Multiple sequence alignment - TraesCS4B01G230000

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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 TraesCS4B01G230000 chr4B 100.000 3815 0 0 1 3815 480926697 480922883 0.000000e+00 7046.0
1 TraesCS4B01G230000 chr4A 90.720 3847 221 65 54 3815 72926156 72922361 0.000000e+00 5001.0
2 TraesCS4B01G230000 chr4D 92.743 2191 101 28 1645 3815 391038888 391036736 0.000000e+00 3112.0
3 TraesCS4B01G230000 chr4D 91.563 1612 85 25 61 1646 391040653 391039067 0.000000e+00 2176.0
4 TraesCS4B01G230000 chr5A 94.643 56 3 0 1 56 57127213 57127158 1.890000e-13 87.9
5 TraesCS4B01G230000 chr5A 94.643 56 3 0 1 56 57135027 57134972 1.890000e-13 87.9


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 TraesCS4B01G230000 chr4B 480922883 480926697 3814 True 7046 7046 100.000 1 3815 1 chr4B.!!$R1 3814
1 TraesCS4B01G230000 chr4A 72922361 72926156 3795 True 5001 5001 90.720 54 3815 1 chr4A.!!$R1 3761
2 TraesCS4B01G230000 chr4D 391036736 391040653 3917 True 2644 3112 92.153 61 3815 2 chr4D.!!$R1 3754

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
328 340 0.620556 AAACTGCACCGGAGATCCAT 59.379 50.0 9.46 0.0 35.14 3.41 F
945 986 0.957395 ACACTGGCCATCGCTTTCTG 60.957 55.0 5.51 0.0 34.44 3.02 F
1372 1442 0.395724 ATTGGATTGGAAGGGGTCGC 60.396 55.0 0.00 0.0 0.00 5.19 F
1545 1619 0.526662 ACTTCTACGAGAACGGCCTG 59.473 55.0 0.00 0.0 44.46 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1152 1199 0.039035 TGGATTGGTTGTAGGTGCCC 59.961 55.000 0.00 0.00 0.00 5.36 R
2566 2830 1.071699 TGGACTGGTACAACAGAAGCC 59.928 52.381 0.24 0.54 40.97 4.35 R
2697 2961 2.054799 TCAGCTTGGTCCTGGTTTAGT 58.945 47.619 0.00 0.00 0.00 2.24 R
3390 3658 0.747283 GGGCCTCTGCAATCTGAGTG 60.747 60.000 0.84 0.00 40.13 3.51 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 5.095691 CCTCAACATTTATCGTATGTGGC 57.904 43.478 0.00 0.00 36.41 5.01
23 24 4.574421 CCTCAACATTTATCGTATGTGGCA 59.426 41.667 0.00 0.00 36.41 4.92
24 25 5.478233 TCAACATTTATCGTATGTGGCAC 57.522 39.130 11.55 11.55 36.41 5.01
25 26 5.182487 TCAACATTTATCGTATGTGGCACT 58.818 37.500 19.83 6.99 36.41 4.40
26 27 6.342111 TCAACATTTATCGTATGTGGCACTA 58.658 36.000 19.83 5.69 36.41 2.74
27 28 6.256975 TCAACATTTATCGTATGTGGCACTAC 59.743 38.462 19.83 16.12 36.41 2.73
28 29 5.914033 ACATTTATCGTATGTGGCACTACT 58.086 37.500 19.83 6.19 35.03 2.57
29 30 7.046292 ACATTTATCGTATGTGGCACTACTA 57.954 36.000 19.83 10.75 35.03 1.82
30 31 7.494211 ACATTTATCGTATGTGGCACTACTAA 58.506 34.615 19.83 10.65 35.03 2.24
31 32 7.652105 ACATTTATCGTATGTGGCACTACTAAG 59.348 37.037 19.83 9.96 35.03 2.18
32 33 6.947644 TTATCGTATGTGGCACTACTAAGA 57.052 37.500 19.83 14.42 0.00 2.10
33 34 7.520451 TTATCGTATGTGGCACTACTAAGAT 57.480 36.000 19.83 19.22 0.00 2.40
34 35 8.625786 TTATCGTATGTGGCACTACTAAGATA 57.374 34.615 19.83 18.39 0.00 1.98
35 36 6.555812 TCGTATGTGGCACTACTAAGATAG 57.444 41.667 19.83 4.90 0.00 2.08
36 37 5.048921 TCGTATGTGGCACTACTAAGATAGC 60.049 44.000 19.83 1.51 0.00 2.97
37 38 5.278315 CGTATGTGGCACTACTAAGATAGCA 60.278 44.000 19.83 0.00 0.00 3.49
38 39 4.386867 TGTGGCACTACTAAGATAGCAC 57.613 45.455 19.83 0.00 0.00 4.40
39 40 4.023980 TGTGGCACTACTAAGATAGCACT 58.976 43.478 19.83 0.00 0.00 4.40
40 41 5.198207 TGTGGCACTACTAAGATAGCACTA 58.802 41.667 19.83 0.00 0.00 2.74
41 42 5.833667 TGTGGCACTACTAAGATAGCACTAT 59.166 40.000 19.83 0.00 0.00 2.12
