Multiple sequence alignment - TraesCS5D01G282600

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 TraesCS5D01G282600 chr5D 100.000 3732 0 0 1 3732 384071351 384067620 0.000000e+00 6892.0
1 TraesCS5D01G282600 chr5B 93.983 3091 79 30 1 3006 460679458 460676390 0.000000e+00 4578.0
2 TraesCS5D01G282600 chr5B 89.706 68 3 2 3082 3148 534911583 534911647 2.390000e-12 84.2
3 TraesCS5D01G282600 chr5A 93.699 1460 50 8 977 2395 484556836 484555378 0.000000e+00 2148.0
4 TraesCS5D01G282600 chr5A 86.268 1420 113 41 2333 3678 484555379 484553968 0.000000e+00 1467.0
5 TraesCS5D01G282600 chr5A 89.536 1013 52 22 1 974 484557884 484556887 0.000000e+00 1234.0
6 TraesCS5D01G282600 chr1D 79.310 435 65 14 3166 3586 310166492 310166915 7.890000e-72 281.0
7 TraesCS5D01G282600 chr1A 77.068 532 86 19 3061 3581 573240520 573241026 1.320000e-69 274.0
8 TraesCS5D01G282600 chr4D 80.545 257 38 4 3355 3603 100339281 100339029 1.770000e-43 187.0
9 TraesCS5D01G282600 chr4B 81.707 164 29 1 3423 3586 41201625 41201787 6.500000e-28 135.0
10 TraesCS5D01G282600 chr3B 87.324 71 6 1 3662 3732 340796094 340796027 1.110000e-10 78.7
11 TraesCS5D01G282600 chr2A 77.519 129 26 1 3604 3732 735691893 735691768 1.440000e-09 75.0


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 TraesCS5D01G282600 chr5D 384067620 384071351 3731 True 6892.000000 6892 100.000000 1 3732 1 chr5D.!!$R1 3731
1 TraesCS5D01G282600 chr5B 460676390 460679458 3068 True 4578.000000 4578 93.983000 1 3006 1 chr5B.!!$R1 3005
2 TraesCS5D01G282600 chr5A 484553968 484557884 3916 True 1616.333333 2148 89.834333 1 3678 3 chr5A.!!$R1 3677
3 TraesCS5D01G282600 chr1A 573240520 573241026 506 False 274.000000 274 77.068000 3061 3581 1 chr1A.!!$F1 520

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
472 512 0.397941 TGGCTAGCCCATGTAGATGC 59.602 55.0 30.81 1.6 39.18 3.91 F
911 985 1.103803 TGCACGTTTTTGGGCACTTA 58.896 45.0 0.00 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2118 2281 2.439507 GGGAGGTATCAGCAATCCTCAA 59.560 50.0 11.34 0.0 45.65 3.02 R
2858 3118 1.327507 GCGTTCTTGAAATTGTCGGC 58.672 50.0 0.00 0.0 0.00 5.54 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
135 143 3.659089 ATACCGCGCTTCTTGCCGT 62.659 57.895 5.56 0.00 38.78 5.68
142 150 0.996462 CGCTTCTTGCCGTATTTCGA 59.004 50.000 0.00 0.00 39.75 3.71
