Multiple sequence alignment - TraesCS2D01G251300

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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 TraesCS2D01G251300 chr2D 100.000 3307 0 0 1 3307 299899198 299895892 0.000000e+00 6107.0
1 TraesCS2D01G251300 chr2D 85.833 120 15 2 782 899 626602873 626602754 3.460000e-25 126.0
2 TraesCS2D01G251300 chr2D 95.349 43 2 0 2427 2469 360992128 360992170 5.920000e-08 69.4
3 TraesCS2D01G251300 chr2A 95.983 2390 55 10 926 3307 376110454 376108098 0.000000e+00 3843.0
4 TraesCS2D01G251300 chr2A 84.305 223 20 9 2616 2834 279056160 279056371 1.560000e-48 204.0
5 TraesCS2D01G251300 chr2A 87.255 102 11 2 752 852 470637891 470637991 7.500000e-22 115.0
6 TraesCS2D01G251300 chr2A 79.545 176 20 11 2670 2841 510852944 510852781 9.700000e-21 111.0
7 TraesCS2D01G251300 chr2A 95.238 42 2 0 2427 2468 315809796 315809755 2.130000e-07 67.6
8 TraesCS2D01G251300 chr2B 94.180 1323 33 10 1991 3307 371158016 371159300 0.000000e+00 1977.0
9 TraesCS2D01G251300 chr2B 97.248 1090 20 3 926 2009 371155371 371156456 0.000000e+00 1838.0
10 TraesCS2D01G251300 chr2B 92.135 267 16 2 58 324 305833769 305833508 4.030000e-99 372.0
11 TraesCS2D01G251300 chr2B 91.791 268 17 3 57 324 399795271 399795009 5.210000e-98 368.0
12 TraesCS2D01G251300 chr4A 94.933 750 36 2 1 750 137536213 137536960 0.000000e+00 1173.0
13 TraesCS2D01G251300 chr4A 92.913 762 45 3 1 754 683771435 683770675 0.000000e+00 1099.0
14 TraesCS2D01G251300 chr1D 93.767 754 41 4 1 750 422325624 422324873 0.000000e+00 1127.0
15 TraesCS2D01G251300 chr1D 93.165 278 16 3 412 688 374638420 374638695 3.970000e-109 405.0
16 TraesCS2D01G251300 chr1D 86.017 236 22 5 412 644 22167149 22166922 3.300000e-60 243.0
17 TraesCS2D01G251300 chr1D 93.023 43 3 0 2427 2469 274943969 274943927 2.760000e-06 63.9
18 TraesCS2D01G251300 chr3A 91.327 761 55 3 1 754 395743757 395744513 0.000000e+00 1029.0
19 TraesCS2D01G251300 chr3A 94.737 38 2 0 2835 2872 374672495 374672458 3.560000e-05 60.2
20 TraesCS2D01G251300 chr5D 91.316 760 44 12 1 753 475521574 475520830 0.000000e+00 1018.0
21 TraesCS2D01G251300 chr5D 93.716 366 23 0 85 450 420900876 420900511 1.730000e-152 549.0
22 TraesCS2D01G251300 chr5D 91.667 300 18 5 447 742 420885069 420884773 3.070000e-110 409.0
23 TraesCS2D01G251300 chr5D 84.375 224 21 7 2615 2834 201312232 201312019 1.200000e-49 207.0
24 TraesCS2D01G251300 chr5B 95.577 520 22 1 234 753 534857723 534858241 0.000000e+00 832.0
25 TraesCS2D01G251300 chr5B 95.417 240 10 1 1 240 534838763 534839001 6.700000e-102 381.0
26 TraesCS2D01G251300 chr5B 95.349 43 2 0 2427 2469 81370511 81370553 5.920000e-08 69.4
27 TraesCS2D01G251300 chr3B 90.370 540 32 13 199 735 28259106 28259628 0.000000e+00 691.0
