Multiple sequence alignment - TraesCS5B01G284400

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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 TraesCS5B01G284400 chr5B 100.000 5175 0 0 1 5175 470029525 470034699 0.000000e+00 9557
1 TraesCS5B01G284400 chr5A 94.344 3713 181 22 740 4438 493190702 493194399 0.000000e+00 5666
2 TraesCS5B01G284400 chr5A 92.074 593 41 5 1 590 493189480 493190069 0.000000e+00 830
3 TraesCS5B01G284400 chr5A 87.535 722 49 15 4474 5175 493194397 493195097 0.000000e+00 797
4 TraesCS5B01G284400 chr5A 86.420 162 13 4 593 747 493190437 493190596 8.910000e-38 169
5 TraesCS5B01G284400 chr5D 95.615 3421 146 4 927 4344 390019322 390022741 0.000000e+00 5483
6 TraesCS5B01G284400 chr5D 93.634 754 29 10 1 747 390018248 390018989 0.000000e+00 1109
7 TraesCS5B01G284400 chr5D 89.778 675 43 16 4471 5140 390022806 390023459 0.000000e+00 841
8 TraesCS5B01G284400 chr5D 98.551 69 1 0 4370 4438 390022741 390022809 7.040000e-24 122


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 TraesCS5B01G284400 chr5B 470029525 470034699 5174 False 9557.00 9557 100.00000 1 5175 1 chr5B.!!$F1 5174
1 TraesCS5B01G284400 chr5A 493189480 493195097 5617 False 1865.50 5666 90.09325 1 5175 4 chr5A.!!$F1 5174
2 TraesCS5B01G284400 chr5D 390018248 390023459 5211 False 1888.75 5483 94.39450 1 5140 4 chr5D.!!$F1 5139

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
749 1243 1.142097 GCCCGGCTACAGAGACTTC 59.858 63.158 0.71 0.0 0.00 3.01 F
1573 2112 0.040425 CCTCAACCTTTTCGCCAACG 60.040 55.000 0.00 0.0 42.01 4.10 F
2337 2876 0.251653 ACTTGAGTAGGAGCGTCCCA 60.252 55.000 1.06 0.0 37.19 4.37 F
2943 3482 0.251787 ACCTGCCCCCATGTTCTTTC 60.252 55.000 0.00 0.0 0.00 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2111 2650 0.378962 AGAGATCGACGAAGGAAGCG 59.621 55.000 0.0 0.0 0.00 4.68 R
2631 3170 1.071471 CTCGCAGTCACCAAGGGTT 59.929 57.895 0.0 0.0 31.02 4.11 R
3935 4474 3.070446 TCAACAACGTCCATTACTCCACT 59.930 43.478 0.0 0.0 0.00 4.00 R
4452 4994 0.106519 ACTGCTCTGTTTTGGCTGGT 60.107 50.000 0.0 0.0 0.00 4.00 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
28 29 4.451900 CATTAATTTCCGCACTCCTAGGT 58.548 43.478 9.08 0.00 0.00 3.08
35 36 3.167485 TCCGCACTCCTAGGTTTAAGAA 58.833 45.455 9.08 0.00 0.00 2.52
37 38 3.306502 CCGCACTCCTAGGTTTAAGAACA 60.307 47.826 9.08 0.00 37.51 3.18
38 39 4.504858 CGCACTCCTAGGTTTAAGAACAT 58.495 43.478 9.08 0.00 37.51 2.71
294 302 8.940768 AAAAGTAAAAATAAGCAGCACTTTCA 57.059 26.923 0.00 0.00 39.97 2.69
549 558 2.111878 CAGATAGCCCTTGCCCCG 59.888 66.667 0.00 0.00 38.69 5.73
