Multiple sequence alignment - TraesCS5A01G134800

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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 TraesCS5A01G134800 chr5A 100.000 2354 0 0 1 2354 304714166 304711813 0.000000e+00 4348.0
1 TraesCS5A01G134800 chr5A 86.690 1435 145 26 944 2354 108744876 108743464 0.000000e+00 1550.0
2 TraesCS5A01G134800 chr5A 84.831 1358 138 52 1047 2354 36031746 36033085 0.000000e+00 1304.0
3 TraesCS5A01G134800 chr5A 91.190 840 71 2 1047 1886 36041236 36042072 0.000000e+00 1138.0
4 TraesCS5A01G134800 chr5A 88.535 157 9 7 770 917 600168550 600168394 5.170000e-42 182.0
5 TraesCS5A01G134800 chr2A 89.979 1407 119 6 954 2340 275352171 275353575 0.000000e+00 1797.0
6 TraesCS5A01G134800 chr2A 90.868 876 78 2 982 1855 661854450 661855325 0.000000e+00 1173.0
7 TraesCS5A01G134800 chr2A 93.771 594 24 8 6 594 366719024 366719609 0.000000e+00 880.0
8 TraesCS5A01G134800 chr2A 88.122 724 65 3 1638 2340 275334459 275335182 0.000000e+00 841.0
9 TraesCS5A01G134800 chr2A 92.334 287 18 3 316 600 30492188 30491904 2.820000e-109 405.0
10 TraesCS5A01G134800 chr1A 93.534 928 42 10 2 917 175839642 175840563 0.000000e+00 1365.0
11 TraesCS5A01G134800 chr1A 92.998 914 45 8 6 906 175864455 175865362 0.000000e+00 1315.0
12 TraesCS5A01G134800 chr1A 91.310 840 68 4 1047 1886 395585335 395584501 0.000000e+00 1142.0
13 TraesCS5A01G134800 chr1A 90.031 652 46 3 1721 2353 209589416 209588765 0.000000e+00 826.0
14 TraesCS5A01G134800 chr1A 88.780 508 53 4 1850 2354 393824305 393824811 9.240000e-174 619.0
15 TraesCS5A01G134800 chr1A 85.989 364 38 13 282 637 243991175 243991533 6.140000e-101 377.0
16 TraesCS5A01G134800 chr1A 91.111 135 6 3 786 914 77376229 77376363 6.690000e-41 178.0
17 TraesCS5A01G134800 chr1A 88.889 81 3 2 818 892 343021138 343021218 6.930000e-16 95.3
18 TraesCS5A01G134800 chr1A 87.654 81 4 3 818 892 343012839 343012919 3.220000e-14 89.8
19 TraesCS5A01G134800 chr1A 94.737 57 1 2 812 868 103987405 103987351 1.160000e-13 87.9
20 TraesCS5A01G134800 chr1A 92.727 55 2 2 815 868 103979263 103979210 6.970000e-11 78.7
21 TraesCS5A01G134800 chr4A 84.120 1461 169 50 941 2354 685920688 685919244 0.000000e+00 1354.0
22 TraesCS5A01G134800 chr4A 91.246 891 78 0 941 1831 685936316 685935426 0.000000e+00 1214.0
23 TraesCS5A01G134800 chr4A 91.794 853 68 2 982 1832 490559437 490560289 0.000000e+00 1186.0
24 TraesCS5A01G134800 chr4A 85.671 656 64 13 1720 2353 414095810 414096457 0.000000e+00 664.0
25 TraesCS5A01G134800 chr4A 87.156 109 7 5 812 914 501429036 501428929 1.480000e-22 117.0
