Multiple sequence alignment - TraesCS4D01G279000

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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 TraesCS4D01G279000 chr4D 100.000 3950 0 0 1 3950 450224102 450220153 0.000000e+00 7295.0
1 TraesCS4D01G279000 chr4A 93.841 3280 131 41 725 3950 16460133 16463395 0.000000e+00 4872.0
2 TraesCS4D01G279000 chr4A 89.030 711 35 12 1 682 16459452 16460148 0.000000e+00 841.0
3 TraesCS4D01G279000 chr4B 95.214 2570 101 9 725 3289 563227154 563224602 0.000000e+00 4045.0
4 TraesCS4D01G279000 chr4B 89.507 629 29 13 69 682 563227745 563227139 0.000000e+00 761.0
5 TraesCS4D01G279000 chr4B 87.905 463 25 5 3304 3743 563224501 563224047 2.100000e-142 516.0
6 TraesCS4D01G279000 chr4B 95.402 174 7 1 3778 3950 563223949 563223776 3.890000e-70 276.0
7 TraesCS4D01G279000 chr4B 95.122 41 2 0 1 41 563227834 563227794 9.160000e-07 65.8
8 TraesCS4D01G279000 chr1A 97.778 45 1 0 3735 3779 501030193 501030237 1.180000e-10 78.7
9 TraesCS4D01G279000 chr7B 94.000 50 2 1 3730 3779 210863483 210863435 1.520000e-09 75.0
10 TraesCS4D01G279000 chr3D 97.619 42 1 0 3736 3777 511899730 511899689 5.480000e-09 73.1
11 TraesCS4D01G279000 chr3D 92.157 51 3 1 3725 3774 253553933 253553983 1.970000e-08 71.3
12 TraesCS4D01G279000 chr6B 90.741 54 3 2 3735 3788 378287141 378287090 1.970000e-08 71.3
13 TraesCS4D01G279000 chr5B 95.556 45 1 1 3731 3775 427246223 427246180 1.970000e-08 71.3
14 TraesCS4D01G279000 chr1D 95.455 44 2 0 3736 3779 22976617 22976574 1.970000e-08 71.3
15 TraesCS4D01G279000 chr7D 92.000 50 3 1 3730 3779 234807860 234807812 7.080000e-08 69.4
16 TraesCS4D01G279000 chr3A 92.000 50 3 1 3725 3774 336610797 336610845 7.080000e-08 69.4


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 TraesCS4D01G279000 chr4D 450220153 450224102 3949 True 7295.00 7295 100.0000 1 3950 1 chr4D.!!$R1 3949
1 TraesCS4D01G279000 chr4A 16459452 16463395 3943 False 2856.50 4872 91.4355 1 3950 2 chr4A.!!$F1 3949
2 TraesCS4D01G279000 chr4B 563223776 563227834 4058 True 1132.76 4045 92.6300 1 3950 5 chr4B.!!$R1 3949

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
690 771 0.030101 GAGTCGGATTCTCGGAGCAG 59.970 60.0 0.0 0.0 0.0 4.24 F
727 808 0.034863 TGGAGTTTAATCACCCGGCC 60.035 55.0 0.0 0.0 0.0 6.13 F
1759 1845 0.038166 GGAGGTGTTCAGGGCAATGA 59.962 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2108 0.407528 TTGACCCAGCCCTGCAATAA 59.592 50.000 0.0 0.0 0.00 1.40 R
2300 2386 3.415457 TGTATGTCACAATGTCTGGCA 57.585 42.857 0.0 0.0 32.95 4.92 R
