Multiple sequence alignment - TraesCS4A01G130600

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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 TraesCS4A01G130600 chr4A 100.000 3824 0 0 1 3824 173629228 173633051 0.000000e+00 7062.0
1 TraesCS4A01G130600 chr4B 91.238 3013 125 40 1 2941 381372618 381375563 0.000000e+00 3973.0
2 TraesCS4A01G130600 chr4B 84.694 98 3 1 3080 3177 381375633 381375718 1.890000e-13 87.9
3 TraesCS4A01G130600 chr4B 97.059 34 1 0 2979 3012 381375577 381375610 1.480000e-04 58.4
4 TraesCS4A01G130600 chr4D 90.290 3100 130 48 1 3012 305139861 305142877 0.000000e+00 3899.0
5 TraesCS4A01G130600 chr4D 82.481 645 103 7 3187 3824 425216663 425217304 1.200000e-154 556.0
6 TraesCS4A01G130600 chr4D 92.661 109 8 0 3069 3177 305142891 305142999 1.420000e-34 158.0
7 TraesCS4A01G130600 chr4D 100.000 30 0 0 3029 3058 305142864 305142893 5.340000e-04 56.5
8 TraesCS4A01G130600 chr5B 98.589 638 9 0 3187 3824 35613668 35613031 0.000000e+00 1129.0
9 TraesCS4A01G130600 chr5B 81.679 262 34 12 1457 1710 267760739 267760484 5.010000e-49 206.0
10 TraesCS4A01G130600 chr6B 97.802 637 14 0 3188 3824 38980423 38979787 0.000000e+00 1099.0
11 TraesCS4A01G130600 chr7A 91.346 624 53 1 3199 3822 55341334 55340712 0.000000e+00 852.0
12 TraesCS4A01G130600 chr5A 90.484 641 60 1 3182 3822 214962267 214961628 0.000000e+00 845.0
13 TraesCS4A01G130600 chr5A 90.484 641 60 1 3182 3822 214969255 214968616 0.000000e+00 845.0
14 TraesCS4A01G130600 chr7D 83.204 643 100 6 3188 3824 568242051 568242691 1.980000e-162 582.0
15 TraesCS4A01G130600 chr7D 81.356 236 38 5 1473 1703 438368646 438368880 1.810000e-43 187.0
16 TraesCS4A01G130600 chr7D 79.386 228 40 4 1477 1699 420742641 420742416 1.840000e-33 154.0
17 TraesCS4A01G130600 chr1D 82.919 644 99 8 3188 3824 57132420 57131781 1.540000e-158 569.0
18 TraesCS4A01G130600 chr3D 82.335 651 102 12 3178 3822 492007187 492007830 1.550000e-153 553.0
19 TraesCS4A01G130600 chr2D 85.484 248 33 2 1463 1710 417544117 417544361 4.900000e-64 255.0
20 TraesCS4A01G130600 chr2B 84.800 250 31 6 1463 1710 489419049 489419293 1.060000e-60 244.0
21 TraesCS4A01G130600 chr2B 91.304 46 4 0 1080 1125 23376534 23376579 3.190000e-06 63.9
22 TraesCS4A01G130600 chr2A 84.836 244 30 6 1469 1710 572615833 572615595 4.940000e-59 239.0
23 TraesCS4A01G130600 chr5D 83.588 262 29 12 1457 1710 238073371 238073626 2.300000e-57 233.0
24 TraesCS4A01G130600 chr7B 80.932 236 39 5 1473 1703 455272025 455271791 8.440000e-42 182.0
25 TraesCS4A01G130600 chr7B 79.736 227 41 5 1477 1699 436787584 436787359 3.950000e-35 159.0


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 TraesCS4A01G130600 chr4A 173629228 173633051 3823 False 7062.000000 7062 100.000 1 3824 1 chr4A.!!$F1 3823
