Multiple sequence alignment - TraesCS2B01G211900

Loading Multiple Alignment...

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 TraesCS2B01G211900 chr2B 100.000 3742 0 0 1 3742 195528348 195532089 0.000000e+00 6911.0
1 TraesCS2B01G211900 chr2B 93.624 596 29 4 1 593 18164681 18164092 0.000000e+00 881.0
2 TraesCS2B01G211900 chr2B 93.148 540 25 6 57 593 214819356 214819886 0.000000e+00 782.0
3 TraesCS2B01G211900 chr2A 88.991 3261 141 80 594 3742 164705860 164702706 0.000000e+00 3832.0
4 TraesCS2B01G211900 chr2D 92.583 2319 90 24 594 2873 136831303 136833578 0.000000e+00 3254.0
5 TraesCS2B01G211900 chr2D 89.161 572 47 8 30 593 318424463 318425027 0.000000e+00 699.0
6 TraesCS2B01G211900 chr2D 94.785 326 6 4 3419 3742 136834138 136834454 7.220000e-137 497.0
7 TraesCS2B01G211900 chr2D 89.583 240 19 5 2428 2661 634861295 634861534 2.180000e-77 300.0
8 TraesCS2B01G211900 chr2D 84.615 299 14 7 2938 3210 136833585 136833877 6.160000e-68 268.0
9 TraesCS2B01G211900 chr2D 85.156 128 12 6 3270 3390 136834012 136834139 1.410000e-24 124.0
10 TraesCS2B01G211900 chr3B 95.616 593 20 3 1 593 720247283 720247869 0.000000e+00 946.0
11 TraesCS2B01G211900 chr3B 94.807 597 25 3 1 597 574693392 574693982 0.000000e+00 926.0
12 TraesCS2B01G211900 chr6B 93.960 596 30 3 1 596 464363989 464363400 0.000000e+00 896.0
13 TraesCS2B01G211900 chr6B 93.086 593 34 5 1 593 557097452 557098037 0.000000e+00 861.0
14 TraesCS2B01G211900 chr4B 90.725 593 38 9 1 593 477222255 477222830 0.000000e+00 774.0
15 TraesCS2B01G211900 chr4B 81.481 108 16 4 1420 1525 74682867 74682762 6.660000e-13 86.1
16 TraesCS2B01G211900 chr5A 88.387 620 45 15 1 593 24137874 24138493 0.000000e+00 721.0
17 TraesCS2B01G211900 chr1D 88.636 572 49 9 30 593 493963969 493963406 0.000000e+00 682.0
18 TraesCS2B01G211900 chr4D 82.407 108 15 4 1420 1525 50771610 50771505 1.430000e-14 91.6
19 TraesCS2B01G211900 chr4A 82.407 108 15 4 1420 1525 546210470 546210575 1.430000e-14 91.6


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 TraesCS2B01G211900 chr2B 195528348 195532089 3741 False 6911.00 6911 100.00000 1 3742 1 chr2B.!!$F1 3741
1 TraesCS2B01G211900 chr2B 18164092 18164681 589 True 881.00 881 93.62400 1 593 1 chr2B.!!$R1 592
2 TraesCS2B01G211900 chr2B 214819356 214819886 530 False 782.00 782 93.14800 57 593 1 chr2B.!!$F2 536
3 TraesCS2B01G211900 chr2A 164702706 164705860 3154 True 3832.00 3832 88.99100 594 3742 1 chr2A.!!$R1 3148
4 TraesCS2B01G211900 chr2D 136831303 136834454 3151 False 1035.75 3254 89.28475 594 3742 4 chr2D.!!$F3 3148
5 TraesCS2B01G211900 chr2D 318424463 318425027 564 False 699.00 699 89.16100 30 593 1 chr2D.!!$F1 563
6 TraesCS2B01G211900 chr3B 720247283 720247869 586 False 946.00 946 95.61600 1 593 1 chr3B.!!$F2 592
7 TraesCS2B01G211900 chr3B 574693392 574693982 590 False 926.00 926 94.80700 1 597 1 chr3B.!!$F1 596
8 TraesCS2B01G211900 chr6B 464363400 464363989 589 True 896.00 896 93.96000 1 596 1 chr6B.!!$R1 595
