Multiple sequence alignment - TraesCS1D01G373000

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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 TraesCS1D01G373000 chr1D 100.000 5179 0 0 1 5179 451128038 451133216 0.000000e+00 9564
1 TraesCS1D01G373000 chr1D 95.082 122 5 1 158 278 451075480 451075601 1.900000e-44 191
2 TraesCS1D01G373000 chr1D 85.542 166 18 5 4653 4814 111413364 111413201 8.920000e-38 169
3 TraesCS1D01G373000 chr1D 82.659 173 23 5 111 280 451068262 451068430 4.180000e-31 147
4 TraesCS1D01G373000 chr1A 92.275 3495 181 51 1 3441 545887220 545890679 0.000000e+00 4876
5 TraesCS1D01G373000 chr1A 88.794 1642 72 42 3481 5058 545890683 545892276 0.000000e+00 1910
6 TraesCS1D01G373000 chr1A 86.471 170 19 4 4653 4820 117885698 117885531 3.190000e-42 183
7 TraesCS1D01G373000 chr1A 85.350 157 19 3 126 280 545867297 545867451 5.370000e-35 159
8 TraesCS1D01G373000 chr1B 95.911 1712 59 7 986 2691 619416871 619418577 0.000000e+00 2763
9 TraesCS1D01G373000 chr1B 96.936 1273 30 2 3139 4402 619419202 619420474 0.000000e+00 2126
10 TraesCS1D01G373000 chr1B 97.862 421 8 1 2692 3112 619418700 619419119 0.000000e+00 726
11 TraesCS1D01G373000 chr1B 85.740 547 58 8 393 924 619416334 619416875 1.260000e-155 560
12 TraesCS1D01G373000 chr1B 91.798 317 16 9 1 311 619415982 619416294 2.860000e-117 433
13 TraesCS1D01G373000 chr1B 93.750 240 11 1 4647 4882 619420806 619421045 1.770000e-94 357
14 TraesCS1D01G373000 chr1B 83.387 313 18 18 4883 5179 619421084 619421378 5.140000e-65 259
15 TraesCS1D01G373000 chr1B 93.519 108 6 1 2728 2835 619419114 619419220 5.370000e-35 159
16 TraesCS1D01G373000 chr1B 84.375 160 23 2 128 285 619398682 619398841 6.940000e-34 156
17 TraesCS1D01G373000 chr1B 88.372 129 5 6 4401 4519 619420578 619420706 4.180000e-31 147
18 TraesCS1D01G373000 chr7D 80.724 1686 226 58 2511 4178 44294056 44295660 0.000000e+00 1221
19 TraesCS1D01G373000 chr7D 77.441 1055 155 44 1233 2259 44292650 44293649 2.110000e-153 553
20 TraesCS1D01G373000 chr7D 92.857 84 4 2 1088 1170 44292368 44292450 2.530000e-23 121
21 TraesCS1D01G373000 chr4A 84.582 934 112 21 2511 3433 655253178 655254090 0.000000e+00 898
22 TraesCS1D01G373000 chr4A 77.395 1075 147 43 1235 2259 655251745 655252773 7.580000e-153 551
23 TraesCS1D01G373000 chr4A 76.790 866 138 47 3508 4363 655254295 655255107 1.330000e-115 427
24 TraesCS1D01G373000 chr4A 87.963 108 11 2 1088 1194 655251458 655251564 5.440000e-25 126
25 TraesCS1D01G373000 chr7A 81.267 1105 155 34 2251 3319 46711916 46713004 0.000000e+00 846
26 TraesCS1D01G373000 chr7A 77.767 1066 155 44 1233 2259 46710837 46711859 9.670000e-162 580
