Multiple sequence alignment - TraesCS2B01G101000

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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 TraesCS2B01G101000 chr2B 100.000 2816 0 0 1 2816 61469467 61466652 0.000000e+00 5201.0
1 TraesCS2B01G101000 chr2A 92.159 2283 147 11 1 2281 233956112 233958364 0.000000e+00 3195.0
2 TraesCS2B01G101000 chr2A 90.294 1257 92 12 1492 2738 233958368 233959604 0.000000e+00 1618.0
3 TraesCS2B01G101000 chr2A 86.721 1235 132 18 463 1684 713921581 713920366 0.000000e+00 1343.0
4 TraesCS2B01G101000 chr2A 85.874 446 57 6 1 444 713921993 713921552 1.180000e-128 470.0
5 TraesCS2B01G101000 chr2A 88.024 167 18 2 2573 2738 233942524 233942359 2.210000e-46 196.0
6 TraesCS2B01G101000 chrUn 89.763 2276 119 36 489 2738 79946865 79949052 0.000000e+00 2808.0
7 TraesCS2B01G101000 chrUn 91.485 1515 77 23 319 1803 79946670 79948162 0.000000e+00 2036.0
8 TraesCS2B01G101000 chr5A 91.210 967 78 2 1006 1972 519654567 519655526 0.000000e+00 1308.0
9 TraesCS2B01G101000 chr5A 90.772 596 39 5 1 592 519640842 519641425 0.000000e+00 782.0
10 TraesCS2B01G101000 chr5A 86.154 650 65 13 2106 2740 519655529 519656168 0.000000e+00 678.0
11 TraesCS2B01G101000 chr5A 88.406 276 23 4 743 1015 519645146 519645415 9.730000e-85 324.0
12 TraesCS2B01G101000 chr5A 88.024 167 18 2 2573 2738 519564693 519564528 2.210000e-46 196.0
13 TraesCS2B01G101000 chr5A 95.763 118 5 0 630 747 519644697 519644814 1.030000e-44 191.0
14 TraesCS2B01G101000 chr5A 97.727 44 1 0 588 631 519643087 519643130 3.010000e-10 76.8
15 TraesCS2B01G101000 chr1B 82.712 1099 135 25 1005 2087 395241812 395240753 0.000000e+00 926.0
16 TraesCS2B01G101000 chr7B 82.455 1100 138 25 1005 2087 501595896 501594835 0.000000e+00 911.0
17 TraesCS2B01G101000 chr4B 81.495 1097 131 31 1005 2087 168717408 168716370 0.000000e+00 835.0
18 TraesCS2B01G101000 chr2D 77.715 534 64 22 1569 2087 640719530 640720023 2.760000e-70 276.0


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 TraesCS2B01G101000 chr2B 61466652 61469467 2815 True 5201.00 5201 100.0000 1 2816 1 chr2B.!!$R1 2815
1 TraesCS2B01G101000 chr2A 233956112 233959604 3492 False 2406.50 3195 91.2265 1 2738 2 chr2A.!!$F1 2737
2 TraesCS2B01G101000 chr2A 713920366 713921993 1627 True 906.50 1343 86.2975 1 1684 2 chr2A.!!$R2 1683
3 TraesCS2B01G101000 chrUn 79946670 79949052 2382 False 2422.00 2808 90.6240 319 2738 2 chrUn.!!$F1 2419
4 TraesCS2B01G101000 chr5A 519654567 519656168 1601 False 993.00 1308 88.6820 1006 2740 2 chr5A.!!$F2 1734
5 TraesCS2B01G101000 chr5A 519640842 519645415 4573 False 343.45 782 93.1670 1 1015 4 chr5A.!!$F1 1014
6 TraesCS2B01G101000 chr1B 395240753 395241812 1059 True 926.00 926 82.7120 1005 2087 1 chr1B.!!$R1 1082
7 TraesCS2B01G101000 chr7B 501594835 501595896 1061 True 911.00 911 82.4550 1005 2087 1 chr7B.!!$R1 1082
8 TraesCS2B01G101000 chr4B 168716370 168717408 1038 True 835.00 835 81.4950 1005 2087 1 chr4B.!!$R1 1082

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
