Multiple sequence alignment - TraesCS6A01G117300

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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 TraesCS6A01G117300 chr6A 100.000 3079 0 0 1 3079 87755706 87758784 0.000000e+00 5686.0
1 TraesCS6A01G117300 chr6A 100.000 2876 0 0 3498 6373 87759203 87762078 0.000000e+00 5312.0
2 TraesCS6A01G117300 chr6A 83.074 1867 219 46 3559 5373 65803828 65802007 0.000000e+00 1607.0
3 TraesCS6A01G117300 chr6A 89.335 647 64 5 1230 1873 65806027 65805383 0.000000e+00 808.0
4 TraesCS6A01G117300 chr6A 82.540 693 75 18 1871 2524 65805122 65804437 9.270000e-158 568.0
5 TraesCS6A01G117300 chr6A 86.073 438 39 14 2650 3079 65804319 65803896 9.740000e-123 451.0
6 TraesCS6A01G117300 chr6A 83.896 385 50 10 5014 5389 80879761 80880142 2.180000e-94 357.0
7 TraesCS6A01G117300 chr6A 88.412 233 19 3 5619 5843 80880170 80880402 2.260000e-69 274.0
8 TraesCS6A01G117300 chr6A 83.399 253 30 7 3780 4025 80879067 80879314 2.310000e-54 224.0
9 TraesCS6A01G117300 chr6A 84.615 234 20 6 1645 1877 22035787 22035569 1.080000e-52 219.0
10 TraesCS6A01G117300 chr6A 84.889 225 17 3 1651 1874 77507351 77507559 1.800000e-50 211.0
11 TraesCS6A01G117300 chr6A 77.871 357 41 13 2467 2791 77508399 77508749 3.030000e-43 187.0
12 TraesCS6A01G117300 chr6A 82.870 216 28 8 5412 5620 540836913 540837126 1.090000e-42 185.0
13 TraesCS6A01G117300 chr6A 81.818 220 35 4 5409 5624 594969408 594969190 5.080000e-41 180.0
14 TraesCS6A01G117300 chr6A 91.781 73 6 0 3007 3079 65804058 65803986 1.130000e-17 102.0
15 TraesCS6A01G117300 chr6D 96.124 3122 65 14 1 3079 69942298 69945406 0.000000e+00 5044.0
16 TraesCS6A01G117300 chr6D 96.019 2361 68 11 3498 5849 69945747 69948090 0.000000e+00 3816.0
17 TraesCS6A01G117300 chr6D 82.845 1877 221 43 3559 5373 48856869 48858706 0.000000e+00 1589.0
18 TraesCS6A01G117300 chr6D 87.670 884 98 11 996 1873 48854435 48855313 0.000000e+00 1018.0
19 TraesCS6A01G117300 chr6D 81.164 1237 143 56 1871 3055 48855573 48856771 0.000000e+00 911.0
20 TraesCS6A01G117300 chr6D 83.837 761 97 18 4668 5412 63730172 63730922 0.000000e+00 701.0
21 TraesCS6A01G117300 chr6D 89.114 542 40 17 5841 6373 69948144 69948675 0.000000e+00 656.0
22 TraesCS6A01G117300 chr6D 87.478 567 49 8 3764 4324 63729180 63729730 9.010000e-178 634.0
23 TraesCS6A01G117300 chr6D 87.861 346 24 10 4323 4666 63729794 63730123 2.150000e-104 390.0
