Multiple sequence alignment - TraesCS3D01G011800

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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 TraesCS3D01G011800 chr3D 100.000 4160 0 0 1 4160 4170264 4166105 0.000000e+00 7683.0
1 TraesCS3D01G011800 chr3D 91.533 1429 111 5 1812 3238 4076805 4078225 0.000000e+00 1960.0
2 TraesCS3D01G011800 chr3D 85.552 1765 187 32 3 1751 4074998 4076710 0.000000e+00 1784.0
3 TraesCS3D01G011800 chr3D 94.279 402 23 0 3255 3656 4078330 4078731 2.130000e-172 616.0
4 TraesCS3D01G011800 chr3D 98.507 67 1 0 3826 3892 4078865 4078931 7.310000e-23 119.0
5 TraesCS3D01G011800 chr3D 98.000 50 1 0 3760 3809 4078820 4078869 2.060000e-13 87.9
6 TraesCS3D01G011800 chr3A 96.079 3239 99 7 3 3238 9612252 9615465 0.000000e+00 5252.0
7 TraesCS3D01G011800 chr3A 94.064 2746 115 7 773 3515 9780258 9777558 0.000000e+00 4124.0
8 TraesCS3D01G011800 chr3A 92.600 473 32 3 6 478 9781347 9780878 0.000000e+00 676.0
9 TraesCS3D01G011800 chr3A 94.068 354 14 2 3235 3587 9615534 9615881 7.920000e-147 531.0
10 TraesCS3D01G011800 chr3A 95.472 265 7 2 471 730 9780517 9780253 6.430000e-113 418.0
11 TraesCS3D01G011800 chr3A 92.737 179 10 2 3550 3725 9777562 9777384 5.340000e-64 255.0
12 TraesCS3D01G011800 chr3A 85.057 261 18 9 3913 4160 9616127 9616379 3.210000e-61 246.0
13 TraesCS3D01G011800 chr3A 81.685 273 23 14 3911 4160 9777119 9776851 7.050000e-48 202.0
14 TraesCS3D01G011800 chr3A 95.181 83 3 1 3811 3892 9777345 9777263 3.380000e-26 130.0
15 TraesCS3D01G011800 chr3A 97.368 38 1 0 3772 3809 9615967 9616004 9.650000e-07 65.8
16 TraesCS3D01G011800 chr3B 91.969 2453 126 22 1146 3542 6667670 6665233 0.000000e+00 3373.0
17 TraesCS3D01G011800 chr3B 86.164 2544 244 52 747 3238 6393441 6395928 0.000000e+00 2649.0
18 TraesCS3D01G011800 chr3B 90.343 1108 72 14 2164 3238 13937795 13936690 0.000000e+00 1421.0
19 TraesCS3D01G011800 chr3B 92.848 741 50 3 3 740 6392657 6393397 0.000000e+00 1072.0
20 TraesCS3D01G011800 chr3B 93.617 376 19 2 1812 2183 13939052 13938678 1.310000e-154 556.0
21 TraesCS3D01G011800 chr3B 88.814 447 25 5 3235 3656 6395997 6396443 3.680000e-145 525.0
22 TraesCS3D01G011800 chr3B 81.942 587 53 21 3254 3806 13936576 13936009 8.200000e-122 448.0
23 TraesCS3D01G011800 chr3B 97.863 234 5 0 988 1221 13939516 13939283 5.010000e-109 405.0
24 TraesCS3D01G011800 chr3B 94.089 203 10 1 1610 1810 13939283 13939081 1.450000e-79 307.0
