Multiple sequence alignment - TraesCS5A01G077600

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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 TraesCS5A01G077600 chr5A 100.000 2708 0 0 1 2708 94741030 94743737 0.000000e+00 5001.0
1 TraesCS5A01G077600 chr5A 82.507 383 34 19 27 384 94735349 94735723 3.390000e-79 305.0
2 TraesCS5A01G077600 chr5A 85.897 78 1 2 2343 2410 426930740 426930663 1.040000e-09 75.0
3 TraesCS5A01G077600 chr5B 91.782 1813 75 21 27 1797 112588311 112586531 0.000000e+00 2455.0
4 TraesCS5A01G077600 chr5B 84.189 487 45 15 2239 2708 112586113 112585642 6.880000e-121 444.0
5 TraesCS5A01G077600 chr5B 80.418 383 39 18 27 384 112589200 112588829 2.670000e-65 259.0
6 TraesCS5A01G077600 chr5B 85.556 90 3 2 2331 2411 382906813 382906901 4.800000e-13 86.1
7 TraesCS5A01G077600 chr5B 85.057 87 3 2 2331 2408 382906285 382906370 2.240000e-11 80.5
8 TraesCS5A01G077600 chr5B 84.444 90 4 2 2331 2411 382907342 382907430 2.240000e-11 80.5
9 TraesCS5A01G077600 chr5D 92.126 1016 48 11 790 1797 103646324 103645333 0.000000e+00 1404.0
10 TraesCS5A01G077600 chr5D 93.100 913 41 10 1059 1958 103654722 103653819 0.000000e+00 1317.0
11 TraesCS5A01G077600 chr5D 94.003 767 25 7 275 1036 103655466 103654716 0.000000e+00 1142.0
12 TraesCS5A01G077600 chr5D 86.449 797 68 19 27 798 103649927 103649146 0.000000e+00 837.0
13 TraesCS5A01G077600 chr5D 85.078 449 39 13 2275 2707 103644919 103644483 1.490000e-117 433.0
14 TraesCS5A01G077600 chr5D 88.462 260 17 8 27 285 103657065 103656818 4.380000e-78 302.0
15 TraesCS5A01G077600 chr5D 80.049 411 22 27 1826 2231 103645260 103644905 1.610000e-62 250.0
16 TraesCS5A01G077600 chr6D 93.376 936 47 7 853 1788 276902588 276903508 0.000000e+00 1371.0
17 TraesCS5A01G077600 chr6D 88.066 729 42 22 27 749 276901810 276902499 0.000000e+00 822.0
18 TraesCS5A01G077600 chr6D 95.862 145 6 0 1805 1949 276903565 276903709 4.510000e-58 235.0
19 TraesCS5A01G077600 chr6D 86.250 80 8 2 2495 2571 83954364 83954285 1.730000e-12 84.2
20 TraesCS5A01G077600 chr6D 92.063 63 0 2 806 868 276902513 276902570 1.730000e-12 84.2
21 TraesCS5A01G077600 chr6D 86.441 59 4 3 2331 2385 25709006 25708948 8.100000e-06 62.1
22 TraesCS5A01G077600 chr6D 86.441 59 4 3 2331 2385 25720779 25720721 8.100000e-06 62.1
23 TraesCS5A01G077600 chrUn 86.250 80 8 2 2495 2571 273240037 273240116 1.730000e-12 84.2
24 TraesCS5A01G077600 chr7D 86.250 80 8 2 2495 2571 307063659 307063580 1.730000e-12 84.2
25 TraesCS5A01G077600 chr7D 86.250 80 8 2 2495 2571 349236881 349236802 1.730000e-12 84.2
