Multiple sequence alignment - TraesCS7D01G165900

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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 TraesCS7D01G165900 chr7D 100.000 4357 0 0 1 4357 115822132 115826488 0.000000e+00 8046.0
1 TraesCS7D01G165900 chr7D 93.318 1721 81 17 2108 3814 116090776 116092476 0.000000e+00 2510.0
2 TraesCS7D01G165900 chr7D 94.151 530 29 2 847 1374 116433002 116433531 0.000000e+00 806.0
3 TraesCS7D01G165900 chr7D 83.227 787 96 14 1867 2638 116434100 116434865 0.000000e+00 689.0
4 TraesCS7D01G165900 chr7D 86.874 579 66 8 2852 3421 116435706 116436283 1.320000e-179 640.0
5 TraesCS7D01G165900 chr7D 94.304 316 14 4 3772 4084 115442454 115442768 8.470000e-132 481.0
6 TraesCS7D01G165900 chr7D 90.000 360 35 1 845 1203 116052181 116052540 8.530000e-127 464.0
7 TraesCS7D01G165900 chr7D 91.304 253 19 1 1586 1835 116063385 116063637 4.170000e-90 342.0
8 TraesCS7D01G165900 chr7D 81.319 455 35 25 1378 1795 116433501 116433942 1.510000e-84 324.0
9 TraesCS7D01G165900 chr7D 88.325 197 15 4 4166 4357 116092630 116092823 3.390000e-56 230.0
10 TraesCS7D01G165900 chr7D 96.460 113 2 1 1867 1977 116063841 116063953 7.440000e-43 185.0
11 TraesCS7D01G165900 chr7D 97.222 36 1 0 1373 1408 115823470 115823505 1.310000e-05 62.1
12 TraesCS7D01G165900 chr7D 97.222 36 1 0 1339 1374 115823504 115823539 1.310000e-05 62.1
13 TraesCS7D01G165900 chr7A 91.258 2082 130 21 1374 3421 120464147 120466210 0.000000e+00 2789.0
14 TraesCS7D01G165900 chr7A 95.104 531 25 1 845 1374 120463651 120464181 0.000000e+00 835.0
15 TraesCS7D01G165900 chr7A 88.000 625 54 10 2850 3461 120218618 120219234 0.000000e+00 719.0
16 TraesCS7D01G165900 chr7A 80.839 715 79 27 847 1552 120217676 120218341 3.890000e-140 508.0
17 TraesCS7D01G165900 chr7A 86.017 472 42 12 3891 4357 120233377 120233829 6.550000e-133 484.0
18 TraesCS7D01G165900 chr7A 89.677 310 20 7 3600 3908 120233063 120233361 6.840000e-103 385.0
19 TraesCS7D01G165900 chr5D 98.140 699 12 1 148 845 514304577 514303879 0.000000e+00 1218.0
20 TraesCS7D01G165900 chr3A 85.600 875 88 14 1 844 203418440 203419307 0.000000e+00 883.0
21 TraesCS7D01G165900 chr7B 83.243 740 93 17 1931 2659 75024820 75025539 0.000000e+00 651.0
22 TraesCS7D01G165900 chr7B 85.616 584 70 8 2852 3421 75026576 75027159 6.230000e-168 601.0
23 TraesCS7D01G165900 chr7B 90.886 395 20 3 847 1240 75024105 75024484 2.320000e-142 516.0
24 TraesCS7D01G165900 chr7B 84.615 520 40 16 3846 4357 74860757 74861244 8.470000e-132 481.0
25 TraesCS7D01G165900 chr7B 91.941 273 21 1 3189 3461 74857667 74857938 8.840000e-102 381.0
26 TraesCS7D01G165900 chr7B 86.416 346 35 3 2850 3193 74857181 74857516 6.880000e-98 368.0
27 TraesCS7D01G165900 chr7B 89.565 115 10 2 1262 1374 75024477 75024591 1.260000e-30 145.0