144 152 2.000447 GCTTCTTGCCGTATTTCGAGT 59.000 47.619 0.00 0.00 42.86 4.18
145 153 2.415512 GCTTCTTGCCGTATTTCGAGTT 59.584 45.455 0.00 0.00 42.86 3.01
146 154 3.725010 GCTTCTTGCCGTATTTCGAGTTG 60.725 47.826 0.00 0.00 42.86 3.16
193 210 1.153349 GGCTCTGCTTCGGTTAGGG 60.153 63.158 0.00 0.00 0.00 3.53
229 248 4.394300 AGGAAAGATGCTCTCGACATTTTG 59.606 41.667 0.00 0.00 0.00 2.44
235 254 1.135859 GCTCTCGACATTTTGTGCTGG 60.136 52.381 0.00 0.00 0.00 4.85
241 260 2.147958 GACATTTTGTGCTGGTCCGTA 58.852 47.619 0.00 0.00 0.00 4.02
242 261 1.877443 ACATTTTGTGCTGGTCCGTAC 59.123 47.619 0.00 0.00 0.00 3.67
281 300 1.009829 GGTGCTGCTTCGATTGTAGG 58.990 55.000 0.00 0.00 0.00 3.18
338 361 1.957695 GTTGGTTGGTCGGTCGGTC 60.958 63.158 0.00 0.00 0.00 4.79
339 362 3.502990 TTGGTTGGTCGGTCGGTCG 62.503 63.158 0.00 0.00 0.00 4.79
340 363 4.729856 GGTTGGTCGGTCGGTCGG 62.730 72.222 0.00 0.00 0.00 4.79
381 421 4.219070 CCAAATTGATGCTCTCCAGTTCAA 59.781 41.667 0.00 0.00 32.10 2.69
420 460 0.965363 TGATCGGCCTTCTTTTGCCC 60.965 55.000 0.00 0.00 45.07 5.36
428 468 2.883888 GCCTTCTTTTGCCCTATGACCA 60.884 50.000 0.00 0.00 0.00 4.02
472 512 0.397941 TGGCTAGCCCATGTAGATGC 59.602 55.000 30.81 1.60 39.18 3.91
499 539 3.522759 TCTCCTGTTGGTGGGTGTATAA 58.477 45.455 0.00 0.00 34.23 0.98
911 985 1.103803 TGCACGTTTTTGGGCACTTA 58.896 45.000 0.00 0.00 0.00 2.24
952 1026 9.003658 TGTTCTGGTCTTTAAAATCATTCTCTC 57.996 33.333 0.00 0.00 0.00 3.20
975 1049 9.268268 TCTCGTTTCATAACCATATGTTTATCC 57.732 33.333 2.72 0.00 39.94 2.59
1902 2043 4.462483 GCTGGAGGTCATTAACATTTTCCA 59.538 41.667 0.00 0.00 0.00 3.53
1945 2086 5.864474 GTCGGGCTACTAAATCATGTCATAG 59.136 44.000 0.00 0.00 0.00 2.23
1974 2115 6.292381 GGAGAATTGTGATGCTAATACGTGTC 60.292 42.308 0.00 0.00 0.00 3.67
2458 2682 6.017830 AGTAAATACCCCAAATTCCGGAAAA 58.982 36.000 23.08 0.00 0.00 2.29
2858 3118 6.083098 TGACATTTATGTTTGGTGACTTGG 57.917 37.500 0.00 0.00 41.95 3.61
2977 3237 4.966168 TCAGCATAATACACCCAGTAGGAA 59.034 41.667 0.00 0.00 39.89 3.36
3000 3260 3.312736 AGTTTGGTGATTGGTTCAGGT 57.687 42.857 0.00 0.00 34.17 4.00
3015 3276 7.859325 TGGTTCAGGTTATAAAAGCATCTAC 57.141 36.000 0.00 0.00 35.49 2.59
3018 3279 6.229936 TCAGGTTATAAAAGCATCTACGGT 57.770 37.500 0.00 0.00 35.49 4.83
3019 3280 6.278363 TCAGGTTATAAAAGCATCTACGGTC 58.722 40.000 0.00 0.00 35.49 4.79