26 TraesCS5A01G077600 chr7D 86.250 80 8 2 2495 2571 382013633 382013554 1.730000e-12 84.2
27 TraesCS5A01G077600 chr4D 86.250 80 8 2 2495 2571 123368880 123368959 1.730000e-12 84.2
28 TraesCS5A01G077600 chr4D 86.250 80 8 2 2495 2571 123579830 123579909 1.730000e-12 84.2
29 TraesCS5A01G077600 chr7B 87.500 56 6 1 2330 2385 712863162 712863216 2.250000e-06 63.9
30 TraesCS5A01G077600 chr2B 92.857 42 3 0 2344 2385 767472392 767472351 8.100000e-06 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5A01G077600 chr5A 94741030 94743737 2707 False 5001.000000 5001 100.000000 1 2708 1 chr5A.!!$F2 2707
1 TraesCS5A01G077600 chr5B 112585642 112589200 3558 True 1052.666667 2455 85.463000 27 2708 3 chr5B.!!$R1 2681
2 TraesCS5A01G077600 chr5D 103644483 103657065 12582 True 812.142857 1404 88.466714 27 2707 7 chr5D.!!$R1 2680
3 TraesCS5A01G077600 chr6D 276901810 276903709 1899 False 628.050000 1371 92.341750 27 1949 4 chr6D.!!$F1 1922

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
894 3220 0.040336 TTCAGCACTCACGACGAGAC 60.04 55.0 0.0 5.36 45.45 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2342 13407 0.250513 GATTCCCTGCGTCTCCAGTT 59.749 55.0 0.0 0.0 0.0 3.16 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
56 946 8.949177 CATGCTGTTAGGATGCATTAATATACA 58.051 33.333 0.00 0.70 43.85 2.29
81 971 6.291377 TCATAAGGCATGGAACTGTCTTATC 58.709 40.000 7.72 0.00 46.10 1.75
82 972 4.851639 AAGGCATGGAACTGTCTTATCT 57.148 40.909 0.00 0.00 39.23 1.98
83 973 5.957771 AAGGCATGGAACTGTCTTATCTA 57.042 39.130 0.00 0.00 39.23 1.98
217 1108 4.864334 GCCCAGAGATGCACCGGG 62.864 72.222 6.32 0.00 40.11 5.73
219 1110 3.790437 CCAGAGATGCACCGGGCT 61.790 66.667 6.32 0.00 45.15 5.19
310 2563 4.446371 CGCCAGGAAGAAGAAGATAATGT 58.554 43.478 0.00 0.00 0.00 2.71
518 2771 4.005650 TGAACTCATGGACAGAATGAAGC 58.994 43.478 0.00 0.00 39.69 3.86
521 2774 4.597004 ACTCATGGACAGAATGAAGCAAT 58.403 39.130 0.00 0.00 39.69 3.56
600 2854 7.493367 AGATTAGTGGAATGAACAGTACTAGC 58.507 38.462 0.00 0.00 0.00 3.42
604 2858 5.877012 AGTGGAATGAACAGTACTAGCATTG 59.123 40.000 16.90 0.00 30.06 2.82
608 2862 6.036517 GGAATGAACAGTACTAGCATTGTGAG 59.963 42.308 16.90 0.00 30.06 3.51
668 2950 2.664402 AAGTGACAGGCTTGGTGAAT 57.336 45.000 0.00 0.00 0.00 2.57
739 3026 2.991190 GTTCGTTCGATCAGGTGCTTAA 59.009 45.455 0.00 0.00 0.00 1.85
771 3058 4.323417 ACCGTGAGCAATATGAAAAGACA 58.677 39.130 0.00 0.00 0.00 3.41
778 3065 3.416277 CAATATGAAAAGACACGGTGCG 58.584 45.455 8.30 0.00 0.00 5.34
