Multiple sequence alignment - TraesCS1A01G279200

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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 TraesCS1A01G279200 chr1A 100.000 3935 0 0 1 3935 474790653 474794587 0.000000e+00 7267
1 TraesCS1A01G279200 chr1A 92.847 1384 96 3 1308 2690 59211692 59210311 0.000000e+00 2004
2 TraesCS1A01G279200 chr1A 92.135 89 7 0 3655 3743 59211684 59211772 4.130000e-25 126
3 TraesCS1A01G279200 chr1D 91.948 3254 165 42 1 3188 375988700 375991922 0.000000e+00 4468
4 TraesCS1A01G279200 chr1D 84.728 681 47 28 3283 3933 375992031 375992684 2.580000e-176 628
5 TraesCS1A01G279200 chr1B 90.694 2869 122 52 899 3647 502217887 502220730 0.000000e+00 3685
6 TraesCS1A01G279200 chr1B 90.000 290 19 5 3646 3935 502220777 502221056 2.230000e-97 366
7 TraesCS1A01G279200 chr1B 95.000 140 6 1 748 886 502217185 502217324 6.620000e-53 219
8 TraesCS1A01G279200 chr5D 92.581 1887 114 12 1308 3188 42725376 42727242 0.000000e+00 2686
9 TraesCS1A01G279200 chr5D 92.475 1887 101 17 1308 3188 249912085 249913936 0.000000e+00 2660
10 TraesCS1A01G279200 chr5D 93.252 163 11 0 1312 1474 42727402 42727240 1.410000e-59 241
11 TraesCS1A01G279200 chr5D 91.667 168 13 1 1308 1474 249914101 249913934 8.500000e-57 231
12 TraesCS1A01G279200 chr5D 92.771 83 6 0 3661 3743 249912087 249912005 1.920000e-23 121
13 TraesCS1A01G279200 chr5D 89.130 92 10 0 3652 3743 249914090 249914181 8.940000e-22 115
14 TraesCS1A01G279200 chr5D 91.358 81 6 1 3661 3741 42725378 42725299 4.160000e-20 110
15 TraesCS1A01G279200 chr2D 91.711 1894 106 22 1308 3188 185365795 185367650 0.000000e+00 2580
16 TraesCS1A01G279200 chr2D 93.258 89 6 0 3655 3743 185369069 185369157 8.870000e-27 132
17 TraesCS1A01G279200 chr2D 93.976 83 5 0 3661 3743 185365797 185365715 4.130000e-25 126
18 TraesCS1A01G279200 chr2A 91.376 1890 124 16 1306 3188 768058800 768060657 0.000000e+00 2551
19 TraesCS1A01G279200 chr2A 92.135 89 7 0 3655 3743 768060813 768060901 4.130000e-25 126
20 TraesCS1A01G279200 chr3B 76.014 2047 336 89 1001 2935 629195163 629193160 0.000000e+00 917
21 TraesCS1A01G279200 chr3A 76.390 1889 301 92 998 2785 615938603 615940447 0.000000e+00 883
22 TraesCS1A01G279200 chr3D 76.047 1027 190 40 1934 2935 473483324 473484319 2.130000e-132 483


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 TraesCS1A01G279200 chr1A 474790653 474794587 3934 False 7267.000000 7267 100.0000 1 3935 1 chr1A.!!$F2 3934
1 TraesCS1A01G279200 chr1A 59210311 59211692 1381 True 2004.000000 2004 92.8470 1308 2690 1 chr1A.!!$R1 1382
2 TraesCS1A01G279200 chr1D 375988700 375992684 3984 False 2548.000000 4468 88.3380 1 3933 2 chr1D.!!$F1 3932
3 TraesCS1A01G279200 chr1B 502217185 502221056 3871 False 1423.333333 3685 91.8980 748 3935 3 chr1B.!!$F1 3187
