Multiple sequence alignment - TraesCS6A01G173800

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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 TraesCS6A01G173800 chr6A 100.000 2662 0 0 1 2662 187273321 187270660 0.000000e+00 4916
1 TraesCS6A01G173800 chr6A 100.000 103 0 0 2795 2897 187270527 187270425 1.060000e-44 191
2 TraesCS6A01G173800 chr6D 92.819 2270 106 26 422 2662 142139694 142137453 0.000000e+00 3236
3 TraesCS6A01G173800 chr6D 91.824 318 16 5 1 317 142141601 142141293 4.430000e-118 435
4 TraesCS6A01G173800 chr6B 92.023 2269 104 33 423 2662 245986315 245984095 0.000000e+00 3116
5 TraesCS6A01G173800 chr6B 91.195 318 15 10 1 317 245988428 245988123 1.240000e-113 420
6 TraesCS6A01G173800 chr7D 86.250 320 44 0 1018 1337 615765520 615765839 5.940000e-92 348
7 TraesCS6A01G173800 chr7D 85.047 321 46 2 1018 1337 615559438 615559119 2.780000e-85 326
8 TraesCS6A01G173800 chr7A 84.688 320 49 0 1018 1337 708319105 708319424 1.300000e-83 320
9 TraesCS6A01G173800 chr5D 83.735 332 51 3 1003 1333 255989609 255989280 7.800000e-81 311
10 TraesCS6A01G173800 chr7B 74.593 799 153 42 1018 1782 708511623 708512405 3.630000e-79 305
11 TraesCS6A01G173800 chr5A 82.229 332 56 3 1003 1333 340270177 340269848 1.700000e-72 283
12 TraesCS6A01G173800 chr5B 81.024 332 60 3 1003 1333 289797868 289797539 7.960000e-66 261
13 TraesCS6A01G173800 chr5B 100.000 59 0 0 2022 2080 309666807 309666749 3.050000e-20 110


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 TraesCS6A01G173800 chr6A 187270425 187273321 2896 True 2553.5 4916 100.0000 1 2897 2 chr6A.!!$R1 2896
1 TraesCS6A01G173800 chr6D 142137453 142141601 4148 True 1835.5 3236 92.3215 1 2662 2 chr6D.!!$R1 2661
2 TraesCS6A01G173800 chr6B 245984095 245988428 4333 True 1768.0 3116 91.6090 1 2662 2 chr6B.!!$R1 2661
3 TraesCS6A01G173800 chr7B 708511623 708512405 782 False 305.0 305 74.5930 1018 1782 1 chr7B.!!$F1 764

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
250 252 0.035534 TCATAAGCGCCAAAGCCTCA 60.036 50.0 2.29 0.0 38.01 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 4973 0.315568 TTTGCCAAATTTCCCCGTCG 59.684 50.0 0.0 0.0 0.0 5.12 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
208 210 3.499918 GGATGGATCACCGATTCATGAAC 59.500 47.826 11.07 4.22 38.28 3.18
