Multiple sequence alignment - TraesCS3B01G164000

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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 TraesCS3B01G164000 chr3B 100.000 3727 0 0 1 3727 161637618 161633892 0.000000e+00 6883
1 TraesCS3B01G164000 chr3D 92.420 2810 109 44 766 3485 110397202 110394407 0.000000e+00 3914
2 TraesCS3B01G164000 chr3D 94.500 600 15 4 4 603 110397854 110397273 0.000000e+00 909
3 TraesCS3B01G164000 chr3D 97.927 193 4 0 3478 3670 110394342 110394150 5.960000e-88 335
4 TraesCS3B01G164000 chr3A 88.050 2728 206 63 888 3558 119693995 119696659 0.000000e+00 3121
5 TraesCS3B01G164000 chr3A 93.729 590 29 4 1 590 119693020 119693601 0.000000e+00 878


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 TraesCS3B01G164000 chr3B 161633892 161637618 3726 True 6883.000000 6883 100.0000 1 3727 1 chr3B.!!$R1 3726
1 TraesCS3B01G164000 chr3D 110394150 110397854 3704 True 1719.333333 3914 94.9490 4 3670 3 chr3D.!!$R1 3666
2 TraesCS3B01G164000 chr3A 119693020 119696659 3639 False 1999.500000 3121 90.8895 1 3558 2 chr3A.!!$F1 3557

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
633 634 0.383949 TTTGCGGGTGAAGCTGAAAC 59.616 50.0 0.0 0.0 35.28 2.78 F
985 1139 0.875059 CACCTCCAAAGCTCGAAACC 59.125 55.0 0.0 0.0 0.00 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1726 0.036388 TGTCCCAAGCAAGGTCGATC 60.036 55.0 0.00 0.00 0.0 3.69 R
2822 3015 0.453390 GATGTAAGCAGCTTGGTGGC 59.547 55.0 18.54 3.61 0.0 5.01 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
37 38 3.713764 AGCCCTATGTGCAGTCTTTAGAT 59.286 43.478 0.00 0.00 0.00 1.98
38 39 4.061596 GCCCTATGTGCAGTCTTTAGATC 58.938 47.826 0.00 0.00 0.00 2.75
64 65 8.840321 CGATAGAAATCTTATGGTCCAAAATGT 58.160 33.333 0.00 0.00 39.76 2.71
82 83 4.819105 ATGTTGAACCTAACATCTCCGA 57.181 40.909 0.00 0.00 45.49 4.55
91 92 6.555463 ACCTAACATCTCCGATTTCCTTAA 57.445 37.500 0.00 0.00 0.00 1.85
188 189 1.196581 CGACACGATTCAATGTTGCCA 59.803 47.619 0.00 0.00 0.00 4.92
222 223 2.483188 GGTCATGTAGGGAAGCCTAACG 60.483 54.545 0.00 0.00 0.00 3.18
250 251 1.029408 TGCTGTCCGTGTTGCTGTTT 61.029 50.000 0.00 0.00 0.00 2.83
266 267 3.317993 GCTGTTTGGTCTTTTTAGCCTCA 59.682 43.478 0.00 0.00 0.00 3.86
267 268 4.202111 GCTGTTTGGTCTTTTTAGCCTCAA 60.202 41.667 0.00 0.00 0.00 3.02
268 269 5.681179 GCTGTTTGGTCTTTTTAGCCTCAAA 60.681 40.000 0.00 0.00 0.00 2.69
454 455 3.073228 CAGGAACCTGGAGACCTCA 57.927 57.895 12.54 0.00 40.17 3.86
539 540 8.649973 ACTAGCTAGTCTGTAATTTATGTTGC 57.350 34.615 20.95 0.00 0.00 4.17
598 599 3.071602 TCTGGTTGCTCTAAGCTGAAACT 59.928 43.478 0.11 0.00 42.97 2.66
599 600 3.817647 CTGGTTGCTCTAAGCTGAAACTT 59.182 43.478 0.11 0.00 42.97 2.66
600 601 4.207165 TGGTTGCTCTAAGCTGAAACTTT 58.793 39.130 0.11 0.00 42.97 2.66
601 602 4.644685 TGGTTGCTCTAAGCTGAAACTTTT 59.355 37.500 0.11 0.00 42.97 2.27
602 603 5.127031 TGGTTGCTCTAAGCTGAAACTTTTT 59.873 36.000 0.11 0.00 42.97 1.94