28 TraesCS2D01G251300 chr3B 80.269 223 32 8 2621 2841 95465238 95465450 1.230000e-34 158.0
29 TraesCS2D01G251300 chr1B 92.401 329 19 3 1 329 377071287 377071609 6.460000e-127 464.0
30 TraesCS2D01G251300 chr1B 97.674 43 1 0 2427 2469 547029500 547029458 1.270000e-09 75.0
31 TraesCS2D01G251300 chr7A 84.581 227 21 10 2612 2834 204736785 204737001 2.590000e-51 213.0
32 TraesCS2D01G251300 chr7A 82.143 224 32 7 2615 2834 19184283 19184064 5.640000e-43 185.0
33 TraesCS2D01G251300 chr7A 82.143 224 26 10 2615 2834 221262533 221262320 2.620000e-41 180.0
34 TraesCS2D01G251300 chr5A 84.821 224 20 7 2615 2834 210535651 210535438 2.590000e-51 213.0
35 TraesCS2D01G251300 chr5A 85.388 219 17 9 2617 2831 444536881 444536674 2.590000e-51 213.0
36 TraesCS2D01G251300 chr5A 93.333 45 3 0 2427 2471 78965502 78965458 2.130000e-07 67.6
37 TraesCS2D01G251300 chr6A 83.482 224 20 10 2616 2834 475430971 475431182 3.370000e-45 193.0
38 TraesCS2D01G251300 chr6A 83.036 224 24 10 2615 2834 504476006 504475793 1.210000e-44 191.0
39 TraesCS2D01G251300 chr6D 79.911 224 30 11 2615 2834 461683313 461683525 2.060000e-32 150.0
40 TraesCS2D01G251300 chr6D 100.000 32 0 0 2837 2868 388957006 388956975 3.560000e-05 60.2
41 TraesCS2D01G251300 chr7D 87.234 94 10 2 813 904 514760258 514760351 4.510000e-19 106.0
42 TraesCS2D01G251300 chr4B 95.349 43 2 0 2427 2469 483511767 483511809 5.920000e-08 69.4
43 TraesCS2D01G251300 chr3D 97.143 35 1 0 2834 2868 522131260 522131294 3.560000e-05 60.2
44 TraesCS2D01G251300 chr3D 94.444 36 2 0 2837 2872 286670441 286670406 4.610000e-04 56.5
45 TraesCS2D01G251300 chr1A 100.000 32 0 0 2837 2868 117215150 117215119 3.560000e-05 60.2
46 TraesCS2D01G251300 chr6B 97.059 34 1 0 2838 2871 691795886 691795853 1.280000e-04 58.4
47 TraesCS2D01G251300 chr4D 100.000 31 0 0 2838 2868 111554005 111553975 1.280000e-04 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 TraesCS2D01G251300 chr2D 299895892 299899198 3306 True 6107.0 6107 100.000 1 3307 1 chr2D.!!$R1 3306
1 TraesCS2D01G251300 chr2A 376108098 376110454 2356 True 3843.0 3843 95.983 926 3307 1 chr2A.!!$R2 2381
2 TraesCS2D01G251300 chr2B 371155371 371159300 3929 False 1907.5 1977 95.714 926 3307 2 chr2B.!!$F1 2381
3 TraesCS2D01G251300 chr4A 137536213 137536960 747 False 1173.0 1173 94.933 1 750 1 chr4A.!!$F1 749
4 TraesCS2D01G251300 chr4A 683770675 683771435 760 True 1099.0 1099 92.913 1 754 1 chr4A.!!$R1 753
5 TraesCS2D01G251300 chr1D 422324873 422325624 751 True 1127.0 1127 93.767 1 750 1 chr1D.!!$R3 749
6 TraesCS2D01G251300 chr3A 395743757 395744513 756 False 1029.0 1029 91.327 1 754 1 chr3A.!!$F1 753
