Multiple sequence alignment - TraesCS6D01G283300

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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 TraesCS6D01G283300 chr6D 100.000 2753 0 0 1 2753 390235707 390232955 0.000000e+00 5084
1 TraesCS6D01G283300 chr6D 87.092 736 47 14 466 1182 390621669 390620963 0.000000e+00 789
2 TraesCS6D01G283300 chr6D 92.708 288 17 3 93 377 390622259 390621973 1.970000e-111 412
3 TraesCS6D01G283300 chr6D 80.471 297 44 9 460 746 390623503 390623211 5.970000e-52 215
4 TraesCS6D01G283300 chr6D 92.708 96 5 1 1 96 390622681 390622588 1.330000e-28 137
5 TraesCS6D01G283300 chr6A 91.796 2316 123 34 436 2709 536772132 536769842 0.000000e+00 3162
6 TraesCS6D01G283300 chr6A 93.793 435 17 8 1 433 536788781 536788355 0.000000e+00 645
7 TraesCS6D01G283300 chr6B 91.269 1993 82 32 17 1964 584032473 584034418 0.000000e+00 2632
8 TraesCS6D01G283300 chr6B 95.724 421 13 3 2279 2697 584034740 584035157 0.000000e+00 673


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 TraesCS6D01G283300 chr6D 390232955 390235707 2752 True 5084.00 5084 100.00000 1 2753 1 chr6D.!!$R1 2752
1 TraesCS6D01G283300 chr6D 390620963 390623503 2540 True 388.25 789 88.24475 1 1182 4 chr6D.!!$R2 1181
2 TraesCS6D01G283300 chr6A 536769842 536772132 2290 True 3162.00 3162 91.79600 436 2709 1 chr6A.!!$R1 2273
3 TraesCS6D01G283300 chr6B 584032473 584035157 2684 False 1652.50 2632 93.49650 17 2697 2 chr6B.!!$F1 2680

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
164 1319 0.035152 ACAATGGCGATGGCTCTGAA 60.035 50.0 0.0 0.0 39.81 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2015 3477 0.457853 TGTCGTCGAGGTTATGCAGC 60.458 55.0 4.85 0.0 0.0 5.25 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
126 1281 1.138661 CTTGGAGCCCAGAGAGTGATC 59.861 57.143 0.00 0.00 33.81 2.92
164 1319 0.035152 ACAATGGCGATGGCTCTGAA 60.035 50.000 0.00 0.00 39.81 3.02
204 1363 1.876416 GCGAGCACCAGGTTTAAGTGA 60.876 52.381 0.00 0.00 33.21 3.41
285 1446 1.541588 GTGGGATTGCACTCTGAAACC 59.458 52.381 3.88 0.00 0.00 3.27
290 1451 4.442753 GGGATTGCACTCTGAAACCAAAAA 60.443 41.667 3.88 0.00 0.00 1.94
345 1507 3.854666 TCATGTTTCTGCTAGACTCTGC 58.145 45.455 0.00 0.00 0.00 4.26
357 1519 5.171476 GCTAGACTCTGCTGTAAACATGAA 58.829 41.667 0.00 0.00 0.00 2.57
377 1539 7.388500 ACATGAATTGGTGGTTTCATTTCAATC 59.612 33.333 0.00 0.00 39.84 2.67
379 1541 7.451732 TGAATTGGTGGTTTCATTTCAATCAT 58.548 30.769 0.00 0.00 34.00 2.45
380 1542 7.937942 TGAATTGGTGGTTTCATTTCAATCATT 59.062 29.630 0.00 0.00 34.00 2.57
381 1543 7.910441 ATTGGTGGTTTCATTTCAATCATTC 57.090 32.000 0.00 0.00 0.00 2.67
382 1544 6.416631 TGGTGGTTTCATTTCAATCATTCA 57.583 33.333 0.00 0.00 0.00 2.57