26 TraesCS5A01G134800 chr4A 94.737 57 1 2 812 868 303660717 303660663 1.160000e-13 87.9
27 TraesCS5A01G134800 chr4A 94.737 57 2 1 812 868 433255045 433254990 1.160000e-13 87.9
28 TraesCS5A01G134800 chrUn 93.787 676 30 5 33 705 318814674 318815340 0.000000e+00 1005.0
29 TraesCS5A01G134800 chrUn 93.787 676 30 5 33 705 318826464 318825798 0.000000e+00 1005.0
30 TraesCS5A01G134800 chrUn 93.787 676 30 5 33 705 356433188 356433854 0.000000e+00 1005.0
31 TraesCS5A01G134800 chr7A 91.132 530 28 12 1 517 407271811 407272334 0.000000e+00 701.0
32 TraesCS5A01G134800 chr7A 91.511 483 36 5 1873 2352 273331190 273330710 0.000000e+00 660.0
33 TraesCS5A01G134800 chr7A 87.814 517 56 7 1842 2354 297073296 297073809 1.200000e-167 599.0
34 TraesCS5A01G134800 chr7A 89.130 138 9 3 786 917 229088108 229087971 1.450000e-37 167.0
35 TraesCS5A01G134800 chr7A 87.075 147 18 1 954 1100 391580150 391580005 5.200000e-37 165.0
36 TraesCS5A01G134800 chr7A 87.640 89 8 3 755 842 379776469 379776383 1.490000e-17 100.0
37 TraesCS5A01G134800 chr7A 95.918 49 2 0 913 961 559410479 559410527 1.940000e-11 80.5
38 TraesCS5A01G134800 chr6A 88.615 527 41 11 1 517 167859558 167859041 7.140000e-175 623.0
39 TraesCS5A01G134800 chr6A 87.879 528 44 13 1 517 282884285 282883767 9.310000e-169 603.0
40 TraesCS5A01G134800 chr6A 81.669 611 86 21 1757 2351 243178201 243178801 3.520000e-133 484.0
41 TraesCS5A01G134800 chr6A 81.178 611 89 21 1757 2352 462752128 462752727 3.540000e-128 468.0
42 TraesCS5A01G134800 chr6A 88.235 68 4 3 853 917 539364576 539364510 6.970000e-11 78.7
43 TraesCS5A01G134800 chr3A 86.803 538 58 13 1826 2354 631663427 631663960 2.610000e-164 588.0
44 TraesCS5A01G134800 chr3A 86.778 537 60 11 1826 2354 631680839 631681372 2.610000e-164 588.0
45 TraesCS5A01G134800 chr3A 90.596 436 31 8 282 712 463563449 463563879 9.440000e-159 569.0
46 TraesCS5A01G134800 chr3A 89.583 192 17 3 725 916 280394625 280394437 8.410000e-60 241.0
47 TraesCS5A01G134800 chr3A 88.000 175 9 5 755 917 420263739 420263913 1.850000e-46 196.0
48 TraesCS5A01G134800 chr3A 87.719 114 6 7 811 917 212804136 212804024 2.460000e-25 126.0
49 TraesCS5A01G134800 chr3A 88.073 109 7 2 812 914 113392506 113392398 8.830000e-25 124.0
50 TraesCS5A01G134800 chr6B 86.709 158 20 1 954 1110 609239835 609239678 8.650000e-40 174.0
51 TraesCS5A01G134800 chr6B 85.443 158 22 1 954 1110 562230608 562230451 1.870000e-36 163.0
52 TraesCS5A01G134800 chr5B 84.177 158 24 1 954 1110 167754929 167754772 4.050000e-33 152.0
