Multiple sequence alignment - TraesCS7A01G329600

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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 TraesCS7A01G329600 chr7A 100.000 4989 0 0 1 4989 481252115 481247127 0.000000e+00 9214.0
1 TraesCS7A01G329600 chr7B 95.135 4645 145 43 252 4863 432505264 432500668 0.000000e+00 7251.0
2 TraesCS7A01G329600 chr7B 90.129 233 17 3 64 294 432505534 432505306 1.050000e-76 298.0
3 TraesCS7A01G329600 chr7B 92.366 131 10 0 4859 4989 432500592 432500462 2.370000e-43 187.0
4 TraesCS7A01G329600 chr7B 90.278 72 6 1 1 71 432505863 432505792 5.320000e-15 93.5
5 TraesCS7A01G329600 chr7D 95.086 4619 131 42 293 4863 416633719 416629149 0.000000e+00 7184.0
6 TraesCS7A01G329600 chr7D 95.623 297 10 3 1 294 416634085 416633789 1.630000e-129 473.0
7 TraesCS7A01G329600 chr7D 90.076 131 12 1 4859 4989 416629076 416628947 8.590000e-38 169.0
8 TraesCS7A01G329600 chr1A 86.878 221 22 2 1801 2020 558332453 558332667 1.790000e-59 241.0


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 TraesCS7A01G329600 chr7A 481247127 481252115 4988 True 9214.000000 9214 100.000 1 4989 1 chr7A.!!$R1 4988
1 TraesCS7A01G329600 chr7B 432500462 432505863 5401 True 1957.375000 7251 91.977 1 4989 4 chr7B.!!$R1 4988
2 TraesCS7A01G329600 chr7D 416628947 416634085 5138 True 2608.666667 7184 93.595 1 4989 3 chr7D.!!$R1 4988

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
714 1086 0.114560 ACGAAAGGGTGGGAGAGAGA 59.885 55.000 0.00 0.0 0.0 3.10 F
975 1352 0.945099 CTGGTAGATGCGCGAGTAGA 59.055 55.000 12.10 0.0 0.0 2.59 F
1643 2026 1.207089 CTGATCGGTGGCCTTACAAGA 59.793 52.381 3.32 0.0 0.0 3.02 F
1646 2029 1.886886 TCGGTGGCCTTACAAGAAAC 58.113 50.000 3.32 0.0 0.0 2.78 F
2086 2469 2.297315 GGTTTCTCCTCCCAAAAAGCTG 59.703 50.000 0.00 0.0 0.0 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1655 2038 0.546267 AGGTCCTGCAGGTGAGATGT 60.546 55.000 31.58 8.48 36.34 3.06 R
2299 2682 0.617413 ACAAGAGATGTCAGGCCAGG 59.383 55.000 5.01 0.00 37.96 4.45 R
2855 3238 4.552166 TTGCCATTTCGCTATTAGCTTC 57.448 40.909 13.55 0.00 39.60 3.86 R
3317 3701 5.213891 ACCACTTCCATGTTGAATTTTCC 57.786 39.130 0.00 0.00 0.00 3.13 R
4034 4423 0.608035 TTGCGAACCCACATTCCTCC 60.608 55.000 0.00 0.00 0.00 4.30 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
34 35 7.571071 ATGATATCTTCTCCTCCACAATCAT 57.429 36.000 3.98 0.00 0.00 2.45