3020 3281 6.046593 CAGGTTATAAAAGCATCTACGGTCA 58.953 40.000 0.00 0.00 35.49 4.02
3023 3284 4.755266 ATAAAAGCATCTACGGTCAGGT 57.245 40.909 0.00 0.00 0.00 4.00
3053 3329 1.140852 CCCCCTCAAATGATAGCACGA 59.859 52.381 0.00 0.00 0.00 4.35
3083 3361 2.180432 AAAACCTGACTTAGACGGGC 57.820 50.000 9.36 0.00 37.30 6.13
3093 3371 1.186917 TTAGACGGGCCCTCAAACGA 61.187 55.000 22.43 0.00 0.00 3.85
3116 3394 2.997315 CTGACCGGCACCCTCTCA 60.997 66.667 0.00 0.00 0.00 3.27
3125 3403 0.761187 GCACCCTCTCATATCCAGCA 59.239 55.000 0.00 0.00 0.00 4.41
3157 3440 1.157751 GATATGGGGAGGTCCGGGA 59.842 63.158 0.00 0.00 36.71 5.14
3190 3473 1.601197 AGACTGACGTGCGACTCCT 60.601 57.895 0.00 0.00 0.00 3.69
3192 3475 2.179517 CTGACGTGCGACTCCTCC 59.820 66.667 0.00 0.00 0.00 4.30
3196 3479 4.135153 CGTGCGACTCCTCCAGGG 62.135 72.222 0.00 0.00 35.41 4.45
3205 3488 0.615850 CTCCTCCAGGGAAACACTCC 59.384 60.000 0.00 0.00 44.58 3.85
3250 3533 2.134287 CCTCCGATGGACCGATGGT 61.134 63.158 0.00 0.00 39.44 3.55
3261 3544 2.430075 CGATGGTGTCGCGTGTCA 60.430 61.111 5.77 1.28 44.33 3.58
3264 3547 3.513768 ATGGTGTCGCGTGTCAGCA 62.514 57.895 25.40 25.40 43.66 4.41
3343 3634 2.003072 ACATCCACATTTCCTCCCCTT 58.997 47.619 0.00 0.00 0.00 3.95
3349 3640 1.203622 ACATTTCCTCCCCTTCCCTCT 60.204 52.381 0.00 0.00 0.00 3.69
3361 3655 2.290323 CCTTCCCTCTACCACCACTTTG 60.290 54.545 0.00 0.00 0.00 2.77
3368 3662 2.151202 CTACCACCACTTTGCAATCGT 58.849 47.619 0.00 0.00 0.00 3.73
3395 3689 0.389817 CTCCACATTTCACTCGCCGA 60.390 55.000 0.00 0.00 0.00 5.54
3439 3733 0.608856 CAAGTAGCCATGCCACCACA 60.609 55.000 0.00 0.00 0.00 4.17
3471 3765 4.404715 TCAGGAGCTACCCTTATGTAACAC 59.595 45.833 0.00 0.00 40.05 3.32
3483 3777 3.307906 TAACACTGGAGCGCCCGT 61.308 61.111 2.29 0.00 37.93 5.28
3486 3780 4.988598 CACTGGAGCGCCCGTTGT 62.989 66.667 2.29 3.16 37.93 3.32
3559 3853 2.036731 TCCGGACGTGGTGGATCT 59.963 61.111 0.00 0.00 0.00 2.75
3560 3854 2.184322 CCGGACGTGGTGGATCTG 59.816 66.667 0.00 0.00 0.00 2.90
3587 3896 1.985116 GCAGGAGGAGGACGAGGTT 60.985 63.158 0.00 0.00 0.00 3.50
3590 3899 0.612453 AGGAGGAGGACGAGGTTGAC 60.612 60.000 0.00 0.00 0.00 3.18
3592 3901 1.228490 AGGAGGACGAGGTTGACGT 60.228 57.895 0.00 0.00 46.58 4.34
3594 3903 1.080705 GAGGACGAGGTTGACGTGG 60.081 63.158 0.00 0.00 43.97 4.94
