Multiple sequence alignment - TraesCS2B01G330700

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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 TraesCS2B01G330700 chr2B 100.000 3062 0 0 1 3062 474901402 474904463 0.000000e+00 5655
1 TraesCS2B01G330700 chr2B 95.696 395 15 2 2305 2698 180567453 180567060 4.310000e-178 634
2 TraesCS2B01G330700 chr2B 97.068 307 8 1 105 411 25364566 25364261 1.630000e-142 516
3 TraesCS2B01G330700 chr2B 96.220 291 10 1 2287 2577 223079643 223079932 2.760000e-130 475
4 TraesCS2B01G330700 chr2B 98.855 262 2 1 537 797 740132057 740132318 1.660000e-127 466
5 TraesCS2B01G330700 chr2B 96.341 164 5 1 4 167 637104107 637103945 5.030000e-68 268
6 TraesCS2B01G330700 chr2B 99.242 132 0 1 2737 2867 408512527 408512658 1.420000e-58 237
7 TraesCS2B01G330700 chr5D 97.226 2884 55 11 1 2867 503288375 503291250 0.000000e+00 4859
8 TraesCS2B01G330700 chr5D 96.317 2878 62 12 1 2867 6179872 6177028 0.000000e+00 4687
9 TraesCS2B01G330700 chr5D 96.939 196 6 0 2867 3062 503231891 503232086 2.280000e-86 329
10 TraesCS2B01G330700 chr5D 96.939 196 6 0 2867 3062 503241672 503241867 2.280000e-86 329
11 TraesCS2B01G330700 chr6D 97.156 2883 56 13 1 2867 45510497 45507625 0.000000e+00 4846
12 TraesCS2B01G330700 chr6D 96.939 196 6 0 2867 3062 389248770 389248965 2.280000e-86 329
13 TraesCS2B01G330700 chr1A 98.159 2227 32 5 1 2219 554459533 554461758 0.000000e+00 3877
14 TraesCS2B01G330700 chr1A 97.832 1199 23 2 1667 2864 554461753 554462949 0.000000e+00 2067
15 TraesCS2B01G330700 chr2D 98.152 2165 30 5 1 2155 9786208 9788372 0.000000e+00 3768
16 TraesCS2B01G330700 chr2D 97.287 1364 31 3 1501 2864 638423033 638424390 0.000000e+00 2309
17 TraesCS2B01G330700 chr4D 95.115 2313 109 3 558 2867 207070648 207068337 0.000000e+00 3642
18 TraesCS2B01G330700 chr4B 96.799 1937 54 5 1 1936 308682708 308680779 0.000000e+00 3227
19 TraesCS2B01G330700 chr1D 97.462 1773 43 1 1095 2867 254433152 254434922 0.000000e+00 3024
20 TraesCS2B01G330700 chr1D 97.020 1510 32 7 1 1500 51877001 51875495 0.000000e+00 2527
21 TraesCS2B01G330700 chr1D 96.939 196 6 0 2867 3062 144238749 144238944 2.280000e-86 329
22 TraesCS2B01G330700 chr5A 96.826 1670 39 7 4 1665 607199027 607197364 0.000000e+00 2778
23 TraesCS2B01G330700 chr3B 95.352 839 35 3 2003 2841 147679434 147678600 0.000000e+00 1330
24 TraesCS2B01G330700 chr3B 90.722 194 10 4 1 194 655009980 655010165 5.070000e-63 252
25 TraesCS2B01G330700 chr3B 99.248 133 1 0 459 591 817305693 817305561 1.100000e-59 241
26 TraesCS2B01G330700 chr3B 94.366 142 7 1 389 529 727508959 727508818 1.850000e-52 217
27 TraesCS2B01G330700 chr3B 98.077 104 2 0 2674 2777 513781006 513781109 6.740000e-42 182