1 TraesCS4A01G130600 chr4B 381372618 381375718 3100 False 1373.100000 3973 90.997 1 3177 3 chr4B.!!$F1 3176
2 TraesCS4A01G130600 chr4D 305139861 305142999 3138 False 1371.166667 3899 94.317 1 3177 3 chr4D.!!$F2 3176
3 TraesCS4A01G130600 chr4D 425216663 425217304 641 False 556.000000 556 82.481 3187 3824 1 chr4D.!!$F1 637
4 TraesCS4A01G130600 chr5B 35613031 35613668 637 True 1129.000000 1129 98.589 3187 3824 1 chr5B.!!$R1 637
5 TraesCS4A01G130600 chr6B 38979787 38980423 636 True 1099.000000 1099 97.802 3188 3824 1 chr6B.!!$R1 636
6 TraesCS4A01G130600 chr7A 55340712 55341334 622 True 852.000000 852 91.346 3199 3822 1 chr7A.!!$R1 623
7 TraesCS4A01G130600 chr5A 214961628 214962267 639 True 845.000000 845 90.484 3182 3822 1 chr5A.!!$R1 640
8 TraesCS4A01G130600 chr5A 214968616 214969255 639 True 845.000000 845 90.484 3182 3822 1 chr5A.!!$R2 640
9 TraesCS4A01G130600 chr7D 568242051 568242691 640 False 582.000000 582 83.204 3188 3824 1 chr7D.!!$F2 636
10 TraesCS4A01G130600 chr1D 57131781 57132420 639 True 569.000000 569 82.919 3188 3824 1 chr1D.!!$R1 636
11 TraesCS4A01G130600 chr3D 492007187 492007830 643 False 553.000000 553 82.335 3178 3822 1 chr3D.!!$F1 644

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
171 172 1.098050 GGATGCTCATCGCTTTTGGT 58.902 50.000 4.02 0.0 38.69 3.67 F
1063 1106 1.000283 CTCTTTCACACACGCCTCTCT 60.000 52.381 0.00 0.0 0.00 3.10 F
2418 2516 0.809636 TGCACCTACCGCATGATTCG 60.810 55.000 0.00 0.0 33.55 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1148 1230 0.912487 TCCACCTCCGCCTGGTTTAT 60.912 55.0 0.0 0.0 35.28 1.40 R
2420 2518 0.108804 GAGCCAGAACCAATCGACGA 60.109 55.0 0.0 0.0 0.00 4.20 R
3791 3941 2.166459 TCTAGATTCACCTCTGTTGGCG 59.834 50.0 0.0 0.0 0.00 5.69 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
83 84 5.105351 AGTGAAAGGTTGAAAACTTTGGGAG 60.105 40.000 10.70 0.00 46.05 4.30
135 136 2.375014 TCCACTTGGGAAAGGGAAAC 57.625 50.000 0.00 0.00 44.80 2.78
171 172 1.098050 GGATGCTCATCGCTTTTGGT 58.902 50.000 4.02 0.00 38.69 3.67
262 267 1.136721 CGTCGCTCCTGTAAACAAACG 60.137 52.381 0.00 0.00 0.00 3.60
296 301 4.031878 GTCTCGAACTAAAAAGATGCGGAG 59.968 45.833 0.00 0.00 0.00 4.63
359 364 1.347707 ACGTGAACTGGATGTGTGGAT 59.652 47.619 0.00 0.00 0.00 3.41
390 395 7.761704 CGAGAGTTACAAATATAGCTGCCATAT 59.238 37.037 0.00 0.00 0.00 1.78
399 404 7.739995 AATATAGCTGCCATATCAACCTCTA 57.260 36.000 0.00 0.00 0.00 2.43
407 412 5.189180 GCCATATCAACCTCTAATCATCCC 58.811 45.833 0.00 0.00 0.00 3.85
511 516 1.246056 TTCTTCTGGCTGCATGTGGC 61.246 55.000 0.50 0.81 45.13 5.01