42 43 6.323996 TGTGGCACTACTAAGATAGCACTATT 59.676 38.462 19.83 0.00 0.00 1.73
43 44 7.504574 TGTGGCACTACTAAGATAGCACTATTA 59.495 37.037 19.83 0.00 0.00 0.98
44 45 8.524487 GTGGCACTACTAAGATAGCACTATTAT 58.476 37.037 11.13 0.00 0.00 1.28
45 46 9.749340 TGGCACTACTAAGATAGCACTATTATA 57.251 33.333 0.00 0.00 0.00 0.98
52 53 8.478877 ACTAAGATAGCACTATTATACATGCCC 58.521 37.037 0.00 0.00 38.92 5.36
64 65 2.961526 ACATGCCCTAACTCGTACAG 57.038 50.000 0.00 0.00 0.00 2.74
69 70 2.232941 TGCCCTAACTCGTACAGGAAAG 59.767 50.000 0.00 0.00 0.00 2.62
96 101 4.180946 CACGAGGGGAGCGAGACG 62.181 72.222 0.00 0.00 0.00 4.18
176 181 1.366494 GAAAACGCCGCGATCGATG 60.366 57.895 21.57 10.19 38.10 3.84
177 182 2.020836 GAAAACGCCGCGATCGATGT 62.021 55.000 21.57 7.72 38.10 3.06
178 183 0.802994 AAAACGCCGCGATCGATGTA 60.803 50.000 21.57 0.00 38.10 2.29
245 250 7.055667 CATGATTACATGGACCTGTAGTACT 57.944 40.000 0.00 0.00 46.95 2.73
262 267 6.781014 TGTAGTACTAGCCCTACAATAATGCT 59.219 38.462 15.93 0.00 40.29 3.79
293 298 2.949106 CCAAGCTTGGCGTCAGTG 59.051 61.111 31.70 6.62 42.21 3.66
328 340 0.620556 AAACTGCACCGGAGATCCAT 59.379 50.000 9.46 0.00 35.14 3.41
330 342 1.227764 CTGCACCGGAGATCCATGG 60.228 63.158 9.46 4.97 35.14 3.66
360 372 1.394572 GCCCGTACGTAACATGGTTTC 59.605 52.381 15.21 0.00 0.00 2.78
361 373 2.932187 GCCCGTACGTAACATGGTTTCT 60.932 50.000 15.21 0.00 0.00 2.52
363 375 2.093152 CCGTACGTAACATGGTTTCTGC 59.907 50.000 15.21 0.00 0.00 4.26
364 376 2.991190 CGTACGTAACATGGTTTCTGCT 59.009 45.455 7.22 0.00 0.00 4.24
365 377 3.430895 CGTACGTAACATGGTTTCTGCTT 59.569 43.478 7.22 0.00 0.00 3.91
368 380 3.880490 ACGTAACATGGTTTCTGCTTTCA 59.120 39.130 0.00 0.00 0.00 2.69
369 381 4.024048 ACGTAACATGGTTTCTGCTTTCAG 60.024 41.667 0.00 0.00 41.67 3.02
382 394 6.309712 TCTGCTTTCAGATTCTCAAACTTG 57.690 37.500 0.00 0.00 43.95 3.16
384 396 6.543465 TCTGCTTTCAGATTCTCAAACTTGAA 59.457 34.615 0.00 0.00 43.95 2.69
385 397 6.498304 TGCTTTCAGATTCTCAAACTTGAAC 58.502 36.000 0.00 0.00 36.64 3.18
386 398 5.917447 GCTTTCAGATTCTCAAACTTGAACC 59.083 40.000 0.00 0.00 36.64 3.62
387 399 6.238869 GCTTTCAGATTCTCAAACTTGAACCT 60.239 38.462 0.00 0.00 36.64 3.50
392 404 9.436957 TCAGATTCTCAAACTTGAACCTTATAC 57.563 33.333 0.00 0.00 36.64 1.47
393 405 8.383619 CAGATTCTCAAACTTGAACCTTATACG 58.616 37.037 0.00 0.00 36.64 3.06
394 406 8.311836 AGATTCTCAAACTTGAACCTTATACGA 58.688 33.333 0.00 0.00 36.64 3.43
395 407 9.099454 GATTCTCAAACTTGAACCTTATACGAT 57.901 33.333 0.00 0.00 36.64 3.73
506 523 4.200838 TCTCTCCAATAACAATGCGTGA 57.799 40.909 0.00 0.00 0.00 4.35
537 554 2.413112 GGATGACATGGATGCGTTATCG 59.587 50.000 0.00 0.00 36.62 2.92
553 570 4.143803 CGTTATCGCGTTGCTGTAGATTAG 60.144 45.833 5.77 0.00 0.00 1.73
618 650 4.274950 GCCACAAGTAGCACAAAAGTAAGA 59.725 41.667 0.00 0.00 0.00 2.10
796 837 1.614241 AAGGCACCTAATCGGCGTCT 61.614 55.000 6.85 0.00 28.94 4.18
797 838 1.591863 GGCACCTAATCGGCGTCTC 60.592 63.158 6.85 0.00 35.61 3.36
882 923 2.364448 GTCCCTCCTCCTCGCCTT 60.364 66.667 0.00 0.00 0.00 4.35
926 967 1.585261 CGCTATATATCCGCGCGCA 60.585 57.895 32.61 11.60 40.42 6.09
945 986 0.957395 ACACTGGCCATCGCTTTCTG 60.957 55.000 5.51 0.00 34.44 3.02
957 998 1.464997 CGCTTTCTGGCTACACCTTTC 59.535 52.381 0.00 0.00 40.22 2.62
1022 1069 2.990479 GAGGAGTTCCATGGCCGT 59.010 61.111 6.96 0.00 38.89 5.68
1269 1320 3.561217 TTGAGCTCGTAACCGCGCA 62.561 57.895 8.75 0.00 46.79 6.09