4 TraesCS1A01G279200 chr5D 42725376 42727242 1866 False 2686.000000 2686 92.5810 1308 3188 1 chr5D.!!$F1 1880
5 TraesCS1A01G279200 chr5D 249912085 249914181 2096 False 1387.500000 2660 90.8025 1308 3743 2 chr5D.!!$F2 2435
6 TraesCS1A01G279200 chr2D 185365795 185369157 3362 False 1356.000000 2580 92.4845 1308 3743 2 chr2D.!!$F1 2435
7 TraesCS1A01G279200 chr2A 768058800 768060901 2101 False 1338.500000 2551 91.7555 1306 3743 2 chr2A.!!$F1 2437
8 TraesCS1A01G279200 chr3B 629193160 629195163 2003 True 917.000000 917 76.0140 1001 2935 1 chr3B.!!$R1 1934
9 TraesCS1A01G279200 chr3A 615938603 615940447 1844 False 883.000000 883 76.3900 998 2785 1 chr3A.!!$F1 1787
10 TraesCS1A01G279200 chr3D 473483324 473484319 995 False 483.000000 483 76.0470 1934 2935 1 chr3D.!!$F1 1001

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
177 178 0.659957 TTTGTTGCGGGCATTTTTGC 59.340 45.0 0.0 0.0 0.0 3.68 F
1272 1930 0.601311 GCTGCAAGTCCTTCTCGTGT 60.601 55.0 0.0 0.0 35.3 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1612 2330 0.846427 TTCATGGCCTTGACCTCCCT 60.846 55.0 20.33 0.0 0.0 4.20 R
2973 3774 0.249657 CTCCTACTCAGCCCGAATGC 60.250 60.0 0.00 0.0 0.0 3.56 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
44 45 4.599047 AGTGAGGCTGACAATATAGAGC 57.401 45.455 6.92 0.00 0.00 4.09
50 51 3.984633 GGCTGACAATATAGAGCGACTTC 59.015 47.826 0.00 0.00 31.89 3.01
58 59 7.268586 ACAATATAGAGCGACTTCAGTTTGAT 58.731 34.615 0.00 0.00 0.00 2.57
93 94 5.498393 AGTACATGGTCTCGAGTTCTAAGA 58.502 41.667 13.13 0.00 0.00 2.10
96 97 6.287589 ACATGGTCTCGAGTTCTAAGAAAT 57.712 37.500 13.13 0.00 0.00 2.17
97 98 6.702329 ACATGGTCTCGAGTTCTAAGAAATT 58.298 36.000 13.13 0.00 0.00 1.82
98 99 7.162082 ACATGGTCTCGAGTTCTAAGAAATTT 58.838 34.615 13.13 0.00 0.00 1.82
99 100 7.661847 ACATGGTCTCGAGTTCTAAGAAATTTT 59.338 33.333 13.13 0.00 0.00 1.82
100 101 8.507249 CATGGTCTCGAGTTCTAAGAAATTTTT 58.493 33.333 13.13 0.00 0.00 1.94
127 128 5.052481 GGCCTAACCCTTTATAGTTGTACG 58.948 45.833 0.00 0.00 0.00 3.67
177 178 0.659957 TTTGTTGCGGGCATTTTTGC 59.340 45.000 0.00 0.00 0.00 3.68
183 184 1.135141 TGCGGGCATTTTTGCACTATC 60.135 47.619 0.00 0.00 35.75 2.08
230 231 4.220693 TGCACAGTCTAGCCATTATTGT 57.779 40.909 0.00 0.00 0.00 2.71
236 237 7.095439 GCACAGTCTAGCCATTATTGTTAGATC 60.095 40.741 0.00 0.00 0.00 2.75
243 244 9.421806 CTAGCCATTATTGTTAGATCAGAAGAG 57.578 37.037 0.00 0.00 0.00 2.85
249 250 9.995003 ATTATTGTTAGATCAGAAGAGGACATC 57.005 33.333 0.00 0.00 0.00 3.06
269 270 1.398451 CGCTCGCACGTCATTTTCTTT 60.398 47.619 0.00 0.00 0.00 2.52
278 279 4.603146 CACGTCATTTTCTTTTCGAAGACG 59.397 41.667 22.64 22.64 45.57 4.18
281 282 5.555631 CGTCATTTTCTTTTCGAAGACGTCA 60.556 40.000 19.50 0.00 40.25 4.35
287 288 6.831727 TTCTTTTCGAAGACGTCATTGTTA 57.168 33.333 19.50 0.14 40.69 2.41