3595 3904 1.521450 GAGGACGAGGTTGACGTGGA 61.521 60.000 0.00 0.00 43.97 4.02
3611 3920 4.838152 GAGGCCGCGGATCTGCAA 62.838 66.667 33.48 0.00 34.15 4.08
3647 3956 1.289160 CCCTTGATTCCCTCCAGTCA 58.711 55.000 0.00 0.00 0.00 3.41
3648 3957 1.211457 CCCTTGATTCCCTCCAGTCAG 59.789 57.143 0.00 0.00 0.00 3.51
3658 3967 0.681564 CTCCAGTCAGAGGCGTAGGT 60.682 60.000 0.00 0.00 0.00 3.08
3678 3987 0.808847 GAAGGCCAACCGTCGTATCC 60.809 60.000 5.01 0.00 42.76 2.59
3679 3988 1.262640 AAGGCCAACCGTCGTATCCT 61.263 55.000 5.01 0.00 42.76 3.24
3680 3989 1.227176 GGCCAACCGTCGTATCCTC 60.227 63.158 0.00 0.00 0.00 3.71
3681 3990 1.227176 GCCAACCGTCGTATCCTCC 60.227 63.158 0.00 0.00 0.00 4.30
3682 3991 1.952102 GCCAACCGTCGTATCCTCCA 61.952 60.000 0.00 0.00 0.00 3.86
3683 3992 0.533491 CCAACCGTCGTATCCTCCAA 59.467 55.000 0.00 0.00 0.00 3.53
3684 3993 1.470979 CCAACCGTCGTATCCTCCAAG 60.471 57.143 0.00 0.00 0.00 3.61
3685 3994 0.175073 AACCGTCGTATCCTCCAAGC 59.825 55.000 0.00 0.00 0.00 4.01
3686 3995 1.299165 CCGTCGTATCCTCCAAGCG 60.299 63.158 0.00 0.00 0.00 4.68
3687 3996 1.299165 CGTCGTATCCTCCAAGCGG 60.299 63.158 0.00 0.00 0.00 5.52
3688 3997 1.721664 CGTCGTATCCTCCAAGCGGA 61.722 60.000 0.00 0.00 39.79 5.54
3706 4015 4.415332 GCAGGAAGCGGACGTCGA 62.415 66.667 9.92 0.00 42.43 4.20
3707 4016 2.504244 CAGGAAGCGGACGTCGAC 60.504 66.667 9.92 5.18 42.43 4.20
3708 4017 4.099170 AGGAAGCGGACGTCGACG 62.099 66.667 34.58 34.58 46.33 5.12
3709 4018 4.093952 GGAAGCGGACGTCGACGA 62.094 66.667 41.52 0.00 43.02 4.20
3710 4019 2.573689 GAAGCGGACGTCGACGAG 60.574 66.667 41.52 29.95 43.02 4.18
3711 4020 3.020026 GAAGCGGACGTCGACGAGA 62.020 63.158 41.52 0.00 43.02 4.04
3712 4021 2.307137 GAAGCGGACGTCGACGAGAT 62.307 60.000 41.52 26.93 43.02 2.75
3713 4022 2.579241 AAGCGGACGTCGACGAGATG 62.579 60.000 41.52 26.90 43.02 2.90
3714 4023 2.648102 CGGACGTCGACGAGATGC 60.648 66.667 41.52 24.40 43.02 3.91
3715 4024 2.792599 GGACGTCGACGAGATGCT 59.207 61.111 41.52 20.46 43.02 3.79
3716 4025 1.136984 GGACGTCGACGAGATGCTT 59.863 57.895 41.52 19.68 43.02 3.91
3717 4026 1.134530 GGACGTCGACGAGATGCTTG 61.135 60.000 41.52 12.23 43.02 4.01
3718 4027 1.734359 GACGTCGACGAGATGCTTGC 61.734 60.000 41.52 15.59 43.02 4.01
3719 4028 2.508891 CGTCGACGAGATGCTTGCC 61.509 63.158 33.35 0.00 43.02 4.52
3720 4029 1.153745 GTCGACGAGATGCTTGCCT 60.154 57.895 0.00 0.00 0.00 4.75
