Multiple sequence alignment - TraesCS3D01G125300

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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 TraesCS3D01G125300 chr3D 100.000 3824 0 0 1 3824 83864803 83860980 0.000000e+00 7062.0
1 TraesCS3D01G125300 chr3B 94.803 2636 73 27 545 3153 132655249 132657847 0.000000e+00 4050.0
2 TraesCS3D01G125300 chr3B 89.001 691 56 14 3149 3824 132658012 132658697 0.000000e+00 837.0
3 TraesCS3D01G125300 chr3B 93.128 553 20 9 1 551 132649035 132649571 0.000000e+00 795.0
4 TraesCS3D01G125300 chr3B 86.809 235 20 4 112 345 564029527 564029303 6.340000e-63 252.0
5 TraesCS3D01G125300 chr3A 91.650 2946 121 47 554 3457 99996650 99993788 0.000000e+00 3962.0
6 TraesCS3D01G125300 chr3A 92.857 434 18 4 1 426 99997170 99996742 5.430000e-173 617.0
7 TraesCS3D01G125300 chr2B 85.385 390 24 6 1351 1739 789616887 789617244 1.300000e-99 374.0
8 TraesCS3D01G125300 chr2B 86.809 235 20 4 112 345 155818725 155818501 6.340000e-63 252.0
9 TraesCS3D01G125300 chr2B 92.593 54 4 0 1343 1396 461896105 461896052 1.140000e-10 78.7
10 TraesCS3D01G125300 chr2B 90.909 55 5 0 1342 1396 212347478 212347424 1.470000e-09 75.0
11 TraesCS3D01G125300 chr2B 95.000 40 2 0 1369 1408 546902928 546902889 3.190000e-06 63.9
12 TraesCS3D01G125300 chr4B 86.809 235 20 4 112 345 5823699 5823475 6.340000e-63 252.0
13 TraesCS3D01G125300 chrUn 86.383 235 21 4 112 345 232880029 232879805 2.950000e-61 246.0
14 TraesCS3D01G125300 chr6B 85.470 234 20 7 112 344 451460460 451460240 8.260000e-57 231.0
15 TraesCS3D01G125300 chr6B 90.164 61 6 0 1369 1429 534509682 534509622 3.170000e-11 80.5
16 TraesCS3D01G125300 chr7D 83.613 238 19 10 109 345 430381142 430380924 5.010000e-49 206.0
17 TraesCS3D01G125300 chr7D 90.769 65 6 0 1369 1433 573007659 573007595 1.890000e-13 87.9
18 TraesCS3D01G125300 chr5D 89.231 65 7 0 1369 1433 448576646 448576710 8.800000e-12 82.4
19 TraesCS3D01G125300 chr6D 95.238 42 2 0 150 191 469270155 469270196 2.470000e-07 67.6


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 TraesCS3D01G125300 chr3D 83860980 83864803 3823 True 7062.0 7062 100.0000 1 3824 1 chr3D.!!$R1 3823
1 TraesCS3D01G125300 chr3B 132655249 132658697 3448 False 2443.5 4050 91.9020 545 3824 2 chr3B.!!$F2 3279
2 TraesCS3D01G125300 chr3B 132649035 132649571 536 False 795.0 795 93.1280 1 551 1 chr3B.!!$F1 550