24 TraesCS6A01G117300 chr6D 82.511 223 34 4 5409 5627 448845072 448844851 2.350000e-44 191.0
25 TraesCS6A01G117300 chr6D 90.411 73 7 0 3007 3079 48856639 48856711 5.260000e-16 97.1
26 TraesCS6A01G117300 chr6D 87.013 77 10 0 2923 2999 69945334 69945410 3.170000e-13 87.9
27 TraesCS6A01G117300 chr6D 85.366 82 6 1 2923 2998 48856723 48856804 5.300000e-11 80.5
28 TraesCS6A01G117300 chr6B 95.081 2704 70 10 420 3079 144960936 144963620 0.000000e+00 4198.0
29 TraesCS6A01G117300 chr6B 94.649 2280 74 17 3498 5772 144963936 144966172 0.000000e+00 3491.0
30 TraesCS6A01G117300 chr6B 88.161 1343 106 30 3764 5088 137383683 137384990 0.000000e+00 1550.0
31 TraesCS6A01G117300 chr6B 81.906 1868 230 48 3559 5373 122296460 122294648 0.000000e+00 1478.0
32 TraesCS6A01G117300 chr6B 80.159 1260 153 57 1871 3079 122297741 122296528 0.000000e+00 852.0
33 TraesCS6A01G117300 chr6B 89.097 642 68 2 1234 1874 122298659 122298019 0.000000e+00 797.0
34 TraesCS6A01G117300 chr6B 91.777 377 27 4 5841 6214 144966434 144966809 7.320000e-144 521.0
35 TraesCS6A01G117300 chr6B 87.135 171 16 4 6209 6373 144967122 144967292 8.430000e-44 189.0
36 TraesCS6A01G117300 chr6B 87.075 147 18 1 5620 5765 137385066 137385212 1.420000e-36 165.0
37 TraesCS6A01G117300 chr6B 98.750 80 0 1 5770 5849 144966302 144966380 2.400000e-29 141.0
38 TraesCS6A01G117300 chr6B 95.000 80 2 1 1 80 144960864 144960941 2.410000e-24 124.0
39 TraesCS6A01G117300 chr6B 86.585 82 5 1 2923 2998 122296606 122296525 1.140000e-12 86.1
40 TraesCS6A01G117300 chr2D 87.719 399 31 10 3498 3883 543110093 543110486 3.500000e-122 449.0
41 TraesCS6A01G117300 chr2D 81.395 344 41 12 1535 1874 543109421 543109745 6.340000e-65 259.0
42 TraesCS6A01G117300 chr2D 96.154 52 1 1 741 791 561838332 561838383 4.090000e-12 84.2
43 TraesCS6A01G117300 chr5D 88.406 345 33 4 3498 3841 23824594 23824932 5.950000e-110 409.0
44 TraesCS6A01G117300 chr1A 87.500 360 34 4 3624 3972 513428541 513428182 7.690000e-109 405.0
45 TraesCS6A01G117300 chr1A 81.324 423 44 22 1456 1874 513429364 513428973 1.730000e-80 311.0
46 TraesCS6A01G117300 chr1A 86.559 186 17 6 5410 5588 398457377 398457193 1.400000e-46 198.0
47 TraesCS6A01G117300 chr1A 82.273 220 31 6 5411 5623 281890576 281890794 3.920000e-42 183.0
48 TraesCS6A01G117300 chr1A 88.679 106 8 3 3498 3602 513428636 513428534 6.710000e-25 126.0
49 TraesCS6A01G117300 chr3A 88.012 342 34 4 3501 3841 723439559 723439224 1.290000e-106 398.0