831 3118 4.510340 GGACTCACTTTGCTTTCTCGTTTA 59.490 41.667 0.00 0.00 0.00 2.01
894 3220 0.040336 TTCAGCACTCACGACGAGAC 60.040 55.000 0.00 5.36 45.45 3.36
896 3222 1.959738 AGCACTCACGACGAGACGA 60.960 57.895 0.00 0.00 45.45 4.20
897 3223 1.510204 GCACTCACGACGAGACGAG 60.510 63.158 0.00 4.42 45.45 4.18
898 3224 1.860759 CACTCACGACGAGACGAGT 59.139 57.895 0.00 5.07 45.45 4.18
899 3225 0.179245 CACTCACGACGAGACGAGTC 60.179 60.000 0.00 0.00 45.45 3.36
954 3287 0.925466 CGTCCGTTGAACGTCAAAGT 59.075 50.000 17.05 0.00 40.58 2.66
1213 3553 2.040606 TCTCCTTCCCCTTCCCGG 59.959 66.667 0.00 0.00 0.00 5.73
1234 12234 3.322466 CCTTCTGGTCCGGGCAGT 61.322 66.667 9.07 0.00 0.00 4.40
1389 12395 3.351416 GTGGGCGGGTTCAACGTC 61.351 66.667 0.00 0.00 34.75 4.34
1644 12650 2.343758 GTCGTCTTCTGCCAGCCA 59.656 61.111 0.00 0.00 0.00 4.75
1651 12657 1.945354 CTTCTGCCAGCCAGCAATGG 61.945 60.000 0.00 0.00 43.52 3.16
1652 12658 2.678934 CTGCCAGCCAGCAATGGT 60.679 61.111 0.00 0.00 43.52 3.55
1653 12659 2.677524 TGCCAGCCAGCAATGGTC 60.678 61.111 0.00 0.00 40.56 4.02
1654 12660 3.818787 GCCAGCCAGCAATGGTCG 61.819 66.667 0.52 0.00 38.91 4.79
1655 12661 2.046023 CCAGCCAGCAATGGTCGA 60.046 61.111 0.00 0.00 0.00 4.20
1656 12662 2.401766 CCAGCCAGCAATGGTCGAC 61.402 63.158 7.13 7.13 0.00 4.20
1710 12716 0.108186 TCGTCGCCGAGAACTAGGTA 60.108 55.000 0.00 0.00 38.40 3.08
1713 12719 1.099879 TCGCCGAGAACTAGGTAGCC 61.100 60.000 0.00 0.00 0.00 3.93
1722 12728 1.797320 ACTAGGTAGCCGGCCATTAA 58.203 50.000 26.15 5.40 0.00 1.40
1729 12735 1.448893 GCCGGCCATTAACGAGTGA 60.449 57.895 18.11 0.00 0.00 3.41
1736 12745 3.063997 GGCCATTAACGAGTGATGTTGAG 59.936 47.826 0.00 0.00 0.00 3.02
1821 12880 4.629092 CCCCTGAGATGCATATGATATCG 58.371 47.826 6.97 2.10 0.00 2.92
1862 12921 7.380333 TCAATGATCCGTTATTATCGTACACAC 59.620 37.037 0.00 0.00 0.00 3.82
1951 13011 4.014406 TCGAGCTACTATGTGGAGTGAAA 58.986 43.478 0.00 0.00 0.00 2.69
1955 13015 5.833082 AGCTACTATGTGGAGTGAAATACG 58.167 41.667 0.00 0.00 0.00 3.06
1961 13021 7.803724 ACTATGTGGAGTGAAATACGTTTTTC 58.196 34.615 20.41 20.41 36.38 2.29
1966 13026 8.030106 TGTGGAGTGAAATACGTTTTTCTTTTT 58.970 29.630 25.14 12.47 36.71 1.94
1994 13058 6.104439 TGAGAAGAATAACGAGTCGAGTAC 57.896 41.667 21.50 6.48 0.00 2.73
2006 13070 4.220572 GAGTCGAGTACAACAAGACAGAC 58.779 47.826 0.00 0.00 32.05 3.51
2015 13079 4.379243 AAGACAGACGCCCCGCAG 62.379 66.667 0.00 0.00 0.00 5.18
2023 13087 3.127533 CGCCCCGCAGAAGAAAGG 61.128 66.667 0.00 0.00 0.00 3.11
2024 13088 2.351276 GCCCCGCAGAAGAAAGGA 59.649 61.111 0.00 0.00 0.00 3.36