295 296 4.866508 AGACGTCATTGTTAGAGAACCA 57.133 40.909 19.50 0.00 34.38 3.67
311 312 3.135530 AGAACCACTCTCTCATTATGGGC 59.864 47.826 0.00 0.00 34.56 5.36
312 313 1.414181 ACCACTCTCTCATTATGGGCG 59.586 52.381 0.00 0.00 34.56 6.13
320 321 2.236146 TCTCATTATGGGCGTCACACTT 59.764 45.455 0.00 0.00 0.00 3.16
358 359 4.122046 TGATGTAGATCGCTTTGACATGG 58.878 43.478 0.00 0.00 31.03 3.66
360 361 1.599542 GTAGATCGCTTTGACATGGCC 59.400 52.381 0.00 0.00 0.00 5.36
378 379 3.834813 TGGCCATCAGAGGTCATATAGTC 59.165 47.826 0.00 0.00 38.62 2.59
392 393 9.367444 AGGTCATATAGTCTGTTTTTCTTTACG 57.633 33.333 0.00 0.00 0.00 3.18
466 467 7.692291 CGACTAGCCTTTAACATTGTGTTTATG 59.308 37.037 0.20 0.00 41.45 1.90
534 535 8.800231 TTTTAATTCGGATGCATATGAATGTG 57.200 30.769 20.56 0.00 35.38 3.21
535 536 7.509141 TTAATTCGGATGCATATGAATGTGT 57.491 32.000 20.56 11.57 35.38 3.72
540 541 6.958255 TCGGATGCATATGAATGTGTTTTAG 58.042 36.000 6.97 0.00 35.38 1.85
541 542 6.542005 TCGGATGCATATGAATGTGTTTTAGT 59.458 34.615 6.97 0.00 35.38 2.24
542 543 6.634035 CGGATGCATATGAATGTGTTTTAGTG 59.366 38.462 6.97 0.00 35.38 2.74
548 549 8.977505 GCATATGAATGTGTTTTAGTGTGTTTT 58.022 29.630 6.97 0.00 35.38 2.43
659 660 5.482908 AGAAAACATCGAACATCTACTGCT 58.517 37.500 0.00 0.00 0.00 4.24
661 662 5.536554 AAACATCGAACATCTACTGCTTG 57.463 39.130 0.00 0.00 0.00 4.01
662 663 4.456280 ACATCGAACATCTACTGCTTGA 57.544 40.909 0.00 0.00 0.00 3.02
663 664 5.016051 ACATCGAACATCTACTGCTTGAT 57.984 39.130 0.00 0.00 0.00 2.57
664 665 5.046529 ACATCGAACATCTACTGCTTGATC 58.953 41.667 0.00 0.00 0.00 2.92
665 666 4.046938 TCGAACATCTACTGCTTGATCC 57.953 45.455 0.00 0.00 0.00 3.36
666 667 3.126831 CGAACATCTACTGCTTGATCCC 58.873 50.000 0.00 0.00 0.00 3.85
667 668 3.430790 CGAACATCTACTGCTTGATCCCA 60.431 47.826 0.00 0.00 0.00 4.37
668 669 3.834489 ACATCTACTGCTTGATCCCAG 57.166 47.619 0.00 0.00 35.26 4.45
669 670 2.437281 ACATCTACTGCTTGATCCCAGG 59.563 50.000 9.16 0.00 33.43 4.45
670 671 2.550277 TCTACTGCTTGATCCCAGGA 57.450 50.000 9.16 0.00 33.43 3.86
671 672 2.832838 TCTACTGCTTGATCCCAGGAA 58.167 47.619 9.16 0.00 33.43 3.36
672 673 3.181329 TCTACTGCTTGATCCCAGGAAA 58.819 45.455 9.16 0.00 33.43 3.13
678 679 2.833943 GCTTGATCCCAGGAAATTTGGT 59.166 45.455 0.00 0.00 33.73 3.67
683 684 7.380423 TTGATCCCAGGAAATTTGGTAAAAA 57.620 32.000 0.00 0.00 33.73 1.94
692 693 7.226325 CAGGAAATTTGGTAAAAAGCACATTCA 59.774 33.333 0.00 0.00 0.00 2.57
701 702 6.928492 GGTAAAAAGCACATTCAAAAGATGGA 59.072 34.615 0.00 0.00 0.00 3.41
703 704 4.796038 AAGCACATTCAAAAGATGGAGG 57.204 40.909 0.00 0.00 0.00 4.30
704 705 3.771216 AGCACATTCAAAAGATGGAGGT 58.229 40.909 0.00 0.00 29.57 3.85
707 708 5.416952 AGCACATTCAAAAGATGGAGGTAAG 59.583 40.000 0.00 0.00 27.17 2.34
708 709 5.415701 GCACATTCAAAAGATGGAGGTAAGA 59.584 40.000 0.00 0.00 27.17 2.10
