Multiple sequence alignment - TraesCS1B01G440200

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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 TraesCS1B01G440200 chr1B 100.000 3530 0 0 1 3530 661894449 661897978 0.000000e+00 6519
1 TraesCS1B01G440200 chr1B 98.956 766 7 1 1 765 673416650 673415885 0.000000e+00 1369
2 TraesCS1B01G440200 chr1B 88.333 120 12 2 3327 3445 661897354 661897472 3.670000e-30 143
3 TraesCS1B01G440200 chr1B 88.333 120 12 2 2906 3024 661897775 661897893 3.670000e-30 143
4 TraesCS1B01G440200 chr1A 94.028 2696 116 16 847 3528 571652885 571655549 0.000000e+00 4045
5 TraesCS1B01G440200 chr1A 87.500 120 12 2 2906 3024 571655360 571655477 6.150000e-28 135
6 TraesCS1B01G440200 chr1A 85.593 118 15 2 3329 3445 571654941 571655057 4.790000e-24 122
7 TraesCS1B01G440200 chr1D 96.220 1746 63 1 1138 2880 475816452 475818197 0.000000e+00 2856
8 TraesCS1B01G440200 chr1D 96.466 283 10 0 848 1130 475815783 475816065 5.340000e-128 468
9 TraesCS1B01G440200 chr1D 78.470 353 55 14 2557 2903 475818519 475818856 9.930000e-51 211
10 TraesCS1B01G440200 chr1D 88.189 127 5 4 3402 3528 475818926 475819042 3.670000e-30 143
11 TraesCS1B01G440200 chr2A 99.086 766 7 0 1 766 238721786 238721021 0.000000e+00 1376
12 TraesCS1B01G440200 chr2B 99.085 765 6 1 1 765 325907355 325906592 0.000000e+00 1373
13 TraesCS1B01G440200 chr2B 98.954 765 8 0 1 765 305755515 305754751 0.000000e+00 1369
14 TraesCS1B01G440200 chr2B 98.575 772 11 0 1 772 217833907 217834678 0.000000e+00 1365
15 TraesCS1B01G440200 chr7A 98.953 764 8 0 1 764 495576826 495576063 0.000000e+00 1367
16 TraesCS1B01G440200 chr6A 98.456 777 11 1 1 776 71107163 71106387 0.000000e+00 1367
17 TraesCS1B01G440200 chr4B 98.953 764 8 0 1 764 75187310 75188073 0.000000e+00 1367
18 TraesCS1B01G440200 chr5B 98.575 772 11 0 1 772 682530841 682530070 0.000000e+00 1365


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 TraesCS1B01G440200 chr1B 661894449 661897978 3529 False 2268.333333 6519 92.222000 1 3530 3 chr1B.!!$F1 3529
1 TraesCS1B01G440200 chr1B 673415885 673416650 765 True 1369.000000 1369 98.956000 1 765 1 chr1B.!!$R1 764
2 TraesCS1B01G440200 chr1A 571652885 571655549 2664 False 1434.000000 4045 89.040333 847 3528 3 chr1A.!!$F1 2681
3 TraesCS1B01G440200 chr1D 475815783 475819042 3259 False 919.500000 2856 89.836250 848 3528 4 chr1D.!!$F1 2680
4 TraesCS1B01G440200 chr2A 238721021 238721786 765 True 1376.000000 1376 99.086000 1 766 1 chr2A.!!$R1 765
5 TraesCS1B01G440200 chr2B 325906592 325907355 763 True 1373.000000 1373 99.085000 1 765 1 chr2B.!!$R2 764
6 TraesCS1B01G440200 chr2B 305754751 305755515 764 True 1369.000000 1369 98.954000 1 765 1 chr2B.!!$R1 764
7 TraesCS1B01G440200 chr2B 217833907 217834678 771 False 1365.000000 1365 98.575000 1 772 1 chr2B.!!$F1 771
