Multiple sequence alignment - TraesCS4D01G075300

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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 TraesCS4D01G075300 chr4D 100.000 3410 0 0 1 3410 49888548 49891957 0.000000e+00 6298.0
1 TraesCS4D01G075300 chr4B 95.450 2044 63 14 797 2820 73469864 73471897 0.000000e+00 3232.0
2 TraesCS4D01G075300 chr4B 98.512 336 5 0 3075 3410 73471891 73472226 8.150000e-166 593.0
3 TraesCS4D01G075300 chr4A 92.264 2107 111 18 760 2836 547204831 547202747 0.000000e+00 2940.0
4 TraesCS4D01G075300 chr4A 83.993 581 62 19 2856 3410 547202693 547202118 2.330000e-146 529.0
5 TraesCS4D01G075300 chr4A 97.059 34 1 0 1974 2007 96107588 96107621 1.320000e-04 58.4
6 TraesCS4D01G075300 chr7D 92.033 728 53 4 1 725 198712480 198711755 0.000000e+00 1018.0
7 TraesCS4D01G075300 chr2D 89.730 740 51 11 1 722 593149905 593150637 0.000000e+00 922.0
8 TraesCS4D01G075300 chr2D 86.889 389 24 13 346 725 15678657 15678287 8.810000e-111 411.0
9 TraesCS4D01G075300 chr2D 86.494 348 25 2 1 326 15678995 15678648 2.500000e-96 363.0
10 TraesCS4D01G075300 chr6D 89.754 732 58 6 1 725 421770608 421769887 0.000000e+00 920.0
11 TraesCS4D01G075300 chr6B 91.365 498 41 2 1 497 634943866 634944362 0.000000e+00 680.0
12 TraesCS4D01G075300 chr6B 80.350 743 101 33 1 710 91246720 91245990 3.900000e-144 521.0
13 TraesCS4D01G075300 chr3A 82.759 754 96 17 1 725 46453119 46453867 2.870000e-180 641.0
14 TraesCS4D01G075300 chr1D 80.662 755 109 22 1 725 165558211 165557464 4.970000e-153 551.0
15 TraesCS4D01G075300 chr7B 78.324 752 116 22 1 720 672411843 672411107 3.120000e-120 442.0
16 TraesCS4D01G075300 chr2B 75.888 676 125 26 1 648 485749192 485748527 9.190000e-81 311.0
17 TraesCS4D01G075300 chr2B 74.859 533 84 24 1 497 768925728 768925210 2.680000e-46 196.0
18 TraesCS4D01G075300 chrUn 81.148 366 54 11 320 677 70162174 70161816 2.590000e-71 279.0
19 TraesCS4D01G075300 chr6A 76.596 564 85 23 94 625 16838417 16838965 2.020000e-67 267.0
20 TraesCS4D01G075300 chr6A 79.717 212 42 1 1 211 216002198 216002409 5.890000e-33 152.0
21 TraesCS4D01G075300 chr3D 80.055 366 61 10 320 678 580594064 580593704 9.390000e-66 261.0


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 TraesCS4D01G075300 chr4D 49888548 49891957 3409 False 6298.0 6298 100.0000 1 3410 1 chr4D.!!$F1 3409
1 TraesCS4D01G075300 chr4B 73469864 73472226 2362 False 1912.5 3232 96.9810 797 3410 2 chr4B.!!$F1 2613
2 TraesCS4D01G075300 chr4A 547202118 547204831 2713 True 1734.5 2940 88.1285 760 3410 2 chr4A.!!$R1 2650