28 TraesCS7D01G165900 chr7B 88.506 87 10 0 2619 2705 75025853 75025939 5.960000e-19 106.0
29 TraesCS7D01G165900 chr5B 80.559 895 112 33 1 844 239009436 239010319 2.210000e-177 632.0
30 TraesCS7D01G165900 chr5B 87.059 170 19 3 1 168 655905148 655905316 5.750000e-44 189.0
31 TraesCS7D01G165900 chr5A 86.458 480 47 9 1 462 99014651 99015130 1.080000e-140 510.0
32 TraesCS7D01G165900 chr5A 86.269 386 44 4 475 852 99016684 99017068 1.130000e-110 411.0
33 TraesCS7D01G165900 chr6B 77.580 901 119 46 1 844 703781655 703782529 6.600000e-128 468.0
34 TraesCS7D01G165900 chr4A 85.017 287 26 12 1 275 201599528 201599247 4.290000e-70 276.0
35 TraesCS7D01G165900 chr4A 88.235 119 14 0 726 844 201597230 201597112 4.540000e-30 143.0
36 TraesCS7D01G165900 chr3B 83.067 313 37 10 1 303 602234234 602233928 2.000000e-68 270.0
37 TraesCS7D01G165900 chr1A 80.347 346 47 16 1 338 8117984 8118316 4.350000e-60 243.0
38 TraesCS7D01G165900 chr1A 85.088 228 26 5 621 844 8119374 8119597 4.380000e-55 226.0
39 TraesCS7D01G165900 chr1B 88.889 171 18 1 675 844 169024129 169024299 4.420000e-50 209.0
40 TraesCS7D01G165900 chr1B 87.059 170 19 3 1 168 169013895 169014063 5.750000e-44 189.0
41 TraesCS7D01G165900 chrUn 79.104 335 31 25 1 327 95403815 95404118 1.240000e-45 195.0
42 TraesCS7D01G165900 chr1D 77.844 334 29 25 1 326 113995197 113995493 9.690000e-37 165.0
43 TraesCS7D01G165900 chr1D 80.198 101 13 4 742 842 478269046 478269139 7.820000e-08 69.4
44 TraesCS7D01G165900 chr6A 82.955 88 13 2 3478 3564 126061605 126061691 1.300000e-10 78.7


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 TraesCS7D01G165900 chr7D 115822132 115826488 4356 False 2723.40 8046 98.148000 1 4357 3 chr7D.!!$F3 4356
1 TraesCS7D01G165900 chr7D 116090776 116092823 2047 False 1370.00 2510 90.821500 2108 4357 2 chr7D.!!$F5 2249
2 TraesCS7D01G165900 chr7D 116433002 116436283 3281 False 614.75 806 86.392750 847 3421 4 chr7D.!!$F6 2574
3 TraesCS7D01G165900 chr7D 116063385 116063953 568 False 263.50 342 93.882000 1586 1977 2 chr7D.!!$F4 391
4 TraesCS7D01G165900 chr7A 120463651 120466210 2559 False 1812.00 2789 93.181000 845 3421 2 chr7A.!!$F3 2576
5 TraesCS7D01G165900 chr7A 120217676 120219234 1558 False 613.50 719 84.419500 847 3461 2 chr7A.!!$F1 2614
6 TraesCS7D01G165900 chr7A 120233063 120233829 766 False 434.50 484 87.847000 3600 4357 2 chr7A.!!$F2 757
7 TraesCS7D01G165900 chr5D 514303879 514304577 698 True 1218.00 1218 98.140000 148 845 1 chr5D.!!$R1 697
8 TraesCS7D01G165900 chr3A 203418440 203419307 867 False 883.00 883 85.600000 1 844 1 chr3A.!!$F1 843
9 TraesCS7D01G165900 chr7B 74857181 74861244 4063 False 410.00 481 87.657333 2850 4357 3 chr7B.!!$F1 1507
10 TraesCS7D01G165900 chr7B 75024105 75027159 3054 False 403.80 651 87.563200 847 3421 5 chr7B.!!$F2 2574