844 4448 0.106918 TGCAAAAAGTGGGTCGGAGT 60.107 50.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2784 7295 0.029267 AGGCCCCTCCTCTCATCAAT 60.029 55.0 0.0 0.0 43.2 2.57 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
109 110 1.830477 TGCAGTGCAAAAGGTTTTCCT 59.170 42.857 17.26 0.00 44.21 3.36
173 174 3.608316 TTCCACAAATTGCATAAGGGC 57.392 42.857 0.00 0.00 0.00 5.19
177 178 2.423185 CACAAATTGCATAAGGGCGAGA 59.577 45.455 0.00 0.00 36.28 4.04
201 202 4.219288 AGTTGAAGAATGATCTTTGGGCAC 59.781 41.667 0.00 0.00 45.91 5.01
246 247 7.671398 AGATTGAATACCAGAAAAACATGGACT 59.329 33.333 0.00 0.00 39.02 3.85
350 353 5.431731 ACCCATTCCCAAAGTGTGATATCTA 59.568 40.000 3.98 0.00 0.00 1.98
398 405 4.322057 ACAGGTTAGCTTCCAATCCATT 57.678 40.909 9.72 0.00 0.00 3.16
503 510 1.167851 AAACCATGCCATGACACTCG 58.832 50.000 6.18 0.00 0.00 4.18
548 581 7.425606 AGTACTTCAAAAACATTCCATGACAC 58.574 34.615 0.00 0.00 0.00 3.67
563 596 3.433306 TGACACCCCACTCTTAATTGG 57.567 47.619 0.00 0.00 0.00 3.16
677 3944 4.414337 AGAATCAGATAAGTGGACTGGC 57.586 45.455 0.00 0.00 33.19 4.85
749 4352 4.337555 GCTGCTCATTGTATGGTTCAAGAT 59.662 41.667 0.00 0.00 0.00 2.40
771 4374 2.303311 GCTGGTAGAGGAGTTTTCCAGT 59.697 50.000 10.08 0.00 46.64 4.00
838 4442 3.642848 AGATGTGAATGCAAAAAGTGGGT 59.357 39.130 0.00 0.00 0.00 4.51
840 4444 2.223688 TGTGAATGCAAAAAGTGGGTCG 60.224 45.455 0.00 0.00 0.00 4.79
841 4445 1.339610 TGAATGCAAAAAGTGGGTCGG 59.660 47.619 0.00 0.00 0.00 4.79
842 4446 1.611491 GAATGCAAAAAGTGGGTCGGA 59.389 47.619 0.00 0.00 0.00 4.55
843 4447 1.247567 ATGCAAAAAGTGGGTCGGAG 58.752 50.000 0.00 0.00 0.00 4.63
844 4448 0.106918 TGCAAAAAGTGGGTCGGAGT 60.107 50.000 0.00 0.00 0.00 3.85
846 4450 1.407618 GCAAAAAGTGGGTCGGAGTTT 59.592 47.619 0.00 0.00 0.00 2.66
847 4451 2.159156 GCAAAAAGTGGGTCGGAGTTTT 60.159 45.455 0.00 0.00 0.00 2.43
848 4452 3.702330 CAAAAAGTGGGTCGGAGTTTTC 58.298 45.455 0.00 0.00 0.00 2.29
881 4487 3.625764 GCCATCATTCCGTAGCTTGTTTA 59.374 43.478 0.00 0.00 0.00 2.01
996 4602 3.126453 AGGGACAAAGCTAGATGGGAAT 58.874 45.455 0.00 0.00 0.00 3.01
1017 4623 9.073475 GGGAATAAAATGTATGGCACTATTGTA 57.927 33.333 0.00 0.00 0.00 2.41
1116 4722 2.009774 CATGGAGGGTTGAAGCTTACG 58.990 52.381 0.00 0.00 0.00 3.18
1185 4791 7.067496 TCATAACAAAAAGGGCCATTACAAA 57.933 32.000 1.49 0.00 0.00 2.83
1188 4794 4.447290 ACAAAAAGGGCCATTACAAACAC 58.553 39.130 1.49 0.00 0.00 3.32
1199 4805 5.382303 CCATTACAAACACGAGAATGTCAC 58.618 41.667 0.00 0.00 30.55 3.67
1213 4819 6.073058 CGAGAATGTCACTCCAAATGAAGAAA 60.073 38.462 0.00 0.00 0.00 2.52
1392 5009 3.330267 CAACTCAAACTCCTGGCTCTAC 58.670 50.000 0.00 0.00 0.00 2.59
1414 5031 5.957798 ACGATTTTCATGATGCAAGAACAT 58.042 33.333 0.00 0.00 0.00 2.71
1600 6007 2.074576 CATCTGCCAGAGTGACAACAG 58.925 52.381 0.00 0.00 0.00 3.16
1601 6008 0.250038 TCTGCCAGAGTGACAACAGC 60.250 55.000 0.00 0.00 0.00 4.40
1602 6009 0.250209 CTGCCAGAGTGACAACAGCT 60.250 55.000 0.00 0.00 0.00 4.24
1603 6010 1.001293 CTGCCAGAGTGACAACAGCTA 59.999 52.381 0.00 0.00 0.00 3.32
1604 6011 1.416030 TGCCAGAGTGACAACAGCTAA 59.584 47.619 0.00 0.00 0.00 3.09
1605 6012 1.801178 GCCAGAGTGACAACAGCTAAC 59.199 52.381 0.00 0.00 0.00 2.34