53 TraesCS5A01G134800 chr3B 80.357 112 17 4 954 1062 360104826 360104935 1.940000e-11 80.5
54 TraesCS5A01G134800 chr3D 94.595 37 2 0 1116 1152 221062907 221062943 9.090000e-05 58.4


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 TraesCS5A01G134800 chr5A 304711813 304714166 2353 True 4348 4348 100.000 1 2354 1 chr5A.!!$R2 2353
1 TraesCS5A01G134800 chr5A 108743464 108744876 1412 True 1550 1550 86.690 944 2354 1 chr5A.!!$R1 1410
2 TraesCS5A01G134800 chr5A 36031746 36033085 1339 False 1304 1304 84.831 1047 2354 1 chr5A.!!$F1 1307
3 TraesCS5A01G134800 chr5A 36041236 36042072 836 False 1138 1138 91.190 1047 1886 1 chr5A.!!$F2 839
4 TraesCS5A01G134800 chr2A 275352171 275353575 1404 False 1797 1797 89.979 954 2340 1 chr2A.!!$F2 1386
5 TraesCS5A01G134800 chr2A 661854450 661855325 875 False 1173 1173 90.868 982 1855 1 chr2A.!!$F4 873
6 TraesCS5A01G134800 chr2A 366719024 366719609 585 False 880 880 93.771 6 594 1 chr2A.!!$F3 588
7 TraesCS5A01G134800 chr2A 275334459 275335182 723 False 841 841 88.122 1638 2340 1 chr2A.!!$F1 702
8 TraesCS5A01G134800 chr1A 175839642 175840563 921 False 1365 1365 93.534 2 917 1 chr1A.!!$F2 915
9 TraesCS5A01G134800 chr1A 175864455 175865362 907 False 1315 1315 92.998 6 906 1 chr1A.!!$F3 900
10 TraesCS5A01G134800 chr1A 395584501 395585335 834 True 1142 1142 91.310 1047 1886 1 chr1A.!!$R4 839
11 TraesCS5A01G134800 chr1A 209588765 209589416 651 True 826 826 90.031 1721 2353 1 chr1A.!!$R3 632
12 TraesCS5A01G134800 chr1A 393824305 393824811 506 False 619 619 88.780 1850 2354 1 chr1A.!!$F7 504
13 TraesCS5A01G134800 chr4A 685919244 685920688 1444 True 1354 1354 84.120 941 2354 1 chr4A.!!$R4 1413
14 TraesCS5A01G134800 chr4A 685935426 685936316 890 True 1214 1214 91.246 941 1831 1 chr4A.!!$R5 890
15 TraesCS5A01G134800 chr4A 490559437 490560289 852 False 1186 1186 91.794 982 1832 1 chr4A.!!$F2 850
16 TraesCS5A01G134800 chr4A 414095810 414096457 647 False 664 664 85.671 1720 2353 1 chr4A.!!$F1 633
17 TraesCS5A01G134800 chrUn 318814674 318815340 666 False 1005 1005 93.787 33 705 1 chrUn.!!$F1 672
18 TraesCS5A01G134800 chrUn 318825798 318826464 666 True 1005 1005 93.787 33 705 1 chrUn.!!$R1 672
19 TraesCS5A01G134800 chrUn 356433188 356433854 666 False 1005 1005 93.787 33 705 1 chrUn.!!$F2 672
20 TraesCS5A01G134800 chr7A 407271811 407272334 523 False 701 701 91.132 1 517 1 chr7A.!!$F2 516
21 TraesCS5A01G134800 chr7A 297073296 297073809 513 False 599 599 87.814 1842 2354 1 chr7A.!!$F1 512
22 TraesCS5A01G134800 chr6A 167859041 167859558 517 True 623 623 88.615 1 517 1 chr6A.!!$R1 516
