Multiple sequence alignment - TraesCS1D01G210400

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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 TraesCS1D01G210400 chr1D 100.000 2627 0 0 1 2627 296480679 296478053 0.000000e+00 4852
1 TraesCS1D01G210400 chr1B 94.233 1526 56 15 596 2104 397995453 397993943 0.000000e+00 2302
2 TraesCS1D01G210400 chr1B 90.972 288 17 6 2340 2627 397991845 397991567 1.910000e-101 379
3 TraesCS1D01G210400 chr1B 88.627 255 8 8 25 273 397996229 397995990 9.200000e-75 291
4 TraesCS1D01G210400 chr1A 93.650 1244 47 16 603 1841 369273629 369272413 0.000000e+00 1831
5 TraesCS1D01G210400 chr1A 90.289 381 26 8 2248 2627 369269187 369268817 3.040000e-134 488
6 TraesCS1D01G210400 chr1A 87.467 375 18 12 25 374 369274215 369273845 3.150000e-109 405
7 TraesCS1D01G210400 chr1A 88.953 344 10 3 1287 1628 369271062 369270745 1.460000e-107 399
8 TraesCS1D01G210400 chr1A 86.256 211 16 9 2410 2618 369271548 369271349 1.580000e-52 217
9 TraesCS1D01G210400 chr3D 89.189 185 17 3 2208 2392 402685809 402685990 7.310000e-56 228
10 TraesCS1D01G210400 chr2D 88.587 184 18 3 2208 2391 314367228 314367408 1.220000e-53 220
11 TraesCS1D01G210400 chr3A 88.525 183 18 3 2208 2390 312002357 312002178 4.400000e-53 219
12 TraesCS1D01G210400 chr5B 88.043 184 19 3 2208 2391 34043387 34043207 5.690000e-52 215
13 TraesCS1D01G210400 chr5B 86.559 186 24 1 2208 2393 508824708 508824892 1.230000e-48 204
14 TraesCS1D01G210400 chr2A 87.234 188 17 7 2208 2391 4831222 4831038 9.530000e-50 207
15 TraesCS1D01G210400 chr6D 87.027 185 21 3 2208 2392 303614208 303614027 3.430000e-49 206
16 TraesCS1D01G210400 chr6B 86.224 196 20 6 2208 2402 422568677 422568488 3.430000e-49 206


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 TraesCS1D01G210400 chr1D 296478053 296480679 2626 True 4852.000000 4852 100.000000 1 2627 1 chr1D.!!$R1 2626
1 TraesCS1D01G210400 chr1B 397991567 397996229 4662 True 990.666667 2302 91.277333 25 2627 3 chr1B.!!$R1 2602
2 TraesCS1D01G210400 chr1A 369268817 369274215 5398 True 668.000000 1831 89.323000 25 2627 5 chr1A.!!$R1 2602

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
654 948 0.243907 TGCGCAGAGAGGAGTGTTAC 59.756 55.0 5.66 0.0 0.0 2.5 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 3990 0.02811 GCTCGTTTCGCCATTGGATC 59.972 55.0 6.95 0.0 0.0 3.36 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
19 20 2.044123 AATGTGGCTAAGCTAGGTGC 57.956 50.000 0.00 0.00 43.29 5.01
209 216 3.845781 ACTTGTGTCATCCTGTGTTCT 57.154 42.857 0.00 0.00 0.00 3.01