2025 13089 1.303317 GCCCCGCAGAAGAAAGGAA 60.303 57.895 0.00 0.00 0.00 3.36
2026 13090 1.308783 GCCCCGCAGAAGAAAGGAAG 61.309 60.000 0.00 0.00 0.00 3.46
2030 13094 2.485814 CCCGCAGAAGAAAGGAAGAAAG 59.514 50.000 0.00 0.00 0.00 2.62
2081 13145 3.262420 TCGAGTTAAAGAGAAGCATGGC 58.738 45.455 0.00 0.00 0.00 4.40
2083 13147 2.685388 GAGTTAAAGAGAAGCATGGCCC 59.315 50.000 0.00 0.00 0.00 5.80
2084 13148 1.401905 GTTAAAGAGAAGCATGGCCCG 59.598 52.381 0.00 0.00 0.00 6.13
2085 13149 0.618458 TAAAGAGAAGCATGGCCCGT 59.382 50.000 0.00 0.00 0.00 5.28
2086 13150 0.251341 AAAGAGAAGCATGGCCCGTT 60.251 50.000 0.00 0.00 0.00 4.44
2087 13151 0.678048 AAGAGAAGCATGGCCCGTTC 60.678 55.000 0.00 0.00 0.00 3.95
2088 13152 2.436646 AGAAGCATGGCCCGTTCG 60.437 61.111 0.00 0.00 0.00 3.95
2089 13153 2.746277 GAAGCATGGCCCGTTCGT 60.746 61.111 0.00 0.00 0.00 3.85
2090 13154 2.282180 AAGCATGGCCCGTTCGTT 60.282 55.556 0.00 0.00 0.00 3.85
2117 13181 4.483243 CGGGGGCTGCACGGTAAT 62.483 66.667 0.50 0.00 0.00 1.89
2158 13222 2.711542 CAACGAAAATCTGGGCCTACT 58.288 47.619 4.53 0.00 0.00 2.57
2159 13223 3.869065 CAACGAAAATCTGGGCCTACTA 58.131 45.455 4.53 0.00 0.00 1.82
2160 13224 3.538634 ACGAAAATCTGGGCCTACTAC 57.461 47.619 4.53 0.00 0.00 2.73
2171 13235 0.384669 GCCTACTACAACCTCGCGAT 59.615 55.000 10.36 0.00 0.00 4.58
2225 13289 8.647143 AAGATCGACAAAACAAATGTGATTTT 57.353 26.923 0.00 0.00 28.02 1.82
2264 13328 9.434420 ACAAATGTGATTTCTTTGTCTCAAAAA 57.566 25.926 0.00 0.00 38.38 1.94
2354 13420 2.831685 AATGTGTAACTGGAGACGCA 57.168 45.000 0.00 0.00 40.15 5.24
2409 13484 0.243907 CCATATGAGCTACGTCCCCG 59.756 60.000 3.65 0.00 40.83 5.73
2423 13498 2.422127 CGTCCCCGTTCTGCATTTAAAT 59.578 45.455 0.00 0.00 0.00 1.40
2427 13502 6.017770 CGTCCCCGTTCTGCATTTAAATTATA 60.018 38.462 0.00 0.00 0.00 0.98
2431 13506 9.541143 CCCCGTTCTGCATTTAAATTATATTTT 57.459 29.630 0.00 0.00 0.00 1.82
2461 13536 8.463930 TTTAATAAGAATAGGAATGTGCCCTG 57.536 34.615 0.00 0.00 35.30 4.45
2479 13558 3.612247 GAAAGGCCGCTGCAGAGGA 62.612 63.158 37.11 0.00 40.13 3.71
2489 13568 1.068679 GCTGCAGAGGAAAAGAGCAAC 60.069 52.381 20.43 0.00 34.45 4.17
2499 13578 0.951558 AAAGAGCAACGCGTTCCATT 59.048 45.000 23.92 9.63 0.00 3.16
2500 13579 0.517316 AAGAGCAACGCGTTCCATTC 59.483 50.000 23.92 16.16 0.00 2.67
2503 13582 1.792057 GCAACGCGTTCCATTCGTG 60.792 57.895 23.92 10.44 43.13 4.35
2518 13599 2.112380 TCGTGTGTGGGTATAGACGA 57.888 50.000 0.00 0.00 40.41 4.20
2537 13618 7.456684 AGACGATCTTTCATTATTCTTCGTG 57.543 36.000 0.00 0.00 38.54 4.35
2548 13629 8.956533 TCATTATTCTTCGTGATATTGACCAA 57.043 30.769 0.00 0.00 0.00 3.67
