Multiple sequence alignment - TraesCS2B01G337800

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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 TraesCS2B01G337800 chr2B 100.000 5743 0 0 1 5743 482723260 482717518 0.000000e+00 10606.0
1 TraesCS2B01G337800 chr2A 93.991 3578 149 17 1 3522 574966865 574963298 0.000000e+00 5356.0
2 TraesCS2B01G337800 chr2A 95.294 2231 81 9 3518 5727 574963266 574961039 0.000000e+00 3517.0
3 TraesCS2B01G337800 chr2A 78.344 157 27 4 5373 5529 121289044 121289193 1.700000e-15 95.3
4 TraesCS2B01G337800 chr2D 94.157 2824 124 23 1 2808 406946308 406943510 0.000000e+00 4263.0
5 TraesCS2B01G337800 chr2D 96.011 2231 67 8 3518 5727 406942785 406940556 0.000000e+00 3607.0
6 TraesCS2B01G337800 chr2D 98.081 469 8 1 3054 3522 406943283 406942816 0.000000e+00 815.0
7 TraesCS2B01G337800 chr2D 98.266 173 3 0 2884 3056 406943510 406943338 2.600000e-78 303.0
8 TraesCS2B01G337800 chr2D 88.043 92 10 1 2495 2585 170277827 170277736 2.190000e-19 108.0
9 TraesCS2B01G337800 chr2D 87.640 89 11 0 2494 2582 236654247 236654335 2.830000e-18 104.0
10 TraesCS2B01G337800 chr4B 74.934 379 54 16 5216 5563 37922562 37922930 1.000000e-27 135.0
11 TraesCS2B01G337800 chr4B 77.707 157 27 5 5373 5529 33625953 33626101 7.930000e-14 89.8
12 TraesCS2B01G337800 chr3D 88.043 92 10 1 2495 2585 501713757 501713666 2.190000e-19 108.0
13 TraesCS2B01G337800 chr1D 88.043 92 10 1 2495 2585 63705207 63705116 2.190000e-19 108.0
14 TraesCS2B01G337800 chr6D 86.957 92 11 1 2495 2585 93317817 93317726 1.020000e-17 102.0
15 TraesCS2B01G337800 chr4D 86.957 92 11 1 2495 2585 50531449 50531358 1.020000e-17 102.0
16 TraesCS2B01G337800 chr7A 77.070 157 29 4 5373 5529 101276053 101276202 3.690000e-12 84.2
17 TraesCS2B01G337800 chr7A 77.273 154 26 6 5374 5526 327910345 327910200 1.330000e-11 82.4
18 TraesCS2B01G337800 chr5A 81.818 99 17 1 5373 5471 66009580 66009677 1.330000e-11 82.4
19 TraesCS2B01G337800 chr1A 82.178 101 13 5 5373 5471 420049794 420049891 1.330000e-11 82.4
20 TraesCS2B01G337800 chr1A 80.392 102 20 0 5373 5474 5260724 5260623 1.720000e-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 TraesCS2B01G337800 chr2B 482717518 482723260 5742 True 10606.0 10606 100.00000 1 5743 1 chr2B.!!$R1 5742
1 TraesCS2B01G337800 chr2A 574961039 574966865 5826 True 4436.5 5356 94.64250 1 5727 2 chr2A.!!$R1 5726