25 TraesCS3D01G011800 chr3B 90.995 211 8 3 890 1100 6667864 6667665 1.470000e-69 274.0
26 TraesCS3D01G011800 chr3B 88.125 160 13 5 3811 3967 6665039 6664883 7.100000e-43 185.0
27 TraesCS3D01G011800 chr3B 84.422 199 12 7 3681 3870 6396502 6396690 1.190000e-40 178.0
28 TraesCS3D01G011800 chr3B 95.082 61 2 1 790 849 6667916 6667856 1.230000e-15 95.3
29 TraesCS3D01G011800 chr3B 77.444 133 13 6 3781 3912 6547012 6546896 3.470000e-06 63.9
30 TraesCS3D01G011800 chrUn 86.164 2544 244 52 747 3238 246339341 246341828 0.000000e+00 2649.0
31 TraesCS3D01G011800 chrUn 92.848 741 50 3 3 740 246338557 246339297 0.000000e+00 1072.0
32 TraesCS3D01G011800 chrUn 88.814 447 25 5 3235 3656 246341897 246342343 3.680000e-145 525.0
33 TraesCS3D01G011800 chrUn 76.427 543 113 11 2562 3095 222639002 222639538 3.170000e-71 279.0
34 TraesCS3D01G011800 chrUn 84.422 199 12 7 3681 3870 246342402 246342590 1.190000e-40 178.0
35 TraesCS3D01G011800 chrUn 77.444 133 13 6 3781 3912 35384044 35384160 3.470000e-06 63.9
36 TraesCS3D01G011800 chrUn 77.444 133 13 6 3781 3912 300614851 300614967 3.470000e-06 63.9
37 TraesCS3D01G011800 chr6A 89.249 1172 80 22 2728 3892 609887984 609889116 0.000000e+00 1424.0
38 TraesCS3D01G011800 chr6A 87.891 735 71 8 3 723 609885886 609886616 0.000000e+00 848.0
39 TraesCS3D01G011800 chr6A 93.788 499 31 0 2199 2697 609887489 609887987 0.000000e+00 750.0
40 TraesCS3D01G011800 chr6A 82.482 274 15 14 3913 4160 609889178 609889444 4.210000e-50 209.0
41 TraesCS3D01G011800 chr5D 77.778 981 197 12 2080 3048 464078547 464079518 5.990000e-163 584.0
42 TraesCS3D01G011800 chr5B 77.079 986 207 10 2076 3050 570935978 570936955 6.080000e-153 551.0
43 TraesCS3D01G011800 chr1B 77.444 133 28 2 1125 1256 9597342 9597473 1.240000e-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 TraesCS3D01G011800 chr3D 4166105 4170264 4159 True 7683.000 7683 100.00000 1 4160 1 chr3D.!!$R1 4159
1 TraesCS3D01G011800 chr3D 4074998 4078931 3933 False 913.380 1960 93.57420 3 3892 5 chr3D.!!$F1 3889
2 TraesCS3D01G011800 chr3A 9612252 9616379 4127 False 1523.700 5252 93.14300 3 4160 4 chr3A.!!$F1 4157
3 TraesCS3D01G011800 chr3A 9776851 9781347 4496 True 967.500 4124 91.95650 6 4160 6 chr3A.!!$R1 4154
4 TraesCS3D01G011800 chr3B 6392657 6396690 4033 False 1106.000 2649 88.06200 3 3870 4 chr3B.!!$F1 3867