709 710 6.096001 GCACATTCAAAAGATGGAGGTAAGAT 59.904 38.462 0.00 0.00 27.17 2.40
710 711 7.283127 GCACATTCAAAAGATGGAGGTAAGATA 59.717 37.037 0.00 0.00 27.17 1.98
711 712 8.616076 CACATTCAAAAGATGGAGGTAAGATAC 58.384 37.037 0.00 0.00 27.17 2.24
716 753 8.602424 TCAAAAGATGGAGGTAAGATACAGAAA 58.398 33.333 0.00 0.00 0.00 2.52
717 754 8.887717 CAAAAGATGGAGGTAAGATACAGAAAG 58.112 37.037 0.00 0.00 0.00 2.62
737 779 2.732412 CTTGAACGAAGCAGAGAGGA 57.268 50.000 0.00 0.00 0.00 3.71
765 817 4.418328 CGGCCCCGGTGATTTCCA 62.418 66.667 0.00 0.00 35.56 3.53
787 839 5.105997 CCATTCACCTTTCACTTTCATCTCC 60.106 44.000 0.00 0.00 0.00 3.71
841 894 4.143389 CGCACTACGTTCTAAAACCAGAAG 60.143 45.833 0.00 0.00 35.25 2.85
852 905 2.177594 AACCAGAAGCAGCCCTCGAG 62.178 60.000 5.13 5.13 0.00 4.04
889 949 2.046988 TCATCACACCAGCCTGCG 60.047 61.111 0.00 0.00 0.00 5.18
995 1626 3.173240 GACGAGTGACGAAGCCGC 61.173 66.667 0.00 0.00 45.77 6.53
1203 1834 2.041265 TCCCTCTTCTCCAGGCCC 59.959 66.667 0.00 0.00 0.00 5.80
1272 1930 0.601311 GCTGCAAGTCCTTCTCGTGT 60.601 55.000 0.00 0.00 35.30 4.49
1569 2287 2.047179 GTGGAGCCCGTCTTGGTC 60.047 66.667 0.00 0.00 35.15 4.02
1612 2330 1.906574 AGAACGAAGCTTATGGGACCA 59.093 47.619 0.00 0.00 0.00 4.02
1836 2570 1.084370 CGTCGGAGAAGCCATCCAAC 61.084 60.000 0.92 0.00 39.69 3.77
2154 2889 1.219124 GGAAGATGACTCGCAGCCA 59.781 57.895 0.00 0.00 31.91 4.75
2282 3017 1.341606 CTGAGAAGGTCGTTCGAAGC 58.658 55.000 0.00 0.00 40.49 3.86
2333 3068 2.491152 CATCACCAATGCCACGGC 59.509 61.111 0.00 0.00 42.35 5.68
2398 3133 0.319555 CGAAGACCTGCTCGACCAAA 60.320 55.000 0.00 0.00 0.00 3.28
2416 3151 2.551459 CAAAGGTTCAGCTCCAACTCTG 59.449 50.000 5.29 0.00 0.00 3.35
2972 3773 3.114616 CTGACCAGCAGTTCGGCG 61.115 66.667 0.00 0.00 39.85 6.46
2973 3774 4.680237 TGACCAGCAGTTCGGCGG 62.680 66.667 7.21 0.00 39.27 6.13
2977 3778 3.434319 CAGCAGTTCGGCGGCATT 61.434 61.111 10.53 0.00 40.81 3.56
2978 3779 3.127533 AGCAGTTCGGCGGCATTC 61.128 61.111 10.53 0.00 40.81 2.67
2979 3780 4.520846 GCAGTTCGGCGGCATTCG 62.521 66.667 10.53 0.00 38.20 3.34
2980 3781 3.864686 CAGTTCGGCGGCATTCGG 61.865 66.667 10.53 0.00 39.69 4.30
2988 3789 2.499205 CGGCATTCGGGCTGAGTA 59.501 61.111 0.00 0.00 42.91 2.59
2989 3790 1.592669 CGGCATTCGGGCTGAGTAG 60.593 63.158 0.00 0.00 42.91 2.57
3025 3841 2.744202 CAGCAGTGGTTAAGGCTTAGTG 59.256 50.000 7.09 2.80 33.60 2.74
3073 3889 6.173339 AGGGCAATGGTATAGTCATAAATCG 58.827 40.000 0.00 0.00 0.00 3.34
3108 3939 4.142381 GCTTGTGTAGGTTTGGATGGAATC 60.142 45.833 0.00 0.00 44.55 2.52
3140 3972 5.235186 GGAACGAGGTTTATCTCATGTGATG 59.765 44.000 18.31 4.45 33.59 3.07
3188 4020 2.607187 CTATTGCTTCTGTCCGTCGTT 58.393 47.619 0.00 0.00 0.00 3.85
3191 4031 2.668280 GCTTCTGTCCGTCGTTGCC 61.668 63.158 0.00 0.00 0.00 4.52
3210 4050 1.802337 CGTCCAGTGTTCACCTCGGA 61.802 60.000 0.00 1.51 0.00 4.55
