Multiple sequence alignment - TraesCS6B01G088700

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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 TraesCS6B01G088700 chr6B 100.000 3317 0 0 1 3317 64323121 64326437 0.000000e+00 6126.0
1 TraesCS6B01G088700 chr6B 77.356 658 102 25 1686 2330 46756691 46756068 2.450000e-91 346.0
2 TraesCS6B01G088700 chr6B 83.004 253 37 4 2980 3231 212415498 212415745 1.200000e-54 224.0
3 TraesCS6B01G088700 chr6B 77.723 202 33 5 365 559 720920795 720920599 2.700000e-21 113.0
4 TraesCS6B01G088700 chr6B 85.047 107 11 2 2438 2540 46755970 46755865 1.630000e-18 104.0
5 TraesCS6B01G088700 chr6B 91.071 56 4 1 2384 2438 46756044 46755989 1.280000e-09 75.0
6 TraesCS6B01G088700 chr6B 78.070 114 17 7 2543 2651 46755275 46755165 7.680000e-07 65.8
7 TraesCS6B01G088700 chr6A 87.590 2224 168 51 794 2947 35179485 35181670 0.000000e+00 2479.0
8 TraesCS6B01G088700 chr6A 85.435 1895 185 40 1 1821 35142701 35144578 0.000000e+00 1886.0
9 TraesCS6B01G088700 chr6A 78.076 1414 236 51 955 2330 26935986 26934609 0.000000e+00 826.0
10 TraesCS6B01G088700 chr6A 80.836 1101 125 43 1902 2947 35144578 35145647 0.000000e+00 785.0
11 TraesCS6B01G088700 chr6A 95.455 352 14 1 2965 3314 35181785 35182136 8.040000e-156 560.0
12 TraesCS6B01G088700 chr6A 87.240 337 37 5 2968 3301 35145754 35146087 2.420000e-101 379.0
13 TraesCS6B01G088700 chr6A 84.190 253 34 4 2980 3231 158945528 158945281 1.190000e-59 241.0
14 TraesCS6B01G088700 chr6A 82.400 125 14 6 2425 2544 26934524 26934403 5.850000e-18 102.0
15 TraesCS6B01G088700 chrUn 85.514 2216 171 61 794 2927 103111303 103113450 0.000000e+00 2176.0
16 TraesCS6B01G088700 chrUn 90.805 1044 70 9 794 1821 103127752 103128785 0.000000e+00 1373.0
17 TraesCS6B01G088700 chrUn 90.885 768 51 9 1902 2650 103128785 103129552 0.000000e+00 1013.0
18 TraesCS6B01G088700 chrUn 89.869 612 52 6 1 605 103109552 103110160 0.000000e+00 778.0
19 TraesCS6B01G088700 chrUn 96.875 192 6 0 3123 3314 103130205 103130396 4.130000e-84 322.0
20 TraesCS6B01G088700 chrUn 77.778 567 92 22 1711 2261 95602433 95601885 5.340000e-83 318.0
21 TraesCS6B01G088700 chrUn 86.713 286 35 3 2997 3281 103113590 103113873 6.910000e-82 315.0
22 TraesCS6B01G088700 chrUn 86.574 216 19 3 2732 2947 103129615 103129820 2.570000e-56 230.0
23 TraesCS6B01G088700 chrUn 92.025 163 13 0 2965 3127 103129934 103130096 2.570000e-56 230.0
24 TraesCS6B01G088700 chrUn 82.123 179 25 4 2669 2847 103120048 103120219 2.670000e-31 147.0
25 TraesCS6B01G088700 chrUn 82.727 110 14 3 2438 2544 95599844 95599737 3.520000e-15 93.5
