Multiple sequence alignment - TraesCS1D01G177200

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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 TraesCS1D01G177200 chr1D 100.000 2786 0 0 1 2786 252482223 252479438 0.000000e+00 5145
1 TraesCS1D01G177200 chr1A 91.250 2617 132 36 206 2786 323188276 323190831 0.000000e+00 3474
2 TraesCS1D01G177200 chr1A 85.590 229 6 6 15 220 323182065 323182289 6.040000e-52 215
3 TraesCS1D01G177200 chr1B 91.367 2583 121 35 224 2768 361011785 361014303 0.000000e+00 3441
4 TraesCS1D01G177200 chr1B 90.000 240 20 3 1 240 361009635 361009870 9.690000e-80 307


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 TraesCS1D01G177200 chr1D 252479438 252482223 2785 True 5145 5145 100.0000 1 2786 1 chr1D.!!$R1 2785
1 TraesCS1D01G177200 chr1A 323188276 323190831 2555 False 3474 3474 91.2500 206 2786 1 chr1A.!!$F2 2580
2 TraesCS1D01G177200 chr1B 361009635 361014303 4668 False 1874 3441 90.6835 1 2768 2 chr1B.!!$F1 2767

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
833 2783 0.034574 ACCAACTCACAAGTGGCACA 60.035 50.0 21.41 0.0 35.36 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 3756 0.179056 CTATACAGGGGGCAACACGG 60.179 60.0 0.0 0.0 46.14 4.94 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
27 28 5.704888 AGAGCGTATAGTTGTATGCTGATC 58.295 41.667 7.25 0.00 44.66 2.92
28 29 5.241728 AGAGCGTATAGTTGTATGCTGATCA 59.758 40.000 7.25 0.00 44.66 2.92
29 30 5.842907 AGCGTATAGTTGTATGCTGATCAA 58.157 37.500 0.00 0.00 43.41 2.57
30 31 6.459066 AGCGTATAGTTGTATGCTGATCAAT 58.541 36.000 0.00 0.00 43.41 2.57
31 32 6.587990 AGCGTATAGTTGTATGCTGATCAATC 59.412 38.462 0.00 0.00 43.41 2.67
32 33 6.366061 GCGTATAGTTGTATGCTGATCAATCA 59.634 38.462 0.00 0.00 34.51 2.57
33 34 7.063898 GCGTATAGTTGTATGCTGATCAATCAT 59.936 37.037 12.88 12.88 36.02 2.45
34 35 8.378421 CGTATAGTTGTATGCTGATCAATCATG 58.622 37.037 16.27 0.00 36.02 3.07
35 36 7.683437 ATAGTTGTATGCTGATCAATCATGG 57.317 36.000 16.27 0.00 36.02 3.66
44 45 4.458397 CTGATCAATCATGGGTAGCACTT 58.542 43.478 0.00 0.00 36.02 3.16
46 47 6.000246 TGATCAATCATGGGTAGCACTTAA 58.000 37.500 0.00 0.00 0.00 1.85
56 57 5.132502 TGGGTAGCACTTAATCAATCATGG 58.867 41.667 0.00 0.00 0.00 3.66
75 76 5.904984 ATGGGTACATGCACTATCCTAAA 57.095 39.130 0.00 0.00 35.57 1.85
104 105 1.379576 GGCTGGCATCTTGGAAGCT 60.380 57.895 0.00 0.00 34.29 3.74
110 111 0.449388 GCATCTTGGAAGCTGGTTCG 59.551 55.000 12.87 0.68 35.80 3.95
154 155 0.900182 TCATCCGGACAGAGTGTGCT 60.900 55.000 6.12 0.00 36.50 4.40