221 223 6.933521 CCGATTCATGAACCTATCATCTTTCT 59.066 38.462 11.07 0.00 45.91 2.52
250 252 0.035534 TCATAAGCGCCAAAGCCTCA 60.036 50.000 2.29 0.00 38.01 3.86
252 254 1.379642 ATAAGCGCCAAAGCCTCAGC 61.380 55.000 2.29 0.00 38.01 4.26
291 293 1.101331 CTTTACCCCGCGAGAGTACT 58.899 55.000 8.23 0.00 0.00 2.73
294 296 1.668419 TACCCCGCGAGAGTACTAAC 58.332 55.000 8.23 0.00 0.00 2.34
317 320 4.576843 GCACGATGCGCATTGTAG 57.423 55.556 36.37 29.41 33.79 2.74
319 322 2.009108 CACGATGCGCATTGTAGCT 58.991 52.632 36.37 16.64 33.79 3.32
321 324 1.368493 CGATGCGCATTGTAGCTGC 60.368 57.895 26.12 7.89 36.26 5.25
322 325 1.009222 GATGCGCATTGTAGCTGCC 60.009 57.895 26.12 4.07 36.24 4.85
324 327 4.241999 GCGCATTGTAGCTGCCGG 62.242 66.667 0.30 0.00 36.24 6.13
326 329 1.889105 CGCATTGTAGCTGCCGGAT 60.889 57.895 5.05 0.00 36.24 4.18
327 330 1.650912 GCATTGTAGCTGCCGGATG 59.349 57.895 5.05 0.00 33.44 3.51
328 331 1.650912 CATTGTAGCTGCCGGATGC 59.349 57.895 5.05 8.59 41.77 3.91
388 3046 2.847327 CACAGAGGTTCATGTGGAGT 57.153 50.000 0.00 0.00 42.46 3.85
395 3053 4.338682 AGAGGTTCATGTGGAGTATACGAC 59.661 45.833 0.00 0.00 0.00 4.34
398 3056 4.360563 GTTCATGTGGAGTATACGACCTG 58.639 47.826 18.08 10.67 0.00 4.00
399 3057 3.893521 TCATGTGGAGTATACGACCTGA 58.106 45.455 18.08 12.24 0.00 3.86
400 3058 3.630769 TCATGTGGAGTATACGACCTGAC 59.369 47.826 18.08 11.86 0.00 3.51
401 3059 2.372264 TGTGGAGTATACGACCTGACC 58.628 52.381 18.08 7.29 0.00 4.02
403 3061 2.358267 GTGGAGTATACGACCTGACCTG 59.642 54.545 18.08 0.00 0.00 4.00
404 3062 2.240414 TGGAGTATACGACCTGACCTGA 59.760 50.000 18.08 0.18 0.00 3.86
405 3063 2.879646 GGAGTATACGACCTGACCTGAG 59.120 54.545 12.65 0.00 0.00 3.35
407 3065 1.337387 GTATACGACCTGACCTGAGGC 59.663 57.143 0.00 0.00 36.46 4.70
408 3066 0.324368 ATACGACCTGACCTGAGGCA 60.324 55.000 0.00 0.00 36.46 4.75
409 3067 0.324368 TACGACCTGACCTGAGGCAT 60.324 55.000 0.00 0.00 36.46 4.40
410 3068 1.153489 CGACCTGACCTGAGGCATG 60.153 63.158 0.00 0.00 36.46 4.06
411 3069 1.222936 GACCTGACCTGAGGCATGG 59.777 63.158 0.00 0.00 36.46 3.66
413 3071 1.136329 ACCTGACCTGAGGCATGGTT 61.136 55.000 0.00 0.00 36.46 3.67
414 3072 0.679002 CCTGACCTGAGGCATGGTTG 60.679 60.000 0.00 0.00 36.59 3.77
426 3102 3.465218 ATGGTTGCCCACTTGCCCA 62.465 57.895 0.00 0.00 45.65 5.36