3 TraesCS3D01G125300 chr3A 99993788 99997170 3382 True 2289.5 3962 92.2535 1 3457 2 chr3A.!!$R1 3456

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
997 1063 0.378257 CTGCACCACTTCACACACAC 59.622 55.0 0.0 0.0 0.0 3.82 F
1255 1321 0.808755 CCAAGGTAATGAACGTGCCC 59.191 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 2021 0.464036 ATGTGGACGTCTGTGTGTGT 59.536 50.0 16.46 0.0 0.0 3.72 R
2877 2964 0.756903 ACCAACTTGTGCTAGGACGT 59.243 50.0 10.02 0.0 0.0 4.34 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
224 233 2.359900 CTAACTTCCTGTGGGTGATGC 58.640 52.381 0.00 0.00 0.00 3.91
260 269 6.196724 TGCCGTAAAAACGATTGTAAAGTTTG 59.803 34.615 0.00 0.00 38.02 2.93
261 270 6.196910 GCCGTAAAAACGATTGTAAAGTTTGT 59.803 34.615 0.00 0.00 38.02 2.83
262 271 7.253717 GCCGTAAAAACGATTGTAAAGTTTGTT 60.254 33.333 0.00 0.00 38.02 2.83
263 272 8.585436 CCGTAAAAACGATTGTAAAGTTTGTTT 58.415 29.630 0.00 0.00 38.02 2.83
327 336 4.199310 CGAGGAAAATACATCCATGTGGT 58.801 43.478 2.26 0.00 41.89 4.16
388 397 2.741553 GCCAACAAACCAAAGGTTCCTG 60.742 50.000 1.34 0.77 46.20 3.86
413 422 4.880886 TTTCATGCATGTAAGATGTCCG 57.119 40.909 25.43 0.00 0.00 4.79
423 432 7.097192 GCATGTAAGATGTCCGGAGATATTTA 58.903 38.462 24.40 17.32 0.00 1.40
426 435 9.877178 ATGTAAGATGTCCGGAGATATTTAATC 57.123 33.333 24.40 13.77 0.00 1.75
438 447 6.465035 GGAGATATTTAATCAGAGGGTGCTGT 60.465 42.308 0.00 0.00 37.20 4.40
454 463 5.639506 GGGTGCTGTATGTATATGCTACTTG 59.360 44.000 0.00 0.00 0.00 3.16
473 482 0.944386 GCAAGGGCACACGTATATGG 59.056 55.000 0.00 0.00 40.72 2.74
536 577 2.317371 AGCTGGACAAGGAGAGAGAA 57.683 50.000 0.00 0.00 0.00 2.87
647 702 3.835978 ACTGCACCACCTTGTAGTACATA 59.164 43.478 3.28 0.00 40.27 2.29
914 980 2.632831 CCCCCATCCATACACACCT 58.367 57.895 0.00 0.00 0.00 4.00
917 983 1.141657 CCCCATCCATACACACCTCAG 59.858 57.143 0.00 0.00 0.00 3.35
920 986 2.158900 CCATCCATACACACCTCAGACC 60.159 54.545 0.00 0.00 0.00 3.85
994 1060 0.467804 TAGCTGCACCACTTCACACA 59.532 50.000 1.02 0.00 0.00 3.72
995 1061 1.097547 AGCTGCACCACTTCACACAC 61.098 55.000 1.02 0.00 0.00 3.82
996 1062 1.375853 GCTGCACCACTTCACACACA 61.376 55.000 0.00 0.00 0.00 3.72
997 1063 0.378257 CTGCACCACTTCACACACAC 59.622 55.000 0.00 0.00 0.00 3.82