630 631 2.800516 TTTTTGCGGGTGAAGCTGA 58.199 47.368 0.00 0.00 35.28 4.26
631 632 1.107114 TTTTTGCGGGTGAAGCTGAA 58.893 45.000 0.00 0.00 35.28 3.02
632 633 1.107114 TTTTGCGGGTGAAGCTGAAA 58.893 45.000 0.00 0.00 35.28 2.69
633 634 0.383949 TTTGCGGGTGAAGCTGAAAC 59.616 50.000 0.00 0.00 35.28 2.78
692 724 3.483558 CAGTCGTTTTGCTTTTCTGAAGC 59.516 43.478 3.91 3.91 43.29 3.86
696 728 3.975035 CGTTTTGCTTTTCTGAAGCCTAC 59.025 43.478 8.15 3.52 42.36 3.18
699 731 2.143122 TGCTTTTCTGAAGCCTACACG 58.857 47.619 8.15 0.00 42.36 4.49
718 759 3.384668 ACGTCAGTGAACAAGTGATCTG 58.615 45.455 0.00 0.00 40.39 2.90
724 765 6.144724 GTCAGTGAACAAGTGATCTGAGTAAC 59.855 42.308 0.00 0.00 40.39 2.50
733 774 6.426646 AGTGATCTGAGTAACTGGTTCTTT 57.573 37.500 0.00 0.00 0.00 2.52
734 775 7.540474 AGTGATCTGAGTAACTGGTTCTTTA 57.460 36.000 0.00 0.00 0.00 1.85
735 776 7.379750 AGTGATCTGAGTAACTGGTTCTTTAC 58.620 38.462 0.00 0.00 0.00 2.01
737 778 7.329717 GTGATCTGAGTAACTGGTTCTTTACTG 59.670 40.741 0.00 0.00 38.40 2.74
739 780 7.120923 TCTGAGTAACTGGTTCTTTACTGTT 57.879 36.000 0.00 0.00 38.40 3.16
740 781 6.984474 TCTGAGTAACTGGTTCTTTACTGTTG 59.016 38.462 0.00 0.00 38.40 3.33
741 782 6.053005 TGAGTAACTGGTTCTTTACTGTTGG 58.947 40.000 0.00 0.00 38.40 3.77
759 824 1.000506 TGGCTCTCAACAGTAACCGTC 59.999 52.381 0.00 0.00 0.00 4.79
760 825 1.272769 GGCTCTCAACAGTAACCGTCT 59.727 52.381 0.00 0.00 0.00 4.18
807 887 3.181424 TGTCTCCCCACAATTCCAATTGA 60.181 43.478 17.12 0.00 46.72 2.57
810 890 4.711355 TCTCCCCACAATTCCAATTGATTC 59.289 41.667 17.12 0.00 46.72 2.52
831 946 5.794687 TCACTTTATGCGGTGAATAAGTG 57.205 39.130 0.00 0.00 39.16 3.16
846 961 0.960364 AAGTGGTGCTATGCAACCCG 60.960 55.000 5.09 0.00 46.96 5.28
861 979 3.933955 GCAACCCGGTTTTAGTTTGTTTT 59.066 39.130 0.00 0.00 0.00 2.43
874 992 7.707774 TTAGTTTGTTTTCCTGCAAAATAGC 57.292 32.000 0.00 0.00 36.79 2.97
877 995 2.968574 TGTTTTCCTGCAAAATAGCCCA 59.031 40.909 0.00 0.00 36.35 5.36
881 999 2.446435 TCCTGCAAAATAGCCCAACTC 58.554 47.619 0.00 0.00 0.00 3.01
884 1002 1.539388 TGCAAAATAGCCCAACTCACG 59.461 47.619 0.00 0.00 0.00 4.35
886 1004 2.432444 CAAAATAGCCCAACTCACGGA 58.568 47.619 0.00 0.00 0.00 4.69
893 1011 1.293498 CCAACTCACGGAGGACCTG 59.707 63.158 0.00 0.00 33.35 4.00
903 1021 1.761174 GAGGACCTGGCCTTTGACA 59.239 57.895 3.32 0.00 38.73 3.58
915 1033 2.867647 GCCTTTGACATGGCCTTTGTTC 60.868 50.000 3.32 3.52 43.11 3.18
916 1034 2.364970 CCTTTGACATGGCCTTTGTTCA 59.635 45.455 3.32 5.97 0.00 3.18
920 1038 2.170166 GACATGGCCTTTGTTCATCCA 58.830 47.619 3.32 0.00 0.00 3.41
921 1039 2.762327 GACATGGCCTTTGTTCATCCAT 59.238 45.455 3.32 0.00 37.99 3.41
923 1041 2.905415 TGGCCTTTGTTCATCCATCT 57.095 45.000 3.32 0.00 0.00 2.90
924 1042 2.726821 TGGCCTTTGTTCATCCATCTC 58.273 47.619 3.32 0.00 0.00 2.75
925 1043 2.041485 TGGCCTTTGTTCATCCATCTCA 59.959 45.455 3.32 0.00 0.00 3.27