9 TraesCS2B01G211900 chr6B 557097452 557098037 585 False 861.00 861 93.08600 1 593 1 chr6B.!!$F1 592
10 TraesCS2B01G211900 chr4B 477222255 477222830 575 False 774.00 774 90.72500 1 593 1 chr4B.!!$F1 592
11 TraesCS2B01G211900 chr5A 24137874 24138493 619 False 721.00 721 88.38700 1 593 1 chr5A.!!$F1 592
12 TraesCS2B01G211900 chr1D 493963406 493963969 563 True 682.00 682 88.63600 30 593 1 chr1D.!!$R1 563

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
678 724 0.033920 CACGAGCCATGCCATAGCTA 59.966 55.0 0.0 0.0 40.8 3.32 F
2032 2133 0.108138 CGATTCTCTCCCACCACCAC 60.108 60.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2285 2387 0.179127 AGTCCTCGATGTGCACGATG 60.179 55.0 13.13 3.93 39.02 3.84 R
2989 3122 0.106318 AAGATTCATCCAGGCCAGGC 60.106 55.0 9.89 1.26 0.00 4.85 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
76 81 3.165875 TCTGCCTTGTACTAAGTCAGCT 58.834 45.455 9.70 0.00 0.00 4.24
77 82 3.193691 TCTGCCTTGTACTAAGTCAGCTC 59.806 47.826 9.70 0.00 0.00 4.09
78 83 2.897326 TGCCTTGTACTAAGTCAGCTCA 59.103 45.455 0.00 0.00 0.00 4.26
79 84 3.515502 TGCCTTGTACTAAGTCAGCTCAT 59.484 43.478 0.00 0.00 0.00 2.90
80 85 4.020218 TGCCTTGTACTAAGTCAGCTCATT 60.020 41.667 0.00 0.00 0.00 2.57
81 86 5.186992 TGCCTTGTACTAAGTCAGCTCATTA 59.813 40.000 0.00 0.00 0.00 1.90
82 87 6.127054 TGCCTTGTACTAAGTCAGCTCATTAT 60.127 38.462 0.00 0.00 0.00 1.28
83 88 6.763610 GCCTTGTACTAAGTCAGCTCATTATT 59.236 38.462 0.00 0.00 0.00 1.40
147 184 1.939934 CACCGAAGTCAAGAACTGCAA 59.060 47.619 0.00 0.00 38.58 4.08
333 376 1.696884 GGAGAGAGCTAGGGATTTGGG 59.303 57.143 0.00 0.00 0.00 4.12
365 408 1.131638 AGACAAGTGAAGCAGGGACA 58.868 50.000 0.00 0.00 0.00 4.02
466 510 1.648467 GGCGCCAATTGTCTGTCTCC 61.648 60.000 24.80 0.00 0.00 3.71
489 533 2.969821 TGGCTGTGGACTAAACCATT 57.030 45.000 0.00 0.00 42.17 3.16
510 554 9.019656 ACCATTACATAGTTTGCAAGTTTATGA 57.980 29.630 22.81 10.17 0.00 2.15
515 559 8.970691 ACATAGTTTGCAAGTTTATGAATGAC 57.029 30.769 22.81 7.40 0.00 3.06
580 624 1.985159 TGCAAGGTTGTGGGTCTCTAT 59.015 47.619 0.00 0.00 0.00 1.98
673 719 1.660560 GAAAGCACGAGCCATGCCAT 61.661 55.000 0.00 0.00 44.53 4.40
674 720 0.394216 AAAGCACGAGCCATGCCATA 60.394 50.000 0.00 0.00 44.53 2.74
675 721 0.816825 AAGCACGAGCCATGCCATAG 60.817 55.000 0.00 0.00 44.53 2.23
676 722 2.901292 GCACGAGCCATGCCATAGC 61.901 63.158 0.00 0.00 37.08 2.97
677 723 1.227764 CACGAGCCATGCCATAGCT 60.228 57.895 0.00 0.00 40.80 3.32
678 724 0.033920 CACGAGCCATGCCATAGCTA 59.966 55.000 0.00 0.00 40.80 3.32
679 725 0.979665 ACGAGCCATGCCATAGCTAT 59.020 50.000 0.00 0.00 40.80 2.97
680 726 2.094026 CACGAGCCATGCCATAGCTATA 60.094 50.000 5.77 0.00 40.80 1.31
681 727 2.093973 ACGAGCCATGCCATAGCTATAC 60.094 50.000 5.77 2.41 40.80 1.47
682 728 2.167281 CGAGCCATGCCATAGCTATACT 59.833 50.000 5.77 0.00 40.80 2.12
683 729 3.381590 CGAGCCATGCCATAGCTATACTA 59.618 47.826 5.77 0.00 40.80 1.82