165 166 2.234661 CAGAGTGTGCTGGTTCCATCTA 59.765 50.000 0.00 0.00 32.26 1.98
191 192 2.230750 GCGTAGAGGGTGTAGACTTGTT 59.769 50.000 0.00 0.00 0.00 2.83
203 204 6.531948 GGTGTAGACTTGTTAGATTAGTGCTG 59.468 42.308 0.00 0.00 0.00 4.41
249 2181 2.922740 ACGGAGTCTTGCTTTTGGTA 57.077 45.000 0.00 0.00 29.74 3.25
257 2189 2.548057 TCTTGCTTTTGGTAGTTGAGCG 59.452 45.455 0.00 0.00 36.17 5.03
259 2191 3.114668 TGCTTTTGGTAGTTGAGCGTA 57.885 42.857 0.00 0.00 36.17 4.42
287 2219 3.469739 TGTTCCCAACCTAAACTCGTTC 58.530 45.455 0.00 0.00 0.00 3.95
293 2225 3.818773 CCAACCTAAACTCGTTCCACAAT 59.181 43.478 0.00 0.00 0.00 2.71
313 2245 1.175983 CCTGGTTTTGGCCGCACTTA 61.176 55.000 0.00 0.00 0.00 2.24
403 2336 1.140312 AGAGTTGAAGGCCCAGACAA 58.860 50.000 0.00 0.00 0.00 3.18
404 2337 1.072965 AGAGTTGAAGGCCCAGACAAG 59.927 52.381 0.00 0.00 0.00 3.16
406 2339 0.823356 GTTGAAGGCCCAGACAAGCA 60.823 55.000 0.00 0.00 0.00 3.91
408 2341 1.676967 GAAGGCCCAGACAAGCAGG 60.677 63.158 0.00 0.00 0.00 4.85
409 2342 2.129555 GAAGGCCCAGACAAGCAGGA 62.130 60.000 0.00 0.00 0.00 3.86
412 2345 0.255890 GGCCCAGACAAGCAGGATAA 59.744 55.000 0.00 0.00 0.00 1.75
416 2349 2.420687 CCCAGACAAGCAGGATAACCTC 60.421 54.545 0.00 0.00 45.94 3.85
417 2350 2.503356 CCAGACAAGCAGGATAACCTCT 59.497 50.000 0.00 0.00 45.94 3.69
418 2351 3.054802 CCAGACAAGCAGGATAACCTCTT 60.055 47.826 0.00 0.00 45.94 2.85
419 2352 4.566488 CCAGACAAGCAGGATAACCTCTTT 60.566 45.833 0.00 0.00 45.94 2.52
420 2353 4.394300 CAGACAAGCAGGATAACCTCTTTG 59.606 45.833 9.33 9.33 45.94 2.77
421 2354 4.042187 AGACAAGCAGGATAACCTCTTTGT 59.958 41.667 14.13 14.13 45.94 2.83
425 2371 5.957771 AGCAGGATAACCTCTTTGTATGA 57.042 39.130 0.00 0.00 45.94 2.15
448 2395 1.639108 GGGGAAGGGTGTTAATCCAGT 59.361 52.381 0.00 0.00 33.48 4.00
461 2408 2.945080 ATCCAGTGATTCGATGCCAT 57.055 45.000 0.00 0.00 0.00 4.40
557 2504 7.812690 ATAAATAGTTCCCAATAAACGGGTC 57.187 36.000 0.00 0.00 44.81 4.46
596 2543 9.764363 ATCATGTAATACATTCGTGTACTTCAT 57.236 29.630 2.67 0.00 36.53 2.57
597 2544 9.244799 TCATGTAATACATTCGTGTACTTCATC 57.755 33.333 2.67 0.00 36.53 2.92
598 2545 9.030301 CATGTAATACATTCGTGTACTTCATCA 57.970 33.333 2.67 0.00 36.53 3.07
599 2546 9.764363 ATGTAATACATTCGTGTACTTCATCAT 57.236 29.630 0.00 0.00 34.67 2.45
600 2547 9.244799 TGTAATACATTCGTGTACTTCATCATC 57.755 33.333 0.00 0.00 0.00 2.92
601 2548 9.244799 GTAATACATTCGTGTACTTCATCATCA 57.755 33.333 0.00 0.00 0.00 3.07
628 2575 3.133003 ACCAAGTAGCTTGCTCATCGTAT 59.867 43.478 0.00 0.00 39.85 3.06
660 2608 7.578169 GTTAGTTAACGAGTTGCTGATAAGT 57.422 36.000 0.00 0.00 0.00 2.24