26 TraesCS6B01G088700 chrUn 85.870 92 7 3 1749 1834 103112409 103112500 3.520000e-15 93.5
27 TraesCS6B01G088700 chr6D 83.004 253 37 4 2980 3231 120672737 120672490 1.200000e-54 224.0
28 TraesCS6B01G088700 chr3B 76.963 191 35 9 48 233 657032845 657033031 2.110000e-17 100.0


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 TraesCS6B01G088700 chr6B 64323121 64326437 3316 False 6126.000000 6126 100.000000 1 3317 1 chr6B.!!$F1 3316
1 TraesCS6B01G088700 chr6A 35179485 35182136 2651 False 1519.500000 2479 91.522500 794 3314 2 chr6A.!!$F2 2520
2 TraesCS6B01G088700 chr6A 35142701 35146087 3386 False 1016.666667 1886 84.503667 1 3301 3 chr6A.!!$F1 3300
3 TraesCS6B01G088700 chr6A 26934403 26935986 1583 True 464.000000 826 80.238000 955 2544 2 chr6A.!!$R2 1589
4 TraesCS6B01G088700 chrUn 103109552 103113873 4321 False 840.625000 2176 86.991500 1 3281 4 chrUn.!!$F2 3280
5 TraesCS6B01G088700 chrUn 103127752 103130396 2644 False 633.600000 1373 91.432800 794 3314 5 chrUn.!!$F3 2520
6 TraesCS6B01G088700 chrUn 95599737 95602433 2696 True 205.750000 318 80.252500 1711 2544 2 chrUn.!!$R1 833

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
817 1788 0.040204 ATCCCAACTCCAAGCCCAAG 59.96 55.0 0.00 0.0 0.00 3.61 F
1587 2595 0.620121 AGAGGAAGAGGAAGGCCAGG 60.62 60.0 5.01 0.0 36.29 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1836 2856 0.243907 TGTCACAGTAGCTTCTCGCC 59.756 55.0 0.00 0.00 40.39 5.54 R
2615 5609 2.159421 GCATGAGTCAGCTGTTGGATTG 60.159 50.0 14.67 7.21 0.00 2.67 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
31 32 6.036300 TGCAAAACTTCTTGATTTTCTTGCTG 59.964 34.615 0.00 0.00 0.00 4.41
53 54 8.774586 TGCTGTTCTCTTAGAAAAAGTTCATAC 58.225 33.333 0.00 0.00 35.75 2.39
94 95 2.126307 CGGTCTGCGACTGGTCAG 60.126 66.667 8.96 0.00 35.49 3.51
108 109 1.592400 GGTCAGACACGATCCGACCA 61.592 60.000 16.88 0.00 44.55 4.02
134 135 1.927895 AAGAATGTGATCGAGCGACC 58.072 50.000 0.00 0.00 0.00 4.79
137 138 0.532573 AATGTGATCGAGCGACCAGT 59.467 50.000 0.00 0.00 0.00 4.00
161 162 1.357079 AGATTGCCTTCTTCTTGGGCT 59.643 47.619 0.00 0.00 45.45 5.19
162 163 2.578021 AGATTGCCTTCTTCTTGGGCTA 59.422 45.455 0.00 0.00 45.45 3.93
207 208 1.024579 CAGCAAACCTATTCGGGCGT 61.025 55.000 0.00 0.00 36.97 5.68
233 234 1.219124 GCTGAACGAGATGCTCCCA 59.781 57.895 0.00 0.00 0.00 4.37
251 252 2.557056 CCCATCATCATCATCCTTGCAC 59.443 50.000 0.00 0.00 0.00 4.57
278 290 2.205022 TGTAATGCTTGGCTTCAGCT 57.795 45.000 0.00 0.00 41.70 4.24