1606 6013 2.806745 GCCAGAGTGACAACAGCTAACA 60.807 50.000 0.00 0.00 0.00 2.41
1688 6102 4.106925 GAGGAGGGGCTGGTGCTG 62.107 72.222 0.00 0.00 39.59 4.41
1696 6110 4.025858 GCTGGTGCTGGCAGAGGA 62.026 66.667 20.86 0.00 36.03 3.71
1697 6111 2.752358 CTGGTGCTGGCAGAGGAA 59.248 61.111 20.86 0.00 0.00 3.36
1698 6112 1.673665 CTGGTGCTGGCAGAGGAAC 60.674 63.158 20.86 9.91 0.00 3.62
1699 6113 2.401699 CTGGTGCTGGCAGAGGAACA 62.402 60.000 20.86 8.90 37.39 3.18
1700 6114 1.228245 GGTGCTGGCAGAGGAACAA 60.228 57.895 20.86 0.00 27.77 2.83
1701 6115 1.239968 GGTGCTGGCAGAGGAACAAG 61.240 60.000 20.86 0.00 27.77 3.16
1702 6116 0.250467 GTGCTGGCAGAGGAACAAGA 60.250 55.000 20.86 0.00 0.00 3.02
1703 6117 0.035881 TGCTGGCAGAGGAACAAGAG 59.964 55.000 20.86 0.00 0.00 2.85
1704 6118 0.676151 GCTGGCAGAGGAACAAGAGG 60.676 60.000 20.86 0.00 0.00 3.69
1705 6119 0.979665 CTGGCAGAGGAACAAGAGGA 59.020 55.000 9.42 0.00 0.00 3.71
1706 6120 0.979665 TGGCAGAGGAACAAGAGGAG 59.020 55.000 0.00 0.00 0.00 3.69
1707 6121 0.251634 GGCAGAGGAACAAGAGGAGG 59.748 60.000 0.00 0.00 0.00 4.30
1708 6122 0.251634 GCAGAGGAACAAGAGGAGGG 59.748 60.000 0.00 0.00 0.00 4.30
1709 6123 1.650528 CAGAGGAACAAGAGGAGGGT 58.349 55.000 0.00 0.00 0.00 4.34
1710 6124 1.552792 CAGAGGAACAAGAGGAGGGTC 59.447 57.143 0.00 0.00 0.00 4.46
1711 6125 1.435168 AGAGGAACAAGAGGAGGGTCT 59.565 52.381 0.00 0.00 0.00 3.85
1712 6126 1.552792 GAGGAACAAGAGGAGGGTCTG 59.447 57.143 0.00 0.00 0.00 3.51
1713 6127 0.615850 GGAACAAGAGGAGGGTCTGG 59.384 60.000 0.00 0.00 0.00 3.86
1714 6128 1.353091 GAACAAGAGGAGGGTCTGGT 58.647 55.000 0.00 0.00 31.45 4.00
1715 6129 1.002544 GAACAAGAGGAGGGTCTGGTG 59.997 57.143 0.00 0.00 30.54 4.17
1716 6130 1.298014 CAAGAGGAGGGTCTGGTGC 59.702 63.158 0.00 0.00 0.00 5.01
1717 6131 1.159664 AAGAGGAGGGTCTGGTGCT 59.840 57.895 0.00 0.00 0.00 4.40
1741 6185 2.239654 CAGAGGAACAATAAGAGGGGCA 59.760 50.000 0.00 0.00 0.00 5.36
1760 6204 0.196118 AGGGAGGGGAACAAGAGGAA 59.804 55.000 0.00 0.00 0.00 3.36
1765 6209 0.609406 GGGGAACAAGAGGAAGTGCC 60.609 60.000 0.00 0.00 32.25 5.01
1799 6249 2.169832 TGCAACTGCTACAAGAGGAC 57.830 50.000 2.95 0.00 42.66 3.85
1811 6261 4.961438 ACAAGAGGACCAAATGCAAATT 57.039 36.364 0.00 0.00 0.00 1.82
1824 6307 6.376581 CCAAATGCAAATTCTAGAAGAGGAGT 59.623 38.462 11.53 1.21 0.00 3.85
1862 6345 2.571653 ACAAGAGCAGGTGCCACTAATA 59.428 45.455 0.00 0.00 43.38 0.98
1870 6353 3.322254 CAGGTGCCACTAATACTAGAGGG 59.678 52.174 0.00 0.00 36.63 4.30
1883 6366 1.200760 TAGAGGGGCAAGAGCAGCAA 61.201 55.000 0.00 0.00 44.61 3.91
1890 6373 0.888285 GCAAGAGCAGCAACTCCTGT 60.888 55.000 0.00 0.00 41.58 4.00
1928 6412 6.547141 CCTTTTTGGAGATGACATGGCTAATA 59.453 38.462 0.00 0.00 38.35 0.98
2120 6605 6.184789 TGTAATACATTTCTGAACCTTCCCC 58.815 40.000 0.00 0.00 0.00 4.81
2141 6626 3.632145 CCTTTGTGCTACTGAACCTTGTT 59.368 43.478 0.00 0.00 0.00 2.83
2211 6707 6.301486 TGCTATGTATGATGCAATCTTCCTT 58.699 36.000 0.00 0.00 45.81 3.36
2338 6839 1.209261 TGTTCTTCTGGCAGTGTGACA 59.791 47.619 15.27 12.45 32.24 3.58
2362 6863 7.117812 ACACACTATATGTAGTTCTGCAACAAC 59.882 37.037 0.00 0.69 40.64 3.32