23 TraesCS5A01G134800 chr6A 282883767 282884285 518 True 603 603 87.879 1 517 1 chr6A.!!$R2 516
24 TraesCS5A01G134800 chr6A 243178201 243178801 600 False 484 484 81.669 1757 2351 1 chr6A.!!$F1 594
25 TraesCS5A01G134800 chr6A 462752128 462752727 599 False 468 468 81.178 1757 2352 1 chr6A.!!$F2 595
26 TraesCS5A01G134800 chr3A 631663427 631663960 533 False 588 588 86.803 1826 2354 1 chr3A.!!$F3 528
27 TraesCS5A01G134800 chr3A 631680839 631681372 533 False 588 588 86.778 1826 2354 1 chr3A.!!$F4 528

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
901 923 0.178891 TCTTCTTCCCCTGCTCTGGT 60.179 55.0 0.0 0.0 0.0 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1907 1.132073 GAAGTAGACGTTCTCGGGACC 59.868 57.143 0.0 0.0 41.85 4.46 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
25 26 3.503363 TCGTTGCTTTCATCTTTGCATCT 59.497 39.130 0.00 0.00 35.27 2.90
27 28 4.682860 CGTTGCTTTCATCTTTGCATCTTT 59.317 37.500 0.00 0.00 35.27 2.52
132 143 8.641498 ATTCACATGGTGTTTCTCTTTAGAAT 57.359 30.769 0.00 0.00 35.58 2.40
211 222 5.323371 ACCGCAACAAACTTGCATTATAT 57.677 34.783 5.93 0.00 45.14 0.86
330 344 1.885887 TCACCCACTTATTGCAAGTGC 59.114 47.619 10.90 0.00 44.62 4.40
422 438 4.592351 TGCCAAATTTCAGATCCTTTGGAA 59.408 37.500 15.16 3.58 46.84 3.53
433 449 5.928264 CAGATCCTTTGGAATTGTTTTGGTC 59.072 40.000 0.00 0.00 34.34 4.02
544 562 0.667993 CAAAGTTCCAGCGCTCCAAA 59.332 50.000 7.13 0.00 0.00 3.28
688 710 1.228367 CATATCCCAGCCAGCCCAC 60.228 63.158 0.00 0.00 0.00 4.61
742 764 2.093075 GTGCTAACCCTAAGTCCTTCCC 60.093 54.545 0.00 0.00 0.00 3.97
782 804 2.920912 TCGTTCCCTTCCACCGCT 60.921 61.111 0.00 0.00 0.00 5.52
868 890 2.561037 GCCGCTAGAGAGGGAGAGC 61.561 68.421 1.26 0.00 37.85 4.09
869 891 1.150536 CCGCTAGAGAGGGAGAGCT 59.849 63.158 0.00 0.00 37.85 4.09
870 892 1.172180 CCGCTAGAGAGGGAGAGCTG 61.172 65.000 0.00 0.00 37.85 4.24
871 893 1.795170 CGCTAGAGAGGGAGAGCTGC 61.795 65.000 0.00 0.00 37.85 5.25
872 894 1.463553 GCTAGAGAGGGAGAGCTGCC 61.464 65.000 0.00 0.00 41.91 4.85
873 895 1.152860 TAGAGAGGGAGAGCTGCCG 60.153 63.158 0.00 0.00 46.59 5.69
874 896 4.219999 GAGAGGGAGAGCTGCCGC 62.220 72.222 3.67 3.67 46.59 6.53
876 898 4.828925 GAGGGAGAGCTGCCGCAC 62.829 72.222 6.89 0.00 46.59 5.34
879 901 4.828925 GGAGAGCTGCCGCACCTC 62.829 72.222 7.51 7.51 39.10 3.85
880 902 4.828925 GAGAGCTGCCGCACCTCC 62.829 72.222 11.38 1.36 39.10 4.30
885 907 3.710722 CTGCCGCACCTCCCTCTT 61.711 66.667 0.00 0.00 0.00 2.85
886 908 3.672295 CTGCCGCACCTCCCTCTTC 62.672 68.421 0.00 0.00 0.00 2.87