7 TraesCS2D01G251300 chr5D 475520830 475521574 744 True 1018.0 1018 91.316 1 753 1 chr5D.!!$R4 752
8 TraesCS2D01G251300 chr5B 534857723 534858241 518 False 832.0 832 95.577 234 753 1 chr5B.!!$F3 519
9 TraesCS2D01G251300 chr3B 28259106 28259628 522 False 691.0 691 90.370 199 735 1 chr3B.!!$F1 536

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
880 898 0.108186 CTTCGGCCTGTGATGCAGTA 60.108 55.0 0.0 0.0 43.55 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2318 3920 0.391263 CCCTCGGACAGGTTACAAGC 60.391 60.0 0.0 0.0 41.51 4.01 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
100 101 3.882326 AGCACACACCTGCTGGCT 61.882 61.111 9.95 0.00 46.10 4.75
105 106 2.851102 ACACCTGCTGGCTGGAGT 60.851 61.111 22.02 17.67 38.26 3.85
224 232 2.188994 GAGCCGAGCTGAGCCATT 59.811 61.111 0.00 0.00 39.88 3.16
270 278 0.325933 ACCCCGTGCTAAAAGTACCC 59.674 55.000 0.00 0.00 0.00 3.69
290 298 3.204526 CCGGTGTAGTTTGTTGTGGTAA 58.795 45.455 0.00 0.00 0.00 2.85
291 299 3.816523 CCGGTGTAGTTTGTTGTGGTAAT 59.183 43.478 0.00 0.00 0.00 1.89
754 772 0.393808 TTGCTATCAAACGGGGCCTC 60.394 55.000 0.84 0.00 0.00 4.70
755 773 1.223487 GCTATCAAACGGGGCCTCA 59.777 57.895 1.96 0.00 0.00 3.86
756 774 0.815615 GCTATCAAACGGGGCCTCAG 60.816 60.000 1.96 0.00 0.00 3.35
757 775 0.541863 CTATCAAACGGGGCCTCAGT 59.458 55.000 1.96 0.00 0.00 3.41
758 776 0.988832 TATCAAACGGGGCCTCAGTT 59.011 50.000 1.96 5.08 35.34 3.16
759 777 0.609131 ATCAAACGGGGCCTCAGTTG 60.609 55.000 12.60 10.69 34.15 3.16
760 778 2.597510 AAACGGGGCCTCAGTTGC 60.598 61.111 12.60 0.00 34.15 4.17
761 779 3.429372 AAACGGGGCCTCAGTTGCA 62.429 57.895 12.60 0.00 34.15 4.08
762 780 2.920076 AAACGGGGCCTCAGTTGCAA 62.920 55.000 12.60 0.00 34.15 4.08
763 781 2.597217 CGGGGCCTCAGTTGCAAA 60.597 61.111 1.96 0.00 0.00 3.68
764 782 2.199652 CGGGGCCTCAGTTGCAAAA 61.200 57.895 1.96 0.00 0.00 2.44
765 783 1.743321 CGGGGCCTCAGTTGCAAAAA 61.743 55.000 1.96 0.00 0.00 1.94
809 827 1.620822 AAAAATCCGCAGCAAGACCT 58.379 45.000 0.00 0.00 0.00 3.85
810 828 0.883833 AAAATCCGCAGCAAGACCTG 59.116 50.000 0.00 0.00 35.93 4.00
811 829 0.250901 AAATCCGCAGCAAGACCTGT 60.251 50.000 0.00 0.00 35.28 4.00
812 830 0.957395 AATCCGCAGCAAGACCTGTG 60.957 55.000 0.00 0.00 41.72 3.66
813 831 2.116983 ATCCGCAGCAAGACCTGTGT 62.117 55.000 0.00 0.00 40.75 3.72
814 832 1.893808 CCGCAGCAAGACCTGTGTT 60.894 57.895 0.00 0.00 40.75 3.32
815 833 1.280746 CGCAGCAAGACCTGTGTTG 59.719 57.895 3.01 3.01 38.27 3.33
826 844 7.481275 CAAGACCTGTGTTGCAAAAATAATT 57.519 32.000 0.00 0.00 0.00 1.40
827 845 7.566709 CAAGACCTGTGTTGCAAAAATAATTC 58.433 34.615 0.00 0.00 0.00 2.17
828 846 6.223120 AGACCTGTGTTGCAAAAATAATTCC 58.777 36.000 0.00 0.00 0.00 3.01
829 847 4.987912 ACCTGTGTTGCAAAAATAATTCCG 59.012 37.500 0.00 0.00 0.00 4.30