661 2609 7.445836 GTTAGTTAACGAGTTGCTGATAAGTG 58.554 38.462 0.00 0.00 0.00 3.16
662 2610 5.539048 AGTTAACGAGTTGCTGATAAGTGT 58.461 37.500 0.00 0.00 0.00 3.55
663 2611 5.989777 AGTTAACGAGTTGCTGATAAGTGTT 59.010 36.000 0.00 0.00 0.00 3.32
664 2612 7.149973 AGTTAACGAGTTGCTGATAAGTGTTA 58.850 34.615 0.00 0.00 0.00 2.41
665 2613 7.654520 AGTTAACGAGTTGCTGATAAGTGTTAA 59.345 33.333 0.00 0.00 0.00 2.01
666 2614 6.854496 AACGAGTTGCTGATAAGTGTTAAA 57.146 33.333 0.00 0.00 0.00 1.52
668 2616 7.254227 ACGAGTTGCTGATAAGTGTTAAAAA 57.746 32.000 0.00 0.00 0.00 1.94
690 2638 5.358298 AAAACGAGTTGCTGATAAGAACC 57.642 39.130 0.00 0.00 0.00 3.62
691 2639 2.973945 ACGAGTTGCTGATAAGAACCC 58.026 47.619 0.00 0.00 0.00 4.11
692 2640 2.301870 ACGAGTTGCTGATAAGAACCCA 59.698 45.455 0.00 0.00 0.00 4.51
693 2641 3.055094 ACGAGTTGCTGATAAGAACCCAT 60.055 43.478 0.00 0.00 0.00 4.00
694 2642 4.161565 ACGAGTTGCTGATAAGAACCCATA 59.838 41.667 0.00 0.00 0.00 2.74
695 2643 5.116180 CGAGTTGCTGATAAGAACCCATAA 58.884 41.667 0.00 0.00 0.00 1.90
696 2644 5.760253 CGAGTTGCTGATAAGAACCCATAAT 59.240 40.000 0.00 0.00 0.00 1.28
720 2669 4.579454 TTATAAGCTCTAACGCACGGAT 57.421 40.909 0.00 0.00 0.00 4.18
734 2683 0.591170 ACGGATGCGAGTTGTTTTGG 59.409 50.000 15.49 0.00 0.00 3.28
833 2783 0.034574 ACCAACTCACAAGTGGCACA 60.035 50.000 21.41 0.00 35.36 4.57
1020 2978 3.003763 AGACCAGCGGGGAAGACC 61.004 66.667 8.08 0.00 41.15 3.85
1080 3038 2.750237 GAACACCCGCACCCCATC 60.750 66.667 0.00 0.00 0.00 3.51
1081 3039 3.561120 GAACACCCGCACCCCATCA 62.561 63.158 0.00 0.00 0.00 3.07
1082 3040 2.837031 GAACACCCGCACCCCATCAT 62.837 60.000 0.00 0.00 0.00 2.45
1083 3041 2.829914 CACCCGCACCCCATCATG 60.830 66.667 0.00 0.00 0.00 3.07
1108 3070 3.647649 CTGGACGACAGCATCCGCA 62.648 63.158 0.00 0.00 40.97 5.69
1158 3120 2.990479 GGTCAGTCCTCCGGCATT 59.010 61.111 0.00 0.00 0.00 3.56
1278 3240 2.275318 CTCGAAAGGATCCTTGTGCTC 58.725 52.381 27.71 19.03 36.26 4.26
1306 3268 0.806102 CTACGGCACATTCCTGTCGG 60.806 60.000 0.00 0.00 31.62 4.79
1389 3351 2.587194 ATGGTCGCTGCATCGCTC 60.587 61.111 4.79 0.92 0.00 5.03
1436 3398 4.760047 GTGCCGCCTCGTCACCAT 62.760 66.667 0.00 0.00 0.00 3.55
1543 3505 0.247460 CACTGTGGAAGCATCGGAGA 59.753 55.000 0.00 0.00 45.75 3.71
1791 3753 2.170817 CCTTACTCCCTTCTAACCCTGC 59.829 54.545 0.00 0.00 0.00 4.85
1792 3754 2.634639 TACTCCCTTCTAACCCTGCA 57.365 50.000 0.00 0.00 0.00 4.41
1793 3755 1.280457 ACTCCCTTCTAACCCTGCAG 58.720 55.000 6.78 6.78 0.00 4.41
1794 3756 0.107459 CTCCCTTCTAACCCTGCAGC 60.107 60.000 8.66 0.00 0.00 5.25