5 TraesCS3D01G011800 chr3B 6664883 6667916 3033 True 981.825 3373 91.54275 790 3967 4 chr3B.!!$R2 3177
6 TraesCS3D01G011800 chr3B 13936009 13939516 3507 True 627.400 1421 91.57080 988 3806 5 chr3B.!!$R3 2818
7 TraesCS3D01G011800 chrUn 246338557 246342590 4033 False 1106.000 2649 88.06200 3 3870 4 chrUn.!!$F4 3867
8 TraesCS3D01G011800 chrUn 222639002 222639538 536 False 279.000 279 76.42700 2562 3095 1 chrUn.!!$F2 533
9 TraesCS3D01G011800 chr6A 609885886 609889444 3558 False 807.750 1424 88.35250 3 4160 4 chr6A.!!$F1 4157
10 TraesCS3D01G011800 chr5D 464078547 464079518 971 False 584.000 584 77.77800 2080 3048 1 chr5D.!!$F1 968
11 TraesCS3D01G011800 chr5B 570935978 570936955 977 False 551.000 551 77.07900 2076 3050 1 chr5B.!!$F1 974

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
239 240 0.464735 ACAGCGTACCAGGTTTGCAA 60.465 50.000 15.92 0.00 0.0 4.08 F
508 880 1.139853 GGAAATCGGATCTCTGTGCCT 59.860 52.381 0.00 0.00 0.0 4.75 F
1613 2118 0.106419 GGTCCGGGGCCAAATGATTA 60.106 55.000 14.16 0.00 0.0 1.75 F
2787 4384 0.040958 GCTTTGGCGCCATATCTTCG 60.041 55.000 33.25 14.25 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1530 2032 4.574013 GGCTCAACATTCTGAACCTGATAG 59.426 45.833 0.00 0.0 30.24 2.08 R
2132 2788 5.298527 ACCTTTGTTTTCCAGTACTTGTAGC 59.701 40.000 0.00 0.0 0.00 3.58 R
2931 4550 0.105039 GGATACCAACAGCCTCCGAG 59.895 60.000 0.00 0.0 0.00 4.63 R
3739 5804 0.034896 ATCTTGTCTGTCCGCGGTTT 59.965 50.000 27.15 0.0 0.00 3.27 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
44 45 3.979101 TGATATCATAATCTGCCGGCA 57.021 42.857 30.59 30.59 0.00 5.69
46 47 4.445453 TGATATCATAATCTGCCGGCATC 58.555 43.478 32.87 20.49 0.00 3.91
47 48 2.865119 ATCATAATCTGCCGGCATCA 57.135 45.000 32.87 20.65 0.00 3.07
239 240 0.464735 ACAGCGTACCAGGTTTGCAA 60.465 50.000 15.92 0.00 0.00 4.08
346 347 3.071874 TCTTCAAGCGGGATGACATTT 57.928 42.857 0.00 0.00 0.00 2.32
356 357 2.424812 GGGATGACATTTAGGCCACCAT 60.425 50.000 5.01 0.00 0.00 3.55
358 359 3.821033 GGATGACATTTAGGCCACCATAC 59.179 47.826 5.01 0.00 0.00 2.39
508 880 1.139853 GGAAATCGGATCTCTGTGCCT 59.860 52.381 0.00 0.00 0.00 4.75
523 898 1.968540 GCCTTCTTCGCTGCACCTT 60.969 57.895 0.00 0.00 0.00 3.50
633 1020 5.799681 ACAACCAAAGCTTCAAACATTTG 57.200 34.783 0.00 0.00 39.48 2.32
826 1279 3.892588 AGCCTATCTTCCTGTACACTAGC 59.107 47.826 0.00 0.00 0.00 3.42
971 1455 6.761099 TCTTAACTCTAGTACCAGCTTCTG 57.239 41.667 0.00 0.00 0.00 3.02