3721 4030 0.100682 GTCGACGAGATGCTTGCCTA 59.899 55.000 0.00 0.00 0.00 3.93
3722 4031 1.032794 TCGACGAGATGCTTGCCTAT 58.967 50.000 0.00 0.00 0.00 2.57
3723 4032 2.031069 GTCGACGAGATGCTTGCCTATA 60.031 50.000 0.00 0.00 0.00 1.31
3724 4033 2.820197 TCGACGAGATGCTTGCCTATAT 59.180 45.455 0.00 0.00 0.00 0.86
3725 4034 2.919859 CGACGAGATGCTTGCCTATATG 59.080 50.000 0.00 0.00 0.00 1.78
3726 4035 3.257393 GACGAGATGCTTGCCTATATGG 58.743 50.000 0.00 0.00 39.35 2.74
3727 4036 2.899900 ACGAGATGCTTGCCTATATGGA 59.100 45.455 0.00 0.00 38.35 3.41
3728 4037 3.056250 ACGAGATGCTTGCCTATATGGAG 60.056 47.826 0.00 0.00 38.35 3.86
3729 4038 3.678252 CGAGATGCTTGCCTATATGGAGG 60.678 52.174 0.00 0.00 39.88 4.30
3730 4039 3.517100 GAGATGCTTGCCTATATGGAGGA 59.483 47.826 0.00 0.00 39.15 3.71
3731 4040 3.518705 AGATGCTTGCCTATATGGAGGAG 59.481 47.826 0.00 0.00 39.15 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
135 143 7.989416 AATACAAGAAACCCAACTCGAAATA 57.011 32.000 0.00 0.00 0.00 1.40
142 150 4.280929 GCCAGAAATACAAGAAACCCAACT 59.719 41.667 0.00 0.00 0.00 3.16
144 152 3.576550 GGCCAGAAATACAAGAAACCCAA 59.423 43.478 0.00 0.00 0.00 4.12
145 153 3.161866 GGCCAGAAATACAAGAAACCCA 58.838 45.455 0.00 0.00 0.00 4.51
146 154 2.163613 CGGCCAGAAATACAAGAAACCC 59.836 50.000 2.24 0.00 0.00 4.11
175 192 1.153349 CCCTAACCGAAGCAGAGCC 60.153 63.158 0.00 0.00 0.00 4.70
193 210 6.596621 AGCATCTTTCCTAGGTTCCTATTTC 58.403 40.000 9.08 0.00 0.00 2.17
229 248 2.431942 CCACGTACGGACCAGCAC 60.432 66.667 21.06 0.00 0.00 4.40
235 254 1.140375 GATCCACCCACGTACGGAC 59.860 63.158 21.06 0.00 0.00 4.79
241 260 2.351276 GCCAAGATCCACCCACGT 59.649 61.111 0.00 0.00 0.00 4.49
242 261 2.040544 GTGCCAAGATCCACCCACG 61.041 63.158 0.00 0.00 0.00 4.94
274 293 5.186198 GCACAGAAACTGATACCCTACAAT 58.814 41.667 5.76 0.00 35.18 2.71
281 300 6.457528 GCTTATCTTGCACAGAAACTGATACC 60.458 42.308 5.76 0.00 34.16 2.73
338 361 0.871722 TGGATGAAAGCAAACGACCG 59.128 50.000 0.00 0.00 0.00 4.79
339 362 1.068541 GGTGGATGAAAGCAAACGACC 60.069 52.381 0.00 0.00 0.00 4.79
340 363 1.606668 TGGTGGATGAAAGCAAACGAC 59.393 47.619 0.00 0.00 0.00 4.34
381 421 1.224592 GAATCAGCCGTCCCCATGT 59.775 57.895 0.00 0.00 0.00 3.21
420 460 3.961480 TGGTCAGTCAGTTGGTCATAG 57.039 47.619 0.00 0.00 0.00 2.23