3 TraesCS4D01G075300 chr7D 198711755 198712480 725 True 1018.0 1018 92.0330 1 725 1 chr7D.!!$R1 724
4 TraesCS4D01G075300 chr2D 593149905 593150637 732 False 922.0 922 89.7300 1 722 1 chr2D.!!$F1 721
5 TraesCS4D01G075300 chr2D 15678287 15678995 708 True 387.0 411 86.6915 1 725 2 chr2D.!!$R1 724
6 TraesCS4D01G075300 chr6D 421769887 421770608 721 True 920.0 920 89.7540 1 725 1 chr6D.!!$R1 724
7 TraesCS4D01G075300 chr6B 91245990 91246720 730 True 521.0 521 80.3500 1 710 1 chr6B.!!$R1 709
8 TraesCS4D01G075300 chr3A 46453119 46453867 748 False 641.0 641 82.7590 1 725 1 chr3A.!!$F1 724
9 TraesCS4D01G075300 chr1D 165557464 165558211 747 True 551.0 551 80.6620 1 725 1 chr1D.!!$R1 724
10 TraesCS4D01G075300 chr7B 672411107 672411843 736 True 442.0 442 78.3240 1 720 1 chr7B.!!$R1 719
11 TraesCS4D01G075300 chr2B 485748527 485749192 665 True 311.0 311 75.8880 1 648 1 chr2B.!!$R1 647
12 TraesCS4D01G075300 chr6A 16838417 16838965 548 False 267.0 267 76.5960 94 625 1 chr6A.!!$F1 531

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
981 1121 0.532862 CCAAACGATCCCCATCTCCG 60.533 60.0 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2968 3161 0.586319 CCAGTAGTTGTGGTTGTGCG 59.414 55.0 0.0 0.0 0.0 5.34 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
56 60 2.359478 CCACTTTAGCGCCCCGTT 60.359 61.111 2.29 0.00 0.00 4.44
80 84 2.472695 TGCATCTTTTCAGTACCGCT 57.527 45.000 0.00 0.00 0.00 5.52
117 122 1.134098 ACCATCCAACTATTCCTGCCG 60.134 52.381 0.00 0.00 0.00 5.69
193 198 1.742308 ACTCCACATGTTACCCCTGT 58.258 50.000 0.00 0.00 0.00 4.00
288 318 0.548926 TGCTGGTAAGATGGGTGGGA 60.549 55.000 0.00 0.00 0.00 4.37
294 324 1.279025 TAAGATGGGTGGGACAGGGC 61.279 60.000 0.00 0.00 41.80 5.19
312 351 3.195396 AGGGCGTGCATGAAAAATTACAT 59.805 39.130 10.93 0.00 0.00 2.29
313 352 4.400884 AGGGCGTGCATGAAAAATTACATA 59.599 37.500 10.93 0.00 0.00 2.29
314 353 4.739716 GGGCGTGCATGAAAAATTACATAG 59.260 41.667 10.93 0.00 0.00 2.23
315 354 4.207019 GGCGTGCATGAAAAATTACATAGC 59.793 41.667 10.93 0.00 0.00 2.97
343 382 3.815856 AGTGAAGAGATGCACATCGAT 57.184 42.857 5.04 0.00 42.48 3.59
439 515 4.762289 ACCTCATAGGAAGTTGGATCAC 57.238 45.455 0.00 0.00 37.67 3.06
497 581 4.216257 CCAAGCAGTACTAAAGTTGCACAT 59.784 41.667 8.94 0.00 35.00 3.21
633 739 6.978343 AAACGGATCTGAATTCGAACATAA 57.022 33.333 9.00 0.00 35.80 1.90
687 797 8.514330 AAAACCCGAATAAATACAAGCAGATA 57.486 30.769 0.00 0.00 0.00 1.98
689 800 7.672983 ACCCGAATAAATACAAGCAGATATG 57.327 36.000 0.00 0.00 0.00 1.78
725 839 1.069358 TGTGACCAGTGTGAACGCATA 59.931 47.619 0.00 0.00 0.00 3.14
726 840 2.139917 GTGACCAGTGTGAACGCATAA 58.860 47.619 0.00 0.00 0.00 1.90
