Multiple sequence alignment - TraesCS7B01G392700

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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 TraesCS7B01G392700 chr7B 100.000 5680 0 0 1 5680 659257488 659263167 0.000000e+00 10490.0
1 TraesCS7B01G392700 chr7B 89.091 55 5 1 5205 5259 669524707 669524654 3.670000e-07 67.6
2 TraesCS7B01G392700 chr7D 94.227 3655 145 18 784 4413 587832865 587836478 0.000000e+00 5520.0
3 TraesCS7B01G392700 chr7D 94.664 1293 38 8 4411 5673 587836507 587837798 0.000000e+00 1977.0
4 TraesCS7B01G392700 chr7D 83.663 808 57 33 1 770 587831998 587832768 0.000000e+00 691.0
5 TraesCS7B01G392700 chr7D 76.538 260 40 13 5208 5452 412652551 412652804 7.730000e-24 122.0
6 TraesCS7B01G392700 chr7A 94.329 2116 85 15 1382 3469 679761462 679763570 0.000000e+00 3210.0
7 TraesCS7B01G392700 chr7A 88.606 1413 98 36 1 1390 679759836 679761208 0.000000e+00 1659.0
8 TraesCS7B01G392700 chr7A 89.854 1301 73 26 4410 5671 679764588 679765868 0.000000e+00 1616.0
9 TraesCS7B01G392700 chr7A 91.798 951 57 13 3473 4413 679763612 679764551 0.000000e+00 1304.0
10 TraesCS7B01G392700 chrUn 90.430 512 21 7 324 834 68602058 68602542 0.000000e+00 649.0
11 TraesCS7B01G392700 chr5A 74.043 235 44 13 5347 5573 512038761 512038986 4.720000e-11 80.5


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 TraesCS7B01G392700 chr7B 659257488 659263167 5679 False 10490.000000 10490 100.000000 1 5680 1 chr7B.!!$F1 5679
1 TraesCS7B01G392700 chr7D 587831998 587837798 5800 False 2729.333333 5520 90.851333 1 5673 3 chr7D.!!$F2 5672
2 TraesCS7B01G392700 chr7A 679759836 679765868 6032 False 1947.250000 3210 91.146750 1 5671 4 chr7A.!!$F1 5670

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
81 82 0.688087 AGGTAAAGCCTCCCTCTCCG 60.688 60.000 0.00 0.00 46.96 4.63 F
821 956 1.213537 GCCGTGCTTACCTCGTGTA 59.786 57.895 0.00 0.00 0.00 2.90 F
968 1103 1.409521 GGAGCTGAGAGCACCTAGAGA 60.410 57.143 0.00 0.00 46.56 3.10 F
972 1107 1.879380 CTGAGAGCACCTAGAGATCGG 59.121 57.143 0.00 0.00 0.00 4.18 F
2429 2884 2.232208 TGTTGCATGTTTGTGGTTGTCA 59.768 40.909 0.00 0.00 0.00 3.58 F
3003 3460 1.435256 AGGGTGCCCAGGTACATATC 58.565 55.000 10.26 0.00 38.92 1.63 F
4194 4713 1.498865 GGCATCCAAGGTCATACGCG 61.499 60.000 3.53 3.53 0.00 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1206 1341 0.385348 CGGCTGAGATGATCTCGTCG 60.385 60.000 20.12 20.12 46.25 5.12 R
1937 2366 2.159043 TCTCCTCAGCGAAATCACATCC 60.159 50.000 0.00 0.00 0.00 3.51 R
2445 2900 3.417069 ACAACCTGCATAGCAAGTACA 57.583 42.857 0.00 0.00 38.41 2.90 R
2446 2901 4.273480 CCATACAACCTGCATAGCAAGTAC 59.727 45.833 0.00 0.00 38.41 2.73 R