3219 4059 3.506067 GTGTTCACCTCGGATTTTTGGAT 59.494 43.478 0.00 0.00 0.00 3.41
3223 4063 3.053693 TCACCTCGGATTTTTGGATGGAT 60.054 43.478 0.00 0.00 0.00 3.41
3224 4064 3.067180 CACCTCGGATTTTTGGATGGATG 59.933 47.826 0.00 0.00 0.00 3.51
3226 4066 3.554934 CTCGGATTTTTGGATGGATGGA 58.445 45.455 0.00 0.00 0.00 3.41
3227 4067 3.287222 TCGGATTTTTGGATGGATGGAC 58.713 45.455 0.00 0.00 0.00 4.02
3228 4068 3.023119 CGGATTTTTGGATGGATGGACA 58.977 45.455 0.00 0.00 0.00 4.02
3230 4070 4.280819 GGATTTTTGGATGGATGGACAGA 58.719 43.478 0.00 0.00 0.00 3.41
3240 4086 2.038952 TGGATGGACAGAAGAACCTGTG 59.961 50.000 0.88 0.00 46.45 3.66
3249 4095 2.175715 AGAAGAACCTGTGGGAAGCTTT 59.824 45.455 0.00 0.00 36.25 3.51
3250 4096 1.986882 AGAACCTGTGGGAAGCTTTG 58.013 50.000 0.00 0.00 36.25 2.77
3251 4097 0.961753 GAACCTGTGGGAAGCTTTGG 59.038 55.000 0.00 0.00 36.25 3.28
3299 4184 1.687493 GTCTGGGACTGGGAGGGAG 60.687 68.421 0.00 0.00 0.00 4.30
3300 4185 2.366167 CTGGGACTGGGAGGGAGG 60.366 72.222 0.00 0.00 0.00 4.30
3338 4226 5.515270 TCGAATAGTAGCTTTGACATGAACG 59.485 40.000 0.00 0.00 0.00 3.95
3344 4232 1.727213 GCTTTGACATGAACGAGCAGC 60.727 52.381 0.00 0.00 0.00 5.25
3448 4347 1.078759 CCTGACCGATCGACAGTTGC 61.079 60.000 27.09 7.69 0.00 4.17
3492 4391 3.115892 TTAAAGAGGGCGCGCACG 61.116 61.111 34.42 0.00 44.07 5.34
3647 5350 0.655733 GCACGCCGTATTGTATTGCT 59.344 50.000 0.00 0.00 0.00 3.91
3656 5755 0.458669 ATTGTATTGCTGCTGCTGCC 59.541 50.000 25.44 12.57 40.48 4.85
3721 5820 2.631428 CCGCCGTTTATGCCGATG 59.369 61.111 0.00 0.00 0.00 3.84
3788 5887 2.974698 GGCCGCGGGATTCTGATG 60.975 66.667 29.38 0.00 0.00 3.07
3792 5891 2.537560 CGCGGGATTCTGATGTGGC 61.538 63.158 0.00 0.00 0.00 5.01
3796 5895 0.815615 GGGATTCTGATGTGGCCGAC 60.816 60.000 0.00 0.00 0.00 4.79
3901 6000 3.490759 GCGGACATGTGCACGAGG 61.491 66.667 18.05 6.51 0.00 4.63
3906 6005 1.626654 GACATGTGCACGAGGAACCG 61.627 60.000 13.13 0.00 0.00 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 5.452496 GCTCTATATTGTCAGCCTCACTTCA 60.452 44.000 0.00 0.00 0.00 3.02
28 29 3.651803 AGTCGCTCTATATTGTCAGCC 57.348 47.619 0.00 0.00 0.00 4.85
31 32 5.836821 ACTGAAGTCGCTCTATATTGTCA 57.163 39.130 0.00 0.00 0.00 3.58
44 45 4.310769 AGAGAACCATCAAACTGAAGTCG 58.689 43.478 0.00 0.00 0.00 4.18
98 99 8.172070 ACAACTATAAAGGGTTAGGCCTAAAAA 58.828 33.333 26.78 4.27 37.43 1.94
99 100 7.701815 ACAACTATAAAGGGTTAGGCCTAAAA 58.298 34.615 26.78 5.14 37.43 1.52
100 101 7.274772 ACAACTATAAAGGGTTAGGCCTAAA 57.725 36.000 26.78 10.76 37.43 1.85
106 107 6.920210 GCTACGTACAACTATAAAGGGTTAGG 59.080 42.308 0.00 0.00 0.00 2.69
115 116 5.972973 CGACCATTGCTACGTACAACTATAA 59.027 40.000 11.16 0.00 0.00 0.98
116 117 5.066375 ACGACCATTGCTACGTACAACTATA 59.934 40.000 11.16 0.00 37.22 1.31
