Multiple sequence alignment - TraesCS3D01G078400

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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 TraesCS3D01G078400 chr3D 100.000 4688 0 0 1 4688 39017943 39022630 0.000000e+00 8658
1 TraesCS3D01G078400 chr3D 86.235 603 74 7 4 601 591384610 591384012 0.000000e+00 645
2 TraesCS3D01G078400 chr3A 93.488 3025 136 34 751 3746 50368217 50365225 0.000000e+00 4438
3 TraesCS3D01G078400 chr3A 89.793 725 44 16 3764 4469 50365176 50364463 0.000000e+00 902
4 TraesCS3D01G078400 chr3A 85.505 614 79 6 1 608 380925664 380925055 2.380000e-177 632
5 TraesCS3D01G078400 chr3A 94.397 232 9 2 4461 4688 50364376 50364145 2.080000e-93 353
6 TraesCS3D01G078400 chr3B 93.603 1876 70 23 2629 4469 61882847 61884707 0.000000e+00 2754
7 TraesCS3D01G078400 chr3B 92.399 1592 67 27 738 2287 61880513 61882092 0.000000e+00 2220
8 TraesCS3D01G078400 chr3B 94.186 172 7 1 2336 2507 61882325 61882493 4.650000e-65 259
9 TraesCS3D01G078400 chr3B 90.164 183 14 2 4461 4640 61884795 61884976 7.840000e-58 235
10 TraesCS3D01G078400 chr3B 90.441 136 8 3 594 726 61880145 61880278 1.730000e-39 174
11 TraesCS3D01G078400 chr3B 95.960 99 4 0 2422 2520 61882493 61882591 1.350000e-35 161
12 TraesCS3D01G078400 chr4A 88.633 607 64 3 2 603 739527302 739526696 0.000000e+00 734
13 TraesCS3D01G078400 chr7B 87.809 607 65 5 1 602 74093275 74092673 0.000000e+00 702
14 TraesCS3D01G078400 chr2D 87.150 607 68 6 1 602 180089509 180090110 0.000000e+00 680
15 TraesCS3D01G078400 chr2D 85.620 605 80 5 5 603 364977458 364978061 3.080000e-176 628
16 TraesCS3D01G078400 chr5D 86.601 612 71 9 1 606 445380213 445379607 0.000000e+00 665
17 TraesCS3D01G078400 chr5A 86.281 605 78 3 1 600 379953695 379954299 0.000000e+00 652
18 TraesCS3D01G078400 chr6A 86.047 602 80 4 1 601 472951852 472952450 1.100000e-180 643
19 TraesCS3D01G078400 chr1D 83.333 126 12 5 4044 4166 196447820 196447701 1.780000e-19 108


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 TraesCS3D01G078400 chr3D 39017943 39022630 4687 False 8658.000000 8658 100.000000 1 4688 1 chr3D.!!$F1 4687
1 TraesCS3D01G078400 chr3D 591384012 591384610 598 True 645.000000 645 86.235000 4 601 1 chr3D.!!$R1 597
2 TraesCS3D01G078400 chr3A 50364145 50368217 4072 True 1897.666667 4438 92.559333 751 4688 3 chr3A.!!$R2 3937
3 TraesCS3D01G078400 chr3A 380925055 380925664 609 True 632.000000 632 85.505000 1 608 1 chr3A.!!$R1 607
4 TraesCS3D01G078400 chr3B 61880145 61884976 4831 False 967.166667 2754 92.792167 594 4640 6 chr3B.!!$F1 4046