830 848 4.143137 CCTGTGTTGCAAAAATAATTCCGC 60.143 41.667 0.00 0.00 0.00 5.54
831 849 4.371786 TGTGTTGCAAAAATAATTCCGCA 58.628 34.783 0.00 0.00 0.00 5.69
832 850 4.811024 TGTGTTGCAAAAATAATTCCGCAA 59.189 33.333 0.00 0.00 34.85 4.85
833 851 5.136711 GTGTTGCAAAAATAATTCCGCAAC 58.863 37.500 15.95 15.95 46.42 4.17
834 852 5.335827 GTTGCAAAAATAATTCCGCAACA 57.664 34.783 17.44 0.00 46.00 3.33
835 853 5.742446 GTTGCAAAAATAATTCCGCAACAA 58.258 33.333 17.44 0.00 46.00 2.83
836 854 5.991328 TGCAAAAATAATTCCGCAACAAA 57.009 30.435 0.00 0.00 0.00 2.83
837 855 6.363577 TGCAAAAATAATTCCGCAACAAAA 57.636 29.167 0.00 0.00 0.00 2.44
838 856 6.195165 TGCAAAAATAATTCCGCAACAAAAC 58.805 32.000 0.00 0.00 0.00 2.43
839 857 5.623264 GCAAAAATAATTCCGCAACAAAACC 59.377 36.000 0.00 0.00 0.00 3.27
840 858 6.512578 GCAAAAATAATTCCGCAACAAAACCT 60.513 34.615 0.00 0.00 0.00 3.50
841 859 6.538189 AAAATAATTCCGCAACAAAACCTG 57.462 33.333 0.00 0.00 0.00 4.00
842 860 4.864704 ATAATTCCGCAACAAAACCTGT 57.135 36.364 0.00 0.00 41.27 4.00
843 861 2.507339 ATTCCGCAACAAAACCTGTG 57.493 45.000 0.00 0.00 38.67 3.66
844 862 1.178276 TTCCGCAACAAAACCTGTGT 58.822 45.000 0.00 0.00 38.67 3.72
845 863 1.178276 TCCGCAACAAAACCTGTGTT 58.822 45.000 0.00 0.00 38.67 3.32
850 868 3.229276 CAACAAAACCTGTGTTGCAGA 57.771 42.857 4.52 0.00 46.63 4.26
851 869 3.583806 CAACAAAACCTGTGTTGCAGAA 58.416 40.909 4.52 0.00 46.63 3.02
852 870 4.183101 CAACAAAACCTGTGTTGCAGAAT 58.817 39.130 4.52 0.00 46.63 2.40
853 871 4.033129 CAACAAAACCTGTGTTGCAGAATG 59.967 41.667 4.52 0.00 46.63 2.67
854 872 6.920570 CAACAAAACCTGTGTTGCAGAATGG 61.921 44.000 4.52 0.00 46.63 3.16
855 873 8.996998 CAACAAAACCTGTGTTGCAGAATGGA 62.997 42.308 4.52 0.00 46.63 3.41
858 876 2.644887 TGTGTTGCAGAATGGAGGC 58.355 52.632 0.00 0.00 38.09 4.70
859 877 0.178995 TGTGTTGCAGAATGGAGGCA 60.179 50.000 0.00 0.00 38.09 4.75
860 878 0.242017 GTGTTGCAGAATGGAGGCAC 59.758 55.000 0.00 0.00 38.09 5.01
861 879 0.895100 TGTTGCAGAATGGAGGCACC 60.895 55.000 0.00 0.00 38.09 5.01
862 880 0.610232 GTTGCAGAATGGAGGCACCT 60.610 55.000 1.84 0.00 38.09 4.00
863 881 0.112995 TTGCAGAATGGAGGCACCTT 59.887 50.000 1.84 0.00 38.09 3.50
864 882 0.322816 TGCAGAATGGAGGCACCTTC 60.323 55.000 1.84 4.08 39.86 3.46
865 883 1.372087 GCAGAATGGAGGCACCTTCG 61.372 60.000 1.84 2.76 39.86 3.79
866 884 0.745845 CAGAATGGAGGCACCTTCGG 60.746 60.000 1.84 1.45 39.86 4.30
867 885 2.044946 AATGGAGGCACCTTCGGC 60.045 61.111 1.84 0.00 39.86 5.54
874 892 2.045926 GCACCTTCGGCCTGTGAT 60.046 61.111 13.65 0.00 31.66 3.06
875 893 2.401766 GCACCTTCGGCCTGTGATG 61.402 63.158 13.65 2.91 31.66 3.07
876 894 2.045926 ACCTTCGGCCTGTGATGC 60.046 61.111 0.00 0.00 0.00 3.91