2553 13634 6.435430 TCTTCGTGATATTGACCAAATTGG 57.565 37.500 11.02 11.02 45.02 3.16
2574 13655 4.158949 TGGTCCTCATTTGCATTTCATGAG 59.841 41.667 14.44 14.44 42.47 2.90
2651 13732 4.268359 GACTCCTGCTCCAGAAAATGATT 58.732 43.478 0.00 0.00 32.44 2.57
2703 13784 1.202557 CCACCTGTGCTTTGCATGTTT 60.203 47.619 0.00 0.00 41.91 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 9.665719 TGCATGTGTTAGAAATAATTACTGAGA 57.334 29.630 0.00 0.00 0.00 3.27
8 9 8.961092 GCATGCATGTGTTAGAAATAATTACTG 58.039 33.333 26.79 0.00 0.00 2.74
9 10 8.906867 AGCATGCATGTGTTAGAAATAATTACT 58.093 29.630 26.79 7.07 0.00 2.24
10 11 8.961092 CAGCATGCATGTGTTAGAAATAATTAC 58.039 33.333 26.79 4.87 0.00 1.89
11 12 8.685427 ACAGCATGCATGTGTTAGAAATAATTA 58.315 29.630 26.79 0.00 42.53 1.40
12 13 7.549839 ACAGCATGCATGTGTTAGAAATAATT 58.450 30.769 26.79 2.59 42.53 1.40
13 14 7.104043 ACAGCATGCATGTGTTAGAAATAAT 57.896 32.000 26.79 3.03 42.53 1.28
14 15 6.513806 ACAGCATGCATGTGTTAGAAATAA 57.486 33.333 26.79 0.00 42.53 1.40
15 16 6.513806 AACAGCATGCATGTGTTAGAAATA 57.486 33.333 29.72 0.00 42.53 1.40
16 17 5.395682 AACAGCATGCATGTGTTAGAAAT 57.604 34.783 29.72 15.68 42.53 2.17
17 18 4.852134 AACAGCATGCATGTGTTAGAAA 57.148 36.364 29.72 0.00 42.53 2.52
18 19 4.395854 CCTAACAGCATGCATGTGTTAGAA 59.604 41.667 40.75 28.04 44.22 2.10
19 20 3.940852 CCTAACAGCATGCATGTGTTAGA 59.059 43.478 40.75 28.44 44.22 2.10
20 21 3.940852 TCCTAACAGCATGCATGTGTTAG 59.059 43.478 37.42 37.42 43.02 2.34
21 22 3.949132 TCCTAACAGCATGCATGTGTTA 58.051 40.909 30.80 30.80 42.53 2.41
22 23 2.794103 TCCTAACAGCATGCATGTGTT 58.206 42.857 31.48 31.48 42.53 3.32
23 24 2.495155 TCCTAACAGCATGCATGTGT 57.505 45.000 26.79 23.79 42.53 3.72
24 25 2.543031 GCATCCTAACAGCATGCATGTG 60.543 50.000 26.79 23.21 42.53 3.21
25 26 1.679680 GCATCCTAACAGCATGCATGT 59.320 47.619 26.79 17.58 42.53 3.21
54 944 4.080129 AGACAGTTCCATGCCTTATGATGT 60.080 41.667 0.00 0.00 39.21 3.06
56 946 4.785346 AGACAGTTCCATGCCTTATGAT 57.215 40.909 0.00 0.00 39.21 2.45
81 971 8.773645 TGCAATGAATCGATATTAAGTTGGTAG 58.226 33.333 0.00 0.00 0.00 3.18
82 972 8.669946 TGCAATGAATCGATATTAAGTTGGTA 57.330 30.769 0.00 0.00 0.00 3.25
83 973 7.566760 TGCAATGAATCGATATTAAGTTGGT 57.433 32.000 0.00 0.00 0.00 3.67
197 1088 1.452651 CGGTGCATCTCTGGGCATT 60.453 57.895 0.00 0.00 42.75 3.56
217 1108 0.098728 AAATGCAATGGCGTACGAGC 59.901 50.000 21.65 13.95 45.35 5.03
219 1110 2.590073 CAAAAATGCAATGGCGTACGA 58.410 42.857 21.65 0.00 45.35 3.43
310 2563 1.831106 TGCTTCCTTGCCGAGAAGATA 59.169 47.619 10.04 0.00 41.69 1.98