8 TraesCS1B01G440200 chr7A 495576063 495576826 763 True 1367.000000 1367 98.953000 1 764 1 chr7A.!!$R1 763
9 TraesCS1B01G440200 chr6A 71106387 71107163 776 True 1367.000000 1367 98.456000 1 776 1 chr6A.!!$R1 775
10 TraesCS1B01G440200 chr4B 75187310 75188073 763 False 1367.000000 1367 98.953000 1 764 1 chr4B.!!$F1 763
11 TraesCS1B01G440200 chr5B 682530070 682530841 771 True 1365.000000 1365 98.575000 1 772 1 chr5B.!!$R1 771

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
876 878 0.114168 AACAAAGCCAGGCCCACATA 59.886 50.0 8.22 0.0 0.0 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2731 3122 0.029167 TGAATGTGCGCACAACTGTG 59.971 50.0 43.14 5.45 45.41 3.66 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
154 155 2.171237 AGCCTGATTTGTGGATCGATGA 59.829 45.455 0.54 0.00 0.00 2.92
363 364 4.819761 GATGTCGGCGGCTGCTCA 62.820 66.667 18.85 14.41 42.25 4.26
537 539 5.494706 TGGGTTGATTCTAAAAGGGATAGGT 59.505 40.000 0.00 0.00 0.00 3.08
766 768 2.537214 GCACGGGCGTTATACTAGTTTC 59.463 50.000 0.00 0.00 0.00 2.78
772 774 6.476706 ACGGGCGTTATACTAGTTTCAATAAC 59.523 38.462 0.00 8.31 33.46 1.89
773 775 6.476380 CGGGCGTTATACTAGTTTCAATAACA 59.524 38.462 19.24 0.00 35.49 2.41
774 776 7.306399 CGGGCGTTATACTAGTTTCAATAACAG 60.306 40.741 19.24 14.58 35.49 3.16
775 777 7.342942 GGCGTTATACTAGTTTCAATAACAGC 58.657 38.462 19.24 19.87 35.49 4.40
776 778 7.055598 GCGTTATACTAGTTTCAATAACAGCG 58.944 38.462 19.24 11.03 35.49 5.18
777 779 7.253883 GCGTTATACTAGTTTCAATAACAGCGT 60.254 37.037 19.24 0.00 35.49 5.07
778 780 9.225201 CGTTATACTAGTTTCAATAACAGCGTA 57.775 33.333 19.24 0.00 35.49 4.42
781 783 6.701432 ACTAGTTTCAATAACAGCGTACAC 57.299 37.500 0.00 0.00 0.00 2.90
782 784 6.453092 ACTAGTTTCAATAACAGCGTACACT 58.547 36.000 0.00 0.00 0.00 3.55
783 785 5.591643 AGTTTCAATAACAGCGTACACTG 57.408 39.130 9.35 9.35 43.59 3.66
784 786 5.294356 AGTTTCAATAACAGCGTACACTGA 58.706 37.500 17.55 0.00 40.25 3.41
785 787 5.756347 AGTTTCAATAACAGCGTACACTGAA 59.244 36.000 17.55 5.64 40.25 3.02
786 788 5.585500 TTCAATAACAGCGTACACTGAAC 57.415 39.130 17.55 0.00 40.25 3.18
787 789 4.623002 TCAATAACAGCGTACACTGAACA 58.377 39.130 17.55 2.61 40.25 3.18
788 790 4.684242 TCAATAACAGCGTACACTGAACAG 59.316 41.667 17.55 0.00 40.25 3.16
789 791 2.596904 AACAGCGTACACTGAACAGT 57.403 45.000 17.55 1.32 43.61 3.55
790 792 2.135664 ACAGCGTACACTGAACAGTC 57.864 50.000 17.55 0.00 40.20 3.51
791 793 1.407618 ACAGCGTACACTGAACAGTCA 59.592 47.619 17.55 0.00 40.20 3.41
792 794 1.787155 CAGCGTACACTGAACAGTCAC 59.213 52.381 4.85 5.54 40.20 3.67
793 795 1.407618 AGCGTACACTGAACAGTCACA 59.592 47.619 4.38 0.00 40.20 3.58
794 796 1.521423 GCGTACACTGAACAGTCACAC 59.479 52.381 4.38 3.03 40.20 3.82
795 797 1.779157 CGTACACTGAACAGTCACACG 59.221 52.381 4.38 10.27 40.20 4.49