524 529 1.337384 ATGTGGCTGCCGGAGTATGA 61.337 55.000 14.98 0.00 0.00 2.15
525 530 1.220749 GTGGCTGCCGGAGTATGAA 59.779 57.895 14.98 0.00 0.00 2.57
556 571 9.959749 GTCAGAGTAATCAAACCAACATTAAAA 57.040 29.630 0.00 0.00 0.00 1.52
558 573 9.743057 CAGAGTAATCAAACCAACATTAAAACA 57.257 29.630 0.00 0.00 0.00 2.83
588 603 9.894783 GTGTATATGTATGAACTACCAGTACTG 57.105 37.037 16.34 16.34 0.00 2.74
611 640 5.015817 TGGTGTGGGTTTATTTAAGGGAGAT 59.984 40.000 0.00 0.00 0.00 2.75
612 641 5.955959 GGTGTGGGTTTATTTAAGGGAGATT 59.044 40.000 0.00 0.00 0.00 2.40
613 642 6.439375 GGTGTGGGTTTATTTAAGGGAGATTT 59.561 38.462 0.00 0.00 0.00 2.17
615 644 8.372459 GTGTGGGTTTATTTAAGGGAGATTTTT 58.628 33.333 0.00 0.00 0.00 1.94
699 728 4.368315 TCGGACGTGAATATTCATTCCAG 58.632 43.478 30.14 25.00 39.99 3.86
700 729 4.098807 TCGGACGTGAATATTCATTCCAGA 59.901 41.667 30.14 26.06 39.99 3.86
732 761 2.982130 CCGGTGGTGGAGGAGAAG 59.018 66.667 0.00 0.00 0.00 2.85
751 780 6.147864 AGAAGATACTCTGAATGTGAGAGC 57.852 41.667 0.00 0.00 40.69 4.09
799 835 1.776667 TGGGGCCTAAGAGGATGAATG 59.223 52.381 0.84 0.00 37.67 2.67
801 837 2.039613 GGGGCCTAAGAGGATGAATGAG 59.960 54.545 0.84 0.00 37.67 2.90
1063 1106 1.000283 CTCTTTCACACACGCCTCTCT 60.000 52.381 0.00 0.00 0.00 3.10
1148 1230 1.934220 GATGTCTGAGGCGTCGGTGA 61.934 60.000 14.58 4.10 0.00 4.02
1439 1527 4.452825 GGGAATCTTGCCTTACTTACTCC 58.547 47.826 0.00 0.00 35.55 3.85
1448 1536 3.306571 GCCTTACTTACTCCCGTGTTTCT 60.307 47.826 0.00 0.00 0.00 2.52
1504 1592 3.964909 GTGGTACTTCTTTTGCCACAAG 58.035 45.455 7.09 0.00 46.29 3.16
1810 1901 6.845758 TCTTTCTGGCTTCATTCATGATTT 57.154 33.333 0.00 0.00 36.56 2.17
1811 1902 6.627243 TCTTTCTGGCTTCATTCATGATTTG 58.373 36.000 0.00 0.00 36.56 2.32
1812 1903 4.380841 TCTGGCTTCATTCATGATTTGC 57.619 40.909 0.00 0.00 36.56 3.68
2024 2116 2.362800 GCGACGTCGACCAAGTCAC 61.363 63.158 39.74 15.89 43.02 3.67
2072 2164 4.402528 CGGTGCCCATTCCGGACA 62.403 66.667 1.83 0.00 42.61 4.02
2390 2482 4.072131 GACATTTGGAAGTACTGAAGCCA 58.928 43.478 0.00 0.00 0.00 4.75
2409 2501 4.514577 CCGGAGCTGCACCTACCG 62.515 72.222 14.15 13.15 42.67 4.02
2418 2516 0.809636 TGCACCTACCGCATGATTCG 60.810 55.000 0.00 0.00 33.55 3.34
2420 2518 0.530650 CACCTACCGCATGATTCGCT 60.531 55.000 0.00 0.00 0.00 4.93
2422 2520 1.278172 CCTACCGCATGATTCGCTCG 61.278 60.000 0.00 0.00 0.00 5.03
2541 2639 2.722487 CGGAGGATTCTCGGGTCG 59.278 66.667 0.47 0.00 40.85 4.79
2542 2640 2.846652 CGGAGGATTCTCGGGTCGG 61.847 68.421 0.47 0.00 40.85 4.79
2543 2641 1.455217 GGAGGATTCTCGGGTCGGA 60.455 63.158 0.00 0.00 40.85 4.55
2562 2660 3.128938 CGGATCGGATCAGGTTACTATCC 59.871 52.174 18.99 0.00 36.59 2.59
2568 2666 4.467795 CGGATCAGGTTACTATCCATCCAT 59.532 45.833 0.00 0.00 39.36 3.41