575 584 1.375326 GGAAAACGGTGCTCCTCCT 59.625 57.895 2.85 0.00 0.00 3.69
590 599 1.957877 CCTCCTCCTAGTCGATGGAAC 59.042 57.143 6.31 0.00 31.23 3.62
639 1019 3.385111 AGTCATAGGATTGACCGAAGACC 59.615 47.826 1.19 0.00 45.80 3.85
677 1057 3.875727 CAGATGCAGAAACCATAGTCCAG 59.124 47.826 0.00 0.00 0.00 3.86
679 1059 4.411540 AGATGCAGAAACCATAGTCCAGAT 59.588 41.667 0.00 0.00 0.00 2.90
749 1243 1.142097 GCCCGGCTACAGAGACTTC 59.858 63.158 0.71 0.00 0.00 3.01
871 1365 2.047274 ACCATTGACGTCCAGGCG 60.047 61.111 14.12 0.84 37.94 5.52
893 1387 4.143473 CGTTTGACGCGTTTACTTGACTAT 60.143 41.667 15.53 0.00 33.65 2.12
895 1389 6.237384 CGTTTGACGCGTTTACTTGACTATAT 60.237 38.462 15.53 0.00 33.65 0.86
905 1399 8.021973 CGTTTACTTGACTATATACAGGGCTAG 58.978 40.741 0.00 0.00 0.00 3.42
906 1400 8.858094 GTTTACTTGACTATATACAGGGCTAGT 58.142 37.037 0.00 0.00 0.00 2.57
913 1408 8.608598 TGACTATATACAGGGCTAGTATGTGTA 58.391 37.037 11.01 5.40 34.28 2.90
950 1483 1.416401 TCGTCTTCCCAGCAGAACTTT 59.584 47.619 0.00 0.00 0.00 2.66
967 1500 1.197721 CTTTCGTGAGTTGTGGCCATC 59.802 52.381 9.72 2.05 0.00 3.51
970 1503 1.167851 CGTGAGTTGTGGCCATCAAT 58.832 50.000 9.72 0.00 0.00 2.57
971 1504 2.027653 TCGTGAGTTGTGGCCATCAATA 60.028 45.455 9.72 3.96 0.00 1.90
978 1511 4.082026 AGTTGTGGCCATCAATAAAAGCTC 60.082 41.667 9.72 1.27 0.00 4.09
1009 1542 0.460284 CCTACGACCGATGCAAGCTT 60.460 55.000 0.00 0.00 0.00 3.74
1011 1544 0.245266 TACGACCGATGCAAGCTTCA 59.755 50.000 0.00 0.00 0.00 3.02
1214 1753 0.251121 ACGTCCAATCCCATGTGCAA 60.251 50.000 0.00 0.00 0.00 4.08
1278 1817 1.664649 CGCGCTGAACCTCAACTCA 60.665 57.895 5.56 0.00 0.00 3.41
1290 1829 1.133181 TCAACTCATCCCACCTGGCA 61.133 55.000 0.00 0.00 0.00 4.92
1350 1889 0.108585 TCAGGACACTCAACCTTGGC 59.891 55.000 0.00 0.00 33.91 4.52
1353 1892 0.951040 GGACACTCAACCTTGGCGAG 60.951 60.000 0.00 0.00 0.00 5.03
1357 1896 0.468226 ACTCAACCTTGGCGAGAACA 59.532 50.000 2.43 0.00 0.00 3.18
1358 1897 1.151668 CTCAACCTTGGCGAGAACAG 58.848 55.000 2.43 0.00 0.00 3.16
1360 1899 0.886490 CAACCTTGGCGAGAACAGCT 60.886 55.000 2.43 0.00 34.52 4.24
1464 2003 2.034066 CCGGCAGCTTTGGGAAGA 59.966 61.111 0.00 0.00 34.71 2.87
1480 2019 0.250234 AAGATGCACTAAGCTGCGGA 59.750 50.000 0.00 0.00 45.94 5.54
1537 2076 0.471591 CCCTGCTCAGATAGGCTCCT 60.472 60.000 0.00 0.00 32.58 3.69
1573 2112 0.040425 CCTCAACCTTTTCGCCAACG 60.040 55.000 0.00 0.00 42.01 4.10
1587 2126 1.671054 CAACGACTTGTCCGGGCAT 60.671 57.895 10.94 0.00 0.00 4.40
1609 2148 2.104331 CGCCGTCGATAGCCAACT 59.896 61.111 0.00 0.00 38.10 3.16
1665 2204 1.229951 TCTGTCAGGGGCCATTCCT 60.230 57.895 4.39 0.00 34.39 3.36