5 TraesCS3D01G078400 chr4A 739526696 739527302 606 True 734.000000 734 88.633000 2 603 1 chr4A.!!$R1 601
6 TraesCS3D01G078400 chr7B 74092673 74093275 602 True 702.000000 702 87.809000 1 602 1 chr7B.!!$R1 601
7 TraesCS3D01G078400 chr2D 180089509 180090110 601 False 680.000000 680 87.150000 1 602 1 chr2D.!!$F1 601
8 TraesCS3D01G078400 chr2D 364977458 364978061 603 False 628.000000 628 85.620000 5 603 1 chr2D.!!$F2 598
9 TraesCS3D01G078400 chr5D 445379607 445380213 606 True 665.000000 665 86.601000 1 606 1 chr5D.!!$R1 605
10 TraesCS3D01G078400 chr5A 379953695 379954299 604 False 652.000000 652 86.281000 1 600 1 chr5A.!!$F1 599
11 TraesCS3D01G078400 chr6A 472951852 472952450 598 False 643.000000 643 86.047000 1 601 1 chr6A.!!$F1 600

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
677 690 0.183731 GCCTCCTCCTATTGGTTGGG 59.816 60.0 7.73 3.35 34.23 4.12 F
1837 2111 0.032952 TCGTCCCAGTAGTTGTGTGC 59.967 55.0 0.00 0.00 0.00 4.57 F
2109 2389 0.534203 TTCCTCAACGACTTGGGTGC 60.534 55.0 0.00 0.00 0.00 5.01 F
3584 4302 0.395586 TGCTGCAACCCTGTTGAACT 60.396 50.0 10.94 0.00 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2666 3384 0.322816 GGTCACCTGTCATGCCATGT 60.323 55.000 4.31 0.0 0.0 3.21 R
3584 4302 1.474320 CCGTTTCTTCCACACCACTGA 60.474 52.381 0.00 0.0 0.0 3.41 R
3591 4309 1.595929 GCCGTCCGTTTCTTCCACA 60.596 57.895 0.00 0.0 0.0 4.17 R
4605 5504 0.769873 CCTAGAGCCCATGAGCCAAT 59.230 55.000 0.00 0.0 0.0 3.16 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
43 44 2.352032 GCTACGTCTCCAGTGGCCT 61.352 63.158 3.51 0.00 39.69 5.19
113 115 4.664851 GCTTCGTTGTTAGTTGTTTCTTCG 59.335 41.667 0.00 0.00 0.00 3.79
126 128 6.596497 AGTTGTTTCTTCGAGTTTTGTTAGGA 59.404 34.615 0.00 0.00 0.00 2.94
213 215 4.419921 GCCCCCGTTCCGATGGTT 62.420 66.667 0.00 0.00 0.00 3.67
221 223 1.399440 CGTTCCGATGGTTCGTCTAGA 59.601 52.381 0.00 0.00 43.97 2.43
238 241 2.888998 GAACGTTGGTGGGCGTGTC 61.889 63.158 5.00 0.00 41.42 3.67
246 249 2.598099 TGGGCGTGTCGAGGTGTA 60.598 61.111 0.00 0.00 0.00 2.90
255 258 1.102222 GTCGAGGTGTATCTCCGGCT 61.102 60.000 0.00 0.00 0.00 5.52
283 286 1.079405 TCGGTGGATTTGCTCGGAC 60.079 57.895 0.00 0.00 0.00 4.79
286 289 0.539986 GGTGGATTTGCTCGGACCTA 59.460 55.000 0.00 0.00 0.00 3.08
307 310 6.157211 CCTAGTTGTTGTTCGTCTATGTTCT 58.843 40.000 0.00 0.00 0.00 3.01
398 401 1.981495 GGTCCTATGAGGCCTTAGCAT 59.019 52.381 6.77 8.88 42.56 3.79
426 429 3.430042 TCCCGACTGTCTACTACAACT 57.570 47.619 6.21 0.00 37.74 3.16