117 118 4.142315 ACGACCATTGCTACGTACAACTAT 60.142 41.667 11.16 2.71 37.22 2.12
127 128 2.550606 TGGAAAACACGACCATTGCTAC 59.449 45.455 0.00 0.00 0.00 3.58
183 184 9.840427 ATTTTCACTTTGGAGATAAATACAACG 57.160 29.630 0.00 0.00 0.00 4.10
230 231 4.211125 AGCGATGTCCTCTTCTGATCTAA 58.789 43.478 0.00 0.00 0.00 2.10
236 237 0.869454 GCGAGCGATGTCCTCTTCTG 60.869 60.000 0.00 0.00 0.00 3.02
243 244 3.248171 GACGTGCGAGCGATGTCC 61.248 66.667 0.00 0.00 35.59 4.02
249 250 0.163788 AAGAAAATGACGTGCGAGCG 59.836 50.000 0.00 0.00 37.94 5.03
269 270 5.366829 TCTCTAACAATGACGTCTTCGAA 57.633 39.130 17.92 0.00 40.62 3.71
295 296 2.101582 GTGACGCCCATAATGAGAGAGT 59.898 50.000 0.00 0.00 0.00 3.24
302 303 3.250762 CCATAAGTGTGACGCCCATAATG 59.749 47.826 0.00 0.00 0.00 1.90
311 312 3.367932 CAGTAGCAACCATAAGTGTGACG 59.632 47.826 0.00 0.00 0.00 4.35
312 313 3.125316 GCAGTAGCAACCATAAGTGTGAC 59.875 47.826 0.00 0.00 41.58 3.67
338 339 2.874701 GCCATGTCAAAGCGATCTACAT 59.125 45.455 0.00 0.00 0.00 2.29
339 340 2.279741 GCCATGTCAAAGCGATCTACA 58.720 47.619 0.00 0.00 0.00 2.74
358 359 4.526262 ACAGACTATATGACCTCTGATGGC 59.474 45.833 0.00 0.00 35.19 4.40
360 361 8.954950 AAAAACAGACTATATGACCTCTGATG 57.045 34.615 0.00 0.00 35.19 3.07
421 422 1.743996 GAGGCAGGGAGATTGAACAC 58.256 55.000 0.00 0.00 0.00 3.32
507 508 9.414295 ACATTCATATGCATCCGAATTAAAATG 57.586 29.630 16.83 11.00 35.03 2.32
606 607 7.359014 GCAATCCGTTCCGAATTACTATAAGAC 60.359 40.741 0.00 0.00 0.00 3.01
613 614 2.936498 CTGCAATCCGTTCCGAATTACT 59.064 45.455 0.00 0.00 0.00 2.24
614 615 2.676342 ACTGCAATCCGTTCCGAATTAC 59.324 45.455 0.00 0.00 0.00 1.89
615 616 2.980568 ACTGCAATCCGTTCCGAATTA 58.019 42.857 0.00 0.00 0.00 1.40
616 617 1.821216 ACTGCAATCCGTTCCGAATT 58.179 45.000 0.00 0.00 0.00 2.17
617 618 2.167693 TCTACTGCAATCCGTTCCGAAT 59.832 45.455 0.00 0.00 0.00 3.34
629 630 5.700832 AGATGTTCGATGTTTTCTACTGCAA 59.299 36.000 0.00 0.00 0.00 4.08
630 631 5.237815 AGATGTTCGATGTTTTCTACTGCA 58.762 37.500 0.00 0.00 0.00 4.41
659 660 7.380423 TTTTTACCAAATTTCCTGGGATCAA 57.620 32.000 0.00 0.00 38.36 2.57
661 662 5.874810 GCTTTTTACCAAATTTCCTGGGATC 59.125 40.000 0.00 0.00 38.36 3.36
662 663 5.309282 TGCTTTTTACCAAATTTCCTGGGAT 59.691 36.000 0.00 0.00 38.36 3.85
663 664 4.656112 TGCTTTTTACCAAATTTCCTGGGA 59.344 37.500 0.00 0.00 38.36 4.37
664 665 4.754618 GTGCTTTTTACCAAATTTCCTGGG 59.245 41.667 0.00 0.00 38.36 4.45
665 666 5.363939 TGTGCTTTTTACCAAATTTCCTGG 58.636 37.500 0.00 0.00 40.05 4.45
666 667 7.226325 TGAATGTGCTTTTTACCAAATTTCCTG 59.774 33.333 0.00 0.00 0.00 3.86
667 668 7.278875 TGAATGTGCTTTTTACCAAATTTCCT 58.721 30.769 0.00 0.00 0.00 3.36
668 669 7.489574 TGAATGTGCTTTTTACCAAATTTCC 57.510 32.000 0.00 0.00 0.00 3.13
669 670 9.780413 TTTTGAATGTGCTTTTTACCAAATTTC 57.220 25.926 0.00 0.00 0.00 2.17
