Multiple sequence alignment - TraesCS4B01G287200

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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 TraesCS4B01G287200 chr4B 100.000 5112 0 0 1 5112 570731523 570736634 0.000000e+00 9441
1 TraesCS4B01G287200 chr4D 93.934 3627 139 38 1 3577 456489497 456493092 0.000000e+00 5404
2 TraesCS4B01G287200 chr4D 95.994 1248 38 5 3876 5112 456493389 456494635 0.000000e+00 2017
3 TraesCS4B01G287200 chr4D 96.283 269 9 1 3608 3876 456493093 456493360 1.690000e-119 440
4 TraesCS4B01G287200 chr4A 95.103 1266 58 3 2604 3868 11366022 11364760 0.000000e+00 1991
5 TraesCS4B01G287200 chr4A 92.181 908 42 15 1724 2602 11367107 11366200 0.000000e+00 1256
6 TraesCS4B01G287200 chr4A 90.380 842 49 15 956 1781 11367932 11367107 0.000000e+00 1077
7 TraesCS4B01G287200 chr4A 94.237 642 23 6 3876 4509 11364722 11364087 0.000000e+00 968
8 TraesCS4B01G287200 chr4A 88.259 741 78 5 37 770 11368762 11368024 0.000000e+00 878
9 TraesCS4B01G287200 chr4A 96.190 525 18 1 4590 5112 11364044 11363520 0.000000e+00 857


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 TraesCS4B01G287200 chr4B 570731523 570736634 5111 False 9441.000000 9441 100.000000 1 5112 1 chr4B.!!$F1 5111
1 TraesCS4B01G287200 chr4D 456489497 456494635 5138 False 2620.333333 5404 95.403667 1 5112 3 chr4D.!!$F1 5111
2 TraesCS4B01G287200 chr4A 11363520 11368762 5242 True 1171.166667 1991 92.725000 37 5112 6 chr4A.!!$R1 5075

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
186 187 0.036765 TGCCGCCAAGAATACTTCGT 60.037 50.000 0.00 0.0 33.70 3.85 F
729 738 0.175760 AGCCATCGCGCTAGAGAAAA 59.824 50.000 5.56 0.0 41.18 2.29 F
1074 1101 0.181350 GCTTCCATACCTCCCACCTG 59.819 60.000 0.00 0.0 0.00 4.00 F
1253 1280 0.319728 TCACACTTGCTCTCAGGCTC 59.680 55.000 0.00 0.0 0.00 4.70 F
1827 1934 1.132881 AGGGGAATCAAAAGGTTGCCA 60.133 47.619 1.53 0.0 37.54 4.92 F
1901 2008 2.168936 TGTGGAAGTACAGAACACCGTT 59.831 45.455 0.00 0.0 31.96 4.44 F
3269 3575 2.554032 GCATGCATATGTTACAGTCCCC 59.446 50.000 14.21 0.0 36.65 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1359 1387 0.028902 GTTTTTCCAACTGCGAGCGT 59.971 50.000 0.00 0.00 0.00 5.07 R
2222 2352 1.451449 TATGGGTGAGGTGGGTTTGT 58.549 50.000 0.00 0.00 0.00 2.83 R
3002 3308 3.006659 TGCTTTTAACCAATCGTGTGC 57.993 42.857 0.00 0.00 0.00 4.57 R
3173 3479 6.931281 GCAATATCTGAGATAGGTTACTGCAA 59.069 38.462 8.30 0.00 0.00 4.08 R
3269 3575 0.248539 GGTAGCTAGTCTTGTCGCCG 60.249 60.000 0.00 0.00 0.00 6.46 R