428 468 5.248020 AGAAGATCATCTTGGTCAGTCAGTT 59.752 40.000 4.06 0.00 36.73 3.16
472 512 1.271054 CCCACCAACAGGAGAAGACTG 60.271 57.143 0.00 0.00 41.64 3.51
499 539 5.709164 AGAATTGCTTTGAGTGCTACTGAAT 59.291 36.000 0.00 0.00 0.00 2.57
911 985 8.088463 AGACCAGAACAGAGAGAATTATGATT 57.912 34.615 0.00 0.00 0.00 2.57
952 1026 7.857569 ACGGATAAACATATGGTTATGAAACG 58.142 34.615 26.90 23.91 37.99 3.60
963 1037 7.803189 GCAAGTGGAAATACGGATAAACATATG 59.197 37.037 0.00 0.00 0.00 1.78
1902 2043 6.985059 GCCCGACATTTAGTTCTAGTATCTTT 59.015 38.462 0.00 0.00 0.00 2.52
1945 2086 6.128445 CGTATTAGCATCACAATTCTCCCATC 60.128 42.308 0.00 0.00 0.00 3.51
1974 2115 9.342308 TCCTATATTTGTTCTTCATAAAGCCAG 57.658 33.333 0.00 0.00 32.18 4.85
2007 2148 6.983890 TCCAAATAAAGTTTCCTTTCAACAGC 59.016 34.615 0.00 0.00 41.18 4.40
2034 2175 4.911390 AGCACTACATAGTTTTCCAAGCT 58.089 39.130 0.00 0.00 33.46 3.74
2035 2176 4.095036 GGAGCACTACATAGTTTTCCAAGC 59.905 45.833 11.28 2.03 36.75 4.01
2118 2281 2.439507 GGGAGGTATCAGCAATCCTCAA 59.560 50.000 11.34 0.00 45.65 3.02
2467 2691 8.418597 AATGCAGCCAGATAATTTCATCTATT 57.581 30.769 0.00 0.00 33.41 1.73
2858 3118 1.327507 GCGTTCTTGAAATTGTCGGC 58.672 50.000 0.00 0.00 0.00 5.54
2908 3168 6.483640 AGAACTTTCAAGAACACAGATACACC 59.516 38.462 0.00 0.00 0.00 4.16
2977 3237 4.141251 ACCTGAACCAATCACCAAACTAGT 60.141 41.667 0.00 0.00 33.47 2.57
3000 3260 6.046593 CACCTGACCGTAGATGCTTTTATAA 58.953 40.000 0.00 0.00 0.00 0.98
3015 3276 1.966451 GGTTTGAGGCACCTGACCG 60.966 63.158 0.00 0.00 0.00 4.79
3018 3279 2.840753 GGGGGTTTGAGGCACCTGA 61.841 63.158 0.00 0.00 34.36 3.86
3019 3280 2.283173 GGGGGTTTGAGGCACCTG 60.283 66.667 0.00 0.00 34.36 4.00
3043 3304 3.316071 TTTTACCGGTTCGTGCTATCA 57.684 42.857 15.04 0.00 0.00 2.15
3068 3344 1.677637 GAGGGCCCGTCTAAGTCAGG 61.678 65.000 18.44 0.00 0.00 3.86
3070 3346 0.543410 TTGAGGGCCCGTCTAAGTCA 60.543 55.000 18.44 10.16 0.00 3.41
3072 3348 0.323957 GTTTGAGGGCCCGTCTAAGT 59.676 55.000 18.44 0.00 0.00 2.24
3074 3350 1.186917 TCGTTTGAGGGCCCGTCTAA 61.187 55.000 18.44 14.27 0.00 2.10
3075 3351 1.607178 TCGTTTGAGGGCCCGTCTA 60.607 57.895 18.44 8.69 0.00 2.59
3076 3352 2.920912 TCGTTTGAGGGCCCGTCT 60.921 61.111 18.44 0.00 0.00 4.18
3077 3353 2.741211 GTCGTTTGAGGGCCCGTC 60.741 66.667 18.44 15.04 0.00 4.79
3083 3361 4.016706 AGGCCGGTCGTTTGAGGG 62.017 66.667 1.90 0.00 0.00 4.30