50 TraesCS6A01G117300 chr3A 84.848 231 19 6 1645 1874 20204312 20204527 1.080000e-52 219.0
51 TraesCS6A01G117300 chr3A 77.904 353 41 12 2470 2791 20205112 20205458 1.090000e-42 185.0
52 TraesCS6A01G117300 chr3D 84.958 359 40 8 3624 3972 455714050 455713696 1.020000e-92 351.0
53 TraesCS6A01G117300 chr4D 83.824 340 53 2 522 860 461578793 461578455 7.970000e-84 322.0
54 TraesCS6A01G117300 chr4A 83.699 319 48 3 528 845 7143792 7144107 1.340000e-76 298.0
55 TraesCS6A01G117300 chr4B 81.493 335 57 4 528 860 577055250 577054919 2.930000e-68 270.0
56 TraesCS6A01G117300 chr5A 84.188 234 21 2 1645 1877 456472692 456472474 5.010000e-51 213.0
57 TraesCS6A01G117300 chr5A 87.692 65 7 1 737 801 6151896 6151959 2.460000e-09 75.0
58 TraesCS6A01G117300 chr1D 84.951 206 23 6 5410 5608 317435947 317435743 1.080000e-47 202.0
59 TraesCS6A01G117300 chr7A 80.645 217 34 7 5411 5620 735935812 735935597 1.840000e-35 161.0
60 TraesCS6A01G117300 chr3B 96.552 58 2 0 17 74 787973468 787973411 5.260000e-16 97.1
61 TraesCS6A01G117300 chr3B 93.103 58 4 0 17 74 821077507 821077450 1.140000e-12 86.1
62 TraesCS6A01G117300 chr5B 92.593 54 2 1 1 54 531551791 531551740 6.850000e-10 76.8


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 TraesCS6A01G117300 chr6A 87755706 87762078 6372 False 5499.000000 5686 100.000000 1 6373 2 chr6A.!!$F4 6372
1 TraesCS6A01G117300 chr6A 65802007 65806027 4020 True 707.200000 1607 86.560600 1230 5373 5 chr6A.!!$R3 4143
2 TraesCS6A01G117300 chr6A 80879067 80880402 1335 False 285.000000 357 85.235667 3780 5843 3 chr6A.!!$F3 2063
3 TraesCS6A01G117300 chr6D 69942298 69948675 6377 False 2400.975000 5044 92.067500 1 6373 4 chr6D.!!$F3 6372
4 TraesCS6A01G117300 chr6D 48854435 48858706 4271 False 739.120000 1589 85.491200 996 5373 5 chr6D.!!$F1 4377
5 TraesCS6A01G117300 chr6D 63729180 63730922 1742 False 575.000000 701 86.392000 3764 5412 3 chr6D.!!$F2 1648
6 TraesCS6A01G117300 chr6B 144960864 144967292 6428 False 1444.000000 4198 93.732000 1 6373 6 chr6B.!!$F2 6372
7 TraesCS6A01G117300 chr6B 137383683 137385212 1529 False 857.500000 1550 87.618000 3764 5765 2 chr6B.!!$F1 2001
8 TraesCS6A01G117300 chr6B 122294648 122298659 4011 True 803.275000 1478 84.436750 1234 5373 4 chr6B.!!$R1 4139
9 TraesCS6A01G117300 chr2D 543109421 543110486 1065 False 354.000000 449 84.557000 1535 3883 2 chr2D.!!$F2 2348