28 TraesCS2B01G330700 chr3B 88.889 153 7 3 2173 2316 672387565 672387414 2.430000e-41 180
29 TraesCS2B01G330700 chrUn 96.939 196 6 0 2867 3062 398828189 398828384 2.280000e-86 329
30 TraesCS2B01G330700 chrUn 96.939 196 6 0 2867 3062 424750761 424750566 2.280000e-86 329
31 TraesCS2B01G330700 chrUn 96.429 196 7 0 2867 3062 216509723 216509528 1.060000e-84 324
32 TraesCS2B01G330700 chr3D 96.939 196 6 0 2867 3062 24148607 24148412 2.280000e-86 329
33 TraesCS2B01G330700 chr3A 96.939 196 6 0 2867 3062 66008736 66008541 2.280000e-86 329


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 TraesCS2B01G330700 chr2B 474901402 474904463 3061 False 5655 5655 100.0000 1 3062 1 chr2B.!!$F3 3061
1 TraesCS2B01G330700 chr5D 503288375 503291250 2875 False 4859 4859 97.2260 1 2867 1 chr5D.!!$F3 2866
2 TraesCS2B01G330700 chr5D 6177028 6179872 2844 True 4687 4687 96.3170 1 2867 1 chr5D.!!$R1 2866
3 TraesCS2B01G330700 chr6D 45507625 45510497 2872 True 4846 4846 97.1560 1 2867 1 chr6D.!!$R1 2866
4 TraesCS2B01G330700 chr1A 554459533 554462949 3416 False 2972 3877 97.9955 1 2864 2 chr1A.!!$F1 2863
5 TraesCS2B01G330700 chr2D 9786208 9788372 2164 False 3768 3768 98.1520 1 2155 1 chr2D.!!$F1 2154
6 TraesCS2B01G330700 chr2D 638423033 638424390 1357 False 2309 2309 97.2870 1501 2864 1 chr2D.!!$F2 1363
7 TraesCS2B01G330700 chr4D 207068337 207070648 2311 True 3642 3642 95.1150 558 2867 1 chr4D.!!$R1 2309
8 TraesCS2B01G330700 chr4B 308680779 308682708 1929 True 3227 3227 96.7990 1 1936 1 chr4B.!!$R1 1935
9 TraesCS2B01G330700 chr1D 254433152 254434922 1770 False 3024 3024 97.4620 1095 2867 1 chr1D.!!$F2 1772
10 TraesCS2B01G330700 chr1D 51875495 51877001 1506 True 2527 2527 97.0200 1 1500 1 chr1D.!!$R1 1499
11 TraesCS2B01G330700 chr5A 607197364 607199027 1663 True 2778 2778 96.8260 4 1665 1 chr5A.!!$R1 1661
12 TraesCS2B01G330700 chr3B 147678600 147679434 834 True 1330 1330 95.3520 2003 2841 1 chr3B.!!$R1 838

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
900 963 4.644498 ACCATTGAAAAAGGGCATTGAAG 58.356 39.13 0.0 0.0 39.47 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2197 2807 0.532862 ATAGGTTCATTGCTCCGGCG 60.533 55.0 0.0 0.0 42.25 6.46 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
900 963 4.644498 ACCATTGAAAAAGGGCATTGAAG 58.356 39.130 0.00 0.00 39.47 3.02
1084 1147 1.001293 GGTTACGAAGGGACCGTTTCT 59.999 52.381 0.03 0.00 40.95 2.52
1326 1389 3.764237 ACTCGTTGGTGTCAATTAGGT 57.236 42.857 0.00 0.00 35.10 3.08
1635 1698 1.043116 TAGGTGCGGCTCTGCTATGT 61.043 55.000 0.00 0.00 35.36 2.29
1833 2443 3.906720 ATGCTATTTGTACCCGTCACT 57.093 42.857 0.00 0.00 0.00 3.41
1913 2523 3.895041 GACTTTGTTTCCCAGGAAATCCA 59.105 43.478 14.68 6.74 44.52 3.41
2071 2681 6.487331 TGGAAACGCTCTTTAATGGAACTTTA 59.513 34.615 0.00 0.00 0.00 1.85