930 1048 6.294397 GGCCTTTGTTCATCCATCTCATTATC 60.294 42.308 0.00 0.00 0.00 1.75
956 1108 2.030958 GCCGTAAACCTCCCACACG 61.031 63.158 0.00 0.00 0.00 4.49
957 1109 2.030958 CCGTAAACCTCCCACACGC 61.031 63.158 0.00 0.00 0.00 5.34
958 1110 2.030958 CGTAAACCTCCCACACGCC 61.031 63.158 0.00 0.00 0.00 5.68
959 1111 1.071814 GTAAACCTCCCACACGCCA 59.928 57.895 0.00 0.00 0.00 5.69
960 1112 1.071814 TAAACCTCCCACACGCCAC 59.928 57.895 0.00 0.00 0.00 5.01
961 1113 1.697082 TAAACCTCCCACACGCCACA 61.697 55.000 0.00 0.00 0.00 4.17
962 1114 2.559922 AAACCTCCCACACGCCACAA 62.560 55.000 0.00 0.00 0.00 3.33
963 1115 2.978010 CCTCCCACACGCCACAAC 60.978 66.667 0.00 0.00 0.00 3.32
964 1116 2.203139 CTCCCACACGCCACAACA 60.203 61.111 0.00 0.00 0.00 3.33
965 1117 2.515057 TCCCACACGCCACAACAC 60.515 61.111 0.00 0.00 0.00 3.32
985 1139 0.875059 CACCTCCAAAGCTCGAAACC 59.125 55.000 0.00 0.00 0.00 3.27
1515 1675 2.994699 CACAAGGCGATGGGGGTA 59.005 61.111 0.00 0.00 0.00 3.69
1551 1711 2.360350 CTCCACAACCTGGCGCAT 60.360 61.111 10.83 0.00 40.39 4.73
1584 1744 1.084370 CGATCGACCTTGCTTGGGAC 61.084 60.000 10.26 0.00 0.00 4.46
1712 1881 1.303155 AGCTTGGCTTCAGGTGAGC 60.303 57.895 0.00 0.00 33.89 4.26
1713 1882 1.601759 GCTTGGCTTCAGGTGAGCA 60.602 57.895 0.00 0.00 0.00 4.26
1717 1886 2.039405 GGCTTCAGGTGAGCAGCAG 61.039 63.158 6.11 0.00 31.35 4.24
1719 1888 1.020333 GCTTCAGGTGAGCAGCAGAG 61.020 60.000 0.00 0.00 30.43 3.35
1777 1946 7.201741 CGAAATCTCTGTCCACTGATAGTTCTA 60.202 40.741 9.08 0.00 32.04 2.10
1986 2170 5.117584 CCAGATCATCTTCCTTCTCTGTTG 58.882 45.833 0.00 0.00 0.00 3.33
2148 2335 2.825836 GGCCTTGATGCTGGACCG 60.826 66.667 0.00 0.00 0.00 4.79
2315 2502 3.119814 GCTGCTTTTAGAGGTTAGGTTGC 60.120 47.826 0.00 0.00 0.00 4.17
2507 2697 6.610741 AAACTGTGACTGAATCTTGAAGTC 57.389 37.500 0.00 0.00 40.61 3.01
2512 2702 3.742882 TGACTGAATCTTGAAGTCTTGCG 59.257 43.478 0.00 0.00 40.79 4.85
2562 2755 8.680903 GTTGATGTTTTTCAGGTATGATGAGAT 58.319 33.333 0.00 0.00 34.73 2.75
2713 2906 6.550938 TGAGATGGAGAAAGAGAATGCTAA 57.449 37.500 0.00 0.00 0.00 3.09
2822 3015 3.919216 TGGTTTATTTTGATGCCAACCG 58.081 40.909 0.00 0.00 37.14 4.44
2879 3072 2.067365 GGTTGGTCACCTTGTCCTTT 57.933 50.000 0.00 0.00 43.29 3.11
2881 3074 1.067060 GTTGGTCACCTTGTCCTTTGC 59.933 52.381 0.00 0.00 0.00 3.68
3019 3241 6.363357 GTGCACTTTGAATGATTGTAGGAAAC 59.637 38.462 10.32 0.00 0.00 2.78
3121 3343 5.509670 GCACAAAGTTTCCTTAGCCTCAAAT 60.510 40.000 0.00 0.00 0.00 2.32
3196 3423 3.960755 GCCCCATCCTAGTTATTTTGCTT 59.039 43.478 0.00 0.00 0.00 3.91
3197 3424 4.038042 GCCCCATCCTAGTTATTTTGCTTC 59.962 45.833 0.00 0.00 0.00 3.86
3198 3425 5.200483 CCCCATCCTAGTTATTTTGCTTCA 58.800 41.667 0.00 0.00 0.00 3.02
3199 3426 5.067805 CCCCATCCTAGTTATTTTGCTTCAC 59.932 44.000 0.00 0.00 0.00 3.18
3200 3427 5.652014 CCCATCCTAGTTATTTTGCTTCACA 59.348 40.000 0.00 0.00 0.00 3.58
3201 3428 6.152661 CCCATCCTAGTTATTTTGCTTCACAA 59.847 38.462 0.00 0.00 36.13 3.33