2392 6895 5.777732 ACTGATGTAAAATTTGGTTGGCCTA 59.222 36.000 3.32 0.00 35.27 3.93
2415 6918 2.374170 GGTTTGAACCCAAGACCTAGGA 59.626 50.000 17.98 0.00 43.43 2.94
2461 6964 4.026744 AGTGAGCTAGCACCAGATTTCTA 58.973 43.478 18.83 0.00 39.59 2.10
2466 6969 7.659390 GTGAGCTAGCACCAGATTTCTAATATT 59.341 37.037 18.83 0.00 32.68 1.28
2500 7005 4.440826 AGCTACTAGTAGAAGCCTGCTA 57.559 45.455 30.09 0.00 36.70 3.49
2525 7030 0.167251 CCGCCGTTTCACGCTTTTAT 59.833 50.000 0.00 0.00 40.91 1.40
2545 7050 3.844577 TCCTGCGACTAGTACAAAGTC 57.155 47.619 15.07 15.07 40.01 3.01
2654 7164 2.284401 CGTGCTCGCAAAAACAAGTTTG 60.284 45.455 0.00 0.00 40.72 2.93
2655 7165 2.920490 GTGCTCGCAAAAACAAGTTTGA 59.080 40.909 0.00 0.00 40.29 2.69
2719 7230 6.828273 TGCACATCCTAAGCAACTTTATGTAT 59.172 34.615 0.00 0.00 34.97 2.29
2724 7235 7.195374 TCCTAAGCAACTTTATGTATCACCT 57.805 36.000 0.00 0.00 0.00 4.00
2725 7236 8.313944 TCCTAAGCAACTTTATGTATCACCTA 57.686 34.615 0.00 0.00 0.00 3.08
2740 7251 6.936335 TGTATCACCTATGCATTTACCTCATG 59.064 38.462 3.54 0.00 0.00 3.07
2741 7252 5.372343 TCACCTATGCATTTACCTCATGT 57.628 39.130 3.54 0.00 0.00 3.21
2742 7253 6.493189 TCACCTATGCATTTACCTCATGTA 57.507 37.500 3.54 0.00 0.00 2.29
2743 7254 6.524734 TCACCTATGCATTTACCTCATGTAG 58.475 40.000 3.54 0.00 0.00 2.74
2760 7271 8.209917 CTCATGTAGGTTTATGAGGGTTTTAC 57.790 38.462 0.00 0.00 44.06 2.01
2761 7272 7.691213 TCATGTAGGTTTATGAGGGTTTTACA 58.309 34.615 0.00 0.00 0.00 2.41
2762 7273 7.827236 TCATGTAGGTTTATGAGGGTTTTACAG 59.173 37.037 0.00 0.00 0.00 2.74
2763 7274 6.478129 TGTAGGTTTATGAGGGTTTTACAGG 58.522 40.000 0.00 0.00 0.00 4.00
2764 7275 4.341487 AGGTTTATGAGGGTTTTACAGGC 58.659 43.478 0.00 0.00 0.00 4.85
2765 7276 4.083565 GGTTTATGAGGGTTTTACAGGCA 58.916 43.478 0.00 0.00 0.00 4.75
2766 7277 4.157840 GGTTTATGAGGGTTTTACAGGCAG 59.842 45.833 0.00 0.00 0.00 4.85
2767 7278 2.514458 ATGAGGGTTTTACAGGCAGG 57.486 50.000 0.00 0.00 0.00 4.85
2768 7279 1.145571 TGAGGGTTTTACAGGCAGGT 58.854 50.000 0.00 0.00 0.00 4.00
2769 7280 1.202879 TGAGGGTTTTACAGGCAGGTG 60.203 52.381 0.00 0.00 0.00 4.00
2770 7281 1.073284 GAGGGTTTTACAGGCAGGTGA 59.927 52.381 0.00 0.00 0.00 4.02
2771 7282 1.497286 AGGGTTTTACAGGCAGGTGAA 59.503 47.619 0.00 0.00 0.00 3.18
2772 7283 2.110011 AGGGTTTTACAGGCAGGTGAAT 59.890 45.455 0.00 0.00 0.00 2.57
2773 7284 2.897326 GGGTTTTACAGGCAGGTGAATT 59.103 45.455 0.00 0.00 0.00 2.17
2774 7285 3.323691 GGGTTTTACAGGCAGGTGAATTT 59.676 43.478 0.00 0.00 0.00 1.82
2775 7286 4.202315 GGGTTTTACAGGCAGGTGAATTTT 60.202 41.667 0.00 0.00 0.00 1.82
2776 7287 4.749598 GGTTTTACAGGCAGGTGAATTTTG 59.250 41.667 0.00 0.00 0.00 2.44
2777 7288 5.452636 GGTTTTACAGGCAGGTGAATTTTGA 60.453 40.000 0.00 0.00 0.00 2.69
2778 7289 6.223120 GTTTTACAGGCAGGTGAATTTTGAT 58.777 36.000 0.00 0.00 0.00 2.57
2779 7290 6.418057 TTTACAGGCAGGTGAATTTTGATT 57.582 33.333 0.00 0.00 0.00 2.57
2780 7291 4.261578 ACAGGCAGGTGAATTTTGATTG 57.738 40.909 0.00 0.00 0.00 2.67
2781 7292 3.896888 ACAGGCAGGTGAATTTTGATTGA 59.103 39.130 0.00 0.00 0.00 2.57
2782 7293 4.344679 ACAGGCAGGTGAATTTTGATTGAA 59.655 37.500 0.00 0.00 0.00 2.69