2 TraesCS2B01G337800 chr2D 406940556 406946308 5752 True 2247.0 4263 96.62875 1 5727 4 chr2D.!!$R2 5726

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
457 459 0.252696 TCTATGTCACTGTGGGCCCT 60.253 55.0 25.70 0.00 0.00 5.19 F
662 664 0.316607 CGAATCTCTGAGCTCGTCCG 60.317 60.0 9.64 1.95 0.00 4.79 F
1043 1049 0.321298 GCCGGTTGCTCAGAGGTAAA 60.321 55.0 1.90 0.00 36.87 2.01 F
1558 1576 0.666913 AGCTCATCGAATGCATTGGC 59.333 50.0 18.59 10.63 41.68 4.52 F
1661 1679 1.068352 AAGGGAAAGGCTGTCAGGGT 61.068 55.0 7.07 0.00 0.00 4.34 F
2166 2184 2.107041 TTGACCACGACCCGAATGCT 62.107 55.0 0.00 0.00 0.00 3.79 F
3778 3942 0.669932 AGTTGCAGAAGAGCTCGCTG 60.670 55.0 25.88 25.88 34.99 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1544 1562 1.679680 CTTCCAGCCAATGCATTCGAT 59.320 47.619 9.53 0.0 41.13 3.59 R
2654 2691 1.120530 ACGGGGCTTAGTATCCACTG 58.879 55.000 0.00 0.0 36.14 3.66 R
2993 3039 1.202879 CCTTGTGCCCTTGTGGAACTA 60.203 52.381 0.00 0.0 44.13 2.24 R
3127 3230 0.237235 GCGAACATTCTCACGGCAAA 59.763 50.000 0.00 0.0 0.00 3.68 R
3216 3319 1.779221 CATTTAATGCCTCCTGCCCA 58.221 50.000 0.00 0.0 40.16 5.36 R
3819 3983 2.159379 GCATCGTCACCTTTTCATTCCC 60.159 50.000 0.00 0.0 0.00 3.97 R
4813 4981 0.543277 CTATCCTTGTCAGGCAGGCA 59.457 55.000 0.00 0.0 40.58 4.75 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
22 23 0.725784 CACAGCGCCGATCAAAACAC 60.726 55.000 2.29 0.00 0.00 3.32
32 33 1.535462 GATCAAAACACGGTCCACAGG 59.465 52.381 0.00 0.00 0.00 4.00
42 43 4.373116 TCCACAGGACCGAAGCGC 62.373 66.667 0.00 0.00 0.00 5.92
105 106 0.473117 AGACCCTGTTCCCCGAGAAA 60.473 55.000 0.00 0.00 35.85 2.52
158 159 0.534203 GACAGGCAAGTCAAACCGGA 60.534 55.000 9.46 0.00 38.40 5.14
160 161 1.600916 AGGCAAGTCAAACCGGAGC 60.601 57.895 9.46 0.00 0.00 4.70
221 222 1.192428 GTCCTACCTCCACCGAACAT 58.808 55.000 0.00 0.00 0.00 2.71
281 282 1.141019 TCGGCGTATGGAGCTGAAC 59.859 57.895 6.85 0.00 45.85 3.18
395 397 1.643868 GCATCGCCACCGTTGATTCA 61.644 55.000 0.00 0.00 36.52 2.57
397 399 0.744414 ATCGCCACCGTTGATTCAGG 60.744 55.000 0.00 0.00 35.54 3.86
408 410 1.942776 TGATTCAGGCTGGAGAGTGA 58.057 50.000 15.73 0.00 0.00 3.41
447 449 0.753262 ATGAGCCGGGTCTATGTCAC 59.247 55.000 31.97 6.48 0.00 3.67
457 459 0.252696 TCTATGTCACTGTGGGCCCT 60.253 55.000 25.70 0.00 0.00 5.19
541 543 1.827315 CGCGCAAACCTGACGAAAGA 61.827 55.000 8.75 0.00 0.00 2.52