1038 1104 4.539293 TCTGACCTAACCCTAGACTACACT 59.461 45.833 0.00 0.00 0.00 3.55
1246 1312 3.012518 CAGCTCCTCAACCAAGGTAATG 58.987 50.000 0.00 0.00 37.69 1.90
1255 1321 0.808755 CCAAGGTAATGAACGTGCCC 59.191 55.000 0.00 0.00 0.00 5.36
1769 1836 2.074230 AAAGCCGTACCACGACGACA 62.074 55.000 0.00 0.00 46.05 4.35
1927 1994 2.464459 CCGCTTCGTCAATGCCCTC 61.464 63.158 0.00 0.00 0.00 4.30
1954 2021 2.420043 GGCGGCGCTCAAGGTATA 59.580 61.111 32.30 0.00 0.00 1.47
1955 2022 1.954651 GGCGGCGCTCAAGGTATAC 60.955 63.158 32.30 6.78 0.00 1.47
1956 2023 1.227147 GCGGCGCTCAAGGTATACA 60.227 57.895 26.86 0.00 0.00 2.29
1976 2043 1.139989 CACACAGACGTCCACATGTC 58.860 55.000 13.01 0.00 38.67 3.06
2170 2242 3.440522 GTGAAAAGCCATCTCCAGGTAAC 59.559 47.826 0.00 0.00 0.00 2.50
2258 2336 8.830580 TGCTGCTTTAATTATGAGTAGAATGAC 58.169 33.333 14.49 2.61 0.00 3.06
2315 2397 8.573035 TGGGTGTGTATCTAAATTGAAGTTTTC 58.427 33.333 0.00 0.00 0.00 2.29
2317 2399 8.287503 GGTGTGTATCTAAATTGAAGTTTTCGT 58.712 33.333 0.00 0.00 0.00 3.85
2318 2400 9.659830 GTGTGTATCTAAATTGAAGTTTTCGTT 57.340 29.630 0.00 0.00 0.00 3.85
2347 2429 0.670546 TTGCGAGCAGAAGTACAGGC 60.671 55.000 0.00 0.00 0.00 4.85
2349 2431 0.456221 GCGAGCAGAAGTACAGGCTA 59.544 55.000 0.00 0.00 36.59 3.93
2355 2437 2.028930 GCAGAAGTACAGGCTACACACT 60.029 50.000 0.00 0.00 0.00 3.55
2826 2908 4.446051 GCCGAGCAGATCAACTACTAATTC 59.554 45.833 0.00 0.00 0.00 2.17
2833 2915 6.312918 GCAGATCAACTACTAATTCAACGGAA 59.687 38.462 0.00 0.00 37.45 4.30
2834 2916 7.011482 GCAGATCAACTACTAATTCAACGGAAT 59.989 37.037 0.00 0.00 45.57 3.01
2853 2935 2.296831 TAATTAAGTAGCGCGCACCA 57.703 45.000 35.10 15.39 0.00 4.17
2856 2938 1.003851 TTAAGTAGCGCGCACCAATC 58.996 50.000 35.10 15.52 0.00 2.67
2859 2941 2.100631 GTAGCGCGCACCAATCAGT 61.101 57.895 35.10 11.76 0.00 3.41
2871 2958 3.885297 CACCAATCAGTTAGCCCCTAATG 59.115 47.826 0.00 0.00 0.00 1.90
2873 2960 4.416848 ACCAATCAGTTAGCCCCTAATGAT 59.583 41.667 0.00 0.00 31.88 2.45
2874 2961 5.006386 CCAATCAGTTAGCCCCTAATGATC 58.994 45.833 0.00 0.00 30.68 2.92
2875 2962 4.543590 ATCAGTTAGCCCCTAATGATCG 57.456 45.455 0.00 0.00 28.32 3.69
2876 2963 3.305720 TCAGTTAGCCCCTAATGATCGT 58.694 45.455 0.00 0.00 0.00 3.73
2877 2964 4.476297 TCAGTTAGCCCCTAATGATCGTA 58.524 43.478 0.00 0.00 0.00 3.43
2878 2965 4.280174 TCAGTTAGCCCCTAATGATCGTAC 59.720 45.833 0.00 0.00 0.00 3.67