4340 4859 2.109126 GGTCTCATCAACGGCCTGC 61.109 63.158 0.00 0.00 0.00 4.85 R
4546 5110 2.809446 TCTGTGTCACGAGTTTCTGTG 58.191 47.619 0.00 0.00 37.44 3.66 R
5639 6245 3.283751 CATGCTTCCACGGGGTTTAATA 58.716 45.455 2.12 0.00 34.93 0.98 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
81 82 0.688087 AGGTAAAGCCTCCCTCTCCG 60.688 60.000 0.00 0.00 46.96 4.63
123 125 1.409427 CCCTCTATCACCAGTTCCGTC 59.591 57.143 0.00 0.00 0.00 4.79
139 141 1.644786 CGTCCCATTCGAACCAAGCC 61.645 60.000 0.00 0.00 0.00 4.35
225 242 1.891060 CTCGGCGTGTCTGTTTGAGC 61.891 60.000 6.85 0.00 0.00 4.26
233 250 3.673338 CGTGTCTGTTTGAGCTCGAATTA 59.327 43.478 19.35 10.82 0.00 1.40
237 254 5.515270 TGTCTGTTTGAGCTCGAATTATACG 59.485 40.000 19.35 5.38 0.00 3.06
241 258 2.647337 TGAGCTCGAATTATACGCGTC 58.353 47.619 18.63 0.00 0.00 5.19
548 586 4.140599 CGCCTTCCGAGAGCTGCT 62.141 66.667 0.00 0.00 40.02 4.24
556 594 2.025441 GAGAGCTGCTCGCGTAGG 59.975 66.667 22.77 0.00 45.59 3.18
657 703 1.280066 GCGCGCATTGATTGGAATTT 58.720 45.000 29.10 0.00 0.00 1.82
675 721 3.130160 GGGCTGCAGTGCTAGTGC 61.130 66.667 17.60 14.33 44.57 4.40
723 775 1.675641 GTGTTGCTGGCCTGTAGGG 60.676 63.158 11.69 0.00 35.18 3.53
770 822 4.382754 CGTTCAGCTTGCTTGATTTTTACC 59.617 41.667 0.00 0.00 0.00 2.85
774 826 5.767665 TCAGCTTGCTTGATTTTTACCACTA 59.232 36.000 0.00 0.00 0.00 2.74
776 828 5.770162 AGCTTGCTTGATTTTTACCACTACT 59.230 36.000 0.00 0.00 0.00 2.57
777 829 6.265422 AGCTTGCTTGATTTTTACCACTACTT 59.735 34.615 0.00 0.00 0.00 2.24
821 956 1.213537 GCCGTGCTTACCTCGTGTA 59.786 57.895 0.00 0.00 0.00 2.90
837 972 2.357637 CGTGTATTGTAAATGCAGGGGG 59.642 50.000 0.00 0.00 0.00 5.40
854 989 2.284995 GAGGGGTGAGGAGCCAGT 60.285 66.667 0.00 0.00 42.06 4.00
855 990 2.284995 AGGGGTGAGGAGCCAGTC 60.285 66.667 0.00 0.00 42.06 3.51
856 991 2.607750 GGGGTGAGGAGCCAGTCA 60.608 66.667 0.00 0.00 42.06 3.41
857 992 2.665603 GGGTGAGGAGCCAGTCAC 59.334 66.667 2.09 2.09 42.06 3.67
858 993 1.915769 GGGTGAGGAGCCAGTCACT 60.916 63.158 9.16 0.00 42.37 3.41
859 994 1.594310 GGTGAGGAGCCAGTCACTC 59.406 63.158 9.16 0.00 42.37 3.51
869 1004 3.056628 CAGTCACTCGCCTGGAATC 57.943 57.895 0.00 0.00 0.00 2.52
892 1027 3.889692 AGGCCCTGGTGTGGTGTG 61.890 66.667 0.00 0.00 0.00 3.82
897 1032 2.192979 CTGGTGTGGTGTGGCAGT 59.807 61.111 0.00 0.00 0.00 4.40
899 1034 2.191908 GGTGTGGTGTGGCAGTGA 59.808 61.111 0.00 0.00 0.00 3.41
922 1057 1.981254 TCACGTCGAAATAACCGGAC 58.019 50.000 9.46 0.00 0.00 4.79
936 1071 6.749036 ATAACCGGACCTTTTAGATGATCT 57.251 37.500 9.46 0.00 0.00 2.75
937 1072 4.408182 ACCGGACCTTTTAGATGATCTG 57.592 45.455 9.46 0.00 0.00 2.90