684 730 4.498850 CGAGCCATGCCATAGCTATACTAG 60.499 50.000 5.77 0.00 40.80 2.57
714 760 1.023513 CAAGCGAGAGAAAGCCCAGG 61.024 60.000 0.00 0.00 0.00 4.45
736 804 1.152226 ATCTCCTCCCGACATCCCC 60.152 63.158 0.00 0.00 0.00 4.81
738 806 3.690206 TCCTCCCGACATCCCCCA 61.690 66.667 0.00 0.00 0.00 4.96
741 809 4.019513 TCCCGACATCCCCCACCT 62.020 66.667 0.00 0.00 0.00 4.00
743 811 3.849951 CCGACATCCCCCACCTCG 61.850 72.222 0.00 0.00 0.00 4.63
828 896 5.125578 CCCTTTATCTTTTCCTCTTTTCCGG 59.874 44.000 0.00 0.00 0.00 5.14
837 905 3.562182 TCCTCTTTTCCGGCTTCTTTTT 58.438 40.909 0.00 0.00 0.00 1.94
854 932 1.956629 TTTCCGTCTCATCTCGCCCC 61.957 60.000 0.00 0.00 0.00 5.80
855 933 3.917760 CCGTCTCATCTCGCCCCC 61.918 72.222 0.00 0.00 0.00 5.40
856 934 4.271816 CGTCTCATCTCGCCCCCG 62.272 72.222 0.00 0.00 0.00 5.73
857 935 4.593864 GTCTCATCTCGCCCCCGC 62.594 72.222 0.00 0.00 0.00 6.13
885 963 0.677098 TTCTACCTCTCGCACTCGCT 60.677 55.000 0.00 0.00 35.30 4.93
964 1057 2.227388 CGTGAAGCAAGCAGATCCTTTT 59.773 45.455 0.00 0.00 0.00 2.27
986 1079 2.365941 GCCTCCCTTATTAGAGCTCGTT 59.634 50.000 8.37 0.00 0.00 3.85
999 1092 0.940047 GCTCGTTATCCGCTAGTGCC 60.940 60.000 0.00 0.00 36.19 5.01
1017 1110 1.773653 GCCATGGAGAAGGAGAGGAAT 59.226 52.381 18.40 0.00 0.00 3.01
1038 1131 2.718073 GGGGTTCTTCGCCGCTCTA 61.718 63.158 0.00 0.00 39.31 2.43
1188 1281 1.298014 GGAGCAGCAGCAGTACCTT 59.702 57.895 3.17 0.00 45.49 3.50
1597 1698 3.929610 GCATCTGGTACTCACTTCACTTC 59.070 47.826 0.00 0.00 0.00 3.01
2007 2108 2.949177 TGCCACCTTTAGCTTCTTCA 57.051 45.000 0.00 0.00 0.00 3.02
2020 2121 2.740256 GCTTCTTCACCCCTCGATTCTC 60.740 54.545 0.00 0.00 0.00 2.87
2021 2122 2.534042 TCTTCACCCCTCGATTCTCT 57.466 50.000 0.00 0.00 0.00 3.10
2022 2123 2.379972 TCTTCACCCCTCGATTCTCTC 58.620 52.381 0.00 0.00 0.00 3.20
2028 2129 0.687757 CCCTCGATTCTCTCCCACCA 60.688 60.000 0.00 0.00 0.00 4.17
2029 2130 0.461961 CCTCGATTCTCTCCCACCAC 59.538 60.000 0.00 0.00 0.00 4.16
2030 2131 0.461961 CTCGATTCTCTCCCACCACC 59.538 60.000 0.00 0.00 0.00 4.61
2031 2132 0.252057 TCGATTCTCTCCCACCACCA 60.252 55.000 0.00 0.00 0.00 4.17
2032 2133 0.108138 CGATTCTCTCCCACCACCAC 60.108 60.000 0.00 0.00 0.00 4.16
2033 2134 0.253327 GATTCTCTCCCACCACCACC 59.747 60.000 0.00 0.00 0.00 4.61
2034 2135 0.475632 ATTCTCTCCCACCACCACCA 60.476 55.000 0.00 0.00 0.00 4.17
2035 2136 1.415672 TTCTCTCCCACCACCACCAC 61.416 60.000 0.00 0.00 0.00 4.16
2036 2137 2.852075 TCTCCCACCACCACCACC 60.852 66.667 0.00 0.00 0.00 4.61
2037 2138 2.854032 CTCCCACCACCACCACCT 60.854 66.667 0.00 0.00 0.00 4.00
2038 2139 2.852075 TCCCACCACCACCACCTC 60.852 66.667 0.00 0.00 0.00 3.85
2039 2140 3.174987 CCCACCACCACCACCTCA 61.175 66.667 0.00 0.00 0.00 3.86
2046 2147 0.880278 CACCACCACCTCACAAGTCG 60.880 60.000 0.00 0.00 0.00 4.18
2108 2210 1.078143 GCAGGGTCTTGATCCGCTT 60.078 57.895 8.65 0.00 0.00 4.68
2111 2213 0.831307 AGGGTCTTGATCCGCTTACC 59.169 55.000 0.00 0.00 0.00 2.85
2114 2216 1.066430 GGTCTTGATCCGCTTACCACA 60.066 52.381 0.00 0.00 0.00 4.17