36 37 6.786461 TGATATCTTCTCCTCCACAATCATCT 59.214 38.462 3.98 0.00 0.00 2.90
40 41 4.750021 TCTCCTCCACAATCATCTCAAG 57.250 45.455 0.00 0.00 0.00 3.02
127 395 0.806868 TACCACTACACGCTTCTCGG 59.193 55.000 0.00 0.00 43.86 4.63
242 515 8.004215 TGAAAGCCTTAATCTAGAGAGAGAGAT 58.996 37.037 0.00 0.00 34.35 2.75
243 516 9.515226 GAAAGCCTTAATCTAGAGAGAGAGATA 57.485 37.037 0.00 0.00 34.35 1.98
244 517 9.520515 AAAGCCTTAATCTAGAGAGAGAGATAG 57.479 37.037 0.00 0.00 34.35 2.08
245 518 8.449423 AGCCTTAATCTAGAGAGAGAGATAGA 57.551 38.462 0.00 0.00 34.35 1.98
255 528 4.832492 AGAGAGAGATAGAGAGAGGAGGT 58.168 47.826 0.00 0.00 0.00 3.85
280 553 6.552859 TGAAACAAGAGCGTAAAATCATCA 57.447 33.333 0.00 0.00 0.00 3.07
375 732 8.903820 ACACCATATTCAGTTTATAAAAGGCTC 58.096 33.333 0.00 0.00 0.00 4.70
385 742 9.994432 CAGTTTATAAAAGGCTCTGTTTCATAG 57.006 33.333 0.00 0.00 0.00 2.23
405 762 8.543862 TCATAGAAGATCATGTGATAATGTGC 57.456 34.615 0.00 0.00 34.37 4.57
535 904 7.416022 AGTATAACATACACTGACGAAGCTAC 58.584 38.462 0.00 0.00 0.00 3.58
546 915 1.475280 ACGAAGCTACGTGCATCCTTA 59.525 47.619 0.00 0.00 44.84 2.69
549 918 1.100510 AGCTACGTGCATCCTTACGA 58.899 50.000 0.00 0.00 45.94 3.43
558 928 6.044046 ACGTGCATCCTTACGATAATTTACA 58.956 36.000 3.64 0.00 42.54 2.41
573 943 8.989980 CGATAATTTACAGGGAGTTTTAGATCC 58.010 37.037 0.00 0.00 34.64 3.36
580 950 4.636206 CAGGGAGTTTTAGATCCGAAAAGG 59.364 45.833 3.90 0.00 42.97 3.11
596 966 7.700811 TCCGAAAAGGTAGAGCTTTTCTCTCT 61.701 42.308 29.75 8.74 44.12 3.10
625 995 2.014010 TGCATTTTCTCTTTGGCCCT 57.986 45.000 0.00 0.00 0.00 5.19
627 997 1.895131 GCATTTTCTCTTTGGCCCTCA 59.105 47.619 0.00 0.00 0.00 3.86
640 1010 6.987403 TTTGGCCCTCAAAGTTTTACTAAT 57.013 33.333 0.00 0.00 40.14 1.73
642 1012 8.480133 TTTGGCCCTCAAAGTTTTACTAATAA 57.520 30.769 0.00 0.00 40.14 1.40
643 1013 7.457024 TGGCCCTCAAAGTTTTACTAATAAC 57.543 36.000 0.00 0.00 0.00 1.89
713 1085 0.977395 AACGAAAGGGTGGGAGAGAG 59.023 55.000 0.00 0.00 0.00 3.20
714 1086 0.114560 ACGAAAGGGTGGGAGAGAGA 59.885 55.000 0.00 0.00 0.00 3.10
975 1352 0.945099 CTGGTAGATGCGCGAGTAGA 59.055 55.000 12.10 0.00 0.00 2.59
1514 1894 4.997395 GGTGATGTCAACTGTCATTGTACT 59.003 41.667 0.00 0.00 0.00 2.73
1515 1895 5.106948 GGTGATGTCAACTGTCATTGTACTG 60.107 44.000 0.00 0.00 0.00 2.74
1516 1896 5.466728 GTGATGTCAACTGTCATTGTACTGT 59.533 40.000 0.00 0.00 33.50 3.55
1517 1897 5.696270 TGATGTCAACTGTCATTGTACTGTC 59.304 40.000 0.00 0.00 31.91 3.51