3307 3488 1.739067 AATCGCAAACCACCTAGAGC 58.261 50.000 0.0 0.0 0.00 4.09 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
39 40 3.133464 CGTGGGCGGCATTGACAT 61.133 61.111 12.47 0.00 0.00 3.06
40 41 2.699768 CGTGGGCGGCATTGACATT 61.700 57.895 12.47 0.00 0.00 2.71
41 42 1.153784 GTGGGCGGCATTGACATTG 60.154 57.895 12.47 0.00 0.00 2.82
42 43 2.349672 TGGGCGGCATTGACATTGG 61.350 57.895 12.47 0.00 0.00 3.16
43 44 2.202783 GGCGGCATTGACATTGGC 60.203 61.111 3.07 12.51 36.38 4.52
44 45 2.572812 GCGGCATTGACATTGGCA 59.427 55.556 19.89 0.00 39.46 4.92
45 46 1.806758 GCGGCATTGACATTGGCAC 60.807 57.895 19.89 9.68 39.46 5.01
46 47 1.885157 CGGCATTGACATTGGCACT 59.115 52.632 19.89 0.00 39.46 4.40
47 48 0.457166 CGGCATTGACATTGGCACTG 60.457 55.000 19.89 5.52 39.46 3.66
57 58 0.035152 ATTGGCACTGGCATTCGAGA 60.035 50.000 6.05 0.00 43.71 4.04
67 68 0.872021 GCATTCGAGACTTCGCCGAT 60.872 55.000 0.00 0.00 46.28 4.18
145 179 4.838152 CGTGGCATCGGTGAGGGG 62.838 72.222 0.00 0.00 0.00 4.79
340 386 0.813184 CCTGCATTTTCATCTGCGGT 59.187 50.000 0.00 0.00 42.07 5.68
489 535 3.343972 GCACGGTGTCATGCTTGT 58.656 55.556 10.24 0.00 38.84 3.16
490 536 1.207593 GCACGGTGTCATGCTTGTC 59.792 57.895 10.24 0.00 38.84 3.18
491 537 1.492873 CACGGTGTCATGCTTGTCG 59.507 57.895 0.00 3.41 0.00 4.35
493 539 0.249699 ACGGTGTCATGCTTGTCGAA 60.250 50.000 0.00 0.00 0.00 3.71
494 540 0.439985 CGGTGTCATGCTTGTCGAAG 59.560 55.000 0.00 0.00 0.00 3.79
686 767 3.823402 CGGAGTCGGATTCTCGGA 58.177 61.111 0.37 0.00 35.32 4.55
687 768 1.649815 CGGAGTCGGATTCTCGGAG 59.350 63.158 0.00 0.00 35.32 4.63
688 769 1.360911 GGAGTCGGATTCTCGGAGC 59.639 63.158 0.00 0.00 33.26 4.70
689 770 1.384989 GGAGTCGGATTCTCGGAGCA 61.385 60.000 0.00 0.00 33.26 4.26
690 771 0.030101 GAGTCGGATTCTCGGAGCAG 59.970 60.000 0.00 0.00 0.00 4.24
691 772 1.590259 GTCGGATTCTCGGAGCAGC 60.590 63.158 0.00 0.00 0.00 5.25
692 773 2.052104 TCGGATTCTCGGAGCAGCA 61.052 57.895 0.00 0.00 0.00 4.41
693 774 1.068753 CGGATTCTCGGAGCAGCAT 59.931 57.895 0.00 0.00 0.00 3.79
694 775 1.220169 CGGATTCTCGGAGCAGCATG 61.220 60.000 0.00 0.00 40.87 4.06
695 776 0.105593 GGATTCTCGGAGCAGCATGA 59.894 55.000 0.00 0.00 39.69 3.07
696 777 1.216122 GATTCTCGGAGCAGCATGAC 58.784 55.000 0.00 0.00 39.69 3.06
697 778 0.529337 ATTCTCGGAGCAGCATGACG 60.529 55.000 0.00 0.00 39.69 4.35
698 779 3.260483 CTCGGAGCAGCATGACGC 61.260 66.667 0.00 0.00 39.69 5.19
714 795 4.681978 GCGTCAGCCCGTGGAGTT 62.682 66.667 0.00 0.00 37.42 3.01
715 796 2.030562 CGTCAGCCCGTGGAGTTT 59.969 61.111 0.00 0.00 0.00 2.66
716 797 1.290955 CGTCAGCCCGTGGAGTTTA 59.709 57.895 0.00 0.00 0.00 2.01
717 798 0.320073 CGTCAGCCCGTGGAGTTTAA 60.320 55.000 0.00 0.00 0.00 1.52