3202 3429 7.253422 CCATCCTAGTTATTTTGCTTCACAAG 58.747 38.462 0.00 0.00 40.06 3.16
3372 3601 5.587043 TCAAACGTCAAGGACAAAATGTACT 59.413 36.000 0.00 0.00 45.16 2.73
3562 3872 5.972107 GCATTAGCTCAATACCATCCAAT 57.028 39.130 0.00 0.00 37.91 3.16
3570 3880 5.239525 GCTCAATACCATCCAATGTAAGGAC 59.760 44.000 0.00 0.00 38.13 3.85
3674 3984 2.317371 TGCCCCTTAAAGCAAATCCA 57.683 45.000 0.00 0.00 35.69 3.41
3675 3985 2.178580 TGCCCCTTAAAGCAAATCCAG 58.821 47.619 0.00 0.00 35.69 3.86
3676 3986 2.179427 GCCCCTTAAAGCAAATCCAGT 58.821 47.619 0.00 0.00 0.00 4.00
3677 3987 2.567169 GCCCCTTAAAGCAAATCCAGTT 59.433 45.455 0.00 0.00 0.00 3.16
3678 3988 3.007940 GCCCCTTAAAGCAAATCCAGTTT 59.992 43.478 0.00 0.00 0.00 2.66
3679 3989 4.504864 GCCCCTTAAAGCAAATCCAGTTTT 60.505 41.667 0.00 0.00 0.00 2.43
3680 3990 4.996758 CCCCTTAAAGCAAATCCAGTTTTG 59.003 41.667 0.00 0.00 39.16 2.44
3681 3991 5.454613 CCCCTTAAAGCAAATCCAGTTTTGT 60.455 40.000 3.80 0.00 38.55 2.83
3682 3992 6.054941 CCCTTAAAGCAAATCCAGTTTTGTT 58.945 36.000 3.80 0.00 38.55 2.83
3683 3993 6.018016 CCCTTAAAGCAAATCCAGTTTTGTTG 60.018 38.462 3.80 0.00 38.55 3.33
3684 3994 6.538381 CCTTAAAGCAAATCCAGTTTTGTTGT 59.462 34.615 3.80 0.00 38.55 3.32
3685 3995 7.065683 CCTTAAAGCAAATCCAGTTTTGTTGTT 59.934 33.333 3.80 0.13 38.55 2.83
3686 3996 6.816134 AAAGCAAATCCAGTTTTGTTGTTT 57.184 29.167 3.80 0.00 38.55 2.83
3687 3997 6.421377 AAGCAAATCCAGTTTTGTTGTTTC 57.579 33.333 3.80 0.00 38.55 2.78
3688 3998 4.875536 AGCAAATCCAGTTTTGTTGTTTCC 59.124 37.500 3.80 0.00 38.55 3.13
3689 3999 4.260172 GCAAATCCAGTTTTGTTGTTTCCG 60.260 41.667 3.80 0.00 38.55 4.30
3690 4000 4.729227 AATCCAGTTTTGTTGTTTCCGT 57.271 36.364 0.00 0.00 0.00 4.69
3691 4001 3.495670 TCCAGTTTTGTTGTTTCCGTG 57.504 42.857 0.00 0.00 0.00 4.94
3692 4002 2.820787 TCCAGTTTTGTTGTTTCCGTGT 59.179 40.909 0.00 0.00 0.00 4.49
3693 4003 3.119779 TCCAGTTTTGTTGTTTCCGTGTC 60.120 43.478 0.00 0.00 0.00 3.67
3694 4004 3.366476 CCAGTTTTGTTGTTTCCGTGTCA 60.366 43.478 0.00 0.00 0.00 3.58
3695 4005 3.606346 CAGTTTTGTTGTTTCCGTGTCAC 59.394 43.478 0.00 0.00 0.00 3.67
3696 4006 2.529136 TTTGTTGTTTCCGTGTCACG 57.471 45.000 18.54 18.54 42.11 4.35
3697 4007 1.440708 TTGTTGTTTCCGTGTCACGT 58.559 45.000 23.01 0.00 40.58 4.49
3698 4008 2.290531 TGTTGTTTCCGTGTCACGTA 57.709 45.000 23.01 5.48 40.58 3.57
3699 4009 1.925847 TGTTGTTTCCGTGTCACGTAC 59.074 47.619 23.01 17.17 40.58 3.67
3700 4010 1.925847 GTTGTTTCCGTGTCACGTACA 59.074 47.619 23.01 19.23 40.58 2.90
3713 4023 5.165676 TGTCACGTACACATATGTTTCTCC 58.834 41.667 5.37 0.00 40.48 3.71
3714 4024 5.165676 GTCACGTACACATATGTTTCTCCA 58.834 41.667 5.37 0.00 40.48 3.86
3715 4025 5.636121 GTCACGTACACATATGTTTCTCCAA 59.364 40.000 5.37 0.00 40.48 3.53
3716 4026 6.312918 GTCACGTACACATATGTTTCTCCAAT 59.687 38.462 5.37 0.00 40.48 3.16
3717 4027 6.312672 TCACGTACACATATGTTTCTCCAATG 59.687 38.462 5.37 0.00 40.48 2.82