727 841 2.742053 GTGACCAGTGTGAACGCATAAT 59.258 45.455 0.00 0.00 0.00 1.28
728 842 3.930229 GTGACCAGTGTGAACGCATAATA 59.070 43.478 0.00 0.00 0.00 0.98
729 843 4.390603 GTGACCAGTGTGAACGCATAATAA 59.609 41.667 0.00 0.00 0.00 1.40
730 844 4.998033 TGACCAGTGTGAACGCATAATAAA 59.002 37.500 0.00 0.00 0.00 1.40
731 845 5.121611 TGACCAGTGTGAACGCATAATAAAG 59.878 40.000 0.00 0.00 0.00 1.85
732 846 5.242434 ACCAGTGTGAACGCATAATAAAGA 58.758 37.500 0.00 0.00 0.00 2.52
733 847 5.880332 ACCAGTGTGAACGCATAATAAAGAT 59.120 36.000 0.00 0.00 0.00 2.40
734 848 7.045416 ACCAGTGTGAACGCATAATAAAGATA 58.955 34.615 0.00 0.00 0.00 1.98
735 849 7.551262 ACCAGTGTGAACGCATAATAAAGATAA 59.449 33.333 0.00 0.00 0.00 1.75
736 850 8.559536 CCAGTGTGAACGCATAATAAAGATAAT 58.440 33.333 0.00 0.00 0.00 1.28
737 851 9.935682 CAGTGTGAACGCATAATAAAGATAATT 57.064 29.630 0.00 0.00 0.00 1.40
765 879 8.358582 ACGAATAAAAAGAGAGGGAGTACTTA 57.641 34.615 0.00 0.00 0.00 2.24
777 891 8.840200 AGAGGGAGTACTTATGATGAACTTTA 57.160 34.615 0.00 0.00 0.00 1.85
811 932 4.788925 TCCTTTCCAAAAGAAGACCTGA 57.211 40.909 1.06 0.00 35.40 3.86
870 991 1.132453 CGCATCGAGTCTGGACTTGTA 59.868 52.381 15.19 5.60 42.66 2.41
872 993 2.480416 GCATCGAGTCTGGACTTGTAGG 60.480 54.545 15.19 8.86 42.66 3.18
944 1081 3.243907 CGAAAGGCCTCCTCCTATTACAG 60.244 52.174 5.23 0.00 34.82 2.74
948 1085 2.373502 GGCCTCCTCCTATTACAGCAAT 59.626 50.000 0.00 0.00 0.00 3.56
954 1094 4.404394 TCCTCCTATTACAGCAATCGAACA 59.596 41.667 0.00 0.00 0.00 3.18
981 1121 0.532862 CCAAACGATCCCCATCTCCG 60.533 60.000 0.00 0.00 0.00 4.63
1089 1236 1.065636 ACCATACTCGACACTCTCGGA 60.066 52.381 0.00 0.00 43.16 4.55
1344 1491 0.246635 TCTTCTACTTCCGCTGCACC 59.753 55.000 0.00 0.00 0.00 5.01
1566 1713 4.933064 CTCCTCGCCATCGCCGTC 62.933 72.222 0.00 0.00 35.26 4.79
1674 1821 2.286578 ATCCCCGGTGGCCCTTTA 60.287 61.111 0.00 0.00 0.00 1.85
1677 1824 2.608550 CCCCGGTGGCCCTTTAAGA 61.609 63.158 0.00 0.00 0.00 2.10
1733 1880 3.974835 TACCGGCGCTGGTCTACGA 62.975 63.158 42.92 23.90 42.62 3.43
1785 1932 2.439553 ATTGGCGGCTTTGGAGGGAA 62.440 55.000 11.43 0.00 0.00 3.97
2038 2185 0.461961 ATTGCCGGAGACTAGACTGC 59.538 55.000 5.05 1.04 0.00 4.40
2109 2256 1.119015 GTGACGATGACGACGACGAC 61.119 60.000 15.32 8.68 42.66 4.34
2110 2257 1.922220 GACGATGACGACGACGACG 60.922 63.158 17.60 17.60 42.66 5.12
2111 2258 2.271024 GACGATGACGACGACGACGA 62.271 60.000 25.15 5.17 41.06 4.20
2112 2259 1.922220 CGATGACGACGACGACGAC 60.922 63.158 25.15 19.21 41.06 4.34
2127 2274 2.205074 GACGACGATGAAGATGGCATT 58.795 47.619 0.00 0.00 0.00 3.56