615 617 0.740868 CTTCGCCTCCATCGCTCAAA 60.741 55.000 0.00 0.00 0.00 2.69
651 653 1.047002 CATCTCCCCTGCGAATCTCT 58.953 55.000 0.00 0.00 0.00 3.10
662 664 0.316607 CGAATCTCTGAGCTCGTCCG 60.317 60.000 9.64 1.95 0.00 4.79
713 715 0.458889 CGCCGGAGAAAACCACGATA 60.459 55.000 5.05 0.00 33.07 2.92
718 720 4.380128 GCCGGAGAAAACCACGATATTTTT 60.380 41.667 5.05 0.00 0.00 1.94
809 815 1.599542 CGAATTCCCTCGCCATCTTTC 59.400 52.381 0.00 0.00 31.04 2.62
984 990 1.129917 TTCACGGGTTGGAACTGGTA 58.870 50.000 0.00 0.00 0.00 3.25
1026 1032 4.341502 TTTTGCTGCTTCGGCGCC 62.342 61.111 19.07 19.07 45.37 6.53
1043 1049 0.321298 GCCGGTTGCTCAGAGGTAAA 60.321 55.000 1.90 0.00 36.87 2.01
1044 1050 1.439679 CCGGTTGCTCAGAGGTAAAC 58.560 55.000 0.00 0.00 0.00 2.01
1057 1067 5.009610 TCAGAGGTAAACTTTGTTTCCATGC 59.990 40.000 0.00 0.00 33.27 4.06
1058 1068 4.892934 AGAGGTAAACTTTGTTTCCATGCA 59.107 37.500 0.00 0.00 0.00 3.96
1192 1207 9.843334 GTACTCCTACGATGATATTTTTAGAGG 57.157 37.037 0.00 0.00 0.00 3.69
1193 1208 7.897864 ACTCCTACGATGATATTTTTAGAGGG 58.102 38.462 0.00 0.00 0.00 4.30
1199 1214 6.055588 CGATGATATTTTTAGAGGGTGTGGT 58.944 40.000 0.00 0.00 0.00 4.16
1350 1365 3.122480 TCCCATCAGCCCTCATCTTTTA 58.878 45.455 0.00 0.00 0.00 1.52
1351 1366 3.527253 TCCCATCAGCCCTCATCTTTTAA 59.473 43.478 0.00 0.00 0.00 1.52
1352 1367 4.017591 TCCCATCAGCCCTCATCTTTTAAA 60.018 41.667 0.00 0.00 0.00 1.52
1353 1368 4.711355 CCCATCAGCCCTCATCTTTTAAAA 59.289 41.667 0.00 0.00 0.00 1.52
1354 1369 5.187576 CCCATCAGCCCTCATCTTTTAAAAA 59.812 40.000 1.66 0.00 0.00 1.94
1420 1435 3.195610 TGTTGACTGGACTATACCTGCTG 59.804 47.826 0.00 0.00 33.18 4.41
1558 1576 0.666913 AGCTCATCGAATGCATTGGC 59.333 50.000 18.59 10.63 41.68 4.52
1661 1679 1.068352 AAGGGAAAGGCTGTCAGGGT 61.068 55.000 7.07 0.00 0.00 4.34
1799 1817 9.639563 TTTGCTATTTATGATGGTCATTTAGGA 57.360 29.630 0.00 0.00 38.26 2.94
1836 1854 7.731054 TGCATACCTACAGGAAAATTTGTTTT 58.269 30.769 1.29 0.00 38.94 2.43
1863 1881 9.191995 CTAATATTTTGAACGAGGCAAGTTTTT 57.808 29.630 0.00 0.00 31.14 1.94
1996 2014 2.987232 AGGCTTATGAAAAGACGGACC 58.013 47.619 0.00 0.00 0.00 4.46
2166 2184 2.107041 TTGACCACGACCCGAATGCT 62.107 55.000 0.00 0.00 0.00 3.79
2172 2190 3.567797 GACCCGAATGCTGAGCGC 61.568 66.667 0.00 0.00 39.77 5.92
2187 2205 4.996113 CGCGGCGCTATTGAAAAT 57.004 50.000 30.54 0.00 0.00 1.82