718 799 1.674817 CGTCAGCCCGTGGAGTTTAAT 60.675 52.381 0.00 0.00 0.00 1.40
719 800 2.007608 GTCAGCCCGTGGAGTTTAATC 58.992 52.381 0.00 0.00 0.00 1.75
720 801 1.626321 TCAGCCCGTGGAGTTTAATCA 59.374 47.619 0.00 0.00 0.00 2.57
721 802 1.737793 CAGCCCGTGGAGTTTAATCAC 59.262 52.381 0.00 0.00 0.00 3.06
722 803 1.092348 GCCCGTGGAGTTTAATCACC 58.908 55.000 0.00 0.00 0.00 4.02
723 804 1.746470 CCCGTGGAGTTTAATCACCC 58.254 55.000 0.00 0.00 0.00 4.61
724 805 1.365699 CCGTGGAGTTTAATCACCCG 58.634 55.000 0.00 2.20 0.00 5.28
725 806 1.365699 CGTGGAGTTTAATCACCCGG 58.634 55.000 0.00 0.00 0.00 5.73
726 807 1.092348 GTGGAGTTTAATCACCCGGC 58.908 55.000 0.00 0.00 0.00 6.13
727 808 0.034863 TGGAGTTTAATCACCCGGCC 60.035 55.000 0.00 0.00 0.00 6.13
768 851 1.822613 TCGGATTCTCGGTCTCGGG 60.823 63.158 0.00 0.00 38.44 5.14
796 879 2.338984 GCGTCAGACCGTGGAGTT 59.661 61.111 0.00 0.00 0.00 3.01
814 897 2.090760 GTTTTTAATTACCCGGCCGGA 58.909 47.619 45.44 27.01 37.50 5.14
852 935 2.222729 CCGAAGGCGTATTTTTCACGAG 60.223 50.000 0.00 0.00 46.14 4.18
865 948 4.909696 TTTCACGAGCAAAGAAAATGGA 57.090 36.364 0.00 0.00 0.00 3.41
877 960 2.952310 AGAAAATGGATAGAAAGCGGGC 59.048 45.455 0.00 0.00 0.00 6.13
919 1002 3.935818 TGACAGAAGGTGGGTTTGTTA 57.064 42.857 0.00 0.00 0.00 2.41
924 1008 5.020795 ACAGAAGGTGGGTTTGTTAGTTTT 58.979 37.500 0.00 0.00 0.00 2.43
972 1058 0.179020 CTCCAAGCCTCCAACACACA 60.179 55.000 0.00 0.00 0.00 3.72
1010 1096 1.545614 CCGTCGGTAATGGCGATTCG 61.546 60.000 2.08 0.62 0.00 3.34
1386 1472 2.164663 CGCATCAAACGCGCTCCTA 61.165 57.895 5.73 0.00 46.98 2.94
1695 1781 5.056480 CCAGGAATCTTGACGTATAATGCA 58.944 41.667 0.00 0.00 0.00 3.96
1724 1810 2.719705 AGGGGTTGTGTAGGAATGGAAA 59.280 45.455 0.00 0.00 0.00 3.13
1737 1823 4.023291 GGAATGGAAAGTGGGATAAAGCA 58.977 43.478 0.00 0.00 0.00 3.91
1759 1845 0.038166 GGAGGTGTTCAGGGCAATGA 59.962 55.000 0.00 0.00 0.00 2.57
1776 1862 4.619227 AACGAGTGTGGGGTGGCG 62.619 66.667 0.00 0.00 0.00 5.69
1945 2031 0.398098 GAGGGGGAAGATGGACCGTA 60.398 60.000 0.00 0.00 0.00 4.02
2680 2766 8.394971 TGTTAAAGAAGAGAAGATGCATGAAA 57.605 30.769 2.46 0.00 0.00 2.69
2724 2810 3.895041 TGGAGAATGAAAAGGTTCAACCC 59.105 43.478 1.75 0.00 46.66 4.11
2832 2918 3.935828 GTGCTAGAGGAATTGAACCAGAC 59.064 47.826 0.00 0.00 0.00 3.51
2910 2996 6.944290 AGGAGTCATTTCAACTTCATGATGAA 59.056 34.615 15.03 7.73 35.99 2.57
2970 3056 8.757307 TCTGAGGGTATTATTTTCCTCCATAT 57.243 34.615 0.00 0.00 43.72 1.78
3019 3105 4.789012 TCAACAATGAGAAATGAAGGCC 57.211 40.909 0.00 0.00 0.00 5.19
3021 3107 5.569355 TCAACAATGAGAAATGAAGGCCTA 58.431 37.500 5.16 0.00 0.00 3.93