2569 2667 5.394663 CGGATCAGGTTACTATCCATCCATC 60.395 48.000 0.00 0.00 39.36 3.51
2598 2700 0.980423 CTCCAGGGATTAGCTAGGCC 59.020 60.000 0.00 0.00 0.00 5.19
2615 2730 7.990055 AGCTAGGCCTCCTTATGTTAATTAAT 58.010 34.615 9.68 0.00 34.61 1.40
2617 2732 9.734984 GCTAGGCCTCCTTATGTTAATTAATTA 57.265 33.333 9.68 3.71 34.61 1.40
2657 2772 9.750125 TTCATATCTTGATCTGTGTGTACATAC 57.250 33.333 15.23 15.23 33.14 2.39
2664 2779 5.126545 TGATCTGTGTGTACATACCACTACC 59.873 44.000 18.72 5.46 35.97 3.18
2666 2781 4.219070 TCTGTGTGTACATACCACTACCAC 59.781 45.833 18.72 9.82 35.97 4.16
2667 2782 3.896272 TGTGTGTACATACCACTACCACA 59.104 43.478 18.72 12.11 32.36 4.17
2668 2783 4.344390 TGTGTGTACATACCACTACCACAA 59.656 41.667 18.72 0.00 32.36 3.33
2669 2784 4.687483 GTGTGTACATACCACTACCACAAC 59.313 45.833 11.42 0.00 0.00 3.32
2670 2785 4.344390 TGTGTACATACCACTACCACAACA 59.656 41.667 0.00 0.00 0.00 3.33
2671 2786 4.927425 GTGTACATACCACTACCACAACAG 59.073 45.833 0.00 0.00 0.00 3.16
2709 2836 0.942962 GCAGTAGCAGCATGATGGTC 59.057 55.000 20.29 11.24 39.69 4.02
2779 2906 2.948979 TGAATCGATTAATTTGGGCGCT 59.051 40.909 11.38 0.00 0.00 5.92
2793 2920 2.758089 GCGCTGTTGATGAGCCAGG 61.758 63.158 0.00 0.00 32.41 4.45
2818 2945 4.555348 CTAGCGCTACTACTAGCTTTGT 57.445 45.455 14.45 0.00 43.07 2.83
2819 2946 5.670149 CTAGCGCTACTACTAGCTTTGTA 57.330 43.478 14.45 0.00 43.07 2.41
2820 2947 6.243811 CTAGCGCTACTACTAGCTTTGTAT 57.756 41.667 14.45 0.00 43.07 2.29
2821 2948 4.861210 AGCGCTACTACTAGCTTTGTATG 58.139 43.478 8.99 0.00 43.07 2.39
2822 2949 3.982058 GCGCTACTACTAGCTTTGTATGG 59.018 47.826 0.00 0.00 43.07 2.74
2823 2950 4.261489 GCGCTACTACTAGCTTTGTATGGA 60.261 45.833 0.00 0.00 43.07 3.41
2824 2951 5.735354 GCGCTACTACTAGCTTTGTATGGAA 60.735 44.000 0.00 0.00 43.07 3.53
2825 2952 6.448006 CGCTACTACTAGCTTTGTATGGAAT 58.552 40.000 0.00 0.00 43.07 3.01
2826 2953 6.583050 CGCTACTACTAGCTTTGTATGGAATC 59.417 42.308 0.00 0.00 43.07 2.52
2827 2954 6.869388 GCTACTACTAGCTTTGTATGGAATCC 59.131 42.308 0.00 0.00 42.11 3.01
2915 3043 2.411069 CGATGCTTGTGTTCTCTCTGTG 59.589 50.000 0.00 0.00 0.00 3.66
2930 3058 0.238289 CTGTGCCGCTTTACACTTGG 59.762 55.000 0.00 0.00 37.68 3.61
2935 3063 2.745281 TGCCGCTTTACACTTGGTAATC 59.255 45.455 0.00 0.00 41.43 1.75
2941 3069 6.348950 CCGCTTTACACTTGGTAATCAATCAA 60.349 38.462 0.00 0.00 41.43 2.57
2942 3070 6.742718 CGCTTTACACTTGGTAATCAATCAAG 59.257 38.462 0.00 0.00 41.43 3.02
2943 3071 7.360861 CGCTTTACACTTGGTAATCAATCAAGA 60.361 37.037 5.08 0.00 41.43 3.02
2944 3072 7.750903 GCTTTACACTTGGTAATCAATCAAGAC 59.249 37.037 5.08 0.00 41.43 3.01
2946 3074 5.547465 ACACTTGGTAATCAATCAAGACGA 58.453 37.500 5.08 0.00 39.97 4.20