2171 2273 1.737008 GAAGGTGAACGGCGAGGAC 60.737 63.158 16.62 6.12 0.00 3.85
2279 2381 2.047274 TACTTCAGCCAGCGCACC 60.047 61.111 11.47 0.00 37.52 5.01
2420 2522 3.341043 ATCATGATCGCGCACGCC 61.341 61.111 8.75 0.00 39.84 5.68
2558 2660 2.892425 GACTGCTTCATCCCGCCG 60.892 66.667 0.00 0.00 0.00 6.46
2735 2840 1.924731 AGATCGTGTGGAGAGTGGAA 58.075 50.000 0.00 0.00 0.00 3.53
2738 2843 2.281539 TCGTGTGGAGAGTGGAAGTA 57.718 50.000 0.00 0.00 0.00 2.24
2740 2845 3.959293 TCGTGTGGAGAGTGGAAGTATA 58.041 45.455 0.00 0.00 0.00 1.47
2753 2858 3.632604 TGGAAGTATAAGGAGCAGACTCG 59.367 47.826 0.00 0.00 44.48 4.18
2855 2988 6.788684 TGTTCATACTACTAGAGATCGAGC 57.211 41.667 0.00 0.00 0.00 5.03
2873 3006 1.012841 GCTCGATTTTCCTCTGCCTG 58.987 55.000 0.00 0.00 0.00 4.85
2874 3007 1.012841 CTCGATTTTCCTCTGCCTGC 58.987 55.000 0.00 0.00 0.00 4.85
2876 3009 0.393537 CGATTTTCCTCTGCCTGCCT 60.394 55.000 0.00 0.00 0.00 4.75
2877 3010 1.101331 GATTTTCCTCTGCCTGCCTG 58.899 55.000 0.00 0.00 0.00 4.85
2878 3011 0.969409 ATTTTCCTCTGCCTGCCTGC 60.969 55.000 0.00 0.00 0.00 4.85
2881 3014 3.085947 CCTCTGCCTGCCTGCCTA 61.086 66.667 0.00 0.00 0.00 3.93
2882 3015 2.505006 CTCTGCCTGCCTGCCTAG 59.495 66.667 0.00 0.00 0.00 3.02
2883 3016 2.284921 TCTGCCTGCCTGCCTAGT 60.285 61.111 0.00 0.00 0.00 2.57
2884 3017 2.124819 CTGCCTGCCTGCCTAGTG 60.125 66.667 0.00 0.00 0.00 2.74
2885 3018 2.607442 TGCCTGCCTGCCTAGTGA 60.607 61.111 0.00 0.00 0.00 3.41
2886 3019 2.189191 CTGCCTGCCTGCCTAGTGAA 62.189 60.000 0.00 0.00 0.00 3.18
2887 3020 1.225704 GCCTGCCTGCCTAGTGAAT 59.774 57.895 0.00 0.00 0.00 2.57
2888 3021 0.817229 GCCTGCCTGCCTAGTGAATC 60.817 60.000 0.00 0.00 0.00 2.52
2889 3022 0.543277 CCTGCCTGCCTAGTGAATCA 59.457 55.000 0.00 0.00 0.00 2.57
2890 3023 1.142465 CCTGCCTGCCTAGTGAATCAT 59.858 52.381 0.00 0.00 0.00 2.45
2891 3024 2.492012 CTGCCTGCCTAGTGAATCATC 58.508 52.381 0.00 0.00 0.00 2.92
2892 3025 1.839354 TGCCTGCCTAGTGAATCATCA 59.161 47.619 0.00 0.00 0.00 3.07
2893 3026 2.440627 TGCCTGCCTAGTGAATCATCAT 59.559 45.455 0.00 0.00 38.01 2.45
2894 3027 2.812591 GCCTGCCTAGTGAATCATCATG 59.187 50.000 0.00 0.00 38.01 3.07
2903 3036 6.479331 CCTAGTGAATCATCATGAGACACTTG 59.521 42.308 24.74 22.46 40.77 3.16
2917 3050 3.802685 AGACACTTGTTCTAACTCGTTGC 59.197 43.478 0.00 0.00 0.00 4.17
2933 3066 2.092838 CGTTGCTTCGAGTTCTTCATCC 59.907 50.000 0.00 0.00 0.00 3.51
2934 3067 1.996292 TGCTTCGAGTTCTTCATCCG 58.004 50.000 0.00 0.00 0.00 4.18
2935 3068 1.272490 TGCTTCGAGTTCTTCATCCGT 59.728 47.619 0.00 0.00 0.00 4.69
2936 3069 1.921230 GCTTCGAGTTCTTCATCCGTC 59.079 52.381 0.00 0.00 0.00 4.79
2937 3070 2.531206 CTTCGAGTTCTTCATCCGTCC 58.469 52.381 0.00 0.00 0.00 4.79
2943 3076 4.116238 GAGTTCTTCATCCGTCCATCTTC 58.884 47.826 0.00 0.00 0.00 2.87
3105 3253 0.315568 GCCATCCGGAGCTGTACTAG 59.684 60.000 11.34 0.00 0.00 2.57
3167 3337 4.767578 AGTGCCACTTGACAGATGATAT 57.232 40.909 0.00 0.00 0.00 1.63