11 TraesCS7D01G165900 chr5B 239009436 239010319 883 False 632.00 632 80.559000 1 844 1 chr5B.!!$F1 843
12 TraesCS7D01G165900 chr5A 99014651 99017068 2417 False 460.50 510 86.363500 1 852 2 chr5A.!!$F1 851
13 TraesCS7D01G165900 chr6B 703781655 703782529 874 False 468.00 468 77.580000 1 844 1 chr6B.!!$F1 843
14 TraesCS7D01G165900 chr4A 201597112 201599528 2416 True 209.50 276 86.626000 1 844 2 chr4A.!!$R1 843
15 TraesCS7D01G165900 chr1A 8117984 8119597 1613 False 234.50 243 82.717500 1 844 2 chr1A.!!$F1 843

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
102 103 0.036732 TGACCCAGATTGAGGTGCAC 59.963 55.000 8.8 8.8 36.17 4.57 F
1780 5899 0.244721 GGTGCCAAACAGAGAATGCC 59.755 55.000 0.0 0.0 0.00 4.40 F
2008 6392 4.028852 TGCTATCTTGCTATATACGCCG 57.971 45.455 0.0 0.0 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 6374 0.037697 TGGGCGGCGTATATAGCAAG 60.038 55.000 9.37 1.18 36.08 4.01 R
2783 7756 1.134946 GCATGAAGGTGCCATGGTTAC 59.865 52.381 14.67 12.79 41.13 2.50 R
3854 11826 0.319641 GGAGGAAGACAACGAGCGTT 60.320 55.000 1.93 1.93 39.13 4.84 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
102 103 0.036732 TGACCCAGATTGAGGTGCAC 59.963 55.000 8.80 8.80 36.17 4.57
338 379 4.789075 GACCTTACGCGAGCGGCA 62.789 66.667 21.69 6.20 43.84 5.69
339 391 4.796231 ACCTTACGCGAGCGGCAG 62.796 66.667 21.69 15.26 43.84 4.85
529 2154 5.652014 TGTGGGAAAGTAATTATGGCAGAAG 59.348 40.000 0.00 0.00 0.00 2.85
685 3087 5.470368 CAACTTCATCGGGATGTATCGTAT 58.530 41.667 8.41 0.00 39.72 3.06
695 3101 4.261656 GGGATGTATCGTATCGGATCATCC 60.262 50.000 18.76 18.76 42.58 3.51
718 3124 1.800681 GAAACCCTTTGGATCGCGG 59.199 57.895 6.13 0.00 34.81 6.46
740 4746 2.022129 GCATCCCCGATTAGCGTCG 61.022 63.158 2.80 2.80 41.13 5.12
777 4783 1.080298 GTCGAACCACGTTCCGGAT 60.080 57.895 4.15 0.00 39.14 4.18
882 4894 3.349006 CGACGCCTGCTGCAAAGT 61.349 61.111 3.02 3.83 41.33 2.66
1171 5184 3.382832 ACAGAGGCCCCTTCGACG 61.383 66.667 0.00 0.00 0.00 5.12
1301 5314 1.743394 CGACAGGCTTATTTTGGGGAC 59.257 52.381 0.00 0.00 0.00 4.46
1311 5324 3.713826 ATTTTGGGGACTCGTGTATGT 57.286 42.857 0.00 0.00 0.00 2.29
1340 5353 4.912766 TCGTTTGGAAATTATTGCGTTGTC 59.087 37.500 0.00 0.00 0.00 3.18
1345 5358 7.778470 TTGGAAATTATTGCGTTGTCTTTTT 57.222 28.000 0.00 0.00 0.00 1.94
1368 5381 8.821686 TTTTAGGATTCTTTTGATGCTATGGA 57.178 30.769 0.00 0.00 0.00 3.41
1369 5382 8.455903 TTTAGGATTCTTTTGATGCTATGGAG 57.544 34.615 0.00 0.00 0.00 3.86
1677 5793 1.226688 AGTGTGATCATCCGTCGCG 60.227 57.895 0.00 0.00 0.00 5.87
1755 5874 8.314751 AGTTAGTACTTACTACTTGGTACTCGA 58.685 37.037 12.70 0.00 42.27 4.04
1780 5899 0.244721 GGTGCCAAACAGAGAATGCC 59.755 55.000 0.00 0.00 0.00 4.40
2006 6390 5.321983 GCATGCTATCTTGCTATATACGC 57.678 43.478 11.37 0.00 39.47 4.42
2007 6391 4.210120 GCATGCTATCTTGCTATATACGCC 59.790 45.833 11.37 0.00 39.47 5.68