2220 2238 3.772387 TGTTTCAAATATGCCAGGTGGA 58.228 40.909 0.00 0.00 37.39 4.02
2232 2250 4.526970 TGCCAGGTGGATCTTCTATTTTC 58.473 43.478 0.00 0.00 37.39 2.29
2268 2291 3.492421 AATCATTGTTACAGGCTTGCG 57.508 42.857 0.00 0.00 0.00 4.85
2295 2318 7.123098 TCCAGTTGTGCATCTGATATTTGATTT 59.877 33.333 14.91 0.00 34.02 2.17
2453 2476 8.812513 ATATGCTTGCTATATTCTTGCCATTA 57.187 30.769 0.00 0.00 0.00 1.90
2524 2547 3.134804 CCTCCGTCCCACAATAGAAGATT 59.865 47.826 0.00 0.00 0.00 2.40
2623 2660 3.569701 TCCAGAAAATGTTGGAAGTGCTC 59.430 43.478 0.00 0.00 40.41 4.26
2764 2809 3.502191 TGCAGCAATTATTTTCCGTCC 57.498 42.857 0.00 0.00 0.00 4.79
2845 2890 7.591426 GCTAACCTTAAAGTGTCTGAACAAATG 59.409 37.037 0.00 0.00 37.08 2.32
2964 3010 4.469657 AGAAAGTGGCAATAGTTCACCAA 58.530 39.130 2.68 0.00 33.03 3.67
2993 3039 9.988350 CTAGTCTTATGCATTATTTTTCACGTT 57.012 29.630 3.54 0.00 0.00 3.99
3142 3245 6.455360 AATCAATATTTGCCGTGAGAATGT 57.545 33.333 0.00 0.00 0.00 2.71
3143 3246 5.895636 TCAATATTTGCCGTGAGAATGTT 57.104 34.783 0.00 0.00 0.00 2.71
3216 3319 9.342308 TCTTCTTATGAAAAGAATGACAGTTGT 57.658 29.630 0.98 0.00 35.90 3.32
3531 3693 8.970859 ATGGAGATTTCTTTGTAAGGATGTAG 57.029 34.615 0.00 0.00 0.00 2.74
3547 3709 4.470304 GGATGTAGTCAACCTTAAGACCCT 59.530 45.833 3.36 0.00 35.38 4.34
3670 3834 5.501156 ACTCCATTTCGCCTATCTTTTCTT 58.499 37.500 0.00 0.00 0.00 2.52
3671 3835 5.946377 ACTCCATTTCGCCTATCTTTTCTTT 59.054 36.000 0.00 0.00 0.00 2.52
3692 3856 4.967084 TTAGTCCTGAACAAAGCTACCA 57.033 40.909 0.00 0.00 0.00 3.25
3707 3871 9.073475 ACAAAGCTACCAACAAAAATATACTCA 57.927 29.630 0.00 0.00 0.00 3.41
3778 3942 0.669932 AGTTGCAGAAGAGCTCGCTG 60.670 55.000 25.88 25.88 34.99 5.18
3819 3983 8.057742 GCATAAATGTGTGTTGAAAAGAAACTG 58.942 33.333 0.00 0.00 26.81 3.16
4480 4646 4.962839 TGGGATAAAACCTAGTACTCCCA 58.037 43.478 9.12 9.12 46.55 4.37
4546 4714 7.378181 ACTAAAGCTGTGACAATTAATTTGGG 58.622 34.615 0.00 0.00 39.80 4.12
4728 4896 5.379732 TGATATATCATGCGTGGTCGTTA 57.620 39.130 11.49 0.00 39.49 3.18
4804 4972 7.292120 AGAGGAGAGCAGAAGGAATTATAACAT 59.708 37.037 0.00 0.00 0.00 2.71
4878 5046 2.754552 TGGAATGCTGGCTGTAAATGAC 59.245 45.455 0.00 0.00 0.00 3.06
4984 5153 9.455847 CAAATAGCCTTCTTCTGTAAATAATGC 57.544 33.333 0.00 0.00 0.00 3.56
5069 5238 2.963599 TCCAACTTGGAGTTTACCCC 57.036 50.000 6.39 0.00 42.67 4.95