1530 2032 3.081061 TGTGTTGAGTACCATGCAATCC 58.919 45.455 0.00 0.00 0.00 3.01
1611 2116 2.278738 GGTCCGGGGCCAAATGAT 59.721 61.111 14.16 0.00 0.00 2.45
1612 2117 1.381191 GGTCCGGGGCCAAATGATT 60.381 57.895 14.16 0.00 0.00 2.57
1613 2118 0.106419 GGTCCGGGGCCAAATGATTA 60.106 55.000 14.16 0.00 0.00 1.75
2132 2788 5.063944 CGTTGTCTGTATTGATCTTCCTTGG 59.936 44.000 0.00 0.00 0.00 3.61
2314 3904 2.110213 GTGTGCTTCCCGGTGACA 59.890 61.111 0.00 0.00 0.00 3.58
2787 4384 0.040958 GCTTTGGCGCCATATCTTCG 60.041 55.000 33.25 14.25 0.00 3.79
2918 4537 0.610174 AATCAGCTGTCTCGGCAAGA 59.390 50.000 14.67 1.56 38.37 3.02
2920 4539 1.447489 CAGCTGTCTCGGCAAGAGG 60.447 63.158 5.25 0.00 46.82 3.69
2921 4540 1.910772 AGCTGTCTCGGCAAGAGGT 60.911 57.895 8.32 0.00 46.82 3.85
2922 4541 1.739562 GCTGTCTCGGCAAGAGGTG 60.740 63.158 8.32 1.81 46.82 4.00
2923 4542 1.079543 CTGTCTCGGCAAGAGGTGG 60.080 63.158 8.32 0.00 46.82 4.61
2924 4543 2.266055 GTCTCGGCAAGAGGTGGG 59.734 66.667 8.32 0.00 46.82 4.61
2925 4544 2.203788 TCTCGGCAAGAGGTGGGT 60.204 61.111 8.32 0.00 46.82 4.51
2926 4545 2.046892 CTCGGCAAGAGGTGGGTG 60.047 66.667 0.94 0.00 43.20 4.61
2927 4546 3.612247 CTCGGCAAGAGGTGGGTGG 62.612 68.421 0.94 0.00 43.20 4.61
2928 4547 4.722700 CGGCAAGAGGTGGGTGGG 62.723 72.222 0.00 0.00 0.00 4.61
2929 4548 3.256960 GGCAAGAGGTGGGTGGGA 61.257 66.667 0.00 0.00 0.00 4.37
2930 4549 2.616458 GGCAAGAGGTGGGTGGGAT 61.616 63.158 0.00 0.00 0.00 3.85
2931 4550 1.077429 GCAAGAGGTGGGTGGGATC 60.077 63.158 0.00 0.00 0.00 3.36
2932 4551 1.566298 GCAAGAGGTGGGTGGGATCT 61.566 60.000 0.00 0.00 0.00 2.75
2933 4552 0.543749 CAAGAGGTGGGTGGGATCTC 59.456 60.000 0.00 0.00 0.00 2.75
2934 4553 0.978146 AAGAGGTGGGTGGGATCTCG 60.978 60.000 0.00 0.00 0.00 4.04
2935 4554 2.365635 AGGTGGGTGGGATCTCGG 60.366 66.667 0.00 0.00 0.00 4.63
3012 4687 0.532573 TCCAGATGAAGCCAGACGAC 59.467 55.000 0.00 0.00 0.00 4.34
3167 4846 7.504403 AGTACATTCCCAGAGTGAAATATCTG 58.496 38.462 0.00 0.00 42.14 2.90
3171 4850 7.126421 ACATTCCCAGAGTGAAATATCTGTACT 59.874 37.037 0.00 0.00 41.13 2.73
3207 4886 6.071320 GGACCAAATTTTATCCTCTAGCCAT 58.929 40.000 9.40 0.00 0.00 4.40
3217 4896 1.117994 CTCTAGCCATCTCAGGTGCA 58.882 55.000 0.00 0.00 0.00 4.57
3287 5172 7.883391 TTCTTAATACGGAGAGAAGACATCT 57.117 36.000 0.00 0.00 42.61 2.90
3297 5182 6.423302 CGGAGAGAAGACATCTAAAATGATGG 59.577 42.308 8.96 0.00 45.78 3.51
3425 5345 7.157050 CATTCAGTTGAATATTTGAATGGCG 57.843 36.000 22.17 7.09 46.56 5.69