2008 6392 4.028852 TGCTATCTTGCTATATACGCCG 57.971 45.455 0.00 0.00 0.00 6.46
2054 6438 5.450453 TGGTTGTGGTTTCCTAAATCTGAA 58.550 37.500 0.00 0.00 0.00 3.02
2176 6564 5.659440 TTTTAAGCATCAGCCTAAAAGGG 57.341 39.130 0.00 0.00 40.10 3.95
2236 6626 9.840427 ATACATAAACATGAAAACTTTCCGAAG 57.160 29.630 0.00 0.00 36.36 3.79
2246 6636 9.838339 ATGAAAACTTTCCGAAGTATCTATCAT 57.162 29.630 0.00 0.00 45.18 2.45
2546 6944 6.306987 ACCAACCTTAACAGAACATGAAGAT 58.693 36.000 0.00 0.00 0.00 2.40
2764 7737 9.319060 ACCAATCAGCTAGATGAGAAGAATATA 57.681 33.333 16.87 0.00 36.96 0.86
2783 7756 9.136323 AGAATATATTTTTCTTTAGCTGGTGGG 57.864 33.333 0.00 0.00 29.12 4.61
2921 8180 4.579869 AGTCGTCCAAAATCTACAATGCT 58.420 39.130 0.00 0.00 0.00 3.79
2927 8186 5.125417 GTCCAAAATCTACAATGCTAAGCCA 59.875 40.000 0.00 0.00 0.00 4.75
2955 8214 1.598701 GGCAAGTGCTGGGGATGTTC 61.599 60.000 2.85 0.00 41.70 3.18
3116 8382 2.353610 CCCAATGAAGTGCAGGGCC 61.354 63.158 0.00 0.00 31.81 5.80
3177 8443 2.295909 AGTAGGAGCGAAGATGAGCATC 59.704 50.000 2.27 2.27 38.09 3.91
3389 8820 8.116753 GGTGTATCTGTATTTTCATCTTCAACG 58.883 37.037 0.00 0.00 0.00 4.10
3393 8824 7.962964 TCTGTATTTTCATCTTCAACGACTT 57.037 32.000 0.00 0.00 0.00 3.01
3396 8827 8.596271 TGTATTTTCATCTTCAACGACTTGTA 57.404 30.769 0.00 0.00 0.00 2.41
3411 8842 6.106673 ACGACTTGTATCCATTTTAGACTGG 58.893 40.000 0.00 0.00 0.00 4.00
3417 8848 6.980577 TGTATCCATTTTAGACTGGGGAATT 58.019 36.000 0.00 0.00 33.13 2.17
3421 8852 7.758820 TCCATTTTAGACTGGGGAATTAGTA 57.241 36.000 0.00 0.00 33.13 1.82
3441 8872 4.833380 AGTAAGAGTAACTCCAACAGCTCA 59.167 41.667 0.00 0.00 0.00 4.26
3463 8894 5.808540 TCACCTATCTTCAAATTAACCGTCG 59.191 40.000 0.00 0.00 0.00 5.12
3482 8916 3.245519 GTCGTTGAAGTTGAGACCAGTTC 59.754 47.826 0.00 0.00 0.00 3.01
3506 8940 5.350640 CCGTAAACTGGCCTTAACTTTAGAG 59.649 44.000 3.32 0.00 0.00 2.43
3513 8947 4.538490 TGGCCTTAACTTTAGAGAATCCCA 59.462 41.667 3.32 0.00 33.66 4.37
3524 8958 8.832735 ACTTTAGAGAATCCCATAAAAGTGGTA 58.167 33.333 0.00 0.00 37.57 3.25
3534 8968 5.340027 CCCATAAAAGTGGTATGTTCTCCCT 60.340 44.000 0.00 0.00 37.57 4.20
3553 8987 2.618045 CCTGCAGGTTTACGGGAAGATT 60.618 50.000 25.53 0.00 33.88 2.40
3625 9059 5.768662 TCTTTCCGTATCTCTAATGTCGGAT 59.231 40.000 5.01 0.00 44.73 4.18
3652 9086 6.947733 GGAATCATATACCAAATGTCCCATGA 59.052 38.462 0.00 0.00 0.00 3.07
3684 9120 3.131755 TCGATCATCTGTGCACTGAATCT 59.868 43.478 27.23 15.51 0.00 2.40
3685 9121 3.245519 CGATCATCTGTGCACTGAATCTG 59.754 47.826 27.23 20.93 0.00 2.90
3686 9122 3.967332 TCATCTGTGCACTGAATCTGA 57.033 42.857 27.23 22.59 0.00 3.27
3687 9123 4.482952 TCATCTGTGCACTGAATCTGAT 57.517 40.909 27.23 9.63 0.00 2.90
3688 9124 4.439968 TCATCTGTGCACTGAATCTGATC 58.560 43.478 27.23 0.00 0.00 2.92
3689 9125 4.161754 TCATCTGTGCACTGAATCTGATCT 59.838 41.667 27.23 8.25 0.00 2.75