2879 2966 3.255149 AGTTAGCCCCTAATGATCGTACG 59.745 47.826 9.53 9.53 0.00 3.67
2880 2967 1.700955 AGCCCCTAATGATCGTACGT 58.299 50.000 16.05 2.33 0.00 3.57
2881 2968 1.612463 AGCCCCTAATGATCGTACGTC 59.388 52.381 16.05 12.39 0.00 4.34
2882 2969 1.336609 GCCCCTAATGATCGTACGTCC 60.337 57.143 16.05 8.80 0.00 4.79
2883 2970 2.236766 CCCCTAATGATCGTACGTCCT 58.763 52.381 16.05 1.08 0.00 3.85
2884 2971 3.415212 CCCCTAATGATCGTACGTCCTA 58.585 50.000 16.05 0.00 0.00 2.94
2885 2972 3.439476 CCCCTAATGATCGTACGTCCTAG 59.561 52.174 16.05 13.45 0.00 3.02
2886 2973 3.119919 CCCTAATGATCGTACGTCCTAGC 60.120 52.174 16.05 0.00 0.00 3.42
2887 2974 3.501062 CCTAATGATCGTACGTCCTAGCA 59.499 47.826 16.05 5.03 0.00 3.49
2888 2975 3.351020 AATGATCGTACGTCCTAGCAC 57.649 47.619 16.05 0.37 0.00 4.40
2977 3064 2.033141 GGCTTGAGTGGAGCAGCA 59.967 61.111 0.00 0.00 41.89 4.41
3012 3099 2.791560 GTCTCATTCGTGATGTGATCGG 59.208 50.000 8.64 0.00 39.61 4.18
3015 3102 4.097286 TCTCATTCGTGATGTGATCGGTAA 59.903 41.667 0.00 0.00 34.32 2.85
3145 3236 7.849804 ATATGACTAGCTTTTGTACACTTGG 57.150 36.000 0.00 0.00 0.00 3.61
3193 3450 6.398918 GGAGATTTGTGTACTGAGCTTTAGA 58.601 40.000 6.00 0.00 0.00 2.10
3221 3485 9.150348 CTGTGTTTGTTCCTTGATTTAAAGTTT 57.850 29.630 0.00 0.00 0.00 2.66
3260 3524 6.757897 TTGTCAGTAAGCAATAATGGAAGG 57.242 37.500 0.00 0.00 30.60 3.46
3275 3544 2.825532 TGGAAGGCCATTTCTTTAGTGC 59.174 45.455 5.01 0.00 39.92 4.40
3329 3598 7.387673 TGTGTCATAACCTGTCTCAGTATTTTG 59.612 37.037 0.00 0.00 0.00 2.44
3424 3702 4.647424 TCTGCACCAAAGTTTACAAAGG 57.353 40.909 0.00 0.00 0.00 3.11
3474 3752 7.786178 TGCATATACATACAGAACTTCAACC 57.214 36.000 0.00 0.00 0.00 3.77
3481 3759 7.581213 ACATACAGAACTTCAACCAATTTCA 57.419 32.000 0.00 0.00 0.00 2.69
3498 3776 7.171337 ACCAATTTCACATCATTTTGTAACTGC 59.829 33.333 0.00 0.00 0.00 4.40
3589 3867 3.003897 TGCAGTTTTTATTCCACGGACAC 59.996 43.478 0.00 0.00 0.00 3.67
3592 3870 5.768317 CAGTTTTTATTCCACGGACACAAT 58.232 37.500 0.00 0.00 0.00 2.71
3593 3871 6.212955 CAGTTTTTATTCCACGGACACAATT 58.787 36.000 0.00 0.00 0.00 2.32
3595 3873 7.223777 CAGTTTTTATTCCACGGACACAATTTT 59.776 33.333 0.00 0.00 0.00 1.82
3713 3993 1.832167 GGCACCTTCCCACAGCAAA 60.832 57.895 0.00 0.00 0.00 3.68
3715 3995 0.823356 GCACCTTCCCACAGCAAAGA 60.823 55.000 0.00 0.00 0.00 2.52