877 895 2.046023 CCTTCGGCCTGTGATGCA 60.046 61.111 0.00 0.00 0.00 3.96
878 896 2.110967 CCTTCGGCCTGTGATGCAG 61.111 63.158 0.00 0.00 44.63 4.41
879 897 1.376424 CTTCGGCCTGTGATGCAGT 60.376 57.895 0.00 0.00 43.55 4.40
880 898 0.108186 CTTCGGCCTGTGATGCAGTA 60.108 55.000 0.00 0.00 43.55 2.74
881 899 0.323302 TTCGGCCTGTGATGCAGTAA 59.677 50.000 0.00 0.00 43.55 2.24
882 900 0.323302 TCGGCCTGTGATGCAGTAAA 59.677 50.000 0.00 0.00 43.55 2.01
883 901 1.065491 TCGGCCTGTGATGCAGTAAAT 60.065 47.619 0.00 0.00 43.55 1.40
884 902 1.745087 CGGCCTGTGATGCAGTAAATT 59.255 47.619 0.00 0.00 43.55 1.82
885 903 2.478370 CGGCCTGTGATGCAGTAAATTG 60.478 50.000 0.00 0.00 43.55 2.32
886 904 2.159198 GGCCTGTGATGCAGTAAATTGG 60.159 50.000 0.00 0.00 43.55 3.16
887 905 2.754552 GCCTGTGATGCAGTAAATTGGA 59.245 45.455 0.00 0.00 43.55 3.53
888 906 3.428045 GCCTGTGATGCAGTAAATTGGAC 60.428 47.826 0.00 0.00 43.55 4.02
889 907 3.181507 CCTGTGATGCAGTAAATTGGACG 60.182 47.826 0.00 0.00 43.55 4.79
890 908 2.746904 TGTGATGCAGTAAATTGGACGG 59.253 45.455 0.00 0.00 0.00 4.79
891 909 1.742831 TGATGCAGTAAATTGGACGGC 59.257 47.619 8.38 8.38 38.33 5.68
892 910 2.017049 GATGCAGTAAATTGGACGGCT 58.983 47.619 14.13 3.75 38.61 5.52
893 911 1.448985 TGCAGTAAATTGGACGGCTC 58.551 50.000 14.13 0.00 38.61 4.70
894 912 0.373716 GCAGTAAATTGGACGGCTCG 59.626 55.000 8.14 0.00 35.45 5.03
895 913 0.373716 CAGTAAATTGGACGGCTCGC 59.626 55.000 0.00 0.00 0.00 5.03
896 914 1.082117 AGTAAATTGGACGGCTCGCG 61.082 55.000 0.00 0.00 0.00 5.87
897 915 1.079875 GTAAATTGGACGGCTCGCGA 61.080 55.000 9.26 9.26 0.00 5.87
898 916 1.079875 TAAATTGGACGGCTCGCGAC 61.080 55.000 3.71 1.87 0.00 5.19
899 917 4.814294 ATTGGACGGCTCGCGACC 62.814 66.667 3.71 11.31 0.00 4.79
1509 1533 3.755628 GAGGTGGAGCGCGTGGTA 61.756 66.667 8.43 0.00 0.00 3.25
1794 1818 2.498167 ACGCAGTTCTTCAAGCTGAAT 58.502 42.857 0.00 0.00 37.78 2.57
1830 1854 1.199097 CTGAACGGCACCCATGTTTAC 59.801 52.381 0.00 0.00 0.00 2.01
2017 3619 2.037367 AGGGCGCAGAGGTAGTCA 59.963 61.111 10.83 0.00 0.00 3.41
2100 3702 0.179081 GGGTGAAGGGATGCTACGTC 60.179 60.000 0.00 0.00 0.00 4.34
2270 3872 2.880719 TAATGGCATGCGCGGTTTGC 62.881 55.000 12.44 13.85 39.92 3.68
2318 3920 5.738370 CAACCGAATAAAAAGCTATCCTCG 58.262 41.667 0.00 0.00 0.00 4.63
2384 3992 2.717639 ACCTTCAACACTTGCTGTCT 57.282 45.000 0.00 0.00 30.29 3.41
2576 4190 9.322773 GATCATGAGAAGAATGATACTGTGAAA 57.677 33.333 0.09 0.00 43.25 2.69
2605 4219 3.137544 TCAAACACTAAGGGCTCCTTCAA 59.862 43.478 9.46 0.00 43.57 2.69
2608 4222 4.178956 ACACTAAGGGCTCCTTCAAAAA 57.821 40.909 9.46 0.00 43.57 1.94
2754 4368 5.924475 TCAAACTCTTCGAAACAATCCTC 57.076 39.130 0.00 0.00 0.00 3.71
2763 4377 6.317642 TCTTCGAAACAATCCTCTGTTTTTCA 59.682 34.615 0.00 0.00 46.84 2.69