938 1073 3.134804 ACCGGACCTTTTAGATGATCTGG 59.865 47.826 9.46 0.00 0.00 3.86
968 1103 1.409521 GGAGCTGAGAGCACCTAGAGA 60.410 57.143 0.00 0.00 46.56 3.10
972 1107 1.879380 CTGAGAGCACCTAGAGATCGG 59.121 57.143 0.00 0.00 0.00 4.18
1266 1401 4.094646 ATGCCCATGTCCGCGTCA 62.095 61.111 4.92 4.31 0.00 4.35
1284 1419 4.616835 GCGTCAAAGAATCCAAAGATTGCT 60.617 41.667 0.00 0.00 42.93 3.91
1322 1457 2.687842 GCTCATTGCCCTTCGAGAG 58.312 57.895 0.00 0.00 35.15 3.20
1601 1998 4.916983 TTTGAACAGTGGAACATCAAGG 57.083 40.909 0.00 0.00 44.52 3.61
1851 2280 6.405953 GCCTGTGCATACTAGTTCTCTCTTTA 60.406 42.308 0.00 0.00 37.47 1.85
1937 2366 6.928492 AGTTTGCATGGGTGTTTTACATAAAG 59.072 34.615 0.00 0.00 0.00 1.85
2189 2618 4.881273 AGTTGACCAATATCGCTTGCATTA 59.119 37.500 0.00 0.00 0.00 1.90
2222 2651 3.997726 ATCATTCCCAATTCCCCATGA 57.002 42.857 0.00 0.00 0.00 3.07
2304 2733 7.903145 TCTAAAGACCACTATTAGCAGTTTGA 58.097 34.615 0.00 0.00 0.00 2.69
2370 2799 5.195940 AGGAGCTTTGTGCATTACATATGT 58.804 37.500 13.93 13.93 45.94 2.29
2422 2877 4.121317 AGGTTTGATGTTGCATGTTTGTG 58.879 39.130 0.00 0.00 0.00 3.33
2423 2878 3.248125 GGTTTGATGTTGCATGTTTGTGG 59.752 43.478 0.00 0.00 0.00 4.17
2424 2879 3.815856 TTGATGTTGCATGTTTGTGGT 57.184 38.095 0.00 0.00 0.00 4.16
2425 2880 3.815856 TGATGTTGCATGTTTGTGGTT 57.184 38.095 0.00 0.00 0.00 3.67
2426 2881 3.455327 TGATGTTGCATGTTTGTGGTTG 58.545 40.909 0.00 0.00 0.00 3.77
2427 2882 3.118847 TGATGTTGCATGTTTGTGGTTGT 60.119 39.130 0.00 0.00 0.00 3.32
2428 2883 2.886081 TGTTGCATGTTTGTGGTTGTC 58.114 42.857 0.00 0.00 0.00 3.18
2429 2884 2.232208 TGTTGCATGTTTGTGGTTGTCA 59.768 40.909 0.00 0.00 0.00 3.58
2430 2885 3.257393 GTTGCATGTTTGTGGTTGTCAA 58.743 40.909 0.00 0.00 0.00 3.18
2431 2886 3.599730 TGCATGTTTGTGGTTGTCAAA 57.400 38.095 0.00 0.00 33.28 2.69
2432 2887 3.930336 TGCATGTTTGTGGTTGTCAAAA 58.070 36.364 0.00 0.00 36.71 2.44
2433 2888 4.511527 TGCATGTTTGTGGTTGTCAAAAT 58.488 34.783 0.00 0.00 36.71 1.82
2434 2889 4.940046 TGCATGTTTGTGGTTGTCAAAATT 59.060 33.333 0.00 0.00 36.71 1.82
2435 2890 5.163784 TGCATGTTTGTGGTTGTCAAAATTG 60.164 36.000 0.00 0.00 36.71 2.32
2436 2891 5.064452 GCATGTTTGTGGTTGTCAAAATTGA 59.936 36.000 0.00 0.00 36.71 2.57
2437 2892 6.402983 GCATGTTTGTGGTTGTCAAAATTGAA 60.403 34.615 0.00 0.00 39.21 2.69
2438 2893 7.679164 GCATGTTTGTGGTTGTCAAAATTGAAT 60.679 33.333 0.00 0.00 39.21 2.57
2439 2894 8.824781 CATGTTTGTGGTTGTCAAAATTGAATA 58.175 29.630 0.00 0.00 39.21 1.75
2440 2895 8.417780 TGTTTGTGGTTGTCAAAATTGAATAG 57.582 30.769 0.00 0.00 39.21 1.73
2441 2896 8.253810 TGTTTGTGGTTGTCAAAATTGAATAGA 58.746 29.630 0.00 0.00 39.21 1.98