3740 4047 0.322816 CCCAGTGCTGCACCTTGTAT 60.323 55.000 27.74 6.65 34.49 2.29 R
4478 4852 0.037303 AACTGTGGACTGGGAGCATG 59.963 55.000 0.00 0.00 0.00 4.06 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
56 57 4.650734 TGAAGCACCATAGTCAACATGAA 58.349 39.130 0.00 0.00 0.00 2.57
134 135 1.148236 GGATACCACCTAGAGCCTCCT 59.852 57.143 0.00 0.00 0.00 3.69
137 138 1.311403 CCACCTAGAGCCTCCTCCA 59.689 63.158 0.00 0.00 38.96 3.86
138 139 0.758685 CCACCTAGAGCCTCCTCCAG 60.759 65.000 0.00 0.00 38.96 3.86
182 183 0.107654 GAGGTGCCGCCAAGAATACT 60.108 55.000 0.00 0.00 40.61 2.12
186 187 0.036765 TGCCGCCAAGAATACTTCGT 60.037 50.000 0.00 0.00 33.70 3.85
224 226 2.903855 GCCATGGGATGTCGCCAG 60.904 66.667 15.13 0.00 0.00 4.85
289 291 3.001533 CACCAAACAACTTCAGCAAATGC 59.998 43.478 0.00 0.00 42.49 3.56
319 327 2.753319 TCAGAATGACACCCGGTGA 58.247 52.632 24.80 2.65 42.56 4.02
326 334 2.122547 ACACCCGGTGACCTCCTT 60.123 61.111 24.80 0.00 36.96 3.36
327 335 1.765597 GACACCCGGTGACCTCCTTT 61.766 60.000 24.80 0.00 36.96 3.11
328 336 1.302511 CACCCGGTGACCTCCTTTG 60.303 63.158 12.68 0.00 35.23 2.77
392 400 1.228800 AAACCCGGTCTCCGTCTCT 60.229 57.895 0.00 0.00 46.80 3.10
423 431 1.957177 TGCCGCCAAAGACATGTTTAA 59.043 42.857 0.00 0.00 0.00 1.52
492 500 1.905843 CCTCCTCGAGGCCGATGAT 60.906 63.158 27.39 0.00 43.29 2.45
535 543 0.535102 CCCAAAAGTCGTCAGCAGGT 60.535 55.000 0.00 0.00 0.00 4.00
568 576 1.210478 CATCCAATCAACGGAGGACCT 59.790 52.381 0.00 0.00 36.41 3.85
570 578 2.542550 TCCAATCAACGGAGGACCTAA 58.457 47.619 0.00 0.00 0.00 2.69
614 622 1.807814 ACACAACCTCCTCTTGGACT 58.192 50.000 0.00 0.00 37.46 3.85
647 656 4.225942 TGATCCTCTGTGATAAACCAAGCT 59.774 41.667 0.00 0.00 0.00 3.74
708 717 0.951558 AAAGCGTGGCAAAAGATCGT 59.048 45.000 0.00 0.00 0.00 3.73
717 726 2.286418 GGCAAAAGATCGTTAGCCATCG 60.286 50.000 14.64 0.00 41.63 3.84
729 738 0.175760 AGCCATCGCGCTAGAGAAAA 59.824 50.000 5.56 0.00 41.18 2.29
764 773 2.032924 GTGAGCGTGTAACAAAAGGCTT 59.967 45.455 0.00 0.00 37.63 4.35
770 779 3.548014 CGTGTAACAAAAGGCTTGAGGTG 60.548 47.826 0.00 0.00 35.74 4.00
771 780 2.360801 TGTAACAAAAGGCTTGAGGTGC 59.639 45.455 0.00 0.00 0.00 5.01
772 781 6.804812 GTGTAACAAAAGGCTTGAGGTGCC 62.805 50.000 0.00 0.00 43.73 5.01
797 824 8.975439 CCACGTGGAAATTTGATACTATACTAC 58.025 37.037 31.31 0.00 37.39 2.73
844 871 5.912892 ACTGTGTTTTGTCCCTATTTTTGG 58.087 37.500 0.00 0.00 0.00 3.28