796 798 2.793585 CGTACACTGAACAGTCACACGT 60.794 50.000 16.90 10.28 40.20 4.49
797 799 3.546616 CGTACACTGAACAGTCACACGTA 60.547 47.826 16.90 9.57 40.20 3.57
798 800 3.079960 ACACTGAACAGTCACACGTAG 57.920 47.619 4.38 0.00 40.20 3.51
799 801 2.223735 ACACTGAACAGTCACACGTAGG 60.224 50.000 4.38 0.00 40.20 3.18
800 802 2.034179 CACTGAACAGTCACACGTAGGA 59.966 50.000 4.38 0.00 40.20 2.94
801 803 2.891580 ACTGAACAGTCACACGTAGGAT 59.108 45.455 1.32 0.00 36.92 3.24
802 804 3.245797 CTGAACAGTCACACGTAGGATG 58.754 50.000 0.00 0.00 0.00 3.51
803 805 2.626266 TGAACAGTCACACGTAGGATGT 59.374 45.455 0.00 0.00 0.00 3.06
805 807 1.272490 ACAGTCACACGTAGGATGTGG 59.728 52.381 14.06 5.48 46.15 4.17
806 808 1.544246 CAGTCACACGTAGGATGTGGA 59.456 52.381 14.06 0.00 46.15 4.02
807 809 1.544691 AGTCACACGTAGGATGTGGAC 59.455 52.381 14.06 7.68 46.15 4.02
808 810 1.271379 GTCACACGTAGGATGTGGACA 59.729 52.381 14.06 0.00 46.15 4.02
809 811 1.271379 TCACACGTAGGATGTGGACAC 59.729 52.381 14.06 0.00 46.15 3.67
810 812 1.272490 CACACGTAGGATGTGGACACT 59.728 52.381 3.91 0.00 43.11 3.55
811 813 1.272490 ACACGTAGGATGTGGACACTG 59.728 52.381 3.91 0.00 39.36 3.66
812 814 1.544246 CACGTAGGATGTGGACACTGA 59.456 52.381 3.91 0.00 31.65 3.41
813 815 2.029380 CACGTAGGATGTGGACACTGAA 60.029 50.000 3.91 0.00 31.65 3.02
814 816 2.029290 ACGTAGGATGTGGACACTGAAC 60.029 50.000 3.91 0.00 0.00 3.18
815 817 2.029380 CGTAGGATGTGGACACTGAACA 60.029 50.000 3.91 0.00 0.00 3.18
816 818 2.847327 AGGATGTGGACACTGAACAG 57.153 50.000 3.91 0.00 0.00 3.16
817 819 2.050144 AGGATGTGGACACTGAACAGT 58.950 47.619 1.32 1.32 43.61 3.55
818 820 2.037772 AGGATGTGGACACTGAACAGTC 59.962 50.000 4.38 0.00 40.20 3.51
825 827 2.072298 GACACTGAACAGTCCATCAGC 58.928 52.381 4.38 0.00 45.50 4.26
826 828 1.417517 ACACTGAACAGTCCATCAGCA 59.582 47.619 4.38 0.00 45.50 4.41
827 829 2.039480 ACACTGAACAGTCCATCAGCAT 59.961 45.455 4.38 0.00 45.50 3.79
828 830 3.261643 ACACTGAACAGTCCATCAGCATA 59.738 43.478 4.38 0.00 45.50 3.14
829 831 4.256110 CACTGAACAGTCCATCAGCATAA 58.744 43.478 4.38 0.00 45.50 1.90
830 832 4.331992 CACTGAACAGTCCATCAGCATAAG 59.668 45.833 4.38 0.00 45.50 1.73
831 833 3.273434 TGAACAGTCCATCAGCATAAGC 58.727 45.455 0.00 0.00 42.56 3.09
832 834 2.338577 ACAGTCCATCAGCATAAGCC 57.661 50.000 0.00 0.00 43.56 4.35
833 835 1.842562 ACAGTCCATCAGCATAAGCCT 59.157 47.619 0.00 0.00 43.56 4.58
834 836 2.240667 ACAGTCCATCAGCATAAGCCTT 59.759 45.455 0.00 0.00 43.56 4.35
835 837 3.285484 CAGTCCATCAGCATAAGCCTTT 58.715 45.455 0.00 0.00 43.56 3.11
836 838 4.080356 ACAGTCCATCAGCATAAGCCTTTA 60.080 41.667 0.00 0.00 43.56 1.85
837 839 4.514441 CAGTCCATCAGCATAAGCCTTTAG 59.486 45.833 0.00 0.00 43.56 1.85
838 840 4.164988 AGTCCATCAGCATAAGCCTTTAGT 59.835 41.667 0.00 0.00 43.56 2.24
839 841 4.513318 GTCCATCAGCATAAGCCTTTAGTC 59.487 45.833 0.00 0.00 43.56 2.59