2247 2394 1.520564 CGCGTGCTACCTTGCCATA 60.521 57.895 0.00 0.00 0.00 2.74
2346 2493 1.523934 CTCGGCGTTCTGTTTTACGTT 59.476 47.619 6.85 0.00 39.80 3.99
2368 2515 3.062763 CTCACAAGAACATTGCTCGAGT 58.937 45.455 15.13 0.00 0.00 4.18
2740 2891 6.114187 ACACATCAGACCACAATAGAGAAA 57.886 37.500 0.00 0.00 0.00 2.52
2836 2987 8.095452 ACAGGGAAGAACTTGTAAGATGATAT 57.905 34.615 0.00 0.00 0.00 1.63
2837 2988 8.552296 ACAGGGAAGAACTTGTAAGATGATATT 58.448 33.333 0.00 0.00 0.00 1.28
2838 2989 9.050601 CAGGGAAGAACTTGTAAGATGATATTC 57.949 37.037 0.00 0.00 0.00 1.75
2839 2990 8.997734 AGGGAAGAACTTGTAAGATGATATTCT 58.002 33.333 0.00 0.00 0.00 2.40
2840 2991 9.050601 GGGAAGAACTTGTAAGATGATATTCTG 57.949 37.037 0.00 0.00 0.00 3.02
2844 2995 8.887717 AGAACTTGTAAGATGATATTCTGTTGC 58.112 33.333 0.00 0.00 0.00 4.17
2845 2996 8.798859 AACTTGTAAGATGATATTCTGTTGCT 57.201 30.769 0.00 0.00 0.00 3.91
2846 2997 8.430801 ACTTGTAAGATGATATTCTGTTGCTC 57.569 34.615 0.00 0.00 0.00 4.26
2847 2998 8.043113 ACTTGTAAGATGATATTCTGTTGCTCA 58.957 33.333 0.00 0.00 0.00 4.26
2848 2999 8.791327 TTGTAAGATGATATTCTGTTGCTCAA 57.209 30.769 0.00 0.00 0.00 3.02
2849 3000 8.429493 TGTAAGATGATATTCTGTTGCTCAAG 57.571 34.615 0.00 0.00 0.00 3.02
2850 3001 8.043113 TGTAAGATGATATTCTGTTGCTCAAGT 58.957 33.333 0.00 0.00 0.00 3.16
2851 3002 9.534565 GTAAGATGATATTCTGTTGCTCAAGTA 57.465 33.333 0.00 0.00 0.00 2.24
2853 3004 9.624373 AAGATGATATTCTGTTGCTCAAGTATT 57.376 29.630 0.00 0.00 0.00 1.89
2854 3005 9.624373 AGATGATATTCTGTTGCTCAAGTATTT 57.376 29.630 0.00 0.00 0.00 1.40
2867 3052 7.422399 TGCTCAAGTATTTTGTTCACCTTAAC 58.578 34.615 0.00 0.00 0.00 2.01
2874 3059 8.576442 AGTATTTTGTTCACCTTAACTTCCATG 58.424 33.333 0.00 0.00 0.00 3.66
2878 3063 6.870971 TGTTCACCTTAACTTCCATGTTAC 57.129 37.500 0.00 0.00 32.84 2.50
2879 3064 5.766174 TGTTCACCTTAACTTCCATGTTACC 59.234 40.000 0.00 0.00 32.84 2.85
2880 3065 4.571919 TCACCTTAACTTCCATGTTACCG 58.428 43.478 0.00 0.00 32.84 4.02
2896 3081 6.308371 TGTTACCGTTTTCTTCAGGATTTC 57.692 37.500 0.00 0.00 0.00 2.17
2897 3082 5.239963 TGTTACCGTTTTCTTCAGGATTTCC 59.760 40.000 0.00 0.00 0.00 3.13
2899 3084 4.407365 ACCGTTTTCTTCAGGATTTCCAT 58.593 39.130 0.00 0.00 38.89 3.41
2900 3085 4.218417 ACCGTTTTCTTCAGGATTTCCATG 59.782 41.667 0.00 0.00 38.89 3.66
2901 3086 4.168760 CGTTTTCTTCAGGATTTCCATGC 58.831 43.478 0.00 0.00 38.89 4.06
2903 3088 5.540911 GTTTTCTTCAGGATTTCCATGCAA 58.459 37.500 0.00 0.00 38.89 4.08
2905 3090 4.038271 TCTTCAGGATTTCCATGCAAGT 57.962 40.909 0.00 0.00 38.89 3.16
2906 3091 4.012374 TCTTCAGGATTTCCATGCAAGTC 58.988 43.478 0.00 0.00 38.89 3.01