850 877 2.533916 TGTCCCTATTTTTGGCATGCA 58.466 42.857 21.36 2.54 0.00 3.96
855 882 5.002516 TCCCTATTTTTGGCATGCAAAAAG 58.997 37.500 27.33 18.53 42.41 2.27
912 939 2.091994 AGCAGGGCAAAGCATCTAATCT 60.092 45.455 0.00 0.00 0.00 2.40
940 967 2.428171 AGGGTCAAATGATCAAATGCCG 59.572 45.455 0.00 0.00 0.00 5.69
994 1021 1.956802 GGAAACGCCCACCAAAGAG 59.043 57.895 0.00 0.00 0.00 2.85
1051 1078 2.824489 GCTCCGCCAAAGCCCTAC 60.824 66.667 0.00 0.00 33.53 3.18
1074 1101 0.181350 GCTTCCATACCTCCCACCTG 59.819 60.000 0.00 0.00 0.00 4.00
1145 1172 5.536260 AGTTTTCGTAGTACAGGGTTCTTC 58.464 41.667 0.38 0.00 0.00 2.87
1146 1173 5.303845 AGTTTTCGTAGTACAGGGTTCTTCT 59.696 40.000 0.38 0.00 0.00 2.85
1147 1174 5.796424 TTTCGTAGTACAGGGTTCTTCTT 57.204 39.130 0.38 0.00 0.00 2.52
1154 1181 1.272147 ACAGGGTTCTTCTTGCCCATC 60.272 52.381 0.00 0.00 44.69 3.51
1201 1228 4.740902 GGGCCCTTGGATAAATCTTGTAT 58.259 43.478 17.04 0.00 0.00 2.29
1253 1280 0.319728 TCACACTTGCTCTCAGGCTC 59.680 55.000 0.00 0.00 0.00 4.70
1262 1289 1.755959 GCTCTCAGGCTCTCAGATTCA 59.244 52.381 0.00 0.00 0.00 2.57
1309 1336 2.642807 CCCAAGAACTCAGGAACCCTAA 59.357 50.000 0.00 0.00 29.64 2.69
1310 1337 3.307762 CCCAAGAACTCAGGAACCCTAAG 60.308 52.174 0.00 0.00 29.64 2.18
1311 1338 3.583086 CCAAGAACTCAGGAACCCTAAGA 59.417 47.826 0.00 0.00 29.64 2.10
1312 1339 4.226168 CCAAGAACTCAGGAACCCTAAGAT 59.774 45.833 0.00 0.00 29.64 2.40
1331 1358 7.383572 CCTAAGATAGAATCCACTGTGATTTCG 59.616 40.741 9.86 0.00 35.15 3.46
1365 1393 2.809601 CTCGGAACCCAACGCTCG 60.810 66.667 0.00 0.00 0.00 5.03
1388 1417 5.390991 CGCAGTTGGAAAAACTCTAAGATCC 60.391 44.000 0.00 0.00 0.00 3.36
1422 1451 5.885352 TGAAGATTTTAGGATTCCGATTGCA 59.115 36.000 0.00 0.00 0.00 4.08
1646 1675 3.504906 ACTGGTCATGTGAGAGCAAATTG 59.495 43.478 0.00 0.00 44.44 2.32
1649 1678 4.341806 TGGTCATGTGAGAGCAAATTGTTT 59.658 37.500 0.00 0.00 42.45 2.83
1650 1679 5.163426 TGGTCATGTGAGAGCAAATTGTTTT 60.163 36.000 0.00 0.00 42.45 2.43
1651 1680 5.754890 GGTCATGTGAGAGCAAATTGTTTTT 59.245 36.000 0.00 0.00 36.11 1.94
1696 1726 9.606631 ATGTCATTTAGTTGAACTAGAGGAATC 57.393 33.333 11.07 2.54 29.48 2.52
1716 1746 4.919774 TCTCTTTGTTACCCAATGCCTA 57.080 40.909 0.00 0.00 31.81 3.93
1718 1748 5.253330 TCTCTTTGTTACCCAATGCCTAAG 58.747 41.667 0.00 0.00 31.81 2.18
1794 1901 2.883386 CCTCTCTTTATTGATGGCCTGC 59.117 50.000 3.32 0.00 0.00 4.85
1814 1921 4.355549 TGCAGATTTTTGATGAGGGGAAT 58.644 39.130 0.00 0.00 0.00 3.01
1826 1933 1.550524 GAGGGGAATCAAAAGGTTGCC 59.449 52.381 0.00 0.00 34.50 4.52