280 292 2.086869 GTAATGCTTGGCTTCAGCTGA 58.913 47.619 13.74 13.74 41.70 4.26
286 298 1.948145 CTTGGCTTCAGCTGATGGATC 59.052 52.381 25.89 12.70 41.70 3.36
287 299 0.913924 TGGCTTCAGCTGATGGATCA 59.086 50.000 25.89 16.15 41.70 2.92
316 328 2.858745 CATCCATCTGTCATCCATGCA 58.141 47.619 0.00 0.00 0.00 3.96
450 463 4.450082 AGAAAGTTGCAACGAAACCTTT 57.550 36.364 23.21 16.46 0.00 3.11
559 572 7.791949 TGTAACAAGACTTTTGTTGCAAAAAG 58.208 30.769 17.98 17.98 46.52 2.27
605 619 4.708726 ATTTTCTGCAGCATAACCTGTC 57.291 40.909 9.47 0.00 35.28 3.51
607 621 2.391616 TCTGCAGCATAACCTGTCTG 57.608 50.000 9.47 0.00 35.28 3.51
608 622 0.731417 CTGCAGCATAACCTGTCTGC 59.269 55.000 0.00 6.16 46.37 4.26
609 623 2.858622 GCAGCATAACCTGTCTGCA 58.141 52.632 8.04 0.00 45.91 4.41
614 671 1.135972 GCATAACCTGTCTGCAACACG 60.136 52.381 0.00 0.00 35.96 4.49
615 672 1.464608 CATAACCTGTCTGCAACACGG 59.535 52.381 0.00 2.58 33.24 4.94
642 699 6.979465 TGTGTTGCAATGATAAAAGATGACA 58.021 32.000 0.59 0.00 0.00 3.58
658 715 0.247736 GACACTCGGCCACTCAATCT 59.752 55.000 2.24 0.00 0.00 2.40
660 717 1.078848 ACTCGGCCACTCAATCTGC 60.079 57.895 2.24 0.00 0.00 4.26
693 764 2.411547 GCTCGCGATTAAAATGATCCGG 60.412 50.000 10.36 0.00 0.00 5.14
756 860 3.953612 TCCTTGCAAATCTTCAGTGTGTT 59.046 39.130 0.00 0.00 0.00 3.32
759 863 4.031418 TGCAAATCTTCAGTGTGTTGTG 57.969 40.909 0.00 0.00 0.00 3.33
767 871 3.645975 GTGTGTTGTGCGGACCGG 61.646 66.667 17.22 0.00 0.00 5.28
782 886 1.296056 ACCGGCGAAAGGAAATCACG 61.296 55.000 9.30 0.00 0.00 4.35
785 889 0.446616 GGCGAAAGGAAATCACGGAC 59.553 55.000 0.00 0.00 0.00 4.79
786 890 0.094730 GCGAAAGGAAATCACGGACG 59.905 55.000 0.00 0.00 0.00 4.79
787 891 0.094730 CGAAAGGAAATCACGGACGC 59.905 55.000 0.00 0.00 0.00 5.19
788 892 0.094730 GAAAGGAAATCACGGACGCG 59.905 55.000 3.53 3.53 0.00 6.01
789 893 0.601841 AAAGGAAATCACGGACGCGT 60.602 50.000 13.85 13.85 0.00 6.01
791 895 1.012486 AGGAAATCACGGACGCGTTC 61.012 55.000 15.53 11.52 0.00 3.95
817 1788 0.040204 ATCCCAACTCCAAGCCCAAG 59.960 55.000 0.00 0.00 0.00 3.61
841 1812 1.186267 AACCCGCGTTCTCTTCTCCT 61.186 55.000 4.92 0.00 0.00 3.69
842 1813 1.139947 CCCGCGTTCTCTTCTCCTC 59.860 63.158 4.92 0.00 0.00 3.71
843 1814 1.139947 CCGCGTTCTCTTCTCCTCC 59.860 63.158 4.92 0.00 0.00 4.30
877 1855 7.416438 CCATCCCTCAAAGATTCAAGATTTCAG 60.416 40.741 0.00 0.00 0.00 3.02
898 1876 1.234821 CACTACAAAAGGCGGCAGAA 58.765 50.000 13.08 0.00 0.00 3.02
971 1965 3.399181 CCCGAACCCTAGCCAGCA 61.399 66.667 0.00 0.00 0.00 4.41
1009 2005 2.745308 CGATGACCCATGGCCTCCA 61.745 63.158 6.09 0.96 38.19 3.86