3125 3403 2.177669 CCCATATCCACCCCAGATTTGT 59.822 50.000 0.00 0.00 0.00 2.83
3172 3455 1.579084 GAGGAGTCGCACGTCAGTCT 61.579 60.000 0.00 0.00 0.00 3.24
3190 3473 1.133363 TTTCGGAGTGTTTCCCTGGA 58.867 50.000 0.00 0.00 43.63 3.86
3192 3475 2.143925 GAGTTTCGGAGTGTTTCCCTG 58.856 52.381 0.00 0.00 43.63 4.45
3215 3498 3.760035 GAGACGAGCTTCGGGCCA 61.760 66.667 4.39 0.00 45.59 5.36
3218 3501 2.776913 GGAGGAGACGAGCTTCGGG 61.777 68.421 9.75 0.00 45.59 5.14
3228 3511 0.824182 ATCGGTCCATCGGAGGAGAC 60.824 60.000 0.00 0.00 38.64 3.36
3279 3570 2.963101 TGCCTTAAATAGCCGAGCTAGA 59.037 45.455 10.64 0.00 44.66 2.43
3300 3591 3.605664 GTTTTGGTGCCAGCGCCT 61.606 61.111 21.94 0.00 46.12 5.52
3302 3593 4.662961 GGGTTTTGGTGCCAGCGC 62.663 66.667 0.00 0.00 0.00 5.92
3343 3634 0.690762 GCAAAGTGGTGGTAGAGGGA 59.309 55.000 0.00 0.00 0.00 4.20
3349 3640 2.147958 GACGATTGCAAAGTGGTGGTA 58.852 47.619 14.44 0.00 0.00 3.25
3361 3655 0.669318 TGGAGTTGGACGACGATTGC 60.669 55.000 0.00 0.00 0.00 3.56
3368 3662 2.104111 AGTGAAATGTGGAGTTGGACGA 59.896 45.455 0.00 0.00 0.00 4.20
3406 3700 1.305219 TACTTGATTGCGGTGGCTGC 61.305 55.000 0.00 0.00 40.82 5.25
3408 3702 1.026718 GCTACTTGATTGCGGTGGCT 61.027 55.000 0.00 0.00 40.82 4.75
3471 3765 2.509336 CTACAACGGGCGCTCCAG 60.509 66.667 7.64 6.31 34.36 3.86
3559 3853 2.235602 CTCCTCCTGCTCCTCCTCCA 62.236 65.000 0.00 0.00 0.00 3.86
3560 3854 1.457455 CTCCTCCTGCTCCTCCTCC 60.457 68.421 0.00 0.00 0.00 4.30
3594 3903 4.838152 TTGCAGATCCGCGGCCTC 62.838 66.667 23.51 19.53 36.83 4.70
3595 3904 4.845580 CTTGCAGATCCGCGGCCT 62.846 66.667 23.51 17.38 36.83 5.19
3609 3918 1.071605 GTTGACTACTGCTCCGCTTG 58.928 55.000 0.00 0.00 0.00 4.01
3611 3920 1.592223 GGTTGACTACTGCTCCGCT 59.408 57.895 0.00 0.00 0.00 5.52
3615 3924 3.618690 ATCAAGGGTTGACTACTGCTC 57.381 47.619 0.00 0.00 43.48 4.26
3621 3930 2.844348 GGAGGGAATCAAGGGTTGACTA 59.156 50.000 0.00 0.00 43.48 2.59
3647 3956 2.359967 GGCCTTCACCTACGCCTCT 61.360 63.158 0.00 0.00 38.41 3.69
3648 3957 2.180159 TTGGCCTTCACCTACGCCTC 62.180 60.000 3.32 0.00 42.15 4.70
3654 3963 1.675219 GACGGTTGGCCTTCACCTA 59.325 57.895 3.32 0.00 33.63 3.08
3658 3967 0.108520 GATACGACGGTTGGCCTTCA 60.109 55.000 3.32 0.00 33.06 3.02
3679 3988 2.665000 CTTCCTGCTCCGCTTGGA 59.335 61.111 0.00 0.00 40.32 3.53