3041 3127 5.289434 GCCTATTGCAGTTTGTTTAGATTGC 59.711 40.000 0.00 0.00 40.77 3.56
3074 3160 8.856153 TTTGCTCCAACAAGTATTTATAGACA 57.144 30.769 0.00 0.00 0.00 3.41
3099 3185 4.796038 AGGTGAGCATGAGAAATTTTGG 57.204 40.909 0.00 0.00 0.00 3.28
3125 3211 5.862924 TCAGCATTAAAATATCGGCTAGC 57.137 39.130 6.04 6.04 0.00 3.42
3138 3224 3.031964 GCTAGCTTGTGCGCACTGG 62.032 63.158 37.59 29.10 45.42 4.00
3247 3339 4.978186 TCTGTACAAGTATCCGTTCTTCG 58.022 43.478 0.00 0.00 39.52 3.79
3288 3380 3.979495 GCTGCTTGACTGACATTCTTTTG 59.021 43.478 0.00 0.00 0.00 2.44
3289 3381 4.543692 CTGCTTGACTGACATTCTTTTGG 58.456 43.478 0.00 0.00 0.00 3.28
3290 3382 3.953612 TGCTTGACTGACATTCTTTTGGT 59.046 39.130 0.00 0.00 0.00 3.67
3295 3387 7.041372 GCTTGACTGACATTCTTTTGGTACTTA 60.041 37.037 0.00 0.00 0.00 2.24
3307 3488 8.365399 TCTTTTGGTACTTATGCATTCTATCG 57.635 34.615 3.54 0.00 0.00 2.92
3322 3503 2.100916 TCTATCGCTCTAGGTGGTTTGC 59.899 50.000 0.00 0.00 0.00 3.68
3342 3523 2.351726 GCGATTTGGTACCATCACACTC 59.648 50.000 17.17 3.51 0.00 3.51
3460 3657 3.316029 CAGATGTGCTTTCTTCACCAACA 59.684 43.478 0.00 0.00 33.71 3.33
3509 3713 2.831526 AGGTGTGCTTTTGTTTTCTGGT 59.168 40.909 0.00 0.00 0.00 4.00
3518 3722 3.762407 TTGTTTTCTGGTCATCGGAGA 57.238 42.857 0.00 0.00 45.75 3.71
3530 3734 3.993081 GTCATCGGAGAAATCTAGCATGG 59.007 47.826 0.00 0.00 43.58 3.66
3640 3844 7.328249 ACAACTACATTTTGCAAATCCGTAATG 59.672 33.333 13.65 14.29 0.00 1.90
3737 3982 4.833390 AGCAGTTCAACCTACCAATCTAC 58.167 43.478 0.00 0.00 0.00 2.59
3738 3983 4.532521 AGCAGTTCAACCTACCAATCTACT 59.467 41.667 0.00 0.00 0.00 2.57
3739 3984 4.870991 GCAGTTCAACCTACCAATCTACTC 59.129 45.833 0.00 0.00 0.00 2.59
3740 3985 5.420409 CAGTTCAACCTACCAATCTACTCC 58.580 45.833 0.00 0.00 0.00 3.85
3741 3986 4.470304 AGTTCAACCTACCAATCTACTCCC 59.530 45.833 0.00 0.00 0.00 4.30
3743 3988 4.287552 TCAACCTACCAATCTACTCCCTC 58.712 47.826 0.00 0.00 0.00 4.30
3744 3989 3.331718 ACCTACCAATCTACTCCCTCC 57.668 52.381 0.00 0.00 0.00 4.30
3746 3991 2.424523 CCTACCAATCTACTCCCTCCGT 60.425 54.545 0.00 0.00 0.00 4.69
3747 3992 3.181436 CCTACCAATCTACTCCCTCCGTA 60.181 52.174 0.00 0.00 0.00 4.02
3748 3993 3.614568 ACCAATCTACTCCCTCCGTAT 57.385 47.619 0.00 0.00 0.00 3.06
3751 3996 3.895656 CCAATCTACTCCCTCCGTATCAA 59.104 47.826 0.00 0.00 0.00 2.57
3754 3999 6.464465 CCAATCTACTCCCTCCGTATCAAAAT 60.464 42.308 0.00 0.00 0.00 1.82
3755 4000 7.256190 CCAATCTACTCCCTCCGTATCAAAATA 60.256 40.741 0.00 0.00 0.00 1.40
3756 4001 8.314751 CAATCTACTCCCTCCGTATCAAAATAT 58.685 37.037 0.00 0.00 0.00 1.28