2783 7294 4.927425 CAGGCAGGTGAATTTTGATTGAAG 59.073 41.667 0.00 0.00 0.00 3.02
2784 7295 4.834496 AGGCAGGTGAATTTTGATTGAAGA 59.166 37.500 0.00 0.00 0.00 2.87
2785 7296 5.482878 AGGCAGGTGAATTTTGATTGAAGAT 59.517 36.000 0.00 0.00 0.00 2.40
2786 7297 6.013984 AGGCAGGTGAATTTTGATTGAAGATT 60.014 34.615 0.00 0.00 0.00 2.40
2787 7298 6.091713 GGCAGGTGAATTTTGATTGAAGATTG 59.908 38.462 0.00 0.00 0.00 2.67
2788 7299 6.869913 GCAGGTGAATTTTGATTGAAGATTGA 59.130 34.615 0.00 0.00 0.00 2.57
2789 7300 7.548075 GCAGGTGAATTTTGATTGAAGATTGAT 59.452 33.333 0.00 0.00 0.00 2.57
2790 7301 8.869897 CAGGTGAATTTTGATTGAAGATTGATG 58.130 33.333 0.00 0.00 0.00 3.07
2791 7302 8.809066 AGGTGAATTTTGATTGAAGATTGATGA 58.191 29.630 0.00 0.00 0.00 2.92
2792 7303 9.084164 GGTGAATTTTGATTGAAGATTGATGAG 57.916 33.333 0.00 0.00 0.00 2.90
2793 7304 9.850628 GTGAATTTTGATTGAAGATTGATGAGA 57.149 29.630 0.00 0.00 0.00 3.27
2795 7306 9.517609 GAATTTTGATTGAAGATTGATGAGAGG 57.482 33.333 0.00 0.00 0.00 3.69
2796 7307 8.818622 ATTTTGATTGAAGATTGATGAGAGGA 57.181 30.769 0.00 0.00 0.00 3.71
2797 7308 7.860918 TTTGATTGAAGATTGATGAGAGGAG 57.139 36.000 0.00 0.00 0.00 3.69
2798 7309 5.926663 TGATTGAAGATTGATGAGAGGAGG 58.073 41.667 0.00 0.00 0.00 4.30
2799 7310 4.767578 TTGAAGATTGATGAGAGGAGGG 57.232 45.455 0.00 0.00 0.00 4.30
2800 7311 3.044156 TGAAGATTGATGAGAGGAGGGG 58.956 50.000 0.00 0.00 0.00 4.79
2801 7312 1.433121 AGATTGATGAGAGGAGGGGC 58.567 55.000 0.00 0.00 0.00 5.80
2802 7313 0.399833 GATTGATGAGAGGAGGGGCC 59.600 60.000 0.00 0.00 0.00 5.80
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
150 151 5.669477 GCCCTTATGCAATTTGTGGAAATA 58.331 37.500 0.00 0.00 31.18 1.40
173 174 6.402983 CCCAAAGATCATTCTTCAACTTCTCG 60.403 42.308 0.00 0.00 41.42 4.04
177 178 4.834496 TGCCCAAAGATCATTCTTCAACTT 59.166 37.500 0.00 0.00 41.42 2.66
201 202 5.578005 ATCTCATTTGTGGATCTTGCAAG 57.422 39.130 20.81 20.81 0.00 4.01
246 247 2.301870 CCTGACTGTGTGCCCTTAACTA 59.698 50.000 0.00 0.00 0.00 2.24
535 568 1.004745 GAGTGGGGTGTCATGGAATGT 59.995 52.381 0.00 0.00 46.80 2.71
563 596 8.371699 AGTTCTCTTGCCTCCAATATATAACTC 58.628 37.037 0.00 0.00 0.00 3.01
677 3944 1.280133 TGGATCTTTGGGCAGAGTCTG 59.720 52.381 16.21 16.21 34.12 3.51
749 4352 2.303022 CTGGAAAACTCCTCTACCAGCA 59.697 50.000 0.00 0.00 38.40 4.41
771 4374 9.258826 CAAATAAATGTTGTTGAAGGATGTCAA 57.741 29.630 0.00 0.00 35.14 3.18
818 4421 3.552684 CGACCCACTTTTTGCATTCACAT 60.553 43.478 0.00 0.00 0.00 3.21
838 4442 1.078708 GGGATGCCGAAAACTCCGA 60.079 57.895 0.00 0.00 0.00 4.55
840 4444 0.740737 CATGGGATGCCGAAAACTCC 59.259 55.000 0.00 0.00 0.00 3.85
881 4487 7.587037 TTCTGGTTCAATTCTTTCATGTCTT 57.413 32.000 0.00 0.00 0.00 3.01
1017 4623 5.801380 ACTTTCGTGTACAAAGGTGGATAT 58.199 37.500 9.90 0.00 35.49 1.63
1116 4722 3.194116 AGTGCATTGTGGATCCATGTTTC 59.806 43.478 19.62 4.90 0.00 2.78
1158 4764 6.667414 TGTAATGGCCCTTTTTGTTATGATCT 59.333 34.615 0.00 0.00 0.00 2.75
1185 4791 3.469008 TTTGGAGTGACATTCTCGTGT 57.531 42.857 0.00 0.00 33.26 4.49
1188 4794 4.931601 TCTTCATTTGGAGTGACATTCTCG 59.068 41.667 0.00 0.00 33.26 4.04