3718 4028 6.312672 CACGTACACATATGTTTCTCCAATGA 59.687 38.462 5.37 0.00 40.48 2.57
3719 4029 6.535150 ACGTACACATATGTTTCTCCAATGAG 59.465 38.462 5.37 0.00 40.48 2.90
3720 4030 6.535150 CGTACACATATGTTTCTCCAATGAGT 59.465 38.462 5.37 0.00 40.48 3.41
3721 4031 7.064609 CGTACACATATGTTTCTCCAATGAGTT 59.935 37.037 5.37 0.00 40.48 3.01
3722 4032 7.149569 ACACATATGTTTCTCCAATGAGTTG 57.850 36.000 5.37 0.00 36.35 3.16
3723 4033 6.942005 ACACATATGTTTCTCCAATGAGTTGA 59.058 34.615 5.37 0.00 36.35 3.18
3724 4034 7.613022 ACACATATGTTTCTCCAATGAGTTGAT 59.387 33.333 5.37 0.00 36.35 2.57
3725 4035 7.913821 CACATATGTTTCTCCAATGAGTTGATG 59.086 37.037 5.37 0.00 39.75 3.07
3726 4036 7.830697 ACATATGTTTCTCCAATGAGTTGATGA 59.169 33.333 1.41 0.00 39.75 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 7.513856 TGCACATAGGGCTAGATACATTTTAA 58.486 34.615 0.00 0.00 0.00 1.52
37 38 9.056005 CATTTTGGACCATAAGATTTCTATCGA 57.944 33.333 0.00 0.00 35.85 3.59
38 39 8.840321 ACATTTTGGACCATAAGATTTCTATCG 58.160 33.333 0.00 0.00 35.85 2.92
64 65 5.045869 AGGAAATCGGAGATGTTAGGTTCAA 60.046 40.000 0.00 0.00 45.12 2.69
82 83 9.860898 GTTAAGATCTGCAAACATTAAGGAAAT 57.139 29.630 0.00 0.00 0.00 2.17
91 92 5.120830 GTCTGACGTTAAGATCTGCAAACAT 59.879 40.000 0.00 0.00 0.00 2.71
188 189 7.410174 TCCCTACATGACCAAAATTTACAGAT 58.590 34.615 0.00 0.00 0.00 2.90
250 251 6.208599 CCACTATTTTGAGGCTAAAAAGACCA 59.791 38.462 14.82 0.86 33.67 4.02
266 267 3.136443 TGATCTCCGGCATCCACTATTTT 59.864 43.478 0.00 0.00 0.00 1.82
267 268 2.705658 TGATCTCCGGCATCCACTATTT 59.294 45.455 0.00 0.00 0.00 1.40
268 269 2.037772 GTGATCTCCGGCATCCACTATT 59.962 50.000 0.00 0.00 0.00 1.73
454 455 8.245195 ACAATTTTACAATCTTACAACAGGGT 57.755 30.769 0.00 0.00 0.00 4.34
495 496 8.887036 AGCTAGTTCCAAAATAAAACAAAAGG 57.113 30.769 0.00 0.00 0.00 3.11
539 540 4.929211 TGAATTATCCATGCTATTCCGACG 59.071 41.667 0.00 0.00 0.00 5.12
612 613 1.107114 TTCAGCTTCACCCGCAAAAA 58.893 45.000 0.00 0.00 0.00 1.94
613 614 1.107114 TTTCAGCTTCACCCGCAAAA 58.893 45.000 0.00 0.00 0.00 2.44
615 616 0.749818 TGTTTCAGCTTCACCCGCAA 60.750 50.000 0.00 0.00 0.00 4.85
617 618 0.598065 AATGTTTCAGCTTCACCCGC 59.402 50.000 0.00 0.00 0.00 6.13
618 619 3.369546 AAAATGTTTCAGCTTCACCCG 57.630 42.857 0.00 0.00 0.00 5.28
619 620 4.280929 AGGTAAAATGTTTCAGCTTCACCC 59.719 41.667 0.00 0.00 0.00 4.61
620 621 5.009610 TGAGGTAAAATGTTTCAGCTTCACC 59.990 40.000 0.00 0.00 0.00 4.02
621 622 6.072112 TGAGGTAAAATGTTTCAGCTTCAC 57.928 37.500 0.00 0.00 0.00 3.18
623 624 7.115378 CACATTGAGGTAAAATGTTTCAGCTTC 59.885 37.037 0.00 0.00 43.94 3.86
626 627 5.634859 CCACATTGAGGTAAAATGTTTCAGC 59.365 40.000 0.00 0.00 43.94 4.26
627 628 6.158598 CCCACATTGAGGTAAAATGTTTCAG 58.841 40.000 0.00 0.00 43.94 3.02
629 630 5.478407 CCCCACATTGAGGTAAAATGTTTC 58.522 41.667 0.00 0.00 43.94 2.78
630 631 4.285775 CCCCCACATTGAGGTAAAATGTTT 59.714 41.667 0.00 0.00 43.94 2.83