2143 2753 7.471819 GCTGGGAATGCCAGAATTATCAATTTA 60.472 37.037 25.31 0.00 37.47 1.40
2146 2756 7.756722 GGGAATGCCAGAATTATCAATTTATCG 59.243 37.037 0.00 0.00 35.15 2.92
2148 2758 8.408043 AATGCCAGAATTATCAATTTATCGGA 57.592 30.769 0.00 0.00 0.00 4.55
2197 2807 3.064207 TGCCGGATTAATCGTATTCTGC 58.936 45.455 5.05 4.19 0.00 4.26
2219 2829 2.427095 GCCGGAGCAATGAACCTATTTT 59.573 45.455 5.05 0.00 39.53 1.82
2352 2964 6.105397 ACTTTTCCGTACTTTGTATCTGGA 57.895 37.500 0.00 0.00 0.00 3.86
2353 2965 6.527423 ACTTTTCCGTACTTTGTATCTGGAA 58.473 36.000 0.00 0.00 32.52 3.53
2374 2986 6.216662 TGGAATACTTCACCTAATTTCCTCCA 59.783 38.462 0.00 0.00 0.00 3.86
2375 2987 7.091993 TGGAATACTTCACCTAATTTCCTCCAT 60.092 37.037 0.00 0.00 0.00 3.41
2530 3142 5.305585 TGTTAGGTCTAGGTGCTTTTCTTG 58.694 41.667 0.00 0.00 0.00 3.02
2628 3246 3.141272 ACCAATTTGACCCTTAGTCCCAA 59.859 43.478 0.00 0.00 45.68 4.12
2867 3489 5.803020 ATCTGTCTTTGGTTTTATCGCTC 57.197 39.130 0.00 0.00 0.00 5.03
2868 3490 4.894784 TCTGTCTTTGGTTTTATCGCTCT 58.105 39.130 0.00 0.00 0.00 4.09
2869 3491 6.032956 TCTGTCTTTGGTTTTATCGCTCTA 57.967 37.500 0.00 0.00 0.00 2.43
2870 3492 6.100004 TCTGTCTTTGGTTTTATCGCTCTAG 58.900 40.000 0.00 0.00 0.00 2.43
2871 3493 6.032956 TGTCTTTGGTTTTATCGCTCTAGA 57.967 37.500 0.00 0.00 0.00 2.43
2872 3494 6.640518 TGTCTTTGGTTTTATCGCTCTAGAT 58.359 36.000 0.00 0.00 34.79 1.98
2873 3495 7.778083 TGTCTTTGGTTTTATCGCTCTAGATA 58.222 34.615 0.00 0.00 32.39 1.98
2874 3496 8.421784 TGTCTTTGGTTTTATCGCTCTAGATAT 58.578 33.333 0.00 0.00 33.60 1.63
2875 3497 8.917655 GTCTTTGGTTTTATCGCTCTAGATATC 58.082 37.037 0.00 0.00 33.60 1.63
2876 3498 8.861086 TCTTTGGTTTTATCGCTCTAGATATCT 58.139 33.333 10.73 10.73 33.60 1.98
2924 3546 9.726438 TTAGTAGTACTATTAGTTACCGATCCC 57.274 37.037 10.82 0.00 29.64 3.85
2925 3547 6.876257 AGTAGTACTATTAGTTACCGATCCCG 59.124 42.308 5.75 0.00 0.00 5.14
2935 3557 2.415010 CGATCCCGGCTCTGTGAG 59.585 66.667 0.00 0.00 0.00 3.51
2936 3558 2.418910 CGATCCCGGCTCTGTGAGT 61.419 63.158 0.00 0.00 31.39 3.41
2937 3559 1.901085 GATCCCGGCTCTGTGAGTT 59.099 57.895 0.00 0.00 31.39 3.01
2938 3560 0.179097 GATCCCGGCTCTGTGAGTTC 60.179 60.000 0.00 0.00 31.39 3.01
2939 3561 0.616111 ATCCCGGCTCTGTGAGTTCT 60.616 55.000 0.00 0.00 31.39 3.01
2940 3562 0.832135 TCCCGGCTCTGTGAGTTCTT 60.832 55.000 0.00 0.00 31.39 2.52
2941 3563 0.035458 CCCGGCTCTGTGAGTTCTTT 59.965 55.000 0.00 0.00 31.39 2.52
2942 3564 1.433534 CCGGCTCTGTGAGTTCTTTC 58.566 55.000 0.00 0.00 31.39 2.62
2943 3565 1.001406 CCGGCTCTGTGAGTTCTTTCT 59.999 52.381 0.00 0.00 31.39 2.52
2944 3566 2.548920 CCGGCTCTGTGAGTTCTTTCTT 60.549 50.000 0.00 0.00 31.39 2.52
2945 3567 2.734079 CGGCTCTGTGAGTTCTTTCTTC 59.266 50.000 0.00 0.00 31.39 2.87