1199 4805 6.127814 TGCTTGAGCTATTTCTTCATTTGGAG 60.128 38.462 4.44 0.00 42.66 3.86
1213 4819 7.733969 TCATAATCTTCTTCTGCTTGAGCTAT 58.266 34.615 4.44 0.00 42.66 2.97
1365 4982 2.350522 CAGGAGTTTGAGTTGGATCCG 58.649 52.381 7.39 0.00 31.97 4.18
1392 5009 5.803461 ACATGTTCTTGCATCATGAAAATCG 59.197 36.000 20.34 8.31 40.64 3.34
1484 5104 7.230747 TGTGAACCTCTCCTAATGAATCAAAA 58.769 34.615 0.00 0.00 0.00 2.44
1600 6007 2.170607 TCCCCTTGACATAGCTGTTAGC 59.829 50.000 0.00 0.00 42.84 3.09
1601 6008 4.446371 CTTCCCCTTGACATAGCTGTTAG 58.554 47.826 0.00 0.00 35.14 2.34
1602 6009 3.199946 CCTTCCCCTTGACATAGCTGTTA 59.800 47.826 0.00 0.00 35.14 2.41
1603 6010 2.025887 CCTTCCCCTTGACATAGCTGTT 60.026 50.000 0.00 0.00 35.14 3.16
1604 6011 1.561542 CCTTCCCCTTGACATAGCTGT 59.438 52.381 0.00 0.00 38.67 4.40
1605 6012 1.748591 GCCTTCCCCTTGACATAGCTG 60.749 57.143 0.00 0.00 0.00 4.24
1606 6013 0.548510 GCCTTCCCCTTGACATAGCT 59.451 55.000 0.00 0.00 0.00 3.32
1688 6102 0.251634 CCTCCTCTTGTTCCTCTGCC 59.748 60.000 0.00 0.00 0.00 4.85
1689 6103 0.251634 CCCTCCTCTTGTTCCTCTGC 59.748 60.000 0.00 0.00 0.00 4.26
1690 6104 1.552792 GACCCTCCTCTTGTTCCTCTG 59.447 57.143 0.00 0.00 0.00 3.35
1691 6105 1.435168 AGACCCTCCTCTTGTTCCTCT 59.565 52.381 0.00 0.00 0.00 3.69
1692 6106 1.552792 CAGACCCTCCTCTTGTTCCTC 59.447 57.143 0.00 0.00 0.00 3.71
1693 6107 1.650528 CAGACCCTCCTCTTGTTCCT 58.349 55.000 0.00 0.00 0.00 3.36
1694 6108 0.615850 CCAGACCCTCCTCTTGTTCC 59.384 60.000 0.00 0.00 0.00 3.62
1695 6109 1.002544 CACCAGACCCTCCTCTTGTTC 59.997 57.143 0.00 0.00 0.00 3.18
1696 6110 1.059913 CACCAGACCCTCCTCTTGTT 58.940 55.000 0.00 0.00 0.00 2.83
1697 6111 1.484444 GCACCAGACCCTCCTCTTGT 61.484 60.000 0.00 0.00 0.00 3.16
1698 6112 1.197430 AGCACCAGACCCTCCTCTTG 61.197 60.000 0.00 0.00 0.00 3.02
1699 6113 1.159664 AGCACCAGACCCTCCTCTT 59.840 57.895 0.00 0.00 0.00 2.85
1700 6114 1.611851 CAGCACCAGACCCTCCTCT 60.612 63.158 0.00 0.00 0.00 3.69
1701 6115 2.664081 CCAGCACCAGACCCTCCTC 61.664 68.421 0.00 0.00 0.00 3.71
1702 6116 2.608988 CCAGCACCAGACCCTCCT 60.609 66.667 0.00 0.00 0.00 3.69
1703 6117 4.416738 GCCAGCACCAGACCCTCC 62.417 72.222 0.00 0.00 0.00 4.30
1704 6118 3.618780 CTGCCAGCACCAGACCCTC 62.619 68.421 0.00 0.00 32.03 4.30
1705 6119 3.644606 CTGCCAGCACCAGACCCT 61.645 66.667 0.00 0.00 32.03 4.34
1706 6120 3.618780 CTCTGCCAGCACCAGACCC 62.619 68.421 0.00 0.00 35.60 4.46
1707 6121 2.046507 CTCTGCCAGCACCAGACC 60.047 66.667 0.00 0.00 35.60 3.85
1708 6122 2.046507 CCTCTGCCAGCACCAGAC 60.047 66.667 0.00 0.00 35.60 3.51
1709 6123 1.842920 TTCCTCTGCCAGCACCAGA 60.843 57.895 0.00 0.00 37.71 3.86
1710 6124 1.673665 GTTCCTCTGCCAGCACCAG 60.674 63.158 0.00 0.00 0.00 4.00
1711 6125 1.993701 TTGTTCCTCTGCCAGCACCA 61.994 55.000 0.00 0.00 0.00 4.17
1712 6126 0.610232 ATTGTTCCTCTGCCAGCACC 60.610 55.000 0.00 0.00 0.00 5.01
1713 6127 2.113860 TATTGTTCCTCTGCCAGCAC 57.886 50.000 0.00 0.00 0.00 4.40
1714 6128 2.305635 TCTTATTGTTCCTCTGCCAGCA 59.694 45.455 0.00 0.00 0.00 4.41
1715 6129 2.941720 CTCTTATTGTTCCTCTGCCAGC 59.058 50.000 0.00 0.00 0.00 4.85
1716 6130 3.539604 CCTCTTATTGTTCCTCTGCCAG 58.460 50.000 0.00 0.00 0.00 4.85