503 510 2.793946 GCGGGTAGTCGTCGCTAA 59.206 61.111 0.00 0.00 45.16 3.09
533 540 8.762426 GTCTACGGATCTGGATGTAATTTTTAC 58.238 37.037 6.47 0.00 0.00 2.01
561 571 3.818210 CTGGTGTTTGTTGTACTGCCATA 59.182 43.478 0.00 0.00 0.00 2.74
572 582 6.658816 TGTTGTACTGCCATAATTGAAGATGT 59.341 34.615 0.00 0.00 0.00 3.06
585 595 7.897575 AATTGAAGATGTATAGATCGGAAGC 57.102 36.000 4.35 0.00 0.00 3.86
625 635 7.619964 AGTGTGGGTATAATTTTTACGAAGG 57.380 36.000 0.00 0.00 0.00 3.46
629 639 7.148440 TGTGGGTATAATTTTTACGAAGGAACG 60.148 37.037 0.00 0.00 39.31 3.95
631 641 7.148440 TGGGTATAATTTTTACGAAGGAACGTG 60.148 37.037 0.00 0.00 46.02 4.49
633 643 6.806388 ATAATTTTTACGAAGGAACGTGGT 57.194 33.333 0.00 0.00 46.02 4.16
634 644 3.948196 TTTTTACGAAGGAACGTGGTG 57.052 42.857 0.00 0.00 46.02 4.17
635 645 2.886862 TTTACGAAGGAACGTGGTGA 57.113 45.000 0.00 0.00 46.02 4.02
636 646 2.138596 TTACGAAGGAACGTGGTGAC 57.861 50.000 0.00 0.00 46.02 3.67
677 690 0.183731 GCCTCCTCCTATTGGTTGGG 59.816 60.000 7.73 3.35 34.23 4.12
678 691 1.893315 CCTCCTCCTATTGGTTGGGA 58.107 55.000 7.73 6.63 34.23 4.37
702 715 8.794553 GGAAATAGGTCGATTAGATTGACTAGA 58.205 37.037 0.00 0.00 42.23 2.43
719 745 5.860941 ACTAGATGAGTCAAGGTACCATG 57.139 43.478 15.94 13.33 29.95 3.66
721 747 5.958380 ACTAGATGAGTCAAGGTACCATGAA 59.042 40.000 20.87 6.92 29.95 2.57
723 749 6.126863 AGATGAGTCAAGGTACCATGAAAA 57.873 37.500 20.87 10.20 0.00 2.29
804 1039 2.631160 TCCCCAAATATACGCCTGTG 57.369 50.000 0.00 0.00 0.00 3.66
850 1085 9.717892 GAAGAAATTAAAGACGCCCTAAATTAG 57.282 33.333 0.00 0.00 0.00 1.73
991 1238 1.620323 GCCCAAAAAGACCAGCAAGAT 59.380 47.619 0.00 0.00 0.00 2.40
1004 1251 1.142465 AGCAAGATAGACAGCCATGGG 59.858 52.381 15.13 0.00 0.00 4.00
1047 1294 2.125673 GTGCAGTACCGTGGCGAT 60.126 61.111 0.00 0.00 0.00 4.58
1152 1399 5.363562 TCTCCATCAAGTACCTCTACGTA 57.636 43.478 0.00 0.00 0.00 3.57
1156 1403 5.237996 TCCATCAAGTACCTCTACGTATTCG 59.762 44.000 0.00 0.00 43.34 3.34
1163 1410 2.109538 CTCTACGTATTCGCCGCCGA 62.110 60.000 0.00 0.00 42.66 5.54
1484 1731 2.125065 CTGCTCTGCTCTGCCCTG 60.125 66.667 0.00 0.00 0.00 4.45
1612 1863 5.494724 TCCTTTGCATGCATCTATAGATCC 58.505 41.667 23.37 4.35 31.21 3.36
1647 1898 2.948979 TGCTTGGTTTCTGTACTTGGTG 59.051 45.455 0.00 0.00 0.00 4.17
1681 1932 4.264253 TGATTTTATGCTGTAGCTGCTGT 58.736 39.130 13.43 0.00 42.66 4.40
1701 1952 4.681744 TGTTCCTGCATGACTTGAAAAAC 58.318 39.130 0.00 0.00 0.00 2.43
1775 2030 4.024048 CAGTGCAGTACGTCCAAGAAAAAT 60.024 41.667 0.00 0.00 0.00 1.82
1776 2031 4.213482 AGTGCAGTACGTCCAAGAAAAATC 59.787 41.667 0.00 0.00 0.00 2.17