1170 2166 1.231641 CCCATCCTCCCTCGTCTCT 59.768 63.158 0.00 0.00 0.00 3.10
1328 2324 3.642741 ATGCCGAGAAGGGGAGGGT 62.643 63.158 0.00 0.00 41.48 4.34
1397 2402 4.446371 CAGAGTTTCAGGTATAAGCCCAG 58.554 47.826 0.00 0.00 0.00 4.45
1399 2404 1.940613 GTTTCAGGTATAAGCCCAGCG 59.059 52.381 0.00 0.00 0.00 5.18
1470 2478 3.181457 TGGCTCATGATCAAGGAGATGAC 60.181 47.826 24.25 14.17 37.00 3.06
1539 2547 4.514577 AAGCCCCGATCTGCGTCG 62.515 66.667 0.00 0.00 41.13 5.12
1587 2595 0.620121 AGAGGAAGAGGAAGGCCAGG 60.620 60.000 5.01 0.00 36.29 4.45
1657 2668 2.629656 GCTGCACCAATTCTGCCGT 61.630 57.895 0.00 0.00 33.36 5.68
1681 2695 3.695606 TCGAGCCACAGCCAGACC 61.696 66.667 0.00 0.00 41.25 3.85
1739 2759 4.691175 CTTCTTGATGATCTCATGTCCGT 58.309 43.478 0.00 0.00 36.57 4.69
1794 2814 0.907486 TGCCTGTCCCTGAATCAGAG 59.093 55.000 12.53 0.00 32.44 3.35
1817 2837 1.136305 CAATTGCAGCTTCTCCATGGG 59.864 52.381 13.02 2.57 0.00 4.00
1856 2879 2.285827 GCGAGAAGCTACTGTGACAT 57.714 50.000 0.00 0.00 44.04 3.06
1860 2883 3.128764 CGAGAAGCTACTGTGACATGGTA 59.871 47.826 0.00 0.00 0.00 3.25
1874 2897 2.273908 TGGTACTCCAGGACGAAGC 58.726 57.895 0.00 0.00 39.03 3.86
1880 2903 2.743928 CCAGGACGAAGCTGGTGC 60.744 66.667 0.00 1.98 33.87 5.01
1951 2974 1.070758 ACTTGTTGATGCCTGTCGTCT 59.929 47.619 0.00 0.00 0.00 4.18
1980 3004 3.718723 AGAGGTCAATTACAGCTCCTCT 58.281 45.455 9.88 9.88 44.40 3.69
1993 3017 1.689273 GCTCCTCTATGTCCGACCATT 59.311 52.381 0.00 0.00 0.00 3.16
2010 3034 2.025981 CCATTCTGGTTCCATGGTGAGA 60.026 50.000 12.58 6.18 33.90 3.27
2019 3058 3.868757 TCCATGGTGAGAAACTACGAG 57.131 47.619 12.58 0.00 0.00 4.18
2138 3183 2.040278 AGACCCAGACAGCAATGCTAAA 59.960 45.455 7.70 0.00 36.40 1.85
2139 3184 3.019564 GACCCAGACAGCAATGCTAAAT 58.980 45.455 7.70 0.00 36.40 1.40
2140 3185 3.434309 ACCCAGACAGCAATGCTAAATT 58.566 40.909 7.70 0.00 36.40 1.82
2268 5190 0.962356 CAAGCTCACCGGCAATTCCT 60.962 55.000 0.00 0.00 34.17 3.36
2271 5193 0.107654 GCTCACCGGCAATTCCTACT 60.108 55.000 0.00 0.00 0.00 2.57
2346 5274 4.275689 CCAGCTTCATGTTCTGTGTGTTTA 59.724 41.667 0.00 0.00 0.00 2.01
2354 5285 6.593770 TCATGTTCTGTGTGTTTATTCGCTAT 59.406 34.615 0.00 0.00 0.00 2.97
2391 5330 1.487558 GCCGTTTACCCCAAGGATAGA 59.512 52.381 0.00 0.00 36.73 1.98
2397 5336 5.756833 CGTTTACCCCAAGGATAGAATACAC 59.243 44.000 0.00 0.00 36.73 2.90
2479 5444 8.367911 TCTGGTTATGTATGTCAGGATACATTC 58.632 37.037 10.56 6.01 43.89 2.67
2493 5461 7.933577 TCAGGATACATTCTTAAGTATTGGCTG 59.066 37.037 1.63 0.00 41.41 4.85
2503 5471 7.175104 TCTTAAGTATTGGCTGAAAGATTGGT 58.825 34.615 1.63 0.00 34.07 3.67