1827 1934 1.132881 AGGGGAATCAAAAGGTTGCCA 60.133 47.619 1.53 0.00 37.54 4.92
1850 1957 4.702131 ACAATTTCTGAAATCTCTTCCCCG 59.298 41.667 15.43 0.78 0.00 5.73
1901 2008 2.168936 TGTGGAAGTACAGAACACCGTT 59.831 45.455 0.00 0.00 31.96 4.44
1937 2044 2.885135 ATTGGCAGGTCAGACAATCA 57.115 45.000 2.17 0.00 43.64 2.57
1939 2046 2.655090 TGGCAGGTCAGACAATCAAA 57.345 45.000 2.17 0.00 0.00 2.69
2063 2192 9.849166 GAGATAAACCATCATACTAAGCTCTAC 57.151 37.037 0.00 0.00 35.96 2.59
2065 2194 9.982651 GATAAACCATCATACTAAGCTCTACAA 57.017 33.333 0.00 0.00 33.46 2.41
2143 2273 8.907222 TGTAATGAGTGTGCATATGTGAATAT 57.093 30.769 4.29 0.00 0.00 1.28
2197 2327 2.694628 TCTTTTGCTGTTTCATGCCTGT 59.305 40.909 0.00 0.00 0.00 4.00
2222 2352 5.047377 CCGGTAACTTGTAAACAGTACCCTA 60.047 44.000 0.00 0.00 31.40 3.53
2277 2407 4.152647 GGTGTCCTCTTTTCCAAATTCCT 58.847 43.478 0.00 0.00 0.00 3.36
2417 2547 7.056006 AGATTTGGACATACAACAGCATATCA 58.944 34.615 0.00 0.00 0.00 2.15
3002 3308 9.796180 AACACTACTAATATCCTACTCCTACTG 57.204 37.037 0.00 0.00 0.00 2.74
3269 3575 2.554032 GCATGCATATGTTACAGTCCCC 59.446 50.000 14.21 0.00 36.65 4.81
3338 3644 9.474920 GAAGTAATTGTTGTTGATCAAAATGGA 57.525 29.630 10.35 0.00 37.81 3.41
3582 3888 3.081710 GGTAAACCCACCTAGCACATT 57.918 47.619 0.00 0.00 35.55 2.71
3631 3938 9.130661 TCTTTTGGATTTGTGATTCTAACAAGA 57.869 29.630 0.00 0.00 38.67 3.02
3830 4137 6.483307 TCTGGAAATCAACTGAGTACAAAGTG 59.517 38.462 0.00 0.00 0.00 3.16
3835 4142 7.391148 AATCAACTGAGTACAAAGTGTTGTT 57.609 32.000 0.00 0.00 46.01 2.83
3943 4309 7.872138 AGGATTCAAGGTTTATCATTGGTCTA 58.128 34.615 0.00 0.00 38.23 2.59
4123 4489 5.048013 TGTCGAGAAATGAGACACACTGTAT 60.048 40.000 0.00 0.00 39.63 2.29
4240 4606 8.225416 ACCCAAGAGACATACATCTAGTACATA 58.775 37.037 0.00 0.00 35.05 2.29
4374 4741 1.829222 AGGAATTGCAATTGCCTGAGG 59.171 47.619 32.26 0.00 41.18 3.86
4478 4852 2.092323 GGTAACCAATGAAGCCTGGAC 58.908 52.381 0.00 0.00 36.49 4.02
4487 4861 2.202236 GAAGCCTGGACATGCTCCCA 62.202 60.000 0.00 6.83 38.49 4.37
4514 4888 5.268544 CACAGTTTCTGTCATGTCAACAAG 58.731 41.667 0.00 0.00 43.43 3.16
4515 4889 4.336433 ACAGTTTCTGTCATGTCAACAAGG 59.664 41.667 0.00 0.00 41.21 3.61
4516 4890 3.885297 AGTTTCTGTCATGTCAACAAGGG 59.115 43.478 0.00 0.00 0.00 3.95
4527 4901 3.843619 TGTCAACAAGGGATCATCCAGTA 59.156 43.478 5.89 0.00 38.64 2.74
4530 4904 4.721274 TCAACAAGGGATCATCCAGTATCA 59.279 41.667 5.89 0.00 38.64 2.15