3169 3339 4.880120 AGTGCCACTTGACAGATGATATTG 59.120 41.667 0.00 0.00 0.00 1.90
3223 3488 3.753797 GGTGCCTCTTCCAGAGTAAAAAG 59.246 47.826 0.21 0.00 40.72 2.27
3256 3521 1.195448 CTTGTCTTGACACGGACATGC 59.805 52.381 2.62 0.00 41.27 4.06
3346 3619 5.388408 ACTTGCTACTAACTACTGGTGTC 57.612 43.478 0.00 0.00 0.00 3.67
3399 3672 1.612950 CCAAATTGTGGTGTGCTGCTA 59.387 47.619 0.00 0.00 43.20 3.49
3400 3673 2.231964 CCAAATTGTGGTGTGCTGCTAT 59.768 45.455 0.00 0.00 43.20 2.97
3401 3674 3.443329 CCAAATTGTGGTGTGCTGCTATA 59.557 43.478 0.00 0.00 43.20 1.31
3408 3681 4.893524 TGTGGTGTGCTGCTATAGTAGTAT 59.106 41.667 17.77 0.00 0.00 2.12
3426 3703 1.063183 ATAGCTTCCTGGGCATCTCC 58.937 55.000 0.00 0.00 0.00 3.71
3465 3745 1.143684 CAGGAGAGGAGAGGAGAGGAG 59.856 61.905 0.00 0.00 0.00 3.69
3466 3746 1.010793 AGGAGAGGAGAGGAGAGGAGA 59.989 57.143 0.00 0.00 0.00 3.71
3468 3748 1.421646 GAGAGGAGAGGAGAGGAGAGG 59.578 61.905 0.00 0.00 0.00 3.69
3472 3752 0.179029 GAGAGGAGAGGAGAGGGACG 60.179 65.000 0.00 0.00 0.00 4.79
3473 3753 0.622154 AGAGGAGAGGAGAGGGACGA 60.622 60.000 0.00 0.00 0.00 4.20
3474 3754 0.179029 GAGGAGAGGAGAGGGACGAG 60.179 65.000 0.00 0.00 0.00 4.18
3475 3755 0.917333 AGGAGAGGAGAGGGACGAGT 60.917 60.000 0.00 0.00 0.00 4.18
3476 3756 0.464916 GGAGAGGAGAGGGACGAGTC 60.465 65.000 0.00 0.00 0.00 3.36
3477 3757 0.812412 GAGAGGAGAGGGACGAGTCG 60.812 65.000 11.85 11.85 0.00 4.18
3723 4025 1.818674 CTGCCCGGTGCTTTATTTTCT 59.181 47.619 14.76 0.00 42.00 2.52
3724 4026 1.816224 TGCCCGGTGCTTTATTTTCTC 59.184 47.619 14.76 0.00 42.00 2.87
3725 4027 2.092323 GCCCGGTGCTTTATTTTCTCT 58.908 47.619 0.00 0.00 36.87 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.207417 TCATCATTTTTCAGGAGTTCTTGACC 59.793 38.462 0.00 0.00 31.40 4.02
76 81 8.996271 CAGTAATAATGAGCTGCAGAATAATGA 58.004 33.333 20.43 0.00 0.00 2.57
77 82 8.235226 CCAGTAATAATGAGCTGCAGAATAATG 58.765 37.037 20.43 2.23 0.00 1.90
78 83 7.392673 CCCAGTAATAATGAGCTGCAGAATAAT 59.607 37.037 20.43 0.00 0.00 1.28
79 84 6.712095 CCCAGTAATAATGAGCTGCAGAATAA 59.288 38.462 20.43 0.00 0.00 1.40
80 85 6.043127 TCCCAGTAATAATGAGCTGCAGAATA 59.957 38.462 20.43 1.80 0.00 1.75
81 86 5.068636 CCCAGTAATAATGAGCTGCAGAAT 58.931 41.667 20.43 4.39 0.00 2.40
82 87 4.164030 TCCCAGTAATAATGAGCTGCAGAA 59.836 41.667 20.43 1.66 0.00 3.02
83 88 3.711190 TCCCAGTAATAATGAGCTGCAGA 59.289 43.478 20.43 0.00 0.00 4.26
147 184 1.995626 AACCTAGCGCCAGGGTCAT 60.996 57.895 25.90 6.39 40.29 3.06
333 376 4.579869 TCACTTGTCTTCTTTATCCCTGC 58.420 43.478 0.00 0.00 0.00 4.85
365 408 2.436646 CTGGAAATCACGCCCGCT 60.437 61.111 0.00 0.00 0.00 5.52
466 510 1.737793 GGTTTAGTCCACAGCCAATCG 59.262 52.381 0.00 0.00 0.00 3.34
510 554 5.069516 ACTTGCAAAAGGTGATCAAGTCATT 59.930 36.000 0.00 0.00 42.31 2.57
515 559 5.005971 CACAAACTTGCAAAAGGTGATCAAG 59.994 40.000 12.32 0.00 39.79 3.02
580 624 5.356190 CAGAATTAGAATGAGGCAAGAGCAA 59.644 40.000 0.00 0.00 44.61 3.91
673 719 5.731591 TGCTCGATGCTACTAGTATAGCTA 58.268 41.667 16.62 0.00 46.54 3.32