454 3130 1.541310 TTGTACTGGGTCGGAGCTGG 61.541 60.000 7.19 3.18 0.00 4.85
457 3133 1.255667 TACTGGGTCGGAGCTGGTTC 61.256 60.000 7.19 0.00 0.00 3.62
470 3146 2.806621 GGTTCGGCGTGGTCGTAC 60.807 66.667 6.85 0.00 39.49 3.67
530 3211 1.654774 CGCGAGCAGTCCAGCTATA 59.345 57.895 0.00 0.00 46.75 1.31
736 3418 2.174639 CCCCACCTGCCATTCTGTTATA 59.825 50.000 0.00 0.00 0.00 0.98
926 3609 3.379445 CGCCACTACCACCGGAGT 61.379 66.667 9.46 7.95 0.00 3.85
954 3637 4.760220 GAGGCCAAGGGGAGGGGA 62.760 72.222 5.01 0.00 35.59 4.81
955 3638 4.767892 AGGCCAAGGGGAGGGGAG 62.768 72.222 5.01 0.00 35.59 4.30
957 3640 4.760220 GCCAAGGGGAGGGGAGGA 62.760 72.222 0.00 0.00 35.59 3.71
990 3673 5.224135 GTTTTTGGTTGTAGTGTGTGTGTT 58.776 37.500 0.00 0.00 0.00 3.32
1035 3718 1.276622 AGTGCGACAGGATAAAGGGT 58.723 50.000 0.00 0.00 0.00 4.34
1299 3982 4.354212 CGCACCGACAACGCTGTG 62.354 66.667 0.00 0.00 35.30 3.66
1596 4327 2.192443 CTCTCGCTCCCCGGACTA 59.808 66.667 0.73 0.00 37.59 2.59
1897 4652 0.179084 CGTCATGACCCGCCAGTAAT 60.179 55.000 20.03 0.00 0.00 1.89
1898 4653 1.067974 CGTCATGACCCGCCAGTAATA 59.932 52.381 20.03 0.00 0.00 0.98
1899 4654 2.482316 CGTCATGACCCGCCAGTAATAA 60.482 50.000 20.03 0.00 0.00 1.40
1904 4659 5.654650 TCATGACCCGCCAGTAATAAAAATT 59.345 36.000 0.00 0.00 0.00 1.82
1983 4755 1.469940 CGCCGCTAGATCTTGTGAAGT 60.470 52.381 17.69 0.00 0.00 3.01
2016 4789 3.665585 GCTGTAGTCGCTTTCTTTTCTGC 60.666 47.826 0.00 0.00 0.00 4.26
2115 4890 3.306989 GCAAGGGGGAAATGGAAAGAAAG 60.307 47.826 0.00 0.00 0.00 2.62
2116 4891 4.159557 CAAGGGGGAAATGGAAAGAAAGA 58.840 43.478 0.00 0.00 0.00 2.52
2117 4892 4.053009 AGGGGGAAATGGAAAGAAAGAG 57.947 45.455 0.00 0.00 0.00 2.85
2118 4893 3.662642 AGGGGGAAATGGAAAGAAAGAGA 59.337 43.478 0.00 0.00 0.00 3.10
2120 4895 4.220821 GGGGGAAATGGAAAGAAAGAGAAC 59.779 45.833 0.00 0.00 0.00 3.01
2121 4896 4.082733 GGGGAAATGGAAAGAAAGAGAACG 60.083 45.833 0.00 0.00 0.00 3.95
2122 4897 4.760204 GGGAAATGGAAAGAAAGAGAACGA 59.240 41.667 0.00 0.00 0.00 3.85
2123 4898 5.240844 GGGAAATGGAAAGAAAGAGAACGAA 59.759 40.000 0.00 0.00 0.00 3.85
2190 4966 3.548770 GGCACAGGAATGAGATGATTGA 58.451 45.455 0.00 0.00 0.00 2.57
2197 4973 2.540265 ATGAGATGATTGAGACCGGC 57.460 50.000 0.00 0.00 0.00 6.13
2200 4976 0.103208 AGATGATTGAGACCGGCGAC 59.897 55.000 9.30 1.53 0.00 5.19