518 2771 2.029020 TCGGACTCACTGAGTGGAATTG 60.029 50.000 16.69 0.97 43.53 2.32
521 2774 1.546029 CATCGGACTCACTGAGTGGAA 59.454 52.381 16.69 1.85 43.53 3.53
600 2854 8.871862 TGAATTTCTGAAACAAAACTCACAATG 58.128 29.630 4.73 0.00 0.00 2.82
604 2858 7.463251 GCAGTGAATTTCTGAAACAAAACTCAC 60.463 37.037 4.73 10.71 35.20 3.51
608 2862 6.645700 TGCAGTGAATTTCTGAAACAAAAC 57.354 33.333 4.73 2.52 35.20 2.43
668 2950 3.056891 GGGAAAAGAATGCATCGGTTCAA 60.057 43.478 0.00 0.00 31.19 2.69
753 3040 4.154015 CACCGTGTCTTTTCATATTGCTCA 59.846 41.667 0.00 0.00 0.00 4.26
778 3065 4.237724 GCTAATTTCAAAACAGAGGCACC 58.762 43.478 0.00 0.00 0.00 5.01
831 3118 2.906389 TGATGCCTACTGTTCTGTTCCT 59.094 45.455 0.00 0.00 0.00 3.36
894 3220 2.571096 GCGACGTCGTCTGACTCG 60.571 66.667 35.48 11.35 43.21 4.18
954 3287 3.841137 TTTGCACTGCAGGGCGCTA 62.841 57.895 34.24 20.15 40.61 4.26
1269 12275 3.997064 CTTGCTCCCCGTCTCGCAG 62.997 68.421 0.00 0.00 33.48 5.18
1530 12536 1.745489 CTGCTTGAAGTACCCGGGC 60.745 63.158 24.08 4.85 0.00 6.13
1575 12581 4.680537 ACGGGCTCCCTGTCGACT 62.681 66.667 17.92 0.00 39.13 4.18
1644 12650 2.959372 TCGACGTCGACCATTGCT 59.041 55.556 34.97 0.00 44.22 3.91
1710 12716 1.449601 CACTCGTTAATGGCCGGCT 60.450 57.895 28.56 9.55 0.00 5.52
1713 12719 1.651987 ACATCACTCGTTAATGGCCG 58.348 50.000 0.00 0.00 0.00 6.13
1722 12728 1.337071 ACGTGTCTCAACATCACTCGT 59.663 47.619 0.00 0.00 37.81 4.18
1729 12735 5.401531 ACACCTTATACGTGTCTCAACAT 57.598 39.130 0.00 0.00 40.40 2.71
1736 12745 7.823149 ATTTTCACTACACCTTATACGTGTC 57.177 36.000 0.00 0.00 43.29 3.67
1792 12804 2.665000 CATCTCAGGGGCACACGT 59.335 61.111 0.00 0.00 0.00 4.49
1797 12809 1.437397 TCATATGCATCTCAGGGGCA 58.563 50.000 0.19 0.00 42.43 5.36
1798 12810 2.803030 ATCATATGCATCTCAGGGGC 57.197 50.000 0.19 0.00 0.00 5.80
1801 12813 4.974888 CGACGATATCATATGCATCTCAGG 59.025 45.833 0.19 0.00 0.00 3.86
1802 12814 5.576895 ACGACGATATCATATGCATCTCAG 58.423 41.667 0.19 0.00 0.00 3.35
1821 12880 5.107453 GGATCATTGACGATTCCATTACGAC 60.107 44.000 0.00 0.00 0.00 4.34
1967 13027 6.072618 ACTCGACTCGTTATTCTTCTCAAAGA 60.073 38.462 0.00 0.00 39.78 2.52
1968 13028 6.087522 ACTCGACTCGTTATTCTTCTCAAAG 58.912 40.000 0.00 0.00 0.00 2.77
1969 13029 6.010294 ACTCGACTCGTTATTCTTCTCAAA 57.990 37.500 0.00 0.00 0.00 2.69
1970 13030 5.624344 ACTCGACTCGTTATTCTTCTCAA 57.376 39.130 0.00 0.00 0.00 3.02
1971 13031 5.640783 TGTACTCGACTCGTTATTCTTCTCA 59.359 40.000 0.00 0.00 0.00 3.27
1972 13032 6.104439 TGTACTCGACTCGTTATTCTTCTC 57.896 41.667 0.00 0.00 0.00 2.87