674 720 4.580868 TGCTCGATGCTACTAGTATAGCT 58.419 43.478 16.62 0.00 46.54 3.32
675 721 4.948608 TGCTCGATGCTACTAGTATAGC 57.051 45.455 10.22 10.22 46.58 2.97
676 722 5.328691 GCTTGCTCGATGCTACTAGTATAG 58.671 45.833 2.33 0.00 43.30 1.31
677 723 4.142881 CGCTTGCTCGATGCTACTAGTATA 60.143 45.833 2.33 0.00 43.37 1.47
678 724 3.365465 CGCTTGCTCGATGCTACTAGTAT 60.365 47.826 2.33 0.00 43.37 2.12
679 725 2.031944 CGCTTGCTCGATGCTACTAGTA 60.032 50.000 1.89 1.89 43.37 1.82
680 726 1.268794 CGCTTGCTCGATGCTACTAGT 60.269 52.381 0.00 0.00 43.37 2.57
681 727 1.002359 TCGCTTGCTCGATGCTACTAG 60.002 52.381 8.07 0.00 43.37 2.57
682 728 1.002359 CTCGCTTGCTCGATGCTACTA 60.002 52.381 8.07 0.00 43.37 1.82
683 729 0.248825 CTCGCTTGCTCGATGCTACT 60.249 55.000 8.07 0.00 43.37 2.57
684 730 0.248661 TCTCGCTTGCTCGATGCTAC 60.249 55.000 8.07 0.00 43.37 3.58
714 760 0.249657 GATGTCGGGAGGAGATGTGC 60.250 60.000 0.00 0.00 0.00 4.57
736 804 3.302347 AAAGAGGCGAGCGAGGTGG 62.302 63.158 0.00 0.00 0.00 4.61
738 806 2.574399 GAAAGAGGCGAGCGAGGT 59.426 61.111 0.00 0.00 0.00 3.85
741 809 1.827399 AAAGGGAAAGAGGCGAGCGA 61.827 55.000 0.00 0.00 0.00 4.93
743 811 1.362406 CGAAAGGGAAAGAGGCGAGC 61.362 60.000 0.00 0.00 0.00 5.03
828 896 3.061429 CGAGATGAGACGGAAAAAGAAGC 59.939 47.826 0.00 0.00 0.00 3.86
837 905 2.833582 GGGGCGAGATGAGACGGA 60.834 66.667 0.00 0.00 0.00 4.69
854 932 4.867599 GTAGAAGGCGACGGGCGG 62.868 72.222 4.96 0.00 44.92 6.13
855 933 4.867599 GGTAGAAGGCGACGGGCG 62.868 72.222 0.00 0.00 44.92 6.13
856 934 3.427598 GAGGTAGAAGGCGACGGGC 62.428 68.421 0.00 0.00 42.51 6.13
857 935 1.726533 GAGAGGTAGAAGGCGACGGG 61.727 65.000 0.00 0.00 0.00 5.28
885 963 4.225267 GGAGTAGAAGGGGAAAGATGTGAA 59.775 45.833 0.00 0.00 0.00 3.18
964 1057 1.964223 CGAGCTCTAATAAGGGAGGCA 59.036 52.381 12.85 0.00 0.00 4.75
986 1079 0.969149 CTCCATGGCACTAGCGGATA 59.031 55.000 6.96 0.00 43.41 2.59
999 1092 3.071312 CCTGATTCCTCTCCTTCTCCATG 59.929 52.174 0.00 0.00 0.00 3.66
1017 1110 4.388499 GCGGCGAAGAACCCCTGA 62.388 66.667 12.98 0.00 0.00 3.86
1038 1131 2.750350 CGCACCACCTCCTCCTTT 59.250 61.111 0.00 0.00 0.00 3.11
1188 1281 2.849964 CGCTATGAGCTGCTCCGGA 61.850 63.158 25.61 2.93 39.60 5.14
1597 1698 0.674581 TGCGAATTCCCAGAGCAGTG 60.675 55.000 0.00 0.00 33.57 3.66
1722 1823 1.810030 GAACTCGGACGCCACCATC 60.810 63.158 0.00 0.00 0.00 3.51
2007 2108 0.688087 GTGGGAGAGAATCGAGGGGT 60.688 60.000 0.00 0.00 42.67 4.95
2020 2121 2.854032 AGGTGGTGGTGGTGGGAG 60.854 66.667 0.00 0.00 0.00 4.30
2021 2122 2.852075 GAGGTGGTGGTGGTGGGA 60.852 66.667 0.00 0.00 0.00 4.37
2022 2123 3.174987 TGAGGTGGTGGTGGTGGG 61.175 66.667 0.00 0.00 0.00 4.61
2028 2129 1.445942 CGACTTGTGAGGTGGTGGT 59.554 57.895 0.00 0.00 0.00 4.16
2029 2130 1.961277 GCGACTTGTGAGGTGGTGG 60.961 63.158 0.00 0.00 0.00 4.61
2030 2131 0.603707 ATGCGACTTGTGAGGTGGTG 60.604 55.000 0.00 0.00 0.00 4.17
2031 2132 0.320771 GATGCGACTTGTGAGGTGGT 60.321 55.000 0.00 0.00 0.00 4.16