2567 5560 2.513159 GCATGTGCTTGCTTGTGTG 58.487 52.632 0.00 0.00 39.57 3.82
2611 5605 5.458126 GCAATTAATCTCTTTTAGCTGCTGC 59.542 40.000 13.43 7.62 40.05 5.25
2615 5609 2.704572 TCTCTTTTAGCTGCTGCCTTC 58.295 47.619 13.43 0.00 40.80 3.46
2651 5645 2.686915 CTCATGCACTTGGGATCCTTTC 59.313 50.000 12.58 0.00 0.00 2.62
2667 5683 3.526019 TCCTTTCCTGTATAGGGTTTGGG 59.474 47.826 5.59 2.35 44.70 4.12
2681 5697 6.464530 AGGGTTTGGGTCTTAATTAGAGTT 57.535 37.500 0.00 0.00 32.23 3.01
2700 5716 4.787598 AGTTCAATGCTTTTCTAACAGCG 58.212 39.130 0.00 0.00 39.04 5.18
2702 5718 3.407698 TCAATGCTTTTCTAACAGCGGA 58.592 40.909 0.00 0.00 39.04 5.54
2782 5799 9.131791 AGTCCTATTTACAGTTTCACATTGTTT 57.868 29.630 0.00 0.00 0.00 2.83
2855 5872 6.464222 TCCATAATTCTCGAACCATATGACC 58.536 40.000 3.65 0.00 0.00 4.02
2921 5938 9.667989 GTCTTAGAAATAGTTTCTCTCCGTATC 57.332 37.037 8.11 0.00 46.62 2.24
2929 5948 4.707448 AGTTTCTCTCCGTATCACTCATGT 59.293 41.667 0.00 0.00 0.00 3.21
2959 5983 6.914654 TCCATCTCATTGGAATTTTGTGAA 57.085 33.333 0.00 0.00 42.82 3.18
2961 5985 7.153985 TCCATCTCATTGGAATTTTGTGAAAC 58.846 34.615 0.00 0.00 42.82 2.78
2962 5986 7.015487 TCCATCTCATTGGAATTTTGTGAAACT 59.985 33.333 0.00 0.00 42.82 2.66
2963 5987 7.117236 CCATCTCATTGGAATTTTGTGAAACTG 59.883 37.037 0.00 0.00 39.25 3.16
2964 5988 7.111247 TCTCATTGGAATTTTGTGAAACTGT 57.889 32.000 0.00 0.00 38.04 3.55
2965 5989 8.231692 TCTCATTGGAATTTTGTGAAACTGTA 57.768 30.769 0.00 0.00 38.04 2.74
2966 5990 8.352201 TCTCATTGGAATTTTGTGAAACTGTAG 58.648 33.333 0.00 0.00 38.04 2.74
3072 6203 3.172229 GTCTGACAGACAAGATAGCCC 57.828 52.381 27.15 0.00 44.45 5.19
3078 6211 3.942115 GACAGACAAGATAGCCCTTTTCC 59.058 47.826 0.00 0.00 0.00 3.13
3141 6387 3.193267 GTGTGCCTGCCATGAAAATCTTA 59.807 43.478 0.00 0.00 0.00 2.10
3148 6394 5.359009 CCTGCCATGAAAATCTTACAGTGAT 59.641 40.000 0.00 0.00 0.00 3.06
3160 6406 8.954950 AATCTTACAGTGATCATAGAACCAAG 57.045 34.615 0.00 0.00 0.00 3.61
3314 6562 8.165267 TCCCCTGATTAACAAGGAAAAGTATA 57.835 34.615 6.81 0.00 32.12 1.47
3315 6563 8.050930 TCCCCTGATTAACAAGGAAAAGTATAC 58.949 37.037 6.81 0.00 32.12 1.47
3316 6564 8.053355 CCCCTGATTAACAAGGAAAAGTATACT 58.947 37.037 0.00 0.00 32.12 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 8.092521 TCTAAGAGAACAGCAAGAAAATCAAG 57.907 34.615 0.00 0.00 0.00 3.02
65 66 0.605319 GCAGACCGGTCAACCATTGA 60.605 55.000 35.00 0.00 37.33 2.57
82 83 1.524008 ATCGTGTCTGACCAGTCGCA 61.524 55.000 5.17 0.14 0.00 5.10
94 95 1.504359 TTTGTTGGTCGGATCGTGTC 58.496 50.000 0.00 0.00 0.00 3.67