1795 3757 1.077429 CCCTTCTAACCCTGCAGCC 60.077 63.158 8.66 0.00 0.00 4.85
1796 3758 1.450312 CCTTCTAACCCTGCAGCCG 60.450 63.158 8.66 2.46 0.00 5.52
1797 3759 1.296715 CTTCTAACCCTGCAGCCGT 59.703 57.895 8.66 3.20 0.00 5.68
1798 3760 1.003839 TTCTAACCCTGCAGCCGTG 60.004 57.895 8.66 0.00 0.00 4.94
1799 3761 1.764571 TTCTAACCCTGCAGCCGTGT 61.765 55.000 8.66 0.00 0.00 4.49
1800 3762 1.302511 CTAACCCTGCAGCCGTGTT 60.303 57.895 8.66 10.80 0.00 3.32
1801 3763 1.577328 CTAACCCTGCAGCCGTGTTG 61.577 60.000 8.66 0.00 0.00 3.33
1845 3809 9.018582 CAAGATTTAGAAGAGGAAACAGGAAAT 57.981 33.333 0.00 0.00 0.00 2.17
1853 3817 9.268282 AGAAGAGGAAACAGGAAATATGTAGTA 57.732 33.333 0.00 0.00 0.00 1.82
1861 3825 7.366847 ACAGGAAATATGTAGTAGCAGTGAT 57.633 36.000 0.00 0.00 0.00 3.06
1879 3843 6.584954 CAGTGATGAAAGTAGAAGAAACGTG 58.415 40.000 0.00 0.00 0.00 4.49
1898 3862 4.166523 CGTGATATAGGATAACAGTGGCG 58.833 47.826 0.00 0.00 0.00 5.69
1920 3884 5.061808 GCGTACTGTATGTAGTTTCAGTTGG 59.938 44.000 8.69 0.00 40.77 3.77
1921 3885 6.384224 CGTACTGTATGTAGTTTCAGTTGGA 58.616 40.000 0.00 0.00 40.77 3.53
1932 3896 5.848406 AGTTTCAGTTGGACAGACTTCTAG 58.152 41.667 0.00 0.00 0.00 2.43
1952 3930 1.269517 GGTTTTTGCACAGAATCGCCA 60.270 47.619 0.00 0.00 0.00 5.69
1957 3935 2.109126 GCACAGAATCGCCACCCTC 61.109 63.158 0.00 0.00 0.00 4.30
1970 3948 2.689983 GCCACCCTCCATGTCAAATTAG 59.310 50.000 0.00 0.00 0.00 1.73
1981 3959 3.495331 TGTCAAATTAGCCTTGAGCCAA 58.505 40.909 0.00 0.00 45.47 4.52
1987 3965 4.525912 ATTAGCCTTGAGCCAACAAAAG 57.474 40.909 0.00 0.00 45.47 2.27
1988 3966 2.071778 AGCCTTGAGCCAACAAAAGA 57.928 45.000 0.00 0.00 45.47 2.52
2059 4038 5.933617 TCCTGTCAGCTTAAATGCAGATAT 58.066 37.500 0.00 0.00 31.49 1.63
2060 4039 6.359804 TCCTGTCAGCTTAAATGCAGATATT 58.640 36.000 0.00 0.00 31.49 1.28
2119 4098 0.471617 AGCAGTAATAGCCTGGCCAG 59.528 55.000 26.87 26.87 0.00 4.85
2121 4100 1.542108 GCAGTAATAGCCTGGCCAGAG 60.542 57.143 34.91 23.71 0.00 3.35
2126 4105 0.621571 ATAGCCTGGCCAGAGTCCAA 60.622 55.000 34.91 12.98 32.41 3.53
2452 4435 5.010112 GGCCCTTCATATCTAAAGCTTTTCC 59.990 44.000 18.47 0.00 0.00 3.13
2559 4542 6.734502 AGCTAGAAGGATAAGGGAAAGTAC 57.265 41.667 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.430000 TGATCAGCATACAACTATACGCTCTA 59.570 38.462 0.00 0.00 0.00 2.43
9 10 8.663025 CCATGATTGATCAGCATACAACTATAC 58.337 37.037 11.41 0.00 40.64 1.47
17 18 4.394300 GCTACCCATGATTGATCAGCATAC 59.606 45.833 11.41 0.00 40.64 2.39
24 25 6.712095 TGATTAAGTGCTACCCATGATTGATC 59.288 38.462 0.00 0.00 0.00 2.92