266 273 6.356186 TCTTTTGGAGGGTTTAGTCTACTC 57.644 41.667 0.00 0.00 0.00 2.59
267 274 6.082707 TCTTTTGGAGGGTTTAGTCTACTCT 58.917 40.000 0.00 0.00 0.00 3.24
271 417 3.382227 GGAGGGTTTAGTCTACTCTGAGC 59.618 52.174 4.19 0.00 0.00 4.26
287 433 3.818210 TCTGAGCTTCGCTAATCTCCTAG 59.182 47.826 0.01 0.00 39.88 3.02
353 503 5.636123 TCCTCTACAAACTTGGCCAAAATA 58.364 37.500 20.91 6.64 0.00 1.40
432 642 9.941325 TGTGCAAATGAAACATTATATTTCCTT 57.059 25.926 0.00 0.00 35.57 3.36
438 648 9.868277 AATGAAACATTATATTTCCTTTTCGCA 57.132 25.926 0.00 0.00 35.57 5.10
439 649 9.868277 ATGAAACATTATATTTCCTTTTCGCAA 57.132 25.926 0.00 0.00 35.57 4.85
440 650 9.698309 TGAAACATTATATTTCCTTTTCGCAAA 57.302 25.926 0.00 0.00 35.57 3.68
469 679 7.823745 AGAAACATTACATTTCCTGTTGAGT 57.176 32.000 0.00 0.00 39.39 3.41
477 687 5.799213 ACATTTCCTGTTGAGTCTAGAAGG 58.201 41.667 0.00 0.00 32.90 3.46
478 688 4.891992 TTTCCTGTTGAGTCTAGAAGGG 57.108 45.455 6.14 0.00 0.00 3.95
479 689 2.821437 TCCTGTTGAGTCTAGAAGGGG 58.179 52.381 6.14 0.00 0.00 4.79
480 690 2.111972 TCCTGTTGAGTCTAGAAGGGGT 59.888 50.000 6.14 0.00 0.00 4.95
481 691 2.234908 CCTGTTGAGTCTAGAAGGGGTG 59.765 54.545 0.00 0.00 0.00 4.61
482 692 1.623811 TGTTGAGTCTAGAAGGGGTGC 59.376 52.381 0.00 0.00 0.00 5.01
483 693 1.623811 GTTGAGTCTAGAAGGGGTGCA 59.376 52.381 0.00 0.00 0.00 4.57
484 694 2.237392 GTTGAGTCTAGAAGGGGTGCAT 59.763 50.000 0.00 0.00 0.00 3.96
485 695 2.551270 TGAGTCTAGAAGGGGTGCATT 58.449 47.619 0.00 0.00 0.00 3.56
487 697 3.055094 TGAGTCTAGAAGGGGTGCATTTC 60.055 47.826 0.00 0.00 0.00 2.17
488 698 2.912956 AGTCTAGAAGGGGTGCATTTCA 59.087 45.455 0.00 0.00 0.00 2.69
491 710 4.706962 GTCTAGAAGGGGTGCATTTCAATT 59.293 41.667 0.00 0.00 0.00 2.32
502 721 4.739228 GTGCATTTCAATTTTTGGCCAAAC 59.261 37.500 30.43 14.87 0.00 2.93
517 736 3.068873 GGCCAAACTTCACAACCATACAA 59.931 43.478 0.00 0.00 0.00 2.41
522 745 7.530010 CCAAACTTCACAACCATACAATAGAG 58.470 38.462 0.00 0.00 0.00 2.43
530 753 7.177744 TCACAACCATACAATAGAGTACTGTCA 59.822 37.037 0.00 0.00 0.00 3.58
542 765 8.879342 ATAGAGTACTGTCAATTTATCACAGC 57.121 34.615 0.00 0.00 41.15 4.40
555 778 0.522626 TCACAGCATTTGCATGGACG 59.477 50.000 5.20 0.00 45.16 4.79
558 781 1.336148 ACAGCATTTGCATGGACGTTG 60.336 47.619 5.20 0.00 45.16 4.10
565 788 0.392863 TGCATGGACGTTGGGATGAG 60.393 55.000 0.00 0.00 0.00 2.90
648 942 0.458197 CTTGAGTGCGCAGAGAGGAG 60.458 60.000 12.22 0.07 0.00 3.69
650 944 1.153862 GAGTGCGCAGAGAGGAGTG 60.154 63.158 12.22 0.00 0.00 3.51
654 948 0.243907 TGCGCAGAGAGGAGTGTTAC 59.756 55.000 5.66 0.00 0.00 2.50
688 982 1.078848 CTCCGTCCAGAGCAAAGGG 60.079 63.158 0.00 0.00 0.00 3.95