631 632 3.837731 CCCCCACATTGAGGTAAAATGTT 59.162 43.478 0.00 0.00 43.94 2.71
632 633 3.440127 CCCCCACATTGAGGTAAAATGT 58.560 45.455 0.00 0.00 46.57 2.71
633 634 2.168313 GCCCCCACATTGAGGTAAAATG 59.832 50.000 0.00 0.00 40.23 2.32
692 724 2.794910 CACTTGTTCACTGACGTGTAGG 59.205 50.000 0.00 0.00 41.89 3.18
696 728 3.183172 CAGATCACTTGTTCACTGACGTG 59.817 47.826 0.00 0.00 42.59 4.49
699 731 4.626042 ACTCAGATCACTTGTTCACTGAC 58.374 43.478 0.00 0.00 32.31 3.51
707 739 5.305644 AGAACCAGTTACTCAGATCACTTGT 59.694 40.000 0.00 0.00 0.00 3.16
718 759 5.049612 GCCAACAGTAAAGAACCAGTTACTC 60.050 44.000 0.00 0.00 38.25 2.59
724 765 3.744660 AGAGCCAACAGTAAAGAACCAG 58.255 45.455 0.00 0.00 0.00 4.00
739 780 1.000506 GACGGTTACTGTTGAGAGCCA 59.999 52.381 0.00 0.00 0.00 4.75
740 781 1.272769 AGACGGTTACTGTTGAGAGCC 59.727 52.381 0.00 0.00 0.00 4.70
741 782 2.726832 AGACGGTTACTGTTGAGAGC 57.273 50.000 0.00 0.00 0.00 4.09
751 816 5.336055 CCATGAGATCATCCTAGACGGTTAC 60.336 48.000 0.00 0.00 33.61 2.50
754 819 3.161067 CCATGAGATCATCCTAGACGGT 58.839 50.000 0.00 0.00 33.61 4.83
810 890 4.394920 ACCACTTATTCACCGCATAAAGTG 59.605 41.667 6.13 6.13 35.24 3.16
831 946 1.248101 AAACCGGGTTGCATAGCACC 61.248 55.000 14.22 0.00 38.71 5.01
843 958 4.364860 CAGGAAAACAAACTAAAACCGGG 58.635 43.478 6.32 0.00 0.00 5.73
846 961 6.729391 TTTGCAGGAAAACAAACTAAAACC 57.271 33.333 0.00 0.00 31.09 3.27
861 979 2.224992 TGAGTTGGGCTATTTTGCAGGA 60.225 45.455 0.00 0.00 34.04 3.86
874 992 1.913762 AGGTCCTCCGTGAGTTGGG 60.914 63.158 0.00 0.00 39.05 4.12
877 995 2.584391 GCCAGGTCCTCCGTGAGTT 61.584 63.158 0.00 0.00 39.05 3.01
881 999 2.895424 AAAGGCCAGGTCCTCCGTG 61.895 63.158 5.01 0.00 39.05 4.94
884 1002 1.002011 GTCAAAGGCCAGGTCCTCC 60.002 63.158 5.01 0.00 34.82 4.30
886 1004 0.038744 CATGTCAAAGGCCAGGTCCT 59.961 55.000 5.01 0.00 38.31 3.85
903 1021 3.294214 GAGATGGATGAACAAAGGCCAT 58.706 45.455 5.01 0.00 41.76 4.40
915 1033 7.523544 CGGCTAGGATAGATAATGAGATGGATG 60.524 44.444 0.00 0.00 42.77 3.51
916 1034 6.493115 CGGCTAGGATAGATAATGAGATGGAT 59.507 42.308 0.00 0.00 42.77 3.41
920 1038 8.688151 GTTTACGGCTAGGATAGATAATGAGAT 58.312 37.037 0.00 0.00 42.77 2.75
921 1039 7.122353 GGTTTACGGCTAGGATAGATAATGAGA 59.878 40.741 0.00 0.00 42.77 3.27
923 1041 6.952358 AGGTTTACGGCTAGGATAGATAATGA 59.048 38.462 0.00 0.00 42.77 2.57
924 1042 7.171630 AGGTTTACGGCTAGGATAGATAATG 57.828 40.000 0.00 0.00 42.77 1.90
925 1043 6.380560 GGAGGTTTACGGCTAGGATAGATAAT 59.619 42.308 0.00 0.00 42.77 1.28
930 1048 2.561858 GGGAGGTTTACGGCTAGGATAG 59.438 54.545 0.00 0.00 43.09 2.08
956 1108 1.040339 TTTGGAGGTGGTGTTGTGGC 61.040 55.000 0.00 0.00 0.00 5.01
957 1109 1.032014 CTTTGGAGGTGGTGTTGTGG 58.968 55.000 0.00 0.00 0.00 4.17
958 1110 0.385390 GCTTTGGAGGTGGTGTTGTG 59.615 55.000 0.00 0.00 0.00 3.33
959 1111 0.258774 AGCTTTGGAGGTGGTGTTGT 59.741 50.000 0.00 0.00 31.08 3.32
960 1112 0.954452 GAGCTTTGGAGGTGGTGTTG 59.046 55.000 0.00 0.00 32.79 3.33