840 842 3.496130 CCATCAGCATAAGCCTTTAGTCG 59.504 47.826 0.00 0.00 43.56 4.18
841 843 3.179443 TCAGCATAAGCCTTTAGTCGG 57.821 47.619 0.00 0.00 43.56 4.79
842 844 2.158957 TCAGCATAAGCCTTTAGTCGGG 60.159 50.000 0.00 0.00 43.56 5.14
843 845 1.838077 AGCATAAGCCTTTAGTCGGGT 59.162 47.619 0.00 0.00 43.56 5.28
844 846 2.238898 AGCATAAGCCTTTAGTCGGGTT 59.761 45.455 0.00 0.00 43.92 4.11
845 847 3.014623 GCATAAGCCTTTAGTCGGGTTT 58.985 45.455 0.00 0.00 41.94 3.27
850 852 7.629866 GCATAAGCCTTTAGTCGGGTTTTATTT 60.630 37.037 0.00 0.00 41.94 1.40
852 854 5.318630 AGCCTTTAGTCGGGTTTTATTTGA 58.681 37.500 0.00 0.00 0.00 2.69
873 875 2.736531 CAACAAAGCCAGGCCCAC 59.263 61.111 8.22 0.00 0.00 4.61
875 877 1.152269 AACAAAGCCAGGCCCACAT 60.152 52.632 8.22 0.00 0.00 3.21
876 878 0.114168 AACAAAGCCAGGCCCACATA 59.886 50.000 8.22 0.00 0.00 2.29
1263 1654 3.084579 CTGCGCAACATCCTCGTC 58.915 61.111 13.05 0.00 0.00 4.20
1595 1986 0.320771 CCCTCCAACTTCCACGACAG 60.321 60.000 0.00 0.00 0.00 3.51
1647 2038 1.142748 CGTCAGGATGGACAGAGGC 59.857 63.158 0.00 0.00 37.66 4.70
1680 2071 3.396570 ACGGAATGGGACCCCGAC 61.397 66.667 8.45 0.00 45.58 4.79
1779 2170 3.423154 CCGCTCAGGTTCAACCGC 61.423 66.667 0.00 0.00 44.90 5.68
1810 2201 1.841556 AAGGGCCTGAAGGTGTCGA 60.842 57.895 6.92 0.00 37.57 4.20
1830 2221 3.541713 GGAGAGGCGCGGAGGATT 61.542 66.667 8.83 0.00 0.00 3.01
1842 2233 2.615912 GCGGAGGATTGAGAAATTCAGG 59.384 50.000 0.00 0.00 37.07 3.86
1935 2326 0.112218 CCTGTGGGGTGGTTCATGAA 59.888 55.000 3.38 3.38 0.00 2.57
1965 2356 0.880278 TGACACTTGAGAAGCGCACC 60.880 55.000 11.47 0.00 0.00 5.01
1986 2377 2.702847 GGTTGACCACCTGACACAC 58.297 57.895 0.00 0.00 43.29 3.82
2034 2425 0.883814 CTCTGCGGGGAATGCTCATC 60.884 60.000 0.00 0.00 0.00 2.92
2037 2428 2.281070 CGGGGAATGCTCATCCGG 60.281 66.667 0.00 0.00 37.87 5.14
2172 2563 0.694771 AGATGAGGGCTCTTGTTGCA 59.305 50.000 0.00 0.00 0.00 4.08
2214 2605 1.159905 TGGGCCTAGGACTGGTGAA 59.840 57.895 16.16 0.00 0.00 3.18
2226 2617 0.901124 CTGGTGAAGAGACAGAGGGG 59.099 60.000 0.00 0.00 34.21 4.79
2277 2668 5.045359 TGAAGGAAGTGACATGGAAGATGAT 60.045 40.000 0.00 0.00 0.00 2.45
2419 2810 2.027385 TCGGAGATGGTGATGACTCAG 58.973 52.381 0.00 0.00 30.18 3.35
2431 2822 3.390967 TGATGACTCAGGTCCACAAGAAA 59.609 43.478 0.00 0.00 41.47 2.52
2442 2833 3.056035 GTCCACAAGAAATCGAGGTACCT 60.056 47.826 16.26 16.26 0.00 3.08
2473 2864 4.816385 AGAGTAATACAACCAATGATGCCG 59.184 41.667 0.00 0.00 0.00 5.69
2609 3000 5.443283 TCATCTTATCTGATTGCAAAGCCT 58.557 37.500 1.71 0.00 0.00 4.58
2654 3045 2.812011 CTGGGTTGTTGGCTAGTGTTAC 59.188 50.000 0.00 0.00 0.00 2.50
2661 3052 4.740268 TGTTGGCTAGTGTTACGTATCAG 58.260 43.478 6.58 0.00 0.00 2.90
2709 3100 4.158209 TCATATTGTGAACAACCTGCATGG 59.842 41.667 0.00 0.00 38.86 3.66
2731 3122 5.526111 TGGTAACACTAAAACTGTCTTCAGC 59.474 40.000 0.00 0.00 46.17 4.26