2907 3092 2.726821 TCAGGATTTCCATGCAAGTCC 58.273 47.619 2.69 2.69 38.89 3.85
2934 3127 1.780919 ACCCTAACCTTTGGAGCACTT 59.219 47.619 0.00 0.00 0.00 3.16
2952 3145 5.068460 AGCACTTGTAAAACAAAGCCATACA 59.932 36.000 11.15 0.00 38.91 2.29
2958 3151 7.721286 TGTAAAACAAAGCCATACATTTTGG 57.279 32.000 1.88 0.00 36.41 3.28
2960 3153 7.987458 TGTAAAACAAAGCCATACATTTTGGAA 59.013 29.630 0.00 0.00 36.41 3.53
2961 3154 7.872113 AAAACAAAGCCATACATTTTGGAAA 57.128 28.000 0.00 0.00 36.41 3.13
2962 3155 7.872113 AAACAAAGCCATACATTTTGGAAAA 57.128 28.000 0.00 0.00 36.41 2.29
2963 3156 8.462589 AAACAAAGCCATACATTTTGGAAAAT 57.537 26.923 0.00 0.00 39.07 1.82
3000 3193 4.202357 ACAACTACTGGAGCAACTGAATCA 60.202 41.667 0.00 0.00 0.00 2.57
3002 3195 4.573900 ACTACTGGAGCAACTGAATCAAG 58.426 43.478 0.00 0.00 0.00 3.02
3003 3196 2.787994 ACTGGAGCAACTGAATCAAGG 58.212 47.619 0.00 0.00 0.00 3.61
3004 3197 2.089980 CTGGAGCAACTGAATCAAGGG 58.910 52.381 0.00 0.00 0.00 3.95
3006 3199 1.615384 GGAGCAACTGAATCAAGGGCT 60.615 52.381 2.51 2.51 35.45 5.19
3023 3238 2.772515 GGGCTAACACCTAATGACCTCT 59.227 50.000 0.00 0.00 0.00 3.69
3058 3273 7.338957 AGAAATAGGAGCCTTCATCAGAAAAAG 59.661 37.037 0.00 0.00 32.35 2.27
3059 3274 4.647564 AGGAGCCTTCATCAGAAAAAGA 57.352 40.909 0.00 0.00 32.35 2.52
3061 3276 5.388654 AGGAGCCTTCATCAGAAAAAGAAA 58.611 37.500 0.00 0.00 32.35 2.52
3077 3295 4.808414 AAGAAAAATCAAGGGCTTAGGC 57.192 40.909 0.00 0.00 37.82 3.93
3205 3423 8.073355 GGATACAAGGAACATACTACAAATCG 57.927 38.462 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 60 4.570772 GCGGTACTGAAAAGATGCATAGAA 59.429 41.667 5.68 0.00 0.00 2.10
80 84 3.304911 TGGTGAAAACTGGACATCCAA 57.695 42.857 1.50 0.00 46.97 3.53
117 122 0.388649 ACGAAGTCGCACATCTCACC 60.389 55.000 0.00 0.00 44.43 4.02
193 198 5.353394 ACTCCTTGTGTAGTTTGAGTTGA 57.647 39.130 0.00 0.00 29.20 3.18
288 318 0.968405 ATTTTTCATGCACGCCCTGT 59.032 45.000 0.00 0.00 0.00 4.00
294 324 5.229887 GTGGCTATGTAATTTTTCATGCACG 59.770 40.000 0.00 0.00 0.00 5.34
312 351 4.382040 GCATCTCTTCACTACTTGTGGCTA 60.382 45.833 0.00 0.00 46.20 3.93
313 352 3.618507 GCATCTCTTCACTACTTGTGGCT 60.619 47.826 0.00 0.00 46.20 4.75
314 353 2.675348 GCATCTCTTCACTACTTGTGGC 59.325 50.000 0.00 0.00 46.20 5.01
315 354 3.681897 GTGCATCTCTTCACTACTTGTGG 59.318 47.826 0.00 0.00 46.20 4.17
330 369 4.142609 ACCTTGTAATCGATGTGCATCT 57.857 40.909 0.00 0.00 35.72 2.90
332 371 5.023533 ACTACCTTGTAATCGATGTGCAT 57.976 39.130 0.00 0.00 0.00 3.96
343 382 1.271707 GCCCTGCCAACTACCTTGTAA 60.272 52.381 0.00 0.00 0.00 2.41
497 581 4.409718 TGGTGCAACTCTGTTAGTACAA 57.590 40.909 2.04 0.00 37.50 2.41