887 909 3.394836 GCCGCACCTCCCTCTTCT 61.395 66.667 0.00 0.00 0.00 2.85
888 910 2.960688 GCCGCACCTCCCTCTTCTT 61.961 63.158 0.00 0.00 0.00 2.52
889 911 1.219393 CCGCACCTCCCTCTTCTTC 59.781 63.158 0.00 0.00 0.00 2.87
890 912 1.219393 CGCACCTCCCTCTTCTTCC 59.781 63.158 0.00 0.00 0.00 3.46
891 913 1.604915 GCACCTCCCTCTTCTTCCC 59.395 63.158 0.00 0.00 0.00 3.97
892 914 1.916206 GCACCTCCCTCTTCTTCCCC 61.916 65.000 0.00 0.00 0.00 4.81
893 915 0.252927 CACCTCCCTCTTCTTCCCCT 60.253 60.000 0.00 0.00 0.00 4.79
894 916 0.252927 ACCTCCCTCTTCTTCCCCTG 60.253 60.000 0.00 0.00 0.00 4.45
895 917 1.631071 CCTCCCTCTTCTTCCCCTGC 61.631 65.000 0.00 0.00 0.00 4.85
896 918 0.620121 CTCCCTCTTCTTCCCCTGCT 60.620 60.000 0.00 0.00 0.00 4.24
897 919 0.618968 TCCCTCTTCTTCCCCTGCTC 60.619 60.000 0.00 0.00 0.00 4.26
898 920 0.620121 CCCTCTTCTTCCCCTGCTCT 60.620 60.000 0.00 0.00 0.00 4.09
899 921 0.540923 CCTCTTCTTCCCCTGCTCTG 59.459 60.000 0.00 0.00 0.00 3.35
900 922 0.540923 CTCTTCTTCCCCTGCTCTGG 59.459 60.000 0.00 0.00 0.00 3.86
901 923 0.178891 TCTTCTTCCCCTGCTCTGGT 60.179 55.000 0.00 0.00 0.00 4.00
902 924 0.251634 CTTCTTCCCCTGCTCTGGTC 59.748 60.000 0.00 0.00 0.00 4.02
903 925 0.473694 TTCTTCCCCTGCTCTGGTCA 60.474 55.000 0.00 0.00 0.00 4.02
904 926 0.473694 TCTTCCCCTGCTCTGGTCAA 60.474 55.000 0.00 0.00 0.00 3.18
905 927 0.322008 CTTCCCCTGCTCTGGTCAAC 60.322 60.000 0.00 0.00 0.00 3.18
906 928 2.046892 CCCCTGCTCTGGTCAACG 60.047 66.667 0.00 0.00 0.00 4.10
907 929 2.743928 CCCTGCTCTGGTCAACGC 60.744 66.667 0.00 0.00 0.00 4.84
908 930 2.743928 CCTGCTCTGGTCAACGCC 60.744 66.667 0.00 0.00 0.00 5.68
909 931 2.031012 CTGCTCTGGTCAACGCCA 59.969 61.111 0.00 0.00 36.97 5.69
910 932 1.597854 CTGCTCTGGTCAACGCCAA 60.598 57.895 0.00 0.00 38.18 4.52
911 933 1.153066 TGCTCTGGTCAACGCCAAA 60.153 52.632 0.00 0.00 38.18 3.28
912 934 1.282875 GCTCTGGTCAACGCCAAAC 59.717 57.895 0.00 0.00 38.18 2.93
913 935 1.949257 CTCTGGTCAACGCCAAACC 59.051 57.895 0.00 0.00 38.18 3.27
914 936 1.841663 CTCTGGTCAACGCCAAACCG 61.842 60.000 0.00 0.00 38.18 4.44
915 937 3.536498 CTGGTCAACGCCAAACCGC 62.536 63.158 0.00 0.00 38.18 5.68
916 938 4.337060 GGTCAACGCCAAACCGCC 62.337 66.667 0.00 0.00 0.00 6.13
917 939 3.587933 GTCAACGCCAAACCGCCA 61.588 61.111 0.00 0.00 0.00 5.69
918 940 3.587933 TCAACGCCAAACCGCCAC 61.588 61.111 0.00 0.00 0.00 5.01
919 941 4.639171 CAACGCCAAACCGCCACC 62.639 66.667 0.00 0.00 0.00 4.61
920 942 4.887190 AACGCCAAACCGCCACCT 62.887 61.111 0.00 0.00 0.00 4.00
921 943 4.887190 ACGCCAAACCGCCACCTT 62.887 61.111 0.00 0.00 0.00 3.50