2442 2897 8.755018 GTTTGTGGTTGTCAAAATTGAATAGAG 58.245 33.333 0.00 0.00 39.21 2.43
2443 2898 7.581213 TGTGGTTGTCAAAATTGAATAGAGT 57.419 32.000 0.00 0.00 39.21 3.24
2444 2899 8.684386 TGTGGTTGTCAAAATTGAATAGAGTA 57.316 30.769 0.00 0.00 39.21 2.59
2445 2900 9.295825 TGTGGTTGTCAAAATTGAATAGAGTAT 57.704 29.630 0.00 0.00 39.21 2.12
2446 2901 9.559958 GTGGTTGTCAAAATTGAATAGAGTATG 57.440 33.333 0.00 0.00 39.21 2.39
2447 2902 9.295825 TGGTTGTCAAAATTGAATAGAGTATGT 57.704 29.630 0.00 0.00 39.21 2.29
2528 2983 1.868997 CAAATGCGCTGGAAGACGT 59.131 52.632 9.73 0.00 36.20 4.34
2565 3020 8.458573 TTTTTGTCTTGCTTTCTGATAGGTTA 57.541 30.769 0.00 0.00 0.00 2.85
2733 3190 4.267349 TGGTAAGACTACTGGAACTTGC 57.733 45.455 0.00 0.00 0.00 4.01
2744 3201 5.046910 ACTGGAACTTGCATTTCATTACG 57.953 39.130 9.99 0.00 0.00 3.18
2816 3273 2.097466 GGCCAATATCACAAGGACGTTG 59.903 50.000 0.00 6.34 42.48 4.10
3003 3460 1.435256 AGGGTGCCCAGGTACATATC 58.565 55.000 10.26 0.00 38.92 1.63
3014 3471 5.817816 CCCAGGTACATATCTTTGTGAAGTC 59.182 44.000 0.00 0.00 34.41 3.01
3045 3505 9.853555 CCTTATTATTGTTGTTCTTGCAATGTA 57.146 29.630 0.00 0.00 34.97 2.29
3186 3654 7.191551 AGCACTTTCATATGATTGTGATTTCG 58.808 34.615 28.04 11.81 32.92 3.46
3456 3926 7.338710 AGAAGTTCAAGCTATATTGCAAGGTA 58.661 34.615 11.72 0.00 34.99 3.08
3591 4101 9.982651 TCTAATATGAAGCTGGAGTTGTTATAC 57.017 33.333 0.00 0.00 0.00 1.47
3600 4110 6.371825 AGCTGGAGTTGTTATACTAAAACTGC 59.628 38.462 0.00 0.00 40.26 4.40
3661 4171 9.866655 AATAGGCCATAATGAACTGAAGAATAA 57.133 29.630 5.01 0.00 0.00 1.40
3664 4174 8.636213 AGGCCATAATGAACTGAAGAATAAATG 58.364 33.333 5.01 0.00 0.00 2.32
3679 4196 8.986477 AAGAATAAATGCACTTCCATAAACAC 57.014 30.769 0.00 0.00 0.00 3.32
3686 4203 4.037446 TGCACTTCCATAAACACCAGAAAC 59.963 41.667 0.00 0.00 0.00 2.78
3790 4307 4.336433 AGCATGGGAACTTCATATGTTTCG 59.664 41.667 1.90 0.00 0.00 3.46
3841 4358 4.558095 GCATTTGAGTGATGTGCTTGTTCT 60.558 41.667 0.00 0.00 33.25 3.01
3865 4382 4.383850 AGTCATCATTCCTGAAGTCTCG 57.616 45.455 0.00 0.00 34.37 4.04
4060 4578 9.069078 CAATCTACAGAAGTTGCATTTACATTG 57.931 33.333 0.00 0.00 0.00 2.82
4194 4713 1.498865 GGCATCCAAGGTCATACGCG 61.499 60.000 3.53 3.53 0.00 6.01
4284 4803 6.154203 TCCTGAGATGATCTGTACATGTTC 57.846 41.667 2.30 0.00 0.00 3.18
4338 4857 9.687210 GATGTATTCTAATGTACATTACCGTCA 57.313 33.333 21.73 16.61 40.56 4.35
4340 4859 7.644945 TGTATTCTAATGTACATTACCGTCACG 59.355 37.037 21.73 11.92 32.50 4.35
4393 4912 3.088532 GTGATGACAAGGTATGGGCAAA 58.911 45.455 0.00 0.00 0.00 3.68
4402 4921 2.831526 AGGTATGGGCAAAAATTTCGCT 59.168 40.909 11.16 0.00 0.00 4.93
4403 4922 3.260632 AGGTATGGGCAAAAATTTCGCTT 59.739 39.130 11.16 0.96 0.00 4.68