3680 3989 3.130160 GCTTCCTGCTCCGCTTGG 61.130 66.667 0.00 0.00 38.95 3.61
3681 3990 3.494336 CGCTTCCTGCTCCGCTTG 61.494 66.667 0.00 0.00 40.11 4.01
3682 3991 4.767255 CCGCTTCCTGCTCCGCTT 62.767 66.667 0.00 0.00 40.11 4.68
3686 3995 3.991536 GACGTCCGCTTCCTGCTCC 62.992 68.421 3.51 0.00 40.11 4.70
3687 3996 2.507324 GACGTCCGCTTCCTGCTC 60.507 66.667 3.51 0.00 40.11 4.26
3688 3997 4.421479 CGACGTCCGCTTCCTGCT 62.421 66.667 10.58 0.00 40.11 4.24
3689 3998 4.415332 TCGACGTCCGCTTCCTGC 62.415 66.667 10.58 0.00 38.37 4.85
3690 3999 2.504244 GTCGACGTCCGCTTCCTG 60.504 66.667 10.58 0.00 38.37 3.86
3691 4000 4.099170 CGTCGACGTCCGCTTCCT 62.099 66.667 29.08 0.00 38.37 3.36
3692 4001 3.996744 CTCGTCGACGTCCGCTTCC 62.997 68.421 34.40 0.00 40.80 3.46
3693 4002 2.307137 ATCTCGTCGACGTCCGCTTC 62.307 60.000 34.40 0.00 40.80 3.86
3694 4003 2.396955 ATCTCGTCGACGTCCGCTT 61.397 57.895 34.40 13.90 40.80 4.68
3695 4004 2.818714 ATCTCGTCGACGTCCGCT 60.819 61.111 34.40 14.91 40.80 5.52
3696 4005 2.648102 CATCTCGTCGACGTCCGC 60.648 66.667 34.40 1.76 40.80 5.54
3697 4006 2.579241 AAGCATCTCGTCGACGTCCG 62.579 60.000 34.40 23.61 40.80 4.79
3698 4007 1.134530 CAAGCATCTCGTCGACGTCC 61.135 60.000 34.40 19.37 40.80 4.79
3699 4008 1.734359 GCAAGCATCTCGTCGACGTC 61.734 60.000 34.40 19.56 40.80 4.34
3700 4009 1.801913 GCAAGCATCTCGTCGACGT 60.802 57.895 34.40 15.71 40.80 4.34
3701 4010 2.508891 GGCAAGCATCTCGTCGACG 61.509 63.158 31.30 31.30 41.45 5.12
3702 4011 0.100682 TAGGCAAGCATCTCGTCGAC 59.899 55.000 5.18 5.18 0.00 4.20
3703 4012 1.032794 ATAGGCAAGCATCTCGTCGA 58.967 50.000 0.00 0.00 0.00 4.20
3704 4013 2.706555 TATAGGCAAGCATCTCGTCG 57.293 50.000 0.00 0.00 0.00 5.12
3705 4014 3.056536 TCCATATAGGCAAGCATCTCGTC 60.057 47.826 0.00 0.00 37.29 4.20
3706 4015 2.899900 TCCATATAGGCAAGCATCTCGT 59.100 45.455 0.00 0.00 37.29 4.18
3707 4016 3.519579 CTCCATATAGGCAAGCATCTCG 58.480 50.000 0.00 0.00 37.29 4.04
3708 4017 3.517100 TCCTCCATATAGGCAAGCATCTC 59.483 47.826 0.00 0.00 36.51 2.75
3709 4018 3.518705 CTCCTCCATATAGGCAAGCATCT 59.481 47.826 0.00 0.00 36.51 2.90
3710 4019 3.871485 CTCCTCCATATAGGCAAGCATC 58.129 50.000 0.00 0.00 36.51 3.91
3711 4020 3.996921 CTCCTCCATATAGGCAAGCAT 57.003 47.619 0.00 0.00 36.51 3.79


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

AutoCloner maintained by Alex Coulton.