3543 5474 3.911260 AGGAAGAGATGGCATGATGATCT 59.089 43.478 3.81 0.00 0.00 2.75
3630 5603 5.236911 CCTGCAAAACATGTAAGTGCAAAAT 59.763 36.000 23.37 0.00 44.05 1.82
3631 5604 6.423302 CCTGCAAAACATGTAAGTGCAAAATA 59.577 34.615 23.37 8.11 44.05 1.40
3669 5692 5.930135 ACAGAAGTTAACTGACACTCCATT 58.070 37.500 9.34 0.00 38.55 3.16
3687 5719 7.437565 CACTCCATTGATTGTACACAGATAGAG 59.562 40.741 0.00 0.00 0.00 2.43
3692 5724 3.484953 TTGTACACAGATAGAGGGGGT 57.515 47.619 0.00 0.00 0.00 4.95
3700 5735 4.594920 CACAGATAGAGGGGGTTGTATCAT 59.405 45.833 0.00 0.00 0.00 2.45
3704 5739 6.013032 CAGATAGAGGGGGTTGTATCATCAAT 60.013 42.308 0.00 0.00 0.00 2.57
3744 5809 3.759618 TGGCTTTCCCATAACTAAAACCG 59.240 43.478 0.00 0.00 39.18 4.44
3745 5810 3.428452 GGCTTTCCCATAACTAAAACCGC 60.428 47.826 0.00 0.00 0.00 5.68
3746 5811 3.729762 GCTTTCCCATAACTAAAACCGCG 60.730 47.826 0.00 0.00 0.00 6.46
3747 5812 2.027003 TCCCATAACTAAAACCGCGG 57.973 50.000 26.86 26.86 0.00 6.46
3748 5813 1.554160 TCCCATAACTAAAACCGCGGA 59.446 47.619 35.90 8.44 0.00 5.54
3749 5814 1.667212 CCCATAACTAAAACCGCGGAC 59.333 52.381 35.90 0.00 0.00 4.79
3750 5815 2.348660 CCATAACTAAAACCGCGGACA 58.651 47.619 35.90 12.36 0.00 4.02
3751 5816 2.350498 CCATAACTAAAACCGCGGACAG 59.650 50.000 35.90 23.05 0.00 3.51
3752 5817 3.255725 CATAACTAAAACCGCGGACAGA 58.744 45.455 35.90 13.33 0.00 3.41
3753 5818 1.505425 AACTAAAACCGCGGACAGAC 58.495 50.000 35.90 0.00 0.00 3.51
3754 5819 0.390124 ACTAAAACCGCGGACAGACA 59.610 50.000 35.90 10.42 0.00 3.41
3755 5820 1.202557 ACTAAAACCGCGGACAGACAA 60.203 47.619 35.90 9.08 0.00 3.18
3756 5821 1.459592 CTAAAACCGCGGACAGACAAG 59.540 52.381 35.90 14.99 0.00 3.16
3757 5822 0.179067 AAAACCGCGGACAGACAAGA 60.179 50.000 35.90 0.00 0.00 3.02
3758 5823 0.034896 AAACCGCGGACAGACAAGAT 59.965 50.000 35.90 0.68 0.00 2.40
3814 5879 5.821470 CCATTCTTCTTATGCTCTGTGTCAT 59.179 40.000 0.00 0.00 0.00 3.06
3967 6167 7.083858 TCTGTTTCAAACAAAAGTTCAGACAG 58.916 34.615 4.13 0.00 41.61 3.51
3971 6171 5.013547 TCAAACAAAAGTTCAGACAGGGAA 58.986 37.500 0.00 0.00 0.00 3.97
3995 6195 5.016782 AGCAGGGAGGGATATATAGACAGAA 59.983 44.000 0.00 0.00 0.00 3.02
4001 6201 6.232581 AGGGATATATAGACAGAATGCTGC 57.767 41.667 0.00 0.00 46.26 5.25
4014 6214 2.428071 GCTGCGCTGTGCTGTTTC 60.428 61.111 18.99 1.97 46.63 2.78
4036 6236 7.426929 TTCTTGCTAGTTCAGAAAAGATCAC 57.573 36.000 0.00 0.00 31.97 3.06