1672 2211 0.849417 AGGGGCCATTCCTTCATCTC 59.151 55.000 4.39 0.00 34.39 2.75
1705 2244 1.639298 CCGCCTCTCTTTGCTTTCGG 61.639 60.000 0.00 0.00 0.00 4.30
1719 2258 3.886505 TGCTTTCGGTCCAGTTTAACAAT 59.113 39.130 0.00 0.00 0.00 2.71
1725 2264 4.449743 TCGGTCCAGTTTAACAATCTTTCG 59.550 41.667 0.00 0.00 0.00 3.46
1744 2283 2.833244 GGACTCATCCCTCCTCCAG 58.167 63.158 0.00 0.00 39.39 3.86
1770 2309 4.039124 TGGAACATTTCTTCCTTGAAAGGC 59.961 41.667 4.08 0.00 46.06 4.35
1776 2315 6.721208 ACATTTCTTCCTTGAAAGGCTTATCA 59.279 34.615 0.00 4.12 46.06 2.15
1779 2318 5.491982 TCTTCCTTGAAAGGCTTATCAGTC 58.508 41.667 0.00 0.00 46.06 3.51
1782 2321 3.372206 CCTTGAAAGGCTTATCAGTCGTG 59.628 47.826 0.00 0.00 39.76 4.35
1785 2324 0.541863 AAGGCTTATCAGTCGTGGGG 59.458 55.000 0.00 0.00 0.00 4.96
1842 2381 1.760029 GCTAACCTCCCTCTTCTCCAG 59.240 57.143 0.00 0.00 0.00 3.86
1994 2533 2.012673 GCAGAATCTTGAATCGCTGGT 58.987 47.619 0.00 0.00 0.00 4.00
2001 2540 2.562738 TCTTGAATCGCTGGTTCTCTCA 59.437 45.455 3.80 0.00 0.00 3.27
2033 2572 1.000955 ACAAGCTACGACTCCAAGTGG 59.999 52.381 0.00 0.00 0.00 4.00
2111 2650 3.532542 CCTCAAACGAATTAGGAGGGAC 58.467 50.000 0.00 0.00 41.12 4.46
2166 2705 2.750712 GCTCGTATATCTGTCCCTCTCC 59.249 54.545 0.00 0.00 0.00 3.71
2212 2751 9.093458 ACATACCTGAAAGAATTGGAAATCTTT 57.907 29.630 2.70 2.70 45.85 2.52
2312 2851 1.584724 GGAGATCTGTCCCTGGGAAA 58.415 55.000 19.06 12.01 31.38 3.13
2326 2865 4.445735 CCCTGGGAAAGAACAACTTGAGTA 60.446 45.833 7.01 0.00 38.98 2.59
2337 2876 0.251653 ACTTGAGTAGGAGCGTCCCA 60.252 55.000 1.06 0.00 37.19 4.37
2478 3017 5.253330 TCCAACAACTTGACAGGGATAATC 58.747 41.667 0.00 0.00 0.00 1.75
2631 3170 6.520021 AGATTATCACATGAAATCCCTCCA 57.480 37.500 0.00 0.00 31.35 3.86
2812 3351 6.089551 CCTCAACACACTTCACTATCTAAACG 59.910 42.308 0.00 0.00 0.00 3.60
2838 3377 4.994852 TCCTTCAATAACTTCGTTGGTGAG 59.005 41.667 0.00 0.00 0.00 3.51
2943 3482 0.251787 ACCTGCCCCCATGTTCTTTC 60.252 55.000 0.00 0.00 0.00 2.62
2949 3488 1.670811 CCCCCATGTTCTTTCGAATCG 59.329 52.381 0.00 0.00 0.00 3.34
3090 3629 1.207089 TCGACTGCAACTATCCAAGGG 59.793 52.381 0.00 0.00 0.00 3.95
3209 3748 2.769602 AACTTAGGCGGAGATAGGGA 57.230 50.000 0.00 0.00 0.00 4.20
3219 3758 1.346068 GGAGATAGGGATGACAGTGCC 59.654 57.143 0.00 0.00 0.00 5.01
3381 3920 1.886542 GGGGACGACTTCAAAGCAATT 59.113 47.619 0.00 0.00 0.00 2.32
3409 3948 4.922206 TGAGTTCATGCCTAATGGAAGTT 58.078 39.130 0.00 0.00 36.86 2.66
3436 3975 1.327303 TTGGTTGCATCCAGACCAAC 58.673 50.000 14.55 0.00 45.69 3.77
3471 4010 7.633789 AGCATTTGGATCTCCTTAAAAGAGTA 58.366 34.615 0.00 0.00 36.82 2.59