4404 4923 4.464597 AGGTATGGGCAAAAATTTCGCTTA 59.535 37.500 11.16 3.32 0.00 3.09
4405 4924 5.046950 AGGTATGGGCAAAAATTTCGCTTAA 60.047 36.000 11.16 0.75 0.00 1.85
4406 4925 5.290885 GGTATGGGCAAAAATTTCGCTTAAG 59.709 40.000 11.16 0.00 0.00 1.85
4407 4926 4.329462 TGGGCAAAAATTTCGCTTAAGT 57.671 36.364 4.02 0.00 0.00 2.24
4408 4927 5.455056 TGGGCAAAAATTTCGCTTAAGTA 57.545 34.783 4.02 0.00 0.00 2.24
4430 4990 6.763610 AGTATTTTTCTTCTAGATCTTGCCCG 59.236 38.462 0.00 0.00 0.00 6.13
4546 5110 5.755849 TGATTTCTGGTTTCTATCCCCTTC 58.244 41.667 0.00 0.00 0.00 3.46
4547 5111 5.252863 TGATTTCTGGTTTCTATCCCCTTCA 59.747 40.000 0.00 0.00 0.00 3.02
4905 5473 9.371136 CTCAGTTGTAATCTATTGTGCTTTCTA 57.629 33.333 0.00 0.00 0.00 2.10
5143 5724 1.872952 GGGTTTTGGCATGTTTTCAGC 59.127 47.619 0.00 0.00 0.00 4.26
5147 5728 4.496175 GGTTTTGGCATGTTTTCAGCTTTG 60.496 41.667 0.00 0.00 0.00 2.77
5208 5789 1.473278 AGTTACTCGGAAAGGAGCTCG 59.527 52.381 7.83 0.00 37.57 5.03
5387 5975 1.154338 GCACATGCACTGTTCGCTC 60.154 57.895 0.00 0.00 41.59 5.03
5478 6067 8.870116 AGCACAGATACATTACATCCTTGTATA 58.130 33.333 0.00 0.00 38.12 1.47
5598 6204 5.323382 ACATTATACCCATGGCTGAATGA 57.677 39.130 23.08 7.12 0.00 2.57
5615 6221 8.193438 GGCTGAATGAGTAAGCAGATAAATTTT 58.807 33.333 0.00 0.00 38.73 1.82
5639 6245 0.179018 GCGGCCCCATTCATAAGTCT 60.179 55.000 0.00 0.00 0.00 3.24
5673 6279 2.417243 GGAAGCATGTGAATTTTCCCCG 60.417 50.000 0.00 0.00 32.93 5.73
5674 6280 2.214376 AGCATGTGAATTTTCCCCGA 57.786 45.000 0.00 0.00 0.00 5.14
5675 6281 2.094675 AGCATGTGAATTTTCCCCGAG 58.905 47.619 0.00 0.00 0.00 4.63
5676 6282 2.091541 GCATGTGAATTTTCCCCGAGA 58.908 47.619 0.00 0.00 0.00 4.04
5677 6283 2.098117 GCATGTGAATTTTCCCCGAGAG 59.902 50.000 0.00 0.00 0.00 3.20
5678 6284 1.821216 TGTGAATTTTCCCCGAGAGC 58.179 50.000 0.00 0.00 0.00 4.09
5679 6285 1.073125 TGTGAATTTTCCCCGAGAGCA 59.927 47.619 0.00 0.00 0.00 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 104 1.409427 GACGGAACTGGTGATAGAGGG 59.591 57.143 0.00 0.00 0.00 4.30
108 109 1.874129 ATGGGACGGAACTGGTGATA 58.126 50.000 0.00 0.00 0.00 2.15
109 110 0.991920 AATGGGACGGAACTGGTGAT 59.008 50.000 0.00 0.00 0.00 3.06
123 125 2.406616 CGGGCTTGGTTCGAATGGG 61.407 63.158 0.00 0.00 0.00 4.00
225 242 2.651701 AGCTGACGCGTATAATTCGAG 58.348 47.619 13.97 0.30 42.32 4.04
233 250 3.900892 CCCGGAGCTGACGCGTAT 61.901 66.667 13.97 0.00 42.32 3.06
523 560 1.081376 CTCGGAAGGCGCCTATACG 60.081 63.158 33.07 31.17 0.00 3.06
525 562 1.524863 GCTCTCGGAAGGCGCCTATA 61.525 60.000 33.07 14.47 0.00 1.31
527 564 3.528370 GCTCTCGGAAGGCGCCTA 61.528 66.667 33.07 13.81 0.00 3.93