1518 1898 4.048504 TGTCAACTGTCATTGTACTGTCG 58.951 43.478 0.00 0.00 31.91 4.35
1519 1899 4.049186 GTCAACTGTCATTGTACTGTCGT 58.951 43.478 0.00 0.00 31.91 4.34
1520 1900 4.506654 GTCAACTGTCATTGTACTGTCGTT 59.493 41.667 0.00 0.00 31.91 3.85
1521 1901 4.506288 TCAACTGTCATTGTACTGTCGTTG 59.494 41.667 0.00 0.00 31.91 4.10
1522 1902 4.054780 ACTGTCATTGTACTGTCGTTGT 57.945 40.909 0.00 0.00 0.00 3.32
1525 1905 6.916440 ACTGTCATTGTACTGTCGTTGTATA 58.084 36.000 0.00 0.00 0.00 1.47
1527 1907 8.033038 ACTGTCATTGTACTGTCGTTGTATATT 58.967 33.333 0.00 0.00 0.00 1.28
1529 1909 8.652463 TGTCATTGTACTGTCGTTGTATATTTG 58.348 33.333 0.00 0.00 0.00 2.32
1581 1963 5.263968 TGTCTTGCTGCCTAATCTACTAC 57.736 43.478 0.00 0.00 0.00 2.73
1643 2026 1.207089 CTGATCGGTGGCCTTACAAGA 59.793 52.381 3.32 0.00 0.00 3.02
1646 2029 1.886886 TCGGTGGCCTTACAAGAAAC 58.113 50.000 3.32 0.00 0.00 2.78
1648 2031 2.633967 TCGGTGGCCTTACAAGAAACTA 59.366 45.455 3.32 0.00 0.00 2.24
1655 2038 6.428771 GTGGCCTTACAAGAAACTACAATGTA 59.571 38.462 3.32 0.00 0.00 2.29
1703 2086 2.781923 TGCATCTACACACAATGCTGT 58.218 42.857 7.92 0.00 44.75 4.40
2086 2469 2.297315 GGTTTCTCCTCCCAAAAAGCTG 59.703 50.000 0.00 0.00 0.00 4.24
2124 2507 9.474920 GATTTTCTATCATCACCTAGAGAGTTG 57.525 37.037 0.00 0.00 0.00 3.16
2131 2514 4.919774 TCACCTAGAGAGTTGAGAGTCT 57.080 45.455 0.00 0.00 38.28 3.24
2299 2682 3.502979 TGTTTTGGTAATTGGTAGTCGGC 59.497 43.478 0.00 0.00 0.00 5.54
2587 2970 6.849697 TCCAGAGGTATATATGTGAACCCTTT 59.150 38.462 0.00 0.00 32.10 3.11
2591 2974 8.376270 AGAGGTATATATGTGAACCCTTTAAGC 58.624 37.037 0.00 0.00 32.10 3.09
2811 3194 5.600908 AACACACCATACGTAACATGTTC 57.399 39.130 15.85 6.18 0.00 3.18
2855 3238 3.855689 ATTTCTTTCCTGCATTGACCG 57.144 42.857 0.00 0.00 0.00 4.79
2880 3263 3.983344 GCTAATAGCGAAATGGCAAATGG 59.017 43.478 0.00 0.00 34.64 3.16
2881 3264 4.499696 GCTAATAGCGAAATGGCAAATGGT 60.500 41.667 0.00 0.00 34.64 3.55
2923 3306 7.642669 CGATAGTTAAAATGCACAATCAGGAT 58.357 34.615 0.00 0.00 0.00 3.24
3064 3448 3.607422 TTGACAAAGAGTGATGTTGCG 57.393 42.857 0.00 0.00 0.00 4.85
3248 3632 2.651455 CAGATGGATGACATGGTGCTT 58.349 47.619 0.00 0.00 40.72 3.91
3317 3701 7.228108 ACACTCATATTATGGCATCTTTCACAG 59.772 37.037 1.65 0.00 0.00 3.66
3319 3703 6.840527 TCATATTATGGCATCTTTCACAGGA 58.159 36.000 1.65 0.00 0.00 3.86
3352 3738 6.983890 ACATGGAAGTGGTTACAATTTTGAAC 59.016 34.615 0.00 0.00 34.65 3.18