3575 4114 4.321899 GCCAAGCAATGTACTTTTGGATGA 60.322 41.667 12.57 0.00 40.52 2.92
3711 4250 1.339151 GCTCCAGGTTTGTCCGATTCT 60.339 52.381 0.00 0.00 41.99 2.40
3751 4290 4.283978 TCCTTAAAACGGTCTACATCACCA 59.716 41.667 0.00 0.00 32.89 4.17
3774 4313 9.807649 ACCAAAATGCTAATATCTTCAAATGTC 57.192 29.630 0.00 0.00 0.00 3.06
3835 4374 6.985653 ATACAAGGAGATGTGTACAGCTAT 57.014 37.500 2.39 0.00 43.41 2.97
3935 4474 5.879763 AGTATGCTGAAATGGCCATACATA 58.120 37.500 21.15 17.54 32.09 2.29
3994 4533 3.528370 ATCGAGAAGGGGTCGCCG 61.528 66.667 0.00 0.00 37.35 6.46
3995 4534 4.728110 TCGAGAAGGGGTCGCCGA 62.728 66.667 0.00 0.00 37.35 5.54
4079 4619 3.239449 TGCCTGACCTCACTTCTTAGAA 58.761 45.455 0.00 0.00 0.00 2.10
4135 4675 9.593134 GTGAGTAGAATGTTGATCAAAGATACT 57.407 33.333 10.35 13.27 0.00 2.12
4149 4689 9.102757 GATCAAAGATACTATCAAAGAGTTGCA 57.897 33.333 0.00 0.00 34.50 4.08
4151 4691 7.550551 TCAAAGATACTATCAAAGAGTTGCAGG 59.449 37.037 0.00 0.00 34.50 4.85
4164 4704 5.994250 AGAGTTGCAGGCTATCAAAGATTA 58.006 37.500 3.37 0.00 0.00 1.75
4169 4709 4.164030 TGCAGGCTATCAAAGATTACCTCA 59.836 41.667 0.00 0.00 0.00 3.86
4170 4710 5.163163 TGCAGGCTATCAAAGATTACCTCAT 60.163 40.000 0.00 0.00 0.00 2.90
4176 4716 8.150945 GGCTATCAAAGATTACCTCATGTAGAA 58.849 37.037 0.00 0.00 0.00 2.10
4222 4762 2.274760 GCCAGATGCCAGAGCCTT 59.725 61.111 0.00 0.00 38.69 4.35
4223 4763 2.119655 GCCAGATGCCAGAGCCTTG 61.120 63.158 0.00 0.00 38.69 3.61
4232 4772 4.235079 TGCCAGAGCCTTGTGTATTTAT 57.765 40.909 0.00 0.00 38.69 1.40
4237 4777 6.223852 CCAGAGCCTTGTGTATTTATCGTAT 58.776 40.000 0.00 0.00 0.00 3.06
4280 4820 6.882610 TCTTCAATTTGTAGCATGTGTCTT 57.117 33.333 0.00 0.00 0.00 3.01
4281 4821 6.902341 TCTTCAATTTGTAGCATGTGTCTTC 58.098 36.000 0.00 0.00 0.00 2.87
4282 4822 6.712095 TCTTCAATTTGTAGCATGTGTCTTCT 59.288 34.615 0.00 0.00 0.00 2.85
4283 4823 7.877612 TCTTCAATTTGTAGCATGTGTCTTCTA 59.122 33.333 0.00 0.00 0.00 2.10
4284 4824 7.364522 TCAATTTGTAGCATGTGTCTTCTAC 57.635 36.000 0.00 0.00 33.80 2.59
4285 4825 6.934083 TCAATTTGTAGCATGTGTCTTCTACA 59.066 34.615 4.97 4.97 39.44 2.74
4292 4834 6.246420 AGCATGTGTCTTCTACATTTTCAC 57.754 37.500 0.00 0.00 41.10 3.18
4312 4854 5.233225 TCACACATCTGCTAGTTTCTTGAG 58.767 41.667 0.00 0.00 0.00 3.02
4316 4858 5.576384 CACATCTGCTAGTTTCTTGAGAGAC 59.424 44.000 0.00 0.00 0.00 3.36
4418 4960 6.538742 GTGACTGAAATTTATCGGAATCCAGA 59.461 38.462 0.00 0.00 0.00 3.86
4436 4978 9.764363 GAATCCAGACAGTATTATTGACATGTA 57.236 33.333 0.00 0.00 0.00 2.29
4438 4980 9.935241 ATCCAGACAGTATTATTGACATGTATC 57.065 33.333 0.00 0.00 0.00 2.24