2837 3231 5.764686 ACCTCTTGATTTGAAAATTTTGGGC 59.235 36.000 8.47 0.00 0.00 5.36
2838 3232 5.764192 CCTCTTGATTTGAAAATTTTGGGCA 59.236 36.000 8.47 0.00 0.00 5.36
2884 3487 4.338118 TGTGTTGATCTGTTTTCAAGGACC 59.662 41.667 0.00 0.00 33.95 4.46
2946 3585 7.721402 TGGCTTTGTTGTTCATACTGTTAAAT 58.279 30.769 0.00 0.00 0.00 1.40
2955 3594 8.542497 TGTTCATACTGTTAAATGTGTCTACC 57.458 34.615 0.00 0.00 0.00 3.18
2972 3611 6.258947 GTGTCTACCTGGAATCTTTAATCTGC 59.741 42.308 0.00 0.00 0.00 4.26
3048 3687 1.784525 GCTGGCTAGCCTTACGTATG 58.215 55.000 33.07 13.86 44.33 2.39
3101 3740 1.452110 TTTGACCGACCTGCATGATG 58.548 50.000 0.00 0.00 0.00 3.07
3151 3790 6.765989 TCCTCCAACGAATATTCACAAATAGG 59.234 38.462 15.57 12.89 31.02 2.57
3218 3862 4.201950 GGCTGCAAATGTACCACTATTGAG 60.202 45.833 0.50 0.00 0.00 3.02
3243 3887 1.995484 GGATGCATGACCGATCATACG 59.005 52.381 2.46 0.00 44.13 3.06
3279 3927 6.213677 TGATACGTATGCAAGGACTATCAAC 58.786 40.000 13.97 0.00 0.00 3.18
3465 4116 4.033894 GCCGAGCGCATGAGTAAT 57.966 55.556 11.47 0.00 37.47 1.89
3468 4119 1.702886 CCGAGCGCATGAGTAATAGG 58.297 55.000 11.47 0.00 0.00 2.57
3469 4120 1.063806 CGAGCGCATGAGTAATAGGC 58.936 55.000 11.47 0.00 0.00 3.93
3470 4121 1.336332 CGAGCGCATGAGTAATAGGCT 60.336 52.381 11.47 0.00 0.00 4.58
3471 4122 2.095212 CGAGCGCATGAGTAATAGGCTA 60.095 50.000 11.47 0.00 0.00 3.93
3472 4123 3.506810 GAGCGCATGAGTAATAGGCTAG 58.493 50.000 11.47 0.00 0.00 3.42
3473 4124 2.894126 AGCGCATGAGTAATAGGCTAGT 59.106 45.455 11.47 0.00 0.00 2.57
3474 4125 4.079970 AGCGCATGAGTAATAGGCTAGTA 58.920 43.478 11.47 0.00 0.00 1.82
3475 4126 4.156922 AGCGCATGAGTAATAGGCTAGTAG 59.843 45.833 11.47 0.00 0.00 2.57
3476 4127 4.416620 CGCATGAGTAATAGGCTAGTAGC 58.583 47.826 14.09 14.09 41.46 3.58
3477 4128 4.082733 CGCATGAGTAATAGGCTAGTAGCA 60.083 45.833 23.24 4.51 44.75 3.49
3478 4129 5.406649 GCATGAGTAATAGGCTAGTAGCAG 58.593 45.833 23.24 1.10 44.75 4.24
3479 4130 5.184096 GCATGAGTAATAGGCTAGTAGCAGA 59.816 44.000 23.24 10.78 44.75 4.26
3480 4131 6.127479 GCATGAGTAATAGGCTAGTAGCAGAT 60.127 42.308 23.24 12.56 44.75 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
154 155 2.809299 GCCTAACAAAGTCAAGACCCGT 60.809 50.000 0.00 0.00 0.00 5.28
363 364 4.598036 AGGGTTTCATCATGATGACCTT 57.402 40.909 33.02 25.69 46.49 3.50
537 539 5.277297 CGTCATGCACTTCTGTTGAAAAGTA 60.277 40.000 0.00 0.00 34.05 2.24
663 665 2.039084 GGGTGATTATGGGGTGCTCTAG 59.961 54.545 0.00 0.00 0.00 2.43
766 768 4.447724 ACTGTTCAGTGTACGCTGTTATTG 59.552 41.667 30.19 20.51 37.70 1.90
772 774 1.787155 GTGACTGTTCAGTGTACGCTG 59.213 52.381 27.05 27.05 37.81 5.18
773 775 1.407618 TGTGACTGTTCAGTGTACGCT 59.592 47.619 10.29 2.24 30.10 5.07
774 776 1.521423 GTGTGACTGTTCAGTGTACGC 59.479 52.381 10.29 11.16 30.10 4.42
775 777 1.779157 CGTGTGACTGTTCAGTGTACG 59.221 52.381 10.29 12.63 30.10 3.67