3757 4002 9.543231 AATCTACTCCCTCCGTATCAAAATATA 57.457 33.333 0.00 0.00 0.00 0.86
3758 4003 8.945195 TCTACTCCCTCCGTATCAAAATATAA 57.055 34.615 0.00 0.00 0.00 0.98
3759 4004 9.021807 TCTACTCCCTCCGTATCAAAATATAAG 57.978 37.037 0.00 0.00 0.00 1.73
3761 4006 7.668492 ACTCCCTCCGTATCAAAATATAAGAC 58.332 38.462 0.00 0.00 0.00 3.01
3762 4007 6.684686 TCCCTCCGTATCAAAATATAAGACG 58.315 40.000 0.00 0.00 0.00 4.18
3763 4008 6.266103 TCCCTCCGTATCAAAATATAAGACGT 59.734 38.462 0.00 0.00 0.00 4.34
3764 4009 6.365247 CCCTCCGTATCAAAATATAAGACGTG 59.635 42.308 0.00 0.00 0.00 4.49
3765 4010 6.921857 CCTCCGTATCAAAATATAAGACGTGT 59.078 38.462 0.00 0.00 0.00 4.49
3766 4011 7.437267 CCTCCGTATCAAAATATAAGACGTGTT 59.563 37.037 2.58 2.58 0.00 3.32
3767 4012 8.706492 TCCGTATCAAAATATAAGACGTGTTT 57.294 30.769 2.22 0.00 0.00 2.83
3768 4013 9.153721 TCCGTATCAAAATATAAGACGTGTTTT 57.846 29.630 2.22 0.00 0.00 2.43
3770 4015 9.961266 CGTATCAAAATATAAGACGTGTTTTGA 57.039 29.630 2.22 7.57 46.44 2.69
3773 4018 8.996988 TCAAAATATAAGACGTGTTTTGACAC 57.003 30.769 2.22 0.00 41.29 3.67
3943 4211 8.487313 TTTAGCATGAACTATTAACATCACGT 57.513 30.769 0.00 0.00 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.608856 TCGAATGCCAGTGCCAATGT 60.609 50.000 0.00 0.00 36.33 2.71
37 38 0.099968 CTCGAATGCCAGTGCCAATG 59.900 55.000 0.00 0.00 36.33 2.82
38 39 0.035152 TCTCGAATGCCAGTGCCAAT 60.035 50.000 0.00 0.00 36.33 3.16
39 40 0.955428 GTCTCGAATGCCAGTGCCAA 60.955 55.000 0.00 0.00 36.33 4.52
40 41 1.375908 GTCTCGAATGCCAGTGCCA 60.376 57.895 0.00 0.00 36.33 4.92
41 42 0.674895 AAGTCTCGAATGCCAGTGCC 60.675 55.000 0.00 0.00 36.33 5.01
42 43 0.723981 GAAGTCTCGAATGCCAGTGC 59.276 55.000 0.00 0.00 38.26 4.40
57 58 4.143333 CCGTCCCATCGGCGAAGT 62.143 66.667 15.93 0.00 43.96 3.01
76 77 2.597805 ACTCGTCCAGTCGGCACT 60.598 61.111 0.00 0.00 0.00 4.40
78 79 2.416244 GAACACTCGTCCAGTCGGCA 62.416 60.000 0.00 0.00 30.26 5.69
115 149 3.204827 CCACGTATGCAGGCAGCC 61.205 66.667 1.84 1.84 44.83 4.85
154 188 4.838152 CTCGGCGGTGTCCCCATG 62.838 72.222 7.21 0.00 0.00 3.66
328 374 1.375396 CCCGACACCGCAGATGAAA 60.375 57.895 0.00 0.00 0.00 2.69
340 386 3.695606 GTGAGAGCAGCCCCGACA 61.696 66.667 0.00 0.00 0.00 4.35
487 533 2.279851 CACACCCACGCTTCGACA 60.280 61.111 0.00 0.00 0.00 4.35
488 534 3.712881 GCACACCCACGCTTCGAC 61.713 66.667 0.00 0.00 0.00 4.20
670 751 1.360911 GCTCCGAGAATCCGACTCC 59.639 63.158 0.00 0.00 0.00 3.85
671 752 0.030101 CTGCTCCGAGAATCCGACTC 59.970 60.000 0.00 0.00 0.00 3.36
672 753 2.010582 GCTGCTCCGAGAATCCGACT 62.011 60.000 0.00 0.00 0.00 4.18
673 754 1.590259 GCTGCTCCGAGAATCCGAC 60.590 63.158 0.00 0.00 0.00 4.79