3690 9126 4.120792 TCTGTGCACTGAATCTGATCTC 57.879 45.455 22.45 0.00 0.00 2.75
3691 9127 3.768215 TCTGTGCACTGAATCTGATCTCT 59.232 43.478 22.45 0.00 0.00 3.10
3692 9128 4.114073 CTGTGCACTGAATCTGATCTCTC 58.886 47.826 19.41 0.00 0.00 3.20
3693 9129 3.768215 TGTGCACTGAATCTGATCTCTCT 59.232 43.478 19.41 0.00 0.00 3.10
3694 9130 4.142204 TGTGCACTGAATCTGATCTCTCTC 60.142 45.833 19.41 0.00 0.00 3.20
3695 9131 4.098349 GTGCACTGAATCTGATCTCTCTCT 59.902 45.833 10.32 0.00 0.00 3.10
3696 9132 4.338964 TGCACTGAATCTGATCTCTCTCTC 59.661 45.833 0.00 0.00 0.00 3.20
3697 9133 4.581824 GCACTGAATCTGATCTCTCTCTCT 59.418 45.833 0.00 0.00 0.00 3.10
3698 9134 5.278169 GCACTGAATCTGATCTCTCTCTCTC 60.278 48.000 0.00 0.00 0.00 3.20
3699 9135 6.060136 CACTGAATCTGATCTCTCTCTCTCT 58.940 44.000 0.00 0.00 0.00 3.10
3700 9136 6.204301 CACTGAATCTGATCTCTCTCTCTCTC 59.796 46.154 0.00 0.00 0.00 3.20
3816 11788 2.778278 GGAGGCCCATCCCCATCA 60.778 66.667 0.00 0.00 32.79 3.07
3818 11790 3.482232 GAGGCCCATCCCCATCACG 62.482 68.421 0.00 0.00 34.51 4.35
3819 11791 3.809013 GGCCCATCCCCATCACGT 61.809 66.667 0.00 0.00 0.00 4.49
3820 11792 2.516930 GCCCATCCCCATCACGTG 60.517 66.667 9.94 9.94 0.00 4.49
3821 11793 2.516930 CCCATCCCCATCACGTGC 60.517 66.667 11.67 0.00 0.00 5.34
3822 11794 2.516930 CCATCCCCATCACGTGCC 60.517 66.667 11.67 0.00 0.00 5.01
3823 11795 2.271821 CATCCCCATCACGTGCCA 59.728 61.111 11.67 0.00 0.00 4.92
3824 11796 1.820906 CATCCCCATCACGTGCCAG 60.821 63.158 11.67 2.56 0.00 4.85
3825 11797 3.704231 ATCCCCATCACGTGCCAGC 62.704 63.158 11.67 0.00 0.00 4.85
3853 11825 4.874977 GGACGCCTAGCCGAGTGC 62.875 72.222 0.00 0.00 41.71 4.40
3854 11826 4.129737 GACGCCTAGCCGAGTGCA 62.130 66.667 0.00 0.00 44.83 4.57
3855 11827 3.642778 GACGCCTAGCCGAGTGCAA 62.643 63.158 0.00 0.00 44.83 4.08
3856 11828 3.188786 CGCCTAGCCGAGTGCAAC 61.189 66.667 0.00 0.00 44.83 4.17
3857 11829 3.188786 GCCTAGCCGAGTGCAACG 61.189 66.667 7.45 7.45 45.86 4.10
3858 11830 3.188786 CCTAGCCGAGTGCAACGC 61.189 66.667 8.71 5.34 45.86 4.84
3875 11847 0.734253 CGCTCGTTGTCTTCCTCCTG 60.734 60.000 0.00 0.00 0.00 3.86
3876 11848 0.390472 GCTCGTTGTCTTCCTCCTGG 60.390 60.000 0.00 0.00 0.00 4.45
3988 12005 0.802607 GATTCTGCCACTCGTCCGTC 60.803 60.000 0.00 0.00 0.00 4.79
4084 12107 4.487412 CCACGCGTACTCCCGGAC 62.487 72.222 13.44 0.00 0.00 4.79
4089 12112 2.832201 CGTACTCCCGGACCTCCC 60.832 72.222 0.73 0.00 0.00 4.30
4093 12116 1.000590 TACTCCCGGACCTCCCCATA 61.001 60.000 0.73 0.00 0.00 2.74
4095 12118 0.693092 CTCCCGGACCTCCCCATAAA 60.693 60.000 0.73 0.00 0.00 1.40
4097 12120 0.626916 CCCGGACCTCCCCATAAAAA 59.373 55.000 0.73 0.00 0.00 1.94
4120 12143 2.412937 CAATCGCGCATTTCCCCC 59.587 61.111 8.75 0.00 0.00 5.40
4151 12176 2.040544 CGCTTCGCAACCTTCCCAT 61.041 57.895 0.00 0.00 0.00 4.00