27 TraesCS1D01G373000 chr7A 78.464 729 101 38 3445 4167 46713081 46713759 4.790000e-115 425
28 TraesCS1D01G373000 chr7A 86.957 115 13 2 1088 1201 46710555 46710668 1.510000e-25 128
29 TraesCS1D01G373000 chr5D 84.100 239 24 6 4654 4882 255564129 255564363 8.730000e-53 219
30 TraesCS1D01G373000 chr5D 81.974 233 28 11 4654 4879 255564437 255564662 8.860000e-43 185
31 TraesCS1D01G373000 chr5B 79.476 229 33 9 4654 4879 286701503 286701720 3.230000e-32 150
32 TraesCS1D01G373000 chr5B 79.310 232 33 9 4654 4882 286701219 286701438 1.160000e-31 148
33 TraesCS1D01G373000 chr5A 88.889 117 11 1 4654 4768 338846863 338846979 5.410000e-30 143
34 TraesCS1D01G373000 chr2D 92.405 79 5 1 126 204 582658386 582658463 1.520000e-20 111


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 TraesCS1D01G373000 chr1D 451128038 451133216 5178 False 9564.000000 9564 100.000000 1 5179 1 chr1D.!!$F3 5178
1 TraesCS1D01G373000 chr1A 545887220 545892276 5056 False 3393.000000 4876 90.534500 1 5058 2 chr1A.!!$F2 5057
2 TraesCS1D01G373000 chr1B 619415982 619421378 5396 False 836.666667 2763 91.919444 1 5179 9 chr1B.!!$F2 5178
3 TraesCS1D01G373000 chr7D 44292368 44295660 3292 False 631.666667 1221 83.674000 1088 4178 3 chr7D.!!$F1 3090
4 TraesCS1D01G373000 chr4A 655251458 655255107 3649 False 500.500000 898 81.682500 1088 4363 4 chr4A.!!$F1 3275
5 TraesCS1D01G373000 chr7A 46710555 46713759 3204 False 494.750000 846 81.113750 1088 4167 4 chr7A.!!$F1 3079
6 TraesCS1D01G373000 chr5D 255564129 255564662 533 False 202.000000 219 83.037000 4654 4882 2 chr5D.!!$F1 228

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
877 918 0.178947 AATAGAGAGGGGGAGAGCCG 60.179 60.000 0.00 0.00 33.83 5.52 F
1230 1282 0.469917 CTGACTCTGGTTGGTGTGGT 59.530 55.000 0.00 0.00 0.00 4.16 F
1532 1744 1.414919 TCTACAAAGTCGGCTTGGTGT 59.585 47.619 20.13 15.48 39.14 4.16 F
2722 3260 0.329596 ATGGAGCCCCTGAGTTGTTC 59.670 55.000 0.00 0.00 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2365 2702 0.167470 CACAAATCCTGCAGCGACTG 59.833 55.000 8.66 10.55 34.12 3.51 R
2697 3235 0.622665 CTCAGGGGCTCCATCAAGTT 59.377 55.000 4.79 0.00 34.83 2.66 R
3441 4045 1.342819 GCATGTTTAGGTTGGCCACAA 59.657 47.619 3.88 0.00 37.19 3.33 R
4646 5616 0.251297 CTGAGGCACCCATGTGGAAA 60.251 55.000 0.00 0.00 42.99 3.13 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
59 61 2.747460 GCACAGGAGCGCAATGGA 60.747 61.111 11.47 0.00 0.00 3.41
60 62 2.117156 GCACAGGAGCGCAATGGAT 61.117 57.895 11.47 0.00 0.00 3.41
61 63 0.815213 GCACAGGAGCGCAATGGATA 60.815 55.000 11.47 0.00 0.00 2.59
62 64 1.224075 CACAGGAGCGCAATGGATAG 58.776 55.000 11.47 0.00 0.00 2.08