5234 5406 3.058160 CCTGTTTGGGCTGCTCCG 61.058 66.667 0.00 0.00 34.94 4.63
5288 5460 1.446016 AACCAAACAGGGTAGCTCCT 58.554 50.000 0.00 0.00 41.32 3.69
5299 5471 2.307098 GGGTAGCTCCTCAATATGCCAT 59.693 50.000 0.00 0.00 36.25 4.40
5322 5494 8.267894 CCATTCCAAGAAAACTAGAATCTAGGA 58.732 37.037 20.18 4.63 0.00 2.94
5409 5582 3.980646 TGTTTTTCCCACGACATTCAG 57.019 42.857 0.00 0.00 0.00 3.02
5410 5583 2.034053 TGTTTTTCCCACGACATTCAGC 59.966 45.455 0.00 0.00 0.00 4.26
5419 5592 3.244009 CCACGACATTCAGCCAGATAGAT 60.244 47.826 0.00 0.00 0.00 1.98
5421 5594 4.813161 CACGACATTCAGCCAGATAGATTT 59.187 41.667 0.00 0.00 0.00 2.17
5451 5624 7.309377 CCACCAAATTTCTCATTCTTGAAGCTA 60.309 37.037 0.00 0.00 0.00 3.32
5452 5625 8.084073 CACCAAATTTCTCATTCTTGAAGCTAA 58.916 33.333 0.00 0.00 0.00 3.09
5454 5627 9.649167 CCAAATTTCTCATTCTTGAAGCTAAAT 57.351 29.630 0.00 0.00 0.00 1.40
5461 5634 9.201989 TCTCATTCTTGAAGCTAAATCTACCTA 57.798 33.333 0.00 0.00 0.00 3.08
5519 5692 3.629398 GCAACTCCTATATGCAACTGCTT 59.371 43.478 2.95 0.00 42.66 3.91
5545 5732 6.434018 AAGTGAAGCTGATTTTGATAGAGC 57.566 37.500 0.00 0.00 0.00 4.09
5564 5751 0.606401 CGGAGCAGTCCCAAACATGT 60.606 55.000 0.00 0.00 40.20 3.21
5566 5753 2.084546 GGAGCAGTCCCAAACATGTAC 58.915 52.381 0.00 0.00 36.76 2.90
5607 5794 6.202762 GGACCTGAAAATTTTAGGCAAAACTG 59.797 38.462 15.39 4.91 36.49 3.16
5641 5828 2.408704 CGCTAGAAGAAACCGTGAACAG 59.591 50.000 0.00 0.00 0.00 3.16
5658 5845 4.892934 TGAACAGTGTTTTATGCCCTCTTT 59.107 37.500 10.45 0.00 0.00 2.52
5727 5914 2.411031 CGTACAACATTTCACAGTCGCC 60.411 50.000 0.00 0.00 0.00 5.54
5728 5915 1.674359 ACAACATTTCACAGTCGCCA 58.326 45.000 0.00 0.00 0.00 5.69
5729 5916 1.603802 ACAACATTTCACAGTCGCCAG 59.396 47.619 0.00 0.00 0.00 4.85
5730 5917 1.872952 CAACATTTCACAGTCGCCAGA 59.127 47.619 0.00 0.00 0.00 3.86
5739 5926 3.972227 GTCGCCAGACAAGTGCAT 58.028 55.556 0.00 0.00 46.32 3.96
5740 5927 2.247790 GTCGCCAGACAAGTGCATT 58.752 52.632 0.00 0.00 46.32 3.56
5741 5928 0.166814 GTCGCCAGACAAGTGCATTC 59.833 55.000 0.00 0.00 46.32 2.67
5742 5929 0.250252 TCGCCAGACAAGTGCATTCA 60.250 50.000 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 0.542333 TCCTGTGGACCGTGTTTTGA 59.458 50.000 0.00 0.00 0.00 2.69
221 222 2.261361 CGGGTCGTCATGTGCTGA 59.739 61.111 0.00 0.00 0.00 4.26
244 245 4.106925 CTGTGGGCCTGGAGGAGC 62.107 72.222 4.53 0.00 37.39 4.70