674 755 1.395045 ATGCTGCTCCGAGAATCCGA 61.395 55.000 0.00 0.00 0.00 4.55
675 756 1.068753 ATGCTGCTCCGAGAATCCG 59.931 57.895 0.00 0.00 0.00 4.18
676 757 0.105593 TCATGCTGCTCCGAGAATCC 59.894 55.000 0.00 0.00 0.00 3.01
677 758 1.216122 GTCATGCTGCTCCGAGAATC 58.784 55.000 0.00 0.00 0.00 2.52
678 759 0.529337 CGTCATGCTGCTCCGAGAAT 60.529 55.000 0.00 0.00 0.00 2.40
679 760 1.153765 CGTCATGCTGCTCCGAGAA 60.154 57.895 0.00 0.00 0.00 2.87
680 761 2.491621 CGTCATGCTGCTCCGAGA 59.508 61.111 0.00 0.00 0.00 4.04
681 762 3.260483 GCGTCATGCTGCTCCGAG 61.260 66.667 0.00 0.00 41.73 4.63
684 765 3.558411 GACGCGTCATGCTGCTCC 61.558 66.667 33.09 2.59 43.27 4.70
685 766 2.796425 CTGACGCGTCATGCTGCTC 61.796 63.158 39.09 12.14 43.27 4.26
686 767 2.812609 CTGACGCGTCATGCTGCT 60.813 61.111 39.09 0.00 43.27 4.24
687 768 4.511443 GCTGACGCGTCATGCTGC 62.511 66.667 39.09 32.93 43.27 5.25
688 769 3.857854 GGCTGACGCGTCATGCTG 61.858 66.667 37.75 29.99 43.27 4.41
697 778 2.775032 TAAACTCCACGGGCTGACGC 62.775 60.000 0.00 0.00 37.37 5.19
698 779 0.320073 TTAAACTCCACGGGCTGACG 60.320 55.000 0.00 0.00 40.31 4.35
699 780 2.007608 GATTAAACTCCACGGGCTGAC 58.992 52.381 0.00 0.00 0.00 3.51
700 781 1.626321 TGATTAAACTCCACGGGCTGA 59.374 47.619 0.00 0.00 0.00 4.26
701 782 1.737793 GTGATTAAACTCCACGGGCTG 59.262 52.381 0.00 0.00 0.00 4.85
702 783 1.339727 GGTGATTAAACTCCACGGGCT 60.340 52.381 0.00 0.00 0.00 5.19
703 784 1.092348 GGTGATTAAACTCCACGGGC 58.908 55.000 0.00 0.00 0.00 6.13
704 785 1.746470 GGGTGATTAAACTCCACGGG 58.254 55.000 6.22 0.00 0.00 5.28
705 786 1.365699 CGGGTGATTAAACTCCACGG 58.634 55.000 6.22 0.00 0.00 4.94
706 787 1.365699 CCGGGTGATTAAACTCCACG 58.634 55.000 0.00 6.86 0.00 4.94
707 788 1.092348 GCCGGGTGATTAAACTCCAC 58.908 55.000 2.18 0.00 0.00 4.02
708 789 0.034863 GGCCGGGTGATTAAACTCCA 60.035 55.000 2.18 0.00 0.00 3.86
709 790 1.093496 CGGCCGGGTGATTAAACTCC 61.093 60.000 20.10 0.00 0.00 3.85
710 791 1.093496 CCGGCCGGGTGATTAAACTC 61.093 60.000 37.42 0.00 0.00 3.01
711 792 1.078001 CCGGCCGGGTGATTAAACT 60.078 57.895 37.42 0.00 0.00 2.66
712 793 1.078285 TCCGGCCGGGTGATTAAAC 60.078 57.895 42.36 0.00 37.00 2.01
713 794 1.222387 CTCCGGCCGGGTGATTAAA 59.778 57.895 42.36 20.85 37.00 1.52
714 795 1.963464 GACTCCGGCCGGGTGATTAA 61.963 60.000 42.36 21.65 37.00 1.40
715 796 2.364579 ACTCCGGCCGGGTGATTA 60.365 61.111 42.36 22.44 37.00 1.75
716 797 3.782443 GACTCCGGCCGGGTGATT 61.782 66.667 42.36 22.52 37.00 2.57
727 808 0.458543 CACACTGGAATCCGACTCCG 60.459 60.000 0.00 0.00 35.55 4.63
786 869 3.752747 CGGGTAATTAAAAACTCCACGGT 59.247 43.478 0.00 0.00 0.00 4.83