776 778 2.805845 ACGTGTGACTGTTCAGTGTAC 58.194 47.619 10.29 9.41 30.10 2.90
777 779 3.004002 CCTACGTGTGACTGTTCAGTGTA 59.996 47.826 10.29 5.33 30.10 2.90
778 780 2.223735 CCTACGTGTGACTGTTCAGTGT 60.224 50.000 10.29 4.47 30.10 3.55
779 781 2.034179 TCCTACGTGTGACTGTTCAGTG 59.966 50.000 10.29 0.00 30.10 3.66
780 782 2.304092 TCCTACGTGTGACTGTTCAGT 58.696 47.619 5.08 5.08 30.10 3.41
781 783 3.245797 CATCCTACGTGTGACTGTTCAG 58.754 50.000 0.00 0.00 30.10 3.02
782 784 2.626266 ACATCCTACGTGTGACTGTTCA 59.374 45.455 0.00 0.00 0.00 3.18
783 785 3.299340 ACATCCTACGTGTGACTGTTC 57.701 47.619 0.00 0.00 0.00 3.18
790 792 1.272490 AGTGTCCACATCCTACGTGTG 59.728 52.381 0.00 0.00 44.99 3.82
791 793 1.272490 CAGTGTCCACATCCTACGTGT 59.728 52.381 0.00 0.00 32.26 4.49
792 794 1.544246 TCAGTGTCCACATCCTACGTG 59.456 52.381 0.00 0.00 0.00 4.49
793 795 1.919240 TCAGTGTCCACATCCTACGT 58.081 50.000 0.00 0.00 0.00 3.57
794 796 2.029380 TGTTCAGTGTCCACATCCTACG 60.029 50.000 0.00 0.00 0.00 3.51
795 797 3.006967 ACTGTTCAGTGTCCACATCCTAC 59.993 47.826 4.58 0.00 0.00 3.18
796 798 3.239449 ACTGTTCAGTGTCCACATCCTA 58.761 45.455 4.58 0.00 0.00 2.94
797 799 2.037772 GACTGTTCAGTGTCCACATCCT 59.962 50.000 10.29 0.00 0.00 3.24
798 800 2.417719 GACTGTTCAGTGTCCACATCC 58.582 52.381 10.29 0.00 0.00 3.51
805 807 2.072298 GCTGATGGACTGTTCAGTGTC 58.928 52.381 10.29 6.45 41.16 3.67
806 808 1.417517 TGCTGATGGACTGTTCAGTGT 59.582 47.619 10.29 0.00 41.16 3.55
807 809 2.174363 TGCTGATGGACTGTTCAGTG 57.826 50.000 10.29 0.00 41.16 3.66
808 810 4.511527 CTTATGCTGATGGACTGTTCAGT 58.488 43.478 5.08 5.08 41.16 3.41
809 811 3.311871 GCTTATGCTGATGGACTGTTCAG 59.688 47.826 4.06 4.06 41.84 3.02
810 812 3.273434 GCTTATGCTGATGGACTGTTCA 58.727 45.455 0.00 0.00 36.03 3.18
811 813 2.615912 GGCTTATGCTGATGGACTGTTC 59.384 50.000 0.13 0.00 39.59 3.18
812 814 2.240667 AGGCTTATGCTGATGGACTGTT 59.759 45.455 0.13 0.00 39.59 3.16
813 815 1.842562 AGGCTTATGCTGATGGACTGT 59.157 47.619 0.13 0.00 39.59 3.55
814 816 2.634815 AGGCTTATGCTGATGGACTG 57.365 50.000 0.13 0.00 39.59 3.51
815 817 3.659183 AAAGGCTTATGCTGATGGACT 57.341 42.857 0.00 0.00 39.59 3.85
816 818 4.455606 ACTAAAGGCTTATGCTGATGGAC 58.544 43.478 0.00 0.00 39.59 4.02
817 819 4.708177 GACTAAAGGCTTATGCTGATGGA 58.292 43.478 0.00 0.00 39.59 3.41
818 820 3.496130 CGACTAAAGGCTTATGCTGATGG 59.504 47.826 0.00 0.00 39.59 3.51
819 821 3.496130 CCGACTAAAGGCTTATGCTGATG 59.504 47.826 0.00 0.00 39.59 3.07
820 822 3.495100 CCCGACTAAAGGCTTATGCTGAT 60.495 47.826 0.00 0.00 39.59 2.90
821 823 2.158957 CCCGACTAAAGGCTTATGCTGA 60.159 50.000 0.00 0.00 39.59 4.26
822 824 2.213499 CCCGACTAAAGGCTTATGCTG 58.787 52.381 0.00 0.00 39.59 4.41
823 825 1.838077 ACCCGACTAAAGGCTTATGCT 59.162 47.619 0.00 0.00 39.59 3.79