922 944 4.341502 CGCCAAACCGCCACCTTG 62.342 66.667 0.00 0.00 0.00 3.61
923 945 3.989787 GCCAAACCGCCACCTTGG 61.990 66.667 0.00 0.00 42.17 3.61
924 946 2.203422 CCAAACCGCCACCTTGGA 60.203 61.111 0.00 0.00 40.96 3.53
925 947 2.268076 CCAAACCGCCACCTTGGAG 61.268 63.158 0.00 0.00 40.96 3.86
926 948 2.597510 AAACCGCCACCTTGGAGC 60.598 61.111 0.00 0.00 40.96 4.70
927 949 3.133365 AAACCGCCACCTTGGAGCT 62.133 57.895 0.00 0.00 40.96 4.09
928 950 3.553095 AACCGCCACCTTGGAGCTC 62.553 63.158 4.71 4.71 40.96 4.09
929 951 4.785453 CCGCCACCTTGGAGCTCC 62.785 72.222 26.78 26.78 40.96 4.70
930 952 4.020617 CGCCACCTTGGAGCTCCA 62.021 66.667 32.00 32.00 45.94 3.86
962 984 2.040278 CACCAGCTCCTCCTCCCT 59.960 66.667 0.00 0.00 0.00 4.20
967 989 2.363147 GCTCCTCCTCCCTCGTGT 60.363 66.667 0.00 0.00 0.00 4.49
980 1002 0.895530 CTCGTGTGGCTCTTTCCCTA 59.104 55.000 0.00 0.00 0.00 3.53
1019 1041 3.524606 GGCGCCGCTACCTCACTA 61.525 66.667 12.58 0.00 0.00 2.74
1023 1045 1.520494 CGCCGCTACCTCACTATAGA 58.480 55.000 6.78 0.00 0.00 1.98
1100 1123 4.749310 CAGCAAGCTCGCCTCCGT 62.749 66.667 0.00 0.00 35.54 4.69
1154 1177 2.548057 GGAATTCGTCAAGTTCAGCACA 59.452 45.455 0.00 0.00 0.00 4.57
1192 1215 4.728102 CTGTTACCCGCGCCGTCA 62.728 66.667 0.00 0.00 0.00 4.35
1209 1232 0.249573 TCACCGTTCGTCTTCAACCC 60.250 55.000 0.00 0.00 0.00 4.11
1341 1364 1.214367 GCAGTCTTCGTTTCGGAACA 58.786 50.000 7.49 0.00 35.44 3.18
1395 1418 0.393808 CCACTAATGTTGACCCCGGG 60.394 60.000 15.80 15.80 0.00 5.73
1396 1419 0.326927 CACTAATGTTGACCCCGGGT 59.673 55.000 21.85 9.59 39.44 5.28
1403 1426 0.755079 GTTGACCCCGGGTATCTACC 59.245 60.000 21.85 5.22 45.71 3.18
1535 1559 0.516877 ACCACGACAATTGACGCATG 59.483 50.000 26.10 18.47 36.73 4.06
1638 1662 2.048444 ATCGCCGTGAGTACCTCTAA 57.952 50.000 0.00 0.00 0.00 2.10
1714 1738 1.343465 CCACGTCAAGTTCCACTACCT 59.657 52.381 0.00 0.00 0.00 3.08
1741 1765 0.038166 TACCACTACCGTCGACCCTT 59.962 55.000 10.58 0.00 0.00 3.95
1858 1901 6.295462 GGACAAATAGTACCACTACTTCCACA 60.295 42.308 0.00 0.00 32.84 4.17
1864 1907 1.269413 ACCACTACTTCCACAACGACG 60.269 52.381 0.00 0.00 0.00 5.12
2145 2238 1.860641 TCTCCATGAGCTACCGGAAA 58.139 50.000 9.46 0.00 0.00 3.13
2214 2310 2.465860 TTCGTTTCCACCACGATGAT 57.534 45.000 0.00 0.00 45.67 2.45
2295 2397 7.391275 ACATGTCATCCGCATCATGATAATAAA 59.609 33.333 8.15 0.00 39.68 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.822026 TGATGACATGATGCAATGCAAAA 58.178 34.783 13.45 3.51 43.62 2.44
27 28 4.664150 ATGATGACATGATGCAATGCAA 57.336 36.364 13.45 0.00 37.45 4.08
54 55 9.357652 CCATACGATTTGATTGTTGAGAAAAAT 57.642 29.630 0.00 0.00 0.00 1.82