134 135 4.205065 AGAAGAAGGCAATCTCTCACTG 57.795 45.455 0.00 0.00 0.00 3.66
137 138 3.307975 CCCAAGAAGAAGGCAATCTCTCA 60.308 47.826 0.00 0.00 0.00 3.27
185 186 0.679640 CCCGAATAGGTTTGCTGGCA 60.680 55.000 0.00 0.00 38.74 4.92
207 208 1.999735 CATCTCGTTCAGCGCCTTAAA 59.000 47.619 2.29 0.00 41.07 1.52
226 227 2.345560 AGGATGATGATGATGGGAGCA 58.654 47.619 0.00 0.00 0.00 4.26
233 234 6.540438 AAAAAGTGCAAGGATGATGATGAT 57.460 33.333 0.00 0.00 0.00 2.45
260 267 2.086869 TCAGCTGAAGCCAAGCATTAC 58.913 47.619 15.67 0.00 43.38 1.89
278 290 1.519234 GCTCGCGTGTGATCCATCA 60.519 57.895 5.77 0.00 0.00 3.07
280 292 0.877649 GATGCTCGCGTGTGATCCAT 60.878 55.000 5.77 1.67 0.00 3.41
286 298 1.520120 AGATGGATGCTCGCGTGTG 60.520 57.895 5.77 0.00 0.00 3.82
287 299 1.520120 CAGATGGATGCTCGCGTGT 60.520 57.895 5.77 0.00 0.00 4.49
316 328 0.878961 GGGAGACAAAGACACGCGTT 60.879 55.000 10.22 0.17 0.00 4.84
398 410 3.458487 ACAGAGGTCTTGTTACAGGGTTT 59.542 43.478 0.00 0.00 0.00 3.27
401 413 3.403038 CAACAGAGGTCTTGTTACAGGG 58.597 50.000 0.00 0.00 0.00 4.45
402 414 2.808543 GCAACAGAGGTCTTGTTACAGG 59.191 50.000 0.00 0.00 0.00 4.00
405 417 4.893424 TTTGCAACAGAGGTCTTGTTAC 57.107 40.909 0.00 0.00 0.00 2.50
430 442 3.924073 ACAAAGGTTTCGTTGCAACTTTC 59.076 39.130 26.09 13.56 36.13 2.62
431 443 3.920446 ACAAAGGTTTCGTTGCAACTTT 58.080 36.364 26.09 15.67 36.13 2.66
434 447 3.633058 CAACAAAGGTTTCGTTGCAAC 57.367 42.857 19.89 19.89 36.13 4.17
503 516 5.827797 TCTTTTGCAACAGAGGTCTTATTGT 59.172 36.000 11.24 0.00 0.00 2.71
579 593 4.692155 AGGTTATGCTGCAGAAAATTTTGC 59.308 37.500 20.43 8.04 40.67 3.68
594 608 1.135972 CGTGTTGCAGACAGGTTATGC 60.136 52.381 11.23 4.25 39.39 3.14
633 690 0.687354 AGTGGCCGAGTGTCATCTTT 59.313 50.000 0.00 0.00 0.00 2.52
642 699 1.078848 GCAGATTGAGTGGCCGAGT 60.079 57.895 0.00 0.00 0.00 4.18
660 717 1.742880 CGCGAGCCATGGGATATGG 60.743 63.158 15.13 1.59 41.99 2.74
721 792 9.649167 AAGATTTGCAAGGATATTTTCTCAAAG 57.351 29.630 0.00 0.00 0.00 2.77
731 835 5.948162 ACACACTGAAGATTTGCAAGGATAT 59.052 36.000 0.00 0.00 0.00 1.63
767 871 0.094730 CGTCCGTGATTTCCTTTCGC 59.905 55.000 0.00 0.00 0.00 4.70
782 886 1.227002 GATGGGAGAGAACGCGTCC 60.227 63.158 14.44 9.13 34.25 4.79
785 889 2.107141 GGGATGGGAGAGAACGCG 59.893 66.667 3.53 3.53 0.00 6.01
786 890 0.744771 GTTGGGATGGGAGAGAACGC 60.745 60.000 0.00 0.00 0.00 4.84
787 891 0.905357 AGTTGGGATGGGAGAGAACG 59.095 55.000 0.00 0.00 0.00 3.95
788 892 1.210722 GGAGTTGGGATGGGAGAGAAC 59.789 57.143 0.00 0.00 0.00 3.01
789 893 1.203428 TGGAGTTGGGATGGGAGAGAA 60.203 52.381 0.00 0.00 0.00 2.87