706 1000 0.673985 GGGCAAAGAAACCGAAAGCT 59.326 50.000 0.00 0.00 0.00 3.74
709 1003 3.056821 GGGCAAAGAAACCGAAAGCTAAT 60.057 43.478 0.00 0.00 0.00 1.73
796 1094 0.889186 TCCCGCCAAAGAAGCAACTC 60.889 55.000 0.00 0.00 0.00 3.01
797 1095 1.207593 CCGCCAAAGAAGCAACTCG 59.792 57.895 0.00 0.00 0.00 4.18
798 1096 1.227999 CCGCCAAAGAAGCAACTCGA 61.228 55.000 0.00 0.00 0.00 4.04
799 1097 0.798776 CGCCAAAGAAGCAACTCGAT 59.201 50.000 0.00 0.00 0.00 3.59
806 1104 3.964221 AAGCAACTCGATCGCGCGA 62.964 57.895 36.65 36.65 38.74 5.87
808 1106 2.860628 GCAACTCGATCGCGCGAAT 61.861 57.895 38.07 24.33 40.13 3.34
874 1172 2.239681 ACACTCTTTCTCCGATCCCT 57.760 50.000 0.00 0.00 0.00 4.20
875 1173 2.104170 ACACTCTTTCTCCGATCCCTC 58.896 52.381 0.00 0.00 0.00 4.30
902 1201 5.378292 TCTCTATACAAAGCATAGCCGAG 57.622 43.478 0.00 0.00 0.00 4.63
903 1202 5.070685 TCTCTATACAAAGCATAGCCGAGA 58.929 41.667 0.00 0.00 0.00 4.04
967 1270 2.380410 CGTCGGTGGCAGCAAGTAC 61.380 63.158 17.80 7.80 0.00 2.73
1631 1934 1.390123 CGTCGCAATTTCGTGAGACAT 59.610 47.619 9.24 0.00 45.43 3.06
1648 1951 3.118775 AGACATACGTGTACATGCATGGT 60.119 43.478 29.41 18.99 39.09 3.55
1731 2034 7.516198 ACTGTGTGATGCTCTTAATTCTTTT 57.484 32.000 0.00 0.00 0.00 2.27
1732 2035 7.365741 ACTGTGTGATGCTCTTAATTCTTTTG 58.634 34.615 0.00 0.00 0.00 2.44
1733 2036 7.013655 ACTGTGTGATGCTCTTAATTCTTTTGT 59.986 33.333 0.00 0.00 0.00 2.83
1764 2067 2.641305 AGCTCCTCATTCATGCTGAAC 58.359 47.619 1.44 0.00 39.45 3.18
1784 2087 2.930040 ACGGTGTGATGCTCTTAATTCG 59.070 45.455 0.00 0.00 0.00 3.34
1845 2149 6.094464 TGGATTGCTTTGATACAAGTGATGAG 59.906 38.462 0.00 0.00 0.00 2.90
1888 2768 1.134128 TGGTTGGATCCCATGACGATG 60.134 52.381 9.90 0.00 31.53 3.84
1973 2865 2.161410 TGGTTGATGACGTTATTGCTGC 59.839 45.455 0.00 0.00 0.00 5.25
1986 2878 2.497107 TTGCTGCTCTTTTGCAAGTC 57.503 45.000 0.00 0.00 42.83 3.01
1999 2891 0.370273 GCAAGTCGTTGGCTATGTCG 59.630 55.000 0.00 0.00 33.87 4.35
2011 2903 5.801350 TGGCTATGTCGATTTTCTTCTTG 57.199 39.130 0.00 0.00 0.00 3.02
2066 2958 5.808540 CCCAAATGTCTTGCTTGATATTGTG 59.191 40.000 3.32 4.54 30.19 3.33
2080 2972 7.040478 GCTTGATATTGTGCCATGAAGGTAATA 60.040 37.037 0.00 0.00 40.61 0.98
2081 2973 8.938801 TTGATATTGTGCCATGAAGGTAATAT 57.061 30.769 0.00 0.00 40.61 1.28
2082 2974 8.938801 TGATATTGTGCCATGAAGGTAATATT 57.061 30.769 0.00 0.00 40.61 1.28
2138 3985 5.420725 TCTACACTAAGGTAGACCGTACA 57.579 43.478 0.00 0.00 43.53 2.90
2139 3986 5.994250 TCTACACTAAGGTAGACCGTACAT 58.006 41.667 0.00 0.00 43.53 2.29
2143 3990 3.624861 ACTAAGGTAGACCGTACATGTCG 59.375 47.826 0.00 6.16 42.08 4.35