95 101 0.883833 GTGTCCAATTCCTGCCTGTG 59.116 55.000 0.00 0.00 0.00 3.66
124 130 8.543293 TTCCCTCTTTCTTCGTATAAATAGGA 57.457 34.615 6.09 0.00 33.14 2.94
232 239 0.538118 GGTGGGTGGTGCGTCTATAA 59.462 55.000 0.00 0.00 0.00 0.98
233 240 1.065998 GGTGGGTGGTGCGTCTATAAA 60.066 52.381 0.00 0.00 0.00 1.40
252 259 2.322422 CGGTCTACGCCGTACTCG 59.678 66.667 0.00 3.34 46.11 4.18
326 344 2.879026 GGCGAGCTTAATTAAAGGGAGG 59.121 50.000 0.00 0.00 35.58 4.30
348 366 1.671742 CCTAGATGGGCCGCGTAAT 59.328 57.895 4.92 0.00 0.00 1.89
352 370 1.961277 GATGGGCCGCGTAATGGAG 60.961 63.158 4.92 0.00 0.00 3.86
358 376 2.202932 CGCGTAATGGAGCCAGCT 60.203 61.111 0.00 0.00 0.00 4.24
359 377 1.067416 CGCGTAATGGAGCCAGCTA 59.933 57.895 0.00 0.00 0.00 3.32
427 447 0.811281 CCGAGCCAAAAAGCCCTAAG 59.189 55.000 0.00 0.00 0.00 2.18
443 463 0.319083 TAAGAAAACCGCGAGCCAGA 59.681 50.000 8.23 0.00 0.00 3.86
584 613 2.799371 GGCACGAGAGGTAGGTCG 59.201 66.667 0.00 0.00 42.04 4.79
600 629 4.212213 AGGTCGTCTCGATTTTATCTCG 57.788 45.455 0.00 0.00 38.42 4.04
619 648 5.631119 TCTCGAGAGATAGAGAGAGAGAGA 58.369 45.833 12.08 0.00 38.46 3.10
621 650 4.767409 TCGAGAGATAGAGAGAGAGAGAGG 59.233 50.000 0.00 0.00 33.31 3.69
623 652 5.710567 CGAGAGATAGAGAGAGAGAGAGGTA 59.289 48.000 0.00 0.00 0.00 3.08
627 656 1.774856 AGAGAGAGAGAGAGGTAGGGC 59.225 57.143 0.00 0.00 0.00 5.19
680 718 2.109799 ATCTGGCCGGATCTTGCG 59.890 61.111 22.11 0.00 0.00 4.85
729 770 2.363795 CTCGGTGGGGTAGGAGCA 60.364 66.667 0.00 0.00 0.00 4.26
732 773 2.040606 GGTGGGGTAGGAGCAGGA 59.959 66.667 0.00 0.00 0.00 3.86
753 794 2.025155 GGAAGATAGAGACGAGGTGCA 58.975 52.381 0.00 0.00 0.00 4.57
774 815 4.052518 GGTGGGTGGGCTGCTGAT 62.053 66.667 0.00 0.00 0.00 2.90
787 828 1.473677 CTGCTGATTTTGCGATTGGGA 59.526 47.619 0.00 0.00 0.00 4.37
788 829 2.100252 CTGCTGATTTTGCGATTGGGAT 59.900 45.455 0.00 0.00 0.00 3.85
792 833 2.426738 TGATTTTGCGATTGGGATCACC 59.573 45.455 0.00 0.00 40.81 4.02
827 868 3.332485 TGCTATTGAGTTAGGGTTTGGGT 59.668 43.478 0.00 0.00 0.00 4.51
828 869 3.694566 GCTATTGAGTTAGGGTTTGGGTG 59.305 47.826 0.00 0.00 0.00 4.61
829 870 4.566907 GCTATTGAGTTAGGGTTTGGGTGA 60.567 45.833 0.00 0.00 0.00 4.02
830 871 3.502123 TTGAGTTAGGGTTTGGGTGAG 57.498 47.619 0.00 0.00 0.00 3.51
877 918 0.178947 AATAGAGAGGGGGAGAGCCG 60.179 60.000 0.00 0.00 33.83 5.52
903 944 2.545952 GGGTGTATGTGATGCTCCTACG 60.546 54.545 0.00 0.00 0.00 3.51
950 995 8.260818 GCTGCTATATGATATAAGGTTTCCTGA 58.739 37.037 0.00 0.00 32.13 3.86
953 998 9.103861 GCTATATGATATAAGGTTTCCTGAAGC 57.896 37.037 0.00 0.00 32.13 3.86
971 1017 4.713814 TGAAGCAGATCAAGAGTGAGGTAT 59.286 41.667 0.00 0.00 37.14 2.73
1039 1088 2.825836 CAATGGAGGGAGCGTGGC 60.826 66.667 0.00 0.00 0.00 5.01