383 1545 6.824553 TGGTGGTTTCATTTCAATCATTCAA 58.175 32.000 0.00 0.00 0.00 2.69
384 1546 7.451732 TGGTGGTTTCATTTCAATCATTCAAT 58.548 30.769 0.00 0.00 0.00 2.57
385 1547 7.388224 TGGTGGTTTCATTTCAATCATTCAATG 59.612 33.333 0.00 0.00 0.00 2.82
386 1548 7.388500 GGTGGTTTCATTTCAATCATTCAATGT 59.612 33.333 0.00 0.00 0.00 2.71
399 1561 2.734755 TCAATGTAATGGAGCTGGGG 57.265 50.000 0.00 0.00 0.00 4.96
400 1562 2.204463 TCAATGTAATGGAGCTGGGGA 58.796 47.619 0.00 0.00 0.00 4.81
401 1563 2.173356 TCAATGTAATGGAGCTGGGGAG 59.827 50.000 0.00 0.00 0.00 4.30
402 1564 0.475906 ATGTAATGGAGCTGGGGAGC 59.524 55.000 0.00 0.00 0.00 4.70
415 1577 4.423231 GGAGCTCCCACCCTTTTG 57.577 61.111 23.19 0.00 34.14 2.44
417 1579 0.895559 GGAGCTCCCACCCTTTTGTG 60.896 60.000 23.19 0.00 35.98 3.33
418 1580 0.178990 GAGCTCCCACCCTTTTGTGT 60.179 55.000 0.87 0.00 34.35 3.72
419 1581 0.468029 AGCTCCCACCCTTTTGTGTG 60.468 55.000 0.00 0.00 34.35 3.82
421 1583 1.032014 CTCCCACCCTTTTGTGTGTG 58.968 55.000 0.00 0.00 34.35 3.82
427 1589 1.543802 ACCCTTTTGTGTGTGTGTGTG 59.456 47.619 0.00 0.00 0.00 3.82
433 1595 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
434 1596 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
462 1625 3.135530 AGAGAGAGAGAGAGAGAGAAGCC 59.864 52.174 0.00 0.00 0.00 4.35
473 1858 0.912006 AGAGAAGCCCCCTCCTTGTC 60.912 60.000 0.00 0.00 34.01 3.18
619 2005 6.690957 TCCTTCTATATTTTGCGCAAATTTCG 59.309 34.615 33.94 20.84 36.43 3.46
627 2013 1.218230 GCGCAAATTTCGGCAAACCA 61.218 50.000 0.30 0.00 34.57 3.67
670 2065 6.486320 GTCCATGGTCCAATTTGTTTGAATTT 59.514 34.615 12.58 0.00 37.53 1.82
671 2066 7.013178 GTCCATGGTCCAATTTGTTTGAATTTT 59.987 33.333 12.58 0.00 37.53 1.82
672 2067 7.013083 TCCATGGTCCAATTTGTTTGAATTTTG 59.987 33.333 12.58 0.00 37.53 2.44
872 2298 2.902846 CTCCGCCGTCCGATCTCT 60.903 66.667 0.00 0.00 40.02 3.10
876 2302 1.360551 CGCCGTCCGATCTCTCAAT 59.639 57.895 0.00 0.00 40.02 2.57
881 2307 1.269309 CGTCCGATCTCTCAATCACCC 60.269 57.143 0.00 0.00 0.00 4.61
897 2323 3.161450 CCGATCCCACCCGTCCAT 61.161 66.667 0.00 0.00 0.00 3.41
961 2391 4.737177 AGCCAGCCAAGCCAGCTC 62.737 66.667 0.00 0.00 38.95 4.09
1238 2676 3.075005 GCTCACGGAGGTGGCCTA 61.075 66.667 3.32 0.00 44.50 3.93
1854 3294 2.558359 ACTTGGTTCCAGCATTTGTAGC 59.442 45.455 0.00 0.00 0.00 3.58
1889 3333 6.129179 TCCTTTTGAAGTTCACAGGAGAAAT 58.871 36.000 21.82 0.00 33.36 2.17
1923 3374 0.843309 TTGTGCAGAGGAGGGAAACA 59.157 50.000 0.00 0.00 0.00 2.83
1944 3395 6.105397 ACAAACTTGCAAATCAGATTGGAT 57.895 33.333 0.00 0.00 30.43 3.41
1997 3459 4.855715 TGTTGTCAGTAGAGTCAAGAGG 57.144 45.455 0.00 0.00 0.00 3.69