4531 4905 5.370584 TCAACAAGGGATCATCCAGTATCAT 59.629 40.000 5.89 0.00 38.64 2.45
4532 4906 5.238624 ACAAGGGATCATCCAGTATCATG 57.761 43.478 5.89 0.00 38.64 3.07
4533 4907 4.662179 ACAAGGGATCATCCAGTATCATGT 59.338 41.667 5.89 0.00 38.64 3.21
4534 4908 5.221803 ACAAGGGATCATCCAGTATCATGTC 60.222 44.000 5.89 0.00 38.64 3.06
4653 5032 2.482316 CCGTAGTCATATTCCGTGCCAA 60.482 50.000 0.00 0.00 0.00 4.52
4743 5122 2.296073 ACGGATACATCTCTCTCCCC 57.704 55.000 0.00 0.00 0.00 4.81
4752 5131 3.238597 CATCTCTCTCCCCCTTCTAAGG 58.761 54.545 1.47 1.47 46.06 2.69
4853 5232 1.678970 GCCCCTCATTGGCGACTTT 60.679 57.895 0.00 0.00 39.48 2.66
4862 5241 1.756408 TTGGCGACTTTGGGACGGTA 61.756 55.000 0.00 0.00 0.00 4.02
4897 5276 2.742372 GTCAACCTGCGGCGACAT 60.742 61.111 12.98 0.00 31.33 3.06
4910 5289 3.854809 GCGGCGACATTAAATTGCTTTTA 59.145 39.130 12.98 0.00 0.00 1.52
5078 5457 1.667830 GTACAGCCTGCGCTTGTCA 60.668 57.895 9.73 0.00 45.55 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 4.072131 GACTATGGTGCTTCAAACCTTGA 58.928 43.478 0.00 0.00 38.60 3.02
134 135 1.066858 GGCATCGTCTCTTTGACTGGA 60.067 52.381 0.00 0.00 43.25 3.86
137 138 2.300152 TGAAGGCATCGTCTCTTTGACT 59.700 45.455 0.00 0.00 43.25 3.41
138 139 2.688507 TGAAGGCATCGTCTCTTTGAC 58.311 47.619 0.00 0.00 42.06 3.18
182 183 1.624813 ACGGGGACTTAATTGGACGAA 59.375 47.619 0.00 0.00 0.00 3.85
186 187 2.026636 CCAAGACGGGGACTTAATTGGA 60.027 50.000 0.00 0.00 38.35 3.53
244 246 4.394920 GGAGCTTCGGTGATAAATGTGAAA 59.605 41.667 0.00 0.00 0.00 2.69
289 291 3.790152 TCATTCTGATGACGGAGACTG 57.210 47.619 0.00 0.00 37.37 3.51
326 334 1.595993 CGAAGGCGGAGTCTCCTCAA 61.596 60.000 17.00 0.00 40.46 3.02
327 335 2.046864 CGAAGGCGGAGTCTCCTCA 61.047 63.158 17.00 0.00 40.46 3.86
328 336 1.995646 GACGAAGGCGGAGTCTCCTC 61.996 65.000 17.00 8.89 40.46 3.71
392 400 2.359850 GGCGGCATTCTGGTGACA 60.360 61.111 3.07 0.00 39.59 3.58
423 431 5.986501 TGGTTACAGAGTTTTTGGTTTGT 57.013 34.783 0.00 0.00 0.00 2.83
492 500 4.607239 ACTTCCCTAAGAGACGTGGAATA 58.393 43.478 0.00 0.00 34.76 1.75
535 543 3.054213 TGATTGGATGCTGATGACCTTCA 60.054 43.478 0.00 0.00 0.00 3.02
568 576 2.068834 TGGCGGAAAACAACCCTTTA 57.931 45.000 0.00 0.00 0.00 1.85
570 578 0.678950 CATGGCGGAAAACAACCCTT 59.321 50.000 0.00 0.00 0.00 3.95
578 586 2.088423 GTGTATGGACATGGCGGAAAA 58.912 47.619 0.00 0.00 38.04 2.29
614 622 5.914898 TCACAGAGGATCAAATAGACGAA 57.085 39.130 0.00 0.00 37.82 3.85
708 717 1.029681 TTCTCTAGCGCGATGGCTAA 58.970 50.000 12.10 0.00 44.36 3.09