1717 6131 2.239654 CCCTCTTATTGTTCCTCTGCCA 59.760 50.000 0.00 0.00 0.00 4.92
1741 6185 0.196118 TTCCTCTTGTTCCCCTCCCT 59.804 55.000 0.00 0.00 0.00 4.20
1765 6209 2.157305 TTGCATTTGCCCCTCTTGCG 62.157 55.000 0.00 0.00 41.18 4.85
1799 6249 6.376581 ACTCCTCTTCTAGAATTTGCATTTGG 59.623 38.462 5.44 0.00 0.00 3.28
1811 6261 6.859112 AGTTGCATTTACTCCTCTTCTAGA 57.141 37.500 0.00 0.00 0.00 2.43
1844 6327 2.472029 AGTATTAGTGGCACCTGCTCT 58.528 47.619 15.27 5.25 41.70 4.09
1855 6338 4.262249 GCTCTTGCCCCTCTAGTATTAGTG 60.262 50.000 0.00 0.00 0.00 2.74
1862 6345 1.621672 GCTGCTCTTGCCCCTCTAGT 61.622 60.000 0.00 0.00 38.71 2.57
1870 6353 1.303155 AGGAGTTGCTGCTCTTGCC 60.303 57.895 0.00 0.00 38.71 4.52
1883 6366 3.166679 GGAGGTTGTAGAAGACAGGAGT 58.833 50.000 0.00 0.00 39.88 3.85
1890 6373 5.640158 TCCAAAAAGGAGGTTGTAGAAGA 57.360 39.130 0.00 0.00 43.07 2.87
1928 6412 5.376625 TCTTGAAGTTCCTGTTGCTGTAAT 58.623 37.500 0.00 0.00 0.00 1.89
2100 6585 5.536497 AAGGGGAAGGTTCAGAAATGTAT 57.464 39.130 0.00 0.00 0.00 2.29
2120 6605 4.576463 AGAACAAGGTTCAGTAGCACAAAG 59.424 41.667 11.28 0.00 0.00 2.77
2161 6646 6.774170 ACATCACAACCATCACATATAGCAAT 59.226 34.615 0.00 0.00 0.00 3.56
2338 6839 7.158697 TGTTGTTGCAGAACTACATATAGTGT 58.841 34.615 10.90 0.00 41.14 3.55
2385 6888 3.757836 GGTTCAAACCCTAGGCCAA 57.242 52.632 5.01 0.00 43.43 4.52
2406 6909 3.264964 ACGACTCTTCTCTTCCTAGGTCT 59.735 47.826 9.08 0.00 0.00 3.85
2415 6918 2.442413 AGCTAGCACGACTCTTCTCTT 58.558 47.619 18.83 0.00 0.00 2.85
2479 6982 3.306472 AGCAGGCTTCTACTAGTAGCT 57.694 47.619 22.87 13.64 38.48 3.32
2480 6983 5.941647 AGTATAGCAGGCTTCTACTAGTAGC 59.058 44.000 22.87 15.25 37.82 3.58
2500 7005 4.926207 GTGAAACGGCGGGAGTAT 57.074 55.556 13.24 0.00 0.00 2.12
2525 7030 3.151554 TGACTTTGTACTAGTCGCAGGA 58.848 45.455 17.88 4.06 43.90 3.86
2545 7050 2.421529 GGCACTTTACAGATACCCCCTG 60.422 54.545 0.00 0.00 37.64 4.45
2615 7121 1.269883 ACGTACGGTGCAAATCAGACA 60.270 47.619 21.06 0.00 0.00 3.41
2654 7164 5.537188 TGCAAAATATGGAAAAGTGGTGTC 58.463 37.500 0.00 0.00 0.00 3.67
2655 7165 5.543507 TGCAAAATATGGAAAAGTGGTGT 57.456 34.783 0.00 0.00 0.00 4.16
2719 7230 5.372343 ACATGAGGTAAATGCATAGGTGA 57.628 39.130 0.00 0.00 0.00 4.02
2740 7251 5.356190 GCCTGTAAAACCCTCATAAACCTAC 59.644 44.000 0.00 0.00 0.00 3.18
2741 7252 5.014333 TGCCTGTAAAACCCTCATAAACCTA 59.986 40.000 0.00 0.00 0.00 3.08
2742 7253 4.202631 TGCCTGTAAAACCCTCATAAACCT 60.203 41.667 0.00 0.00 0.00 3.50
2743 7254 4.083565 TGCCTGTAAAACCCTCATAAACC 58.916 43.478 0.00 0.00 0.00 3.27
2744 7255 4.157840 CCTGCCTGTAAAACCCTCATAAAC 59.842 45.833 0.00 0.00 0.00 2.01
2745 7256 4.202631 ACCTGCCTGTAAAACCCTCATAAA 60.203 41.667 0.00 0.00 0.00 1.40
2746 7257 3.332485 ACCTGCCTGTAAAACCCTCATAA 59.668 43.478 0.00 0.00 0.00 1.90
2747 7258 2.916934 ACCTGCCTGTAAAACCCTCATA 59.083 45.455 0.00 0.00 0.00 2.15
2748 7259 1.710809 ACCTGCCTGTAAAACCCTCAT 59.289 47.619 0.00 0.00 0.00 2.90
2749 7260 1.145571 ACCTGCCTGTAAAACCCTCA 58.854 50.000 0.00 0.00 0.00 3.86
2750 7261 1.073284 TCACCTGCCTGTAAAACCCTC 59.927 52.381 0.00 0.00 0.00 4.30