4152 12177 1.508088 GCTTCGCAACCTTCCCATG 59.492 57.895 0.00 0.00 0.00 3.66
4161 12186 2.679092 CTTCCCATGCCAGAGCCA 59.321 61.111 0.00 0.00 38.69 4.75
4259 12290 3.267860 GCCTCTCGCCATTGCTCG 61.268 66.667 0.00 0.00 34.43 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 0.689080 ATCTGGGTCAGCGTCCATCT 60.689 55.000 0.00 0.00 31.95 2.90
102 103 1.945394 CATTCTGGCCTCTTGGAATCG 59.055 52.381 3.32 0.00 34.57 3.34
134 136 3.430453 CCCATGAACCCAGTACATGTTT 58.570 45.455 2.30 0.00 39.47 2.83
144 147 1.496001 CATCAGATCCCCATGAACCCA 59.504 52.381 0.00 0.00 0.00 4.51
146 149 1.144503 AGCATCAGATCCCCATGAACC 59.855 52.381 0.00 0.00 0.00 3.62
291 315 2.728435 GGTAACCGGAGTGCGGGAT 61.728 63.158 27.61 17.50 37.87 3.85
437 504 1.967319 TCTTCAAACCACCAGTCTGC 58.033 50.000 0.00 0.00 0.00 4.26
695 3101 1.173913 GATCCAAAGGGTTTCGGGTG 58.826 55.000 0.00 0.00 34.93 4.61
718 3124 1.668151 GCTAATCGGGGATGCGGAC 60.668 63.158 0.00 0.00 0.00 4.79
740 4746 4.091655 TCGACGAGAGATATACATCTTCGC 59.908 45.833 12.46 7.28 41.78 4.70
882 4894 1.891919 GCGTGGTTCTTGTGCTGGA 60.892 57.895 0.00 0.00 0.00 3.86
988 5001 1.639635 ATCGGCATTGCTCTCCCCTT 61.640 55.000 8.82 0.00 0.00 3.95
989 5002 2.049627 GATCGGCATTGCTCTCCCCT 62.050 60.000 8.82 0.00 0.00 4.79
1154 5167 3.382832 CGTCGAAGGGGCCTCTGT 61.383 66.667 5.46 0.00 0.00 3.41
1301 5314 2.561733 ACGATCCACACATACACGAG 57.438 50.000 0.00 0.00 0.00 4.18
1311 5324 5.406649 GCAATAATTTCCAAACGATCCACA 58.593 37.500 0.00 0.00 0.00 4.17
1677 5793 0.952010 ATGCCAAACACGGTCCGTAC 60.952 55.000 18.38 3.36 38.32 3.67
1755 5874 5.625197 GCATTCTCTGTTTGGCACCATTATT 60.625 40.000 0.00 0.00 0.00 1.40
1844 6138 3.066760 GTGAAACAGCTGGCAACTAAAGT 59.933 43.478 19.93 0.00 36.32 2.66
1993 6374 0.037697 TGGGCGGCGTATATAGCAAG 60.038 55.000 9.37 1.18 36.08 4.01
2006 6390 0.537371 AGTTTTGGAGTCTTGGGCGG 60.537 55.000 0.00 0.00 0.00 6.13
2007 6391 1.266989 GAAGTTTTGGAGTCTTGGGCG 59.733 52.381 0.00 0.00 0.00 6.13
2008 6392 2.294512 CAGAAGTTTTGGAGTCTTGGGC 59.705 50.000 0.00 0.00 0.00 5.36
2054 6438 7.093377 TGGAACTAACGGTTATACATACCAGTT 60.093 37.037 0.29 0.64 38.41 3.16
2523 6921 6.127897 GGATCTTCATGTTCTGTTAAGGTTGG 60.128 42.308 0.00 0.00 0.00 3.77
2764 7737 5.245301 GGTTACCCACCAGCTAAAGAAAAAT 59.755 40.000 0.00 0.00 46.42 1.82
2783 7756 1.134946 GCATGAAGGTGCCATGGTTAC 59.865 52.381 14.67 12.79 41.13 2.50
2927 8186 1.410153 CCAGCACTTGCCAAAGAACTT 59.590 47.619 0.00 0.00 43.38 2.66
2955 8214 3.538634 TGATGATTGAGGTGAGAGCAG 57.461 47.619 0.00 0.00 0.00 4.24
3177 8443 1.419922 GCATGTCGTTACAGCACCG 59.580 57.895 0.00 0.00 39.49 4.94
3396 8827 7.226059 ACTAATTCCCCAGTCTAAAATGGAT 57.774 36.000 0.00 0.00 39.02 3.41
3411 8842 7.618137 TGTTGGAGTTACTCTTACTAATTCCC 58.382 38.462 12.41 0.00 31.83 3.97
3417 8848 6.008331 TGAGCTGTTGGAGTTACTCTTACTA 58.992 40.000 12.41 2.25 0.00 1.82