764 773 0.179004 AATTTCCACGTGGCACCTCA 60.179 50.000 30.25 8.69 34.44 3.86
770 779 5.751243 ATAGTATCAAATTTCCACGTGGC 57.249 39.130 30.25 11.44 34.44 5.01
771 780 8.975439 GTAGTATAGTATCAAATTTCCACGTGG 58.025 37.037 29.26 29.26 0.00 4.94
772 781 9.745880 AGTAGTATAGTATCAAATTTCCACGTG 57.254 33.333 9.08 9.08 0.00 4.49
813 840 4.885325 AGGGACAAAACACAGTAAACGATT 59.115 37.500 0.00 0.00 0.00 3.34
816 843 5.934935 ATAGGGACAAAACACAGTAAACG 57.065 39.130 0.00 0.00 0.00 3.60
817 844 8.813282 CAAAAATAGGGACAAAACACAGTAAAC 58.187 33.333 0.00 0.00 0.00 2.01
819 846 7.493367 CCAAAAATAGGGACAAAACACAGTAA 58.507 34.615 0.00 0.00 0.00 2.24
822 849 4.749598 GCCAAAAATAGGGACAAAACACAG 59.250 41.667 0.00 0.00 0.00 3.66
823 850 4.162320 TGCCAAAAATAGGGACAAAACACA 59.838 37.500 0.00 0.00 0.00 3.72
824 851 4.698575 TGCCAAAAATAGGGACAAAACAC 58.301 39.130 0.00 0.00 0.00 3.32
912 939 7.229306 GCATTTGATCATTTGACCCTCTACATA 59.771 37.037 0.00 0.00 0.00 2.29
940 967 7.903995 TTGATCATTTGCCCTGTTTTATTTC 57.096 32.000 0.00 0.00 0.00 2.17
994 1021 1.863267 CAGGAGACAGCCATCGAATC 58.137 55.000 0.00 0.00 0.00 2.52
1051 1078 0.918983 TGGGAGGTATGGAAGCAAGG 59.081 55.000 0.00 0.00 0.00 3.61
1074 1101 2.757980 TACCTGTTCTTTGGGGCGCC 62.758 60.000 21.18 21.18 0.00 6.53
1145 1172 2.409870 GGAACTGCGGATGGGCAAG 61.410 63.158 0.00 0.00 43.39 4.01
1146 1173 2.361104 GGAACTGCGGATGGGCAA 60.361 61.111 0.00 0.00 43.39 4.52
1147 1174 4.424711 GGGAACTGCGGATGGGCA 62.425 66.667 0.00 0.00 41.45 5.36
1154 1181 1.750399 CAGATTGGGGGAACTGCGG 60.750 63.158 0.00 0.00 0.00 5.69
1201 1228 6.780901 TGACCCCAATTATGTTGTGTACTAA 58.219 36.000 0.00 0.00 0.00 2.24
1253 1280 3.446161 ACCAATGTGGCAATGAATCTGAG 59.554 43.478 0.00 0.00 42.67 3.35
1262 1289 3.265737 TGAGTAGGTACCAATGTGGCAAT 59.734 43.478 15.94 0.00 42.67 3.56
1309 1336 5.053145 GCGAAATCACAGTGGATTCTATCT 58.947 41.667 0.00 0.00 36.51 1.98
1310 1337 5.053145 AGCGAAATCACAGTGGATTCTATC 58.947 41.667 0.00 2.63 36.51 2.08
1311 1338 5.028549 AGCGAAATCACAGTGGATTCTAT 57.971 39.130 0.00 0.00 36.51 1.98
1312 1339 4.471904 AGCGAAATCACAGTGGATTCTA 57.528 40.909 0.00 0.00 36.51 2.10
1359 1387 0.028902 GTTTTTCCAACTGCGAGCGT 59.971 50.000 0.00 0.00 0.00 5.07
1365 1393 5.707764 AGGATCTTAGAGTTTTTCCAACTGC 59.292 40.000 2.21 0.00 0.00 4.40
1404 1433 8.690884 TCAAATATTGCAATCGGAATCCTAAAA 58.309 29.630 16.86 0.00 34.62 1.52
1414 1443 5.163622 ACTCAGGTTCAAATATTGCAATCGG 60.164 40.000 16.86 4.28 0.00 4.18