3720 4000 4.280677 CACCTTCCCACAGCAAAGAAAATA 59.719 41.667 0.00 0.00 0.00 1.40
3728 4008 6.599244 CCCACAGCAAAGAAAATATAGTCTCA 59.401 38.462 0.00 0.00 0.00 3.27
3732 4012 7.148573 ACAGCAAAGAAAATATAGTCTCACACG 60.149 37.037 0.00 0.00 0.00 4.49
3749 4029 2.294074 CACGAAACCCAAACTTCTCCA 58.706 47.619 0.00 0.00 0.00 3.86
3757 4037 5.319043 ACCCAAACTTCTCCAGATAAACA 57.681 39.130 0.00 0.00 0.00 2.83
3759 4039 5.770162 ACCCAAACTTCTCCAGATAAACAAG 59.230 40.000 0.00 0.00 0.00 3.16
3760 4040 5.335976 CCCAAACTTCTCCAGATAAACAAGC 60.336 44.000 0.00 0.00 0.00 4.01
3763 4043 2.024176 TCTCCAGATAAACAAGCCGC 57.976 50.000 0.00 0.00 0.00 6.53
3764 4044 1.277842 TCTCCAGATAAACAAGCCGCA 59.722 47.619 0.00 0.00 0.00 5.69
3765 4045 1.398390 CTCCAGATAAACAAGCCGCAC 59.602 52.381 0.00 0.00 0.00 5.34
3768 4048 1.135689 CAGATAAACAAGCCGCACCAC 60.136 52.381 0.00 0.00 0.00 4.16
3770 4050 0.881118 ATAAACAAGCCGCACCACTG 59.119 50.000 0.00 0.00 0.00 3.66
3771 4051 0.464735 TAAACAAGCCGCACCACTGT 60.465 50.000 0.00 0.00 0.00 3.55
3772 4052 2.003658 AAACAAGCCGCACCACTGTG 62.004 55.000 0.00 0.00 45.65 3.66
3773 4053 2.591429 CAAGCCGCACCACTGTGA 60.591 61.111 9.86 0.00 45.76 3.58
3807 4091 1.911357 AGAACCATCTGTCAGCATCCA 59.089 47.619 0.00 0.00 33.59 3.41
3815 4099 3.415212 TCTGTCAGCATCCAGGAAAAAG 58.585 45.455 0.00 0.00 0.00 2.27
3816 4100 1.888512 TGTCAGCATCCAGGAAAAAGC 59.111 47.619 0.00 0.00 0.00 3.51
3817 4101 2.165998 GTCAGCATCCAGGAAAAAGCT 58.834 47.619 0.00 0.00 0.00 3.74
3818 4102 3.244875 TGTCAGCATCCAGGAAAAAGCTA 60.245 43.478 8.30 0.00 0.00 3.32
3819 4103 3.376546 GTCAGCATCCAGGAAAAAGCTAG 59.623 47.826 8.30 0.00 0.00 3.42
3820 4104 3.264193 TCAGCATCCAGGAAAAAGCTAGA 59.736 43.478 8.30 6.65 0.00 2.43
3822 4106 4.096081 CAGCATCCAGGAAAAAGCTAGAAG 59.904 45.833 8.30 0.00 0.00 2.85
3823 4107 4.018960 AGCATCCAGGAAAAAGCTAGAAGA 60.019 41.667 7.16 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 119 3.217626 AGAACCTTGCAAGTCCAAGAAG 58.782 45.455 24.35 9.35 43.79 2.85
118 120 3.117888 AGAGAACCTTGCAAGTCCAAGAA 60.118 43.478 24.35 0.00 43.79 2.52
224 233 1.444836 TTTACGGCAGGGAATCAACG 58.555 50.000 0.00 0.00 0.00 4.10
260 269 7.375053 TGCCTCATTTTTGTGATAGGTTAAAC 58.625 34.615 0.00 0.00 0.00 2.01
261 270 7.531857 TGCCTCATTTTTGTGATAGGTTAAA 57.468 32.000 0.00 0.00 0.00 1.52
262 271 7.147915 GGATGCCTCATTTTTGTGATAGGTTAA 60.148 37.037 0.00 0.00 0.00 2.01