1973 13033 6.072838 TGTTGTACTCGACTCGTTATTCTTCT 60.073 38.462 0.00 0.00 0.00 2.85
1974 13034 6.082338 TGTTGTACTCGACTCGTTATTCTTC 58.918 40.000 0.00 0.00 0.00 2.87
1975 13035 6.005583 TGTTGTACTCGACTCGTTATTCTT 57.994 37.500 0.00 0.00 0.00 2.52
1982 13042 2.615447 TGTCTTGTTGTACTCGACTCGT 59.385 45.455 0.00 0.00 0.00 4.18
1987 13047 2.603892 GCGTCTGTCTTGTTGTACTCGA 60.604 50.000 0.00 0.00 0.00 4.04
1994 13058 2.317609 CGGGGCGTCTGTCTTGTTG 61.318 63.158 0.00 0.00 0.00 3.33
2006 13070 3.127533 CCTTTCTTCTGCGGGGCG 61.128 66.667 0.00 0.00 0.00 6.13
2015 13079 7.694886 TCTCGTTTTTCTTTCTTCCTTTCTTC 58.305 34.615 0.00 0.00 0.00 2.87
2023 13087 5.107259 GCCTCTCTCTCGTTTTTCTTTCTTC 60.107 44.000 0.00 0.00 0.00 2.87
2024 13088 4.752604 GCCTCTCTCTCGTTTTTCTTTCTT 59.247 41.667 0.00 0.00 0.00 2.52
2025 13089 4.311606 GCCTCTCTCTCGTTTTTCTTTCT 58.688 43.478 0.00 0.00 0.00 2.52
2026 13090 3.122111 CGCCTCTCTCTCGTTTTTCTTTC 59.878 47.826 0.00 0.00 0.00 2.62
2030 13094 1.721926 CACGCCTCTCTCTCGTTTTTC 59.278 52.381 0.00 0.00 33.84 2.29
2060 13124 3.262420 GCCATGCTTCTCTTTAACTCGA 58.738 45.455 0.00 0.00 0.00 4.04
2063 13127 2.728007 GGGCCATGCTTCTCTTTAACT 58.272 47.619 4.39 0.00 0.00 2.24
2077 13141 2.030958 GAACGAACGAACGGGCCAT 61.031 57.895 4.39 0.00 37.61 4.40
2081 13145 1.007038 TGGAGAACGAACGAACGGG 60.007 57.895 0.14 0.00 37.61 5.28
2117 13181 2.117858 TGCCAGCCCAGCATTTCA 59.882 55.556 0.00 0.00 34.69 2.69
2136 13200 1.215382 GGCCCAGATTTTCGTTGCC 59.785 57.895 0.00 0.00 0.00 4.52
2158 13222 1.216977 CACCCATCGCGAGGTTGTA 59.783 57.895 20.35 0.00 32.72 2.41
2159 13223 2.047274 CACCCATCGCGAGGTTGT 60.047 61.111 20.35 13.33 32.72 3.32
2160 13224 2.819595 CCACCCATCGCGAGGTTG 60.820 66.667 20.35 15.95 32.72 3.77
2237 13301 7.990541 TTGAGACAAAGAAATCACATTTGTG 57.009 32.000 7.22 4.29 44.76 3.33
2268 13332 9.077885 GAAGAGAAGAAGATATCACATAGGAGT 57.922 37.037 5.32 0.00 0.00 3.85
2269 13333 8.522830 GGAAGAGAAGAAGATATCACATAGGAG 58.477 40.741 5.32 0.00 0.00 3.69
2270 13334 7.453126 GGGAAGAGAAGAAGATATCACATAGGA 59.547 40.741 5.32 0.00 0.00 2.94
2271 13335 7.310361 GGGGAAGAGAAGAAGATATCACATAGG 60.310 44.444 5.32 0.00 0.00 2.57
2272 13336 7.234371 TGGGGAAGAGAAGAAGATATCACATAG 59.766 40.741 5.32 0.00 0.00 2.23
2273 13337 7.075797 TGGGGAAGAGAAGAAGATATCACATA 58.924 38.462 5.32 0.00 0.00 2.29
2337 13402 0.317160 CCTGCGTCTCCAGTTACACA 59.683 55.000 0.00 0.00 0.00 3.72
2338 13403 0.389948 CCCTGCGTCTCCAGTTACAC 60.390 60.000 0.00 0.00 0.00 2.90
2339 13404 0.541063 TCCCTGCGTCTCCAGTTACA 60.541 55.000 0.00 0.00 0.00 2.41