1422 1451 7.184862 AGAATCCCAACTCAGGTTCAAATATT 58.815 34.615 0.00 0.00 32.73 1.28
1468 1497 1.333931 TCTTGATAGACTGTAGGCGCG 59.666 52.381 0.00 0.00 0.00 6.86
1480 1509 3.391965 GGAGCAGAGCACATCTTGATAG 58.608 50.000 0.00 0.00 35.47 2.08
1655 1684 2.946564 TGACATAATATCGCTGCTCCG 58.053 47.619 0.00 0.00 0.00 4.63
1656 1685 5.869753 AAATGACATAATATCGCTGCTCC 57.130 39.130 0.00 0.00 0.00 4.70
1657 1686 7.588143 ACTAAATGACATAATATCGCTGCTC 57.412 36.000 0.00 0.00 0.00 4.26
1691 1721 4.142160 GGCATTGGGTAACAAAGAGATTCC 60.142 45.833 0.00 0.00 43.46 3.01
1696 1726 4.399303 CCTTAGGCATTGGGTAACAAAGAG 59.601 45.833 0.00 0.00 43.46 2.85
1716 1746 6.712114 AAAATTTAATTGGGTTAGGGCCTT 57.288 33.333 13.45 0.00 0.00 4.35
1718 1748 6.242396 ACAAAAATTTAATTGGGTTAGGGCC 58.758 36.000 0.00 0.00 0.00 5.80
1720 1750 9.126151 ACAAACAAAAATTTAATTGGGTTAGGG 57.874 29.630 7.36 0.00 0.00 3.53
1794 1901 6.534475 TTGATTCCCCTCATCAAAAATCTG 57.466 37.500 0.00 0.00 37.64 2.90
1814 1921 4.161189 TCAGAAATTGTGGCAACCTTTTGA 59.839 37.500 0.00 0.00 34.24 2.69
1826 1933 5.392380 CGGGGAAGAGATTTCAGAAATTGTG 60.392 44.000 9.84 0.00 0.00 3.33
1827 1934 4.702131 CGGGGAAGAGATTTCAGAAATTGT 59.298 41.667 9.84 0.99 0.00 2.71
1850 1957 2.964740 TGTATGAGTTGCAGCTCACTC 58.035 47.619 32.03 25.71 46.72 3.51
1871 1978 3.646162 TCTGTACTTCCACATTGTCTGGT 59.354 43.478 0.00 0.00 0.00 4.00
1901 2008 3.681594 GCCAATCACCTCGGAAGTGAATA 60.682 47.826 13.03 0.00 46.67 1.75
1937 2044 8.985315 ACATGATATGGTGATATTGAGTGTTT 57.015 30.769 0.00 0.00 33.60 2.83
1939 2046 8.843262 CAAACATGATATGGTGATATTGAGTGT 58.157 33.333 0.00 0.00 33.60 3.55
2063 2192 5.817816 AGCGGTAGAGGATGACTAAAATTTG 59.182 40.000 0.00 0.00 0.00 2.32
2065 2194 5.615925 AGCGGTAGAGGATGACTAAAATT 57.384 39.130 0.00 0.00 0.00 1.82
2066 2195 5.615925 AAGCGGTAGAGGATGACTAAAAT 57.384 39.130 0.00 0.00 0.00 1.82
2143 2273 9.733556 ACAATTTCATAGACAATAACAGGTGTA 57.266 29.630 0.00 0.00 0.00 2.90
2197 2327 4.262420 GGGTACTGTTTACAAGTTACCGGA 60.262 45.833 9.46 0.00 31.50 5.14
2222 2352 1.451449 TATGGGTGAGGTGGGTTTGT 58.549 50.000 0.00 0.00 0.00 2.83
2753 3059 9.768215 TGATTAAAGGAGGGAAGAAATAACAAT 57.232 29.630 0.00 0.00 0.00 2.71
3002 3308 3.006659 TGCTTTTAACCAATCGTGTGC 57.993 42.857 0.00 0.00 0.00 4.57
3173 3479 6.931281 GCAATATCTGAGATAGGTTACTGCAA 59.069 38.462 8.30 0.00 0.00 4.08
3182 3488 7.101700 TGCTGTAATGCAATATCTGAGATAGG 58.898 38.462 8.30 4.23 40.29 2.57
3269 3575 0.248539 GGTAGCTAGTCTTGTCGCCG 60.249 60.000 0.00 0.00 0.00 6.46