263 272 6.321181 GGATGCCTCATTTTTGTGATAGGTTA 59.679 38.462 0.00 0.00 0.00 2.85
327 336 4.051167 CTGGCCACCCATCCAGCA 62.051 66.667 0.00 0.00 42.79 4.41
388 397 6.211515 GGACATCTTACATGCATGAAAATCC 58.788 40.000 32.75 21.60 0.00 3.01
413 422 5.936956 CAGCACCCTCTGATTAAATATCTCC 59.063 44.000 0.00 0.00 36.19 3.71
423 432 6.705302 CATATACATACAGCACCCTCTGATT 58.295 40.000 0.00 0.00 37.51 2.57
426 435 4.020751 AGCATATACATACAGCACCCTCTG 60.021 45.833 0.00 0.00 39.86 3.35
454 463 0.944386 CCATATACGTGTGCCCTTGC 59.056 55.000 0.00 0.00 38.26 4.01
472 481 5.941555 ATGAACCTAGCTAGTATATGCCC 57.058 43.478 19.31 0.75 0.00 5.36
473 482 7.386851 TCAAATGAACCTAGCTAGTATATGCC 58.613 38.462 19.31 2.53 0.00 4.40
482 521 6.814954 AGGAAGATCAAATGAACCTAGCTA 57.185 37.500 0.00 0.00 0.00 3.32
511 550 0.608640 CTCCTTGTCCAGCTACCGTT 59.391 55.000 0.00 0.00 0.00 4.44
513 552 0.457851 CTCTCCTTGTCCAGCTACCG 59.542 60.000 0.00 0.00 0.00 4.02
906 972 4.553144 GGGGGTCTGAGGTGTGTA 57.447 61.111 0.00 0.00 0.00 2.90
939 1005 5.971493 AGGGAAGCTCCAGTATATTACTCT 58.029 41.667 0.00 0.00 38.64 3.24
975 1041 0.467804 TGTGTGAAGTGGTGCAGCTA 59.532 50.000 18.08 0.37 0.00 3.32
976 1042 1.097547 GTGTGTGAAGTGGTGCAGCT 61.098 55.000 18.08 0.00 0.00 4.24
994 1060 0.392998 GGCGAGGAATCCATGTGTGT 60.393 55.000 0.61 0.00 0.00 3.72
995 1061 1.431488 CGGCGAGGAATCCATGTGTG 61.431 60.000 0.00 0.00 0.00 3.82
996 1062 1.153369 CGGCGAGGAATCCATGTGT 60.153 57.895 0.00 0.00 0.00 3.72
997 1063 1.153369 ACGGCGAGGAATCCATGTG 60.153 57.895 16.62 0.00 0.00 3.21
1246 1312 3.670377 GGGCAGTTGGGCACGTTC 61.670 66.667 0.00 0.00 45.66 3.95
1735 1802 1.975327 CTTTCTGTCAGCCTCCCGA 59.025 57.895 0.00 0.00 0.00 5.14
1856 1923 4.796231 CCGGTTCGTCTGCGGAGG 62.796 72.222 9.00 9.00 38.89 4.30
1954 2021 0.464036 ATGTGGACGTCTGTGTGTGT 59.536 50.000 16.46 0.00 0.00 3.72
1955 2022 0.861185 CATGTGGACGTCTGTGTGTG 59.139 55.000 16.46 3.91 0.00 3.82
1956 2023 0.464036 ACATGTGGACGTCTGTGTGT 59.536 50.000 16.46 12.56 0.00 3.72
1976 2043 8.837788 TGCATCCAAATAGTTACTAGATCATG 57.162 34.615 0.00 0.00 0.00 3.07
2170 2242 7.464311 GCAAGATGCGTGATGATGAGATTATAG 60.464 40.741 0.00 0.00 31.71 1.31
2320 2402 2.163412 ACTTCTGCTCGCAACACAAAAA 59.837 40.909 0.00 0.00 0.00 1.94
2321 2403 1.742831 ACTTCTGCTCGCAACACAAAA 59.257 42.857 0.00 0.00 0.00 2.44