2947 3075 5.639506 ACACTTGGTAATCAATCAAGACGAG 59.360 40.000 5.08 0.00 39.97 4.18
2970 3115 1.135731 GACGAGACGAGAGGCACTG 59.864 63.158 0.00 0.00 46.78 3.66
2998 3143 2.934932 TGGTGCTGCTCATGGGGA 60.935 61.111 0.00 0.00 0.00 4.81
2999 3144 2.439156 GGTGCTGCTCATGGGGAC 60.439 66.667 0.00 0.00 0.00 4.46
3059 3204 5.753721 AATCTAGCAAGGGGAGATATGAC 57.246 43.478 0.00 0.00 29.71 3.06
3062 3207 3.784511 AGCAAGGGGAGATATGACATG 57.215 47.619 0.00 0.00 0.00 3.21
3063 3208 2.374504 AGCAAGGGGAGATATGACATGG 59.625 50.000 0.00 0.00 0.00 3.66
3064 3209 2.373169 GCAAGGGGAGATATGACATGGA 59.627 50.000 0.00 0.00 0.00 3.41
3065 3210 3.009916 GCAAGGGGAGATATGACATGGAT 59.990 47.826 0.00 0.00 0.00 3.41
3066 3211 4.586884 CAAGGGGAGATATGACATGGATG 58.413 47.826 0.00 0.00 0.00 3.51
3067 3212 3.187942 AGGGGAGATATGACATGGATGG 58.812 50.000 0.00 0.00 0.00 3.51
3068 3213 3.181391 AGGGGAGATATGACATGGATGGA 60.181 47.826 0.00 0.00 0.00 3.41
3069 3214 3.784763 GGGGAGATATGACATGGATGGAT 59.215 47.826 0.00 0.00 0.00 3.41
3070 3215 4.384978 GGGGAGATATGACATGGATGGATG 60.385 50.000 0.00 0.00 0.00 3.51
3071 3216 4.384978 GGGAGATATGACATGGATGGATGG 60.385 50.000 0.00 0.00 0.00 3.51
3072 3217 4.472470 GGAGATATGACATGGATGGATGGA 59.528 45.833 0.00 0.00 0.00 3.41
3126 3271 2.485122 CGGGCTTGTTTGGATCGC 59.515 61.111 0.00 0.00 0.00 4.58
3170 3315 4.120331 GCATGGCGTCCAGTTGGC 62.120 66.667 4.90 2.87 36.75 4.52
3177 3322 2.027625 CGTCCAGTTGGCGAACTCC 61.028 63.158 11.57 2.14 40.68 3.85
3178 3323 1.371558 GTCCAGTTGGCGAACTCCT 59.628 57.895 11.57 0.00 40.68 3.69
3179 3324 0.670854 GTCCAGTTGGCGAACTCCTC 60.671 60.000 11.57 1.41 40.68 3.71
3180 3325 0.832135 TCCAGTTGGCGAACTCCTCT 60.832 55.000 11.57 0.00 40.68 3.69
3718 3868 1.283029 TCTGCTTGGGAGATTGGGAAG 59.717 52.381 0.00 0.00 0.00 3.46
3791 3941 9.593134 CATAGAGCCTTATGATGGAATTACTAC 57.407 37.037 0.00 0.00 33.75 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 6.818142 CCAAAGTTTTCAACCTTTCACTCATT 59.182 34.615 0.00 0.00 0.00 2.57
105 106 2.029073 AAGTGGACAGGACACGCG 59.971 61.111 3.53 3.53 43.41 6.01
262 267 3.388345 AGTTCGAGACTTTCTTGGGTC 57.612 47.619 0.00 0.00 33.92 4.46
296 301 1.443802 CGTTCCCTTCTGCTTTCTCC 58.556 55.000 0.00 0.00 0.00 3.71
359 364 4.980434 GCTATATTTGTAACTCTCGCGGAA 59.020 41.667 6.13 0.00 0.00 4.30
511 516 2.673368 GACTTTGTTCATACTCCGGCAG 59.327 50.000 0.00 0.00 0.00 4.85
514 519 4.177026 CTCTGACTTTGTTCATACTCCGG 58.823 47.826 0.00 0.00 0.00 5.14
515 520 4.810790 ACTCTGACTTTGTTCATACTCCG 58.189 43.478 0.00 0.00 0.00 4.63
518 523 9.778741 TTTGATTACTCTGACTTTGTTCATACT 57.221 29.630 0.00 0.00 0.00 2.12
519 524 9.813080 GTTTGATTACTCTGACTTTGTTCATAC 57.187 33.333 0.00 0.00 0.00 2.39
524 529 7.122055 TGTTGGTTTGATTACTCTGACTTTGTT 59.878 33.333 0.00 0.00 0.00 2.83