548 586 3.826754 CCAGCAGAGCCTACGCGA 61.827 66.667 15.93 0.00 41.18 5.87
576 614 0.667487 CGAGGAAAGCAAGACGAGCA 60.667 55.000 0.00 0.00 0.00 4.26
583 621 1.004918 ACGACCCGAGGAAAGCAAG 60.005 57.895 0.00 0.00 0.00 4.01
657 703 2.348620 CACTAGCACTGCAGCCCA 59.651 61.111 15.27 0.00 34.23 5.36
675 721 1.140589 CACCTGACGGCTGCTCTAG 59.859 63.158 0.00 0.00 0.00 2.43
696 742 3.286751 CAGCAACACACCACCCCG 61.287 66.667 0.00 0.00 0.00 5.73
697 743 2.912025 CCAGCAACACACCACCCC 60.912 66.667 0.00 0.00 0.00 4.95
698 744 3.605664 GCCAGCAACACACCACCC 61.606 66.667 0.00 0.00 0.00 4.61
699 745 3.605664 GGCCAGCAACACACCACC 61.606 66.667 0.00 0.00 0.00 4.61
700 746 2.519302 AGGCCAGCAACACACCAC 60.519 61.111 5.01 0.00 0.00 4.16
704 750 1.073025 CCTACAGGCCAGCAACACA 59.927 57.895 5.01 0.00 0.00 3.72
723 775 3.612955 CGATCTAGAAGAAGAATCGGGGC 60.613 52.174 0.00 0.00 0.00 5.80
774 826 9.788889 TGATGCAAGAGATCATGATTAATAAGT 57.211 29.630 10.14 0.00 0.00 2.24
776 828 9.788889 ACTGATGCAAGAGATCATGATTAATAA 57.211 29.630 10.14 0.00 0.00 1.40
777 829 9.216117 CACTGATGCAAGAGATCATGATTAATA 57.784 33.333 10.14 0.00 0.00 0.98
821 956 1.062962 CCCTCCCCCTGCATTTACAAT 60.063 52.381 0.00 0.00 0.00 2.71
837 972 2.284995 ACTGGCTCCTCACCCCTC 60.285 66.667 0.00 0.00 0.00 4.30
854 989 1.410517 GATGAGATTCCAGGCGAGTGA 59.589 52.381 0.00 0.00 0.00 3.41
855 990 1.137675 TGATGAGATTCCAGGCGAGTG 59.862 52.381 0.00 0.00 0.00 3.51
856 991 1.411977 CTGATGAGATTCCAGGCGAGT 59.588 52.381 0.00 0.00 0.00 4.18
857 992 1.270199 CCTGATGAGATTCCAGGCGAG 60.270 57.143 0.00 0.00 40.69 5.03
858 993 0.755079 CCTGATGAGATTCCAGGCGA 59.245 55.000 0.00 0.00 40.69 5.54
859 994 3.302375 CCTGATGAGATTCCAGGCG 57.698 57.895 0.00 0.00 40.69 5.52
865 1000 0.842635 ACCAGGGCCTGATGAGATTC 59.157 55.000 34.84 0.00 32.44 2.52
866 1001 0.549950 CACCAGGGCCTGATGAGATT 59.450 55.000 34.84 6.61 32.44 2.40
869 1004 1.077930 CACACCAGGGCCTGATGAG 60.078 63.158 34.69 23.24 32.44 2.90
892 1027 2.022129 CGACGTGAAGGTCACTGCC 61.022 63.158 0.00 0.00 44.85 4.85
897 1032 3.319755 GGTTATTTCGACGTGAAGGTCA 58.680 45.455 0.00 0.00 37.99 4.02
899 1034 2.331194 CGGTTATTTCGACGTGAAGGT 58.669 47.619 0.00 0.00 37.99 3.50
914 1049 5.163343 CCAGATCATCTAAAAGGTCCGGTTA 60.163 44.000 0.00 0.00 0.00 2.85
922 1057 5.996513 CACCATCTCCAGATCATCTAAAAGG 59.003 44.000 0.00 0.00 31.21 3.11
936 1071 0.041684 TCAGCTCCTCACCATCTCCA 59.958 55.000 0.00 0.00 0.00 3.86
937 1072 0.752054 CTCAGCTCCTCACCATCTCC 59.248 60.000 0.00 0.00 0.00 3.71
938 1073 1.682854 CTCTCAGCTCCTCACCATCTC 59.317 57.143 0.00 0.00 0.00 2.75
1206 1341 0.385348 CGGCTGAGATGATCTCGTCG 60.385 60.000 20.12 20.12 46.25 5.12