2946 3568 3.070748 GGCTCTGTGAGTTCTTTCTTCC 58.929 50.000 0.00 0.00 31.39 3.46
2947 3569 2.734079 GCTCTGTGAGTTCTTTCTTCCG 59.266 50.000 0.00 0.00 31.39 4.30
2948 3570 3.800604 GCTCTGTGAGTTCTTTCTTCCGT 60.801 47.826 0.00 0.00 31.39 4.69
2949 3571 3.717707 TCTGTGAGTTCTTTCTTCCGTG 58.282 45.455 0.00 0.00 0.00 4.94
2950 3572 3.383505 TCTGTGAGTTCTTTCTTCCGTGA 59.616 43.478 0.00 0.00 0.00 4.35
2951 3573 4.039245 TCTGTGAGTTCTTTCTTCCGTGAT 59.961 41.667 0.00 0.00 0.00 3.06
2952 3574 4.058124 TGTGAGTTCTTTCTTCCGTGATG 58.942 43.478 0.00 0.00 0.00 3.07
2953 3575 4.202212 TGTGAGTTCTTTCTTCCGTGATGA 60.202 41.667 0.00 0.00 0.00 2.92
2954 3576 4.750098 GTGAGTTCTTTCTTCCGTGATGAA 59.250 41.667 0.00 0.00 0.00 2.57
2955 3577 4.750098 TGAGTTCTTTCTTCCGTGATGAAC 59.250 41.667 0.00 0.00 33.84 3.18
2956 3578 4.962155 AGTTCTTTCTTCCGTGATGAACT 58.038 39.130 0.00 0.00 36.40 3.01
2957 3579 4.752101 AGTTCTTTCTTCCGTGATGAACTG 59.248 41.667 0.00 6.77 37.99 3.16
2958 3580 4.336889 TCTTTCTTCCGTGATGAACTGT 57.663 40.909 2.98 0.00 0.00 3.55
2959 3581 4.307432 TCTTTCTTCCGTGATGAACTGTC 58.693 43.478 2.98 0.00 0.00 3.51
2960 3582 2.347697 TCTTCCGTGATGAACTGTCG 57.652 50.000 0.00 0.00 0.00 4.35
2961 3583 1.067846 TCTTCCGTGATGAACTGTCGG 60.068 52.381 0.00 0.00 42.12 4.79
2962 3584 0.669318 TTCCGTGATGAACTGTCGGC 60.669 55.000 0.00 0.00 40.81 5.54
2963 3585 1.374125 CCGTGATGAACTGTCGGCA 60.374 57.895 0.00 0.00 35.01 5.69
2964 3586 1.626654 CCGTGATGAACTGTCGGCAC 61.627 60.000 0.00 0.00 35.01 5.01
2965 3587 1.626654 CGTGATGAACTGTCGGCACC 61.627 60.000 0.00 0.00 30.67 5.01
2966 3588 1.003839 TGATGAACTGTCGGCACCC 60.004 57.895 0.00 0.00 0.00 4.61
2976 3598 2.046314 CGGCACCCGTCCTTCATT 60.046 61.111 0.00 0.00 42.73 2.57
2977 3599 1.674322 CGGCACCCGTCCTTCATTT 60.674 57.895 0.00 0.00 42.73 2.32
2978 3600 1.241315 CGGCACCCGTCCTTCATTTT 61.241 55.000 0.00 0.00 42.73 1.82
2979 3601 0.966179 GGCACCCGTCCTTCATTTTT 59.034 50.000 0.00 0.00 0.00 1.94
2998 3620 3.876274 TTTTCTCTGTGGATCGAGGAG 57.124 47.619 0.00 2.57 0.00 3.69
2999 3621 2.808906 TTCTCTGTGGATCGAGGAGA 57.191 50.000 6.34 6.34 0.00 3.71
3000 3622 2.808906 TCTCTGTGGATCGAGGAGAA 57.191 50.000 7.53 0.00 31.28 2.87
3001 3623 3.087370 TCTCTGTGGATCGAGGAGAAA 57.913 47.619 7.53 0.00 31.28 2.52
3002 3624 3.020274 TCTCTGTGGATCGAGGAGAAAG 58.980 50.000 7.53 0.00 31.28 2.62
3003 3625 2.100584 CTCTGTGGATCGAGGAGAAAGG 59.899 54.545 0.00 0.00 0.00 3.11
3004 3626 1.137872 CTGTGGATCGAGGAGAAAGGG 59.862 57.143 0.00 0.00 0.00 3.95
3005 3627 0.466124 GTGGATCGAGGAGAAAGGGG 59.534 60.000 0.00 0.00 0.00 4.79
3006 3628 0.691078 TGGATCGAGGAGAAAGGGGG 60.691 60.000 0.00 0.00 0.00 5.40
3007 3629 1.448069 GATCGAGGAGAAAGGGGGC 59.552 63.158 0.00 0.00 0.00 5.80
3008 3630 1.003573 ATCGAGGAGAAAGGGGGCT 59.996 57.895 0.00 0.00 0.00 5.19