824 826 2.327200 ACCCGACTAAAGGCTTATGC 57.673 50.000 0.00 0.00 38.76 3.14
825 827 6.937436 ATAAAACCCGACTAAAGGCTTATG 57.063 37.500 0.00 0.00 0.00 1.90
826 828 7.612633 TCAAATAAAACCCGACTAAAGGCTTAT 59.387 33.333 0.00 0.00 0.00 1.73
827 829 6.941436 TCAAATAAAACCCGACTAAAGGCTTA 59.059 34.615 0.00 0.00 0.00 3.09
828 830 5.771165 TCAAATAAAACCCGACTAAAGGCTT 59.229 36.000 0.00 0.00 0.00 4.35
829 831 5.318630 TCAAATAAAACCCGACTAAAGGCT 58.681 37.500 0.00 0.00 0.00 4.58
830 832 5.632244 TCAAATAAAACCCGACTAAAGGC 57.368 39.130 0.00 0.00 0.00 4.35
831 833 5.392703 GGCTCAAATAAAACCCGACTAAAGG 60.393 44.000 0.00 0.00 0.00 3.11
832 834 5.392703 GGGCTCAAATAAAACCCGACTAAAG 60.393 44.000 0.00 0.00 0.00 1.85
833 835 4.460034 GGGCTCAAATAAAACCCGACTAAA 59.540 41.667 0.00 0.00 0.00 1.85
834 836 4.011698 GGGCTCAAATAAAACCCGACTAA 58.988 43.478 0.00 0.00 0.00 2.24
835 837 3.009253 TGGGCTCAAATAAAACCCGACTA 59.991 43.478 0.00 0.00 44.00 2.59
836 838 2.224917 TGGGCTCAAATAAAACCCGACT 60.225 45.455 0.00 0.00 44.00 4.18
837 839 2.164338 TGGGCTCAAATAAAACCCGAC 58.836 47.619 0.00 0.00 44.00 4.79
838 840 2.559231 GTTGGGCTCAAATAAAACCCGA 59.441 45.455 0.00 0.00 44.00 5.14
839 841 2.297597 TGTTGGGCTCAAATAAAACCCG 59.702 45.455 0.00 0.00 44.00 5.28
840 842 4.344359 TTGTTGGGCTCAAATAAAACCC 57.656 40.909 0.00 0.00 41.24 4.11
841 843 4.213270 GCTTTGTTGGGCTCAAATAAAACC 59.787 41.667 0.00 0.00 34.88 3.27
842 844 4.213270 GGCTTTGTTGGGCTCAAATAAAAC 59.787 41.667 0.00 1.39 34.88 2.43
843 845 4.141620 TGGCTTTGTTGGGCTCAAATAAAA 60.142 37.500 0.00 1.61 34.88 1.52
844 846 3.389329 TGGCTTTGTTGGGCTCAAATAAA 59.611 39.130 0.00 5.18 34.88 1.40
845 847 2.968574 TGGCTTTGTTGGGCTCAAATAA 59.031 40.909 0.00 0.00 34.88 1.40
850 852 1.531365 CCTGGCTTTGTTGGGCTCA 60.531 57.895 0.00 0.00 0.00 4.26
852 854 2.919328 GCCTGGCTTTGTTGGGCT 60.919 61.111 12.43 0.00 39.68 5.19
873 875 1.893808 GGCGTGATGGGCTGGTATG 60.894 63.158 0.00 0.00 0.00 2.39
875 877 4.155733 CGGCGTGATGGGCTGGTA 62.156 66.667 0.00 0.00 33.11 3.25
1595 1986 4.865865 GGTACCTGAGGCAGATGC 57.134 61.111 4.06 0.00 41.14 3.91
1707 2098 2.512355 GGCCCGATTCTCCTCCTCC 61.512 68.421 0.00 0.00 0.00 4.30
1779 2170 3.058160 CCCTTGGGCAGCTTCACG 61.058 66.667 0.00 0.00 0.00 4.35
1797 2188 1.608717 CTCCCCTCGACACCTTCAGG 61.609 65.000 0.00 0.00 42.17 3.86
1830 2221 2.754552 CGGCATTTCCCTGAATTTCTCA 59.245 45.455 0.00 0.00 0.00 3.27
1935 2326 5.489792 TCTCAAGTGTCAGGCTTAGAATT 57.510 39.130 0.00 0.00 0.00 2.17
1983 2374 1.192803 GGAACTCCTCCCGGAAGTGT 61.193 60.000 0.73 0.00 39.29 3.55
1986 2377 2.893398 CGGAACTCCTCCCGGAAG 59.107 66.667 0.73 0.00 41.87 3.46
2034 2425 2.034066 AACATGTCAGGGTGCCGG 59.966 61.111 0.00 0.00 0.00 6.13
2037 2428 2.679837 CACATAGAACATGTCAGGGTGC 59.320 50.000 0.00 0.00 0.00 5.01
2172 2563 2.657237 CGAGGGAAGCGTGGAACT 59.343 61.111 0.00 0.00 31.75 3.01