27 28 6.698008 TTGATTAAGTGCTACCCATGATTG 57.302 37.500 0.00 0.00 0.00 2.67
28 29 7.062322 TGATTGATTAAGTGCTACCCATGATT 58.938 34.615 0.00 0.00 0.00 2.57
29 30 6.604171 TGATTGATTAAGTGCTACCCATGAT 58.396 36.000 0.00 0.00 0.00 2.45
30 31 6.000246 TGATTGATTAAGTGCTACCCATGA 58.000 37.500 0.00 0.00 0.00 3.07
31 32 6.294342 CCATGATTGATTAAGTGCTACCCATG 60.294 42.308 0.00 0.00 0.00 3.66
32 33 5.771666 CCATGATTGATTAAGTGCTACCCAT 59.228 40.000 0.00 0.00 0.00 4.00
33 34 5.132502 CCATGATTGATTAAGTGCTACCCA 58.867 41.667 0.00 0.00 0.00 4.51
34 35 4.520492 CCCATGATTGATTAAGTGCTACCC 59.480 45.833 0.00 0.00 0.00 3.69
35 36 5.133221 ACCCATGATTGATTAAGTGCTACC 58.867 41.667 0.00 0.00 0.00 3.18
56 57 5.530915 TGCATTTTAGGATAGTGCATGTACC 59.469 40.000 10.59 0.00 40.51 3.34
75 76 1.324740 ATGCCAGCCGTTGATGCATT 61.325 50.000 0.00 0.00 0.00 3.56
84 85 1.377725 CTTCCAAGATGCCAGCCGT 60.378 57.895 0.00 0.00 0.00 5.68
110 111 2.828128 GCTTGATACAGCGGCAGCC 61.828 63.158 4.82 0.00 46.67 4.85
165 166 3.155501 GTCTACACCCTCTACGCCATAT 58.844 50.000 0.00 0.00 0.00 1.78
174 175 7.122948 CACTAATCTAACAAGTCTACACCCTCT 59.877 40.741 0.00 0.00 0.00 3.69
175 176 7.259161 CACTAATCTAACAAGTCTACACCCTC 58.741 42.308 0.00 0.00 0.00 4.30
191 192 4.929819 TGCGTAATCCAGCACTAATCTA 57.070 40.909 0.00 0.00 38.59 1.98
203 204 0.096454 GCGAACCACTTGCGTAATCC 59.904 55.000 0.00 0.00 0.00 3.01
249 2181 4.634443 GGGAACAATACAATACGCTCAACT 59.366 41.667 0.00 0.00 0.00 3.16
287 2219 0.321346 GGCCAAAACCAGGATTGTGG 59.679 55.000 0.00 0.00 44.01 4.17
293 2225 2.909965 GTGCGGCCAAAACCAGGA 60.910 61.111 2.24 0.00 0.00 3.86
313 2245 0.322546 GGGGCCTCTGTTTTCACGAT 60.323 55.000 0.84 0.00 0.00 3.73
403 2336 5.957771 TCATACAAAGAGGTTATCCTGCT 57.042 39.130 0.00 0.00 45.24 4.24
404 2337 5.406780 CGATCATACAAAGAGGTTATCCTGC 59.593 44.000 0.00 0.00 45.24 4.85
408 2341 5.011738 TCCCCGATCATACAAAGAGGTTATC 59.988 44.000 0.00 0.00 0.00 1.75
409 2342 4.905456 TCCCCGATCATACAAAGAGGTTAT 59.095 41.667 0.00 0.00 0.00 1.89
412 2345 2.759355 TCCCCGATCATACAAAGAGGT 58.241 47.619 0.00 0.00 0.00 3.85
415 2348 2.438021 CCCTTCCCCGATCATACAAAGA 59.562 50.000 0.00 0.00 0.00 2.52
416 2349 2.172717 ACCCTTCCCCGATCATACAAAG 59.827 50.000 0.00 0.00 0.00 2.77
417 2350 2.092646 CACCCTTCCCCGATCATACAAA 60.093 50.000 0.00 0.00 0.00 2.83
418 2351 1.488812 CACCCTTCCCCGATCATACAA 59.511 52.381 0.00 0.00 0.00 2.41
419 2352 1.128200 CACCCTTCCCCGATCATACA 58.872 55.000 0.00 0.00 0.00 2.29
420 2353 1.129058 ACACCCTTCCCCGATCATAC 58.871 55.000 0.00 0.00 0.00 2.39