3421 8852 3.244249 GGTGAGCTGTTGGAGTTACTCTT 60.244 47.826 12.41 0.00 0.00 2.85
3441 8872 5.727434 ACGACGGTTAATTTGAAGATAGGT 58.273 37.500 0.00 0.00 0.00 3.08
3463 8894 2.544267 CGGAACTGGTCTCAACTTCAAC 59.456 50.000 0.00 0.00 0.00 3.18
3482 8916 5.240121 TCTAAAGTTAAGGCCAGTTTACGG 58.760 41.667 5.01 0.00 0.00 4.02
3506 8940 7.013369 GGAGAACATACCACTTTTATGGGATTC 59.987 40.741 0.00 0.00 40.82 2.52
3513 8947 5.193679 GCAGGGAGAACATACCACTTTTAT 58.806 41.667 0.00 0.00 0.00 1.40
3524 8958 2.615493 CGTAAACCTGCAGGGAGAACAT 60.615 50.000 35.42 11.03 40.27 2.71
3534 8968 2.871096 AATCTTCCCGTAAACCTGCA 57.129 45.000 0.00 0.00 0.00 4.41
3553 8987 2.093128 GCCAAGGAGAAACGGGAAGATA 60.093 50.000 0.00 0.00 0.00 1.98
3595 9029 5.786264 TTAGAGATACGGAAAGATGGACC 57.214 43.478 0.00 0.00 0.00 4.46
3625 9059 5.135191 TGGGACATTTGGTATATGATTCCCA 59.865 40.000 9.09 9.09 41.97 4.37
3652 9086 4.201891 GCACAGATGATCGAAATTGCTCTT 60.202 41.667 0.00 0.00 0.00 2.85
3684 9120 5.462240 AGAGAGAGAGAGAGAGAGAGATCA 58.538 45.833 0.00 0.00 0.00 2.92
3685 9121 5.774690 AGAGAGAGAGAGAGAGAGAGAGATC 59.225 48.000 0.00 0.00 0.00 2.75
3686 9122 5.714863 AGAGAGAGAGAGAGAGAGAGAGAT 58.285 45.833 0.00 0.00 0.00 2.75
3687 9123 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
3688 9124 5.221422 GGAAGAGAGAGAGAGAGAGAGAGAG 60.221 52.000 0.00 0.00 0.00 3.20
3689 9125 4.651503 GGAAGAGAGAGAGAGAGAGAGAGA 59.348 50.000 0.00 0.00 0.00 3.10
3690 9126 4.653341 AGGAAGAGAGAGAGAGAGAGAGAG 59.347 50.000 0.00 0.00 0.00 3.20
3691 9127 4.624913 AGGAAGAGAGAGAGAGAGAGAGA 58.375 47.826 0.00 0.00 0.00 3.10
3692 9128 5.365021 AAGGAAGAGAGAGAGAGAGAGAG 57.635 47.826 0.00 0.00 0.00 3.20
3693 9129 5.779241 AAAGGAAGAGAGAGAGAGAGAGA 57.221 43.478 0.00 0.00 0.00 3.10
3694 9130 6.840780 AAAAAGGAAGAGAGAGAGAGAGAG 57.159 41.667 0.00 0.00 0.00 3.20
3720 9156 5.520748 AGGAAGAAAGAGAGAGAGAGTCT 57.479 43.478 0.00 0.00 38.71 3.24
3721 9157 6.434340 AGAAAGGAAGAAAGAGAGAGAGAGTC 59.566 42.308 0.00 0.00 0.00 3.36
3722 9158 6.314917 AGAAAGGAAGAAAGAGAGAGAGAGT 58.685 40.000 0.00 0.00 0.00 3.24
3835 11807 4.554363 CACTCGGCTAGGCGTCCG 62.554 72.222 34.02 25.08 46.52 4.79
3836 11808 4.874977 GCACTCGGCTAGGCGTCC 62.875 72.222 34.02 18.51 40.25 4.79
3837 11809 3.642778 TTGCACTCGGCTAGGCGTC 62.643 63.158 34.02 22.07 45.15 5.19
3838 11810 3.691342 TTGCACTCGGCTAGGCGT 61.691 61.111 34.02 16.79 45.15 5.68
3839 11811 3.188786 GTTGCACTCGGCTAGGCG 61.189 66.667 31.00 31.00 45.15 5.52
3840 11812 3.188786 CGTTGCACTCGGCTAGGC 61.189 66.667 6.15 6.15 45.15 3.93
3841 11813 3.188786 GCGTTGCACTCGGCTAGG 61.189 66.667 11.50 0.00 45.15 3.02
3842 11814 2.125912 AGCGTTGCACTCGGCTAG 60.126 61.111 11.50 0.00 45.15 3.42
3843 11815 2.126071 GAGCGTTGCACTCGGCTA 60.126 61.111 11.50 0.00 45.15 3.93
3854 11826 0.319641 GGAGGAAGACAACGAGCGTT 60.320 55.000 1.93 1.93 39.13 4.84