1099 1151 2.351777 CCTCAAGTGTCGGAGGTGA 58.648 57.895 0.00 0.00 44.59 4.02
1186 1238 4.541973 AACCTCGGTATTAAACTCCGTT 57.458 40.909 13.26 2.36 43.94 4.44
1201 1253 3.423154 GTTTCGCCTCGGCAGTGG 61.423 66.667 8.87 0.09 42.06 4.00
1230 1282 0.469917 CTGACTCTGGTTGGTGTGGT 59.530 55.000 0.00 0.00 0.00 4.16
1306 1498 2.282040 AAGCACAGCAGTGGAGGC 60.282 61.111 11.54 0.00 45.98 4.70
1422 1620 2.611292 GCCAGGTGATGATCTTTCTTCG 59.389 50.000 0.00 0.00 0.00 3.79
1446 1644 6.319658 CGGCTATGCTTTATCCCATGATTTAT 59.680 38.462 0.00 0.00 32.18 1.40
1455 1653 9.559958 CTTTATCCCATGATTTATTTATGTCGC 57.440 33.333 0.00 0.00 32.18 5.19
1532 1744 1.414919 TCTACAAAGTCGGCTTGGTGT 59.585 47.619 20.13 15.48 39.14 4.16
1737 1980 3.706086 ACTCCCAAATCTGTGTTTGCTTT 59.294 39.130 0.00 0.00 37.67 3.51
1879 2126 5.198207 TGTGCCAAATGAGATCATCTGAAT 58.802 37.500 0.00 0.00 35.10 2.57
2023 2280 8.082242 ACTCAATACAAAGTTAATGGTTCTTGC 58.918 33.333 0.00 0.00 0.00 4.01
2365 2702 9.220767 GGTTTTATTGATATCACCATACTCCTC 57.779 37.037 4.48 0.00 0.00 3.71
2509 2924 6.423182 TCCAAATACTGTAAATCCTCCCTTG 58.577 40.000 0.00 0.00 0.00 3.61
2527 2942 7.066525 CCTCCCTTGTTTGTTTTATCGCTATTA 59.933 37.037 0.00 0.00 0.00 0.98
2722 3260 0.329596 ATGGAGCCCCTGAGTTGTTC 59.670 55.000 0.00 0.00 0.00 3.18
2807 3345 3.012518 CTGGATCTTGGTTGTGGTGATC 58.987 50.000 0.00 0.00 34.48 2.92
2826 3364 8.723365 TGGTGATCCATATATTTGGTTTCTACT 58.277 33.333 11.44 0.00 39.03 2.57
2985 3523 4.141287 CAATGTTGAAGGTCACCCTGTTA 58.859 43.478 0.00 0.00 41.56 2.41
3216 3813 1.308069 GCATTTCTCCGGAAGCTGCA 61.308 55.000 18.04 0.00 39.53 4.41
3462 4066 0.246360 GTGGCCAACCTAAACATGCC 59.754 55.000 7.24 0.00 39.33 4.40
3768 4549 6.122850 TCTTGATATTGCAGGAAAATGACG 57.877 37.500 0.00 0.00 0.00 4.35
3914 4695 4.458397 CTTGACATGGATGCTCAGGTAAT 58.542 43.478 0.00 0.00 31.42 1.89
3981 4767 7.329962 AGCATCACACATTTGTTATCATGTTTG 59.670 33.333 0.00 0.00 31.66 2.93
4003 4789 1.670674 CCAACCATGCTTCATGTGTGC 60.671 52.381 6.12 0.00 39.94 4.57
4081 4869 2.037902 TGGAACAACAGGCGAATGTAGA 59.962 45.455 0.00 0.00 31.92 2.59
4083 4871 2.831685 ACAACAGGCGAATGTAGACA 57.168 45.000 0.00 0.00 31.70 3.41
4086 4874 4.827692 ACAACAGGCGAATGTAGACATAA 58.172 39.130 0.00 0.00 35.10 1.90
4087 4875 5.242434 ACAACAGGCGAATGTAGACATAAA 58.758 37.500 0.00 0.00 35.10 1.40
4088 4876 5.703592 ACAACAGGCGAATGTAGACATAAAA 59.296 36.000 0.00 0.00 35.10 1.52
4124 4912 3.318017 CGATGAAAACACGAAGAGGAGT 58.682 45.455 0.00 0.00 0.00 3.85
4183 4971 6.366877 TCGAAACGGGTTAAGAGATAACTTTG 59.633 38.462 0.00 0.00 42.93 2.77
4414 5330 9.695526 CCTTGAAAAAGATAACATCAAATGTGA 57.304 29.630 0.00 0.00 44.07 3.58
4420 5336 9.814899 AAAAGATAACATCAAATGTGACAAACA 57.185 25.926 0.00 0.00 44.07 2.83