2152 3999 2.135139 CCGTACATGTCGATCCAATGG 58.865 52.381 16.06 0.00 0.00 3.16
2172 4019 0.316689 CGAAACGAGCACAAACACCC 60.317 55.000 0.00 0.00 0.00 4.61
2173 4020 1.021968 GAAACGAGCACAAACACCCT 58.978 50.000 0.00 0.00 0.00 4.34
2190 4037 4.221041 ACACCCTCTCTCTTACTACAAAGC 59.779 45.833 0.00 0.00 0.00 3.51
2208 4055 1.207329 AGCCCTTTGACGTCAGGTATC 59.793 52.381 19.11 9.39 0.00 2.24
2228 4075 9.784531 AGGTATCTAGGTTTGAATATTGTGATG 57.215 33.333 0.00 0.00 0.00 3.07
2230 4077 9.778741 GTATCTAGGTTTGAATATTGTGATGGA 57.221 33.333 0.00 0.00 0.00 3.41
2231 4078 8.915057 ATCTAGGTTTGAATATTGTGATGGAG 57.085 34.615 0.00 0.00 0.00 3.86
2279 6807 4.770795 TGCTAGGTTGGCTAGATTTTCTC 58.229 43.478 0.00 0.00 0.00 2.87
2303 6863 2.818751 TGTTGGTTGGTTTGAGGAGT 57.181 45.000 0.00 0.00 0.00 3.85
2330 6890 6.435430 TGAATCAAATTGTACCATTCCTCG 57.565 37.500 0.00 0.00 0.00 4.63
2331 6891 5.943416 TGAATCAAATTGTACCATTCCTCGT 59.057 36.000 0.00 0.00 0.00 4.18
2336 6896 6.711194 TCAAATTGTACCATTCCTCGTAAACA 59.289 34.615 0.00 0.00 0.00 2.83
2406 7034 3.037549 ACAAAAAGCCCTTTGATGTCCA 58.962 40.909 13.49 0.00 38.35 4.02
2408 7036 2.978156 AAAGCCCTTTGATGTCCAGA 57.022 45.000 0.00 0.00 0.00 3.86
2476 7104 1.004440 AACCGAGAGCAGCCAACTC 60.004 57.895 0.00 0.00 0.00 3.01
2522 7150 9.220767 GTTCTTTCTTGTACCATATCATATCCC 57.779 37.037 0.00 0.00 0.00 3.85
2551 7179 5.103728 TGGGTGATAATCCAAAGCCAGATAA 60.104 40.000 0.00 0.00 35.36 1.75
2567 7195 4.082125 CAGATAAATGGCTAATGGGGTCC 58.918 47.826 0.00 0.00 0.00 4.46
2595 7223 1.135199 GCAGCACCATTGTCCATGAAG 60.135 52.381 0.00 0.00 34.31 3.02
2603 7231 0.107643 TTGTCCATGAAGCACGGACA 59.892 50.000 10.90 10.90 36.31 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.044123 GCACCTAGCTTAGCCACATT 57.956 50.000 0.00 0.00 41.15 2.71
1 2 3.788672 GCACCTAGCTTAGCCACAT 57.211 52.632 0.00 0.00 41.15 3.21
7 8 6.493518 CCTAGTGGAGTAGCACCTAGCTTAG 61.494 52.000 0.00 0.00 43.91 2.18
8 9 4.689150 CCTAGTGGAGTAGCACCTAGCTTA 60.689 50.000 0.00 0.00 43.91 3.09
9 10 3.942042 CCTAGTGGAGTAGCACCTAGCTT 60.942 52.174 0.00 0.00 43.91 3.74
10 11 2.423660 CCTAGTGGAGTAGCACCTAGCT 60.424 54.545 0.00 0.00 46.69 3.32
11 12 1.957877 CCTAGTGGAGTAGCACCTAGC 59.042 57.143 0.00 0.00 38.63 3.42
12 13 2.952978 CACCTAGTGGAGTAGCACCTAG 59.047 54.545 0.00 0.00 37.04 3.02
13 14 2.579400 TCACCTAGTGGAGTAGCACCTA 59.421 50.000 0.00 0.00 37.04 3.08
14 15 1.358103 TCACCTAGTGGAGTAGCACCT 59.642 52.381 0.00 0.00 37.04 4.00
15 16 1.751924 CTCACCTAGTGGAGTAGCACC 59.248 57.143 0.00 0.00 37.04 5.01