796 879 2.503895 TTCCGGCCGGGTAATTAAAA 57.496 45.000 42.36 24.46 37.00 1.52
819 902 1.287041 GCCTTCGGTTTTAGACGCGT 61.287 55.000 13.85 13.85 0.00 6.01
845 928 5.937540 TCTATCCATTTTCTTTGCTCGTGAA 59.062 36.000 0.00 0.00 0.00 3.18
852 935 4.800471 CCGCTTTCTATCCATTTTCTTTGC 59.200 41.667 0.00 0.00 0.00 3.68
865 948 1.451387 CGTTGGGCCCGCTTTCTAT 60.451 57.895 19.37 0.00 0.00 1.98
877 960 2.997986 AGCATTACGTAAACTCGTTGGG 59.002 45.455 12.81 0.00 43.80 4.12
919 1002 4.374399 CTTCAAGCTGGAATTGCAAAACT 58.626 39.130 3.39 0.00 0.00 2.66
924 1008 0.604578 GCCTTCAAGCTGGAATTGCA 59.395 50.000 16.68 0.00 0.00 4.08
950 1034 1.239347 GTGTTGGAGGCTTGGAGTTC 58.761 55.000 0.00 0.00 0.00 3.01
972 1058 1.373748 CGAACGGTGGTGGATTCGT 60.374 57.895 0.00 0.00 39.21 3.85
1044 1130 2.126424 GTCGAGCGTCTGGTGGAC 60.126 66.667 0.00 0.00 42.61 4.02
1045 1131 3.371063 GGTCGAGCGTCTGGTGGA 61.371 66.667 0.00 0.00 0.00 4.02
1371 1457 1.521681 GGCTAGGAGCGCGTTTGAT 60.522 57.895 8.43 0.00 43.62 2.57
1695 1781 2.158667 CCTACACAACCCCTTCAACACT 60.159 50.000 0.00 0.00 0.00 3.55
1724 1810 1.566231 CCTCCCTTGCTTTATCCCACT 59.434 52.381 0.00 0.00 0.00 4.00
1737 1823 1.360393 TTGCCCTGAACACCTCCCTT 61.360 55.000 0.00 0.00 0.00 3.95
1759 1845 4.619227 CGCCACCCCACACTCGTT 62.619 66.667 0.00 0.00 0.00 3.85
1953 2039 4.532834 ACTCTCTCATCTCCCTCAAGTAC 58.467 47.826 0.00 0.00 0.00 2.73
2022 2108 0.407528 TTGACCCAGCCCTGCAATAA 59.592 50.000 0.00 0.00 0.00 1.40
2300 2386 3.415457 TGTATGTCACAATGTCTGGCA 57.585 42.857 0.00 0.00 32.95 4.92
2680 2766 9.643693 CTCCATCATGTTAAGCAAATTAAAAGT 57.356 29.630 0.00 0.00 35.16 2.66
2724 2810 7.853377 AATCATATTATACGTCACAGTGTCG 57.147 36.000 17.19 17.19 35.19 4.35
2910 2996 2.967887 AGCAAACCCTTTCTGAAGCATT 59.032 40.909 0.00 0.00 0.00 3.56
2970 3056 9.639563 TTAACCATAGCATCAATAAGATTCCAA 57.360 29.630 0.00 0.00 33.72 3.53
3019 3105 6.389091 TGGCAATCTAAACAAACTGCAATAG 58.611 36.000 0.00 0.00 0.00 1.73
3021 3107 5.212532 TGGCAATCTAAACAAACTGCAAT 57.787 34.783 0.00 0.00 0.00 3.56
3041 3127 3.070015 ACTTGTTGGAGCAAAAATCCTGG 59.930 43.478 0.00 0.00 37.74 4.45
3074 3160 6.395629 CAAAATTTCTCATGCTCACCTTCAT 58.604 36.000 0.00 0.00 0.00 2.57
3099 3185 6.305693 AGCCGATATTTTAATGCTGAACTC 57.694 37.500 0.00 0.00 0.00 3.01
3125 3211 3.259425 GAAGGCCAGTGCGCACAAG 62.259 63.158 39.21 29.84 38.85 3.16
3138 3224 3.382546 TCCACTACGGTAATGTAGAAGGC 59.617 47.826 7.84 0.00 43.65 4.35
3201 3293 7.549134 AGAACAATATTGCATCTTACGAAGTCA 59.451 33.333 15.48 0.00 43.93 3.41
3239 3331 6.726230 TCTACTATCAGAATTCCGAAGAACG 58.274 40.000 0.65 0.00 42.18 3.95