1261 1396 3.609807 GCAATCTTTGGATTCTTTGACGC 59.390 43.478 0.00 0.00 39.87 5.19
1266 1401 9.783081 AACATAAAAGCAATCTTTGGATTCTTT 57.217 25.926 0.00 0.00 41.40 2.52
1284 1419 4.469657 AGCCAGGTGTCAAGAACATAAAA 58.530 39.130 0.00 0.00 40.80 1.52
1322 1457 3.149196 TGCAGAAACTTCTCCCACAATC 58.851 45.455 0.00 0.00 34.74 2.67
1764 2193 4.578871 TCATGACCCTGTGTATCAAAGTG 58.421 43.478 0.00 0.00 0.00 3.16
1851 2280 5.745312 TCACTATGAATATCTCGGCCAAT 57.255 39.130 2.24 0.00 0.00 3.16
1937 2366 2.159043 TCTCCTCAGCGAAATCACATCC 60.159 50.000 0.00 0.00 0.00 3.51
1992 2421 6.073385 GGGAGAATTTTCTTCGAAACGTAAGT 60.073 38.462 0.00 0.00 46.94 2.24
2222 2651 4.227300 TGGCCTTGAGGATACAAGTAATGT 59.773 41.667 3.32 0.00 43.72 2.71
2304 2733 7.337942 AGACTAAGATTTTTCGGCATCTCAATT 59.662 33.333 0.00 0.00 0.00 2.32
2432 2887 9.429359 GCATAGCAAGTACATACTCTATTCAAT 57.571 33.333 0.00 0.00 34.99 2.57
2433 2888 8.421002 TGCATAGCAAGTACATACTCTATTCAA 58.579 33.333 0.00 0.00 34.76 2.69
2434 2889 7.951591 TGCATAGCAAGTACATACTCTATTCA 58.048 34.615 0.00 0.00 34.76 2.57
2435 2890 7.543868 CCTGCATAGCAAGTACATACTCTATTC 59.456 40.741 0.00 0.00 38.41 1.75
2436 2891 7.015682 ACCTGCATAGCAAGTACATACTCTATT 59.984 37.037 0.00 0.00 38.41 1.73
2437 2892 6.495181 ACCTGCATAGCAAGTACATACTCTAT 59.505 38.462 0.00 0.00 38.41 1.98
2438 2893 5.833667 ACCTGCATAGCAAGTACATACTCTA 59.166 40.000 0.00 0.00 38.41 2.43
2439 2894 4.651503 ACCTGCATAGCAAGTACATACTCT 59.348 41.667 0.00 0.00 38.41 3.24
2440 2895 4.950050 ACCTGCATAGCAAGTACATACTC 58.050 43.478 0.00 0.00 38.41 2.59
2441 2896 5.118990 CAACCTGCATAGCAAGTACATACT 58.881 41.667 0.00 0.00 38.41 2.12
2442 2897 4.876107 ACAACCTGCATAGCAAGTACATAC 59.124 41.667 0.00 0.00 38.41 2.39
2443 2898 5.097742 ACAACCTGCATAGCAAGTACATA 57.902 39.130 0.00 0.00 38.41 2.29
2444 2899 3.955471 ACAACCTGCATAGCAAGTACAT 58.045 40.909 0.00 0.00 38.41 2.29
2445 2900 3.417069 ACAACCTGCATAGCAAGTACA 57.583 42.857 0.00 0.00 38.41 2.90
2446 2901 4.273480 CCATACAACCTGCATAGCAAGTAC 59.727 45.833 0.00 0.00 38.41 2.73
2447 2902 4.450976 CCATACAACCTGCATAGCAAGTA 58.549 43.478 0.00 0.00 38.41 2.24
2565 3020 8.063770 AGGAAATCATTCATAACCAGGAATTCT 58.936 33.333 5.23 0.00 33.01 2.40
3003 3460 9.329913 CAATAATAAGGAAACGACTTCACAAAG 57.670 33.333 0.00 0.00 35.55 2.77
3014 3471 7.593273 TGCAAGAACAACAATAATAAGGAAACG 59.407 33.333 0.00 0.00 0.00 3.60
3049 3509 7.227156 ACAGGGGAATATAATCTAGCAAACTG 58.773 38.462 0.00 0.00 0.00 3.16
3070 3531 4.687483 GTCAAAGCATGAATTTGGAACAGG 59.313 41.667 18.33 0.00 39.09 4.00
3186 3654 7.751793 CCCATTTAAAAATACAGACGTGGTTAC 59.248 37.037 0.00 0.00 0.00 2.50
3205 3674 7.290714 CCACAAGTACTATACTACCCCCATTTA 59.709 40.741 0.00 0.00 38.26 1.40