422 438 6.204495 CCATTTTTGAATCCGACCAAAACAAT 59.796 34.615 9.01 1.90 40.60 2.71
433 449 4.178545 ACTTGAGCCATTTTTGAATCCG 57.821 40.909 0.00 0.00 0.00 4.18
742 764 1.476007 GGGAGAGATGTGGATCGGGG 61.476 65.000 0.00 0.00 33.34 5.73
751 773 1.096416 GAACGACGAGGGAGAGATGT 58.904 55.000 0.00 0.00 0.00 3.06
752 774 0.382515 GGAACGACGAGGGAGAGATG 59.617 60.000 0.00 0.00 0.00 2.90
828 850 0.540830 ATCGAGGGAGGAGGGAATCG 60.541 60.000 0.00 0.00 0.00 3.34
868 890 3.672295 GAAGAGGGAGGTGCGGCAG 62.672 68.421 1.18 0.00 0.00 4.85
869 891 3.706373 GAAGAGGGAGGTGCGGCA 61.706 66.667 0.00 0.00 0.00 5.69
870 892 2.860972 GAAGAAGAGGGAGGTGCGGC 62.861 65.000 0.00 0.00 0.00 6.53
871 893 1.219393 GAAGAAGAGGGAGGTGCGG 59.781 63.158 0.00 0.00 0.00 5.69
872 894 1.219393 GGAAGAAGAGGGAGGTGCG 59.781 63.158 0.00 0.00 0.00 5.34
873 895 1.604915 GGGAAGAAGAGGGAGGTGC 59.395 63.158 0.00 0.00 0.00 5.01
874 896 0.252927 AGGGGAAGAAGAGGGAGGTG 60.253 60.000 0.00 0.00 0.00 4.00
875 897 0.252927 CAGGGGAAGAAGAGGGAGGT 60.253 60.000 0.00 0.00 0.00 3.85
876 898 1.631071 GCAGGGGAAGAAGAGGGAGG 61.631 65.000 0.00 0.00 0.00 4.30
877 899 0.620121 AGCAGGGGAAGAAGAGGGAG 60.620 60.000 0.00 0.00 0.00 4.30
878 900 0.618968 GAGCAGGGGAAGAAGAGGGA 60.619 60.000 0.00 0.00 0.00 4.20
879 901 0.620121 AGAGCAGGGGAAGAAGAGGG 60.620 60.000 0.00 0.00 0.00 4.30
880 902 0.540923 CAGAGCAGGGGAAGAAGAGG 59.459 60.000 0.00 0.00 0.00 3.69
881 903 0.540923 CCAGAGCAGGGGAAGAAGAG 59.459 60.000 0.00 0.00 0.00 2.85
882 904 0.178891 ACCAGAGCAGGGGAAGAAGA 60.179 55.000 0.00 0.00 0.00 2.87
883 905 0.251634 GACCAGAGCAGGGGAAGAAG 59.748 60.000 0.00 0.00 0.00 2.85
884 906 0.473694 TGACCAGAGCAGGGGAAGAA 60.474 55.000 0.00 0.00 0.00 2.52
885 907 0.473694 TTGACCAGAGCAGGGGAAGA 60.474 55.000 0.00 0.00 0.00 2.87
886 908 0.322008 GTTGACCAGAGCAGGGGAAG 60.322 60.000 0.00 0.00 0.00 3.46
887 909 1.761174 GTTGACCAGAGCAGGGGAA 59.239 57.895 0.00 0.00 0.00 3.97
888 910 2.583441 CGTTGACCAGAGCAGGGGA 61.583 63.158 0.00 0.00 0.00 4.81
889 911 2.046892 CGTTGACCAGAGCAGGGG 60.047 66.667 0.00 0.00 0.00 4.79
890 912 2.743928 GCGTTGACCAGAGCAGGG 60.744 66.667 0.00 0.00 0.00 4.45
891 913 2.743928 GGCGTTGACCAGAGCAGG 60.744 66.667 0.00 0.00 0.00 4.85
892 914 1.165907 TTTGGCGTTGACCAGAGCAG 61.166 55.000 0.00 0.00 41.82 4.24
893 915 1.153066 TTTGGCGTTGACCAGAGCA 60.153 52.632 0.00 0.00 41.82 4.26
894 916 1.282875 GTTTGGCGTTGACCAGAGC 59.717 57.895 0.00 0.00 41.82 4.09
895 917 1.841663 CGGTTTGGCGTTGACCAGAG 61.842 60.000 0.00 0.00 41.82 3.35