4437 5354 5.640732 ACAAACAGTTGTTTTGCTACAGAG 58.359 37.500 7.48 0.00 46.01 3.35
4462 5389 3.195041 CGGTGTGTACTCACTGTGG 57.805 57.895 22.95 10.21 44.14 4.17
4483 5410 3.751175 GGACGACATGAAAATTCACCAGA 59.249 43.478 0.00 0.00 40.49 3.86
4566 5517 6.639632 TTTTCTAACTCATCAGCTTGCTTT 57.360 33.333 0.00 0.00 0.00 3.51
4573 5524 5.555017 ACTCATCAGCTTGCTTTAAGAAGA 58.445 37.500 0.00 0.00 38.76 2.87
4603 5554 2.132300 GGGGGCTGCACAAAGAAAA 58.868 52.632 3.46 0.00 0.00 2.29
4607 5558 2.611224 GGGGCTGCACAAAGAAAATCAG 60.611 50.000 3.46 0.00 0.00 2.90
4615 5566 8.801913 GCTGCACAAAGAAAATCAGAATATAAC 58.198 33.333 0.00 0.00 0.00 1.89
4644 5614 7.104939 CCCAAAAGAAATGAATCCATGCTTTA 58.895 34.615 0.00 0.00 37.29 1.85
4645 5615 7.607223 CCCAAAAGAAATGAATCCATGCTTTAA 59.393 33.333 0.00 0.00 37.29 1.52
4646 5616 9.169592 CCAAAAGAAATGAATCCATGCTTTAAT 57.830 29.630 0.00 0.00 37.29 1.40
4650 5620 8.953368 AGAAATGAATCCATGCTTTAATTTCC 57.047 30.769 17.14 7.13 32.36 3.13
4651 5621 8.542080 AGAAATGAATCCATGCTTTAATTTCCA 58.458 29.630 17.14 0.00 32.36 3.53
4828 5811 4.790140 CGAAAAGAAAAGATGCCTCGAATG 59.210 41.667 0.00 0.00 0.00 2.67
4832 5815 2.806945 AAAGATGCCTCGAATGGGAA 57.193 45.000 0.00 0.00 0.00 3.97
4933 6129 7.168972 CACAAATTTCAAAGCGGAATAAGAACA 59.831 33.333 0.00 0.00 0.00 3.18
4937 6133 2.467566 AAGCGGAATAAGAACACGGT 57.532 45.000 0.00 0.00 36.80 4.83
4938 6134 3.598019 AAGCGGAATAAGAACACGGTA 57.402 42.857 0.00 0.00 34.65 4.02
4939 6135 3.160777 AGCGGAATAAGAACACGGTAG 57.839 47.619 0.00 0.00 33.21 3.18
4941 6137 2.199236 CGGAATAAGAACACGGTAGGC 58.801 52.381 0.00 0.00 0.00 3.93
4942 6138 2.417651 CGGAATAAGAACACGGTAGGCA 60.418 50.000 0.00 0.00 0.00 4.75
4945 6141 4.094442 GGAATAAGAACACGGTAGGCAAAG 59.906 45.833 0.00 0.00 0.00 2.77
4946 6142 1.235724 AAGAACACGGTAGGCAAAGC 58.764 50.000 0.00 0.00 0.00 3.51
4947 6143 0.396811 AGAACACGGTAGGCAAAGCT 59.603 50.000 0.00 0.00 0.00 3.74
4958 6166 6.996282 ACGGTAGGCAAAGCTGTAATAATTAT 59.004 34.615 0.00 0.00 0.00 1.28
4978 6186 4.708726 ATGTAGAAATCAACAAGCAGGC 57.291 40.909 0.00 0.00 0.00 4.85
4979 6187 3.754965 TGTAGAAATCAACAAGCAGGCT 58.245 40.909 0.00 0.00 0.00 4.58
4980 6188 3.503363 TGTAGAAATCAACAAGCAGGCTG 59.497 43.478 10.94 10.94 0.00 4.85
4981 6189 1.271656 AGAAATCAACAAGCAGGCTGC 59.728 47.619 31.56 31.56 45.46 5.25
5033 6242 0.519077 GCTTTTCTCCTTGGTGCGAG 59.481 55.000 0.00 0.00 0.00 5.03
5058 6267 1.775385 AATAAATGGTTGGAGCCGGG 58.225 50.000 2.18 0.00 0.00 5.73
5080 6289 4.400251 AGGGGGCGAGCTGGTAGT 62.400 66.667 0.00 0.00 0.00 2.73
5088 6304 2.222886 GCGAGCTGGTAGTAGATGAGA 58.777 52.381 0.00 0.00 0.00 3.27