525 530 6.601613 TGTTGGTTTGATTACTCTGACTTTGT 59.398 34.615 0.00 0.00 0.00 2.83
581 596 6.150474 CCTTAAATAAACCCACACCAGTACTG 59.850 42.308 16.34 16.34 0.00 2.74
588 603 4.925836 TCTCCCTTAAATAAACCCACACC 58.074 43.478 0.00 0.00 0.00 4.16
589 604 7.476540 AAATCTCCCTTAAATAAACCCACAC 57.523 36.000 0.00 0.00 0.00 3.82
630 659 4.500887 CGTTGGACAGAACCTGACTTCTTA 60.501 45.833 0.45 0.00 35.18 2.10
699 728 4.083862 GGCCGGTGTCCTGTCCTC 62.084 72.222 1.90 0.00 0.00 3.71
732 761 4.300189 ACGCTCTCACATTCAGAGTATC 57.700 45.455 0.00 0.00 39.81 2.24
775 807 1.141858 CATCCTCTTAGGCCCCAACTC 59.858 57.143 0.00 0.00 34.61 3.01
799 835 5.552870 TGTCCTAATCTTAATGGCTCCTC 57.447 43.478 0.00 0.00 0.00 3.71
801 837 5.685728 ACTTGTCCTAATCTTAATGGCTCC 58.314 41.667 0.00 0.00 0.00 4.70
1008 1051 2.556782 GGTTTAGGAACAAGGGAAGGGG 60.557 54.545 0.00 0.00 37.51 4.79
1063 1106 1.153329 GACGCCGAGAGAGAGGAGA 60.153 63.158 0.00 0.00 0.00 3.71
1122 1183 1.219124 GCCTCAGACATCTCCGCAA 59.781 57.895 0.00 0.00 0.00 4.85
1123 1184 2.895680 GCCTCAGACATCTCCGCA 59.104 61.111 0.00 0.00 0.00 5.69
1148 1230 0.912487 TCCACCTCCGCCTGGTTTAT 60.912 55.000 0.00 0.00 35.28 1.40
1216 1304 4.289101 TCCTCGTCCGTGGGGTGA 62.289 66.667 7.82 0.00 33.83 4.02
1448 1536 3.712907 GGCCTTGCCTGTCCGGTA 61.713 66.667 0.00 0.00 46.69 4.02
1504 1592 2.125793 GTCGGGTACTTGCGGTCC 60.126 66.667 0.00 0.00 0.00 4.46
1810 1901 8.768019 GCGAATCATATATCATATTTAGCAGCA 58.232 33.333 0.00 0.00 0.00 4.41
1811 1902 7.948895 CGCGAATCATATATCATATTTAGCAGC 59.051 37.037 0.00 0.00 0.00 5.25
1812 1903 8.972349 ACGCGAATCATATATCATATTTAGCAG 58.028 33.333 15.93 0.00 0.00 4.24
2017 2109 3.058914 GTGGACTTGAAATCGGTGACTTG 60.059 47.826 0.00 0.00 0.00 3.16
2024 2116 2.350522 CAGAGGTGGACTTGAAATCGG 58.649 52.381 0.00 0.00 0.00 4.18
2072 2164 2.375174 TGCTGTTCCATCTTAACCTGGT 59.625 45.455 0.00 0.00 34.03 4.00
2199 2291 4.704103 TGCCCCGAGACCTGCTCT 62.704 66.667 0.00 0.00 41.66 4.09
2335 2427 0.869028 GCGGGGTACTCGTCGAATTC 60.869 60.000 0.00 0.00 0.00 2.17
2418 2516 1.696832 GCCAGAACCAATCGACGAGC 61.697 60.000 3.01 0.00 0.00 5.03
2420 2518 0.108804 GAGCCAGAACCAATCGACGA 60.109 55.000 0.00 0.00 0.00 4.20
2422 2520 0.389948 ACGAGCCAGAACCAATCGAC 60.390 55.000 0.00 0.00 37.16 4.20
2476 2574 2.040278 ACCACTAACACCAGCATCACAT 59.960 45.455 0.00 0.00 0.00 3.21
2539 2637 2.359981 AGTAACCTGATCCGATCCGA 57.640 50.000 5.91 0.00 0.00 4.55
2540 2638 3.128938 GGATAGTAACCTGATCCGATCCG 59.871 52.174 5.91 0.00 30.33 4.18
2541 2639 4.087182 TGGATAGTAACCTGATCCGATCC 58.913 47.826 5.91 0.00 41.85 3.36
2542 2640 5.163499 GGATGGATAGTAACCTGATCCGATC 60.163 48.000 1.01 1.01 41.85 3.69