896 918 1.890041 CGGTTTGGCGTTGACCAGA 60.890 57.895 0.00 0.00 41.82 3.86
897 919 2.637025 CGGTTTGGCGTTGACCAG 59.363 61.111 0.00 0.00 41.82 4.00
898 920 3.587933 GCGGTTTGGCGTTGACCA 61.588 61.111 0.00 0.00 38.16 4.02
899 921 4.337060 GGCGGTTTGGCGTTGACC 62.337 66.667 0.00 0.00 0.00 4.02
906 928 3.989787 CCAAGGTGGCGGTTTGGC 61.990 66.667 1.56 0.00 45.12 4.52
907 929 2.203422 TCCAAGGTGGCGGTTTGG 60.203 61.111 7.22 7.22 42.12 3.28
908 930 2.919494 GCTCCAAGGTGGCGGTTTG 61.919 63.158 0.00 0.00 37.47 2.93
909 931 2.597510 GCTCCAAGGTGGCGGTTT 60.598 61.111 0.00 0.00 37.47 3.27
910 932 3.553095 GAGCTCCAAGGTGGCGGTT 62.553 63.158 0.87 0.00 32.50 4.44
911 933 4.021925 GAGCTCCAAGGTGGCGGT 62.022 66.667 0.87 0.00 35.42 5.68
912 934 4.785453 GGAGCTCCAAGGTGGCGG 62.785 72.222 28.43 0.00 37.47 6.13
913 935 4.020617 TGGAGCTCCAAGGTGGCG 62.021 66.667 33.41 0.00 44.35 5.69
962 984 0.606604 GTAGGGAAAGAGCCACACGA 59.393 55.000 0.00 0.00 0.00 4.35
967 989 0.118346 TGGAGGTAGGGAAAGAGCCA 59.882 55.000 0.00 0.00 0.00 4.75
1011 1033 3.386078 CACAGCCACATCTATAGTGAGGT 59.614 47.826 15.04 7.65 39.30 3.85
1019 1041 1.064906 AGCAAGCACAGCCACATCTAT 60.065 47.619 0.00 0.00 0.00 1.98
1023 1045 2.927580 GCAGCAAGCACAGCCACAT 61.928 57.895 0.00 0.00 44.79 3.21
1077 1099 1.153489 GGCGAGCTTGCTGATGAGA 60.153 57.895 25.01 0.00 34.52 3.27
1167 1190 2.599757 GCGGGTAACAGGGGAGGTT 61.600 63.158 0.00 0.00 39.74 3.50
1192 1215 1.070275 GGGGTTGAAGACGAACGGT 59.930 57.895 0.00 0.00 0.00 4.83
1310 1333 4.785453 GACTGCAAGGGGCCTCCG 62.785 72.222 0.00 0.00 43.89 4.63
1311 1334 2.828480 GAAGACTGCAAGGGGCCTCC 62.828 65.000 0.00 0.00 43.89 4.30
1341 1364 0.403271 AGTGCCATCAGCTTCTTGGT 59.597 50.000 7.88 0.00 44.23 3.67
1403 1426 3.751698 TCGATCATAGAGGTCCACGTATG 59.248 47.826 0.00 0.00 0.00 2.39
1419 1442 0.892063 TGACGGTTCCACATCGATCA 59.108 50.000 0.00 0.00 0.00 2.92
1474 1498 2.146342 CAGTCTTGGTTCTTGCGATGT 58.854 47.619 0.00 0.00 0.00 3.06
1493 1517 2.747686 GGGTCTTCGGACTTGCCA 59.252 61.111 0.00 0.00 43.94 4.92
1535 1559 3.721035 ACACGACAAAAGTAGTGGTACC 58.279 45.455 4.43 4.43 38.78 3.34
1714 1738 2.421073 CGACGGTAGTGGTACTCATGAA 59.579 50.000 0.00 0.00 0.00 2.57
1741 1765 2.915659 ACGTCCACGGAGGCTTCA 60.916 61.111 5.70 0.00 44.95 3.02
1858 1901 2.647297 GTTCTCGGGACCGTCGTT 59.353 61.111 10.90 0.00 40.74 3.85
1864 1907 1.132073 GAAGTAGACGTTCTCGGGACC 59.868 57.143 0.00 0.00 41.85 4.46
2145 2238 3.259930 GCCACGGCAACATAACGT 58.740 55.556 2.36 0.00 42.17 3.99
2214 2310 9.287373 TGACATGAGCATATTATGAAGCATTTA 57.713 29.630 7.87 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.