2223 4999 3.940852 GGGGAAATTTGGCAAATCATGTC 59.059 43.478 24.51 17.83 0.00 3.06
2276 5052 0.392461 TAGCAGGTTCCGTTGATGGC 60.392 55.000 0.00 0.00 0.00 4.40
2281 5057 0.804989 GGTTCCGTTGATGGCTTGAG 59.195 55.000 0.00 0.00 0.00 3.02
2285 5061 2.176045 TCCGTTGATGGCTTGAGACTA 58.824 47.619 0.00 0.00 0.00 2.59
2287 5063 1.929836 CGTTGATGGCTTGAGACTAGC 59.070 52.381 0.00 0.00 37.91 3.42
2288 5064 2.675032 CGTTGATGGCTTGAGACTAGCA 60.675 50.000 7.37 0.00 40.42 3.49
2290 5066 3.189618 TGATGGCTTGAGACTAGCATG 57.810 47.619 7.37 0.00 40.42 4.06
2291 5067 2.502947 TGATGGCTTGAGACTAGCATGT 59.497 45.455 7.37 0.00 40.42 3.21
2292 5068 3.706086 TGATGGCTTGAGACTAGCATGTA 59.294 43.478 7.37 0.00 40.42 2.29
2293 5069 3.808466 TGGCTTGAGACTAGCATGTAG 57.192 47.619 7.37 0.00 40.42 2.74
2345 5121 1.827969 CCGTGGTTCTCTCTGAATCCT 59.172 52.381 0.00 0.00 34.98 3.24
2362 5138 9.281371 TCTGAATCCTTGCTATAATCAAATCTG 57.719 33.333 0.00 0.00 0.00 2.90
2384 5160 0.034896 AAGCCCTTCCGTGTGTACTG 59.965 55.000 0.00 0.00 0.00 2.74
2387 5163 0.670546 CCCTTCCGTGTGTACTGCTG 60.671 60.000 0.00 0.00 0.00 4.41
2388 5164 1.291877 CCTTCCGTGTGTACTGCTGC 61.292 60.000 0.00 0.00 0.00 5.25
2456 5232 4.111375 ACTACTGGAACGCACAATCTAG 57.889 45.455 0.00 0.00 0.00 2.43
2476 5252 2.169789 CATGACGAAGGCTGGAGCG 61.170 63.158 0.00 0.00 43.26 5.03
2534 5310 3.951979 GAACCATTCGAATCGAGCATT 57.048 42.857 7.92 0.00 37.14 3.56
2536 5312 1.331756 ACCATTCGAATCGAGCATTGC 59.668 47.619 7.92 0.00 37.14 3.56
2811 5587 4.637771 CCAGCCGGGTAGGAAAAG 57.362 61.111 5.47 0.00 45.00 2.27
2812 5588 1.749258 CCAGCCGGGTAGGAAAAGC 60.749 63.158 5.47 0.00 45.00 3.51
2813 5589 1.299976 CAGCCGGGTAGGAAAAGCT 59.700 57.895 5.47 0.00 45.00 3.74
2814 5590 0.322546 CAGCCGGGTAGGAAAAGCTT 60.323 55.000 5.47 0.00 45.00 3.74
2815 5591 0.322546 AGCCGGGTAGGAAAAGCTTG 60.323 55.000 3.10 0.00 45.00 4.01
2816 5592 1.934220 GCCGGGTAGGAAAAGCTTGC 61.934 60.000 2.18 0.00 45.00 4.01
2817 5593 1.313091 CCGGGTAGGAAAAGCTTGCC 61.313 60.000 0.00 4.97 45.00 4.52
2818 5594 1.644786 CGGGTAGGAAAAGCTTGCCG 61.645 60.000 0.00 0.00 0.00 5.69
2819 5595 1.506718 GGTAGGAAAAGCTTGCCGC 59.493 57.895 0.00 3.96 39.57 6.53
2841 5617 1.388547 GCTGTTCGCCAAATATCCCA 58.611 50.000 0.00 0.00 0.00 4.37
2842 5618 1.334869 GCTGTTCGCCAAATATCCCAG 59.665 52.381 0.00 0.00 0.00 4.45