2214 2605 1.083706 ATTGGGCCCCTCTGTCTCT 59.916 57.895 22.27 0.00 0.00 3.10
2277 2668 4.311606 TGTCCGAAAAATCATCGTCTTCA 58.688 39.130 0.00 0.00 38.60 3.02
2400 2791 1.068281 CCTGAGTCATCACCATCTCCG 59.932 57.143 0.00 0.00 0.00 4.63
2419 2810 2.474410 ACCTCGATTTCTTGTGGACC 57.526 50.000 0.00 0.00 0.00 4.46
2431 2822 5.262804 ACTCTTTGACTTAGGTACCTCGAT 58.737 41.667 20.32 4.33 0.00 3.59
2494 2885 3.071479 GTTGTCTGCCGTCAGGAAATAA 58.929 45.455 0.00 0.00 40.69 1.40
2609 3000 4.701651 CAGGGCACATCAAAAGACATAGAA 59.298 41.667 0.00 0.00 0.00 2.10
2654 3045 1.196749 CTCACGTGCTCGCTGATACG 61.197 60.000 11.67 0.00 41.18 3.06
2661 3052 0.179171 TAAGCTACTCACGTGCTCGC 60.179 55.000 11.67 10.50 41.18 5.03
2709 3100 6.036735 TGTGCTGAAGACAGTTTTAGTGTTAC 59.963 38.462 0.00 0.00 45.04 2.50
2731 3122 0.029167 TGAATGTGCGCACAACTGTG 59.971 50.000 43.14 5.45 45.41 3.66
2738 3129 2.159430 TGTCTATTGTGAATGTGCGCAC 59.841 45.455 33.11 33.11 35.63 5.34
2837 3231 4.869861 TCACAAGGTATGATCAATCACGTG 59.130 41.667 9.94 9.94 40.03 4.49
2838 3232 5.084818 TCACAAGGTATGATCAATCACGT 57.915 39.130 0.00 0.00 40.03 4.49
2884 3487 2.799412 GACTCTTGACAGCTCACACTTG 59.201 50.000 0.00 0.00 0.00 3.16
2946 3585 7.331026 CAGATTAAAGATTCCAGGTAGACACA 58.669 38.462 0.00 0.00 0.00 3.72
2955 3594 8.680903 ACTAACAATGCAGATTAAAGATTCCAG 58.319 33.333 0.00 0.00 0.00 3.86
3048 3687 5.753438 TGTTATTCTAATGATGTGCTCGGTC 59.247 40.000 0.00 0.00 0.00 4.79
3087 3726 0.107993 AGTGTCATCATGCAGGTCGG 60.108 55.000 0.00 0.00 0.00 4.79
3162 3801 8.131455 TCTTTCAGTCATGCGAAATATAGTTC 57.869 34.615 2.80 2.80 31.10 3.01
3218 3862 2.423185 TGATCGGTCATGCATCCAAAAC 59.577 45.455 0.00 0.00 0.00 2.43
3243 3887 5.163903 TGCATACGTATCAACATGTCACAAC 60.164 40.000 4.74 0.00 0.00 3.32
3429 4078 3.243877 CGGCGATACATCAAAAGACAGAG 59.756 47.826 0.00 0.00 0.00 3.35
3430 4079 3.119280 TCGGCGATACATCAAAAGACAGA 60.119 43.478 4.99 0.00 0.00 3.41
3464 4115 9.707957 AAATATGACTATCTGCTACTAGCCTAT 57.292 33.333 5.58 2.18 41.51 2.57
3465 4116 9.535170 AAAATATGACTATCTGCTACTAGCCTA 57.465 33.333 5.58 0.00 41.51 3.93
3468 4119 9.698309 TTCAAAATATGACTATCTGCTACTAGC 57.302 33.333 0.61 0.61 38.79 3.42
3471 4122 9.890629 TTGTTCAAAATATGACTATCTGCTACT 57.109 29.630 0.00 0.00 37.92 2.57
3474 4125 9.399797 TGATTGTTCAAAATATGACTATCTGCT 57.600 29.630 0.00 0.00 37.92 4.24
3475 4126 9.661187 CTGATTGTTCAAAATATGACTATCTGC 57.339 33.333 0.00 0.00 37.92 4.26
3476 4127 9.661187 GCTGATTGTTCAAAATATGACTATCTG 57.339 33.333 0.00 0.00 37.92 2.90
3477 4128 9.399797 TGCTGATTGTTCAAAATATGACTATCT 57.600 29.630 0.00 0.00 37.92 1.98
3479 4130 9.961265 CATGCTGATTGTTCAAAATATGACTAT 57.039 29.630 0.00 0.00 37.92 2.12
3480 4131 9.176460 TCATGCTGATTGTTCAAAATATGACTA 57.824 29.630 0.00 0.00 37.92 2.59


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

AutoCloner maintained by Alex Coulton.