2030 3492 1.809619 TGCGCTGCATAACCTCGAC 60.810 57.895 9.73 0.00 31.71 4.20
2031 3493 2.860628 GCGCTGCATAACCTCGACG 61.861 63.158 0.00 0.00 0.00 5.12
2038 3500 1.921243 CATAACCTCGACGACATGCA 58.079 50.000 0.00 0.00 0.00 3.96
2041 3531 1.808411 AACCTCGACGACATGCATTT 58.192 45.000 0.00 0.00 0.00 2.32
2042 3532 2.665649 ACCTCGACGACATGCATTTA 57.334 45.000 0.00 0.00 0.00 1.40
2066 3556 3.440173 ACATTGTAATTTGGAGAGCACCG 59.560 43.478 0.00 0.00 0.00 4.94
2067 3557 2.851263 TGTAATTTGGAGAGCACCGT 57.149 45.000 0.00 0.00 0.00 4.83
2068 3558 2.695359 TGTAATTTGGAGAGCACCGTC 58.305 47.619 0.00 0.00 0.00 4.79
2071 3561 1.270907 ATTTGGAGAGCACCGTCTCT 58.729 50.000 1.24 0.48 45.48 3.10
2072 3562 1.048601 TTTGGAGAGCACCGTCTCTT 58.951 50.000 1.24 0.00 43.05 2.85
2073 3563 1.048601 TTGGAGAGCACCGTCTCTTT 58.951 50.000 1.24 0.00 43.05 2.52
2080 3570 3.191791 AGAGCACCGTCTCTTTAGAAGTC 59.808 47.826 0.00 0.00 40.32 3.01
2081 3571 2.891580 AGCACCGTCTCTTTAGAAGTCA 59.108 45.455 0.00 0.00 32.16 3.41
2128 3618 5.068067 ACCAATGTTGCTAACTTTAACCGTT 59.932 36.000 0.00 0.00 0.00 4.44
2162 3652 2.925563 GTTTGCTGCATTAGGAATGTGC 59.074 45.455 1.84 10.30 41.01 4.57
2163 3653 1.836802 TGCTGCATTAGGAATGTGCA 58.163 45.000 0.00 13.75 45.69 4.57
2167 3657 2.009051 TGCATTAGGAATGTGCAGTCG 58.991 47.619 0.00 0.00 43.30 4.18
2168 3658 2.009774 GCATTAGGAATGTGCAGTCGT 58.990 47.619 0.00 0.82 41.01 4.34
2169 3659 3.194861 GCATTAGGAATGTGCAGTCGTA 58.805 45.455 0.00 0.00 41.01 3.43
2192 3683 7.221067 CGTAGTAGAAGAATGTTCTTAAGCCTG 59.779 40.741 7.91 0.00 46.84 4.85
2195 3686 8.157476 AGTAGAAGAATGTTCTTAAGCCTGAAA 58.843 33.333 7.91 0.00 46.84 2.69
2197 3688 8.414629 AGAAGAATGTTCTTAAGCCTGAAATT 57.585 30.769 7.91 0.00 46.84 1.82
2199 3690 7.765695 AGAATGTTCTTAAGCCTGAAATTCA 57.234 32.000 0.00 0.00 32.55 2.57
2207 3698 8.181904 TCTTAAGCCTGAAATTCAAATCTGTT 57.818 30.769 0.00 0.00 0.00 3.16
2211 3702 7.530426 AGCCTGAAATTCAAATCTGTTAGTT 57.470 32.000 0.00 0.00 0.00 2.24
2227 3719 8.080083 TCTGTTAGTTTAAATTCGGTGAACTC 57.920 34.615 0.00 0.00 33.13 3.01
2230 3722 3.749609 AGTTTAAATTCGGTGAACTCCCG 59.250 43.478 0.00 0.00 46.83 5.14
2234 3726 0.399075 ATTCGGTGAACTCCCGGTTT 59.601 50.000 0.00 0.00 45.51 3.27
2235 3727 1.047002 TTCGGTGAACTCCCGGTTTA 58.953 50.000 0.00 0.00 45.51 2.01
2239 3731 2.354403 CGGTGAACTCCCGGTTTATCTT 60.354 50.000 0.00 0.00 41.78 2.40
2241 3733 4.077108 GGTGAACTCCCGGTTTATCTTTT 58.923 43.478 0.00 0.00 38.41 2.27
2242 3734 4.082949 GGTGAACTCCCGGTTTATCTTTTG 60.083 45.833 0.00 0.00 38.41 2.44
2243 3735 4.758165 GTGAACTCCCGGTTTATCTTTTGA 59.242 41.667 0.00 0.00 38.41 2.69
2244 3736 5.001232 TGAACTCCCGGTTTATCTTTTGAG 58.999 41.667 0.00 0.00 38.41 3.02