10 TraesCS6A01G117300 chr1A 513428182 513429364 1182 True 280.666667 405 85.834333 1456 3972 3 chr1A.!!$R2 2516
11 TraesCS6A01G117300 chr3A 20204312 20205458 1146 False 202.000000 219 81.376000 1645 2791 2 chr3A.!!$F1 1146

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
654 656 0.108585 TGCTCAAGGGACTGTTCACC 59.891 55.000 0.00 0.0 40.86 4.02 F
735 737 1.541672 CACACCCCCTCCAGGTTTT 59.458 57.895 0.00 0.0 34.56 2.43 F
2511 2856 0.098552 TGCAAAGTGAACTGTGTGCG 59.901 50.000 2.68 0.0 33.71 5.34 F
3724 4108 0.373716 CCGCTTTGGAGATACGCAAC 59.626 55.000 0.00 0.0 42.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2453 2798 0.982852 CCTGTCCTATGTGGGGCTGA 60.983 60.000 0.00 0.0 32.72 4.26 R
2548 2901 1.893137 TGGTGACGAGCAGATGTTAGT 59.107 47.619 0.00 0.0 0.00 2.24 R
4267 4678 2.498905 CAATCAACAATCTGTGCGTCG 58.501 47.619 0.00 0.0 0.00 5.12 R
5435 6036 0.102481 CCCTAGAACTACGCGCATGT 59.898 55.000 5.73 0.0 0.00 3.21 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
149 150 1.079438 GACAGGAGGGACCAGAGGT 59.921 63.158 0.00 0.00 42.04 3.85
166 167 2.355837 TCTGCGTCACCGTTGCTC 60.356 61.111 0.00 0.00 36.15 4.26
174 175 1.339929 GTCACCGTTGCTCCCAATTTT 59.660 47.619 0.00 0.00 32.75 1.82
413 414 3.471680 ACTGAGTTCCTCTGACTTTTGC 58.528 45.455 5.31 0.00 34.33 3.68
423 424 6.349300 TCCTCTGACTTTTGCATAGGATAAC 58.651 40.000 0.00 0.00 34.77 1.89
592 593 1.880340 GGCATTCTCAGCGGACTCG 60.880 63.158 0.00 0.00 39.81 4.18
654 656 0.108585 TGCTCAAGGGACTGTTCACC 59.891 55.000 0.00 0.00 40.86 4.02
668 670 4.163458 ACTGTTCACCTAGTTGTGGAAGAA 59.837 41.667 0.07 0.00 36.87 2.52
735 737 1.541672 CACACCCCCTCCAGGTTTT 59.458 57.895 0.00 0.00 34.56 2.43
804 806 2.810767 GCCACTCGGTTTCTCTCCTTTT 60.811 50.000 0.00 0.00 33.28 2.27
815 817 5.476091 TTCTCTCCTTTTCTTCCTCTCAC 57.524 43.478 0.00 0.00 0.00 3.51
860 862 7.925043 TCAAGCCGTTGTAAATTTTATCCTA 57.075 32.000 0.00 0.00 34.98 2.94
877 879 2.712087 TCCTAGGTTTTGGGTTGTGCTA 59.288 45.455 9.08 0.00 0.00 3.49
1416 1430 3.175240 CACGCTCGCCGACTTCAG 61.175 66.667 2.37 0.00 41.02 3.02
1507 1521 3.640407 GTCACCCTCCTGCAGCCA 61.640 66.667 8.66 0.00 0.00 4.75
1603 1619 3.674997 TCACAGTTTCCACAGCTAATCC 58.325 45.455 0.00 0.00 0.00 3.01
1686 1702 1.805871 GCAGCTTCAGAAGGAGATCGG 60.806 57.143 12.30 0.00 0.00 4.18
2325 2656 6.970043 TGCGATTGGTTATTGTAACATTAAGC 59.030 34.615 0.00 0.00 32.16 3.09
2453 2798 2.782341 AGATTAGAAATGCTCCAGCCCT 59.218 45.455 0.00 0.00 41.18 5.19