2751 7262 1.145571 TCACCTGCCTGTAAAACCCT 58.854 50.000 0.00 0.00 0.00 4.34
2752 7263 1.989706 TTCACCTGCCTGTAAAACCC 58.010 50.000 0.00 0.00 0.00 4.11
2753 7264 4.600692 AAATTCACCTGCCTGTAAAACC 57.399 40.909 0.00 0.00 0.00 3.27
2754 7265 5.596845 TCAAAATTCACCTGCCTGTAAAAC 58.403 37.500 0.00 0.00 0.00 2.43
2755 7266 5.860941 TCAAAATTCACCTGCCTGTAAAA 57.139 34.783 0.00 0.00 0.00 1.52
2756 7267 6.041409 TCAATCAAAATTCACCTGCCTGTAAA 59.959 34.615 0.00 0.00 0.00 2.01
2757 7268 5.538053 TCAATCAAAATTCACCTGCCTGTAA 59.462 36.000 0.00 0.00 0.00 2.41
2758 7269 5.076182 TCAATCAAAATTCACCTGCCTGTA 58.924 37.500 0.00 0.00 0.00 2.74
2759 7270 3.896888 TCAATCAAAATTCACCTGCCTGT 59.103 39.130 0.00 0.00 0.00 4.00
2760 7271 4.524316 TCAATCAAAATTCACCTGCCTG 57.476 40.909 0.00 0.00 0.00 4.85
2761 7272 4.834496 TCTTCAATCAAAATTCACCTGCCT 59.166 37.500 0.00 0.00 0.00 4.75
2762 7273 5.138125 TCTTCAATCAAAATTCACCTGCC 57.862 39.130 0.00 0.00 0.00 4.85
2763 7274 6.869913 TCAATCTTCAATCAAAATTCACCTGC 59.130 34.615 0.00 0.00 0.00 4.85
2764 7275 8.869897 CATCAATCTTCAATCAAAATTCACCTG 58.130 33.333 0.00 0.00 0.00 4.00
2765 7276 8.809066 TCATCAATCTTCAATCAAAATTCACCT 58.191 29.630 0.00 0.00 0.00 4.00
2766 7277 8.991243 TCATCAATCTTCAATCAAAATTCACC 57.009 30.769 0.00 0.00 0.00 4.02
2767 7278 9.850628 TCTCATCAATCTTCAATCAAAATTCAC 57.149 29.630 0.00 0.00 0.00 3.18
2769 7280 9.517609 CCTCTCATCAATCTTCAATCAAAATTC 57.482 33.333 0.00 0.00 0.00 2.17
2770 7281 9.251440 TCCTCTCATCAATCTTCAATCAAAATT 57.749 29.630 0.00 0.00 0.00 1.82
2771 7282 8.818622 TCCTCTCATCAATCTTCAATCAAAAT 57.181 30.769 0.00 0.00 0.00 1.82
2772 7283 7.338703 CCTCCTCTCATCAATCTTCAATCAAAA 59.661 37.037 0.00 0.00 0.00 2.44
2773 7284 6.827251 CCTCCTCTCATCAATCTTCAATCAAA 59.173 38.462 0.00 0.00 0.00 2.69
2774 7285 6.354938 CCTCCTCTCATCAATCTTCAATCAA 58.645 40.000 0.00 0.00 0.00 2.57
2775 7286 5.163227 CCCTCCTCTCATCAATCTTCAATCA 60.163 44.000 0.00 0.00 0.00 2.57
2776 7287 5.307204 CCCTCCTCTCATCAATCTTCAATC 58.693 45.833 0.00 0.00 0.00 2.67
2777 7288 4.104420 CCCCTCCTCTCATCAATCTTCAAT 59.896 45.833 0.00 0.00 0.00 2.57
2778 7289 3.457380 CCCCTCCTCTCATCAATCTTCAA 59.543 47.826 0.00 0.00 0.00 2.69
2779 7290 3.044156 CCCCTCCTCTCATCAATCTTCA 58.956 50.000 0.00 0.00 0.00 3.02
2780 7291 2.224499 GCCCCTCCTCTCATCAATCTTC 60.224 54.545 0.00 0.00 0.00 2.87
2781 7292 1.773653 GCCCCTCCTCTCATCAATCTT 59.226 52.381 0.00 0.00 0.00 2.40
2782 7293 1.433121 GCCCCTCCTCTCATCAATCT 58.567 55.000 0.00 0.00 0.00 2.40
2783 7294 0.399833 GGCCCCTCCTCTCATCAATC 59.600 60.000 0.00 0.00 0.00 2.67
2784 7295 0.029267 AGGCCCCTCCTCTCATCAAT 60.029 55.000 0.00 0.00 43.20 2.57
2785 7296 0.642156 TAGGCCCCTCCTCTCATCAA 59.358 55.000 0.00 0.00 43.20 2.57
2786 7297 0.105453 GTAGGCCCCTCCTCTCATCA 60.105 60.000 0.00 0.00 43.20 3.07
2787 7298 0.834261 GGTAGGCCCCTCCTCTCATC 60.834 65.000 0.00 0.00 43.20 2.92
2788 7299 1.237458 GGTAGGCCCCTCCTCTCAT 59.763 63.158 0.00 0.00 43.20 2.90
2789 7300 2.696893 GGTAGGCCCCTCCTCTCA 59.303 66.667 0.00 0.00 43.20 3.27


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

AutoCloner maintained by Alex Coulton.