791 895 1.211457 CTTGGAGTTGGGATGGGAGAG 59.789 57.143 0.00 0.00 0.00 3.20
817 1788 3.733960 GAGAACGCGGGTTTGGGC 61.734 66.667 19.59 6.49 36.24 5.36
841 1812 2.842462 AGGGATGGCGCGTATGGA 60.842 61.111 8.43 0.00 0.00 3.41
842 1813 2.357517 GAGGGATGGCGCGTATGG 60.358 66.667 8.43 0.00 0.00 2.74
843 1814 0.813610 TTTGAGGGATGGCGCGTATG 60.814 55.000 8.43 0.00 0.00 2.39
877 1855 2.200170 CTGCCGCCTTTTGTAGTGCC 62.200 60.000 0.00 0.00 0.00 5.01
910 1896 2.823154 GTTTGGGATTGGTGGATCGAAA 59.177 45.455 0.00 0.00 0.00 3.46
1009 2005 2.014550 CCATGGGAAGGATGGGGGT 61.015 63.158 2.85 0.00 37.33 4.95
1155 2151 1.456705 GCCAGAGACGAGGGAGGAT 60.457 63.158 0.00 0.00 0.00 3.24
1156 2152 2.043852 GCCAGAGACGAGGGAGGA 60.044 66.667 0.00 0.00 0.00 3.71
1159 2155 2.043852 GAGGCCAGAGACGAGGGA 60.044 66.667 5.01 0.00 0.00 4.20
1221 2217 0.321298 GGCCGAAGAAGTACCAGCAA 60.321 55.000 0.00 0.00 0.00 3.91
1296 2292 4.120331 GCATGCCACGTGCCCTTC 62.120 66.667 10.91 0.00 40.16 3.46
1311 2307 4.332543 ACCCTCCCCTTCTCGGCA 62.333 66.667 0.00 0.00 0.00 5.69
1470 2478 1.341606 GAACTGTCTCGCCTTTCTCG 58.658 55.000 0.00 0.00 0.00 4.04
1587 2595 4.500116 GCCGGAGCTGAGTCGTCC 62.500 72.222 5.05 0.00 35.50 4.79
1681 2695 1.081892 CCATCCGAGCAGTTGTTCAG 58.918 55.000 0.00 0.00 0.00 3.02
1739 2759 0.532573 GACTTGATCAGGCGTGAGGA 59.467 55.000 15.18 0.70 35.66 3.71
1794 2814 1.538047 TGGAGAAGCTGCAATTGACC 58.462 50.000 10.34 0.00 0.00 4.02
1833 2853 2.951745 CAGTAGCTTCTCGCCGCG 60.952 66.667 6.39 6.39 40.39 6.46
1836 2856 0.243907 TGTCACAGTAGCTTCTCGCC 59.756 55.000 0.00 0.00 40.39 5.54
1838 2858 2.094494 ACCATGTCACAGTAGCTTCTCG 60.094 50.000 0.00 0.00 0.00 4.04
1842 2865 3.195825 GGAGTACCATGTCACAGTAGCTT 59.804 47.826 0.00 0.00 35.97 3.74
1856 2879 0.251653 AGCTTCGTCCTGGAGTACCA 60.252 55.000 0.00 0.00 44.76 3.25
1918 2941 1.352352 CAACAAGTCACCCAGGAGGAT 59.648 52.381 0.00 0.00 39.89 3.24
1951 2974 5.188555 AGCTGTAATTGACCTCTGATTCAGA 59.811 40.000 15.39 15.39 38.25 3.27
1993 3017 2.711009 AGTTTCTCACCATGGAACCAGA 59.289 45.455 21.47 10.45 0.00 3.86
2019 3058 1.838073 AACCACCATGGAGGACGGTC 61.838 60.000 32.26 0.00 43.10 4.79
2046 3085 5.945310 TGATCAGAATTATCAAGAAGGGGG 58.055 41.667 0.00 0.00 30.52 5.40
2097 3136 2.113986 AAGTCAGTGGGCAGTGGC 59.886 61.111 8.47 8.47 36.65 5.01
2120 3165 5.779529 ATAATTTAGCATTGCTGTCTGGG 57.220 39.130 21.31 0.00 40.10 4.45
2268 5190 4.445453 GTGATTGCATCATCCACTCAGTA 58.555 43.478 0.00 0.00 42.04 2.74
2271 5193 2.026075 TGGTGATTGCATCATCCACTCA 60.026 45.455 6.86 0.00 39.69 3.41
2333 5261 5.220605 GGGATAGCGAATAAACACACAGAAC 60.221 44.000 0.00 0.00 0.00 3.01