2511 2856 0.098552 TGCAAAGTGAACTGTGTGCG 59.901 50.000 2.68 0.00 33.71 5.34
2540 2893 8.220755 TGTCTTTAATACATCAGCCATTTACC 57.779 34.615 0.00 0.00 0.00 2.85
2548 2901 4.227300 ACATCAGCCATTTACCCTTGAGTA 59.773 41.667 0.00 0.00 0.00 2.59
2551 2904 5.027460 TCAGCCATTTACCCTTGAGTACTA 58.973 41.667 0.00 0.00 0.00 1.82
2766 3141 6.600822 ACTCCAGATTGATGTCCAAATTAGTG 59.399 38.462 0.00 0.00 38.43 2.74
2880 3257 2.413239 CGATGACCTGATGTTGTTGTGC 60.413 50.000 0.00 0.00 0.00 4.57
3724 4108 0.373716 CCGCTTTGGAGATACGCAAC 59.626 55.000 0.00 0.00 42.00 4.17
3762 4146 5.591472 TCCACTTTTCATCAGAATATGCCAG 59.409 40.000 0.00 0.00 32.89 4.85
3841 4238 9.759473 TCTCTTCCTTGGAATTTGATAAAGAAT 57.241 29.630 2.24 0.00 0.00 2.40
4060 4469 3.882888 AGGCTCATGAAAAACTGACGAAA 59.117 39.130 0.00 0.00 0.00 3.46
4150 4561 4.333649 GCTGGATTGATTGAATGACGAGAA 59.666 41.667 0.00 0.00 0.00 2.87
4179 4590 9.257651 GTCTAACTCTTTTACTTTCTGTTGCTA 57.742 33.333 0.00 0.00 0.00 3.49
4525 5005 1.732732 CGAGACTGAGGGTAAACTGCG 60.733 57.143 0.00 0.00 0.00 5.18
4666 5176 2.633488 GTGATCCTTGTGAGGCCTTAC 58.367 52.381 20.46 20.46 43.21 2.34
4699 5257 1.269206 CCGCTGTTTGTGCAGAAACAT 60.269 47.619 34.03 0.00 43.22 2.71
4852 5419 1.160137 GTGTTCGGAAGCTGCTTCAT 58.840 50.000 35.27 8.41 41.77 2.57
4976 5551 9.872721 TCATTAATAAAGCATGCATCTTTTCAA 57.127 25.926 21.98 15.35 35.58 2.69
5201 5793 5.222079 TGTACCTGCTTCACAATGTAGAA 57.778 39.130 0.00 0.00 0.00 2.10
5210 5802 2.419673 TCACAATGTAGAATTGCAGCCG 59.580 45.455 0.00 0.00 32.55 5.52
5267 5859 2.546645 AAATGTGCAGGCAATCGGCG 62.547 55.000 0.00 0.00 46.16 6.46
5419 6020 3.112263 TGGAATACCCAGTACTCCCTTG 58.888 50.000 0.00 0.00 40.82 3.61
5435 6036 0.824109 CTTGGTCTCGGTGCATAGGA 59.176 55.000 0.00 0.00 0.00 2.94
5926 6728 8.862325 AACTGACTTTGGAATCACACATATTA 57.138 30.769 0.00 0.00 0.00 0.98
5927 6729 9.466497 AACTGACTTTGGAATCACACATATTAT 57.534 29.630 0.00 0.00 0.00 1.28
6001 6803 6.497437 TGAAACAAACATCATCTGACACTTG 58.503 36.000 0.00 0.00 0.00 3.16
6058 6864 2.612972 GGTCATGCTGAGACGGAAAGAA 60.613 50.000 0.00 0.00 36.87 2.52
6060 6866 2.562738 TCATGCTGAGACGGAAAGAAGA 59.437 45.455 0.00 0.00 0.00 2.87
6062 6868 1.273606 TGCTGAGACGGAAAGAAGAGG 59.726 52.381 0.00 0.00 0.00 3.69
6063 6869 2.003196 CTGAGACGGAAAGAAGAGGC 57.997 55.000 0.00 0.00 0.00 4.70
6065 6871 0.526662 GAGACGGAAAGAAGAGGCGA 59.473 55.000 0.00 0.00 0.00 5.54
6066 6872 0.528470 AGACGGAAAGAAGAGGCGAG 59.472 55.000 0.00 0.00 0.00 5.03