4439 4981 9.147732 TCCAGACAGTATTATTGACATGTATCT 57.852 33.333 0.00 0.00 0.00 1.98
4459 5001 3.478780 GGTCTGTACCACCAGCCA 58.521 61.111 6.27 0.00 45.98 4.75
4460 5002 1.758592 GGTCTGTACCACCAGCCAA 59.241 57.895 6.27 0.00 45.98 4.52
4461 5003 0.109723 GGTCTGTACCACCAGCCAAA 59.890 55.000 6.27 0.00 45.98 3.28
4462 5004 1.477923 GGTCTGTACCACCAGCCAAAA 60.478 52.381 6.27 0.00 45.98 2.44
4463 5005 1.607148 GTCTGTACCACCAGCCAAAAC 59.393 52.381 0.00 0.00 32.32 2.43
4464 5006 1.213182 TCTGTACCACCAGCCAAAACA 59.787 47.619 0.00 0.00 32.32 2.83
4465 5007 1.608590 CTGTACCACCAGCCAAAACAG 59.391 52.381 0.00 0.00 0.00 3.16
4466 5008 1.213182 TGTACCACCAGCCAAAACAGA 59.787 47.619 0.00 0.00 0.00 3.41
4467 5009 1.880027 GTACCACCAGCCAAAACAGAG 59.120 52.381 0.00 0.00 0.00 3.35
4468 5010 1.109323 ACCACCAGCCAAAACAGAGC 61.109 55.000 0.00 0.00 0.00 4.09
4469 5011 1.108727 CCACCAGCCAAAACAGAGCA 61.109 55.000 0.00 0.00 0.00 4.26
4470 5012 0.313043 CACCAGCCAAAACAGAGCAG 59.687 55.000 0.00 0.00 0.00 4.24
4471 5013 0.106519 ACCAGCCAAAACAGAGCAGT 60.107 50.000 0.00 0.00 0.00 4.40
4472 5014 1.142870 ACCAGCCAAAACAGAGCAGTA 59.857 47.619 0.00 0.00 0.00 2.74
4473 5015 2.224867 ACCAGCCAAAACAGAGCAGTAT 60.225 45.455 0.00 0.00 0.00 2.12
4493 5037 6.004574 AGTATATAGCTCGACTTCCATGACA 58.995 40.000 0.00 0.00 0.00 3.58
4554 5098 3.200605 AGCACATATCATCCAAGTGGTGA 59.799 43.478 0.00 1.61 39.20 4.02
4561 5105 2.705658 TCATCCAAGTGGTGACAAGAGT 59.294 45.455 0.00 0.00 46.06 3.24
4565 5109 2.158900 CCAAGTGGTGACAAGAGTCTGT 60.159 50.000 0.00 0.00 46.06 3.41
4603 5147 4.927978 TGAACCCCAATAACAAACAGTG 57.072 40.909 0.00 0.00 0.00 3.66
4625 5169 8.245491 CAGTGACATCATATGTTTCCATGAAAA 58.755 33.333 1.90 0.00 45.03 2.29
4627 5171 9.590451 GTGACATCATATGTTTCCATGAAAAAT 57.410 29.630 1.90 0.00 45.03 1.82
4843 5400 3.244875 TGACCTTTGCAGCTATTTCCTCA 60.245 43.478 0.00 0.00 0.00 3.86
4869 5426 5.789710 GCATTTGCATTTTCAGCTATGTT 57.210 34.783 0.00 0.00 41.59 2.71
4870 5427 6.173191 GCATTTGCATTTTCAGCTATGTTT 57.827 33.333 0.00 0.00 41.59 2.83
4871 5428 6.019152 GCATTTGCATTTTCAGCTATGTTTG 58.981 36.000 0.00 0.00 41.59 2.93
4872 5429 6.128499 GCATTTGCATTTTCAGCTATGTTTGA 60.128 34.615 0.00 0.00 41.59 2.69
4873 5430 7.453034 CATTTGCATTTTCAGCTATGTTTGAG 58.547 34.615 0.00 0.00 0.00 3.02
4874 5431 4.487948 TGCATTTTCAGCTATGTTTGAGC 58.512 39.130 0.00 0.00 40.42 4.26
4910 5467 5.073478 GCTTGAAACACGAGTCTATTTTCG 58.927 41.667 0.00 0.00 42.26 3.46
4920 5477 7.597743 ACACGAGTCTATTTTCGTTGTATTCTT 59.402 33.333 0.00 0.00 46.87 2.52
4921 5478 8.433126 CACGAGTCTATTTTCGTTGTATTCTTT 58.567 33.333 0.00 0.00 46.87 2.52