2246 3738 5.237236 ACTCCCGGTTTATCTTTTGAGAA 57.763 39.130 0.00 0.00 0.00 2.87
2247 3739 5.001874 ACTCCCGGTTTATCTTTTGAGAAC 58.998 41.667 0.00 0.00 28.36 3.01
2248 3740 5.221864 ACTCCCGGTTTATCTTTTGAGAACT 60.222 40.000 0.00 0.00 32.46 3.01
2249 3741 6.013984 ACTCCCGGTTTATCTTTTGAGAACTA 60.014 38.462 0.00 0.00 32.46 2.24
2250 3742 6.168389 TCCCGGTTTATCTTTTGAGAACTAC 58.832 40.000 0.00 0.00 32.46 2.73
2251 3743 6.013984 TCCCGGTTTATCTTTTGAGAACTACT 60.014 38.462 0.00 0.00 32.46 2.57
2252 3744 6.313164 CCCGGTTTATCTTTTGAGAACTACTC 59.687 42.308 0.00 0.00 45.11 2.59
2253 3745 7.097834 CCGGTTTATCTTTTGAGAACTACTCT 58.902 38.462 0.00 0.00 45.13 3.24
2254 3746 8.248945 CCGGTTTATCTTTTGAGAACTACTCTA 58.751 37.037 0.00 0.00 45.13 2.43
2255 3747 9.804758 CGGTTTATCTTTTGAGAACTACTCTAT 57.195 33.333 0.00 0.00 45.13 1.98
2281 3773 8.644216 TCTACTTAACATCTTAACCTGTGTTGA 58.356 33.333 0.00 0.00 36.34 3.18
2286 3786 9.959749 TTAACATCTTAACCTGTGTTGATTTTC 57.040 29.630 0.00 0.00 36.34 2.29
2357 3857 3.784178 TCTTCTTCAGACCTGGAGATGT 58.216 45.455 16.26 0.00 44.18 3.06
2533 4034 1.047002 CTCCTCCATCTTCAGGCGAT 58.953 55.000 0.00 0.00 0.00 4.58
2542 4043 5.815740 TCCATCTTCAGGCGATAAAGTTAAC 59.184 40.000 0.00 0.00 0.00 2.01
2543 4044 5.584649 CCATCTTCAGGCGATAAAGTTAACA 59.415 40.000 8.61 0.00 0.00 2.41
2544 4045 6.238211 CCATCTTCAGGCGATAAAGTTAACAG 60.238 42.308 8.61 0.00 0.00 3.16
2617 4123 2.486951 GCAGTGGCATTGCTATCAAG 57.513 50.000 25.50 0.00 40.72 3.02
2645 4151 4.084287 ACCAAGATCATGTTGCATTCTGT 58.916 39.130 0.00 0.00 0.00 3.41
2647 4153 5.124457 ACCAAGATCATGTTGCATTCTGTAC 59.876 40.000 0.00 0.00 0.00 2.90
2683 4190 3.455543 TGTCCATCCATGACTTATGCTCA 59.544 43.478 0.00 0.00 35.37 4.26
2703 4210 1.234615 AAAAGGCGTCGGGTGTGATG 61.235 55.000 0.00 0.00 0.00 3.07
2709 4216 1.289109 CGTCGGGTGTGATGTGTTCC 61.289 60.000 0.00 0.00 0.00 3.62
2710 4217 0.034896 GTCGGGTGTGATGTGTTCCT 59.965 55.000 0.00 0.00 0.00 3.36
2711 4218 1.274167 GTCGGGTGTGATGTGTTCCTA 59.726 52.381 0.00 0.00 0.00 2.94
2712 4219 1.274167 TCGGGTGTGATGTGTTCCTAC 59.726 52.381 0.00 0.00 0.00 3.18
2713 4220 1.001520 CGGGTGTGATGTGTTCCTACA 59.998 52.381 0.00 0.00 34.63 2.74
2714 4221 2.549134 CGGGTGTGATGTGTTCCTACAA 60.549 50.000 0.00 0.00 35.69 2.41
2715 4222 3.686016 GGGTGTGATGTGTTCCTACAAT 58.314 45.455 0.00 0.00 35.69 2.71
2716 4223 4.079253 GGGTGTGATGTGTTCCTACAATT 58.921 43.478 0.00 0.00 35.69 2.32
2717 4224 5.250200 GGGTGTGATGTGTTCCTACAATTA 58.750 41.667 0.00 0.00 35.69 1.40
2718 4225 5.123344 GGGTGTGATGTGTTCCTACAATTAC 59.877 44.000 0.00 0.00 35.69 1.89
2719 4226 5.163893 GGTGTGATGTGTTCCTACAATTACG 60.164 44.000 0.00 0.00 35.69 3.18
2720 4227 4.390603 TGTGATGTGTTCCTACAATTACGC 59.609 41.667 0.00 0.00 35.69 4.42