3353 3739 6.531503 TGGAAGTGGTTACAATTTTGAACA 57.468 33.333 0.00 0.00 34.65 3.18
3672 4059 3.005155 GTGATTAATTGAGCCATCCTGCC 59.995 47.826 0.00 0.00 0.00 4.85
3679 4066 0.613012 GAGCCATCCTGCCCTTTTGT 60.613 55.000 0.00 0.00 0.00 2.83
3790 4177 6.650427 AACTTTCCTTGTCCTAATTGTTCC 57.350 37.500 0.00 0.00 0.00 3.62
3867 4254 6.708054 CCCTGTAGATCTTAATTAGTTGCTGG 59.292 42.308 0.00 0.00 0.00 4.85
3868 4255 7.275920 CCTGTAGATCTTAATTAGTTGCTGGT 58.724 38.462 0.00 0.00 0.00 4.00
3892 4279 3.011949 TGGCAGAATTCGCTGAAAAAC 57.988 42.857 17.53 4.69 38.14 2.43
3905 4292 8.867248 TTCGCTGAAAAACAATTTAAACAAAC 57.133 26.923 0.00 0.00 0.00 2.93
3940 4328 4.090090 TGCTCCTCCTCTTACCTATATGC 58.910 47.826 0.00 0.00 0.00 3.14
3991 4379 4.732938 GCCATTCAGCAGACAAATTAGAGC 60.733 45.833 0.00 0.00 0.00 4.09
4013 4402 1.019278 GTGGATGTGATTGCGACCGT 61.019 55.000 0.00 0.00 0.00 4.83
4034 4423 3.743521 TGTCAGTGAGGACATTTCAAGG 58.256 45.455 0.00 0.00 42.56 3.61
4068 4457 0.391130 CGCAATCCAAGGGAACTCGA 60.391 55.000 0.00 0.00 42.68 4.04
4069 4458 1.087501 GCAATCCAAGGGAACTCGAC 58.912 55.000 0.00 0.00 42.68 4.20
4070 4459 1.610624 GCAATCCAAGGGAACTCGACA 60.611 52.381 0.00 0.00 42.68 4.35
4141 4530 4.320275 GGAGTGAACGGAAAAAGATTGGAC 60.320 45.833 0.00 0.00 0.00 4.02
4152 4541 2.280797 ATTGGACGTGCGTGCTGT 60.281 55.556 16.33 3.47 37.36 4.40
4173 4562 4.061596 GTCAAAGAGCTTGCTTCTACAGT 58.938 43.478 0.00 0.00 34.76 3.55
4360 4755 3.521560 TGGACGTGCTATGATGTTTCTC 58.478 45.455 8.99 0.00 0.00 2.87
4394 4789 1.082679 CAGATGAGAGTGCTGTGGCG 61.083 60.000 0.00 0.00 42.25 5.69
4489 4884 1.005630 GACGCAGAGAGCAGTGGTT 60.006 57.895 0.00 0.00 46.13 3.67
4490 4885 1.005630 ACGCAGAGAGCAGTGGTTC 60.006 57.895 0.00 0.00 46.13 3.62
4491 4886 1.005748 CGCAGAGAGCAGTGGTTCA 60.006 57.895 0.00 0.00 46.13 3.18
4492 4887 0.390866 CGCAGAGAGCAGTGGTTCAT 60.391 55.000 0.00 0.00 46.13 2.57
4493 4888 1.134995 CGCAGAGAGCAGTGGTTCATA 60.135 52.381 0.00 0.00 46.13 2.15
4494 4889 2.548875 GCAGAGAGCAGTGGTTCATAG 58.451 52.381 0.00 0.00 44.79 2.23
4495 4890 2.167281 GCAGAGAGCAGTGGTTCATAGA 59.833 50.000 0.00 0.00 44.79 1.98
4579 5000 7.282332 TGGTGACACATGTTTTGAATGATAA 57.718 32.000 8.08 0.00 33.40 1.75
4648 5069 4.152938 AGTTAAGGCACCGTCGAAATTAAC 59.847 41.667 0.00 2.68 33.80 2.01
4702 5123 2.892425 CGCTCCGGATCAACCAGC 60.892 66.667 3.57 1.21 38.90 4.85
4707 5128 1.377725 CCGGATCAACCAGCTTGCT 60.378 57.895 0.00 0.00 38.90 3.91