4938 5495 8.992349 TGTATTCTTTCTCTCCATCCTTCAATA 58.008 33.333 0.00 0.00 0.00 1.90
4959 5516 9.249053 TCAATAATTGGAACATTAAAGTAGGCA 57.751 29.630 0.00 0.00 39.30 4.75
4960 5517 9.868277 CAATAATTGGAACATTAAAGTAGGCAA 57.132 29.630 0.00 0.00 39.30 4.52
4990 5549 7.777095 AGATTCCTAGATTATAACGATGCCTC 58.223 38.462 0.00 0.00 0.00 4.70
5008 5567 8.495949 CGATGCCTCGTCAAATTAGTAAATTAT 58.504 33.333 2.94 0.00 40.07 1.28
5070 5631 2.238646 TGCCGTACCTTGATTCCTTGAT 59.761 45.455 0.00 0.00 0.00 2.57
5074 5635 5.424757 CCGTACCTTGATTCCTTGATGTTA 58.575 41.667 0.00 0.00 0.00 2.41
5136 5699 3.008266 TGGTCTCTCTCATGCATTCAACA 59.992 43.478 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.004752 AGGAGTGCGGAAATTAATGCT 57.995 42.857 0.00 0.00 0.00 3.79
10 11 3.434940 AAACCTAGGAGTGCGGAAATT 57.565 42.857 17.98 0.00 0.00 1.82
14 15 2.811410 TCTTAAACCTAGGAGTGCGGA 58.189 47.619 17.98 3.50 0.00 5.54
20 21 5.529060 GCCATCATGTTCTTAAACCTAGGAG 59.471 44.000 17.98 1.70 34.28 3.69
241 244 4.024387 TGCAGACATTTTCCACTCGTTTAC 60.024 41.667 0.00 0.00 0.00 2.01
248 251 8.806146 ACTTTTTATATGCAGACATTTTCCACT 58.194 29.630 0.00 0.00 37.74 4.00
279 282 3.004734 GGTGTGTTGAAAGTGCTGCTTAT 59.995 43.478 0.00 0.00 36.17 1.73
283 286 0.592247 CGGTGTGTTGAAAGTGCTGC 60.592 55.000 0.00 0.00 0.00 5.25
294 302 2.479566 AGCATCATCTTCGGTGTGTT 57.520 45.000 0.00 0.00 0.00 3.32
422 430 5.722021 ATGCTTTGGTACCCTTTAAACTG 57.278 39.130 10.07 0.00 0.00 3.16
549 558 1.802337 GCACCGTTTTCCCCTTCACC 61.802 60.000 0.00 0.00 0.00 4.02
555 564 1.674651 GAGGAGCACCGTTTTCCCC 60.675 63.158 0.00 0.00 41.83 4.81
575 584 2.025226 AGTGAGGTTCCATCGACTAGGA 60.025 50.000 0.00 0.00 0.00 2.94
590 599 1.439679 GCGTTTCCCTAACAGTGAGG 58.560 55.000 0.00 0.00 36.50 3.86
677 1057 3.808174 GCTACCACTCAATTAACGGGATC 59.192 47.826 0.00 0.00 0.00 3.36
679 1059 2.835764 AGCTACCACTCAATTAACGGGA 59.164 45.455 0.00 0.00 0.00 5.14
732 1112 0.684805 AGGAAGTCTCTGTAGCCGGG 60.685 60.000 2.18 0.00 0.00 5.73
749 1243 4.984205 GACTAGAGTCGTTGGAGTTTAGG 58.016 47.826 0.00 0.00 35.58 2.69
793 1287 5.392595 GCTGAAGTATGAACGTCTTCTCTCT 60.393 44.000 13.23 0.00 38.52 3.10
797 1291 3.057456 ACGCTGAAGTATGAACGTCTTCT 60.057 43.478 13.23 0.00 38.52 2.85
871 1365 3.580794 AGTCAAGTAAACGCGTCAAAC 57.419 42.857 14.44 11.47 0.00 2.93
893 1387 9.848710 GAGATATACACATACTAGCCCTGTATA 57.151 37.037 10.35 10.35 35.68 1.47
895 1389 7.929959 AGAGATATACACATACTAGCCCTGTA 58.070 38.462 0.00 0.00 0.00 2.74
913 1408 7.338449 GGGAAGACGAGAAGCTAATAGAGATAT 59.662 40.741 0.00 0.00 0.00 1.63
950 1483 0.107643 TTGATGGCCACAACTCACGA 59.892 50.000 8.16 0.00 0.00 4.35