2032 2133 1.354337 CGATGCGACTTGTGAGGTGG 61.354 60.000 0.00 0.00 0.00 4.61
2033 2134 1.959899 GCGATGCGACTTGTGAGGTG 61.960 60.000 0.00 0.00 0.00 4.00
2034 2135 1.738099 GCGATGCGACTTGTGAGGT 60.738 57.895 0.00 0.00 0.00 3.85
2035 2136 1.291184 TTGCGATGCGACTTGTGAGG 61.291 55.000 0.00 0.00 0.00 3.86
2036 2137 0.512518 TTTGCGATGCGACTTGTGAG 59.487 50.000 0.00 0.00 0.00 3.51
2037 2138 1.128507 GATTTGCGATGCGACTTGTGA 59.871 47.619 0.00 0.00 0.00 3.58
2038 2139 1.129251 AGATTTGCGATGCGACTTGTG 59.871 47.619 0.00 0.00 0.00 3.33
2039 2140 1.442769 AGATTTGCGATGCGACTTGT 58.557 45.000 0.00 0.00 0.00 3.16
2046 2147 4.285292 CATGGTAAGAAGATTTGCGATGC 58.715 43.478 0.00 0.00 0.00 3.91
2108 2210 3.246112 AACAGGCCGGCTGTGGTA 61.246 61.111 28.56 0.00 34.97 3.25
2138 2240 1.667830 CTTCTTCTCGCCCACGCAA 60.668 57.895 0.00 0.00 39.84 4.85
2279 2381 2.512286 ATGTGCACGATGAGCCCG 60.512 61.111 13.13 0.00 0.00 6.13
2285 2387 0.179127 AGTCCTCGATGTGCACGATG 60.179 55.000 13.13 3.93 39.02 3.84
2288 2390 4.079090 GAGTCCTCGATGTGCACG 57.921 61.111 13.13 0.00 0.00 5.34
2495 2597 1.440893 CACCTCCTCGATGCTCCAG 59.559 63.158 0.00 0.00 0.00 3.86
2558 2660 4.530857 CCGGACCTGATGTCGGCC 62.531 72.222 0.00 0.00 45.46 6.13
2735 2840 3.117813 ACTCCGAGTCTGCTCCTTATACT 60.118 47.826 0.00 0.00 38.49 2.12
2738 2843 2.028130 CACTCCGAGTCTGCTCCTTAT 58.972 52.381 0.00 0.00 38.49 1.73
2740 2845 0.251386 TCACTCCGAGTCTGCTCCTT 60.251 55.000 0.00 0.00 38.49 3.36
2753 2858 1.936547 CTGCGGCTAATTCTTCACTCC 59.063 52.381 0.00 0.00 0.00 3.85
2826 2956 8.695284 CGATCTCTAGTAGTATGAACAAATTGC 58.305 37.037 0.00 0.00 0.00 3.56
2855 2988 1.012841 GCAGGCAGAGGAAAATCGAG 58.987 55.000 0.00 0.00 0.00 4.04
2873 3006 2.627515 TGATGATTCACTAGGCAGGC 57.372 50.000 0.00 0.00 0.00 4.85
2874 3007 4.040095 TCTCATGATGATTCACTAGGCAGG 59.960 45.833 0.00 0.00 33.85 4.85
2876 3009 4.406649 TGTCTCATGATGATTCACTAGGCA 59.593 41.667 0.00 0.00 33.85 4.75
2877 3010 4.749099 GTGTCTCATGATGATTCACTAGGC 59.251 45.833 16.93 0.00 33.85 3.93
2878 3011 6.159299 AGTGTCTCATGATGATTCACTAGG 57.841 41.667 21.94 0.63 37.93 3.02
2880 3013 6.939622 ACAAGTGTCTCATGATGATTCACTA 58.060 36.000 22.86 2.31 38.36 2.74
2881 3014 5.802465 ACAAGTGTCTCATGATGATTCACT 58.198 37.500 19.44 19.44 39.75 3.41
2882 3015 6.370994 AGAACAAGTGTCTCATGATGATTCAC 59.629 38.462 16.65 16.65 33.85 3.18
2883 3016 6.470278 AGAACAAGTGTCTCATGATGATTCA 58.530 36.000 0.00 0.00 36.00 2.57
2884 3017 6.981762 AGAACAAGTGTCTCATGATGATTC 57.018 37.500 0.00 0.00 0.00 2.52
2885 3018 8.099537 AGTTAGAACAAGTGTCTCATGATGATT 58.900 33.333 0.00 0.00 0.00 2.57
2886 3019 7.619050 AGTTAGAACAAGTGTCTCATGATGAT 58.381 34.615 0.00 0.00 0.00 2.45
2887 3020 6.997655 AGTTAGAACAAGTGTCTCATGATGA 58.002 36.000 0.00 0.00 0.00 2.92
2888 3021 6.034363 CGAGTTAGAACAAGTGTCTCATGATG 59.966 42.308 0.00 0.00 0.00 3.07
2889 3022 6.096036 CGAGTTAGAACAAGTGTCTCATGAT 58.904 40.000 0.00 0.00 0.00 2.45
2890 3023 5.009710 ACGAGTTAGAACAAGTGTCTCATGA 59.990 40.000 0.00 0.00 0.00 3.07