1777 2032 4.213482 GTGCAGTACGTCCAAGAAAAATCT 59.787 41.667 0.00 0.00 0.00 2.40
1778 2033 4.213270 TGCAGTACGTCCAAGAAAAATCTG 59.787 41.667 0.00 0.00 0.00 2.90
1779 2034 4.213482 GCAGTACGTCCAAGAAAAATCTGT 59.787 41.667 0.00 0.00 0.00 3.41
1780 2035 5.679906 CAGTACGTCCAAGAAAAATCTGTG 58.320 41.667 0.00 0.00 0.00 3.66
1837 2111 0.032952 TCGTCCCAGTAGTTGTGTGC 59.967 55.000 0.00 0.00 0.00 4.57
1894 2171 0.886490 AGGAGACAGCAAAGTTGGCG 60.886 55.000 0.00 0.00 36.08 5.69
1899 2176 2.165437 AGACAGCAAAGTTGGCGAAAAA 59.835 40.909 0.00 0.00 36.08 1.94
1900 2177 2.535574 GACAGCAAAGTTGGCGAAAAAG 59.464 45.455 0.00 0.00 36.08 2.27
1901 2178 1.258720 CAGCAAAGTTGGCGAAAAAGC 59.741 47.619 0.00 0.00 36.08 3.51
1903 2180 1.258720 GCAAAGTTGGCGAAAAAGCAG 59.741 47.619 0.00 0.00 39.27 4.24
1904 2181 2.808244 CAAAGTTGGCGAAAAAGCAGA 58.192 42.857 0.00 0.00 39.27 4.26
1905 2182 2.781945 AAGTTGGCGAAAAAGCAGAG 57.218 45.000 0.00 0.00 39.27 3.35
1909 2186 1.167851 TGGCGAAAAAGCAGAGATGG 58.832 50.000 0.00 0.00 39.27 3.51
1915 2192 4.333926 GCGAAAAAGCAGAGATGGTAGATT 59.666 41.667 0.00 0.00 37.05 2.40
1982 2262 2.159379 GCCTCGCCACCTTTATTTTCTG 60.159 50.000 0.00 0.00 0.00 3.02
2012 2292 2.065899 TGTCCTTCCAAACAACCCAG 57.934 50.000 0.00 0.00 0.00 4.45
2080 2360 5.885230 TGCACGATCTGATTTTCTCAAAT 57.115 34.783 0.00 0.00 35.12 2.32
2109 2389 0.534203 TTCCTCAACGACTTGGGTGC 60.534 55.000 0.00 0.00 0.00 5.01
2110 2390 1.966451 CCTCAACGACTTGGGTGCC 60.966 63.158 0.00 0.00 0.00 5.01
2165 2450 2.026822 TCAGGGGCAATCTTCTCACTTC 60.027 50.000 0.00 0.00 0.00 3.01
2173 2458 6.226052 GGCAATCTTCTCACTTCCAAATTTT 58.774 36.000 0.00 0.00 0.00 1.82
2174 2459 6.367149 GGCAATCTTCTCACTTCCAAATTTTC 59.633 38.462 0.00 0.00 0.00 2.29
2175 2460 6.925165 GCAATCTTCTCACTTCCAAATTTTCA 59.075 34.615 0.00 0.00 0.00 2.69
2176 2461 7.439056 GCAATCTTCTCACTTCCAAATTTTCAA 59.561 33.333 0.00 0.00 0.00 2.69
2265 2550 1.753073 CATCCTTGATCCCCTTTGTGC 59.247 52.381 0.00 0.00 0.00 4.57
2285 2570 5.592282 TGTGCTGTTCTAGGATTGTTGAAAA 59.408 36.000 0.00 0.00 0.00 2.29
2439 2919 4.006319 CCTCCCTCAAACTGAATTCTCAC 58.994 47.826 7.05 0.00 0.00 3.51
2466 3031 1.395045 ATCTCGCCGATCCTCTGCAA 61.395 55.000 0.00 0.00 0.00 4.08
2546 3216 0.801251 GTGCCATCACTGTCAAGCTC 59.199 55.000 0.00 0.00 40.03 4.09
2559 3229 1.612442 AAGCTCCCGGCCTGACTAA 60.612 57.895 0.00 0.00 43.05 2.24
2560 3230 0.983378 AAGCTCCCGGCCTGACTAAT 60.983 55.000 0.00 0.00 43.05 1.73
2561 3231 1.069935 GCTCCCGGCCTGACTAATC 59.930 63.158 0.00 0.00 34.27 1.75