670 671 9.786105 CTTTTGAATGTGCTTTTTACCAAATTT 57.214 25.926 0.00 0.00 0.00 1.82
671 672 9.171877 TCTTTTGAATGTGCTTTTTACCAAATT 57.828 25.926 0.00 0.00 0.00 1.82
672 673 8.729805 TCTTTTGAATGTGCTTTTTACCAAAT 57.270 26.923 0.00 0.00 0.00 2.32
678 679 7.153985 CCTCCATCTTTTGAATGTGCTTTTTA 58.846 34.615 0.00 0.00 0.00 1.52
683 684 3.771216 ACCTCCATCTTTTGAATGTGCT 58.229 40.909 0.00 0.00 0.00 4.40
692 693 7.554476 GCTTTCTGTATCTTACCTCCATCTTTT 59.446 37.037 0.00 0.00 0.00 2.27
701 702 5.869888 CGTTCAAGCTTTCTGTATCTTACCT 59.130 40.000 0.00 0.00 0.00 3.08
703 704 6.946229 TCGTTCAAGCTTTCTGTATCTTAC 57.054 37.500 0.00 0.00 0.00 2.34
704 705 7.582435 CTTCGTTCAAGCTTTCTGTATCTTA 57.418 36.000 0.00 0.00 0.00 2.10
737 779 3.069318 GGGGCCGTCGTCTCTCTT 61.069 66.667 0.00 0.00 0.00 2.85
765 817 4.697352 CGGAGATGAAAGTGAAAGGTGAAT 59.303 41.667 0.00 0.00 0.00 2.57
787 839 5.118990 AGGATGAAAATGGACATAGACACG 58.881 41.667 0.00 0.00 0.00 4.49
1612 2330 0.846427 TTCATGGCCTTGACCTCCCT 60.846 55.000 20.33 0.00 0.00 4.20
1673 2401 1.541118 TCCTTCAGGTCCATGGGCA 60.541 57.895 20.13 0.00 36.34 5.36
1764 2492 1.274712 CTGCCTCCTCCTTCTTGAGT 58.725 55.000 0.00 0.00 0.00 3.41
2398 3133 1.346068 GACAGAGTTGGAGCTGAACCT 59.654 52.381 0.00 0.00 36.07 3.50
2416 3151 0.531200 ACGGGGAAGTCTTCGATGAC 59.469 55.000 20.62 20.62 37.23 3.06
2658 3411 2.126965 GCGCTGTTGCTGCTGAAG 60.127 61.111 0.00 0.00 36.40 3.02
2733 3498 2.358003 ACGCACTGCTCTTCCTGC 60.358 61.111 0.00 0.00 0.00 4.85
2972 3773 1.227674 CCTACTCAGCCCGAATGCC 60.228 63.158 0.00 0.00 0.00 4.40
2973 3774 0.249657 CTCCTACTCAGCCCGAATGC 60.250 60.000 0.00 0.00 0.00 3.56
2974 3775 1.115467 ACTCCTACTCAGCCCGAATG 58.885 55.000 0.00 0.00 0.00 2.67
2975 3776 2.091775 ACTACTCCTACTCAGCCCGAAT 60.092 50.000 0.00 0.00 0.00 3.34
2977 3778 0.917533 ACTACTCCTACTCAGCCCGA 59.082 55.000 0.00 0.00 0.00 5.14
2978 3779 1.765230 AACTACTCCTACTCAGCCCG 58.235 55.000 0.00 0.00 0.00 6.13
2979 3780 3.367321 AGAAACTACTCCTACTCAGCCC 58.633 50.000 0.00 0.00 0.00 5.19
2980 3781 5.172205 CAAAGAAACTACTCCTACTCAGCC 58.828 45.833 0.00 0.00 0.00 4.85
2981 3782 4.627900 GCAAAGAAACTACTCCTACTCAGC 59.372 45.833 0.00 0.00 0.00 4.26
2982 3783 5.784177 TGCAAAGAAACTACTCCTACTCAG 58.216 41.667 0.00 0.00 0.00 3.35
2983 3784 5.784177 CTGCAAAGAAACTACTCCTACTCA 58.216 41.667 0.00 0.00 0.00 3.41
2984 3785 4.627900 GCTGCAAAGAAACTACTCCTACTC 59.372 45.833 0.00 0.00 0.00 2.59
2985 3786 4.040461 TGCTGCAAAGAAACTACTCCTACT 59.960 41.667 0.00 0.00 0.00 2.57
2986 3787 4.315803 TGCTGCAAAGAAACTACTCCTAC 58.684 43.478 0.00 0.00 0.00 3.18
2987 3788 4.040461 ACTGCTGCAAAGAAACTACTCCTA 59.960 41.667 3.02 0.00 0.00 2.94
2988 3789 3.181450 ACTGCTGCAAAGAAACTACTCCT 60.181 43.478 3.02 0.00 0.00 3.69
2989 3790 3.058639 CACTGCTGCAAAGAAACTACTCC 60.059 47.826 3.02 0.00 0.00 3.85