2794 4408 9.836076 ATCTCATATAATGCAATCAAACAATCG 57.164 29.630 0.00 0.00 0.00 3.34
2795 4409 9.054922 TCTCATATAATGCAATCAAACAATCGA 57.945 29.630 0.00 0.00 0.00 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 3.500982 CATCAATACTGTGTTTTGCGGG 58.499 45.455 0.00 0.00 0.00 6.13
100 101 3.340928 CTGAGCATGTTGATCAACTCCA 58.659 45.455 32.57 21.82 42.67 3.86
153 154 0.536460 TGGTTGTTTCTTCCTCCGGC 60.536 55.000 0.00 0.00 0.00 6.13
224 232 1.375908 GAGGCGAGTGCATGGAACA 60.376 57.895 0.00 0.00 45.35 3.18
270 278 4.273969 ACATTACCACAACAAACTACACCG 59.726 41.667 0.00 0.00 0.00 4.94
443 453 4.319177 CCTGTCGTCTTTGGAGAAATCTT 58.681 43.478 0.00 0.00 32.66 2.40
487 500 1.254284 ACTCGCTACTTGCTCTGGCT 61.254 55.000 0.00 0.00 40.11 4.75
790 808 1.270550 CAGGTCTTGCTGCGGATTTTT 59.729 47.619 0.00 0.00 0.00 1.94
791 809 0.883833 CAGGTCTTGCTGCGGATTTT 59.116 50.000 0.00 0.00 0.00 1.82
792 810 0.250901 ACAGGTCTTGCTGCGGATTT 60.251 50.000 0.00 0.00 0.00 2.17
793 811 0.957395 CACAGGTCTTGCTGCGGATT 60.957 55.000 0.00 0.00 0.00 3.01
794 812 1.376424 CACAGGTCTTGCTGCGGAT 60.376 57.895 0.00 0.00 0.00 4.18
795 813 2.031012 CACAGGTCTTGCTGCGGA 59.969 61.111 0.00 0.00 0.00 5.54
796 814 1.893808 AACACAGGTCTTGCTGCGG 60.894 57.895 0.00 0.00 0.00 5.69
797 815 1.280746 CAACACAGGTCTTGCTGCG 59.719 57.895 0.00 0.00 0.00 5.18
798 816 1.008079 GCAACACAGGTCTTGCTGC 60.008 57.895 5.34 0.00 39.79 5.25
799 817 0.740149 TTGCAACACAGGTCTTGCTG 59.260 50.000 12.45 0.00 42.77 4.41
800 818 1.473258 TTTGCAACACAGGTCTTGCT 58.527 45.000 12.45 0.00 42.77 3.91
801 819 2.292103 TTTTGCAACACAGGTCTTGC 57.708 45.000 0.00 5.59 42.67 4.01
802 820 7.307337 GGAATTATTTTTGCAACACAGGTCTTG 60.307 37.037 0.00 0.00 0.00 3.02
803 821 6.705825 GGAATTATTTTTGCAACACAGGTCTT 59.294 34.615 0.00 0.00 0.00 3.01
804 822 6.223120 GGAATTATTTTTGCAACACAGGTCT 58.777 36.000 0.00 0.00 0.00 3.85
805 823 5.118510 CGGAATTATTTTTGCAACACAGGTC 59.881 40.000 0.00 0.00 0.00 3.85
806 824 4.987912 CGGAATTATTTTTGCAACACAGGT 59.012 37.500 0.00 0.00 0.00 4.00
807 825 4.143137 GCGGAATTATTTTTGCAACACAGG 60.143 41.667 0.00 0.00 0.00 4.00
808 826 4.447054 TGCGGAATTATTTTTGCAACACAG 59.553 37.500 0.00 0.00 0.00 3.66
809 827 4.371786 TGCGGAATTATTTTTGCAACACA 58.628 34.783 0.00 0.00 0.00 3.72
810 828 4.981389 TGCGGAATTATTTTTGCAACAC 57.019 36.364 0.00 0.00 0.00 3.32
813 831 5.991328 TTGTTGCGGAATTATTTTTGCAA 57.009 30.435 0.00 0.00 39.73 4.08
814 832 5.991328 TTTGTTGCGGAATTATTTTTGCA 57.009 30.435 0.00 0.00 0.00 4.08
815 833 5.623264 GGTTTTGTTGCGGAATTATTTTTGC 59.377 36.000 0.00 0.00 0.00 3.68
816 834 6.850317 CAGGTTTTGTTGCGGAATTATTTTTG 59.150 34.615 0.00 0.00 0.00 2.44
817 835 6.540551 ACAGGTTTTGTTGCGGAATTATTTTT 59.459 30.769 0.00 0.00 36.31 1.94