2891 3024 5.223382 ACGAGTTAGAACAAGTGTCTCATG 58.777 41.667 0.00 0.00 0.00 3.07
2892 3025 5.455056 ACGAGTTAGAACAAGTGTCTCAT 57.545 39.130 0.00 0.00 0.00 2.90
2893 3026 4.913335 ACGAGTTAGAACAAGTGTCTCA 57.087 40.909 0.00 0.00 0.00 3.27
2894 3027 4.085004 GCAACGAGTTAGAACAAGTGTCTC 60.085 45.833 0.00 0.00 0.00 3.36
2917 3050 2.094700 TGGACGGATGAAGAACTCGAAG 60.095 50.000 0.00 0.00 0.00 3.79
2933 3066 6.392625 TCCTATTTACAGAGAAGATGGACG 57.607 41.667 0.00 0.00 0.00 4.79
2934 3067 6.183360 TGCTCCTATTTACAGAGAAGATGGAC 60.183 42.308 0.00 0.00 0.00 4.02
2935 3068 5.899547 TGCTCCTATTTACAGAGAAGATGGA 59.100 40.000 0.00 0.00 0.00 3.41
2936 3069 6.166984 TGCTCCTATTTACAGAGAAGATGG 57.833 41.667 0.00 0.00 0.00 3.51
2937 3070 9.770097 TTTATGCTCCTATTTACAGAGAAGATG 57.230 33.333 0.00 0.00 0.00 2.90
2943 3076 9.330063 TCAACATTTATGCTCCTATTTACAGAG 57.670 33.333 0.00 0.00 0.00 3.35
2989 3122 0.106318 AAGATTCATCCAGGCCAGGC 60.106 55.000 9.89 1.26 0.00 4.85
3066 3213 3.306780 GGCCTACAAGAGTCAGCAGTAAA 60.307 47.826 0.00 0.00 0.00 2.01
3068 3215 1.825474 GGCCTACAAGAGTCAGCAGTA 59.175 52.381 0.00 0.00 0.00 2.74
3069 3216 0.610687 GGCCTACAAGAGTCAGCAGT 59.389 55.000 0.00 0.00 0.00 4.40
3070 3217 0.610174 TGGCCTACAAGAGTCAGCAG 59.390 55.000 3.32 0.00 0.00 4.24
3071 3218 1.208052 GATGGCCTACAAGAGTCAGCA 59.792 52.381 3.32 0.00 0.00 4.41
3072 3219 1.474143 GGATGGCCTACAAGAGTCAGC 60.474 57.143 3.32 0.00 0.00 4.26
3105 3253 5.120674 GGTAACACGAACCCACAATTAGTAC 59.879 44.000 0.00 0.00 0.00 2.73
3167 3337 8.492415 AATAAGCATCAGTACTAGGTATCCAA 57.508 34.615 0.00 0.00 0.00 3.53
3169 3339 9.209175 CAAAATAAGCATCAGTACTAGGTATCC 57.791 37.037 0.00 0.00 0.00 2.59
3229 3494 1.670811 CGTGTCAAGACAAGCAAAGGT 59.329 47.619 4.20 0.00 43.77 3.50
3256 3521 5.473846 ACTGATCTATCTGGGTACGTACATG 59.526 44.000 26.02 15.02 0.00 3.21
3346 3619 2.534298 CAAGATCTGTACTGCCACTCG 58.466 52.381 0.00 0.00 0.00 4.18
3399 3672 5.011982 TGCCCAGGAAGCTATACTACTAT 57.988 43.478 0.00 0.00 0.00 2.12
3400 3673 4.464652 TGCCCAGGAAGCTATACTACTA 57.535 45.455 0.00 0.00 0.00 1.82
3401 3674 3.330126 TGCCCAGGAAGCTATACTACT 57.670 47.619 0.00 0.00 0.00 2.57
3408 3681 1.402896 CGGAGATGCCCAGGAAGCTA 61.403 60.000 0.00 0.00 0.00 3.32
3426 3703 1.730451 GGACCAACCAAACACACCCG 61.730 60.000 0.00 0.00 38.79 5.28
3465 3745 2.435586 TCGTCCGACTCGTCCCTC 60.436 66.667 0.00 0.00 0.00 4.30
3466 3746 2.745492 GTCGTCCGACTCGTCCCT 60.745 66.667 12.31 0.00 41.57 4.20
3468 3748 2.175322 GTGTCGTCCGACTCGTCC 59.825 66.667 19.30 1.08 44.80 4.79
3472 3752 2.404995 ATCCCGTGTCGTCCGACTC 61.405 63.158 19.30 14.95 44.80 3.36
3473 3753 2.360852 ATCCCGTGTCGTCCGACT 60.361 61.111 19.30 0.00 44.80 4.18
3474 3754 2.202570 CATCCCGTGTCGTCCGAC 60.203 66.667 12.66 12.66 44.77 4.79
3475 3755 3.445687 CCATCCCGTGTCGTCCGA 61.446 66.667 0.00 0.00 0.00 4.55
3477 3757 3.385749 ATGCCATCCCGTGTCGTCC 62.386 63.158 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.