2347 2429 2.202440 CGGCCGTCGAGTGTGTAG 60.202 66.667 19.50 0.00 42.43 2.74
2826 2908 4.442705 CGCGCTACTTAATTATTCCGTTG 58.557 43.478 5.56 0.00 0.00 4.10
2833 2915 2.828877 TGGTGCGCGCTACTTAATTAT 58.171 42.857 33.29 0.00 0.00 1.28
2834 2916 2.296831 TGGTGCGCGCTACTTAATTA 57.703 45.000 33.29 5.03 0.00 1.40
2853 2935 4.348168 ACGATCATTAGGGGCTAACTGATT 59.652 41.667 0.00 0.00 31.35 2.57
2856 2938 3.753294 ACGATCATTAGGGGCTAACTG 57.247 47.619 0.00 0.00 0.00 3.16
2859 2941 3.225104 ACGTACGATCATTAGGGGCTAA 58.775 45.455 24.41 0.00 0.00 3.09
2871 2958 2.097142 ACTTGTGCTAGGACGTACGATC 59.903 50.000 24.41 15.06 0.00 3.69
2873 2960 1.527034 ACTTGTGCTAGGACGTACGA 58.473 50.000 24.41 0.00 0.00 3.43
2874 2961 1.983605 CAACTTGTGCTAGGACGTACG 59.016 52.381 15.01 15.01 0.00 3.67
2875 2962 2.288640 ACCAACTTGTGCTAGGACGTAC 60.289 50.000 10.02 0.00 0.00 3.67
2876 2963 1.965643 ACCAACTTGTGCTAGGACGTA 59.034 47.619 10.02 0.00 0.00 3.57
2877 2964 0.756903 ACCAACTTGTGCTAGGACGT 59.243 50.000 10.02 0.00 0.00 4.34
2878 2965 2.736144 TACCAACTTGTGCTAGGACG 57.264 50.000 10.02 0.00 0.00 4.79
2879 2966 4.565564 CGTTATACCAACTTGTGCTAGGAC 59.434 45.833 7.56 7.56 0.00 3.85
2880 2967 4.463539 TCGTTATACCAACTTGTGCTAGGA 59.536 41.667 0.00 0.00 0.00 2.94
2881 2968 4.751060 TCGTTATACCAACTTGTGCTAGG 58.249 43.478 0.00 0.00 0.00 3.02
2882 2969 5.647589 TCTCGTTATACCAACTTGTGCTAG 58.352 41.667 0.00 0.00 0.00 3.42
2883 2970 5.648178 TCTCGTTATACCAACTTGTGCTA 57.352 39.130 0.00 0.00 0.00 3.49
2884 2971 4.530710 TCTCGTTATACCAACTTGTGCT 57.469 40.909 0.00 0.00 0.00 4.40
2885 2972 5.121768 ACAATCTCGTTATACCAACTTGTGC 59.878 40.000 0.00 0.00 0.00 4.57
2886 2973 6.721571 ACAATCTCGTTATACCAACTTGTG 57.278 37.500 0.00 0.00 0.00 3.33
2887 2974 7.739498 AAACAATCTCGTTATACCAACTTGT 57.261 32.000 0.00 0.00 0.00 3.16
2888 2975 8.504005 AGAAAACAATCTCGTTATACCAACTTG 58.496 33.333 0.00 0.00 0.00 3.16
3012 3099 3.377172 CCCTCACAAATCCATCCGTTTAC 59.623 47.826 0.00 0.00 0.00 2.01
3015 3102 1.955208 GCCCTCACAAATCCATCCGTT 60.955 52.381 0.00 0.00 0.00 4.44
3145 3236 7.998964 TCCCAAATAATTATCTCTTCCTCCAAC 59.001 37.037 0.00 0.00 0.00 3.77
3193 3450 6.463995 TTAAATCAAGGAACAAACACAGCT 57.536 33.333 0.00 0.00 0.00 4.24
3221 3485 8.604640 TTACTGACAATTCACACCGTTTATTA 57.395 30.769 0.00 0.00 0.00 0.98