2336 5264 3.245284 CGGGATAGCGAATAAACACACAG 59.755 47.826 0.00 0.00 0.00 3.66
2346 5274 2.233676 TGCATGTATCGGGATAGCGAAT 59.766 45.455 0.00 0.00 0.00 3.34
2354 5285 1.522806 GCGGTTGCATGTATCGGGA 60.523 57.895 8.55 0.00 42.15 5.14
2391 5330 5.759273 TGGTACAAGCTACAAAACGTGTATT 59.241 36.000 0.00 0.00 37.49 1.89
2479 5444 7.396540 ACCAATCTTTCAGCCAATACTTAAG 57.603 36.000 0.00 0.00 0.00 1.85
2487 5452 4.406456 ACACATACCAATCTTTCAGCCAA 58.594 39.130 0.00 0.00 0.00 4.52
2493 5461 9.113838 AGATGACAATACACATACCAATCTTTC 57.886 33.333 0.00 0.00 0.00 2.62
2566 5559 7.517614 TTGCAGTTTACAACATAGGAAATCA 57.482 32.000 0.00 0.00 0.00 2.57
2567 5560 8.986477 AATTGCAGTTTACAACATAGGAAATC 57.014 30.769 0.00 0.00 0.00 2.17
2588 5581 5.975939 GGCAGCAGCTAAAAGAGATTAATTG 59.024 40.000 0.00 0.00 41.70 2.32
2597 5590 2.566833 TGAAGGCAGCAGCTAAAAGA 57.433 45.000 0.00 0.00 41.70 2.52
2611 5605 2.746362 GAGTCAGCTGTTGGATTGAAGG 59.254 50.000 14.67 0.00 0.00 3.46
2615 5609 2.159421 GCATGAGTCAGCTGTTGGATTG 60.159 50.000 14.67 7.21 0.00 2.67
2651 5645 5.703730 TTAAGACCCAAACCCTATACAGG 57.296 43.478 0.00 0.00 42.22 4.00
2681 5697 3.407698 TCCGCTGTTAGAAAAGCATTGA 58.592 40.909 5.32 0.00 39.47 2.57
2700 5716 6.780457 TCAATTTCATCAATTTCTCCCTCC 57.220 37.500 0.00 0.00 32.24 4.30
2702 5718 7.452501 TGAGTTCAATTTCATCAATTTCTCCCT 59.547 33.333 0.00 0.00 32.24 4.20
2752 5769 9.654663 AATGTGAAACTGTAAATAGGACTAGTC 57.345 33.333 14.87 14.87 38.04 2.59
2855 5872 7.703621 GTGACTTTGTCCAATATTCATTCCATG 59.296 37.037 0.00 0.00 0.00 3.66
2863 5880 6.801539 TCTGTGTGACTTTGTCCAATATTC 57.198 37.500 0.00 0.00 0.00 1.75
2864 5881 7.765695 AATCTGTGTGACTTTGTCCAATATT 57.234 32.000 0.00 0.00 0.00 1.28
2865 5882 9.113838 GATAATCTGTGTGACTTTGTCCAATAT 57.886 33.333 0.00 0.00 0.00 1.28
2866 5883 8.321353 AGATAATCTGTGTGACTTTGTCCAATA 58.679 33.333 0.00 0.00 0.00 1.90
2875 5892 4.707448 AGACCGAGATAATCTGTGTGACTT 59.293 41.667 0.00 0.00 0.00 3.01
3066 6197 4.228824 TGTATACGAGGGAAAAGGGCTAT 58.771 43.478 0.00 0.00 0.00 2.97
3072 6203 6.392354 TGTACAGTTGTATACGAGGGAAAAG 58.608 40.000 0.00 0.00 32.54 2.27
3078 6211 5.510674 CGTTCTTGTACAGTTGTATACGAGG 59.489 44.000 0.00 0.00 34.68 4.63
3141 6387 6.613271 AGATACCTTGGTTCTATGATCACTGT 59.387 38.462 0.00 0.00 0.00 3.55
3148 6394 6.867519 TGAACAGATACCTTGGTTCTATGA 57.132 37.500 0.00 0.00 40.12 2.15
3160 6406 9.654663 ACTGAAGTACTTAAATGAACAGATACC 57.345 33.333 19.44 0.53 0.00 2.73


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

AutoCloner maintained by Alex Coulton.