2630 3305 6.545298 AGATCTTTGATTTAGACCTGCAATCC 59.455 38.462 0.00 0.00 0.00 3.01
2666 3384 1.814394 GACAAGCACATGAATGGCTGA 59.186 47.619 0.00 0.00 35.49 4.26
2829 3547 3.387947 GACCACCCCGTCGTCCAT 61.388 66.667 0.00 0.00 0.00 3.41
2896 3614 1.904771 CACCCGGAGTATTGCCAGA 59.095 57.895 0.73 0.00 0.00 3.86
3431 4149 4.493747 GGACCTCGACTTCGGCGG 62.494 72.222 7.21 2.90 40.29 6.13
3584 4302 0.395586 TGCTGCAACCCTGTTGAACT 60.396 50.000 10.94 0.00 0.00 3.01
3591 4309 1.213296 ACCCTGTTGAACTCAGTGGT 58.787 50.000 0.00 0.00 34.30 4.16
3717 4442 4.458295 CCTAGCATAATGCCCAATCTCAAG 59.542 45.833 0.00 0.00 46.52 3.02
3784 4552 4.686972 GATCTTGTTCGTCTGATCCATCA 58.313 43.478 0.00 0.00 35.16 3.07
3820 4588 2.397549 TCATAAGCATGCTCATCGTCG 58.602 47.619 22.93 0.00 31.73 5.12
3978 4774 7.753309 TTATTAGTGAAAGCAAACTAAGGCA 57.247 32.000 0.00 0.00 41.02 4.75
4000 4797 5.230182 CAAGGGAATGAAACTTTTACTGGC 58.770 41.667 0.00 0.00 0.00 4.85
4146 4944 5.481473 TCAAAGCAATCCCTTCTTTTATGCT 59.519 36.000 0.00 0.00 43.89 3.79
4167 4965 0.179145 CGTACTACTGGCTCCAACGG 60.179 60.000 2.99 0.00 0.00 4.44
4330 5129 8.709646 CGTCCTTACACATTATCTAATTTAGCC 58.290 37.037 0.00 0.00 0.00 3.93
4393 5193 4.381185 CCCGGTTGCCTAAAGTTTTATTCC 60.381 45.833 0.00 0.00 0.00 3.01
4557 5453 6.707608 TCTGAGAATGGTTCCATATTGATTCG 59.292 38.462 4.67 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 1.258445 CCTAAGGCCACTGGAGACGT 61.258 60.000 5.01 0.00 0.00 4.34
221 223 2.898343 GACACGCCCACCAACGTT 60.898 61.111 0.00 0.00 41.32 3.99
238 241 1.101635 TCAGCCGGAGATACACCTCG 61.102 60.000 5.05 0.00 34.08 4.63
246 249 2.733956 GAGGATAGATCAGCCGGAGAT 58.266 52.381 5.05 7.76 37.96 2.75
283 286 6.157211 AGAACATAGACGAACAACAACTAGG 58.843 40.000 0.00 0.00 0.00 3.02
286 289 5.815740 ACAAGAACATAGACGAACAACAACT 59.184 36.000 0.00 0.00 0.00 3.16
307 310 1.271163 GGATCCAACCCGAAGACACAA 60.271 52.381 6.95 0.00 0.00 3.33
359 362 0.311790 CAGCGCACCAGAACAACAAT 59.688 50.000 11.47 0.00 0.00 2.71
398 401 0.536687 AGACAGTCGGGAAGTCGTCA 60.537 55.000 0.00 0.00 37.36 4.35
426 429 2.967397 CGGAGTCGGGCACAACTA 59.033 61.111 0.00 0.00 0.00 2.24
482 485 4.248402 CGACGACTACCCGCAAAA 57.752 55.556 0.00 0.00 0.00 2.44
487 490 0.247974 CACTTAGCGACGACTACCCG 60.248 60.000 0.00 0.00 0.00 5.28
489 492 0.807496 ACCACTTAGCGACGACTACC 59.193 55.000 0.00 0.00 0.00 3.18
503 510 2.311463 CATCCAGATCCGTAGACCACT 58.689 52.381 0.00 0.00 0.00 4.00
533 540 6.142817 GCAGTACAACAAACACCAGAAATAG 58.857 40.000 0.00 0.00 0.00 1.73
547 557 6.658816 ACATCTTCAATTATGGCAGTACAACA 59.341 34.615 0.00 0.00 0.00 3.33