2543 2641 4.712337 GGATGGATAGTAACCTGATCCGAT 59.288 45.833 0.00 0.00 41.85 4.18
2562 2660 1.415659 GGAGGTCTGTCTGGATGGATG 59.584 57.143 0.00 0.00 0.00 3.51
2568 2666 1.079256 CCCTGGAGGTCTGTCTGGA 59.921 63.158 0.00 0.00 0.00 3.86
2569 2667 0.326048 ATCCCTGGAGGTCTGTCTGG 60.326 60.000 0.00 0.00 36.75 3.86
2615 2730 9.542462 CAAGATATGAACCGAGGACTAATTTAA 57.458 33.333 0.00 0.00 0.00 1.52
2617 2732 7.792032 TCAAGATATGAACCGAGGACTAATTT 58.208 34.615 0.00 0.00 34.30 1.82
2628 2743 5.111989 ACACACAGATCAAGATATGAACCG 58.888 41.667 11.28 0.70 42.54 4.44
2657 2772 3.935203 CAGAATAGCTGTTGTGGTAGTGG 59.065 47.826 11.92 0.00 39.85 4.00
2666 2781 7.130917 GCTAATCACAATCAGAATAGCTGTTG 58.869 38.462 0.00 0.00 45.14 3.33
2667 2782 6.825213 TGCTAATCACAATCAGAATAGCTGTT 59.175 34.615 10.49 0.00 42.31 3.16
2668 2783 6.351711 TGCTAATCACAATCAGAATAGCTGT 58.648 36.000 10.49 0.00 42.31 4.40
2669 2784 6.482641 ACTGCTAATCACAATCAGAATAGCTG 59.517 38.462 12.54 12.54 42.31 4.24
2670 2785 6.590068 ACTGCTAATCACAATCAGAATAGCT 58.410 36.000 10.49 0.00 42.31 3.32
2671 2786 6.857777 ACTGCTAATCACAATCAGAATAGC 57.142 37.500 0.00 0.00 42.22 2.97
2746 2873 9.956720 AAATTAATCGATTCACAAATGGATCTC 57.043 29.630 15.25 0.00 38.81 2.75
2779 2906 1.676635 GCTGCCTGGCTCATCAACA 60.677 57.895 21.03 0.00 0.00 3.33
2813 2940 4.701956 ACAAAGCGGATTCCATACAAAG 57.298 40.909 3.09 0.00 0.00 2.77
2814 2941 5.650266 ACATACAAAGCGGATTCCATACAAA 59.350 36.000 3.09 0.00 0.00 2.83
2815 2942 5.189928 ACATACAAAGCGGATTCCATACAA 58.810 37.500 3.09 0.00 0.00 2.41
2816 2943 4.776349 ACATACAAAGCGGATTCCATACA 58.224 39.130 3.09 0.00 0.00 2.29
2817 2944 5.756347 TGTACATACAAAGCGGATTCCATAC 59.244 40.000 3.09 0.00 32.40 2.39
2818 2945 5.919755 TGTACATACAAAGCGGATTCCATA 58.080 37.500 3.09 0.00 32.40 2.74
2819 2946 4.776349 TGTACATACAAAGCGGATTCCAT 58.224 39.130 3.09 0.00 32.40 3.41
2820 2947 4.209307 TGTACATACAAAGCGGATTCCA 57.791 40.909 3.09 0.00 32.40 3.53
2821 2948 4.574828 ACATGTACATACAAAGCGGATTCC 59.425 41.667 8.32 0.00 39.99 3.01
2822 2949 5.734855 ACATGTACATACAAAGCGGATTC 57.265 39.130 8.32 0.00 39.99 2.52
2823 2950 5.526111 GGTACATGTACATACAAAGCGGATT 59.474 40.000 31.52 0.00 39.99 3.01
2824 2951 5.054477 GGTACATGTACATACAAAGCGGAT 58.946 41.667 31.52 0.00 39.99 4.18
2825 2952 4.081586 TGGTACATGTACATACAAAGCGGA 60.082 41.667 31.52 0.00 39.99 5.54
2826 2953 4.033587 GTGGTACATGTACATACAAAGCGG 59.966 45.833 31.52 0.00 44.52 5.52
2827 2954 4.033587 GGTGGTACATGTACATACAAAGCG 59.966 45.833 31.52 0.00 44.52 4.68
2915 3043 2.745281 TGATTACCAAGTGTAAAGCGGC 59.255 45.455 0.00 0.00 42.51 6.53
2930 3058 5.452944 GTCGAGTCTCGTCTTGATTGATTAC 59.547 44.000 21.15 4.36 41.35 1.89
2935 3063 2.159693 TCGTCGAGTCTCGTCTTGATTG 60.160 50.000 21.15 3.27 41.35 2.67