16 17 1.751924 CCTCACCTAGTGGAGTAGCAC 59.248 57.143 7.02 0.00 37.04 4.40
17 18 1.639108 TCCTCACCTAGTGGAGTAGCA 59.361 52.381 7.02 0.00 35.06 3.49
18 19 2.438800 TCCTCACCTAGTGGAGTAGC 57.561 55.000 7.02 0.00 35.06 3.58
23 24 1.689575 GCCATCTCCTCACCTAGTGGA 60.690 57.143 0.00 0.00 37.56 4.02
62 63 1.078759 CAGCTACTAGTGGCGTGCAC 61.079 60.000 23.51 6.82 42.26 4.57
209 216 4.726583 AGTACCTAGAGTGACAGAACACA 58.273 43.478 0.00 0.00 42.45 3.72
271 417 6.146898 GCTTAAGACTAGGAGATTAGCGAAG 58.853 44.000 6.67 0.00 0.00 3.79
331 481 4.871933 ATTTTGGCCAAGTTTGTAGAGG 57.128 40.909 19.48 0.00 0.00 3.69
441 651 9.883142 TCAACAGGAAATGTAATGTTTCTTTTT 57.117 25.926 0.00 0.00 43.00 1.94
442 652 9.533253 CTCAACAGGAAATGTAATGTTTCTTTT 57.467 29.630 0.00 0.00 43.00 2.27
443 653 8.695456 ACTCAACAGGAAATGTAATGTTTCTTT 58.305 29.630 0.00 0.00 43.00 2.52
444 654 8.237811 ACTCAACAGGAAATGTAATGTTTCTT 57.762 30.769 0.00 0.00 43.00 2.52
445 655 7.721399 AGACTCAACAGGAAATGTAATGTTTCT 59.279 33.333 0.00 0.00 43.00 2.52
446 656 7.875971 AGACTCAACAGGAAATGTAATGTTTC 58.124 34.615 0.00 0.00 43.00 2.78
447 657 7.823745 AGACTCAACAGGAAATGTAATGTTT 57.176 32.000 0.00 0.00 43.00 2.83
448 658 8.375506 TCTAGACTCAACAGGAAATGTAATGTT 58.624 33.333 0.00 0.00 43.00 2.71
449 659 7.907389 TCTAGACTCAACAGGAAATGTAATGT 58.093 34.615 0.00 0.00 43.00 2.71
450 660 8.777865 TTCTAGACTCAACAGGAAATGTAATG 57.222 34.615 0.00 0.00 43.00 1.90
451 661 8.043710 CCTTCTAGACTCAACAGGAAATGTAAT 58.956 37.037 0.20 0.00 43.00 1.89
452 662 7.386851 CCTTCTAGACTCAACAGGAAATGTAA 58.613 38.462 0.20 0.00 43.00 2.41
453 663 6.070767 CCCTTCTAGACTCAACAGGAAATGTA 60.071 42.308 7.37 0.00 43.00 2.29
454 664 5.280215 CCCTTCTAGACTCAACAGGAAATGT 60.280 44.000 7.37 0.00 46.97 2.71
455 665 5.181748 CCCTTCTAGACTCAACAGGAAATG 58.818 45.833 7.37 0.00 0.00 2.32
456 666 4.226168 CCCCTTCTAGACTCAACAGGAAAT 59.774 45.833 7.37 0.00 0.00 2.17
457 667 3.583086 CCCCTTCTAGACTCAACAGGAAA 59.417 47.826 7.37 0.00 0.00 3.13
458 668 3.173965 CCCCTTCTAGACTCAACAGGAA 58.826 50.000 7.37 0.00 0.00 3.36
459 669 2.111972 ACCCCTTCTAGACTCAACAGGA 59.888 50.000 7.37 0.00 0.00 3.86
460 670 2.234908 CACCCCTTCTAGACTCAACAGG 59.765 54.545 0.00 0.00 0.00 4.00
461 671 2.354203 GCACCCCTTCTAGACTCAACAG 60.354 54.545 0.00 0.00 0.00 3.16
462 672 1.623811 GCACCCCTTCTAGACTCAACA 59.376 52.381 0.00 0.00 0.00 3.33
469 679 4.591321 ATTGAAATGCACCCCTTCTAGA 57.409 40.909 0.00 0.00 0.00 2.43
477 687 2.228582 GGCCAAAAATTGAAATGCACCC 59.771 45.455 0.00 0.00 0.00 4.61
478 688 2.883386 TGGCCAAAAATTGAAATGCACC 59.117 40.909 0.61 0.00 0.00 5.01
479 689 4.564940 TTGGCCAAAAATTGAAATGCAC 57.435 36.364 17.98 0.00 0.00 4.57