737 851 9.638176 AGTACTCCCTCTCTTTTTATTCGTATA 57.362 33.333 0.00 0.00 0.00 1.47
738 852 8.536340 AGTACTCCCTCTCTTTTTATTCGTAT 57.464 34.615 0.00 0.00 0.00 3.06
739 853 7.951347 AGTACTCCCTCTCTTTTTATTCGTA 57.049 36.000 0.00 0.00 0.00 3.43
740 854 6.854091 AGTACTCCCTCTCTTTTTATTCGT 57.146 37.500 0.00 0.00 0.00 3.85
741 855 9.250624 CATAAGTACTCCCTCTCTTTTTATTCG 57.749 37.037 0.00 0.00 0.00 3.34
745 859 9.488762 TCATCATAAGTACTCCCTCTCTTTTTA 57.511 33.333 0.00 0.00 0.00 1.52
746 860 8.380742 TCATCATAAGTACTCCCTCTCTTTTT 57.619 34.615 0.00 0.00 0.00 1.94
747 861 7.979786 TCATCATAAGTACTCCCTCTCTTTT 57.020 36.000 0.00 0.00 0.00 2.27
748 862 7.621683 AGTTCATCATAAGTACTCCCTCTCTTT 59.378 37.037 0.00 0.00 0.00 2.52
749 863 7.129425 AGTTCATCATAAGTACTCCCTCTCTT 58.871 38.462 0.00 0.00 0.00 2.85
750 864 6.678547 AGTTCATCATAAGTACTCCCTCTCT 58.321 40.000 0.00 0.00 0.00 3.10
751 865 6.969993 AGTTCATCATAAGTACTCCCTCTC 57.030 41.667 0.00 0.00 0.00 3.20
752 866 7.741554 AAAGTTCATCATAAGTACTCCCTCT 57.258 36.000 0.00 0.00 0.00 3.69
777 891 7.403231 TCTTTTGGAAAGGATCAGGTCTACTAT 59.597 37.037 0.00 0.00 0.00 2.12
785 901 4.460731 GGTCTTCTTTTGGAAAGGATCAGG 59.539 45.833 0.00 0.00 33.07 3.86
811 932 9.898152 TTTTGGATTTTATTTCAGTTGTCCTTT 57.102 25.926 0.00 0.00 0.00 3.11
842 963 3.046390 CCAGACTCGATGCGAAAGATAC 58.954 50.000 0.00 0.00 34.74 2.24
870 991 4.467107 GGGTCTCCTCGCCTCCCT 62.467 72.222 0.00 0.00 35.63 4.20
872 993 3.151022 CAGGGTCTCCTCGCCTCC 61.151 72.222 0.00 0.00 42.67 4.30
944 1081 2.175811 GCCGTGGTGTTCGATTGC 59.824 61.111 0.00 0.00 0.00 3.56
948 1085 3.402095 TTTGGGCCGTGGTGTTCGA 62.402 57.895 0.00 0.00 0.00 3.71
954 1094 2.359478 GATCGTTTGGGCCGTGGT 60.359 61.111 0.00 0.00 0.00 4.16
981 1121 1.783031 TATCTTCTCGGTCTCGCGGC 61.783 60.000 6.13 0.00 36.13 6.53
986 1126 1.068194 CCGCCATATCTTCTCGGTCTC 60.068 57.143 0.00 0.00 35.75 3.36
987 1127 0.962489 CCGCCATATCTTCTCGGTCT 59.038 55.000 0.00 0.00 35.75 3.85
1065 1212 0.530744 GAGTGTCGAGTATGGTGGCA 59.469 55.000 0.00 0.00 0.00 4.92
1089 1236 0.891373 CGATGCGGGTGATATCCTCT 59.109 55.000 0.00 0.00 0.00 3.69
1566 1713 1.376037 GAACCAGAAGGCGGTGAGG 60.376 63.158 0.00 0.00 36.67 3.86
1671 1818 4.757149 GCCAGCTCAAGAAGAACTCTTAAA 59.243 41.667 0.00 0.00 42.84 1.52
1672 1819 4.319177 GCCAGCTCAAGAAGAACTCTTAA 58.681 43.478 0.00 0.00 42.84 1.85
1674 1821 2.551938 GGCCAGCTCAAGAAGAACTCTT 60.552 50.000 0.00 0.00 45.80 2.85
1677 1824 0.767375 TGGCCAGCTCAAGAAGAACT 59.233 50.000 0.00 0.00 0.00 3.01
1877 2024 1.818060 TCGAATTGGGTGAATTGCCAG 59.182 47.619 0.00 0.00 34.18 4.85