2843 5619 2.643551 CTGTTCGCCAAATATCCCAGT 58.356 47.619 0.00 0.00 0.00 4.00
2844 5620 2.355756 CTGTTCGCCAAATATCCCAGTG 59.644 50.000 0.00 0.00 0.00 3.66
2845 5621 1.065551 GTTCGCCAAATATCCCAGTGC 59.934 52.381 0.00 0.00 0.00 4.40
2846 5622 0.254462 TCGCCAAATATCCCAGTGCA 59.746 50.000 0.00 0.00 0.00 4.57
2847 5623 0.664761 CGCCAAATATCCCAGTGCAG 59.335 55.000 0.00 0.00 0.00 4.41
2848 5624 1.746861 CGCCAAATATCCCAGTGCAGA 60.747 52.381 0.00 0.00 0.00 4.26
2849 5625 2.378038 GCCAAATATCCCAGTGCAGAA 58.622 47.619 0.00 0.00 0.00 3.02
2850 5626 2.099756 GCCAAATATCCCAGTGCAGAAC 59.900 50.000 0.00 0.00 0.00 3.01
2851 5627 3.355378 CCAAATATCCCAGTGCAGAACA 58.645 45.455 0.00 0.00 0.00 3.18
2852 5628 3.379372 CCAAATATCCCAGTGCAGAACAG 59.621 47.826 0.00 0.00 0.00 3.16
2853 5629 2.338577 ATATCCCAGTGCAGAACAGC 57.661 50.000 0.00 0.00 0.00 4.40
2854 5630 0.983467 TATCCCAGTGCAGAACAGCA 59.017 50.000 0.00 0.00 43.35 4.41
2870 5646 2.125147 CAAAGGATGCCCGCGAGA 60.125 61.111 8.23 0.00 37.58 4.04
2871 5647 2.176273 CAAAGGATGCCCGCGAGAG 61.176 63.158 8.23 0.00 37.58 3.20
2883 5659 3.004283 CGAGAGCTGCGCAATCTG 58.996 61.111 24.88 14.96 0.00 2.90
2884 5660 2.708255 GAGAGCTGCGCAATCTGC 59.292 61.111 24.88 18.63 40.69 4.26
2885 5661 1.814586 GAGAGCTGCGCAATCTGCT 60.815 57.895 24.88 22.76 42.25 4.24
2886 5662 2.708255 GAGCTGCGCAATCTGCTC 59.292 61.111 26.91 26.91 45.85 4.26
2887 5663 2.821688 GAGCTGCGCAATCTGCTCC 61.822 63.158 29.22 16.47 46.05 4.70
2888 5664 3.885521 GCTGCGCAATCTGCTCCC 61.886 66.667 13.05 0.00 42.25 4.30
2889 5665 3.207669 CTGCGCAATCTGCTCCCC 61.208 66.667 13.05 0.00 42.25 4.81
2890 5666 4.802051 TGCGCAATCTGCTCCCCC 62.802 66.667 8.16 0.00 42.25 5.40
2891 5667 4.802051 GCGCAATCTGCTCCCCCA 62.802 66.667 0.30 0.00 42.25 4.96
2892 5668 2.045045 CGCAATCTGCTCCCCCAA 60.045 61.111 0.00 0.00 42.25 4.12
2893 5669 2.117156 CGCAATCTGCTCCCCCAAG 61.117 63.158 0.00 0.00 42.25 3.61
2894 5670 1.000396 GCAATCTGCTCCCCCAAGT 60.000 57.895 0.00 0.00 40.96 3.16
2895 5671 0.613012 GCAATCTGCTCCCCCAAGTT 60.613 55.000 0.00 0.00 40.96 2.66
2896 5672 1.928868 CAATCTGCTCCCCCAAGTTT 58.071 50.000 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 1.667830 CACAGTGGCGTGTACCCTG 60.668 63.158 0.00 0.00 35.39 4.45
208 210 6.436847 TGAGCAGGAGATAGAAAGATGATAGG 59.563 42.308 0.00 0.00 0.00 2.57