421 2354 1.887797 AACACCCTTCCCCGATCATA 58.112 50.000 0.00 0.00 0.00 2.15
425 2371 1.493446 GGATTAACACCCTTCCCCGAT 59.507 52.381 0.00 0.00 0.00 4.18
448 2395 3.740832 GTCAATCGTATGGCATCGAATCA 59.259 43.478 20.17 2.53 39.45 2.57
461 2408 0.880441 TTCGTGTCCCGTCAATCGTA 59.120 50.000 0.00 0.00 37.94 3.43
576 2523 9.981114 ATGATGATGAAGTACACGAATGTATTA 57.019 29.630 0.00 0.00 43.21 0.98
577 2524 8.768019 CATGATGATGAAGTACACGAATGTATT 58.232 33.333 0.00 0.00 43.21 1.89
578 2525 7.386025 CCATGATGATGAAGTACACGAATGTAT 59.614 37.037 0.00 0.00 43.21 2.29
596 2543 4.769688 CAAGCTACTTGGTACCATGATGA 58.230 43.478 29.21 15.14 37.77 2.92
597 2544 3.313526 GCAAGCTACTTGGTACCATGATG 59.686 47.826 29.21 21.23 41.31 3.07
598 2545 3.545703 GCAAGCTACTTGGTACCATGAT 58.454 45.455 29.21 17.47 41.31 2.45
599 2546 2.985896 GCAAGCTACTTGGTACCATGA 58.014 47.619 29.21 10.26 41.31 3.07
668 2616 4.215613 GGGTTCTTATCAGCAACTCGTTTT 59.784 41.667 0.00 0.00 0.00 2.43
670 2618 3.244422 TGGGTTCTTATCAGCAACTCGTT 60.244 43.478 0.00 0.00 0.00 3.85
671 2619 2.301870 TGGGTTCTTATCAGCAACTCGT 59.698 45.455 0.00 0.00 0.00 4.18
672 2620 2.972625 TGGGTTCTTATCAGCAACTCG 58.027 47.619 0.00 0.00 0.00 4.18
673 2621 7.573968 AATTATGGGTTCTTATCAGCAACTC 57.426 36.000 0.00 0.00 0.00 3.01
674 2622 7.961326 AAATTATGGGTTCTTATCAGCAACT 57.039 32.000 0.00 0.00 0.00 3.16
688 2636 8.565416 GCGTTAGAGCTTATAAAAATTATGGGT 58.435 33.333 0.00 0.00 0.00 4.51
689 2637 8.564574 TGCGTTAGAGCTTATAAAAATTATGGG 58.435 33.333 0.00 0.00 38.13 4.00
690 2638 9.382244 GTGCGTTAGAGCTTATAAAAATTATGG 57.618 33.333 0.00 0.00 38.13 2.74
691 2639 9.092322 CGTGCGTTAGAGCTTATAAAAATTATG 57.908 33.333 0.00 0.00 38.13 1.90
692 2640 8.280497 CCGTGCGTTAGAGCTTATAAAAATTAT 58.720 33.333 0.00 0.00 38.13 1.28
693 2641 7.492020 TCCGTGCGTTAGAGCTTATAAAAATTA 59.508 33.333 0.00 0.00 38.13 1.40
694 2642 6.314400 TCCGTGCGTTAGAGCTTATAAAAATT 59.686 34.615 0.00 0.00 38.13 1.82
695 2643 5.813672 TCCGTGCGTTAGAGCTTATAAAAAT 59.186 36.000 0.00 0.00 38.13 1.82
696 2644 5.170021 TCCGTGCGTTAGAGCTTATAAAAA 58.830 37.500 0.00 0.00 38.13 1.94
720 2669 3.701241 GTTGAATCCAAAACAACTCGCA 58.299 40.909 0.00 0.00 40.13 5.10
734 2683 5.873179 TGGACTTTTGGATACGTTGAATC 57.127 39.130 0.00 0.00 42.51 2.52
782 2732 1.396301 CGAGCTGCTGTTTTCTGGATC 59.604 52.381 7.01 0.00 0.00 3.36
833 2783 7.457060 GCTCGAAGAAAATACGAAAGAAATCT 58.543 34.615 0.00 0.00 34.09 2.40
1078 3036 2.124570 GTCCAGGTGCGCCATGAT 60.125 61.111 20.59 0.00 37.19 2.45
1080 3038 4.758251 TCGTCCAGGTGCGCCATG 62.758 66.667 20.59 13.39 37.19 3.66