2721 4228 4.390603 GTGATGTGTTCCTACAATTACGCA 59.609 41.667 0.00 0.00 35.69 5.24
2722 4229 4.629634 TGATGTGTTCCTACAATTACGCAG 59.370 41.667 0.00 0.00 35.69 5.18
2723 4230 3.997762 TGTGTTCCTACAATTACGCAGT 58.002 40.909 0.00 0.00 39.69 4.40
2724 4231 4.382291 TGTGTTCCTACAATTACGCAGTT 58.618 39.130 0.00 0.00 37.84 3.16
2725 4232 4.449743 TGTGTTCCTACAATTACGCAGTTC 59.550 41.667 0.00 0.00 37.84 3.01
2726 4233 4.689345 GTGTTCCTACAATTACGCAGTTCT 59.311 41.667 0.00 0.00 37.84 3.01
2727 4234 4.688879 TGTTCCTACAATTACGCAGTTCTG 59.311 41.667 0.00 0.00 37.78 3.02
2728 4235 3.259064 TCCTACAATTACGCAGTTCTGC 58.741 45.455 13.97 13.97 37.78 4.26
2739 4246 3.375911 GCAGTTCTGCGTCTTTATCAC 57.624 47.619 9.04 0.00 0.00 3.06
2740 4247 2.996621 GCAGTTCTGCGTCTTTATCACT 59.003 45.455 9.04 0.00 0.00 3.41
2741 4248 3.061429 GCAGTTCTGCGTCTTTATCACTC 59.939 47.826 9.04 0.00 0.00 3.51
2742 4249 4.489810 CAGTTCTGCGTCTTTATCACTCT 58.510 43.478 0.00 0.00 0.00 3.24
2743 4250 4.325741 CAGTTCTGCGTCTTTATCACTCTG 59.674 45.833 0.00 0.00 0.00 3.35
2744 4251 2.881074 TCTGCGTCTTTATCACTCTGC 58.119 47.619 0.00 0.00 0.00 4.26
2745 4252 2.493675 TCTGCGTCTTTATCACTCTGCT 59.506 45.455 0.00 0.00 0.00 4.24
2746 4253 2.602211 CTGCGTCTTTATCACTCTGCTG 59.398 50.000 0.00 0.00 0.00 4.41
2747 4254 2.029020 TGCGTCTTTATCACTCTGCTGT 60.029 45.455 0.00 0.00 0.00 4.40
2748 4255 2.346847 GCGTCTTTATCACTCTGCTGTG 59.653 50.000 0.00 0.00 39.15 3.66
2749 4256 3.579709 CGTCTTTATCACTCTGCTGTGT 58.420 45.455 0.00 0.00 38.90 3.72
2750 4257 4.733850 CGTCTTTATCACTCTGCTGTGTA 58.266 43.478 0.00 0.00 38.90 2.90
2751 4258 5.161358 CGTCTTTATCACTCTGCTGTGTAA 58.839 41.667 0.00 0.00 38.90 2.41
2752 4259 5.807520 CGTCTTTATCACTCTGCTGTGTAAT 59.192 40.000 0.00 0.00 38.90 1.89
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.466167 CAGTTCTCCTGCGTTTGATGG 59.534 52.381 0.00 0.00 33.59 3.51
1 2 2.146342 ACAGTTCTCCTGCGTTTGATG 58.854 47.619 0.00 0.00 45.68 3.07
2 3 2.550830 ACAGTTCTCCTGCGTTTGAT 57.449 45.000 0.00 0.00 45.68 2.57
8 831 0.318441 TCCAGAACAGTTCTCCTGCG 59.682 55.000 13.27 1.87 45.68 5.18
12 835 4.020128 ACCTTGTATCCAGAACAGTTCTCC 60.020 45.833 13.27 0.49 38.11 3.71
126 1281 4.621068 TGTTTGACAGACAGCTTCAAAG 57.379 40.909 10.12 0.00 39.34 2.77
164 1319 3.557898 CGCTGCATCATATTCCCTACCTT 60.558 47.826 0.00 0.00 0.00 3.50
301 1463 1.253593 CCCAGCAGCCTTTTCTTCCC 61.254 60.000 0.00 0.00 0.00 3.97
345 1507 6.511416 TGAAACCACCAATTCATGTTTACAG 58.489 36.000 0.00 0.00 30.94 2.74
357 1519 7.451732 TGAATGATTGAAATGAAACCACCAAT 58.548 30.769 0.00 0.00 0.00 3.16
377 1539 3.319972 CCCCAGCTCCATTACATTGAATG 59.680 47.826 3.16 3.16 36.70 2.67