4758 5180 6.581542 ACGAGTAGTTTTTGTTATCGACTCTG 59.418 38.462 0.00 0.00 32.99 3.35
4788 5210 9.999009 CTGTTAGATGAAATGACGTACTACTAA 57.001 33.333 0.00 0.00 0.00 2.24
4868 5370 6.937436 ATATGACAGTGATGTACTACACGA 57.063 37.500 13.92 4.54 41.22 4.35
4972 5474 7.340743 TGGTCATAAAAGTGGTAATGTATTGGG 59.659 37.037 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 6.618311 GGAGAACCATGGCTCAACTTGAGA 62.618 50.000 20.98 3.08 40.35 3.27
36 37 2.553028 GGAGAACCATGGCTCAACTTGA 60.553 50.000 17.32 0.00 35.97 3.02
40 41 2.633488 GTAGGAGAACCATGGCTCAAC 58.367 52.381 17.32 11.65 38.94 3.18
127 395 7.539436 TGATGTGTGTAGAGAAAGAGATGTAC 58.461 38.462 0.00 0.00 0.00 2.90
166 435 3.581755 TGTATTTCTCCTTCGAACCGTG 58.418 45.455 0.00 0.00 0.00 4.94
172 441 4.495422 GAGCAGTTGTATTTCTCCTTCGA 58.505 43.478 0.00 0.00 0.00 3.71
242 515 6.732487 TCTTGTTTCATACCTCCTCTCTCTA 58.268 40.000 0.00 0.00 0.00 2.43
243 516 5.584913 TCTTGTTTCATACCTCCTCTCTCT 58.415 41.667 0.00 0.00 0.00 3.10
244 517 5.681179 GCTCTTGTTTCATACCTCCTCTCTC 60.681 48.000 0.00 0.00 0.00 3.20
245 518 4.161377 GCTCTTGTTTCATACCTCCTCTCT 59.839 45.833 0.00 0.00 0.00 3.10
255 528 8.175069 GTGATGATTTTACGCTCTTGTTTCATA 58.825 33.333 0.00 0.00 0.00 2.15
303 660 3.444034 TGTCATACTTCTCCTTCTCCACG 59.556 47.826 0.00 0.00 0.00 4.94
385 742 5.450171 GCTGCACATTATCACATGATCTTC 58.550 41.667 0.00 0.00 36.05 2.87
463 830 1.556911 CTAGTGCAAGAGGGGTGACAT 59.443 52.381 0.00 0.00 0.00 3.06
523 892 0.917259 GATGCACGTAGCTTCGTCAG 59.083 55.000 15.97 7.11 45.94 3.51
529 898 1.475280 TCGTAAGGATGCACGTAGCTT 59.525 47.619 10.54 5.14 40.96 3.74
535 904 6.346598 CCTGTAAATTATCGTAAGGATGCACG 60.347 42.308 0.00 0.00 39.48 5.34
546 915 9.543783 GATCTAAAACTCCCTGTAAATTATCGT 57.456 33.333 0.00 0.00 0.00 3.73
549 918 8.711170 TCGGATCTAAAACTCCCTGTAAATTAT 58.289 33.333 0.00 0.00 0.00 1.28
558 928 4.288887 ACCTTTTCGGATCTAAAACTCCCT 59.711 41.667 0.00 0.00 36.31 4.20
671 1041 0.740149 ACGGTGACACACGTGAGTTA 59.260 50.000 25.01 15.02 46.40 2.24
672 1042 1.514087 ACGGTGACACACGTGAGTT 59.486 52.632 25.01 5.17 46.40 3.01
713 1085 0.923358 TCTCTCCCCCTCTCTGACTC 59.077 60.000 0.00 0.00 0.00 3.36
714 1086 1.217689 CATCTCTCCCCCTCTCTGACT 59.782 57.143 0.00 0.00 0.00 3.41
1581 1963 6.039829 TGACAGAGTGAGCCATAATGTACTAG 59.960 42.308 0.00 0.00 0.00 2.57
1643 2026 5.643777 GCAGGTGAGATGTACATTGTAGTTT 59.356 40.000 10.30 0.00 0.00 2.66