480 690 4.643784 AGTTTGGCCAAAAATTGAAATGCA 59.356 33.333 31.92 2.68 31.33 3.96
481 691 5.185668 AGTTTGGCCAAAAATTGAAATGC 57.814 34.783 31.92 15.32 31.33 3.56
482 692 6.692249 GTGAAGTTTGGCCAAAAATTGAAATG 59.308 34.615 31.92 0.00 36.25 2.32
483 693 6.376581 TGTGAAGTTTGGCCAAAAATTGAAAT 59.623 30.769 31.92 11.92 36.25 2.17
484 694 5.707298 TGTGAAGTTTGGCCAAAAATTGAAA 59.293 32.000 31.92 16.16 36.25 2.69
485 695 5.248640 TGTGAAGTTTGGCCAAAAATTGAA 58.751 33.333 31.92 16.20 36.25 2.69
487 697 5.331098 GTTGTGAAGTTTGGCCAAAAATTG 58.669 37.500 31.92 0.00 36.25 2.32
488 698 4.397730 GGTTGTGAAGTTTGGCCAAAAATT 59.602 37.500 31.92 26.96 38.69 1.82
491 710 2.303022 TGGTTGTGAAGTTTGGCCAAAA 59.697 40.909 31.92 14.42 31.33 2.44
502 721 8.035394 ACAGTACTCTATTGTATGGTTGTGAAG 58.965 37.037 0.00 0.00 0.00 3.02
517 736 8.478066 TGCTGTGATAAATTGACAGTACTCTAT 58.522 33.333 0.00 0.00 39.48 1.98
522 745 7.008628 GCAAATGCTGTGATAAATTGACAGTAC 59.991 37.037 0.00 0.00 39.48 2.73
530 753 5.813672 GTCCATGCAAATGCTGTGATAAATT 59.186 36.000 6.97 0.00 42.66 1.82
535 758 1.133598 CGTCCATGCAAATGCTGTGAT 59.866 47.619 6.97 0.00 42.66 3.06
542 765 0.887247 TCCCAACGTCCATGCAAATG 59.113 50.000 0.00 0.00 0.00 2.32
555 778 4.262036 GGTTGAAGAAAACCTCATCCCAAC 60.262 45.833 0.00 0.00 45.25 3.77
591 814 1.606885 GCAGAGGAGAGCAGAGCAGT 61.607 60.000 0.00 0.00 0.00 4.40
594 817 0.179103 GAAGCAGAGGAGAGCAGAGC 60.179 60.000 0.00 0.00 0.00 4.09
648 942 3.699538 GGGATTCCATTTCCAGGTAACAC 59.300 47.826 4.80 0.00 41.41 3.32
650 944 4.207955 GAGGGATTCCATTTCCAGGTAAC 58.792 47.826 4.80 0.00 34.77 2.50
654 948 2.371658 GGAGGGATTCCATTTCCAGG 57.628 55.000 4.80 0.00 46.01 4.45
688 982 3.636282 TTAGCTTTCGGTTTCTTTGCC 57.364 42.857 0.00 0.00 0.00 4.52
706 1000 3.188460 GCTTCAAAAGTCGTGCTCCATTA 59.812 43.478 0.00 0.00 0.00 1.90
709 1003 0.944386 GCTTCAAAAGTCGTGCTCCA 59.056 50.000 0.00 0.00 0.00 3.86
796 1094 3.138375 ATCGAATTCGCGCGATCG 58.862 55.556 36.63 36.63 43.03 3.69
799 1097 1.327988 GATCGATCGAATTCGCGCGA 61.328 55.000 31.47 31.47 43.91 5.87
806 1104 6.971602 ACAGTACTGTATGATCGATCGAATT 58.028 36.000 26.91 6.38 42.90 2.17
808 1106 6.704937 AGTACAGTACTGTATGATCGATCGAA 59.295 38.462 32.53 6.97 46.36 3.71
874 1172 3.414759 TGCTTTGTATAGAGAGGGGGA 57.585 47.619 0.00 0.00 0.00 4.81
875 1173 4.323104 GCTATGCTTTGTATAGAGAGGGGG 60.323 50.000 6.82 0.00 31.47 5.40
928 1227 1.060937 GCAGCTATTGTTGCGTCGG 59.939 57.895 0.00 0.00 40.35 4.79
961 1264 2.618839 GCGCGGCGTATGTACTTG 59.381 61.111 24.46 0.00 0.00 3.16
1095 1398 1.636570 CGACGAGCCAGAAGACGAGA 61.637 60.000 0.00 0.00 0.00 4.04