379 1541 2.580322 TCCCCAGCTCCATTACATTGAA 59.420 45.455 0.00 0.00 0.00 2.69
380 1542 2.173356 CTCCCCAGCTCCATTACATTGA 59.827 50.000 0.00 0.00 0.00 2.57
381 1543 2.579873 CTCCCCAGCTCCATTACATTG 58.420 52.381 0.00 0.00 0.00 2.82
382 1544 1.133668 GCTCCCCAGCTCCATTACATT 60.134 52.381 0.00 0.00 43.09 2.71
383 1545 0.475906 GCTCCCCAGCTCCATTACAT 59.524 55.000 0.00 0.00 43.09 2.29
384 1546 1.915228 GCTCCCCAGCTCCATTACA 59.085 57.895 0.00 0.00 43.09 2.41
385 1547 4.887615 GCTCCCCAGCTCCATTAC 57.112 61.111 0.00 0.00 43.09 1.89
399 1561 0.178990 ACACAAAAGGGTGGGAGCTC 60.179 55.000 4.71 4.71 43.08 4.09
400 1562 0.468029 CACACAAAAGGGTGGGAGCT 60.468 55.000 0.00 0.00 45.09 4.09
401 1563 0.755327 ACACACAAAAGGGTGGGAGC 60.755 55.000 2.12 0.00 45.09 4.70
402 1564 1.032014 CACACACAAAAGGGTGGGAG 58.968 55.000 2.12 0.00 45.09 4.30
403 1565 0.333312 ACACACACAAAAGGGTGGGA 59.667 50.000 7.18 0.00 45.09 4.37
406 1568 1.543802 ACACACACACACAAAAGGGTG 59.456 47.619 0.00 0.00 44.35 4.61
407 1569 1.543802 CACACACACACACAAAAGGGT 59.456 47.619 0.00 0.00 0.00 4.34
410 1572 2.979151 CACACACACACACACACAAAAG 59.021 45.455 0.00 0.00 0.00 2.27
415 1577 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
417 1579 1.128507 CTCACACACACACACACACAC 59.871 52.381 0.00 0.00 0.00 3.82
418 1580 1.001406 TCTCACACACACACACACACA 59.999 47.619 0.00 0.00 0.00 3.72
419 1581 1.660607 CTCTCACACACACACACACAC 59.339 52.381 0.00 0.00 0.00 3.82
421 1583 2.159240 TCTCTCTCACACACACACACAC 60.159 50.000 0.00 0.00 0.00 3.82
427 1589 3.407698 TCTCTCTCTCTCTCACACACAC 58.592 50.000 0.00 0.00 0.00 3.82
433 1595 4.646945 TCTCTCTCTCTCTCTCTCTCTCAC 59.353 50.000 0.00 0.00 0.00 3.51
434 1596 4.871822 TCTCTCTCTCTCTCTCTCTCTCA 58.128 47.826 0.00 0.00 0.00 3.27
462 1625 5.710409 TTTATTAGAAGGACAAGGAGGGG 57.290 43.478 0.00 0.00 0.00 4.79
569 1954 0.396435 TTCAGTCACGGGCTGAACAT 59.604 50.000 17.04 0.00 44.90 2.71
619 2005 2.352715 CGGAAGAAATTCCTGGTTTGCC 60.353 50.000 5.55 0.00 38.96 4.52
627 2013 3.585732 TGGACTTACCGGAAGAAATTCCT 59.414 43.478 9.46 0.00 42.61 3.36
642 2028 5.835819 TCAAACAAATTGGACCATGGACTTA 59.164 36.000 21.47 4.98 39.62 2.24
872 2298 1.632018 GGGTGGGATCGGGTGATTGA 61.632 60.000 0.00 0.00 34.09 2.57
876 2302 4.707768 ACGGGTGGGATCGGGTGA 62.708 66.667 0.00 0.00 0.00 4.02
881 2307 1.523711 CAATGGACGGGTGGGATCG 60.524 63.158 0.00 0.00 0.00 3.69
897 2323 3.443479 AGGGGTTTGGGTGGGCAA 61.443 61.111 0.00 0.00 0.00 4.52
1237 2675 1.521010 CGAGGGAGTCGCTCTCGTA 60.521 63.158 28.46 0.00 43.03 3.43
1238 2676 2.820479 CGAGGGAGTCGCTCTCGT 60.820 66.667 28.46 0.75 43.03 4.18
1854 3294 7.009540 GTGAACTTCAAAAGGAATTGACACAAG 59.990 37.037 0.00 0.00 38.95 3.16