1349 1419 4.396790 GTCCACTTGGCATTTCGGTTATTA 59.603 41.667 0.00 0.00 34.44 0.98
1372 1442 0.395724 ATTGGATTGGAAGGGGTCGC 60.396 55.000 0.00 0.00 0.00 5.19
1392 1462 2.641305 CCTTGATCTTCTGCCTCCTTG 58.359 52.381 0.00 0.00 0.00 3.61
1462 1536 2.692041 CCTCATGGGGATTCTTCTTTGC 59.308 50.000 5.34 0.00 0.00 3.68
1490 1564 2.285144 GGGGAAGGTCGGGGAGAA 60.285 66.667 0.00 0.00 0.00 2.87
1545 1619 0.526662 ACTTCTACGAGAACGGCCTG 59.473 55.000 0.00 0.00 44.46 4.85
1600 1674 2.112190 TCACCAATATCTACACCGCCA 58.888 47.619 0.00 0.00 0.00 5.69
1680 1934 3.456380 TTTCAGGGAGAAATGGGAAGG 57.544 47.619 0.00 0.00 41.17 3.46
1686 1940 2.492088 GGGAGAAATGGGAAGGTTTTCG 59.508 50.000 0.00 0.00 33.98 3.46
1694 1948 1.411246 GGGAAGGTTTTCGGTGCTTTT 59.589 47.619 0.00 0.00 33.98 2.27
1707 1961 2.938869 GTGCTTTTTCACCTGCTCATC 58.061 47.619 0.00 0.00 0.00 2.92
1708 1962 2.294233 GTGCTTTTTCACCTGCTCATCA 59.706 45.455 0.00 0.00 0.00 3.07
1709 1963 2.294233 TGCTTTTTCACCTGCTCATCAC 59.706 45.455 0.00 0.00 0.00 3.06
1710 1964 2.555757 GCTTTTTCACCTGCTCATCACT 59.444 45.455 0.00 0.00 0.00 3.41
1713 1967 2.680312 TTCACCTGCTCATCACTAGC 57.320 50.000 0.00 0.00 40.50 3.42
1714 1968 1.857965 TCACCTGCTCATCACTAGCT 58.142 50.000 0.00 0.00 40.73 3.32
1715 1969 2.182827 TCACCTGCTCATCACTAGCTT 58.817 47.619 0.00 0.00 40.73 3.74
1716 1970 2.093816 TCACCTGCTCATCACTAGCTTG 60.094 50.000 0.00 0.00 40.73 4.01
1717 1971 1.297664 CCTGCTCATCACTAGCTTGC 58.702 55.000 0.00 0.00 40.73 4.01
1718 1972 1.134461 CCTGCTCATCACTAGCTTGCT 60.134 52.381 0.00 0.00 40.73 3.91
1721 1975 2.762887 TGCTCATCACTAGCTTGCTACT 59.237 45.455 0.00 0.00 40.73 2.57
1722 1976 3.954258 TGCTCATCACTAGCTTGCTACTA 59.046 43.478 0.00 0.00 40.73 1.82
1723 1977 4.402474 TGCTCATCACTAGCTTGCTACTAA 59.598 41.667 0.00 0.00 40.73 2.24
1724 1978 4.981674 GCTCATCACTAGCTTGCTACTAAG 59.018 45.833 0.00 0.00 37.01 2.18
1725 1979 5.521906 TCATCACTAGCTTGCTACTAAGG 57.478 43.478 0.00 0.00 0.00 2.69
1726 1980 3.802948 TCACTAGCTTGCTACTAAGGC 57.197 47.619 0.00 0.00 0.00 4.35
1739 1993 5.240844 TGCTACTAAGGCTTTTTGTTCCTTC 59.759 40.000 4.45 0.00 40.42 3.46
1796 2050 2.358737 CACAGCTTGACCCGGTCC 60.359 66.667 15.24 0.00 0.00 4.46
1838 2092 5.170803 CGATTCGTTTGCATGAGATCATTTG 59.829 40.000 0.00 0.00 33.61 2.32
1867 2121 7.228507 GTCAATGCAGGTACATGGTCATATTTA 59.771 37.037 9.91 0.00 0.00 1.40
1875 2130 9.131791 AGGTACATGGTCATATTTATTTGAACC 57.868 33.333 0.00 0.00 0.00 3.62
1951 2210 8.832521 TGATATACTTGTAAAAACGGCATAAGG 58.167 33.333 0.00 0.00 0.00 2.69
1986 2245 3.959449 TCATCCCTGTTCTCTCAGAGATG 59.041 47.826 4.85 10.46 45.53 2.90
2121 2380 1.887242 GCTGAAGGTGCACACGTCA 60.887 57.895 20.43 18.75 0.00 4.35
2128 2387 4.277174 TGAAGGTGCACACGTCAAATAAAT 59.723 37.500 20.43 0.00 0.00 1.40
2323 2582 2.393271 ATTGCTTCTTCCAGTCCTCG 57.607 50.000 0.00 0.00 0.00 4.63
2330 2589 3.165087 TCTTCCAGTCCTCGAGGTAAA 57.835 47.619 30.17 16.35 36.34 2.01
2337 2596 5.068723 TCCAGTCCTCGAGGTAAATCATAAC 59.931 44.000 30.17 17.42 36.34 1.89
2378 2642 8.888716 GTTTTAAAAAGCCCAGAAAAAGAATCA 58.111 29.630 1.31 0.00 0.00 2.57
2438 2702 3.134623 TCGACTTCTACATCAATGGGCAT 59.865 43.478 0.00 0.00 0.00 4.40
2448 2712 0.968901 CAATGGGCATGACCACTGCT 60.969 55.000 26.45 3.24 44.72 4.24
2480 2744 1.071605 GCAGCAGAGACAGGTTAACG 58.928 55.000 0.00 0.00 0.00 3.18
2561 2825 7.608761 ACTTGTTGAAGTTGTCTAACCTTAACA 59.391 33.333 0.00 0.00 39.56 2.41
2563 2827 6.036300 TGTTGAAGTTGTCTAACCTTAACACG 59.964 38.462 0.00 0.00 37.52 4.49