1344 1647 2.046892 CTGGGCTGGTGGAAGTCG 60.047 66.667 0.00 0.00 0.00 4.18
1614 1917 2.344441 ACGTATGTCTCACGAAATTGCG 59.656 45.455 3.68 3.68 41.91 4.85
1631 1934 2.342179 CACACCATGCATGTACACGTA 58.658 47.619 24.58 0.00 0.00 3.57
1648 1951 6.680810 ACTACTGTAGTTAATTACACGCACA 58.319 36.000 14.53 0.00 34.86 4.57
1764 2067 2.285220 CCGAATTAAGAGCATCACACCG 59.715 50.000 0.00 0.00 37.82 4.94
1888 2768 0.801067 AATAACGACGCTCAGACGCC 60.801 55.000 0.00 0.00 41.46 5.68
1893 2773 4.386230 CAACAAGAAATAACGACGCTCAG 58.614 43.478 0.00 0.00 0.00 3.35
1973 2865 1.334869 AGCCAACGACTTGCAAAAGAG 59.665 47.619 0.00 0.00 0.00 2.85
1986 2878 4.330074 AGAAGAAAATCGACATAGCCAACG 59.670 41.667 0.00 0.00 0.00 4.10
2011 2903 5.008316 ACGACCCACACAAGAAAGAAATAAC 59.992 40.000 0.00 0.00 0.00 1.89
2106 3953 9.924650 GTCTACCTTAGTGTAGATTTTCAGAAA 57.075 33.333 11.64 0.00 46.45 2.52
2107 3954 8.529476 GGTCTACCTTAGTGTAGATTTTCAGAA 58.471 37.037 11.64 0.00 46.45 3.02
2108 3955 7.148120 CGGTCTACCTTAGTGTAGATTTTCAGA 60.148 40.741 11.64 0.00 46.45 3.27
2109 3956 6.973474 CGGTCTACCTTAGTGTAGATTTTCAG 59.027 42.308 11.64 0.87 46.45 3.02
2110 3957 6.435277 ACGGTCTACCTTAGTGTAGATTTTCA 59.565 38.462 11.64 0.00 46.45 2.69
2111 3958 6.861144 ACGGTCTACCTTAGTGTAGATTTTC 58.139 40.000 11.64 2.70 46.45 2.29
2112 3959 6.847421 ACGGTCTACCTTAGTGTAGATTTT 57.153 37.500 11.64 0.95 46.45 1.82
2113 3960 6.886459 TGTACGGTCTACCTTAGTGTAGATTT 59.114 38.462 11.64 4.95 46.45 2.17
2114 3961 6.418101 TGTACGGTCTACCTTAGTGTAGATT 58.582 40.000 11.64 5.19 46.45 2.40
2115 3962 5.994250 TGTACGGTCTACCTTAGTGTAGAT 58.006 41.667 11.64 2.65 46.45 1.98
2116 3963 5.420725 TGTACGGTCTACCTTAGTGTAGA 57.579 43.478 6.52 6.52 43.70 2.59
2117 3964 5.587844 ACATGTACGGTCTACCTTAGTGTAG 59.412 44.000 0.00 0.00 39.67 2.74
2118 3965 5.500234 ACATGTACGGTCTACCTTAGTGTA 58.500 41.667 0.00 0.00 0.00 2.90
2119 3966 4.338879 ACATGTACGGTCTACCTTAGTGT 58.661 43.478 0.00 0.00 0.00 3.55
2120 3967 4.495349 CGACATGTACGGTCTACCTTAGTG 60.495 50.000 0.00 0.00 33.11 2.74
2121 3968 3.624861 CGACATGTACGGTCTACCTTAGT 59.375 47.826 0.00 0.00 33.11 2.24
2122 3969 3.873361 TCGACATGTACGGTCTACCTTAG 59.127 47.826 14.72 0.08 33.11 2.18
2123 3970 3.872696 TCGACATGTACGGTCTACCTTA 58.127 45.455 14.72 0.00 33.11 2.69
2124 3971 2.715046 TCGACATGTACGGTCTACCTT 58.285 47.619 14.72 0.00 33.11 3.50
2125 3972 2.408271 TCGACATGTACGGTCTACCT 57.592 50.000 14.72 0.00 33.11 3.08
2126 3973 2.031333 GGATCGACATGTACGGTCTACC 60.031 54.545 21.80 9.65 40.20 3.18
2127 3974 2.615447 TGGATCGACATGTACGGTCTAC 59.385 50.000 21.80 12.25 40.20 2.59