1889 3333 6.149308 CCTCTGCACAACACATAATACAGAAA 59.851 38.462 0.00 0.00 32.94 2.52
1923 3374 6.600882 AGATCCAATCTGATTTGCAAGTTT 57.399 33.333 0.00 0.00 38.44 2.66
1944 3395 5.075900 AGAAAATTTCCCCTTTGGTCCTAGA 59.924 40.000 1.57 0.00 34.77 2.43
1997 3459 3.831729 CGCATATGTGTGCATGGAC 57.168 52.632 10.90 10.90 45.30 4.02
2015 3477 0.457853 TGTCGTCGAGGTTATGCAGC 60.458 55.000 4.85 0.00 0.00 5.25
2023 3485 2.665649 TAAATGCATGTCGTCGAGGT 57.334 45.000 0.00 0.00 0.00 3.85
2027 3489 5.737353 ACAATGTATAAATGCATGTCGTCG 58.263 37.500 0.00 0.00 33.33 5.12
2028 3490 9.663904 AATTACAATGTATAAATGCATGTCGTC 57.336 29.630 0.00 0.00 33.33 4.20
2041 3531 6.481976 CGGTGCTCTCCAAATTACAATGTATA 59.518 38.462 0.00 0.00 0.00 1.47
2042 3532 5.296780 CGGTGCTCTCCAAATTACAATGTAT 59.703 40.000 0.00 0.00 0.00 2.29
2055 3545 1.819288 CTAAAGAGACGGTGCTCTCCA 59.181 52.381 9.50 2.71 44.18 3.86
2056 3546 2.093106 TCTAAAGAGACGGTGCTCTCC 58.907 52.381 9.50 0.00 44.18 3.71
2057 3547 3.191791 ACTTCTAAAGAGACGGTGCTCTC 59.808 47.826 9.50 0.00 44.18 3.20
2064 3554 8.934507 AATTTATCTGACTTCTAAAGAGACGG 57.065 34.615 0.00 0.00 0.00 4.79
2071 3561 9.436957 GTGGACTGAATTTATCTGACTTCTAAA 57.563 33.333 0.00 0.00 0.00 1.85
2072 3562 8.593679 TGTGGACTGAATTTATCTGACTTCTAA 58.406 33.333 0.00 0.00 0.00 2.10
2073 3563 8.134202 TGTGGACTGAATTTATCTGACTTCTA 57.866 34.615 0.00 0.00 0.00 2.10
2080 3570 7.246311 GTGTTGATGTGGACTGAATTTATCTG 58.754 38.462 0.00 0.00 0.00 2.90
2081 3571 6.375455 GGTGTTGATGTGGACTGAATTTATCT 59.625 38.462 0.00 0.00 0.00 1.98
2112 3602 3.628487 ACTGCAAACGGTTAAAGTTAGCA 59.372 39.130 0.00 0.00 27.90 3.49
2113 3603 4.219143 ACTGCAAACGGTTAAAGTTAGC 57.781 40.909 0.00 0.00 27.90 3.09
2117 3607 2.804647 GCAACTGCAAACGGTTAAAGT 58.195 42.857 0.00 0.00 43.73 2.66
2140 3630 3.367703 GCACATTCCTAATGCAGCAAACT 60.368 43.478 0.00 0.00 42.69 2.66
2157 3647 5.105716 ACATTCTTCTACTACGACTGCACAT 60.106 40.000 0.00 0.00 0.00 3.21
2162 3652 9.279904 CTTAAGAACATTCTTCTACTACGACTG 57.720 37.037 10.11 0.00 43.72 3.51
2163 3653 7.969508 GCTTAAGAACATTCTTCTACTACGACT 59.030 37.037 10.11 0.00 43.72 4.18
2164 3654 7.220491 GGCTTAAGAACATTCTTCTACTACGAC 59.780 40.741 10.11 0.00 43.72 4.34
2165 3655 7.122353 AGGCTTAAGAACATTCTTCTACTACGA 59.878 37.037 10.11 0.00 43.72 3.43
2166 3656 7.221067 CAGGCTTAAGAACATTCTTCTACTACG 59.779 40.741 10.11 0.00 43.72 3.51
2167 3657 8.251721 TCAGGCTTAAGAACATTCTTCTACTAC 58.748 37.037 10.11 0.00 43.72 2.73
2168 3658 8.362464 TCAGGCTTAAGAACATTCTTCTACTA 57.638 34.615 10.11 0.00 43.72 1.82
2169 3659 7.246171 TCAGGCTTAAGAACATTCTTCTACT 57.754 36.000 10.11 3.30 43.72 2.57
2197 3688 9.058174 TCACCGAATTTAAACTAACAGATTTGA 57.942 29.630 0.00 0.00 0.00 2.69