3009 3631 1.051556 ATCGAGGAGAAAGGGGGCTC 61.052 60.000 0.00 0.00 0.00 4.70
3012 3634 4.491409 GGAGAAAGGGGGCTCCGC 62.491 72.222 0.00 0.00 41.10 5.54
3013 3635 3.717294 GAGAAAGGGGGCTCCGCA 61.717 66.667 0.00 0.00 41.52 5.69
3014 3636 3.689002 GAGAAAGGGGGCTCCGCAG 62.689 68.421 0.00 0.00 41.52 5.18
3030 3652 2.432444 CGCAGGAAAAGGATTGTACCA 58.568 47.619 0.00 0.00 0.00 3.25
3031 3653 3.016736 CGCAGGAAAAGGATTGTACCAT 58.983 45.455 0.00 0.00 0.00 3.55
3032 3654 3.181497 CGCAGGAAAAGGATTGTACCATG 60.181 47.826 0.00 0.00 0.00 3.66
3033 3655 4.016444 GCAGGAAAAGGATTGTACCATGA 58.984 43.478 0.00 0.00 0.00 3.07
3034 3656 4.096984 GCAGGAAAAGGATTGTACCATGAG 59.903 45.833 0.00 0.00 0.00 2.90
3035 3657 5.500234 CAGGAAAAGGATTGTACCATGAGA 58.500 41.667 0.00 0.00 0.00 3.27
3036 3658 5.587844 CAGGAAAAGGATTGTACCATGAGAG 59.412 44.000 0.00 0.00 0.00 3.20
3037 3659 5.488919 AGGAAAAGGATTGTACCATGAGAGA 59.511 40.000 0.00 0.00 0.00 3.10
3038 3660 6.012508 AGGAAAAGGATTGTACCATGAGAGAA 60.013 38.462 0.00 0.00 0.00 2.87
3039 3661 6.317391 GGAAAAGGATTGTACCATGAGAGAAG 59.683 42.308 0.00 0.00 0.00 2.85
3040 3662 4.414337 AGGATTGTACCATGAGAGAAGC 57.586 45.455 0.00 0.00 0.00 3.86
3041 3663 3.776969 AGGATTGTACCATGAGAGAAGCA 59.223 43.478 0.00 0.00 0.00 3.91
3042 3664 3.873952 GGATTGTACCATGAGAGAAGCAC 59.126 47.826 0.00 0.00 0.00 4.40
3043 3665 4.507710 GATTGTACCATGAGAGAAGCACA 58.492 43.478 0.00 0.00 0.00 4.57
3044 3666 3.599730 TGTACCATGAGAGAAGCACAG 57.400 47.619 0.00 0.00 0.00 3.66
3045 3667 3.165071 TGTACCATGAGAGAAGCACAGA 58.835 45.455 0.00 0.00 0.00 3.41
3046 3668 3.194329 TGTACCATGAGAGAAGCACAGAG 59.806 47.826 0.00 0.00 0.00 3.35
3047 3669 2.255406 ACCATGAGAGAAGCACAGAGT 58.745 47.619 0.00 0.00 0.00 3.24
3048 3670 2.636893 ACCATGAGAGAAGCACAGAGTT 59.363 45.455 0.00 0.00 0.00 3.01
3049 3671 3.260740 CCATGAGAGAAGCACAGAGTTC 58.739 50.000 0.00 0.00 0.00 3.01
3050 3672 3.306571 CCATGAGAGAAGCACAGAGTTCA 60.307 47.826 0.00 0.00 0.00 3.18
3051 3673 4.313282 CATGAGAGAAGCACAGAGTTCAA 58.687 43.478 0.00 0.00 0.00 2.69
3052 3674 3.722147 TGAGAGAAGCACAGAGTTCAAC 58.278 45.455 0.00 0.00 0.00 3.18
3053 3675 3.063485 GAGAGAAGCACAGAGTTCAACC 58.937 50.000 0.00 0.00 0.00 3.77
3054 3676 2.147150 GAGAAGCACAGAGTTCAACCC 58.853 52.381 0.00 0.00 0.00 4.11
3055 3677 0.868406 GAAGCACAGAGTTCAACCCG 59.132 55.000 0.00 0.00 0.00 5.28
3056 3678 1.166531 AAGCACAGAGTTCAACCCGC 61.167 55.000 0.00 0.00 0.00 6.13
3057 3679 1.598130 GCACAGAGTTCAACCCGCT 60.598 57.895 0.00 0.00 0.00 5.52
3058 3680 1.166531 GCACAGAGTTCAACCCGCTT 61.167 55.000 0.00 0.00 0.00 4.68
3059 3681 0.868406 CACAGAGTTCAACCCGCTTC 59.132 55.000 0.00 0.00 0.00 3.86
3060 3682 0.468226 ACAGAGTTCAACCCGCTTCA 59.532 50.000 0.00 0.00 0.00 3.02