2941 3069 1.072116 CGTCTCGTCGAGTCTCGTCT 61.072 60.000 21.15 0.00 41.35 4.18
2942 3070 1.069924 TCGTCTCGTCGAGTCTCGTC 61.070 60.000 21.15 15.02 41.35 4.20
2943 3071 1.080907 TCGTCTCGTCGAGTCTCGT 60.081 57.895 21.15 0.00 41.35 4.18
2944 3072 3.764645 TCGTCTCGTCGAGTCTCG 58.235 61.111 21.15 16.33 42.10 4.04
2980 3125 2.753043 CCCCATGAGCAGCACCAC 60.753 66.667 0.00 0.00 0.00 4.16
3017 3162 5.592688 AGATTTCGGAAGGTTGTCTCAAAAA 59.407 36.000 0.00 0.00 0.00 1.94
3018 3163 5.130350 AGATTTCGGAAGGTTGTCTCAAAA 58.870 37.500 0.00 0.00 0.00 2.44
3019 3164 4.714632 AGATTTCGGAAGGTTGTCTCAAA 58.285 39.130 0.00 0.00 0.00 2.69
3020 3165 4.351874 AGATTTCGGAAGGTTGTCTCAA 57.648 40.909 0.00 0.00 0.00 3.02
3021 3166 4.620803 GCTAGATTTCGGAAGGTTGTCTCA 60.621 45.833 0.00 0.00 0.00 3.27
3022 3167 3.866327 GCTAGATTTCGGAAGGTTGTCTC 59.134 47.826 0.00 0.00 0.00 3.36
3023 3168 3.260884 TGCTAGATTTCGGAAGGTTGTCT 59.739 43.478 0.00 0.00 0.00 3.41
3024 3169 3.596214 TGCTAGATTTCGGAAGGTTGTC 58.404 45.455 0.00 0.00 0.00 3.18
3025 3170 3.695830 TGCTAGATTTCGGAAGGTTGT 57.304 42.857 0.00 0.00 0.00 3.32
3026 3171 3.375299 CCTTGCTAGATTTCGGAAGGTTG 59.625 47.826 0.00 0.00 41.94 3.77
3027 3172 3.610911 CCTTGCTAGATTTCGGAAGGTT 58.389 45.455 0.00 0.00 41.94 3.50
3059 3204 3.732048 TGATCCATCCATCCATCCATG 57.268 47.619 0.00 0.00 0.00 3.66
3062 3207 2.310945 ACCATGATCCATCCATCCATCC 59.689 50.000 0.00 0.00 0.00 3.51
3063 3208 3.733883 ACCATGATCCATCCATCCATC 57.266 47.619 0.00 0.00 0.00 3.51
3064 3209 4.480777 AAACCATGATCCATCCATCCAT 57.519 40.909 0.00 0.00 0.00 3.41
3065 3210 3.962063 CAAAACCATGATCCATCCATCCA 59.038 43.478 0.00 0.00 0.00 3.41
3066 3211 3.322828 CCAAAACCATGATCCATCCATCC 59.677 47.826 0.00 0.00 0.00 3.51
3067 3212 3.322828 CCCAAAACCATGATCCATCCATC 59.677 47.826 0.00 0.00 0.00 3.51
3068 3213 3.311091 CCCAAAACCATGATCCATCCAT 58.689 45.455 0.00 0.00 0.00 3.41
3069 3214 2.749600 CCCAAAACCATGATCCATCCA 58.250 47.619 0.00 0.00 0.00 3.41
3070 3215 1.413812 GCCCAAAACCATGATCCATCC 59.586 52.381 0.00 0.00 0.00 3.51
3071 3216 1.413812 GGCCCAAAACCATGATCCATC 59.586 52.381 0.00 0.00 0.00 3.51
3072 3217 1.499368 GGCCCAAAACCATGATCCAT 58.501 50.000 0.00 0.00 0.00 3.41
3105 3250 3.561120 ATCCAAACAAGCCCGCGGA 62.561 57.895 30.73 1.48 0.00 5.54
3126 3271 1.318576 GTGCTCCGGGAATAATTGGG 58.681 55.000 0.00 0.00 0.00 4.12
3153 3298 4.120331 GCCAACTGGACGCCATGC 62.120 66.667 0.00 0.00 37.39 4.06
3718 3868 2.273449 CCCCTCCTGCATGACACC 59.727 66.667 0.00 0.00 0.00 4.16
3741 3891 3.004734 CCACAGCGTTTCCTCTGAAATTT 59.995 43.478 0.00 0.00 42.20 1.82
3791 3941 2.166459 TCTAGATTCACCTCTGTTGGCG 59.834 50.000 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.