2038 2185 4.130118 GGTACCCTCAGTTCAGCAATATG 58.870 47.826 0.00 0.00 0.00 1.78
2109 2256 1.262417 CCAATGCCATCTTCATCGTCG 59.738 52.381 0.00 0.00 0.00 5.12
2110 2257 1.605710 CCCAATGCCATCTTCATCGTC 59.394 52.381 0.00 0.00 0.00 4.20
2111 2258 1.064463 ACCCAATGCCATCTTCATCGT 60.064 47.619 0.00 0.00 0.00 3.73
2112 2259 1.683943 ACCCAATGCCATCTTCATCG 58.316 50.000 0.00 0.00 0.00 3.84
2127 2274 2.615465 CCCTGATGAGCCCAACCCA 61.615 63.158 0.00 0.00 0.00 4.51
2247 2394 4.820744 ATGCCGAGCCCCGCAATT 62.821 61.111 0.00 0.00 36.84 2.32
2307 2454 4.515404 GTGATGGACACCGGTAGC 57.485 61.111 6.87 1.12 43.05 3.58
2346 2493 3.243873 ACTCGAGCAATGTTCTTGTGAGA 60.244 43.478 13.61 0.00 0.00 3.27
2368 2515 3.191162 GTGGAGCACTGCATAACAAATGA 59.809 43.478 3.30 0.00 32.40 2.57
2836 2987 6.972328 GTGAACAAAATACTTGAGCAACAGAA 59.028 34.615 0.00 0.00 0.00 3.02
2837 2988 6.459573 GGTGAACAAAATACTTGAGCAACAGA 60.460 38.462 0.00 0.00 0.00 3.41
2838 2989 5.687285 GGTGAACAAAATACTTGAGCAACAG 59.313 40.000 0.00 0.00 0.00 3.16
2839 2990 5.359576 AGGTGAACAAAATACTTGAGCAACA 59.640 36.000 0.00 0.00 0.00 3.33
2840 2991 5.831997 AGGTGAACAAAATACTTGAGCAAC 58.168 37.500 0.00 0.00 0.00 4.17
2842 2993 7.284489 AGTTAAGGTGAACAAAATACTTGAGCA 59.716 33.333 0.00 0.00 0.00 4.26
2843 2994 7.649057 AGTTAAGGTGAACAAAATACTTGAGC 58.351 34.615 0.00 0.00 0.00 4.26
2844 2995 9.665264 GAAGTTAAGGTGAACAAAATACTTGAG 57.335 33.333 0.00 0.00 0.00 3.02
2845 2996 8.626526 GGAAGTTAAGGTGAACAAAATACTTGA 58.373 33.333 0.00 0.00 0.00 3.02
2846 2997 8.410141 TGGAAGTTAAGGTGAACAAAATACTTG 58.590 33.333 0.00 0.00 0.00 3.16
2847 2998 8.528044 TGGAAGTTAAGGTGAACAAAATACTT 57.472 30.769 0.00 0.00 0.00 2.24
2848 2999 8.576442 CATGGAAGTTAAGGTGAACAAAATACT 58.424 33.333 0.00 0.00 0.00 2.12
2849 3000 8.357402 ACATGGAAGTTAAGGTGAACAAAATAC 58.643 33.333 0.00 0.00 0.00 1.89
2850 3001 8.472007 ACATGGAAGTTAAGGTGAACAAAATA 57.528 30.769 0.00 0.00 0.00 1.40
2851 3002 7.360113 ACATGGAAGTTAAGGTGAACAAAAT 57.640 32.000 0.00 0.00 0.00 1.82
2853 3004 6.783708 AACATGGAAGTTAAGGTGAACAAA 57.216 33.333 0.00 0.00 0.00 2.83
2854 3005 6.263617 GGTAACATGGAAGTTAAGGTGAACAA 59.736 38.462 0.00 0.00 35.88 2.83
2867 3052 5.334879 CCTGAAGAAAACGGTAACATGGAAG 60.335 44.000 0.00 0.00 0.00 3.46
2874 3059 5.239963 TGGAAATCCTGAAGAAAACGGTAAC 59.760 40.000 0.44 0.00 36.82 2.50
2878 3063 4.737054 CATGGAAATCCTGAAGAAAACGG 58.263 43.478 0.44 0.00 36.82 4.44
2879 3064 4.168760 GCATGGAAATCCTGAAGAAAACG 58.831 43.478 0.44 0.00 36.82 3.60
2880 3065 5.138125 TGCATGGAAATCCTGAAGAAAAC 57.862 39.130 0.44 0.00 36.82 2.43
2896 3081 0.883833 GTTCTGTGGGACTTGCATGG 59.116 55.000 4.44 0.00 0.00 3.66