3061 3683 1.134220 ACAGAGTTCAACCCGCTTCAA 60.134 47.619 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
792 849 9.532697 CCATGAATTTGATTCGATTTGTTTTTC 57.467 29.630 0.00 0.00 42.15 2.29
793 850 9.270640 TCCATGAATTTGATTCGATTTGTTTTT 57.729 25.926 0.00 0.00 42.15 1.94
794 851 8.830201 TCCATGAATTTGATTCGATTTGTTTT 57.170 26.923 0.00 0.00 42.15 2.43
795 852 9.439500 AATCCATGAATTTGATTCGATTTGTTT 57.561 25.926 0.00 0.00 42.15 2.83
796 853 9.439500 AAATCCATGAATTTGATTCGATTTGTT 57.561 25.926 0.00 0.00 42.15 2.83
799 856 9.533253 GGTAAATCCATGAATTTGATTCGATTT 57.467 29.630 0.00 13.98 38.80 2.17
800 857 8.694540 TGGTAAATCCATGAATTTGATTCGATT 58.305 29.630 0.00 0.00 41.93 3.34
801 858 8.236585 TGGTAAATCCATGAATTTGATTCGAT 57.763 30.769 0.00 0.00 41.93 3.59
802 859 7.637631 TGGTAAATCCATGAATTTGATTCGA 57.362 32.000 0.00 0.00 41.93 3.71
900 963 3.926616 TCTGTGGACGATTTCTTTCTCC 58.073 45.455 0.00 0.00 0.00 3.71
1326 1389 4.777896 AGAGCTACAAAAGTCCATAGACCA 59.222 41.667 0.00 0.00 44.72 4.02
1486 1549 0.105246 AACCAACCAGATTGCCCCAA 60.105 50.000 0.00 0.00 36.93 4.12
1635 1698 0.249447 CGGTCGCTCCATGAATAGCA 60.249 55.000 12.98 0.00 38.70 3.49
1833 2443 5.132502 CCAATAGCACTCATCCATAAACCA 58.867 41.667 0.00 0.00 0.00 3.67
1913 2523 0.543277 TTCAGGATCTTCCGCTGCAT 59.457 50.000 0.00 0.00 42.75 3.96
1960 2570 5.048573 ACGCACGAATACCCTTGTTTAAAAT 60.049 36.000 0.00 0.00 0.00 1.82
1969 2579 0.539986 ATCCACGCACGAATACCCTT 59.460 50.000 0.00 0.00 0.00 3.95
2143 2753 6.978674 TGAGATCCAAGTAGTTTATCCGAT 57.021 37.500 0.00 0.00 0.00 4.18
2146 2756 7.600752 GCTACATGAGATCCAAGTAGTTTATCC 59.399 40.741 19.00 6.35 44.56 2.59
2148 2758 7.445945 GGCTACATGAGATCCAAGTAGTTTAT 58.554 38.462 19.00 0.00 44.56 1.40
2197 2807 0.532862 ATAGGTTCATTGCTCCGGCG 60.533 55.000 0.00 0.00 42.25 6.46
2219 2829 1.629353 TGGTACGAAATGGGCCACTTA 59.371 47.619 9.28 0.00 0.00 2.24
2352 2964 9.004231 ACTATGGAGGAAATTAGGTGAAGTATT 57.996 33.333 0.00 0.00 0.00 1.89
2353 2965 8.568617 ACTATGGAGGAAATTAGGTGAAGTAT 57.431 34.615 0.00 0.00 0.00 2.12
2374 2986 1.413077 GCCACCGAAGCCTAAGACTAT 59.587 52.381 0.00 0.00 0.00 2.12
2375 2987 0.822164 GCCACCGAAGCCTAAGACTA 59.178 55.000 0.00 0.00 0.00 2.59
2530 3142 8.613482 GCCAAAATAAAGATCCTTGAGTACTAC 58.387 37.037 0.00 0.00 0.00 2.73
2898 3520 9.726438 GGGATCGGTAACTAATAGTACTACTAA 57.274 37.037 4.31 0.00 33.89 2.24
2899 3521 8.035394 CGGGATCGGTAACTAATAGTACTACTA 58.965 40.741 4.31 0.00 34.82 1.82
2900 3522 6.876257 CGGGATCGGTAACTAATAGTACTACT 59.124 42.308 4.31 0.00 0.00 2.57
2901 3523 7.066374 CGGGATCGGTAACTAATAGTACTAC 57.934 44.000 4.31 0.00 0.00 2.73
2918 3540 1.949847 AACTCACAGAGCCGGGATCG 61.950 60.000 6.65 4.70 32.04 3.69
2919 3541 0.179097 GAACTCACAGAGCCGGGATC 60.179 60.000 3.56 3.56 32.04 3.36