3855 11827 1.179814 AGGAGGAAGACAACGAGCGT 61.180 55.000 0.00 0.00 0.00 5.07
3856 11828 0.734253 CAGGAGGAAGACAACGAGCG 60.734 60.000 0.00 0.00 0.00 5.03
3857 11829 0.390472 CCAGGAGGAAGACAACGAGC 60.390 60.000 0.00 0.00 36.89 5.03
3858 11830 1.203523 CTCCAGGAGGAAGACAACGAG 59.796 57.143 8.88 0.00 45.19 4.18
3900 11905 0.436531 CGTTTCTGCTGCTTCGTCTC 59.563 55.000 0.00 0.00 0.00 3.36
3988 12005 4.938226 GTCAGTTTCTGGAGGTGGATTTAG 59.062 45.833 0.00 0.00 31.51 1.85
4044 12061 0.883370 GGGTGACGTTTGGAGTGGTC 60.883 60.000 0.00 0.00 0.00 4.02
4077 12100 0.253254 TTTTATGGGGAGGTCCGGGA 60.253 55.000 0.00 0.00 36.71 5.14
4095 12118 2.147436 AATGCGCGATTGGTGTTTTT 57.853 40.000 12.10 0.00 0.00 1.94
4097 12120 1.668628 GGAAATGCGCGATTGGTGTTT 60.669 47.619 12.10 0.00 0.00 2.83
4098 12121 0.109319 GGAAATGCGCGATTGGTGTT 60.109 50.000 12.10 0.00 0.00 3.32
4099 12122 1.506262 GGAAATGCGCGATTGGTGT 59.494 52.632 12.10 0.00 0.00 4.16
4101 12124 2.414785 GGGGAAATGCGCGATTGGT 61.415 57.895 12.10 0.00 0.00 3.67
4102 12125 2.412937 GGGGAAATGCGCGATTGG 59.587 61.111 12.10 0.00 0.00 3.16
4103 12126 1.737355 ATGGGGGAAATGCGCGATTG 61.737 55.000 12.10 0.00 0.00 2.67
4104 12127 1.042559 AATGGGGGAAATGCGCGATT 61.043 50.000 12.10 3.86 0.00 3.34
4105 12128 1.042559 AAATGGGGGAAATGCGCGAT 61.043 50.000 12.10 0.00 0.00 4.58
4106 12129 0.394488 TAAATGGGGGAAATGCGCGA 60.394 50.000 12.10 0.00 0.00 5.87
4107 12130 0.673437 ATAAATGGGGGAAATGCGCG 59.327 50.000 0.00 0.00 0.00 6.86
4108 12131 2.908688 AATAAATGGGGGAAATGCGC 57.091 45.000 0.00 0.00 0.00 6.09
4109 12132 3.387699 AGGAAATAAATGGGGGAAATGCG 59.612 43.478 0.00 0.00 0.00 4.73
4110 12133 5.368145 GAAGGAAATAAATGGGGGAAATGC 58.632 41.667 0.00 0.00 0.00 3.56
4151 12176 3.294493 GCGGTTTTGGCTCTGGCA 61.294 61.111 0.00 0.00 40.87 4.92
4152 12177 4.404654 CGCGGTTTTGGCTCTGGC 62.405 66.667 0.00 0.00 37.82 4.85
4161 12186 2.742738 CGGAATACGGCGCGGTTTT 61.743 57.895 26.10 22.93 39.42 2.43
4200 12225 3.860536 GCCAAAACGAGTAGAAGCTAGAG 59.139 47.826 0.00 0.00 0.00 2.43
4201 12226 3.672511 CGCCAAAACGAGTAGAAGCTAGA 60.673 47.826 0.00 0.00 34.06 2.43
4202 12227 2.599082 CGCCAAAACGAGTAGAAGCTAG 59.401 50.000 0.00 0.00 34.06 3.42
4203 12228 2.602878 CGCCAAAACGAGTAGAAGCTA 58.397 47.619 0.00 0.00 34.06 3.32
4204 12229 1.429463 CGCCAAAACGAGTAGAAGCT 58.571 50.000 0.00 0.00 34.06 3.74
4205 12230 0.179222 GCGCCAAAACGAGTAGAAGC 60.179 55.000 0.00 0.00 34.06 3.86
4208 12233 0.249531 TGTGCGCCAAAACGAGTAGA 60.250 50.000 4.18 0.00 34.06 2.59
4213 12244 2.950673 GGATGTGCGCCAAAACGA 59.049 55.556 4.18 0.00 34.06 3.85
4259 12290 0.107459 GGAACAGATGTCAGGGAGGC 60.107 60.000 0.00 0.00 0.00 4.70
4305 12336 2.204461 TGTCAGTCCCGAGCGGAAA 61.204 57.895 11.05 0.00 44.47 3.13


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

AutoCloner maintained by Alex Coulton.