1081 3039 4.760047 GTCGTCCAGGTGCGCCAT 62.760 66.667 20.59 0.08 37.19 4.40
1108 3070 2.573869 CGACCATGACCTGAGCGT 59.426 61.111 0.00 0.00 0.00 5.07
1267 3229 1.446792 CGTCAGCGAGCACAAGGAT 60.447 57.895 0.00 0.00 41.33 3.24
1389 3351 2.431942 GTCCGCCTGTGTACACGG 60.432 66.667 25.27 25.27 46.97 4.94
1394 3356 0.888619 CTTCTCTGTCCGCCTGTGTA 59.111 55.000 0.00 0.00 0.00 2.90
1518 3480 3.357079 GCTTCCACAGTGGCCACG 61.357 66.667 29.68 24.87 37.47 4.94
1520 3482 1.303561 GATGCTTCCACAGTGGCCA 60.304 57.895 15.64 0.00 37.47 5.36
1793 3755 2.260088 TATACAGGGGGCAACACGGC 62.260 60.000 0.00 0.00 46.14 5.68
1794 3756 0.179056 CTATACAGGGGGCAACACGG 60.179 60.000 0.00 0.00 46.14 4.94
1795 3757 0.828022 TCTATACAGGGGGCAACACG 59.172 55.000 0.00 0.00 46.14 4.49
1796 3758 1.557832 TGTCTATACAGGGGGCAACAC 59.442 52.381 0.00 0.00 42.03 3.32
1797 3759 1.959710 TGTCTATACAGGGGGCAACA 58.040 50.000 0.00 0.00 39.74 3.33
1808 3770 9.959749 CCTCTTCTAAATCTTGACTGTCTATAC 57.040 37.037 9.51 0.00 0.00 1.47
1845 3809 8.747538 TCTACTTTCATCACTGCTACTACATA 57.252 34.615 0.00 0.00 0.00 2.29
1853 3817 5.406780 CGTTTCTTCTACTTTCATCACTGCT 59.593 40.000 0.00 0.00 0.00 4.24
1861 3825 8.963725 TCCTATATCACGTTTCTTCTACTTTCA 58.036 33.333 0.00 0.00 0.00 2.69
1879 3843 6.512342 AGTACGCCACTGTTATCCTATATC 57.488 41.667 0.00 0.00 35.62 1.63
1898 3862 7.149973 TGTCCAACTGAAACTACATACAGTAC 58.850 38.462 0.00 0.00 41.73 2.73
1920 3884 4.574828 TGTGCAAAAACCTAGAAGTCTGTC 59.425 41.667 0.00 0.00 0.00 3.51
1921 3885 4.523083 TGTGCAAAAACCTAGAAGTCTGT 58.477 39.130 0.00 0.00 0.00 3.41
1932 3896 1.269517 TGGCGATTCTGTGCAAAAACC 60.270 47.619 0.00 0.00 0.00 3.27
1952 3930 2.582636 AGGCTAATTTGACATGGAGGGT 59.417 45.455 0.00 0.00 0.00 4.34
1957 3935 3.181483 GGCTCAAGGCTAATTTGACATGG 60.181 47.826 0.00 0.00 41.46 3.66
1970 3948 4.082026 ACATATCTTTTGTTGGCTCAAGGC 60.082 41.667 0.00 0.00 41.50 4.35
2005 3984 4.353777 ACCAGCCTCTAACACTATTCTCA 58.646 43.478 0.00 0.00 0.00 3.27
2013 3992 4.327680 AGAATTCAACCAGCCTCTAACAC 58.672 43.478 8.44 0.00 0.00 3.32
2073 4052 1.275666 AATGTCGGGGTGTGAGATCA 58.724 50.000 0.00 0.00 0.00 2.92
2076 4055 2.614481 GCTTTAATGTCGGGGTGTGAGA 60.614 50.000 0.00 0.00 0.00 3.27
2077 4056 1.737793 GCTTTAATGTCGGGGTGTGAG 59.262 52.381 0.00 0.00 0.00 3.51
2452 4435 3.865745 CAGGTTTATGCTGTAACTCCGAG 59.134 47.826 0.00 0.00 0.00 4.63
2559 4542 3.354089 ACACGAAAAAGTCCTTGCATG 57.646 42.857 0.00 0.00 0.00 4.06


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

AutoCloner maintained by Alex Coulton.