818 836 6.018343 CACAGGTTTTGTTGCGGAATTATTTT 60.018 34.615 0.00 0.00 38.16 1.82
819 837 5.465056 CACAGGTTTTGTTGCGGAATTATTT 59.535 36.000 0.00 0.00 38.16 1.40
820 838 4.987912 CACAGGTTTTGTTGCGGAATTATT 59.012 37.500 0.00 0.00 38.16 1.40
821 839 4.038642 ACACAGGTTTTGTTGCGGAATTAT 59.961 37.500 0.00 0.00 38.16 1.28
822 840 3.381908 ACACAGGTTTTGTTGCGGAATTA 59.618 39.130 0.00 0.00 38.16 1.40
823 841 2.167487 ACACAGGTTTTGTTGCGGAATT 59.833 40.909 0.00 0.00 38.16 2.17
824 842 1.754226 ACACAGGTTTTGTTGCGGAAT 59.246 42.857 0.00 0.00 38.16 3.01
825 843 1.178276 ACACAGGTTTTGTTGCGGAA 58.822 45.000 0.00 0.00 38.16 4.30
826 844 1.135257 CAACACAGGTTTTGTTGCGGA 60.135 47.619 2.50 0.00 45.36 5.54
827 845 1.276415 CAACACAGGTTTTGTTGCGG 58.724 50.000 2.50 0.00 45.36 5.69
840 858 0.178995 TGCCTCCATTCTGCAACACA 60.179 50.000 0.00 0.00 30.85 3.72
841 859 0.242017 GTGCCTCCATTCTGCAACAC 59.758 55.000 0.00 0.00 36.65 3.32
842 860 0.895100 GGTGCCTCCATTCTGCAACA 60.895 55.000 0.00 0.00 42.23 3.33
843 861 0.610232 AGGTGCCTCCATTCTGCAAC 60.610 55.000 0.00 0.00 42.98 4.17
844 862 0.112995 AAGGTGCCTCCATTCTGCAA 59.887 50.000 0.00 0.00 36.65 4.08
845 863 0.322816 GAAGGTGCCTCCATTCTGCA 60.323 55.000 0.00 0.00 39.02 4.41
846 864 1.372087 CGAAGGTGCCTCCATTCTGC 61.372 60.000 0.00 0.00 39.02 4.26
847 865 2.772739 CGAAGGTGCCTCCATTCTG 58.227 57.895 0.00 0.00 39.02 3.02
859 877 2.809861 CTGCATCACAGGCCGAAGGT 62.810 60.000 0.00 0.00 44.67 3.50
860 878 2.110967 CTGCATCACAGGCCGAAGG 61.111 63.158 0.00 0.00 45.40 3.46
861 879 3.494378 CTGCATCACAGGCCGAAG 58.506 61.111 0.00 0.00 43.19 3.79
869 887 2.746904 CCGTCCAATTTACTGCATCACA 59.253 45.455 0.00 0.00 0.00 3.58
870 888 2.477863 GCCGTCCAATTTACTGCATCAC 60.478 50.000 0.00 0.00 0.00 3.06
871 889 1.742831 GCCGTCCAATTTACTGCATCA 59.257 47.619 0.00 0.00 0.00 3.07
872 890 2.017049 AGCCGTCCAATTTACTGCATC 58.983 47.619 6.80 0.00 30.40 3.91
873 891 2.017049 GAGCCGTCCAATTTACTGCAT 58.983 47.619 6.80 0.00 30.40 3.96
874 892 1.448985 GAGCCGTCCAATTTACTGCA 58.551 50.000 6.80 0.00 30.40 4.41
875 893 0.373716 CGAGCCGTCCAATTTACTGC 59.626 55.000 0.00 0.00 0.00 4.40
876 894 0.373716 GCGAGCCGTCCAATTTACTG 59.626 55.000 0.00 0.00 0.00 2.74
877 895 1.082117 CGCGAGCCGTCCAATTTACT 61.082 55.000 0.00 0.00 0.00 2.24
878 896 1.079875 TCGCGAGCCGTCCAATTTAC 61.080 55.000 3.71 0.00 38.35 2.01
879 897 1.079875 GTCGCGAGCCGTCCAATTTA 61.080 55.000 10.24 0.00 38.35 1.40
880 898 2.047655 TCGCGAGCCGTCCAATTT 60.048 55.556 3.71 0.00 38.35 1.82
881 899 2.813908 GTCGCGAGCCGTCCAATT 60.814 61.111 10.24 0.00 38.35 2.32
882 900 4.814294 GGTCGCGAGCCGTCCAAT 62.814 66.667 27.12 0.00 43.34 3.16
913 931 2.202690 TCAATCGGGCGTGCTACG 60.203 61.111 4.61 4.61 45.88 3.51