2128 3975 2.921821 TGGATCGACATGTACGGTCTA 58.078 47.619 21.80 16.78 40.20 2.59
2129 3976 1.758936 TGGATCGACATGTACGGTCT 58.241 50.000 21.80 8.48 40.20 3.85
2130 3977 2.572191 TTGGATCGACATGTACGGTC 57.428 50.000 17.33 17.33 39.71 4.79
2131 3978 2.483013 CCATTGGATCGACATGTACGGT 60.483 50.000 14.72 9.69 0.00 4.83
2132 3979 2.135139 CCATTGGATCGACATGTACGG 58.865 52.381 14.72 2.12 0.00 4.02
2133 3980 1.526887 GCCATTGGATCGACATGTACG 59.473 52.381 6.95 4.78 0.00 3.67
2134 3981 1.526887 CGCCATTGGATCGACATGTAC 59.473 52.381 6.95 0.00 0.00 2.90
2135 3982 1.410882 TCGCCATTGGATCGACATGTA 59.589 47.619 6.95 0.00 0.00 2.29
2136 3983 0.177836 TCGCCATTGGATCGACATGT 59.822 50.000 6.95 0.00 0.00 3.21
2137 3984 1.298602 TTCGCCATTGGATCGACATG 58.701 50.000 6.95 0.00 31.48 3.21
2138 3985 1.670811 GTTTCGCCATTGGATCGACAT 59.329 47.619 6.95 0.00 31.48 3.06
2139 3986 1.083489 GTTTCGCCATTGGATCGACA 58.917 50.000 6.95 0.00 31.48 4.35
2143 3990 0.028110 GCTCGTTTCGCCATTGGATC 59.972 55.000 6.95 0.00 0.00 3.36
2152 3999 0.928451 GGTGTTTGTGCTCGTTTCGC 60.928 55.000 0.00 0.00 0.00 4.70
2172 4019 5.669164 AAGGGCTTTGTAGTAAGAGAGAG 57.331 43.478 0.00 0.00 0.00 3.20
2173 4020 5.794894 CAAAGGGCTTTGTAGTAAGAGAGA 58.205 41.667 0.00 0.00 43.52 3.10
2190 4037 3.068307 CCTAGATACCTGACGTCAAAGGG 59.932 52.174 23.37 20.83 37.94 3.95
2198 4045 7.926555 ACAATATTCAAACCTAGATACCTGACG 59.073 37.037 0.00 0.00 0.00 4.35
2202 4049 9.784531 CATCACAATATTCAAACCTAGATACCT 57.215 33.333 0.00 0.00 0.00 3.08
2208 4055 8.737168 TTCTCCATCACAATATTCAAACCTAG 57.263 34.615 0.00 0.00 0.00 3.02
2279 6807 4.148838 TCCTCAAACCAACCAACAATAGG 58.851 43.478 0.00 0.00 0.00 2.57
2381 7009 6.052360 GGACATCAAAGGGCTTTTTGTTTTA 58.948 36.000 12.39 0.00 38.77 1.52
2406 7034 7.390440 TCAAAATGTATTGTTCGAGTGGATTCT 59.610 33.333 0.00 0.00 0.00 2.40
2408 7036 7.040755 TGTCAAAATGTATTGTTCGAGTGGATT 60.041 33.333 0.00 0.00 0.00 3.01
2476 7104 7.740519 AGAACATCTCGAACTTTTGTTTTTG 57.259 32.000 0.00 0.00 43.66 2.44
2522 7150 3.290710 CTTTGGATTATCACCCACCAGG 58.709 50.000 0.00 0.00 43.78 4.45
2551 7179 0.106015 GCAGGACCCCATTAGCCATT 60.106 55.000 0.00 0.00 0.00 3.16
2583 7211 3.955145 TCCGTGCTTCATGGACAAT 57.045 47.368 3.77 0.00 43.70 2.71
2587 7215 1.974265 TTTTGTCCGTGCTTCATGGA 58.026 45.000 3.77 3.77 46.01 3.41
2588 7216 2.034558 AGTTTTTGTCCGTGCTTCATGG 59.965 45.455 0.00 0.00 41.56 3.66
2589 7217 3.354089 AGTTTTTGTCCGTGCTTCATG 57.646 42.857 0.00 0.00 0.00 3.07
2595 7223 1.871039 TGAGCTAGTTTTTGTCCGTGC 59.129 47.619 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.