3338 3644 3.609175 CGACAATTGAAGTTCGCCACAAT 60.609 43.478 13.59 0.00 34.99 2.71
3420 3726 6.772716 TGCAGATATCATTAAAAGGAAGACCC 59.227 38.462 5.32 0.00 36.73 4.46
3437 3743 5.563876 ACTGAGAATGGATGTGCAGATAT 57.436 39.130 0.00 0.00 0.00 1.63
3740 4047 0.322816 CCCAGTGCTGCACCTTGTAT 60.323 55.000 27.74 6.65 34.49 2.29
3746 4053 0.895100 TGAATTCCCAGTGCTGCACC 60.895 55.000 27.74 11.30 34.49 5.01
3752 4059 2.778299 TGTACTGTGAATTCCCAGTGC 58.222 47.619 27.52 26.15 41.77 4.40
3943 4309 6.320672 CAGCTCAGGAATAATTTGGTCAAGAT 59.679 38.462 0.00 0.00 0.00 2.40
3954 4320 7.660617 CAGACAATCATACAGCTCAGGAATAAT 59.339 37.037 0.00 0.00 0.00 1.28
3958 4324 4.467438 TCAGACAATCATACAGCTCAGGAA 59.533 41.667 0.00 0.00 0.00 3.36
3962 4328 5.349061 ACATCAGACAATCATACAGCTCA 57.651 39.130 0.00 0.00 0.00 4.26
4123 4489 2.325583 CTGCTAAGGCGGGTAAATGA 57.674 50.000 0.00 0.00 40.90 2.57
4154 4520 3.188460 GGAGAACAAAAACAGCAGCGATA 59.812 43.478 0.00 0.00 0.00 2.92
4240 4606 6.189859 TGAGCCTTGAATTTCAGGAATGTAT 58.810 36.000 9.88 0.00 0.00 2.29
4478 4852 0.037303 AACTGTGGACTGGGAGCATG 59.963 55.000 0.00 0.00 0.00 4.06
4487 4861 3.134623 TGACATGACAGAAACTGTGGACT 59.865 43.478 9.15 0.00 45.44 3.85
4514 4888 4.829968 CAGACATGATACTGGATGATCCC 58.170 47.826 9.36 0.00 35.03 3.85
4515 4889 4.252073 GCAGACATGATACTGGATGATCC 58.748 47.826 4.05 4.05 36.96 3.36
4516 4890 4.891260 TGCAGACATGATACTGGATGATC 58.109 43.478 0.00 0.00 35.05 2.92
4527 4901 5.128919 GGGTTTATCTTCTGCAGACATGAT 58.871 41.667 18.03 20.57 32.83 2.45
4530 4904 3.535561 CGGGTTTATCTTCTGCAGACAT 58.464 45.455 18.03 13.92 32.83 3.06
4531 4905 2.354704 CCGGGTTTATCTTCTGCAGACA 60.355 50.000 18.03 6.45 32.83 3.41
4532 4906 2.280628 CCGGGTTTATCTTCTGCAGAC 58.719 52.381 18.03 3.09 32.83 3.51
4533 4907 1.406887 GCCGGGTTTATCTTCTGCAGA 60.407 52.381 13.74 13.74 35.33 4.26
4534 4908 1.017387 GCCGGGTTTATCTTCTGCAG 58.983 55.000 7.63 7.63 0.00 4.41
4600 4977 7.986320 TGATGAATTGTTTTTCACCAAATCTGT 59.014 29.630 0.00 0.00 38.37 3.41
4653 5032 3.507622 GCTTCTTGCTCATTTGTAGGGTT 59.492 43.478 0.00 0.00 38.95 4.11
4743 5122 7.531955 TGCACTAGAAGCACACCTTAGAAGG 62.532 48.000 6.77 6.77 43.76 3.46
4853 5232 0.979187 GGACCTCCAATACCGTCCCA 60.979 60.000 0.00 0.00 39.13 4.37
4897 5276 7.448469 AGCTCCAAGACTCTAAAAGCAATTTAA 59.552 33.333 8.42 0.00 33.20 1.52
5009 5388 2.717639 ATCCTAAGAAAGGCGCACAT 57.282 45.000 10.83 0.00 46.10 3.21


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

AutoCloner maintained by Alex Coulton.