914 932 0.739813 AACTCAATCGGGCGTGCTAC 60.740 55.000 0.00 0.00 0.00 3.58
915 933 0.036765 AAACTCAATCGGGCGTGCTA 60.037 50.000 0.00 0.00 0.00 3.49
916 934 0.889186 AAAACTCAATCGGGCGTGCT 60.889 50.000 0.00 0.00 0.00 4.40
917 935 0.454452 GAAAACTCAATCGGGCGTGC 60.454 55.000 0.00 0.00 0.00 5.34
918 936 0.179225 CGAAAACTCAATCGGGCGTG 60.179 55.000 0.00 0.00 35.49 5.34
919 937 1.908066 GCGAAAACTCAATCGGGCGT 61.908 55.000 0.00 0.00 39.38 5.68
920 938 1.226018 GCGAAAACTCAATCGGGCG 60.226 57.895 0.00 0.00 39.38 6.13
921 939 1.226018 CGCGAAAACTCAATCGGGC 60.226 57.895 0.00 0.00 43.38 6.13
923 941 1.068474 AGTCGCGAAAACTCAATCGG 58.932 50.000 12.06 0.00 39.38 4.18
924 942 2.856091 AAGTCGCGAAAACTCAATCG 57.144 45.000 12.06 0.00 41.81 3.34
1119 1143 1.823169 CGGGGGAGGACTTTTCGACA 61.823 60.000 0.00 0.00 0.00 4.35
1125 1149 2.757077 CAAGCGGGGGAGGACTTT 59.243 61.111 0.00 0.00 0.00 2.66
1479 1503 2.994995 ACCTCGCCGATGACCACA 60.995 61.111 0.00 0.00 0.00 4.17
1509 1533 3.575351 GACACGCCCTTCGCTGACT 62.575 63.158 0.00 0.00 43.23 3.41
1794 1818 4.320129 CCGTTCAGTTTGATGCACACATAA 60.320 41.667 0.00 0.00 36.35 1.90
1830 1854 6.437928 ACAAACAGCAACAACTATACATGTG 58.562 36.000 9.11 0.00 0.00 3.21
1835 1859 5.941948 AGGACAAACAGCAACAACTATAC 57.058 39.130 0.00 0.00 0.00 1.47
1836 1860 6.058833 TCAAGGACAAACAGCAACAACTATA 58.941 36.000 0.00 0.00 0.00 1.31
1837 1861 4.887071 TCAAGGACAAACAGCAACAACTAT 59.113 37.500 0.00 0.00 0.00 2.12
2017 3619 2.663196 GTAGCAGGCCTGTTCCGT 59.337 61.111 32.81 15.33 0.00 4.69
2123 3725 1.509373 AGCAGGAGCATTGAGGATCT 58.491 50.000 0.00 0.00 45.49 2.75
2124 3726 2.549778 GGTAGCAGGAGCATTGAGGATC 60.550 54.545 0.00 0.00 45.49 3.36
2270 3872 5.625251 CAAGTTTGGAACATCAGATCGAAG 58.375 41.667 0.00 0.00 39.30 3.79
2318 3920 0.391263 CCCTCGGACAGGTTACAAGC 60.391 60.000 0.00 0.00 41.51 4.01
2384 3992 4.352893 TCTATCCATCTCCACAACACTCA 58.647 43.478 0.00 0.00 0.00 3.41
2576 4190 5.652452 GGAGCCCTTAGTGTTTGATGTAAAT 59.348 40.000 0.00 0.00 0.00 1.40
2768 4382 9.836076 CGATTGTTTGATTGCATTATATGAGAT 57.164 29.630 0.00 0.00 0.00 2.75
2769 4383 9.054922 TCGATTGTTTGATTGCATTATATGAGA 57.945 29.630 0.00 0.00 0.00 3.27
2770 4384 9.667989 TTCGATTGTTTGATTGCATTATATGAG 57.332 29.630 0.00 0.00 0.00 2.90
2775 4389 8.819974 GGATTTTCGATTGTTTGATTGCATTAT 58.180 29.630 0.00 0.00 0.00 1.28
2776 4390 8.034215 AGGATTTTCGATTGTTTGATTGCATTA 58.966 29.630 0.00 0.00 0.00 1.90
2895 4509 5.221722 ACACAGATATCTGATAACCGCCATT 60.222 40.000 34.16 8.73 46.59 3.16
2896 4510 4.284490 ACACAGATATCTGATAACCGCCAT 59.716 41.667 34.16 9.23 46.59 4.40
2901 4515 6.073385 TCGTACGACACAGATATCTGATAACC 60.073 42.308 34.16 18.01 46.59 2.85


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

AutoCloner maintained by Alex Coulton.