961 1113 0.535102 CGAGCTTTGGAGGTGGTGTT 60.535 55.000 0.00 0.00 32.79 3.32
962 1114 1.071471 CGAGCTTTGGAGGTGGTGT 59.929 57.895 0.00 0.00 32.79 4.16
963 1115 0.250295 TTCGAGCTTTGGAGGTGGTG 60.250 55.000 0.00 0.00 32.79 4.17
964 1116 0.472471 TTTCGAGCTTTGGAGGTGGT 59.528 50.000 0.00 0.00 32.79 4.16
965 1117 0.875059 GTTTCGAGCTTTGGAGGTGG 59.125 55.000 0.00 0.00 32.79 4.61
985 1139 3.814268 CATTTGGCCGGTGGAGCG 61.814 66.667 1.90 0.00 0.00 5.03
1551 1711 0.867329 CGATCGCATTGAGCTCGACA 60.867 55.000 5.59 0.00 41.77 4.35
1566 1726 0.036388 TGTCCCAAGCAAGGTCGATC 60.036 55.000 0.00 0.00 0.00 3.69
1701 1870 0.607112 TCTCTGCTGCTCACCTGAAG 59.393 55.000 0.00 0.00 0.00 3.02
1712 1881 1.288350 CTTCCGCATTCTCTCTGCTG 58.712 55.000 0.00 0.00 37.48 4.41
1713 1882 0.901124 ACTTCCGCATTCTCTCTGCT 59.099 50.000 0.00 0.00 37.48 4.24
1717 1886 2.370281 TCACACTTCCGCATTCTCTC 57.630 50.000 0.00 0.00 0.00 3.20
1719 1888 5.294306 TCAATATTCACACTTCCGCATTCTC 59.706 40.000 0.00 0.00 0.00 2.87
1729 1898 7.087409 TCGCATCAATTCAATATTCACACTT 57.913 32.000 0.00 0.00 0.00 3.16
1777 1946 6.014584 TGACATATGACAAGTAGACAACAGGT 60.015 38.462 10.38 0.00 0.00 4.00
1812 1996 9.836864 TTTACAACAATCTGACATAGCTCATAT 57.163 29.630 0.00 0.00 0.00 1.78
1859 2043 3.937706 GACAGGCATATCACCATATCTGC 59.062 47.826 0.00 0.00 0.00 4.26
1986 2170 8.638565 GTTATGACAATGTATTTTTGACAGTGC 58.361 33.333 3.38 0.00 44.57 4.40
2085 2270 9.112725 TCTAATCATCAACATATTGGTCAAGTG 57.887 33.333 0.00 0.00 36.39 3.16
2148 2335 6.655425 AGCCAATTAACTTTTGGACTAGTCTC 59.345 38.462 21.88 12.69 45.35 3.36
2256 2443 3.189080 CCATCATTTCGCACACTTTCAGA 59.811 43.478 0.00 0.00 0.00 3.27
2265 2452 2.406616 ACGGCCCATCATTTCGCAC 61.407 57.895 0.00 0.00 0.00 5.34
2562 2755 3.490761 GCTTGCAACTTCAGGTTTAAGCA 60.491 43.478 11.46 0.00 45.21 3.91
2688 2881 6.003859 AGCATTCTCTTTCTCCATCTCAAT 57.996 37.500 0.00 0.00 0.00 2.57
2713 2906 6.664816 TCAGGTGAGATTTTAGCCATTCAAAT 59.335 34.615 0.00 0.00 0.00 2.32
2822 3015 0.453390 GATGTAAGCAGCTTGGTGGC 59.547 55.000 18.54 3.61 0.00 5.01
2879 3072 8.506196 AAGGTCCAATAAGTAGAATATAGGCA 57.494 34.615 0.00 0.00 0.00 4.75
2915 3108 9.563748 TCTTTTTCATAGATGTGATCATGCATA 57.436 29.630 0.00 0.00 34.06 3.14
3019 3241 6.128007 ACAACTTGAACACTTAGTGAGGTTTG 60.128 38.462 20.07 14.56 36.96 2.93
3023 3245 5.584649 TCAACAACTTGAACACTTAGTGAGG 59.415 40.000 20.07 0.00 32.63 3.86
3134 3356 7.471399 GCCCAACTTTCCTAATTATGGGTTATG 60.471 40.741 16.03 0.38 46.21 1.90
3136 3358 5.894964 GCCCAACTTTCCTAATTATGGGTTA 59.105 40.000 16.03 0.00 46.21 2.85
3196 3423 6.704493 GTCCTTGTATTAGTTGTGACTTGTGA 59.296 38.462 0.00 0.00 37.33 3.58
3197 3424 6.706270 AGTCCTTGTATTAGTTGTGACTTGTG 59.294 38.462 0.00 0.00 37.33 3.33
3198 3425 6.827727 AGTCCTTGTATTAGTTGTGACTTGT 58.172 36.000 0.00 0.00 37.33 3.16
3199 3426 8.873830 CATAGTCCTTGTATTAGTTGTGACTTG 58.126 37.037 0.00 0.00 37.33 3.16