2340 13405 0.606604 TTCCCTGCGTCTCCAGTTAC 59.393 55.000 0.00 0.00 0.00 2.50
2341 13406 1.480954 GATTCCCTGCGTCTCCAGTTA 59.519 52.381 0.00 0.00 0.00 2.24
2342 13407 0.250513 GATTCCCTGCGTCTCCAGTT 59.749 55.000 0.00 0.00 0.00 3.16
2354 13420 2.987125 CACGGGGTTCGATTCCCT 59.013 61.111 20.64 7.57 44.07 4.20
2436 13511 8.278639 TCAGGGCACATTCCTATTCTTATTAAA 58.721 33.333 0.00 0.00 32.49 1.52
2437 13512 7.811282 TCAGGGCACATTCCTATTCTTATTAA 58.189 34.615 0.00 0.00 32.49 1.40
2438 13513 7.387265 TCAGGGCACATTCCTATTCTTATTA 57.613 36.000 0.00 0.00 32.49 0.98
2439 13514 6.266131 TCAGGGCACATTCCTATTCTTATT 57.734 37.500 0.00 0.00 32.49 1.40
2440 13515 5.912149 TCAGGGCACATTCCTATTCTTAT 57.088 39.130 0.00 0.00 32.49 1.73
2441 13516 5.708736 TTCAGGGCACATTCCTATTCTTA 57.291 39.130 0.00 0.00 32.49 2.10
2442 13517 4.591321 TTCAGGGCACATTCCTATTCTT 57.409 40.909 0.00 0.00 32.49 2.52
2443 13518 4.530875 CTTTCAGGGCACATTCCTATTCT 58.469 43.478 0.00 0.00 32.49 2.40
2444 13519 3.633986 CCTTTCAGGGCACATTCCTATTC 59.366 47.826 0.00 0.00 32.49 1.75
2445 13520 3.635591 CCTTTCAGGGCACATTCCTATT 58.364 45.455 0.00 0.00 32.49 1.73
2446 13521 3.303351 CCTTTCAGGGCACATTCCTAT 57.697 47.619 0.00 0.00 32.49 2.57
2447 13522 2.806945 CCTTTCAGGGCACATTCCTA 57.193 50.000 0.00 0.00 32.49 2.94
2461 13536 3.130160 CCTCTGCAGCGGCCTTTC 61.130 66.667 10.36 0.00 40.13 2.62
2466 13541 1.642952 CTCTTTTCCTCTGCAGCGGC 61.643 60.000 18.27 0.31 41.68 6.53
2467 13542 1.642952 GCTCTTTTCCTCTGCAGCGG 61.643 60.000 16.99 16.99 0.00 5.52
2479 13558 0.951558 ATGGAACGCGTTGCTCTTTT 59.048 45.000 37.07 18.04 0.00 2.27
2489 13568 1.154672 CACACACGAATGGAACGCG 60.155 57.895 3.53 3.53 0.00 6.01
2499 13578 2.112380 TCGTCTATACCCACACACGA 57.888 50.000 0.00 0.00 34.08 4.35
2500 13579 2.617308 AGATCGTCTATACCCACACACG 59.383 50.000 0.00 0.00 0.00 4.49
2503 13582 5.258456 TGAAAGATCGTCTATACCCACAC 57.742 43.478 1.81 0.00 0.00 3.82
2548 13629 5.486735 TGAAATGCAAATGAGGACCAATT 57.513 34.783 0.00 0.00 0.00 2.32
2553 13634 5.571784 TCTCATGAAATGCAAATGAGGAC 57.428 39.130 21.87 0.36 46.21 3.85
2557 13638 8.007405 AGATGATTCTCATGAAATGCAAATGA 57.993 30.769 0.00 0.00 46.21 2.57
2558 13639 8.648557 AAGATGATTCTCATGAAATGCAAATG 57.351 30.769 0.00 0.00 46.21 2.32
2590 13671 1.080995 CGAGCACCTGAAGCTACTGC 61.081 60.000 0.00 0.00 43.58 4.40
2618 13699 3.567397 GAGCAGGAGTCCAGGATAAGTA 58.433 50.000 12.86 0.00 0.00 2.24
2651 13732 3.870538 ATAAGGAGCATGATTCAGGCA 57.129 42.857 23.61 4.52 43.99 4.75


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

AutoCloner maintained by Alex Coulton.