2920 3542 0.616111 AGAACTCACAGAGCCGGGAT 60.616 55.000 2.18 0.00 32.04 3.85
2921 3543 0.832135 AAGAACTCACAGAGCCGGGA 60.832 55.000 2.18 0.00 32.04 5.14
2922 3544 0.035458 AAAGAACTCACAGAGCCGGG 59.965 55.000 2.18 0.00 32.04 5.73
2923 3545 1.001406 AGAAAGAACTCACAGAGCCGG 59.999 52.381 0.00 0.00 32.04 6.13
2924 3546 2.447244 AGAAAGAACTCACAGAGCCG 57.553 50.000 0.00 0.00 32.04 5.52
2925 3547 3.070748 GGAAGAAAGAACTCACAGAGCC 58.929 50.000 0.00 0.00 32.04 4.70
2926 3548 2.734079 CGGAAGAAAGAACTCACAGAGC 59.266 50.000 0.00 0.00 32.04 4.09
2927 3549 3.738282 CACGGAAGAAAGAACTCACAGAG 59.262 47.826 0.00 0.00 35.52 3.35
2928 3550 3.383505 TCACGGAAGAAAGAACTCACAGA 59.616 43.478 0.00 0.00 0.00 3.41
2929 3551 3.717707 TCACGGAAGAAAGAACTCACAG 58.282 45.455 0.00 0.00 0.00 3.66
2930 3552 3.812156 TCACGGAAGAAAGAACTCACA 57.188 42.857 0.00 0.00 0.00 3.58
2931 3553 4.307432 TCATCACGGAAGAAAGAACTCAC 58.693 43.478 0.00 0.00 0.00 3.51
2932 3554 4.600692 TCATCACGGAAGAAAGAACTCA 57.399 40.909 0.00 0.00 0.00 3.41
2933 3555 4.991687 AGTTCATCACGGAAGAAAGAACTC 59.008 41.667 14.30 0.00 40.12 3.01
2934 3556 4.752101 CAGTTCATCACGGAAGAAAGAACT 59.248 41.667 14.30 14.30 42.51 3.01
2935 3557 4.511826 ACAGTTCATCACGGAAGAAAGAAC 59.488 41.667 0.00 0.00 37.11 3.01
2936 3558 4.703897 ACAGTTCATCACGGAAGAAAGAA 58.296 39.130 0.00 0.00 0.00 2.52
2937 3559 4.307432 GACAGTTCATCACGGAAGAAAGA 58.693 43.478 0.00 0.00 0.00 2.52
2938 3560 3.121944 CGACAGTTCATCACGGAAGAAAG 59.878 47.826 0.00 0.00 0.00 2.62
2939 3561 3.057019 CGACAGTTCATCACGGAAGAAA 58.943 45.455 0.00 0.00 0.00 2.52
2940 3562 2.609491 CCGACAGTTCATCACGGAAGAA 60.609 50.000 0.00 0.00 45.31 2.52
2941 3563 1.067846 CCGACAGTTCATCACGGAAGA 60.068 52.381 0.00 0.00 45.31 2.87
2942 3564 1.350193 CCGACAGTTCATCACGGAAG 58.650 55.000 0.00 0.00 45.31 3.46
2943 3565 0.669318 GCCGACAGTTCATCACGGAA 60.669 55.000 0.00 0.00 45.31 4.30
2944 3566 1.080093 GCCGACAGTTCATCACGGA 60.080 57.895 0.00 0.00 45.31 4.69
2945 3567 1.374125 TGCCGACAGTTCATCACGG 60.374 57.895 0.00 0.00 45.26 4.94
2946 3568 1.626654 GGTGCCGACAGTTCATCACG 61.627 60.000 0.00 0.00 0.00 4.35
2947 3569 1.298859 GGGTGCCGACAGTTCATCAC 61.299 60.000 0.00 0.00 0.00 3.06
2948 3570 1.003839 GGGTGCCGACAGTTCATCA 60.004 57.895 0.00 0.00 0.00 3.07
2949 3571 3.890674 GGGTGCCGACAGTTCATC 58.109 61.111 0.00 0.00 0.00 2.92
2960 3582 0.966179 AAAAATGAAGGACGGGTGCC 59.034 50.000 0.00 0.00 0.00 5.01
2977 3599 3.832490 TCTCCTCGATCCACAGAGAAAAA 59.168 43.478 0.00 0.00 36.65 1.94
2978 3600 3.431415 TCTCCTCGATCCACAGAGAAAA 58.569 45.455 0.00 0.00 36.65 2.29
2979 3601 3.087370 TCTCCTCGATCCACAGAGAAA 57.913 47.619 0.00 0.00 36.65 2.52
2980 3602 2.808906 TCTCCTCGATCCACAGAGAA 57.191 50.000 0.00 0.00 36.65 2.87