1646 2029 4.758688 TGCAGGTGAGATGTACATTGTAG 58.241 43.478 10.30 0.00 0.00 2.74
1648 2031 3.603532 CTGCAGGTGAGATGTACATTGT 58.396 45.455 10.30 0.16 0.00 2.71
1655 2038 0.546267 AGGTCCTGCAGGTGAGATGT 60.546 55.000 31.58 8.48 36.34 3.06
2086 2469 9.590451 TGATGATAGAAAATCCAAAATGCTTTC 57.410 29.630 0.00 0.00 0.00 2.62
2097 2480 8.189119 ACTCTCTAGGTGATGATAGAAAATCC 57.811 38.462 0.00 0.00 0.00 3.01
2124 2507 9.863845 AAGCTCTACTTATTGTTTAAGACTCTC 57.136 33.333 0.00 0.00 36.62 3.20
2202 2585 5.491982 ACTAACTTGCTTGAAGGTCATAGG 58.508 41.667 0.00 0.00 35.78 2.57
2265 2648 2.192263 ACCAAAACAACCCAACCACAT 58.808 42.857 0.00 0.00 0.00 3.21
2299 2682 0.617413 ACAAGAGATGTCAGGCCAGG 59.383 55.000 5.01 0.00 37.96 4.45
2309 2692 5.856986 CAGTTCAATGCAAGAACAAGAGATG 59.143 40.000 27.01 16.46 45.93 2.90
2472 2855 6.017934 CCAGGGATGTTGTATTAAATGACTCG 60.018 42.308 0.00 0.00 0.00 4.18
2796 3179 8.182227 TCTGACTAAGAGAACATGTTACGTATG 58.818 37.037 11.95 4.01 0.00 2.39
2855 3238 4.552166 TTGCCATTTCGCTATTAGCTTC 57.448 40.909 13.55 0.00 39.60 3.86
2880 3263 7.689953 ACTATCGTACGATTTTACAATCCAC 57.310 36.000 33.47 0.00 36.18 4.02
2881 3264 9.800433 TTAACTATCGTACGATTTTACAATCCA 57.200 29.630 33.47 12.32 36.18 3.41
3064 3448 6.657541 TGGGTAACACAATTCTTCCTACATTC 59.342 38.462 0.00 0.00 39.74 2.67
3248 3632 7.095910 TGTACTTAAATTTCCACGTAATCGGA 58.904 34.615 0.00 0.00 41.85 4.55
3317 3701 5.213891 ACCACTTCCATGTTGAATTTTCC 57.786 39.130 0.00 0.00 0.00 3.13
3319 3703 7.118496 TGTAACCACTTCCATGTTGAATTTT 57.882 32.000 0.00 0.00 0.00 1.82
3375 3761 6.245408 AGTCACCATATTCAGGTTTAGCAAA 58.755 36.000 0.00 0.00 37.23 3.68
3672 4059 5.261209 TCACAAATTCACCTGACAAAAGG 57.739 39.130 0.00 0.00 43.57 3.11
3790 4177 0.856641 CAGGTTGGTACGTGTGAACG 59.143 55.000 0.00 0.00 35.85 3.95
3863 4250 2.061028 CGAATTCTGCCAAAAACCAGC 58.939 47.619 3.52 0.00 0.00 4.85
3867 4254 3.011949 TCAGCGAATTCTGCCAAAAAC 57.988 42.857 15.47 0.00 34.19 2.43
3868 4255 3.724508 TTCAGCGAATTCTGCCAAAAA 57.275 38.095 15.47 5.79 34.19 1.94
3872 4259 2.360483 TGTTTTTCAGCGAATTCTGCCA 59.640 40.909 15.47 5.36 34.19 4.92
3905 4292 2.363359 GGAGGAGCATAAATTTGGCAGG 59.637 50.000 16.02 0.00 0.00 4.85
3940 4328 2.477825 CCTCGGACAATCTGCATACAG 58.522 52.381 0.00 0.00 45.95 2.74
3991 4379 1.064505 GGTCGCAATCACATCCACATG 59.935 52.381 0.00 0.00 35.92 3.21
4034 4423 0.608035 TTGCGAACCCACATTCCTCC 60.608 55.000 0.00 0.00 0.00 4.30