561 571 7.675062 AGCTTCCGATCTATACATCTTCAATT 58.325 34.615 0.00 0.00 0.00 2.32
572 582 7.837202 TTTTCGAAAAAGCTTCCGATCTATA 57.163 32.000 20.56 0.00 0.00 1.31
604 614 7.148423 ACGTTCCTTCGTAAAAATTATACCCAC 60.148 37.037 0.00 0.00 42.35 4.61
608 618 7.689400 CACCACGTTCCTTCGTAAAAATTATAC 59.311 37.037 0.00 0.00 42.27 1.47
625 635 2.094649 CCTCCTTCTAGTCACCACGTTC 60.095 54.545 0.00 0.00 0.00 3.95
629 639 2.494073 CTCACCTCCTTCTAGTCACCAC 59.506 54.545 0.00 0.00 0.00 4.16
630 640 2.110188 ACTCACCTCCTTCTAGTCACCA 59.890 50.000 0.00 0.00 0.00 4.17
631 641 2.810164 ACTCACCTCCTTCTAGTCACC 58.190 52.381 0.00 0.00 0.00 4.02
633 643 5.258216 ACTAACTCACCTCCTTCTAGTCA 57.742 43.478 0.00 0.00 0.00 3.41
634 644 6.391537 CAAACTAACTCACCTCCTTCTAGTC 58.608 44.000 0.00 0.00 0.00 2.59
635 645 5.279556 GCAAACTAACTCACCTCCTTCTAGT 60.280 44.000 0.00 0.00 0.00 2.57
636 646 5.172205 GCAAACTAACTCACCTCCTTCTAG 58.828 45.833 0.00 0.00 0.00 2.43
702 715 8.877864 TTTATTTTCATGGTACCTTGACTCAT 57.122 30.769 25.79 19.47 31.27 2.90
850 1085 8.126074 CGTACATCTTCTCTCTATATATGGCAC 58.874 40.741 0.00 0.00 0.00 5.01
931 1170 3.839293 CTCTGCTCGGCTTATATACCAC 58.161 50.000 0.00 0.00 0.00 4.16
1004 1251 3.453070 GAGATCTCCAGCCCCGTGC 62.453 68.421 12.00 0.00 41.71 5.34
1334 1581 3.760035 GGAGGAAGTCGGCTGCGA 61.760 66.667 0.00 0.00 0.00 5.10
1612 1863 5.587388 AACCAAGCAGTGATAAATGGATG 57.413 39.130 4.62 0.00 0.00 3.51
1647 1898 7.710896 ACAGCATAAAATCAAGCTTATTCCTC 58.289 34.615 0.00 0.00 34.61 3.71
1681 1932 4.998671 TGTTTTTCAAGTCATGCAGGAA 57.001 36.364 0.92 0.00 0.00 3.36
1775 2030 4.530553 TCTTAATTGCTCCCACTACACAGA 59.469 41.667 0.00 0.00 0.00 3.41
1776 2031 4.832248 TCTTAATTGCTCCCACTACACAG 58.168 43.478 0.00 0.00 0.00 3.66
1777 2032 4.901197 TCTTAATTGCTCCCACTACACA 57.099 40.909 0.00 0.00 0.00 3.72
1778 2033 5.648092 ACAATCTTAATTGCTCCCACTACAC 59.352 40.000 0.00 0.00 45.16 2.90
1779 2034 5.815581 ACAATCTTAATTGCTCCCACTACA 58.184 37.500 0.00 0.00 45.16 2.74
1780 2035 6.555315 CAACAATCTTAATTGCTCCCACTAC 58.445 40.000 0.00 0.00 45.16 2.73
1894 2171 5.067023 CCCAATCTACCATCTCTGCTTTTTC 59.933 44.000 0.00 0.00 0.00 2.29
1899 2176 2.769209 ACCCAATCTACCATCTCTGCT 58.231 47.619 0.00 0.00 0.00 4.24
1900 2177 3.567478 AACCCAATCTACCATCTCTGC 57.433 47.619 0.00 0.00 0.00 4.26
1901 2178 4.901849 TCCTAACCCAATCTACCATCTCTG 59.098 45.833 0.00 0.00 0.00 3.35
1903 2180 5.148502 TCTCCTAACCCAATCTACCATCTC 58.851 45.833 0.00 0.00 0.00 2.75
1904 2181 5.151454 CTCTCCTAACCCAATCTACCATCT 58.849 45.833 0.00 0.00 0.00 2.90