978 1511 2.678836 CGGTCGTAGGATAGATAGCAGG 59.321 54.545 0.00 0.00 0.00 4.85
1009 1542 1.895020 CGGGGGAAAGGACACGATGA 61.895 60.000 0.00 0.00 0.00 2.92
1011 1544 2.987125 CGGGGGAAAGGACACGAT 59.013 61.111 0.00 0.00 0.00 3.73
1203 1742 2.672651 CGCCACTTGCACATGGGA 60.673 61.111 15.59 0.00 41.33 4.37
1207 1746 1.376424 CTCCTCGCCACTTGCACAT 60.376 57.895 0.00 0.00 41.33 3.21
1214 1753 1.668294 CAAGTGACTCCTCGCCACT 59.332 57.895 0.00 0.00 42.34 4.00
1296 1835 1.087771 CCAAGAACGGCGGGATACAC 61.088 60.000 13.24 0.00 39.74 2.90
1297 1836 1.219664 CCAAGAACGGCGGGATACA 59.780 57.895 13.24 0.00 39.74 2.29
1300 1839 4.796495 GCCCAAGAACGGCGGGAT 62.796 66.667 13.24 0.00 43.21 3.85
1350 1889 2.680913 CCCGCCAAAGCTGTTCTCG 61.681 63.158 0.00 0.00 36.60 4.04
1353 1892 3.273080 CTGCCCGCCAAAGCTGTTC 62.273 63.158 0.00 0.00 36.60 3.18
1464 2003 0.533755 GGATCCGCAGCTTAGTGCAT 60.534 55.000 0.00 0.00 44.21 3.96
1480 2019 8.309486 AAGGAGGTTATTCCTGAGATTGAGGAT 61.309 40.741 0.00 0.00 46.90 3.24
1506 2045 1.198713 GAGCAGGGATCTCACCTTGA 58.801 55.000 0.00 0.00 38.98 3.02
1537 2076 6.445139 AGGTTGAGGATCTCTAGATTTTCCAA 59.555 38.462 14.70 4.74 34.37 3.53
1573 2112 1.594331 GGAATATGCCCGGACAAGTC 58.406 55.000 0.73 0.00 0.00 3.01
1575 2114 1.507141 GCGGAATATGCCCGGACAAG 61.507 60.000 0.73 0.00 46.55 3.16
1587 2126 1.174078 TGGCTATCGACGGCGGAATA 61.174 55.000 12.58 0.31 38.28 1.75
1609 2148 2.210116 GAGTGTTTGGAGCGAAGACAA 58.790 47.619 0.00 0.00 0.00 3.18
1665 2204 1.372582 GCATGCGACCAAGAGATGAA 58.627 50.000 0.00 0.00 0.00 2.57
1705 2244 4.758165 TCCCGAAAGATTGTTAAACTGGAC 59.242 41.667 0.00 0.00 0.00 4.02
1795 2334 2.125713 TGCAGGTATCGTGCCACG 60.126 61.111 11.80 11.80 43.45 4.94
1842 2381 4.994852 TGGTTGTAGCTCATGTAGAACAAC 59.005 41.667 19.32 19.32 44.65 3.32
1902 2441 3.079578 CTCAATTCTCTGCAGCTTGGAA 58.920 45.455 9.47 10.76 0.00 3.53
1906 2445 2.358015 GAGCTCAATTCTCTGCAGCTT 58.642 47.619 9.47 0.00 40.58 3.74
1972 2511 2.031807 CCAGCGATTCAAGATTCTGCAG 59.968 50.000 7.63 7.63 0.00 4.41
1994 2533 5.180117 GCTTGTAGCAGATTGTTTGAGAGAA 59.820 40.000 0.00 0.00 41.89 2.87
2001 2540 4.389077 GTCGTAGCTTGTAGCAGATTGTTT 59.611 41.667 0.00 0.00 45.56 2.83
2033 2572 1.168714 GGTGGACATGAAGTTCCAGC 58.831 55.000 14.32 14.32 38.11 4.85
2111 2650 0.378962 AGAGATCGACGAAGGAAGCG 59.621 55.000 0.00 0.00 0.00 4.68
2166 2705 3.899360 TGTTCCCTAGTATCCGGTTATGG 59.101 47.826 0.00 2.06 0.00 2.74
2212 2751 1.559682 GGATAGGACCTGCAACTGGAA 59.440 52.381 3.53 0.00 0.00 3.53
2312 2851 2.628657 ACGCTCCTACTCAAGTTGTTCT 59.371 45.455 2.11 0.00 0.00 3.01
2337 2876 5.989477 TGAGTAAGATTTCCGATGGTCAAT 58.011 37.500 0.00 0.00 0.00 2.57