2897 3082 0.883833 GGTTCTGTGGGACTTGCATG 59.116 55.000 0.00 0.00 0.00 4.06
2899 3084 1.150536 GGGTTCTGTGGGACTTGCA 59.849 57.895 0.00 0.00 0.00 4.08
2900 3085 0.690762 TAGGGTTCTGTGGGACTTGC 59.309 55.000 0.00 0.00 0.00 4.01
2901 3086 2.552373 GGTTAGGGTTCTGTGGGACTTG 60.552 54.545 0.00 0.00 0.00 3.16
2903 3088 1.132495 AGGTTAGGGTTCTGTGGGACT 60.132 52.381 0.00 0.00 0.00 3.85
2905 3090 2.107552 CAAAGGTTAGGGTTCTGTGGGA 59.892 50.000 0.00 0.00 0.00 4.37
2906 3091 2.514803 CAAAGGTTAGGGTTCTGTGGG 58.485 52.381 0.00 0.00 0.00 4.61
2907 3092 2.107552 TCCAAAGGTTAGGGTTCTGTGG 59.892 50.000 0.00 0.00 37.27 4.17
2934 3127 7.500992 TCCAAAATGTATGGCTTTGTTTTACA 58.499 30.769 0.00 0.00 37.88 2.41
2952 3145 5.220758 GGTTGTGCGAAACATTTTCCAAAAT 60.221 36.000 4.00 0.00 38.99 1.82
2958 3151 3.182967 TGTGGTTGTGCGAAACATTTTC 58.817 40.909 4.00 0.00 38.99 2.29
2960 3153 2.926838 GTTGTGGTTGTGCGAAACATTT 59.073 40.909 4.00 0.00 38.99 2.32
2961 3154 2.165437 AGTTGTGGTTGTGCGAAACATT 59.835 40.909 4.00 0.00 38.99 2.71
2962 3155 1.748493 AGTTGTGGTTGTGCGAAACAT 59.252 42.857 4.00 0.00 38.99 2.71
2963 3156 1.169577 AGTTGTGGTTGTGCGAAACA 58.830 45.000 4.00 0.00 36.85 2.83
2964 3157 2.353579 AGTAGTTGTGGTTGTGCGAAAC 59.646 45.455 0.00 0.00 0.00 2.78
2965 3158 2.353269 CAGTAGTTGTGGTTGTGCGAAA 59.647 45.455 0.00 0.00 0.00 3.46
2966 3159 1.937223 CAGTAGTTGTGGTTGTGCGAA 59.063 47.619 0.00 0.00 0.00 4.70
2967 3160 1.577468 CAGTAGTTGTGGTTGTGCGA 58.423 50.000 0.00 0.00 0.00 5.10
2968 3161 0.586319 CCAGTAGTTGTGGTTGTGCG 59.414 55.000 0.00 0.00 0.00 5.34
2969 3162 1.873591 CTCCAGTAGTTGTGGTTGTGC 59.126 52.381 0.00 0.00 36.37 4.57
3000 3193 3.190439 AGGTCATTAGGTGTTAGCCCTT 58.810 45.455 0.00 0.00 33.35 3.95
3002 3195 2.772515 AGAGGTCATTAGGTGTTAGCCC 59.227 50.000 0.00 0.00 0.00 5.19
3003 3196 4.894114 TCTAGAGGTCATTAGGTGTTAGCC 59.106 45.833 0.00 0.00 0.00 3.93
3004 3197 5.595133 ACTCTAGAGGTCATTAGGTGTTAGC 59.405 44.000 23.50 0.00 0.00 3.09
3006 3199 7.179966 TCAACTCTAGAGGTCATTAGGTGTTA 58.820 38.462 23.50 0.00 0.00 2.41
3023 3238 6.440647 TGAAGGCTCCTATTTCTTCAACTCTA 59.559 38.462 0.00 0.00 41.48 2.43
3058 3273 3.118992 CCTGCCTAAGCCCTTGATTTTTC 60.119 47.826 0.00 0.00 38.69 2.29
3059 3274 2.833943 CCTGCCTAAGCCCTTGATTTTT 59.166 45.455 0.00 0.00 38.69 1.94
3061 3276 1.961919 GCCTGCCTAAGCCCTTGATTT 60.962 52.381 0.00 0.00 38.69 2.17
3077 3295 2.886523 TCTCATGTTTCAAAGTGGCCTG 59.113 45.455 3.32 0.00 0.00 4.85
3205 3423 2.463876 GCAGCACCTTTCTGTTGAAAC 58.536 47.619 0.00 0.00 37.27 2.78


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

AutoCloner maintained by Alex Coulton.