4068 4457 1.374190 CCAGCCAGCTCAACTCTGT 59.626 57.895 0.00 0.00 0.00 3.41
4069 4458 1.376942 CCCAGCCAGCTCAACTCTG 60.377 63.158 0.00 0.00 0.00 3.35
4070 4459 2.600729 CCCCAGCCAGCTCAACTCT 61.601 63.158 0.00 0.00 0.00 3.24
4141 4530 1.202568 CTCTTTGACAGCACGCACG 59.797 57.895 0.00 0.00 0.00 5.34
4152 4541 4.060900 CACTGTAGAAGCAAGCTCTTTGA 58.939 43.478 0.00 0.00 39.21 2.69
4173 4562 0.684535 TCCTCAACTTGGATGTCGCA 59.315 50.000 0.00 0.00 0.00 5.10
4360 4755 5.963594 TCTCATCTGATTCTTCTGTGACAG 58.036 41.667 6.18 6.18 0.00 3.51
4489 4884 7.234166 ACATGTGTCACCATCTATGATCTATGA 59.766 37.037 0.00 0.00 0.00 2.15
4490 4885 7.384477 ACATGTGTCACCATCTATGATCTATG 58.616 38.462 0.00 0.00 0.00 2.23
4491 4886 7.550597 ACATGTGTCACCATCTATGATCTAT 57.449 36.000 0.00 0.00 0.00 1.98
4492 4887 6.983906 ACATGTGTCACCATCTATGATCTA 57.016 37.500 0.00 0.00 0.00 1.98
4493 4888 5.883685 ACATGTGTCACCATCTATGATCT 57.116 39.130 0.00 0.00 0.00 2.75
4494 4889 6.932356 AAACATGTGTCACCATCTATGATC 57.068 37.500 0.00 0.00 0.00 2.92
4495 4890 7.114754 AGAAAACATGTGTCACCATCTATGAT 58.885 34.615 0.00 0.00 0.00 2.45
4515 4910 3.500680 GTGTCACCATCGGCTAAAGAAAA 59.499 43.478 0.00 0.00 0.00 2.29
4519 4915 2.093306 TGTGTCACCATCGGCTAAAG 57.907 50.000 0.00 0.00 0.00 1.85
4579 5000 1.463444 GGCAGAGCATTTTACGTCGTT 59.537 47.619 1.78 0.00 0.00 3.85
4648 5069 4.758674 CCTGAATGCACATCTACCATTAGG 59.241 45.833 0.00 0.00 42.21 2.69
4690 5111 0.449388 GAAGCAAGCTGGTTGATCCG 59.551 55.000 22.54 0.00 38.31 4.18
4707 5128 1.302993 GGTGGGTTTAGGCAGCGAA 60.303 57.895 0.00 0.00 0.00 4.70
4758 5180 8.240883 AGTACGTCATTTCATCTAACAGAAAC 57.759 34.615 0.00 0.00 36.65 2.78
4835 5257 7.295322 ACATCACTGTCATATATACTGCAGT 57.705 36.000 25.12 25.12 37.63 4.40
4841 5263 9.756461 CGTGTAGTACATCACTGTCATATATAC 57.244 37.037 6.21 0.00 38.24 1.47
4866 5368 6.215477 ACGTGCACATTCTATTATCAATCG 57.785 37.500 18.64 0.00 0.00 3.34
4868 5370 6.203530 CAGGACGTGCACATTCTATTATCAAT 59.796 38.462 18.64 0.00 0.00 2.57
4952 5454 8.298140 CGTTTTCCCAATACATTACCACTTTTA 58.702 33.333 0.00 0.00 0.00 1.52
4963 5465 2.041891 TCCCCACGTTTTCCCAATACAT 59.958 45.455 0.00 0.00 0.00 2.29
4967 5469 2.089600 TTTCCCCACGTTTTCCCAAT 57.910 45.000 0.00 0.00 0.00 3.16
4968 5470 1.689273 CATTTCCCCACGTTTTCCCAA 59.311 47.619 0.00 0.00 0.00 4.12


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

AutoCloner maintained by Alex Coulton.