3200 3427 8.041323 CCATAGTCCTTGTATTAGTTGTGACTT 58.959 37.037 0.00 0.00 37.33 3.01
3201 3428 7.399191 TCCATAGTCCTTGTATTAGTTGTGACT 59.601 37.037 0.00 0.00 39.97 3.41
3202 3429 7.491696 GTCCATAGTCCTTGTATTAGTTGTGAC 59.508 40.741 0.00 0.00 0.00 3.67
3247 3474 6.317642 CCGTCCATTTCATTCAATTGGTAGTA 59.682 38.462 5.42 0.00 36.99 1.82
3250 3477 5.257262 TCCGTCCATTTCATTCAATTGGTA 58.743 37.500 5.42 0.00 36.99 3.25
3270 3497 3.470709 AGTGGCTCAATCAATACATCCG 58.529 45.455 0.00 0.00 0.00 4.18
3347 3576 4.668289 ACATTTTGTCCTTGACGTTTGAC 58.332 39.130 0.00 0.00 34.95 3.18
3394 3623 0.446222 GCGTGTTGTGGAATGCGTAT 59.554 50.000 0.00 0.00 0.00 3.06
3396 3625 1.719725 TTGCGTGTTGTGGAATGCGT 61.720 50.000 0.00 0.00 0.00 5.24
3397 3626 1.009108 TTGCGTGTTGTGGAATGCG 60.009 52.632 0.00 0.00 0.00 4.73
3464 3702 8.658499 TTCTTACTTTAGTGAAGACTCAAACC 57.342 34.615 0.99 0.00 38.77 3.27
3471 3709 9.387123 CAAATGCTTTCTTACTTTAGTGAAGAC 57.613 33.333 0.99 0.00 38.77 3.01
3562 3872 0.611200 CCCCACATGACGTCCTTACA 59.389 55.000 14.12 0.00 0.00 2.41
3570 3880 2.124983 CTCAGGCCCCACATGACG 60.125 66.667 0.00 0.00 0.00 4.35
3660 3970 7.538303 ACAACAAAACTGGATTTGCTTTAAG 57.462 32.000 7.75 0.00 42.68 1.85
3670 3980 3.445805 ACACGGAAACAACAAAACTGGAT 59.554 39.130 0.00 0.00 0.00 3.41
3671 3981 2.820787 ACACGGAAACAACAAAACTGGA 59.179 40.909 0.00 0.00 0.00 3.86
3672 3982 3.175929 GACACGGAAACAACAAAACTGG 58.824 45.455 0.00 0.00 0.00 4.00
3673 3983 3.606346 GTGACACGGAAACAACAAAACTG 59.394 43.478 0.00 0.00 0.00 3.16
3674 3984 3.668491 CGTGACACGGAAACAACAAAACT 60.668 43.478 20.26 0.00 38.08 2.66
3675 3985 2.590712 CGTGACACGGAAACAACAAAAC 59.409 45.455 20.26 0.00 38.08 2.43
3676 3986 2.852748 CGTGACACGGAAACAACAAAA 58.147 42.857 20.26 0.00 38.08 2.44
3677 3987 2.529136 CGTGACACGGAAACAACAAA 57.471 45.000 20.26 0.00 38.08 2.83
3690 4000 5.165676 GGAGAAACATATGTGTACGTGACA 58.834 41.667 9.63 0.73 37.67 3.58
3691 4001 5.165676 TGGAGAAACATATGTGTACGTGAC 58.834 41.667 9.63 0.00 37.67 3.67
3692 4002 5.394224 TGGAGAAACATATGTGTACGTGA 57.606 39.130 9.63 0.00 37.67 4.35
3693 4003 6.312672 TCATTGGAGAAACATATGTGTACGTG 59.687 38.462 9.63 2.32 37.67 4.49
3694 4004 6.403049 TCATTGGAGAAACATATGTGTACGT 58.597 36.000 9.63 0.00 37.67 3.57
3695 4005 6.535150 ACTCATTGGAGAAACATATGTGTACG 59.465 38.462 9.63 0.00 44.26 3.67
3696 4006 7.849804 ACTCATTGGAGAAACATATGTGTAC 57.150 36.000 9.63 4.25 44.26 2.90
3697 4007 8.100164 TCAACTCATTGGAGAAACATATGTGTA 58.900 33.333 9.63 0.00 44.26 2.90
3698 4008 6.942005 TCAACTCATTGGAGAAACATATGTGT 59.058 34.615 9.63 2.93 44.26 3.72
3699 4009 7.381766 TCAACTCATTGGAGAAACATATGTG 57.618 36.000 9.63 0.00 44.26 3.21
3700 4010 7.830697 TCATCAACTCATTGGAGAAACATATGT 59.169 33.333 1.41 1.41 44.26 2.29
3701 4011 8.217131 TCATCAACTCATTGGAGAAACATATG 57.783 34.615 0.00 0.00 44.26 1.78


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

AutoCloner maintained by Alex Coulton.