2566 2830 2.068837 TGTCTAACCTTAACACGCGG 57.931 50.000 12.47 1.27 0.00 6.46
2661 2925 4.340097 CAGCCAAATGATGATAAGCTCCAA 59.660 41.667 0.00 0.00 0.00 3.53
2853 3117 4.288626 TGGCAGGAGAATTAGTTTGGTAGT 59.711 41.667 0.00 0.00 0.00 2.73
2961 3226 4.142600 GCGCTGAAGAAATATTGAACTGGT 60.143 41.667 0.00 0.00 0.00 4.00
2974 3239 4.898829 TGAACTGGTTGTGAATTGTCTG 57.101 40.909 0.00 0.00 0.00 3.51
3020 3285 3.156293 CATGGTGTCCATTGGTTCTGAA 58.844 45.455 1.86 0.00 42.23 3.02
3021 3286 2.582052 TGGTGTCCATTGGTTCTGAAC 58.418 47.619 12.05 12.05 0.00 3.18
3022 3287 2.174639 TGGTGTCCATTGGTTCTGAACT 59.825 45.455 19.05 0.00 0.00 3.01
3023 3288 3.222603 GGTGTCCATTGGTTCTGAACTT 58.777 45.455 19.05 3.39 0.00 2.66
3024 3289 3.253432 GGTGTCCATTGGTTCTGAACTTC 59.747 47.826 19.05 5.31 0.00 3.01
3025 3290 4.137543 GTGTCCATTGGTTCTGAACTTCT 58.862 43.478 19.05 2.57 0.00 2.85
3026 3291 4.023707 GTGTCCATTGGTTCTGAACTTCTG 60.024 45.833 19.05 13.04 0.00 3.02
3027 3292 4.141505 TGTCCATTGGTTCTGAACTTCTGA 60.142 41.667 19.05 8.00 0.00 3.27
3053 3318 6.015095 TGCATACATAAGTCACAGGGATCTAG 60.015 42.308 0.00 0.00 0.00 2.43
3059 3324 3.987745 AGTCACAGGGATCTAGTGATGT 58.012 45.455 15.00 6.68 43.35 3.06
3175 3442 7.141363 GCATATTGGTATCAGGATTCAACAAC 58.859 38.462 0.00 0.00 0.00 3.32
3204 3471 7.013655 TGCAAAGACTATTTTCTTCAGCTTTCT 59.986 33.333 9.98 0.00 37.41 2.52
3205 3472 7.864882 GCAAAGACTATTTTCTTCAGCTTTCTT 59.135 33.333 0.00 0.00 34.60 2.52
3206 3473 9.741647 CAAAGACTATTTTCTTCAGCTTTCTTT 57.258 29.630 0.00 0.00 34.60 2.52
3207 3474 9.958234 AAAGACTATTTTCTTCAGCTTTCTTTC 57.042 29.630 0.00 0.00 34.60 2.62
3223 3490 4.497473 TCTTTCACAAATAAAGGGCACG 57.503 40.909 0.00 0.00 35.18 5.34
3390 3658 2.497273 AGGTCATGCATTAAGTTTGGGC 59.503 45.455 0.00 0.00 0.00 5.36
3431 3699 5.453198 CCCCTAACTGCATTTTCAAGTGTTT 60.453 40.000 0.00 0.00 0.00 2.83
3439 3707 5.749588 TGCATTTTCAAGTGTTTCATGACAG 59.250 36.000 0.00 0.00 0.00 3.51
3460 3728 7.491048 TGACAGAAAAAGTTGCCAAGAAAATAC 59.509 33.333 0.00 0.00 0.00 1.89
3514 3782 6.423604 AGAATAATTTTGTGGCAAAAACTCGG 59.576 34.615 1.39 0.00 32.12 4.63
3515 3783 3.810310 ATTTTGTGGCAAAAACTCGGA 57.190 38.095 1.39 0.00 32.12 4.55
3558 3828 6.691754 TCACTTCAGACATGCAAACTAAAA 57.308 33.333 0.00 0.00 0.00 1.52
3559 3829 6.728200 TCACTTCAGACATGCAAACTAAAAG 58.272 36.000 0.00 1.42 0.00 2.27
3560 3830 6.318648 TCACTTCAGACATGCAAACTAAAAGT 59.681 34.615 0.00 2.00 0.00 2.66
3561 3831 7.497579 TCACTTCAGACATGCAAACTAAAAGTA 59.502 33.333 0.00 0.00 0.00 2.24
3563 3833 6.554334 TCAGACATGCAAACTAAAAGTACC 57.446 37.500 0.00 0.00 0.00 3.34
3564 3834 6.296026 TCAGACATGCAAACTAAAAGTACCT 58.704 36.000 0.00 0.00 0.00 3.08
3685 3960 3.423539 AAGCCACATGAAAGCTGTCTA 57.576 42.857 5.28 0.00 36.84 2.59
3748 4025 5.026121 ACACCAGTGAATCCATCTTAGAGA 58.974 41.667 4.48 0.00 0.00 3.10
3749 4026 5.128499 ACACCAGTGAATCCATCTTAGAGAG 59.872 44.000 4.48 0.00 0.00 3.20
3776 4053 4.592778 ACCCCAATGAGCAACAGTTAAATT 59.407 37.500 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.574421 TGCCACATACGATAAATGTTGAGG 59.426 41.667 0.00 0.00 35.39 3.86
1 2 5.294306 AGTGCCACATACGATAAATGTTGAG 59.706 40.000 0.00 0.00 35.39 3.02
2 3 5.182487 AGTGCCACATACGATAAATGTTGA 58.818 37.500 0.00 0.00 35.39 3.18
3 4 5.484173 AGTGCCACATACGATAAATGTTG 57.516 39.130 0.00 0.00 35.39 3.33
4 5 6.346096 AGTAGTGCCACATACGATAAATGTT 58.654 36.000 0.00 0.00 35.39 2.71