1905 2182 4.902448 ACTCTCCTAACCCAATCTACCATC 59.098 45.833 0.00 0.00 0.00 3.51
1909 2186 4.287552 TGGACTCTCCTAACCCAATCTAC 58.712 47.826 0.00 0.00 37.46 2.59
1915 2192 1.132657 TGGTTGGACTCTCCTAACCCA 60.133 52.381 14.77 0.00 42.18 4.51
1982 2262 1.239347 GGAAGGACAAAGTGTGCCTC 58.761 55.000 0.00 0.00 39.72 4.70
2012 2292 3.004024 CTTGACAACATGCAAGTGGAC 57.996 47.619 2.88 0.00 37.35 4.02
2080 2360 4.385825 AGTCGTTGAGGAACAAAGCATAA 58.614 39.130 0.00 0.00 40.36 1.90
2109 2389 8.800370 TCTGATCTAGCTAAGATATACACAGG 57.200 38.462 0.00 0.00 45.35 4.00
2265 2550 9.185192 GTTTCATTTTCAACAATCCTAGAACAG 57.815 33.333 0.00 0.00 0.00 3.16
2356 2836 0.969149 CAGCACCTCAGTGGAGTGTA 59.031 55.000 12.96 0.00 44.69 2.90
2357 2837 1.750930 CAGCACCTCAGTGGAGTGT 59.249 57.895 12.96 1.11 44.69 3.55
2358 2838 1.670406 GCAGCACCTCAGTGGAGTG 60.670 63.158 8.58 8.58 44.69 3.51
2466 3031 6.458232 TTACTGTGTTGCCAGTACAAAATT 57.542 33.333 0.00 0.00 45.17 1.82
2546 3216 0.758734 TGATGATTAGTCAGGCCGGG 59.241 55.000 2.18 0.00 37.87 5.73
2666 3384 0.322816 GGTCACCTGTCATGCCATGT 60.323 55.000 4.31 0.00 0.00 3.21
2709 3427 2.672651 TTGATGGCCGTGCACAGG 60.673 61.111 18.64 19.06 0.00 4.00
3169 3887 1.692519 ACCATTGCCGTAGTATCCCTC 59.307 52.381 0.00 0.00 0.00 4.30
3584 4302 1.474320 CCGTTTCTTCCACACCACTGA 60.474 52.381 0.00 0.00 0.00 3.41
3591 4309 1.595929 GCCGTCCGTTTCTTCCACA 60.596 57.895 0.00 0.00 0.00 4.17
3717 4442 4.780815 TCATCCCTATGTTCCATGACAAC 58.219 43.478 0.00 0.00 34.50 3.32
3813 4581 4.389664 AAGTTGTTGATTGACGACGATG 57.610 40.909 0.00 0.00 38.65 3.84
3820 4588 7.391016 GCTGTGTTTTTAAGTTGTTGATTGAC 58.609 34.615 0.00 0.00 0.00 3.18
3947 4743 8.950403 AGTTTGCTTTCACTAATAATTCGTTC 57.050 30.769 0.00 0.00 0.00 3.95
3978 4774 4.022329 CGCCAGTAAAAGTTTCATTCCCTT 60.022 41.667 0.00 0.00 0.00 3.95
4000 4797 5.516339 GGCTGTGTTTTATCAAATCCAATCG 59.484 40.000 0.00 0.00 0.00 3.34
4146 4944 0.245539 GTTGGAGCCAGTAGTACGCA 59.754 55.000 3.46 0.00 0.00 5.24
4167 4965 4.880120 TGATGAAAAGAGAGATGGATGCAC 59.120 41.667 0.00 0.00 0.00 4.57
4328 5127 6.985059 AGTTTAGAGATTACGGATTGTTAGGC 59.015 38.462 0.00 0.00 0.00 3.93
4359 5159 1.619332 GGCAACCGGGAATTAACCAAA 59.381 47.619 6.32 0.00 0.00 3.28
4362 5162 2.423446 TAGGCAACCGGGAATTAACC 57.577 50.000 6.32 0.00 37.17 2.85
4393 5193 9.294030 GTGCAAATCTAATTGACCAAGATTTAG 57.706 33.333 11.13 8.28 44.25 1.85
4526 5422 2.493675 TGGAACCATTCTCAGAGTCTCG 59.506 50.000 0.00 0.00 0.00 4.04
4605 5504 0.769873 CCTAGAGCCCATGAGCCAAT 59.230 55.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.