252 254 1.455408 GGTTGGCGAAAAAGCGAAATG 59.545 47.619 0.00 0.00 36.64 2.32
260 262 1.687660 GGGGTAAAGGTTGGCGAAAAA 59.312 47.619 0.00 0.00 0.00 1.94
369 3027 2.847327 ACTCCACATGAACCTCTGTG 57.153 50.000 0.00 0.00 41.89 3.66
385 3043 2.879646 CCTCAGGTCAGGTCGTATACTC 59.120 54.545 0.56 0.00 0.00 2.59
388 3046 1.064240 TGCCTCAGGTCAGGTCGTATA 60.064 52.381 0.00 0.00 35.72 1.47
395 3053 0.679002 CAACCATGCCTCAGGTCAGG 60.679 60.000 0.00 0.00 37.07 3.86
411 3069 2.521708 ACTGGGCAAGTGGGCAAC 60.522 61.111 0.00 0.00 45.66 4.17
426 3102 0.473886 ACCCAGTACAAGCCCTCACT 60.474 55.000 0.00 0.00 0.00 3.41
436 3112 1.982395 CCAGCTCCGACCCAGTACA 60.982 63.158 0.00 0.00 0.00 2.90
441 3117 3.691342 CGAACCAGCTCCGACCCA 61.691 66.667 0.00 0.00 0.00 4.51
454 3130 1.444895 ATGTACGACCACGCCGAAC 60.445 57.895 0.00 0.00 43.96 3.95
457 3133 1.444724 TTCATGTACGACCACGCCG 60.445 57.895 0.00 0.00 43.96 6.46
470 3146 1.429021 CGGCCGTTCCATGTTCATG 59.571 57.895 19.50 5.88 34.01 3.07
530 3211 1.068125 GGCCGTTAAAAACTGGCGAAT 60.068 47.619 14.73 0.00 45.52 3.34
584 3265 4.455533 GGTTTGAATTTTGAATTGGAGGGC 59.544 41.667 0.00 0.00 0.00 5.19
736 3418 2.665185 GAGGCGGTGTCGTTTGCT 60.665 61.111 0.00 0.00 38.89 3.91
776 3458 3.142838 GTCGCCGGGGTACAGCTA 61.143 66.667 19.13 0.00 0.00 3.32
915 3598 1.228769 AGCAGACACTCCGGTGGTA 60.229 57.895 8.63 0.00 46.85 3.25
916 3599 2.524394 AGCAGACACTCCGGTGGT 60.524 61.111 8.63 2.97 46.85 4.16
917 3600 2.262915 GAGCAGACACTCCGGTGG 59.737 66.667 8.63 2.00 46.85 4.61
926 3609 2.440385 CTTGGCCTCACGAGCAGACA 62.440 60.000 3.32 0.00 0.00 3.41
953 3636 3.073209 ACCAAAAACCTTCTCCTCTCCTC 59.927 47.826 0.00 0.00 0.00 3.71
954 3637 3.056832 ACCAAAAACCTTCTCCTCTCCT 58.943 45.455 0.00 0.00 0.00 3.69
955 3638 3.510531 ACCAAAAACCTTCTCCTCTCC 57.489 47.619 0.00 0.00 0.00 3.71
956 3639 4.207955 ACAACCAAAAACCTTCTCCTCTC 58.792 43.478 0.00 0.00 0.00 3.20
957 3640 4.251103 ACAACCAAAAACCTTCTCCTCT 57.749 40.909 0.00 0.00 0.00 3.69
1015 3698 1.628846 ACCCTTTATCCTGTCGCACTT 59.371 47.619 0.00 0.00 0.00 3.16
1296 3979 2.158813 GGAGTTCCAGTGGTTCTTCACA 60.159 50.000 9.54 0.00 39.93 3.58
1299 3982 2.610727 CGAGGAGTTCCAGTGGTTCTTC 60.611 54.545 9.54 10.35 38.89 2.87
1560 4291 0.816018 GCGAGAGAGAGGTGATCGGA 60.816 60.000 0.00 0.00 34.11 4.55
1898 4653 9.033481 GGTTTTACTACTGGCGTTTTAATTTTT 57.967 29.630 0.00 0.00 0.00 1.94