6067 6873 0.458716 GACGGAAAGAAGAGGCGAGG 60.459 60.000 0.00 0.00 0.00 4.63
6068 6874 1.153549 CGGAAAGAAGAGGCGAGGG 60.154 63.158 0.00 0.00 0.00 4.30
6069 6875 1.450491 GGAAAGAAGAGGCGAGGGC 60.450 63.158 0.00 0.00 38.90 5.19
6091 6898 3.664025 CGGCTTTGAAGACTTTTTAAGCG 59.336 43.478 16.76 11.65 39.00 4.68
6107 6914 2.380410 GCGTCTACAACTGGGCACG 61.380 63.158 0.00 0.00 0.00 5.34
6118 6925 3.670377 GGGCACGCCAAACCAGTC 61.670 66.667 10.83 0.00 37.98 3.51
6137 6944 1.966493 CTCAAACATCCGGGCGAACG 61.966 60.000 0.00 0.00 0.00 3.95
6152 6959 1.669502 CGAACGACCCGGTTACATTGA 60.670 52.381 0.00 0.00 0.00 2.57
6164 6971 6.751888 CCCGGTTACATTGATCAGAAAAATTC 59.248 38.462 0.00 0.00 0.00 2.17
6190 6997 0.099436 GACATGCGTCTCAAATGGGC 59.901 55.000 0.00 0.00 39.22 5.36
6191 6998 0.322816 ACATGCGTCTCAAATGGGCT 60.323 50.000 0.00 0.00 0.00 5.19
6192 6999 0.379669 CATGCGTCTCAAATGGGCTC 59.620 55.000 0.00 0.00 0.00 4.70
6193 7000 0.035152 ATGCGTCTCAAATGGGCTCA 60.035 50.000 0.00 0.00 0.00 4.26
6194 7001 0.035152 TGCGTCTCAAATGGGCTCAT 60.035 50.000 0.00 0.00 34.56 2.90
6198 7005 1.599542 GTCTCAAATGGGCTCATACGC 59.400 52.381 0.00 0.00 32.44 4.42
6240 7366 3.775866 TCGTATCCAACCCAAATGTAGGA 59.224 43.478 0.00 0.00 0.00 2.94
6248 7374 5.445069 CAACCCAAATGTAGGATGGACATA 58.555 41.667 0.00 0.00 36.50 2.29
6303 7430 0.476023 TAGGCCTACCCCCACAAACA 60.476 55.000 8.91 0.00 36.11 2.83
6314 7441 1.688197 CCCACAAACAGCACCAAATCT 59.312 47.619 0.00 0.00 0.00 2.40
6318 7450 3.317711 CACAAACAGCACCAAATCTACCA 59.682 43.478 0.00 0.00 0.00 3.25
6319 7451 3.957497 ACAAACAGCACCAAATCTACCAA 59.043 39.130 0.00 0.00 0.00 3.67
6347 7479 2.045926 CCTGCCTTCCTCCAACCG 60.046 66.667 0.00 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.035056 GCCACTACAGCAATGACCCT 60.035 55.000 0.00 0.00 0.00 4.34
13 14 2.284754 TTTCCATGCCACTACAGCAA 57.715 45.000 0.00 0.00 44.83 3.91
166 167 1.750778 AGCTACGGATGCAAAATTGGG 59.249 47.619 0.00 0.00 0.00 4.12
174 175 2.100197 ACTGAAGTAGCTACGGATGCA 58.900 47.619 17.99 11.42 0.00 3.96
314 315 4.783036 CGCTGTTTTGATGTGAGATTTACG 59.217 41.667 0.00 0.00 0.00 3.18
413 414 6.932356 AGACATGCAACTTGTTATCCTATG 57.068 37.500 0.00 0.00 0.00 2.23
423 424 4.567971 AGAGAGAGAAGACATGCAACTTG 58.432 43.478 8.48 0.00 0.00 3.16
592 593 1.168714 GGTGGTGAAGATCAAGGTGC 58.831 55.000 0.00 0.00 0.00 5.01
654 656 2.833631 ACCGGTTCTTCCACAACTAG 57.166 50.000 0.00 0.00 35.57 2.57
668 670 0.976590 GCTCCCTCTCCTTAACCGGT 60.977 60.000 0.00 0.00 0.00 5.28