4057 6270 1.526575 ATCTGCCCTGTTTGCGGTTG 61.527 55.000 0.00 0.00 36.47 3.77
4121 6345 1.069978 GGAGGGAGCAGCAGTATCTTC 59.930 57.143 0.00 0.00 0.00 2.87
4132 6356 0.179089 AGTATCTTCGCTGCTGCTGG 60.179 55.000 14.03 3.81 36.97 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.471609 TCAAATCTACTATGTTATTCACCGACA 58.528 33.333 0.00 0.00 0.00 4.35
1 2 8.867112 TCAAATCTACTATGTTATTCACCGAC 57.133 34.615 0.00 0.00 0.00 4.79
18 19 6.763135 GCCGGCAGATTATGATATCAAATCTA 59.237 38.462 24.80 9.88 37.76 1.98
37 38 2.102554 CGGTATTTTGATGCCGGCA 58.897 52.632 34.80 34.80 44.35 5.69
44 45 6.183360 ACAGTGGTTTCAAACGGTATTTTGAT 60.183 34.615 0.00 0.00 43.38 2.57
46 47 5.231147 CACAGTGGTTTCAAACGGTATTTTG 59.769 40.000 0.00 0.00 37.75 2.44
47 48 5.344884 CACAGTGGTTTCAAACGGTATTTT 58.655 37.500 0.00 0.00 0.00 1.82
239 240 3.306780 CCTGACAGTTACGGAGGTGAAAT 60.307 47.826 0.93 0.00 0.00 2.17
346 347 2.023791 TGACTACAGGTATGGTGGCCTA 60.024 50.000 3.32 0.00 33.07 3.93
356 357 4.562757 GGTCACTGCAATTGACTACAGGTA 60.563 45.833 21.54 0.00 42.63 3.08
358 359 2.744202 GGTCACTGCAATTGACTACAGG 59.256 50.000 21.54 2.02 42.63 4.00
460 461 3.451894 GCAACCAGCCCCCAATCG 61.452 66.667 0.00 0.00 37.23 3.34
508 880 1.159285 CATCAAGGTGCAGCGAAGAA 58.841 50.000 10.78 0.00 0.00 2.52
523 898 0.251634 TCCATAACTGCGCACCATCA 59.748 50.000 5.66 0.00 0.00 3.07
633 1020 5.707298 TCCTCCTCATCTTCATTTTTCACAC 59.293 40.000 0.00 0.00 0.00 3.82
826 1279 6.317789 TGATTGCTGGTTTTCTTAGTCAAG 57.682 37.500 0.00 0.00 0.00 3.02
971 1455 0.107312 ACAGATGCAGGATCAGGCAC 60.107 55.000 12.07 7.28 43.75 5.01
1369 1871 9.722184 CAGGAACATGTAATCTGATCTCAATAT 57.278 33.333 14.22 0.00 0.00 1.28
1370 1872 8.708378 ACAGGAACATGTAATCTGATCTCAATA 58.292 33.333 21.90 0.00 0.00 1.90
1530 2032 4.574013 GGCTCAACATTCTGAACCTGATAG 59.426 45.833 0.00 0.00 30.24 2.08
2020 2574 8.888579 ACATGTATAAAGTTATGGAGCTGTAC 57.111 34.615 0.00 0.00 0.00 2.90
2132 2788 5.298527 ACCTTTGTTTTCCAGTACTTGTAGC 59.701 40.000 0.00 0.00 0.00 3.58
2787 4384 5.988561 CCCAAAGCTATAGACATCAGACTTC 59.011 44.000 3.21 0.00 0.00 3.01
2918 4537 2.365635 CCGAGATCCCACCCACCT 60.366 66.667 0.00 0.00 0.00 4.00
2919 4538 2.365105 TCCGAGATCCCACCCACC 60.365 66.667 0.00 0.00 0.00 4.61
2920 4539 2.435693 CCTCCGAGATCCCACCCAC 61.436 68.421 0.00 0.00 0.00 4.61
2921 4540 2.041922 CCTCCGAGATCCCACCCA 60.042 66.667 0.00 0.00 0.00 4.51
2922 4541 3.551407 GCCTCCGAGATCCCACCC 61.551 72.222 0.00 0.00 0.00 4.61