281 282 1.004918 ACGGGTCCAAGCGAGAAAG 60.005 57.895 0.00 0.00 0.00 2.62
311 312 1.078143 GCGACAGGGGAGCAGAAAT 60.078 57.895 0.00 0.00 0.00 2.17
365 367 1.880340 GGCGATGCTTCCGTCTGAG 60.880 63.158 0.00 0.00 0.00 3.35
395 397 1.685421 GAGCCTCACTCTCCAGCCT 60.685 63.158 0.00 0.00 42.62 4.58
397 399 1.391157 ATCGAGCCTCACTCTCCAGC 61.391 60.000 0.00 0.00 43.85 4.85
408 410 1.443407 CACCGGATCAATCGAGCCT 59.557 57.895 9.46 0.00 46.10 4.58
447 449 4.087892 CAGACGGAGGGCCCACAG 62.088 72.222 27.56 21.99 34.14 3.66
457 459 0.965866 CTCAGCAGGGTACAGACGGA 60.966 60.000 0.00 0.00 0.00 4.69
718 720 3.222603 GGCCACAGAAAAGAAGAAGGAA 58.777 45.455 0.00 0.00 0.00 3.36
809 815 2.623915 GCACCCTGACAGCAAGCAG 61.624 63.158 0.00 0.00 0.00 4.24
984 990 2.633481 GGCCATATCTCGTAAACTCCCT 59.367 50.000 0.00 0.00 0.00 4.20
1026 1032 2.457366 AGTTTACCTCTGAGCAACCG 57.543 50.000 0.00 0.00 0.00 4.44
1057 1067 7.281991 GCAATTAGCAAAGAAAATACTGGTG 57.718 36.000 0.00 0.00 44.79 4.17
1100 1115 7.569240 CCTCACAGGAAAAATCCTACTCTATT 58.431 38.462 0.00 0.00 37.67 1.73
1101 1116 6.408662 GCCTCACAGGAAAAATCCTACTCTAT 60.409 42.308 0.00 0.00 37.67 1.98
1102 1117 5.104900 GCCTCACAGGAAAAATCCTACTCTA 60.105 44.000 0.00 0.00 37.67 2.43
1103 1118 4.323868 GCCTCACAGGAAAAATCCTACTCT 60.324 45.833 0.00 0.00 37.67 3.24
1106 1121 3.691609 CAGCCTCACAGGAAAAATCCTAC 59.308 47.826 0.00 0.00 37.67 3.18
1186 1201 3.335786 TCTCTAGGAACCACACCCTCTAA 59.664 47.826 0.00 0.00 34.11 2.10
1187 1202 2.924302 TCTCTAGGAACCACACCCTCTA 59.076 50.000 0.00 0.00 34.11 2.43
1190 1205 1.897647 GCTCTCTAGGAACCACACCCT 60.898 57.143 0.00 0.00 36.60 4.34
1191 1206 0.537653 GCTCTCTAGGAACCACACCC 59.462 60.000 0.00 0.00 0.00 4.61
1192 1207 1.267121 TGCTCTCTAGGAACCACACC 58.733 55.000 0.00 0.00 0.00 4.16
1193 1208 3.330267 CTTTGCTCTCTAGGAACCACAC 58.670 50.000 0.00 0.00 32.11 3.82
1199 1214 4.090090 AGTACAGCTTTGCTCTCTAGGAA 58.910 43.478 0.00 0.00 36.40 3.36
1355 1370 4.936685 AGAAGATGAGGGCTAGGTTTTT 57.063 40.909 0.00 0.00 0.00 1.94
1359 1374 4.591072 GTCATAAGAAGATGAGGGCTAGGT 59.409 45.833 0.00 0.00 36.51 3.08
1360 1375 4.590647 TGTCATAAGAAGATGAGGGCTAGG 59.409 45.833 0.00 0.00 36.51 3.02
1443 1461 2.706190 AGCAGGTGAGGTGTAGTTCTTT 59.294 45.455 0.00 0.00 0.00 2.52
1544 1562 1.679680 CTTCCAGCCAATGCATTCGAT 59.320 47.619 9.53 0.00 41.13 3.59
1572 1590 7.715249 AGAACAGTCAGCAAGAGTAAATTAACA 59.285 33.333 0.00 0.00 0.00 2.41