5 6 5.914033 AGTAGTGCCACATACGATAAATGT 58.086 37.500 0.00 0.00 38.08 2.71
6 7 7.865889 TCTTAGTAGTGCCACATACGATAAATG 59.134 37.037 0.00 0.00 0.00 2.32
7 8 7.948357 TCTTAGTAGTGCCACATACGATAAAT 58.052 34.615 0.00 0.00 0.00 1.40
8 9 7.337480 TCTTAGTAGTGCCACATACGATAAA 57.663 36.000 0.00 0.00 0.00 1.40
9 10 6.947644 TCTTAGTAGTGCCACATACGATAA 57.052 37.500 0.00 0.00 0.00 1.75
10 11 7.148289 GCTATCTTAGTAGTGCCACATACGATA 60.148 40.741 0.00 0.25 0.00 2.92
11 12 6.349445 GCTATCTTAGTAGTGCCACATACGAT 60.349 42.308 0.00 0.00 0.00 3.73
12 13 5.048921 GCTATCTTAGTAGTGCCACATACGA 60.049 44.000 0.00 0.00 0.00 3.43
13 14 5.154932 GCTATCTTAGTAGTGCCACATACG 58.845 45.833 0.00 0.00 0.00 3.06
14 15 5.921408 GTGCTATCTTAGTAGTGCCACATAC 59.079 44.000 0.00 0.00 0.00 2.39
15 16 5.833667 AGTGCTATCTTAGTAGTGCCACATA 59.166 40.000 0.00 0.00 0.00 2.29
16 17 4.651503 AGTGCTATCTTAGTAGTGCCACAT 59.348 41.667 0.00 0.00 0.00 3.21
17 18 4.023980 AGTGCTATCTTAGTAGTGCCACA 58.976 43.478 0.00 0.00 0.00 4.17
18 19 4.657436 AGTGCTATCTTAGTAGTGCCAC 57.343 45.455 0.00 0.00 0.00 5.01
19 20 6.978674 AATAGTGCTATCTTAGTAGTGCCA 57.021 37.500 0.00 0.00 0.00 4.92
26 27 8.478877 GGGCATGTATAATAGTGCTATCTTAGT 58.521 37.037 0.00 0.00 37.70 2.24
27 28 8.700051 AGGGCATGTATAATAGTGCTATCTTAG 58.300 37.037 0.00 0.00 37.70 2.18
28 29 8.609617 AGGGCATGTATAATAGTGCTATCTTA 57.390 34.615 0.00 0.00 37.70 2.10
29 30 7.502060 AGGGCATGTATAATAGTGCTATCTT 57.498 36.000 0.00 0.00 37.70 2.40
30 31 8.478877 GTTAGGGCATGTATAATAGTGCTATCT 58.521 37.037 0.00 0.00 37.70 1.98
31 32 8.478877 AGTTAGGGCATGTATAATAGTGCTATC 58.521 37.037 0.00 0.00 37.70 2.08
32 33 8.380742 AGTTAGGGCATGTATAATAGTGCTAT 57.619 34.615 0.00 0.00 37.70 2.97
33 34 7.362660 CGAGTTAGGGCATGTATAATAGTGCTA 60.363 40.741 0.00 0.00 37.70 3.49
34 35 6.572509 CGAGTTAGGGCATGTATAATAGTGCT 60.573 42.308 0.00 0.00 37.70 4.40
35 36 5.577164 CGAGTTAGGGCATGTATAATAGTGC 59.423 44.000 0.00 0.00 36.88 4.40
36 37 6.688578 ACGAGTTAGGGCATGTATAATAGTG 58.311 40.000 0.00 0.00 0.00 2.74
37 38 6.912951 ACGAGTTAGGGCATGTATAATAGT 57.087 37.500 0.00 0.00 0.00 2.12
38 39 7.823665 TGTACGAGTTAGGGCATGTATAATAG 58.176 38.462 0.00 0.00 0.00 1.73
39 40 7.094075 CCTGTACGAGTTAGGGCATGTATAATA 60.094 40.741 0.00 0.00 0.00 0.98
40 41 6.295123 CCTGTACGAGTTAGGGCATGTATAAT 60.295 42.308 0.00 0.00 0.00 1.28
41 42 5.010314 CCTGTACGAGTTAGGGCATGTATAA 59.990 44.000 0.00 0.00 0.00 0.98
42 43 4.521639 CCTGTACGAGTTAGGGCATGTATA 59.478 45.833 0.00 0.00 0.00 1.47
43 44 3.321111 CCTGTACGAGTTAGGGCATGTAT 59.679 47.826 0.00 0.00 0.00 2.29
44 45 2.691526 CCTGTACGAGTTAGGGCATGTA 59.308 50.000 0.00 0.00 0.00 2.29
45 46 1.480954 CCTGTACGAGTTAGGGCATGT 59.519 52.381 0.00 0.00 0.00 3.21
46 47 1.754803 TCCTGTACGAGTTAGGGCATG 59.245 52.381 0.00 0.00 32.39 4.06
47 48 2.154567 TCCTGTACGAGTTAGGGCAT 57.845 50.000 0.00 0.00 32.39 4.40
48 49 1.927487 TTCCTGTACGAGTTAGGGCA 58.073 50.000 0.00 0.00 32.39 5.36
49 50 2.418334 CCTTTCCTGTACGAGTTAGGGC 60.418 54.545 0.00 0.00 32.39 5.19
50 51 2.830321 ACCTTTCCTGTACGAGTTAGGG 59.170 50.000 0.00 0.00 32.39 3.53
51 52 4.991472 GTACCTTTCCTGTACGAGTTAGG 58.009 47.826 0.00 0.00 30.30 2.69
82 85 3.066233 GAACCGTCTCGCTCCCCTC 62.066 68.421 0.00 0.00 0.00 4.30
83 86 3.069318 GAACCGTCTCGCTCCCCT 61.069 66.667 0.00 0.00 0.00 4.79
84 87 3.358076 CTGAACCGTCTCGCTCCCC 62.358 68.421 0.00 0.00 0.00 4.81
88 91 0.318784 GTGAACTGAACCGTCTCGCT 60.319 55.000 0.00 0.00 0.00 4.93