3260 3524 8.652810 AATCAATTATGCACTAAAGAAATGGC 57.347 30.769 0.00 0.00 0.00 4.40
3341 3618 3.836365 TTGGATATCAGGCGAACATCA 57.164 42.857 4.83 0.00 0.00 3.07
3404 3682 4.385358 ACCTTTGTAAACTTTGGTGCAG 57.615 40.909 0.00 0.00 0.00 4.41
3458 3736 7.424803 TGTGAAATTGGTTGAAGTTCTGTATG 58.575 34.615 4.17 0.00 39.04 2.39
3467 3745 8.145316 ACAAAATGATGTGAAATTGGTTGAAG 57.855 30.769 0.00 0.00 30.82 3.02
3474 3752 8.074474 TGCAGTTACAAAATGATGTGAAATTG 57.926 30.769 0.00 0.00 34.75 2.32
3481 3759 8.140628 TGTACATTTGCAGTTACAAAATGATGT 58.859 29.630 18.28 9.11 42.45 3.06
3498 3776 6.746104 TCAAACAAGCGAAATGTACATTTG 57.254 33.333 32.90 24.63 40.77 2.32
3549 3827 2.621526 TGCAGACACTTCTCTCGTGTAA 59.378 45.455 0.00 0.00 44.95 2.41
3553 3831 1.323412 ACTGCAGACACTTCTCTCGT 58.677 50.000 23.35 0.00 0.00 4.18
3708 3988 7.097192 TCGTGTGAGACTATATTTTCTTTGCT 58.903 34.615 0.00 0.00 0.00 3.91
3710 3990 9.530129 GTTTCGTGTGAGACTATATTTTCTTTG 57.470 33.333 0.00 0.00 0.00 2.77
3713 3993 6.817140 GGGTTTCGTGTGAGACTATATTTTCT 59.183 38.462 0.00 0.00 30.26 2.52
3715 3995 6.469410 TGGGTTTCGTGTGAGACTATATTTT 58.531 36.000 0.00 0.00 30.26 1.82
3720 4000 4.062991 GTTTGGGTTTCGTGTGAGACTAT 58.937 43.478 0.00 0.00 30.26 2.12
3728 4008 2.294979 GGAGAAGTTTGGGTTTCGTGT 58.705 47.619 0.00 0.00 0.00 4.49
3732 4012 6.264518 TGTTTATCTGGAGAAGTTTGGGTTTC 59.735 38.462 0.00 0.00 0.00 2.78
3749 4029 1.165270 GTGGTGCGGCTTGTTTATCT 58.835 50.000 0.00 0.00 0.00 1.98
3757 4037 2.116983 ATCTCACAGTGGTGCGGCTT 62.117 55.000 0.00 0.00 44.87 4.35
3759 4039 2.046892 ATCTCACAGTGGTGCGGC 60.047 61.111 0.00 0.00 44.87 6.53
3760 4040 2.393768 GCATCTCACAGTGGTGCGG 61.394 63.158 0.00 0.00 44.87 5.69
3763 4043 1.596603 TGTTGCATCTCACAGTGGTG 58.403 50.000 0.00 0.00 46.66 4.17
3764 4044 2.346766 TTGTTGCATCTCACAGTGGT 57.653 45.000 0.00 0.00 0.00 4.16
3765 4045 3.079578 AGATTGTTGCATCTCACAGTGG 58.920 45.455 0.00 0.00 0.00 4.00
3768 4048 5.064452 GGTTCTAGATTGTTGCATCTCACAG 59.936 44.000 0.00 0.00 0.00 3.66
3770 4050 4.937620 TGGTTCTAGATTGTTGCATCTCAC 59.062 41.667 0.00 0.00 0.00 3.51
3771 4051 5.164620 TGGTTCTAGATTGTTGCATCTCA 57.835 39.130 0.00 0.00 0.00 3.27
3772 4052 6.018098 CAGATGGTTCTAGATTGTTGCATCTC 60.018 42.308 0.00 0.00 0.00 2.75
3773 4053 5.821470 CAGATGGTTCTAGATTGTTGCATCT 59.179 40.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.