5099 6315 5.538433 GGTAGTAGATGAGAAGGAAGCAGAT 59.462 44.000 0.00 0.00 0.00 2.90
5105 6321 1.205893 GAGAAGGAAGCAGATGGACGT 59.794 52.381 0.00 0.00 0.00 4.34
5121 6337 4.446413 GTAGGCGGGGGTCACGTG 62.446 72.222 9.94 9.94 0.00 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 52 3.535561 AGCATATACCTATCCATTGCGC 58.464 45.455 0.00 0.00 33.99 6.09
59 61 3.306780 GGACACCGCAAGCATATACCTAT 60.307 47.826 0.00 0.00 0.00 2.57
60 62 2.036733 GGACACCGCAAGCATATACCTA 59.963 50.000 0.00 0.00 0.00 3.08
61 63 1.202651 GGACACCGCAAGCATATACCT 60.203 52.381 0.00 0.00 0.00 3.08
62 64 1.226746 GGACACCGCAAGCATATACC 58.773 55.000 0.00 0.00 0.00 2.73
122 128 3.351416 GGTGCCGTTTCGTGGTCC 61.351 66.667 0.00 0.00 0.00 4.46
124 130 3.485346 ATGGGTGCCGTTTCGTGGT 62.485 57.895 0.00 0.00 0.00 4.16
252 259 2.348411 ATAGTACCACATTGGCAGCC 57.652 50.000 3.66 3.66 42.67 4.85
286 294 2.556114 GCCCTGCAAGCCAAGGATATAT 60.556 50.000 0.36 0.00 0.00 0.86
296 307 3.976701 TAAGCTCGCCCTGCAAGCC 62.977 63.158 3.72 0.00 0.00 4.35
348 366 3.085947 CCTGGCTAGCTGGCTCCA 61.086 66.667 22.23 11.23 42.34 3.86
384 404 2.759795 GGCCTTTGAGTGGGCTCT 59.240 61.111 0.00 0.00 46.80 4.09
408 428 0.811281 CTTAGGGCTTTTTGGCTCGG 59.189 55.000 0.00 0.00 41.48 4.63
427 447 0.309612 TTTTCTGGCTCGCGGTTTTC 59.690 50.000 6.13 0.00 0.00 2.29
452 472 4.530857 CACGGGATGGACGAGGGC 62.531 72.222 0.00 0.00 34.93 5.19
512 536 2.646143 GCGCGAGGAGGTAGGATC 59.354 66.667 12.10 0.00 0.00 3.36
572 596 2.243602 ATCGAGACGACCTACCTCTC 57.756 55.000 0.00 0.00 39.18 3.20
600 629 6.153680 CCTACCTCTCTCTCTCTCTATCTCTC 59.846 50.000 0.00 0.00 0.00 3.20
606 635 2.976882 GCCCTACCTCTCTCTCTCTCTA 59.023 54.545 0.00 0.00 0.00 2.43
619 648 2.614013 CCCCCAAGTGCCCTACCT 60.614 66.667 0.00 0.00 0.00 3.08
621 650 2.675371 GTCCCCCAAGTGCCCTAC 59.325 66.667 0.00 0.00 0.00 3.18
623 652 4.974438 TCGTCCCCCAAGTGCCCT 62.974 66.667 0.00 0.00 0.00 5.19
627 656 1.302511 CCAAGTCGTCCCCCAAGTG 60.303 63.158 0.00 0.00 0.00 3.16
729 770 2.781174 ACCTCGTCTCTATCTTCCTCCT 59.219 50.000 0.00 0.00 0.00 3.69
732 773 2.303175 GCACCTCGTCTCTATCTTCCT 58.697 52.381 0.00 0.00 0.00 3.36
774 815 1.916506 TGGTGATCCCAATCGCAAAA 58.083 45.000 0.84 0.00 42.99 2.44
787 828 4.307032 AGCAGGTAAAATCAGTGGTGAT 57.693 40.909 0.00 0.00 46.01 3.06
788 829 3.788227 AGCAGGTAAAATCAGTGGTGA 57.212 42.857 0.00 0.00 37.02 4.02
792 833 6.992063 ACTCAATAGCAGGTAAAATCAGTG 57.008 37.500 0.00 0.00 0.00 3.66
800 841 6.177610 CAAACCCTAACTCAATAGCAGGTAA 58.822 40.000 0.00 0.00 29.77 2.85
827 868 2.281276 CAGCAGCACCAGCACTCA 60.281 61.111 0.00 0.00 45.49 3.41
828 869 0.959372 ATTCAGCAGCACCAGCACTC 60.959 55.000 0.00 0.00 45.49 3.51
829 870 0.538977 AATTCAGCAGCACCAGCACT 60.539 50.000 0.00 0.00 45.49 4.40