1899 4654 8.196103 TGGTTTTACTACTGGCGTTTTAATTTT 58.804 29.630 0.00 0.00 0.00 1.82
1904 4659 5.120519 CGATGGTTTTACTACTGGCGTTTTA 59.879 40.000 0.00 0.00 0.00 1.52
2016 4789 1.597663 AGGAACGCAAACAGAACGAAG 59.402 47.619 0.00 0.00 0.00 3.79
2080 4854 3.793144 CTTGCCGACTTCGCAGCC 61.793 66.667 0.00 0.00 38.18 4.85
2083 4857 4.697756 CCCCTTGCCGACTTCGCA 62.698 66.667 0.00 0.00 38.18 5.10
2197 4973 0.315568 TTTGCCAAATTTCCCCGTCG 59.684 50.000 0.00 0.00 0.00 5.12
2200 4976 2.758736 TGATTTGCCAAATTTCCCCG 57.241 45.000 3.82 0.00 0.00 5.73
2276 5052 6.148948 GCTACATCTACATGCTAGTCTCAAG 58.851 44.000 0.00 0.00 32.57 3.02
2281 5057 4.551388 GGTGCTACATCTACATGCTAGTC 58.449 47.826 0.00 0.00 32.57 2.59
2285 5061 1.069204 CCGGTGCTACATCTACATGCT 59.931 52.381 0.00 0.00 32.57 3.79
2287 5063 1.202521 TGCCGGTGCTACATCTACATG 60.203 52.381 1.90 0.00 38.71 3.21
2288 5064 1.119684 TGCCGGTGCTACATCTACAT 58.880 50.000 1.90 0.00 38.71 2.29
2290 5066 1.502231 CATGCCGGTGCTACATCTAC 58.498 55.000 1.90 0.00 38.71 2.59
2291 5067 0.249868 GCATGCCGGTGCTACATCTA 60.250 55.000 6.36 0.00 41.82 1.98
2292 5068 1.524621 GCATGCCGGTGCTACATCT 60.525 57.895 6.36 0.00 41.82 2.90
2293 5069 3.025619 GCATGCCGGTGCTACATC 58.974 61.111 6.36 0.00 41.82 3.06
2332 5108 7.846101 TGATTATAGCAAGGATTCAGAGAGA 57.154 36.000 0.00 0.00 0.00 3.10
2333 5109 8.899427 TTTGATTATAGCAAGGATTCAGAGAG 57.101 34.615 0.00 0.00 0.00 3.20
2345 5121 6.490040 GGGCTTACCAGATTTGATTATAGCAA 59.510 38.462 0.00 0.00 39.85 3.91
2362 5138 0.609662 TACACACGGAAGGGCTTACC 59.390 55.000 0.00 0.00 38.93 2.85
2384 5160 2.675348 GTTTGATCACAGAGGTAGCAGC 59.325 50.000 0.00 0.00 0.00 5.25
2387 5163 3.334583 TGGTTTGATCACAGAGGTAGC 57.665 47.619 0.00 0.00 0.00 3.58
2388 5164 5.063204 TGTTTGGTTTGATCACAGAGGTAG 58.937 41.667 0.00 0.00 0.00 3.18
2476 5252 2.677979 GCTCGGGCTTGTCGTTTCC 61.678 63.158 0.00 0.00 35.22 3.13
2534 5310 1.057275 TTGTGGTACTGTCCCCAGCA 61.057 55.000 0.00 0.38 42.81 4.41
2536 5312 2.158667 ACTTTTGTGGTACTGTCCCCAG 60.159 50.000 0.00 0.00 44.68 4.45
2794 5570 1.749258 GCTTTTCCTACCCGGCTGG 60.749 63.158 3.88 3.88 41.37 4.85
2795 5571 0.322546 AAGCTTTTCCTACCCGGCTG 60.323 55.000 0.00 0.00 0.00 4.85
2796 5572 0.322546 CAAGCTTTTCCTACCCGGCT 60.323 55.000 0.00 0.00 0.00 5.52