3456 3926 7.951347 AGATAGCAATCCAGAAAAGAAACAT 57.049 32.000 0.00 0.00 31.98 2.71
3469 3939 6.959639 TCCATTAACCAAAGATAGCAATCC 57.040 37.500 0.00 0.00 31.98 3.01
3591 4101 7.865707 ACTGAATTTCTGTACTGCAGTTTTAG 58.134 34.615 27.06 18.19 45.23 1.85
3600 4110 9.877178 AGAGGTAATTACTGAATTTCTGTACTG 57.123 33.333 15.05 0.00 36.62 2.74
3661 4171 4.406456 TCTGGTGTTTATGGAAGTGCATT 58.594 39.130 0.00 0.00 0.00 3.56
3664 4174 4.278419 AGTTTCTGGTGTTTATGGAAGTGC 59.722 41.667 0.00 0.00 0.00 4.40
3679 4196 5.916883 CAGAGTTTGCACATTAAGTTTCTGG 59.083 40.000 0.00 0.00 0.00 3.86
3790 4307 5.569059 CCAGAAGACAATTTATTCAACACGC 59.431 40.000 0.00 0.00 0.00 5.34
3841 4358 5.163612 CGAGACTTCAGGAATGATGACTACA 60.164 44.000 0.00 0.00 0.00 2.74
4060 4578 7.909777 GTTAGCAAGTAACTCAAGGAAAAAC 57.090 36.000 0.00 0.00 38.44 2.43
4251 4770 6.044046 CAGATCATCTCAGGAAAGAAGTCAG 58.956 44.000 0.00 0.00 0.00 3.51
4284 4803 8.958119 TGTAAGGGTTATGCACTAAATAGAAG 57.042 34.615 0.00 0.00 0.00 2.85
4338 4857 2.434884 CTCATCAACGGCCTGCGT 60.435 61.111 0.00 0.00 0.00 5.24
4340 4859 2.109126 GGTCTCATCAACGGCCTGC 61.109 63.158 0.00 0.00 0.00 4.85
4403 4922 9.614792 GGGCAAGATCTAGAAGAAAAATACTTA 57.385 33.333 0.00 0.00 0.00 2.24
4404 4923 7.281100 CGGGCAAGATCTAGAAGAAAAATACTT 59.719 37.037 0.00 0.00 0.00 2.24
4405 4924 6.763610 CGGGCAAGATCTAGAAGAAAAATACT 59.236 38.462 0.00 0.00 0.00 2.12
4406 4925 6.761714 TCGGGCAAGATCTAGAAGAAAAATAC 59.238 38.462 0.00 0.00 0.00 1.89
4407 4926 6.884832 TCGGGCAAGATCTAGAAGAAAAATA 58.115 36.000 0.00 0.00 0.00 1.40
4408 4927 5.745227 TCGGGCAAGATCTAGAAGAAAAAT 58.255 37.500 0.00 0.00 0.00 1.82
4472 5036 7.498900 CACTGGGAAAGTATTGCAATACAGATA 59.501 37.037 37.95 22.91 42.87 1.98
4546 5110 2.809446 TCTGTGTCACGAGTTTCTGTG 58.191 47.619 0.00 0.00 37.44 3.66
4547 5111 3.448686 CTTCTGTGTCACGAGTTTCTGT 58.551 45.455 0.00 0.00 0.00 3.41
4905 5473 7.699878 AGGTGAAGGACTTAAAGGAAACATAT 58.300 34.615 0.00 0.00 0.00 1.78
4927 5495 5.195756 AGAGATTAAAGAGGGAGAGAGAGGT 59.804 44.000 0.00 0.00 0.00 3.85
5147 5728 8.421784 TCACCTTCCTCAGAATATATGTACAAC 58.578 37.037 0.00 0.00 0.00 3.32
5214 5795 8.761575 GAATTGTTCAAAATTCAAGCTCCATA 57.238 30.769 5.09 0.00 43.22 2.74
5452 6041 5.994250 ACAAGGATGTAATGTATCTGTGCT 58.006 37.500 0.00 0.00 38.24 4.40
5524 6114 8.608185 TGGAGCCTGATATTTTTAAAATTCCT 57.392 30.769 8.28 0.00 0.00 3.36
5598 6204 6.555315 CGCAAGGAAAATTTATCTGCTTACT 58.445 36.000 10.75 0.00 0.00 2.24
5639 6245 3.283751 CATGCTTCCACGGGGTTTAATA 58.716 45.455 2.12 0.00 34.93 0.98


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

AutoCloner maintained by Alex Coulton.