1661 1679 2.232941 CCCGTAGCTAACCTTGACTTGA 59.767 50.000 0.00 0.00 0.00 3.02
1799 1817 5.208890 TGTAGGTATGCAGGAACAGTATCT 58.791 41.667 0.00 0.00 0.00 1.98
1836 1854 7.681939 AACTTGCCTCGTTCAAAATATTAGA 57.318 32.000 0.00 0.00 0.00 2.10
1887 1905 9.562408 TCACCAAAAATACTAGTGAATGTAACA 57.438 29.630 5.39 0.00 34.68 2.41
1891 1909 9.520515 AAGATCACCAAAAATACTAGTGAATGT 57.479 29.630 5.39 0.00 40.56 2.71
1919 1937 8.912988 ACTCTTCCTGAAATGACACAATAAAAA 58.087 29.630 0.00 0.00 0.00 1.94
1923 1941 8.352201 CAAAACTCTTCCTGAAATGACACAATA 58.648 33.333 0.00 0.00 0.00 1.90
1959 1977 2.157738 GCCTTTGTGATTGCTCTGTCT 58.842 47.619 0.00 0.00 0.00 3.41
1996 2014 4.100035 TGGAGTATGTGACAGAATAGCCTG 59.900 45.833 0.00 0.00 39.93 4.85
2172 2190 2.616842 ACCCTTATTTTCAATAGCGCCG 59.383 45.455 2.29 0.00 0.00 6.46
2175 2193 5.576447 AACCACCCTTATTTTCAATAGCG 57.424 39.130 0.00 0.00 0.00 4.26
2187 2205 6.931840 GCATATTTGAAACAAAACCACCCTTA 59.068 34.615 0.00 0.00 0.00 2.69
2242 2265 7.035004 GCAAGCCTGTAACAATGATTTCAATA 58.965 34.615 0.00 0.00 0.00 1.90
2268 2291 5.355071 TCAAATATCAGATGCACAACTGGAC 59.645 40.000 14.46 0.00 35.20 4.02
2295 2318 9.434275 TCCTGATATTCCAGAACAAGATTAGTA 57.566 33.333 0.00 0.00 36.29 1.82
2359 2382 9.997482 TTGACATCACTAAAAACTTTTCACTAC 57.003 29.630 0.00 0.00 0.00 2.73
2654 2691 1.120530 ACGGGGCTTAGTATCCACTG 58.879 55.000 0.00 0.00 36.14 3.66
2764 2809 8.925161 TCAAATTCAGTGAAAACCTTAAAGTG 57.075 30.769 10.14 0.00 0.00 3.16
2845 2890 9.525409 TTTTGAGTTGTAACACTAGTACTTCTC 57.475 33.333 0.00 4.16 0.00 2.87
2964 3010 8.903820 GTGAAAAATAATGCATAAGACTAGGGT 58.096 33.333 0.00 0.00 0.00 4.34
2993 3039 1.202879 CCTTGTGCCCTTGTGGAACTA 60.203 52.381 0.00 0.00 44.13 2.24
3127 3230 0.237235 GCGAACATTCTCACGGCAAA 59.763 50.000 0.00 0.00 0.00 3.68
3216 3319 1.779221 CATTTAATGCCTCCTGCCCA 58.221 50.000 0.00 0.00 40.16 5.36
3294 3397 9.962783 CAAAATTACCTACTAGCTACTAATCGT 57.037 33.333 0.00 0.00 0.00 3.73
3367 3493 2.162008 TCAATGTCCACATCACAATGCG 59.838 45.455 0.00 0.00 36.26 4.73
3531 3693 6.148976 GTCATGTTAAGGGTCTTAAGGTTGAC 59.851 42.308 1.85 14.41 0.00 3.18
3547 3709 5.010719 AGTCGGAAGTTCTGAGTCATGTTAA 59.989 40.000 14.86 0.00 29.74 2.01
3670 3834 5.298989 TGGTAGCTTTGTTCAGGACTAAA 57.701 39.130 0.00 0.00 0.00 1.85
3671 3835 4.967084 TGGTAGCTTTGTTCAGGACTAA 57.033 40.909 0.00 0.00 0.00 2.24