2923 4542 2.444895 AGCCTCCGAGATCCCACC 60.445 66.667 0.00 0.00 0.00 4.61
2924 4543 1.617947 AACAGCCTCCGAGATCCCAC 61.618 60.000 0.00 0.00 0.00 4.61
2925 4544 1.306141 AACAGCCTCCGAGATCCCA 60.306 57.895 0.00 0.00 0.00 4.37
2926 4545 1.144936 CAACAGCCTCCGAGATCCC 59.855 63.158 0.00 0.00 0.00 3.85
2927 4546 1.144936 CCAACAGCCTCCGAGATCC 59.855 63.158 0.00 0.00 0.00 3.36
2928 4547 1.112113 TACCAACAGCCTCCGAGATC 58.888 55.000 0.00 0.00 0.00 2.75
2929 4548 1.689273 GATACCAACAGCCTCCGAGAT 59.311 52.381 0.00 0.00 0.00 2.75
2930 4549 1.112113 GATACCAACAGCCTCCGAGA 58.888 55.000 0.00 0.00 0.00 4.04
2931 4550 0.105039 GGATACCAACAGCCTCCGAG 59.895 60.000 0.00 0.00 0.00 4.63
2932 4551 0.616395 TGGATACCAACAGCCTCCGA 60.616 55.000 0.00 0.00 0.00 4.55
2933 4552 0.469917 ATGGATACCAACAGCCTCCG 59.530 55.000 0.00 0.00 36.95 4.63
2934 4553 1.490490 TGATGGATACCAACAGCCTCC 59.510 52.381 0.00 0.00 36.95 4.30
2935 4554 2.843701 CTGATGGATACCAACAGCCTC 58.156 52.381 13.37 0.00 44.88 4.70
3164 4843 7.255906 TTTGGTCCAAAACTACGATAGTACAGA 60.256 37.037 14.89 0.00 39.47 3.41
3167 4846 7.838771 ATTTGGTCCAAAACTACGATAGTAC 57.161 36.000 20.76 0.00 41.92 2.73
3217 4896 5.563475 GCACACAAATATTGACTTGCTGAGT 60.563 40.000 0.00 0.00 42.70 3.41
3274 5159 7.254727 GCACCATCATTTTAGATGTCTTCTCTC 60.255 40.741 0.00 0.00 43.00 3.20
3287 5172 9.499479 ACATTTACAATTTGCACCATCATTTTA 57.501 25.926 0.00 0.00 0.00 1.52
3297 5182 5.177327 CCAGGTTCACATTTACAATTTGCAC 59.823 40.000 0.00 0.00 0.00 4.57
3534 5465 0.552848 AACCCCGGCAAGATCATCAT 59.447 50.000 0.00 0.00 0.00 2.45
3543 5474 0.923358 AGGATATGAAACCCCGGCAA 59.077 50.000 0.00 0.00 0.00 4.52
3631 5604 9.683069 GTTAACTTCTGTTGTGAAATGATGAAT 57.317 29.630 0.00 0.00 37.59 2.57
3669 5692 3.967326 CCCCCTCTATCTGTGTACAATCA 59.033 47.826 0.00 0.00 0.00 2.57
3687 5719 4.762251 GCTCTTATTGATGATACAACCCCC 59.238 45.833 0.00 0.00 32.50 5.40
3692 5724 7.345691 TCCTTTGGCTCTTATTGATGATACAA 58.654 34.615 0.00 0.00 0.00 2.41
3700 5735 3.846588 ACCTCTCCTTTGGCTCTTATTGA 59.153 43.478 0.00 0.00 0.00 2.57
3704 5739 1.909302 CCACCTCTCCTTTGGCTCTTA 59.091 52.381 0.00 0.00 0.00 2.10
3734 5799 1.202557 TGTCTGTCCGCGGTTTTAGTT 60.203 47.619 27.15 0.00 0.00 2.24
3735 5800 0.390124 TGTCTGTCCGCGGTTTTAGT 59.610 50.000 27.15 0.00 0.00 2.24
3736 5801 1.459592 CTTGTCTGTCCGCGGTTTTAG 59.540 52.381 27.15 18.11 0.00 1.85