2199 3690 9.673454 GTTCACCGAATTTAAACTAACAGATTT 57.327 29.630 0.00 0.00 0.00 2.17
2227 3719 6.171213 AGTAGTTCTCAAAAGATAAACCGGG 58.829 40.000 6.32 0.00 0.00 5.73
2254 3746 9.436957 CAACACAGGTTAAGATGTTAAGTAGAT 57.563 33.333 0.00 0.00 34.87 1.98
2255 3747 8.644216 TCAACACAGGTTAAGATGTTAAGTAGA 58.356 33.333 0.00 0.00 34.87 2.59
2256 3748 8.827177 TCAACACAGGTTAAGATGTTAAGTAG 57.173 34.615 0.00 0.00 34.87 2.57
2257 3749 9.787435 AATCAACACAGGTTAAGATGTTAAGTA 57.213 29.630 0.00 0.00 34.87 2.24
2258 3750 8.691661 AATCAACACAGGTTAAGATGTTAAGT 57.308 30.769 0.00 0.00 34.87 2.24
2259 3751 9.965824 AAAATCAACACAGGTTAAGATGTTAAG 57.034 29.630 0.00 0.00 34.87 1.85
2260 3752 9.959749 GAAAATCAACACAGGTTAAGATGTTAA 57.040 29.630 0.00 0.00 34.87 2.01
2263 3755 7.651808 CAGAAAATCAACACAGGTTAAGATGT 58.348 34.615 0.00 0.00 34.87 3.06
2265 3757 6.265196 TGCAGAAAATCAACACAGGTTAAGAT 59.735 34.615 0.00 0.00 34.87 2.40
2266 3758 5.592282 TGCAGAAAATCAACACAGGTTAAGA 59.408 36.000 0.00 0.00 34.87 2.10
2268 3760 5.359576 ACTGCAGAAAATCAACACAGGTTAA 59.640 36.000 23.35 0.00 34.87 2.01
2298 3798 3.374745 GTGTTGCAAATCCTTGTGACAG 58.625 45.455 0.00 0.00 33.27 3.51
2357 3857 2.683933 GCCTTCCTCCCTCCGTCA 60.684 66.667 0.00 0.00 0.00 4.35
2542 4043 9.254133 GGATACATAGCTATACATTACATGCTG 57.746 37.037 5.77 0.00 32.72 4.41
2543 4044 8.138074 CGGATACATAGCTATACATTACATGCT 58.862 37.037 5.77 0.00 34.92 3.79
2544 4045 7.096023 GCGGATACATAGCTATACATTACATGC 60.096 40.741 5.77 0.00 0.00 4.06
2617 4123 2.950433 CAACATGATCTTGGTTGCCAC 58.050 47.619 12.76 0.00 35.95 5.01
2645 4151 2.296752 TGGACACGACGAAATGGAAGTA 59.703 45.455 0.00 0.00 0.00 2.24
2647 4153 1.790755 TGGACACGACGAAATGGAAG 58.209 50.000 0.00 0.00 0.00 3.46
2683 4190 0.536460 ATCACACCCGACGCCTTTTT 60.536 50.000 0.00 0.00 0.00 1.94
2703 4210 4.689345 AGAACTGCGTAATTGTAGGAACAC 59.311 41.667 0.00 0.00 34.61 3.32
2720 4227 4.325741 CAGAGTGATAAAGACGCAGAACTG 59.674 45.833 0.00 0.00 0.00 3.16
2721 4228 4.489810 CAGAGTGATAAAGACGCAGAACT 58.510 43.478 0.00 0.00 0.00 3.01
2722 4229 3.061429 GCAGAGTGATAAAGACGCAGAAC 59.939 47.826 0.00 0.00 0.00 3.01
2723 4230 3.056536 AGCAGAGTGATAAAGACGCAGAA 60.057 43.478 0.00 0.00 0.00 3.02
2724 4231 2.493675 AGCAGAGTGATAAAGACGCAGA 59.506 45.455 0.00 0.00 0.00 4.26
2725 4232 2.602211 CAGCAGAGTGATAAAGACGCAG 59.398 50.000 0.00 0.00 0.00 5.18
2726 4233 2.029020 ACAGCAGAGTGATAAAGACGCA 60.029 45.455 0.00 0.00 0.00 5.24
2727 4234 2.346847 CACAGCAGAGTGATAAAGACGC 59.653 50.000 0.00 0.00 42.05 5.19
2728 4235 3.579709 ACACAGCAGAGTGATAAAGACG 58.420 45.455 10.38 0.00 42.05 4.18


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

AutoCloner maintained by Alex Coulton.