90 93 2.052157 GAAGTGAACTGAACCGTCTCG 58.948 52.381 0.00 0.00 0.00 4.04
96 101 1.897560 CCAGGGAAGTGAACTGAACC 58.102 55.000 0.00 0.00 34.21 3.62
176 181 1.264826 GCTGAGGCTCGCTAGTACTAC 59.735 57.143 19.31 0.00 35.22 2.73
177 182 1.595466 GCTGAGGCTCGCTAGTACTA 58.405 55.000 19.31 1.89 35.22 1.82
178 183 1.104577 GGCTGAGGCTCGCTAGTACT 61.105 60.000 23.42 0.00 38.73 2.73
209 214 2.290832 TGTAATCATGCTGCCCTGTTGA 60.291 45.455 0.00 0.00 0.00 3.18
245 250 2.367241 TGCGAGCATTATTGTAGGGCTA 59.633 45.455 0.00 0.00 34.44 3.93
262 267 1.302431 CTTGGTCCACCATGTGCGA 60.302 57.895 0.00 0.00 46.97 5.10
293 298 5.902432 GTGCAGTTTTACGAACTCTTTTCTC 59.098 40.000 0.00 0.00 0.00 2.87
360 372 6.309712 TCAAGTTTGAGAATCTGAAAGCAG 57.690 37.500 0.00 0.00 36.77 4.24
361 373 6.460123 GGTTCAAGTTTGAGAATCTGAAAGCA 60.460 38.462 0.00 0.00 38.61 3.91
363 375 7.269477 AGGTTCAAGTTTGAGAATCTGAAAG 57.731 36.000 0.00 0.00 38.61 2.62
364 376 7.645058 AAGGTTCAAGTTTGAGAATCTGAAA 57.355 32.000 0.00 0.00 35.50 2.69
365 377 8.924511 ATAAGGTTCAAGTTTGAGAATCTGAA 57.075 30.769 0.00 0.00 35.50 3.02
368 380 8.311836 TCGTATAAGGTTCAAGTTTGAGAATCT 58.688 33.333 0.00 0.00 36.80 2.40
369 381 8.475331 TCGTATAAGGTTCAAGTTTGAGAATC 57.525 34.615 0.00 0.00 38.61 2.52
371 383 9.582431 CTATCGTATAAGGTTCAAGTTTGAGAA 57.418 33.333 0.00 0.00 38.61 2.87
373 385 7.707035 AGCTATCGTATAAGGTTCAAGTTTGAG 59.293 37.037 0.00 0.00 38.61 3.02
375 387 7.491372 TGAGCTATCGTATAAGGTTCAAGTTTG 59.509 37.037 0.00 0.00 0.00 2.93
376 388 7.553334 TGAGCTATCGTATAAGGTTCAAGTTT 58.447 34.615 0.00 0.00 0.00 2.66
377 389 7.108841 TGAGCTATCGTATAAGGTTCAAGTT 57.891 36.000 0.00 0.00 0.00 2.66
378 390 6.710597 TGAGCTATCGTATAAGGTTCAAGT 57.289 37.500 0.00 0.00 0.00 3.16
379 391 7.804614 GATGAGCTATCGTATAAGGTTCAAG 57.195 40.000 0.00 0.00 0.00 3.02
416 428 2.552315 TGACTTGGATGAGTTTTTCGCC 59.448 45.455 0.00 0.00 0.00 5.54
417 429 3.896648 TGACTTGGATGAGTTTTTCGC 57.103 42.857 0.00 0.00 0.00 4.70
418 430 5.611796 TCATGACTTGGATGAGTTTTTCG 57.388 39.130 0.00 0.00 0.00 3.46
420 432 4.083110 CGCTCATGACTTGGATGAGTTTTT 60.083 41.667 10.58 0.00 45.89 1.94
506 523 2.577563 TCCATGTCATCCTTCCATGTGT 59.422 45.455 0.00 0.00 35.34 3.72
541 558 5.414789 TGGTTTAGTGCTAATCTACAGCA 57.585 39.130 0.00 0.00 46.47 4.41
569 591 1.759445 AGACGTCCAGGATCATCTTGG 59.241 52.381 13.01 9.63 44.20 3.61
580 602 2.811317 GGCGCTTGAGACGTCCAG 60.811 66.667 13.01 7.29 0.00 3.86
584 606 1.956170 CTTGTGGCGCTTGAGACGT 60.956 57.895 7.64 0.00 0.00 4.34
641 673 1.332195 GTGGCCAGCCTTTCTTTTCT 58.668 50.000 5.11 0.00 36.94 2.52
674 706 0.886043 GTGCATGTCACTGTCTGCCA 60.886 55.000 11.51 0.00 42.38 4.92
796 837 1.372872 CGATGGACAGTGTGTGCGA 60.373 57.895 0.00 0.00 41.94 5.10
797 838 3.015293 GCGATGGACAGTGTGTGCG 62.015 63.158 0.00 0.00 41.94 5.34
882 923 1.953642 CCACACACACGCACGATCA 60.954 57.895 0.00 0.00 0.00 2.92
926 967 0.957395 CAGAAAGCGATGGCCAGTGT 60.957 55.000 13.05 0.00 41.24 3.55
945 986 3.501062 GTGTGGTTAAGAAAGGTGTAGCC 59.499 47.826 0.00 0.00 37.58 3.93
957 998 2.677003 CGGCGGCAGTGTGGTTAAG 61.677 63.158 10.53 0.00 0.00 1.85
984 1029 1.077501 CATGGTTGATGGCCGGACT 60.078 57.895 9.82 0.00 0.00 3.85
1089 1136 3.249189 TTCTTGGCCGGGTGCTCT 61.249 61.111 2.18 0.00 40.92 4.09
1152 1199 0.039035 TGGATTGGTTGTAGGTGCCC 59.961 55.000 0.00 0.00 0.00 5.36
1269 1320 4.060038 CAACGACCCTACCGCGGT 62.060 66.667 36.01 36.01 35.88 5.68