830 871 0.388134 CAATTCAGCAGCACCAGCAC 60.388 55.000 0.00 0.00 45.49 4.40
859 900 1.068943 TCGGCTCTCCCCCTCTCTAT 61.069 60.000 0.00 0.00 0.00 1.98
877 918 0.588252 GCATCACATACACCCGCATC 59.412 55.000 0.00 0.00 0.00 3.91
903 944 3.366781 GCAGCAAAGGAAGAAATCAGTCC 60.367 47.826 0.00 0.00 0.00 3.85
950 995 6.040391 GTCTATACCTCACTCTTGATCTGCTT 59.960 42.308 0.00 0.00 0.00 3.91
953 998 5.561919 GCGTCTATACCTCACTCTTGATCTG 60.562 48.000 0.00 0.00 0.00 2.90
971 1017 3.807538 GCGACACGGGAGCGTCTA 61.808 66.667 0.00 0.00 39.66 2.59
1086 1138 0.822532 ACGAGTTCACCTCCGACACT 60.823 55.000 0.00 0.00 36.82 3.55
1154 1206 2.758737 CGAGGTTAGGAGGGGCGT 60.759 66.667 0.00 0.00 0.00 5.68
1186 1238 4.373116 GACCACTGCCGAGGCGAA 62.373 66.667 9.78 0.00 45.51 4.70
1201 1253 1.342819 ACCAGAGTCAGTTCTGCAGAC 59.657 52.381 18.03 11.89 42.58 3.51
1230 1282 1.347378 TCTCCAGCTGCAACACACATA 59.653 47.619 8.66 0.00 0.00 2.29
1332 1530 1.528309 CTGTCCCTGGCACCGTTTT 60.528 57.895 0.00 0.00 0.00 2.43
1422 1620 5.990120 AAATCATGGGATAAAGCATAGCC 57.010 39.130 0.00 0.00 32.09 3.93
1446 1644 6.007936 AGCAACAACATAAAGCGACATAAA 57.992 33.333 0.00 0.00 0.00 1.40
1455 1653 6.724263 TGACTACACAAGCAACAACATAAAG 58.276 36.000 0.00 0.00 0.00 1.85
1737 1980 6.000246 TGTATGCTTTATCCCTGTTCATGA 58.000 37.500 0.00 0.00 0.00 3.07
1879 2126 6.723298 ATTCACCACAAGGAATTGTTTACA 57.277 33.333 0.00 0.00 38.69 2.41
1907 2157 6.817765 ACACTAGCAATAAAAAGCTGCTTA 57.182 33.333 16.31 0.00 43.83 3.09
1924 2174 7.706607 TGGTCGAATCAATCTCAAATACACTAG 59.293 37.037 0.00 0.00 0.00 2.57
2023 2280 2.601314 TCAATACGAATTCGAAGGTGCG 59.399 45.455 33.05 14.19 43.02 5.34
2365 2702 0.167470 CACAAATCCTGCAGCGACTG 59.833 55.000 8.66 10.55 34.12 3.51
2509 2924 8.628882 AGGCAAATAATAGCGATAAAACAAAC 57.371 30.769 0.00 0.00 0.00 2.93
2527 2942 5.263599 TCATGTACATGGAAGAAGGCAAAT 58.736 37.500 30.56 0.00 39.24 2.32
2697 3235 0.622665 CTCAGGGGCTCCATCAAGTT 59.377 55.000 4.79 0.00 34.83 2.66
2746 3284 7.360691 CGAAGCAACTCCATCTTATTGATATGG 60.361 40.741 0.00 0.00 41.33 2.74
2807 3345 9.868277 TGCAAAAAGTAGAAACCAAATATATGG 57.132 29.630 0.00 0.00 46.38 2.74
2985 3523 5.193099 AGTAGGAACTTGGCCATTATGTT 57.807 39.130 6.09 9.97 41.75 2.71
3216 3813 7.977853 CCAGTATCTTCAGCTAATTTTGCAATT 59.022 33.333 0.00 0.00 36.52 2.32
3441 4045 1.342819 GCATGTTTAGGTTGGCCACAA 59.657 47.619 3.88 0.00 37.19 3.33
3462 4066 5.574830 GCGTATATTAGACAAGGATGCAGAG 59.425 44.000 0.00 0.00 0.00 3.35
3768 4549 3.236005 GAGTTTTCTCTTCTCGTCCGTC 58.764 50.000 0.00 0.00 43.12 4.79
3914 4695 3.131400 GGGTTGGTTAGCACAAAGAAACA 59.869 43.478 0.00 0.00 0.00 2.83
3981 4767 1.888512 ACACATGAAGCATGGTTGGTC 59.111 47.619 16.18 1.03 45.16 4.02