3247 3339 6.229733 AGCAGCATTCTACTATCAGAATTCC 58.770 40.000 0.65 0.00 41.46 3.01
3288 3380 5.715070 AGAGCGATAGAATGCATAAGTACC 58.285 41.667 0.00 0.00 39.76 3.34
3289 3381 6.970043 CCTAGAGCGATAGAATGCATAAGTAC 59.030 42.308 0.00 0.00 39.76 2.73
3290 3382 6.659668 ACCTAGAGCGATAGAATGCATAAGTA 59.340 38.462 0.00 0.00 39.76 2.24
3295 3387 3.056250 CCACCTAGAGCGATAGAATGCAT 60.056 47.826 0.00 0.00 39.76 3.96
3307 3488 1.739067 AATCGCAAACCACCTAGAGC 58.261 50.000 0.00 0.00 0.00 4.09
3322 3503 3.370978 GTGAGTGTGATGGTACCAAATCG 59.629 47.826 20.76 0.00 0.00 3.34
3342 3523 4.214545 TGCCTACAGAAAATTACAACGGTG 59.785 41.667 0.00 0.00 0.00 4.94
3438 3635 3.316029 TGTTGGTGAAGAAAGCACATCTG 59.684 43.478 0.00 0.00 37.99 2.90
3509 3713 3.643320 ACCATGCTAGATTTCTCCGATGA 59.357 43.478 0.00 0.00 0.00 2.92
3518 3722 9.118300 CTGAGAAATTTAGACCATGCTAGATTT 57.882 33.333 7.93 7.93 37.67 2.17
3596 3800 7.926018 TGTAGTTGTATATCAGGCATTAGTGTG 59.074 37.037 0.00 0.00 0.00 3.82
3597 3801 8.018537 TGTAGTTGTATATCAGGCATTAGTGT 57.981 34.615 0.00 0.00 0.00 3.55
3633 3837 4.274705 TGGCAATATGTTACTGCATTACGG 59.725 41.667 0.00 0.00 37.83 4.02
3640 3844 6.391227 AATAACCTGGCAATATGTTACTGC 57.609 37.500 0.00 0.00 35.28 4.40
3737 3982 6.807230 CGTCTTATATTTTGATACGGAGGGAG 59.193 42.308 0.00 0.00 0.00 4.30
3738 3983 6.266103 ACGTCTTATATTTTGATACGGAGGGA 59.734 38.462 0.00 0.00 33.44 4.20
3739 3984 6.365247 CACGTCTTATATTTTGATACGGAGGG 59.635 42.308 0.00 0.00 33.44 4.30
3740 3985 6.921857 ACACGTCTTATATTTTGATACGGAGG 59.078 38.462 0.00 0.00 33.44 4.30
3741 3986 7.925703 ACACGTCTTATATTTTGATACGGAG 57.074 36.000 0.00 0.00 33.44 4.63
3743 3988 9.205916 CAAAACACGTCTTATATTTTGATACGG 57.794 33.333 2.36 0.00 40.89 4.02
3744 3989 9.961266 TCAAAACACGTCTTATATTTTGATACG 57.039 29.630 6.39 0.00 41.77 3.06
3747 3992 9.607285 GTGTCAAAACACGTCTTATATTTTGAT 57.393 29.630 12.13 0.00 45.72 2.57
3748 3993 8.996988 GTGTCAAAACACGTCTTATATTTTGA 57.003 30.769 6.39 6.39 45.84 2.69
3765 4010 6.475076 GCAATGTTGTTGTGATAGTGTCAAAA 59.525 34.615 0.00 0.00 38.90 2.44
3766 4011 5.976534 GCAATGTTGTTGTGATAGTGTCAAA 59.023 36.000 0.00 0.00 38.90 2.69
3767 4012 5.067023 TGCAATGTTGTTGTGATAGTGTCAA 59.933 36.000 0.00 0.00 38.90 3.18
3768 4013 4.578105 TGCAATGTTGTTGTGATAGTGTCA 59.422 37.500 0.00 0.00 0.00 3.58
3770 4015 5.512753 TTGCAATGTTGTTGTGATAGTGT 57.487 34.783 0.00 0.00 0.00 3.55
3771 4016 6.825284 TTTTGCAATGTTGTTGTGATAGTG 57.175 33.333 0.00 0.00 0.00 2.74
3772 4017 8.436046 AAATTTTGCAATGTTGTTGTGATAGT 57.564 26.923 0.00 0.00 0.00 2.12
3776 4043 8.032952 TGTTAAATTTTGCAATGTTGTTGTGA 57.967 26.923 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.