3692 3856 9.860898 GAGGAAGCAAATGAGTATATTTTTGTT 57.139 29.630 0.00 0.00 32.88 2.83
3707 3871 3.462021 GATAGAGCGTGAGGAAGCAAAT 58.538 45.455 0.00 0.00 35.48 2.32
3778 3942 7.278868 ACACATTTATGCTCTTCTTAGTAGTGC 59.721 37.037 6.07 6.07 33.84 4.40
3819 3983 2.159379 GCATCGTCACCTTTTCATTCCC 60.159 50.000 0.00 0.00 0.00 3.97
3894 4058 5.351189 CACACGATCATGTTCTACATTTCCA 59.649 40.000 0.00 0.00 36.53 3.53
3926 4090 2.376518 ACCGATGGCATTAAGATCCCAT 59.623 45.455 0.00 0.00 40.60 4.00
4480 4646 2.346803 CGACAGTTGATTTGGATCGGT 58.653 47.619 0.00 0.00 34.91 4.69
4531 4699 5.016173 CCCTCTGACCCAAATTAATTGTCA 58.984 41.667 15.27 15.27 37.32 3.58
4546 4714 2.419297 CCAATGTGCTACTCCCTCTGAC 60.419 54.545 0.00 0.00 0.00 3.51
4728 4896 6.815089 TGCAACAAATTTACATCTTGAACCT 58.185 32.000 0.00 0.00 0.00 3.50
4804 4972 1.340889 GTCAGGCAGGCAATGTTTTGA 59.659 47.619 0.00 0.00 34.60 2.69
4813 4981 0.543277 CTATCCTTGTCAGGCAGGCA 59.457 55.000 0.00 0.00 40.58 4.75
4878 5046 4.619760 TGAACTTACAATCGAGCTAACACG 59.380 41.667 0.00 0.00 0.00 4.49
4984 5153 6.376581 ACCCTGAGCTTTGAATATCTGAAAAG 59.623 38.462 0.00 0.00 33.67 2.27
5002 5171 1.669115 CACAACGGAGCACCCTGAG 60.669 63.158 4.25 0.00 0.00 3.35
5027 5196 2.065899 TGAAGACAACCCACCCAAAG 57.934 50.000 0.00 0.00 0.00 2.77
5234 5406 4.459330 AGCAGAGATGAATTTTAGGGAGC 58.541 43.478 0.00 0.00 0.00 4.70
5288 5460 6.855763 AGTTTTCTTGGAATGGCATATTGA 57.144 33.333 0.00 0.00 0.00 2.57
5421 5594 7.790027 TCAAGAATGAGAAATTTGGTGGAAAA 58.210 30.769 0.00 0.00 0.00 2.29
5454 5627 9.998106 GTTTATCATATTTGGCTTCTAGGTAGA 57.002 33.333 0.00 0.00 0.00 2.59
5461 5634 7.059156 AGAGCAGTTTATCATATTTGGCTTCT 58.941 34.615 0.00 0.00 0.00 2.85
5519 5692 7.361542 GCTCTATCAAAATCAGCTTCACTTTGA 60.362 37.037 10.70 10.70 39.56 2.69
5545 5732 0.606401 ACATGTTTGGGACTGCTCCG 60.606 55.000 0.00 0.00 37.46 4.63
5564 5751 9.967451 TTCAGGTCCACATTTTATCAAATAGTA 57.033 29.630 0.00 0.00 30.90 1.82
5607 5794 7.590689 GGTTTCTTCTAGCGTGTCTATGTATAC 59.409 40.741 0.00 0.00 0.00 1.47
5637 5824 4.649218 ACAAAGAGGGCATAAAACACTGTT 59.351 37.500 0.00 0.00 0.00 3.16
5641 5828 4.988540 GGAAACAAAGAGGGCATAAAACAC 59.011 41.667 0.00 0.00 0.00 3.32
5658 5845 5.277825 CGCAAATTTTCAGTGTAGGAAACA 58.722 37.500 0.00 0.00 34.23 2.83


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

AutoCloner maintained by Alex Coulton.