4035 4823 3.632145 GCTTCCCTCACAAAGAACTTCAA 59.368 43.478 0.00 0.00 0.00 2.69
4124 4912 1.135112 AGAGCATTGTACATGTCGCGA 60.135 47.619 3.71 3.71 0.00 5.87
4167 4955 3.939592 AGCCGCCAAAGTTATCTCTTAAC 59.060 43.478 0.00 0.00 40.50 2.01
4420 5336 7.352739 CGTTAATTCTCTGTAGCAAAACAACT 58.647 34.615 0.00 0.00 0.00 3.16
4460 5387 3.481453 TGGTGAATTTTCATGTCGTCCA 58.519 40.909 0.00 0.00 39.73 4.02
4462 5389 5.356882 TTCTGGTGAATTTTCATGTCGTC 57.643 39.130 0.00 0.00 39.73 4.20
4483 5410 8.924511 TCTGTTTTATTCTTCAGTCAGGATTT 57.075 30.769 0.00 0.00 0.00 2.17
4644 5614 1.203162 TGAGGCACCCATGTGGAAATT 60.203 47.619 0.00 0.00 42.99 1.82
4645 5615 0.409092 TGAGGCACCCATGTGGAAAT 59.591 50.000 0.00 0.00 42.99 2.17
4646 5616 0.251297 CTGAGGCACCCATGTGGAAA 60.251 55.000 0.00 0.00 42.99 3.13
4647 5617 1.133181 TCTGAGGCACCCATGTGGAA 61.133 55.000 0.00 0.00 42.99 3.53
4648 5618 1.538629 TCTGAGGCACCCATGTGGA 60.539 57.895 0.00 0.00 42.99 4.02
4649 5619 1.077930 CTCTGAGGCACCCATGTGG 60.078 63.158 0.00 0.00 42.99 4.17
4650 5620 0.904649 TACTCTGAGGCACCCATGTG 59.095 55.000 9.85 0.00 45.65 3.21
4651 5621 1.885049 ATACTCTGAGGCACCCATGT 58.115 50.000 9.85 0.00 0.00 3.21
4656 5626 1.409427 AGCGTAATACTCTGAGGCACC 59.591 52.381 9.85 0.00 0.00 5.01
4769 5748 4.274950 TGTTCTTTCTTCGTGGTTTGATCC 59.725 41.667 0.00 0.00 0.00 3.36
4828 5811 2.087646 GACTTGCCTGTGAGATTTCCC 58.912 52.381 0.00 0.00 0.00 3.97
4832 5815 3.777106 TCTTGACTTGCCTGTGAGATT 57.223 42.857 0.00 0.00 0.00 2.40
4902 5924 6.917217 TTCCGCTTTGAAATTTGTGATTTT 57.083 29.167 0.00 0.00 0.00 1.82
4933 6129 2.781681 ATTACAGCTTTGCCTACCGT 57.218 45.000 0.00 0.00 0.00 4.83
4938 6134 9.627123 TTCTACATAATTATTACAGCTTTGCCT 57.373 29.630 0.00 0.00 0.00 4.75
4958 6166 3.503363 CAGCCTGCTTGTTGATTTCTACA 59.497 43.478 0.00 0.00 0.00 2.74
4985 6193 4.463879 CTCCCGTCTGGCAGCCTG 62.464 72.222 14.15 13.09 0.00 4.85
4986 6194 2.589610 TATCTCCCGTCTGGCAGCCT 62.590 60.000 14.15 0.00 0.00 4.58
5033 6242 3.489229 GGCTCCAACCATTTATTTCGCTC 60.489 47.826 0.00 0.00 0.00 5.03
5041 6250 1.208844 TCCCCGGCTCCAACCATTTA 61.209 55.000 0.00 0.00 0.00 1.40
5058 6267 4.247380 CAGCTCGCCCCCTCATCC 62.247 72.222 0.00 0.00 0.00 3.51
5080 6289 4.343526 GTCCATCTGCTTCCTTCTCATCTA 59.656 45.833 0.00 0.00 0.00 1.98
5088 6304 1.482593 CCTACGTCCATCTGCTTCCTT 59.517 52.381 0.00 0.00 0.00 3.36
5121 6337 2.680370 GGACCACCCCACATCCTCC 61.680 68.421 0.00 0.00 0.00 4.30
5122 6338 1.281925 ATGGACCACCCCACATCCTC 61.282 60.000 0.00 0.00 39.34 3.71
5123 6339 1.230281 ATGGACCACCCCACATCCT 60.230 57.895 0.00 0.00 39.34 3.24


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

AutoCloner maintained by Alex Coulton.