1349 1419 4.215109 CGACCCCTTCCAATCCAATAAAT 58.785 43.478 0.00 0.00 0.00 1.40
1372 1442 2.641305 CAAGGAGGCAGAAGATCAAGG 58.359 52.381 0.00 0.00 0.00 3.61
1462 1536 1.077212 CCTTCCCCATCTGCACCAG 60.077 63.158 0.00 0.00 0.00 4.00
1490 1564 0.109086 CACGAAGTCGATGTCCAGCT 60.109 55.000 7.87 0.00 41.61 4.24
1545 1619 4.077184 TGGTCATGGACGCCCGTC 62.077 66.667 12.07 12.07 43.87 4.79
1666 1920 2.492088 CCGAAAACCTTCCCATTTCTCC 59.508 50.000 0.00 0.00 32.28 3.71
1667 1921 3.057526 CACCGAAAACCTTCCCATTTCTC 60.058 47.826 0.00 0.00 32.28 2.87
1694 1948 2.182827 AGCTAGTGATGAGCAGGTGAA 58.817 47.619 0.00 0.00 42.69 3.18
1699 1953 2.312722 AGCAAGCTAGTGATGAGCAG 57.687 50.000 0.00 0.00 42.69 4.24
1704 1958 4.054671 GCCTTAGTAGCAAGCTAGTGATG 58.945 47.826 17.41 8.98 34.39 3.07
1705 1959 3.964031 AGCCTTAGTAGCAAGCTAGTGAT 59.036 43.478 17.41 0.00 34.39 3.06
1707 1961 3.810310 AGCCTTAGTAGCAAGCTAGTG 57.190 47.619 17.41 4.48 34.39 2.74
1708 1962 4.828072 AAAGCCTTAGTAGCAAGCTAGT 57.172 40.909 13.43 13.43 36.32 2.57
1709 1963 5.412904 ACAAAAAGCCTTAGTAGCAAGCTAG 59.587 40.000 1.29 0.00 0.00 3.42
1710 1964 5.313712 ACAAAAAGCCTTAGTAGCAAGCTA 58.686 37.500 0.00 0.00 0.00 3.32
1713 1967 5.241728 AGGAACAAAAAGCCTTAGTAGCAAG 59.758 40.000 0.00 0.00 0.00 4.01
1714 1968 5.137551 AGGAACAAAAAGCCTTAGTAGCAA 58.862 37.500 0.00 0.00 0.00 3.91
1715 1969 4.725490 AGGAACAAAAAGCCTTAGTAGCA 58.275 39.130 0.00 0.00 0.00 3.49
1716 1970 5.335740 GGAAGGAACAAAAAGCCTTAGTAGC 60.336 44.000 0.00 0.00 41.85 3.58
1717 1971 5.768164 TGGAAGGAACAAAAAGCCTTAGTAG 59.232 40.000 0.00 0.00 41.85 2.57
1718 1972 5.697067 TGGAAGGAACAAAAAGCCTTAGTA 58.303 37.500 0.00 0.00 41.85 1.82
1721 1975 4.542697 ACTGGAAGGAACAAAAAGCCTTA 58.457 39.130 0.00 0.00 41.85 2.69
1722 1976 3.374764 ACTGGAAGGAACAAAAAGCCTT 58.625 40.909 0.00 0.00 44.32 4.35
1723 1977 3.032265 ACTGGAAGGAACAAAAAGCCT 57.968 42.857 0.00 0.00 39.30 4.58
1724 1978 3.384789 AGAACTGGAAGGAACAAAAAGCC 59.615 43.478 0.00 0.00 39.30 4.35
1725 1979 4.655762 AGAACTGGAAGGAACAAAAAGC 57.344 40.909 0.00 0.00 39.30 3.51
1775 2029 1.741770 CCGGGTCAAGCTGTGCTAC 60.742 63.158 0.00 0.00 38.25 3.58
1777 2031 3.537206 GACCGGGTCAAGCTGTGCT 62.537 63.158 22.10 0.00 42.56 4.40
1796 2050 3.004283 CTCATCGAGCTTGCGCAG 58.996 61.111 11.31 6.32 39.10 5.18
1838 2092 2.819608 ACCATGTACCTGCATTGACAAC 59.180 45.455 0.00 0.00 0.00 3.32
1927 2185 7.501225 AGCCTTATGCCGTTTTTACAAGTATAT 59.499 33.333 0.00 0.00 42.71 0.86
1943 2202 5.065914 TGAATGATAGTCAAGCCTTATGCC 58.934 41.667 0.00 0.00 42.71 4.40
1951 2210 4.712476 ACAGGGATGAATGATAGTCAAGC 58.288 43.478 0.00 0.00 0.00 4.01
1986 2245 3.254892 GTCGATGAAGAAGAACTCCACC 58.745 50.000 0.00 0.00 0.00 4.61
2128 2387 9.109393 GCTTTGTAACTAACATGGATGAGAATA 57.891 33.333 0.00 0.00 38.10 1.75
2164 2423 5.374071 AGAATTTACGGAAAAGGAGTGTGT 58.626 37.500 0.00 0.00 0.00 3.72
2205 2464 4.409570 CAGTTGATTTCTTCATTGCCTCG 58.590 43.478 0.00 0.00 33.34 4.63
2245 2504 2.158623 TCCTCATGGTATGATGCCCAAC 60.159 50.000 0.00 0.00 38.85 3.77
2378 2642 6.351286 GGAAGGGCATGAAAGTGTCATAAAAT 60.351 38.462 0.00 0.00 45.69 1.82
2448 2712 3.076621 CTCTGCTGCTAATGTGTTCCAA 58.923 45.455 0.00 0.00 0.00 3.53
2561 2825 1.666872 GTACAACAGAAGCCCGCGT 60.667 57.895 4.92 0.00 0.00 6.01
2563 2827 1.298859 CTGGTACAACAGAAGCCCGC 61.299 60.000 0.00 0.00 40.97 6.13
2566 2830 1.071699 TGGACTGGTACAACAGAAGCC 59.928 52.381 0.24 0.54 40.97 4.35