2981 3603 2.808906 TTCTCCTCGATCCACAGAGA 57.191 50.000 0.00 0.00 36.65 3.10
2982 3604 2.100584 CCTTTCTCCTCGATCCACAGAG 59.899 54.545 0.00 0.00 0.00 3.35
2983 3605 2.103373 CCTTTCTCCTCGATCCACAGA 58.897 52.381 0.00 0.00 0.00 3.41
2984 3606 1.137872 CCCTTTCTCCTCGATCCACAG 59.862 57.143 0.00 0.00 0.00 3.66
2985 3607 1.195115 CCCTTTCTCCTCGATCCACA 58.805 55.000 0.00 0.00 0.00 4.17
2986 3608 0.466124 CCCCTTTCTCCTCGATCCAC 59.534 60.000 0.00 0.00 0.00 4.02
2987 3609 0.691078 CCCCCTTTCTCCTCGATCCA 60.691 60.000 0.00 0.00 0.00 3.41
2988 3610 2.046009 GCCCCCTTTCTCCTCGATCC 62.046 65.000 0.00 0.00 0.00 3.36
2989 3611 1.051556 AGCCCCCTTTCTCCTCGATC 61.052 60.000 0.00 0.00 0.00 3.69
2990 3612 1.003573 AGCCCCCTTTCTCCTCGAT 59.996 57.895 0.00 0.00 0.00 3.59
2991 3613 1.686110 GAGCCCCCTTTCTCCTCGA 60.686 63.158 0.00 0.00 0.00 4.04
2992 3614 2.736826 GGAGCCCCCTTTCTCCTCG 61.737 68.421 1.30 0.00 44.19 4.63
2993 3615 2.736826 CGGAGCCCCCTTTCTCCTC 61.737 68.421 6.70 0.00 45.12 3.71
2994 3616 2.689034 CGGAGCCCCCTTTCTCCT 60.689 66.667 6.70 0.00 45.12 3.69
3007 3629 1.826385 ACAATCCTTTTCCTGCGGAG 58.174 50.000 0.00 0.00 31.21 4.63
3008 3630 2.617021 GGTACAATCCTTTTCCTGCGGA 60.617 50.000 0.00 0.00 0.00 5.54
3009 3631 1.743394 GGTACAATCCTTTTCCTGCGG 59.257 52.381 0.00 0.00 0.00 5.69
3010 3632 2.432444 TGGTACAATCCTTTTCCTGCG 58.568 47.619 0.00 0.00 31.92 5.18
3025 3647 3.194542 ACTCTGTGCTTCTCTCATGGTAC 59.805 47.826 0.00 0.00 0.00 3.34
3026 3648 3.435275 ACTCTGTGCTTCTCTCATGGTA 58.565 45.455 0.00 0.00 0.00 3.25
3027 3649 2.255406 ACTCTGTGCTTCTCTCATGGT 58.745 47.619 0.00 0.00 0.00 3.55
3028 3650 3.260740 GAACTCTGTGCTTCTCTCATGG 58.739 50.000 0.00 0.00 0.00 3.66
3029 3651 3.922910 TGAACTCTGTGCTTCTCTCATG 58.077 45.455 0.00 0.00 0.00 3.07
3030 3652 4.314121 GTTGAACTCTGTGCTTCTCTCAT 58.686 43.478 0.00 0.00 0.00 2.90
3031 3653 3.493350 GGTTGAACTCTGTGCTTCTCTCA 60.493 47.826 0.00 0.00 0.00 3.27
3032 3654 3.063485 GGTTGAACTCTGTGCTTCTCTC 58.937 50.000 0.00 0.00 0.00 3.20
3033 3655 2.224402 GGGTTGAACTCTGTGCTTCTCT 60.224 50.000 0.00 0.00 0.00 3.10
3034 3656 2.147150 GGGTTGAACTCTGTGCTTCTC 58.853 52.381 0.00 0.00 0.00 2.87
3035 3657 1.541233 CGGGTTGAACTCTGTGCTTCT 60.541 52.381 0.00 0.00 0.00 2.85
3036 3658 0.868406 CGGGTTGAACTCTGTGCTTC 59.132 55.000 0.00 0.00 0.00 3.86
3037 3659 1.166531 GCGGGTTGAACTCTGTGCTT 61.167 55.000 0.00 0.00 0.00 3.91
3038 3660 1.598130 GCGGGTTGAACTCTGTGCT 60.598 57.895 0.00 0.00 0.00 4.40
3039 3661 1.166531 AAGCGGGTTGAACTCTGTGC 61.167 55.000 0.00 0.00 0.00 4.57
3040 3662 0.868406 GAAGCGGGTTGAACTCTGTG 59.132 55.000 0.00 0.00 0.00 3.66
3041 3663 0.468226 TGAAGCGGGTTGAACTCTGT 59.532 50.000 0.00 0.00 0.00 3.41
3042 3664 1.593196 TTGAAGCGGGTTGAACTCTG 58.407 50.000 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.