3737 5802 1.068895 TCTTGTCTGTCCGCGGTTTTA 59.931 47.619 27.15 1.49 0.00 1.52
3738 5803 0.179067 TCTTGTCTGTCCGCGGTTTT 60.179 50.000 27.15 0.00 0.00 2.43
3739 5804 0.034896 ATCTTGTCTGTCCGCGGTTT 59.965 50.000 27.15 0.00 0.00 3.27
3740 5805 0.034896 AATCTTGTCTGTCCGCGGTT 59.965 50.000 27.15 4.55 0.00 4.44
3741 5806 0.670546 CAATCTTGTCTGTCCGCGGT 60.671 55.000 27.15 0.00 0.00 5.68
3742 5807 1.970917 GCAATCTTGTCTGTCCGCGG 61.971 60.000 22.12 22.12 0.00 6.46
3743 5808 1.016130 AGCAATCTTGTCTGTCCGCG 61.016 55.000 0.00 0.00 0.00 6.46
3744 5809 0.445436 CAGCAATCTTGTCTGTCCGC 59.555 55.000 0.00 0.00 31.91 5.54
3745 5810 0.445436 GCAGCAATCTTGTCTGTCCG 59.555 55.000 12.59 0.00 35.88 4.79
3746 5811 1.527034 TGCAGCAATCTTGTCTGTCC 58.473 50.000 0.00 2.86 35.88 4.02
3747 5812 3.844577 ATTGCAGCAATCTTGTCTGTC 57.155 42.857 15.33 8.02 35.88 3.51
3748 5813 4.304110 CAAATTGCAGCAATCTTGTCTGT 58.696 39.130 21.10 0.00 35.88 3.41
3749 5814 3.678072 CCAAATTGCAGCAATCTTGTCTG 59.322 43.478 21.10 10.96 32.43 3.51
3750 5815 3.575256 TCCAAATTGCAGCAATCTTGTCT 59.425 39.130 21.10 1.30 32.43 3.41
3751 5816 3.916761 TCCAAATTGCAGCAATCTTGTC 58.083 40.909 21.10 0.00 32.43 3.18
3752 5817 3.306502 CCTCCAAATTGCAGCAATCTTGT 60.307 43.478 21.10 2.48 32.43 3.16
3753 5818 3.259064 CCTCCAAATTGCAGCAATCTTG 58.741 45.455 21.10 22.30 32.43 3.02
3754 5819 2.901839 ACCTCCAAATTGCAGCAATCTT 59.098 40.909 21.10 13.83 32.43 2.40
3755 5820 2.532843 ACCTCCAAATTGCAGCAATCT 58.467 42.857 21.10 4.30 32.43 2.40
3756 5821 3.323751 AACCTCCAAATTGCAGCAATC 57.676 42.857 21.10 0.00 32.43 2.67
3757 5822 3.834231 AGTAACCTCCAAATTGCAGCAAT 59.166 39.130 15.33 15.33 35.39 3.56
3758 5823 3.005684 CAGTAACCTCCAAATTGCAGCAA 59.994 43.478 11.07 11.07 0.00 3.91
3814 5879 9.137459 TGAATAACAAACAGAGATTTGGGTTTA 57.863 29.630 3.52 0.00 42.74 2.01
3967 6167 2.344093 TATATCCCTCCCTGCTTCCC 57.656 55.000 0.00 0.00 0.00 3.97
3971 6171 4.546195 TCTGTCTATATATCCCTCCCTGCT 59.454 45.833 0.00 0.00 0.00 4.24
4001 6201 0.867746 TAGCAAGAAACAGCACAGCG 59.132 50.000 0.00 0.00 0.00 5.18
4014 6214 6.791887 TGTGATCTTTTCTGAACTAGCAAG 57.208 37.500 0.00 0.00 0.00 4.01
4036 6236 1.213537 CCGCAAACAGGGCAGATTG 59.786 57.895 0.00 0.00 0.00 2.67
4127 6351 1.453562 TGAAACAGCAGCACCAGCA 60.454 52.632 0.00 0.00 45.49 4.41
4132 6356 2.849880 TGAAAGTGAAACAGCAGCAC 57.150 45.000 0.00 0.00 41.43 4.40


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

AutoCloner maintained by Alex Coulton.