2661 2925 4.623863 ACCCTTGCCCATCATAAAAGAAT 58.376 39.130 0.00 0.00 0.00 2.40
2697 2961 2.054799 TCAGCTTGGTCCTGGTTTAGT 58.945 47.619 0.00 0.00 0.00 2.24
2961 3226 6.647334 TCCTTTATTGCAGACAATTCACAA 57.353 33.333 0.00 0.00 44.21 3.33
2974 3239 3.622627 GCATCTCTGCTCCTTTATTGC 57.377 47.619 0.00 0.00 45.32 3.56
2999 3264 2.794103 TCAGAACCAATGGACACCATG 58.206 47.619 6.16 0.00 44.40 3.66
3020 3285 6.643388 TGTGACTTATGTATGCATCAGAAGT 58.357 36.000 25.49 25.49 45.70 3.01
3021 3286 6.202379 CCTGTGACTTATGTATGCATCAGAAG 59.798 42.308 21.50 21.50 39.20 2.85
3022 3287 6.051074 CCTGTGACTTATGTATGCATCAGAA 58.949 40.000 11.40 4.33 36.58 3.02
3023 3288 5.453762 CCCTGTGACTTATGTATGCATCAGA 60.454 44.000 11.40 0.00 36.58 3.27
3024 3289 4.753610 CCCTGTGACTTATGTATGCATCAG 59.246 45.833 0.19 1.06 36.58 2.90
3025 3290 4.408596 TCCCTGTGACTTATGTATGCATCA 59.591 41.667 0.19 1.39 36.58 3.07
3026 3291 4.960938 TCCCTGTGACTTATGTATGCATC 58.039 43.478 0.19 0.00 36.58 3.91
3027 3292 5.309020 AGATCCCTGTGACTTATGTATGCAT 59.691 40.000 3.79 3.79 39.03 3.96
3053 3318 6.426980 TTCTCTAAATGCACATCACATCAC 57.573 37.500 0.00 0.00 0.00 3.06
3059 3324 7.571080 TGCATATTTCTCTAAATGCACATCA 57.429 32.000 4.82 0.00 36.28 3.07
3138 3405 2.091541 CCAATATGCAAAGGTCACCGT 58.908 47.619 0.00 0.00 0.00 4.83
3175 3442 5.855395 GCTGAAGAAAATAGTCTTTGCACTG 59.145 40.000 0.00 0.00 37.98 3.66
3204 3471 2.959707 ACCGTGCCCTTTATTTGTGAAA 59.040 40.909 0.00 0.00 0.00 2.69
3205 3472 2.588620 ACCGTGCCCTTTATTTGTGAA 58.411 42.857 0.00 0.00 0.00 3.18
3206 3473 2.279935 ACCGTGCCCTTTATTTGTGA 57.720 45.000 0.00 0.00 0.00 3.58
3207 3474 3.056304 CAAACCGTGCCCTTTATTTGTG 58.944 45.455 0.00 0.00 0.00 3.33
3223 3490 3.194005 TCTCTCTTCCACACACAAACC 57.806 47.619 0.00 0.00 0.00 3.27
3319 3587 2.494870 ACATTGTGGTAGACCGTAGACC 59.505 50.000 0.00 0.00 39.43 3.85
3320 3588 3.863142 ACATTGTGGTAGACCGTAGAC 57.137 47.619 0.00 0.00 39.43 2.59
3321 3589 4.281435 TGAAACATTGTGGTAGACCGTAGA 59.719 41.667 0.00 0.00 39.43 2.59
3322 3590 4.562082 TGAAACATTGTGGTAGACCGTAG 58.438 43.478 0.00 0.00 39.43 3.51
3323 3591 4.281435 TCTGAAACATTGTGGTAGACCGTA 59.719 41.667 0.00 0.00 39.43 4.02
3324 3592 3.070446 TCTGAAACATTGTGGTAGACCGT 59.930 43.478 0.00 0.00 39.43 4.83
3325 3593 3.432252 GTCTGAAACATTGTGGTAGACCG 59.568 47.826 12.82 0.00 39.43 4.79
3390 3658 0.747283 GGGCCTCTGCAATCTGAGTG 60.747 60.000 0.84 0.00 40.13 3.51
3431 3699 4.644234 TCTTGGCAACTTTTTCTGTCATGA 59.356 37.500 0.00 0.00 31.25 3.07
3439 3707 9.529325 AAGTAGTATTTTCTTGGCAACTTTTTC 57.471 29.630 0.00 0.00 37.61 2.29
3460 3728 5.565592 TGTAATTTGCATGCCTGAAGTAG 57.434 39.130 16.68 0.00 0.00 2.57
3496 3764 3.594603 TTCCGAGTTTTTGCCACAAAA 57.405 38.095 1.50 1.50 0.00 2.44
3559 3829 2.737252 CGAGTTTTTGCCAGAGAGGTAC 59.263 50.000 0.00 0.00 40.61 3.34
3560 3830 2.289444 CCGAGTTTTTGCCAGAGAGGTA 60.289 50.000 0.00 0.00 40.61 3.08
3561 3831 1.543429 CCGAGTTTTTGCCAGAGAGGT 60.543 52.381 0.00 0.00 40.61 3.85
3563 3833 0.519077 GCCGAGTTTTTGCCAGAGAG 59.481 55.000 0.00 0.00 0.00 3.20
3564 3834 0.179032 TGCCGAGTTTTTGCCAGAGA 60.179 50.000 0.00 0.00 0.00 3.10
3709 3984 8.239038 TCACTGGTGTTAAAACATTATGGAAA 57.761 30.769 0.00 0.00 41.59 3.13
3748 4025 3.010584 ACTGTTGCTCATTGGGGTAATCT 59.989 43.478 0.00 0.00 0.00 2.40
3749 4026 3.356290 ACTGTTGCTCATTGGGGTAATC 58.644 45.455 0.00 0.00 0.00 1.75
3776 4053 0.400213 ATGGCCGTGGAGAGTTTTGA 59.600 50.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.