815 817 0.456653 GGCTATTGGCACACAAAGCG 60.457 55.000 0.00 0.00 43.46 4.68
860 862 2.632512 CCATTAGCACAACCCAAAACCT 59.367 45.455 0.00 0.00 0.00 3.50
877 879 7.364149 ACAAATGTTGGCATCATATACCATT 57.636 32.000 11.24 0.00 33.50 3.16
962 964 0.186386 ACTGCTCCTCCGGCTAGTAT 59.814 55.000 0.00 0.00 0.00 2.12
1209 1222 2.124693 GGGAGCGAGGGAGTGAGAG 61.125 68.421 0.00 0.00 0.00 3.20
1210 1223 2.043852 GGGAGCGAGGGAGTGAGA 60.044 66.667 0.00 0.00 0.00 3.27
1211 1224 2.043450 AGGGAGCGAGGGAGTGAG 60.043 66.667 0.00 0.00 0.00 3.51
1212 1225 2.043852 GAGGGAGCGAGGGAGTGA 60.044 66.667 0.00 0.00 0.00 3.41
1213 1226 3.522731 CGAGGGAGCGAGGGAGTG 61.523 72.222 0.00 0.00 0.00 3.51
1327 1341 3.696518 TAGCACCCGGATGGCCTCT 62.697 63.158 0.73 0.00 37.83 3.69
1603 1619 1.209127 GTGGGCATTTCCACGAACG 59.791 57.895 0.00 0.00 46.31 3.95
1686 1702 2.356793 CCGCGAGCTCATGATCCC 60.357 66.667 15.40 0.00 0.00 3.85
2071 2394 1.139853 GAAGACCAGGATCGAAGCCAT 59.860 52.381 9.96 0.00 0.00 4.40
2453 2798 0.982852 CCTGTCCTATGTGGGGCTGA 60.983 60.000 0.00 0.00 32.72 4.26
2511 2856 6.135290 TGGCTGATGTATTAAAGACAATGC 57.865 37.500 0.00 3.73 0.00 3.56
2540 2893 4.142359 ACGAGCAGATGTTAGTACTCAAGG 60.142 45.833 0.00 0.00 0.00 3.61
2548 2901 1.893137 TGGTGACGAGCAGATGTTAGT 59.107 47.619 0.00 0.00 0.00 2.24
2551 2904 2.479566 ATTGGTGACGAGCAGATGTT 57.520 45.000 0.00 0.00 0.00 2.71
2766 3141 3.570125 CCTGAACTTTTTCTGGGGACTTC 59.430 47.826 3.08 0.00 43.77 3.01
2880 3257 8.794553 AGGTAATTCCTCGTATAGTCACTAATG 58.205 37.037 0.00 0.00 44.42 1.90
2909 3286 5.499004 AGCCAGATTACAAGTCCAAGTAA 57.501 39.130 0.00 0.00 34.99 2.24
2910 3287 5.720041 ACTAGCCAGATTACAAGTCCAAGTA 59.280 40.000 0.00 0.00 0.00 2.24
3041 3418 1.606224 GCAAGTCAACCAGGCCATTTG 60.606 52.381 5.01 4.97 0.00 2.32
3724 4108 6.991938 TGAAAAGTGGAATTGGAATACCTTG 58.008 36.000 0.00 0.00 37.04 3.61
3762 4146 7.435068 TCATAAGCAAAACACCTTCTAGAAC 57.565 36.000 0.00 0.00 0.00 3.01
3841 4238 3.006940 GGAAACACATGTAGCCAATCGA 58.993 45.455 0.00 0.00 0.00 3.59
3976 4382 3.418684 ACTGGTTAAGCACAACTAGGG 57.581 47.619 15.12 0.00 40.30 3.53
4060 4469 5.880901 ACATCCTGGATTTTAGAGTGTTGT 58.119 37.500 6.42 0.00 0.00 3.32
4150 4561 9.057089 CAACAGAAAGTAAAAGAGTTAGACCAT 57.943 33.333 0.00 0.00 0.00 3.55
4231 4642 9.236006 ACTGATACACTTTCATCATTAAGCTTT 57.764 29.630 3.20 0.00 31.05 3.51
4267 4678 2.498905 CAATCAACAATCTGTGCGTCG 58.501 47.619 0.00 0.00 0.00 5.12