2797 5573 1.934220 GCAAGCTTTTCCTACCCGGC 61.934 60.000 0.00 0.00 0.00 6.13
2798 5574 1.313091 GGCAAGCTTTTCCTACCCGG 61.313 60.000 0.00 0.00 0.00 5.73
2799 5575 1.644786 CGGCAAGCTTTTCCTACCCG 61.645 60.000 0.00 0.00 0.00 5.28
2800 5576 1.934220 GCGGCAAGCTTTTCCTACCC 61.934 60.000 0.00 0.00 44.04 3.69
2801 5577 1.506718 GCGGCAAGCTTTTCCTACC 59.493 57.895 0.00 0.00 44.04 3.18
2823 5599 2.355756 CACTGGGATATTTGGCGAACAG 59.644 50.000 0.00 0.00 0.00 3.16
2824 5600 2.364632 CACTGGGATATTTGGCGAACA 58.635 47.619 0.00 0.00 0.00 3.18
2825 5601 1.065551 GCACTGGGATATTTGGCGAAC 59.934 52.381 0.00 0.00 0.00 3.95
2826 5602 1.340502 TGCACTGGGATATTTGGCGAA 60.341 47.619 0.00 0.00 0.00 4.70
2827 5603 0.254462 TGCACTGGGATATTTGGCGA 59.746 50.000 0.00 0.00 0.00 5.54
2828 5604 0.664761 CTGCACTGGGATATTTGGCG 59.335 55.000 0.00 0.00 0.00 5.69
2829 5605 2.057137 TCTGCACTGGGATATTTGGC 57.943 50.000 0.00 0.00 0.00 4.52
2830 5606 3.355378 TGTTCTGCACTGGGATATTTGG 58.645 45.455 0.00 0.00 0.00 3.28
2831 5607 3.181493 GCTGTTCTGCACTGGGATATTTG 60.181 47.826 0.00 0.00 0.00 2.32
2832 5608 3.019564 GCTGTTCTGCACTGGGATATTT 58.980 45.455 0.00 0.00 0.00 1.40
2833 5609 2.025981 TGCTGTTCTGCACTGGGATATT 60.026 45.455 0.48 0.00 38.12 1.28
2834 5610 1.561076 TGCTGTTCTGCACTGGGATAT 59.439 47.619 0.48 0.00 38.12 1.63
2835 5611 0.983467 TGCTGTTCTGCACTGGGATA 59.017 50.000 0.48 0.00 38.12 2.59
2836 5612 0.111061 TTGCTGTTCTGCACTGGGAT 59.889 50.000 4.00 0.00 43.20 3.85
2837 5613 0.106769 TTTGCTGTTCTGCACTGGGA 60.107 50.000 4.00 0.00 43.20 4.37
2838 5614 0.313043 CTTTGCTGTTCTGCACTGGG 59.687 55.000 4.00 0.00 43.20 4.45
2839 5615 0.313043 CCTTTGCTGTTCTGCACTGG 59.687 55.000 4.00 5.99 43.20 4.00
2840 5616 1.311859 TCCTTTGCTGTTCTGCACTG 58.688 50.000 4.00 1.34 43.20 3.66
2841 5617 1.884579 CATCCTTTGCTGTTCTGCACT 59.115 47.619 4.00 0.00 43.20 4.40
2842 5618 2.342910 CATCCTTTGCTGTTCTGCAC 57.657 50.000 4.00 0.00 43.20 4.57
2853 5629 2.125147 TCTCGCGGGCATCCTTTG 60.125 61.111 6.13 0.00 0.00 2.77
2854 5630 2.187946 CTCTCGCGGGCATCCTTT 59.812 61.111 6.13 0.00 0.00 3.11
2855 5631 4.537433 GCTCTCGCGGGCATCCTT 62.537 66.667 6.13 0.00 0.00 3.36
2876 5652 0.613012 AACTTGGGGGAGCAGATTGC 60.613 55.000 0.00 0.00 45.46 3.56
2877 5653 1.928868 AAACTTGGGGGAGCAGATTG 58.071 50.000 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.