3025 3841 9.930693 CCTTAATCAGACCTTAATCATACTACC 57.069 37.037 0.00 0.00 0.00 3.18
3073 3889 8.911662 CAAACCTACACAAGCATGTAATAAAAC 58.088 33.333 0.00 0.00 37.82 2.43
3108 3939 5.126067 AGATAAACCTCGTTCCATTCCATG 58.874 41.667 0.00 0.00 0.00 3.66
3109 3940 5.104527 TGAGATAAACCTCGTTCCATTCCAT 60.105 40.000 0.00 0.00 35.99 3.41
3110 3941 4.224147 TGAGATAAACCTCGTTCCATTCCA 59.776 41.667 0.00 0.00 35.99 3.53
3111 3942 4.766375 TGAGATAAACCTCGTTCCATTCC 58.234 43.478 0.00 0.00 35.99 3.01
3112 3943 5.817816 ACATGAGATAAACCTCGTTCCATTC 59.182 40.000 0.00 0.00 35.99 2.67
3113 3944 5.586243 CACATGAGATAAACCTCGTTCCATT 59.414 40.000 0.00 0.00 35.99 3.16
3114 3945 5.104941 TCACATGAGATAAACCTCGTTCCAT 60.105 40.000 0.00 0.00 35.99 3.41
3115 3946 4.221924 TCACATGAGATAAACCTCGTTCCA 59.778 41.667 0.00 0.00 35.99 3.53
3140 3972 1.933853 ACAGCACGAGACAAACAAGTC 59.066 47.619 0.00 0.00 38.81 3.01
3188 4020 2.110213 GGTGAACACTGGACGGCA 59.890 61.111 4.96 0.00 0.00 5.69
3191 4031 1.372997 CCGAGGTGAACACTGGACG 60.373 63.158 4.96 5.98 0.00 4.79
3210 4050 5.582953 TCTTCTGTCCATCCATCCAAAAAT 58.417 37.500 0.00 0.00 0.00 1.82
3219 4059 2.038952 CACAGGTTCTTCTGTCCATCCA 59.961 50.000 0.00 0.00 45.24 3.41
3223 4063 0.764890 CCCACAGGTTCTTCTGTCCA 59.235 55.000 0.00 0.00 45.24 4.02
3224 4064 1.056660 TCCCACAGGTTCTTCTGTCC 58.943 55.000 0.00 0.00 45.24 4.02
3227 4067 1.072965 AGCTTCCCACAGGTTCTTCTG 59.927 52.381 0.00 0.00 40.40 3.02
3228 4068 1.439543 AGCTTCCCACAGGTTCTTCT 58.560 50.000 0.00 0.00 0.00 2.85
3230 4070 2.310538 CAAAGCTTCCCACAGGTTCTT 58.689 47.619 0.00 0.00 33.27 2.52
3240 4086 3.763897 ACATATGAACACCAAAGCTTCCC 59.236 43.478 10.38 0.00 0.00 3.97
3249 4095 5.009510 CCAAAGTGACAACATATGAACACCA 59.990 40.000 10.38 0.00 39.06 4.17
3250 4096 5.009610 ACCAAAGTGACAACATATGAACACC 59.990 40.000 10.38 0.00 39.06 4.16
3251 4097 6.072112 ACCAAAGTGACAACATATGAACAC 57.928 37.500 10.38 12.56 38.80 3.32
3299 4184 4.065281 CGACAGACACGGTCCCCC 62.065 72.222 1.06 0.00 32.18 5.40
3300 4185 1.885163 ATTCGACAGACACGGTCCCC 61.885 60.000 0.00 0.00 32.18 4.81
3492 4391 3.249973 GACCGGCAAAGGAACGTGC 62.250 63.158 0.00 0.00 42.21 5.34
3656 5755 1.367312 CGCGATGAATGAAGCAGCG 60.367 57.895 0.00 0.00 46.69 5.18
3721 5820 3.047877 CCGAACCAACCGACCAGC 61.048 66.667 0.00 0.00 0.00 4.85
3771 5870 2.974698 CATCAGAATCCCGCGGCC 60.975 66.667 22.85 8.36 0.00 6.13
3796 5895 1.683790 CTAAACAAGTCGAGCCGGCG 61.684 60.000 23.20 8.11 36.23 6.46
3810 5909 5.610552 GCGCTGATCATTATCACGACTAAAC 60.611 44.000 0.00 0.00 37.20 2.01
3820 5919 1.417592 CGCCGCGCTGATCATTATC 59.582 57.895 5.56 0.00 0.00 1.75
3901 6000 3.373565 CCCTTGGCCTTGCGGTTC 61.374 66.667 3.32 0.00 0.00 3.62
3906 6005 3.313524 CAACCCCCTTGGCCTTGC 61.314 66.667 3.32 0.00 37.83 4.01


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

AutoCloner maintained by Alex Coulton.