4525 5005 3.418684 TTTCTCTAGGTTCAAGGCACC 57.581 47.619 0.00 0.00 34.06 5.01
4699 5257 5.893824 TCAAAGAGATGGACAGCTAGTATCA 59.106 40.000 0.00 0.00 0.00 2.15
4811 5377 4.588528 ACAAATTTGAAGCCTATGTGGTGT 59.411 37.500 24.64 0.00 38.35 4.16
4852 5419 1.071987 CTGTGGCAGCAGTCCTTGA 59.928 57.895 0.00 0.00 0.00 3.02
5201 5793 1.838112 TGAAATTCTCCGGCTGCAAT 58.162 45.000 0.50 0.00 0.00 3.56
5210 5802 8.545229 ACGAATCATCTCATATGAAATTCTCC 57.455 34.615 6.90 0.00 0.00 3.71
5403 6004 1.720533 AGACCAAGGGAGTACTGGGTA 59.279 52.381 0.00 0.00 44.94 3.69
5419 6020 0.753262 ATGTCCTATGCACCGAGACC 59.247 55.000 0.00 0.00 0.00 3.85
5435 6036 0.102481 CCCTAGAACTACGCGCATGT 59.898 55.000 5.73 0.00 0.00 3.21
5612 6216 8.993424 ACATAAACAAAGATATGTACTCCCTCT 58.007 33.333 0.00 0.00 40.12 3.69
5860 6662 9.869844 GTTAGTTCTAATACAATGCATGATGAC 57.130 33.333 0.00 0.00 0.00 3.06
5933 6735 6.551385 GGCTCAACCTATCTGAATGTAATG 57.449 41.667 0.00 0.00 34.51 1.90
6001 6803 2.813908 CCACGGCTCGTTGCTACC 60.814 66.667 0.00 0.00 38.32 3.18
6062 6868 3.804193 CTTCAAAGCCGCCCTCGC 61.804 66.667 0.00 0.00 0.00 5.03
6063 6869 2.047274 TCTTCAAAGCCGCCCTCG 60.047 61.111 0.00 0.00 0.00 4.63
6065 6871 0.178990 AAAGTCTTCAAAGCCGCCCT 60.179 50.000 0.00 0.00 0.00 5.19
6066 6872 0.673985 AAAAGTCTTCAAAGCCGCCC 59.326 50.000 0.00 0.00 0.00 6.13
6067 6873 2.509052 AAAAAGTCTTCAAAGCCGCC 57.491 45.000 0.00 0.00 0.00 6.13
6068 6874 3.425525 GCTTAAAAAGTCTTCAAAGCCGC 59.574 43.478 12.30 0.00 34.64 6.53
6069 6875 3.664025 CGCTTAAAAAGTCTTCAAAGCCG 59.336 43.478 15.46 10.02 36.79 5.52
6091 6898 2.033194 GGCGTGCCCAGTTGTAGAC 61.033 63.158 0.00 0.00 0.00 2.59
6107 6914 2.029918 GGATGTTTGAGACTGGTTTGGC 60.030 50.000 0.00 0.00 0.00 4.52
6118 6925 1.794222 GTTCGCCCGGATGTTTGAG 59.206 57.895 0.73 0.00 0.00 3.02
6137 6944 3.536956 TCTGATCAATGTAACCGGGTC 57.463 47.619 6.32 0.00 0.00 4.46
6145 6952 8.546597 TGAGTCGAATTTTTCTGATCAATGTA 57.453 30.769 0.00 0.00 0.00 2.29
6152 6959 6.402983 GCATGTCTGAGTCGAATTTTTCTGAT 60.403 38.462 0.00 0.00 0.00 2.90
6190 6997 1.005630 GCCAGCCTAGGCGTATGAG 60.006 63.158 27.83 14.85 46.12 2.90
6191 6998 3.138625 GCCAGCCTAGGCGTATGA 58.861 61.111 27.83 0.00 46.12 2.15
6198 7005 4.632974 GATGCCGGCCAGCCTAGG 62.633 72.222 26.77 3.67 0.00 3.02
6303 7430 1.272480 GGGGTTGGTAGATTTGGTGCT 60.272 52.381 0.00 0.00 0.00 4.40
6327 7459 1.492993 GGTTGGAGGAAGGCAGGAGT 61.493 60.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.