2455 2994 4.715534 TTATCCCTGTCAAGTTGTTGGA 57.284 40.909 2.11 5.48 34.09 3.53
2478 3017 5.066505 GCTGATGTTGAATAAACTAGTGGGG 59.933 44.000 0.00 0.00 39.70 4.96
2483 3022 7.332926 AGAGTGTGCTGATGTTGAATAAACTAG 59.667 37.037 0.00 0.00 39.70 2.57
2631 3170 1.071471 CTCGCAGTCACCAAGGGTT 59.929 57.895 0.00 0.00 31.02 4.11
2784 3323 4.835615 AGATAGTGAAGTGTGTTGAGGTCT 59.164 41.667 0.00 0.00 0.00 3.85
2943 3482 5.738370 AGTTTGTTCTTCTTTGACGATTCG 58.262 37.500 4.14 4.14 0.00 3.34
2949 3488 7.257722 TCAATGGAAGTTTGTTCTTCTTTGAC 58.742 34.615 14.56 0.00 42.19 3.18
3119 3658 6.227298 TGGAGAAACCATTTGTTGCTTTTA 57.773 33.333 0.00 0.00 43.33 1.52
3209 3748 3.765511 AGCAACAATATTGGCACTGTCAT 59.234 39.130 19.37 0.00 0.00 3.06
3381 3920 4.701651 CCATTAGGCATGAACTCAAAGACA 59.298 41.667 0.00 0.00 34.31 3.41
3409 3948 4.943705 GTCTGGATGCAACCAATCTTCTAA 59.056 41.667 17.27 0.00 39.59 2.10
3436 3975 4.462133 AGATCCAAATGCTTCTCCTCATG 58.538 43.478 0.00 0.00 0.00 3.07
3471 4010 3.384168 TCCCACATCCAGTAGTATGCTT 58.616 45.455 0.00 0.00 0.00 3.91
3711 4250 4.469469 AAGGAAACATGGGGAAGAAAGA 57.531 40.909 0.00 0.00 0.00 2.52
3774 4313 6.942005 TCCAGCACCATATTCTATAACATTGG 59.058 38.462 0.00 0.00 0.00 3.16
3787 4326 5.057843 AGATCACATTTCCAGCACCATAT 57.942 39.130 0.00 0.00 0.00 1.78
3878 4417 7.701539 TTAATCCTTGTATGAACATGCTGTT 57.298 32.000 0.00 1.82 44.37 3.16
3880 4419 8.627403 AGATTTAATCCTTGTATGAACATGCTG 58.373 33.333 0.78 0.00 34.97 4.41
3935 4474 3.070446 TCAACAACGTCCATTACTCCACT 59.930 43.478 0.00 0.00 0.00 4.00
3994 4533 5.652994 AAGTAGAAGAGTCATCTGTGGTC 57.347 43.478 8.14 0.00 35.37 4.02
3995 4534 6.426646 AAAAGTAGAAGAGTCATCTGTGGT 57.573 37.500 8.14 0.00 35.37 4.16
4135 4675 5.357742 TGATAGCCTGCAACTCTTTGATA 57.642 39.130 0.00 0.00 34.24 2.15
4149 4689 6.506538 ACATGAGGTAATCTTTGATAGCCT 57.493 37.500 0.00 0.00 0.00 4.58
4151 4691 9.202273 CTTCTACATGAGGTAATCTTTGATAGC 57.798 37.037 0.00 0.00 0.00 2.97
4164 4704 9.588096 AAAATTAAACCTTCTTCTACATGAGGT 57.412 29.630 0.00 0.00 0.00 3.85
4266 4806 6.934083 TGAAAATGTAGAAGACACATGCTACA 59.066 34.615 9.96 9.96 44.88 2.74
4280 4820 6.701340 ACTAGCAGATGTGTGAAAATGTAGA 58.299 36.000 0.00 0.00 0.00 2.59
4281 4821 6.974932 ACTAGCAGATGTGTGAAAATGTAG 57.025 37.500 0.00 0.00 0.00 2.74
4282 4822 7.661437 AGAAACTAGCAGATGTGTGAAAATGTA 59.339 33.333 0.00 0.00 0.00 2.29
4283 4823 6.488006 AGAAACTAGCAGATGTGTGAAAATGT 59.512 34.615 0.00 0.00 0.00 2.71
4284 4824 6.906659 AGAAACTAGCAGATGTGTGAAAATG 58.093 36.000 0.00 0.00 0.00 2.32
4285 4825 7.229306 TCAAGAAACTAGCAGATGTGTGAAAAT 59.771 33.333 0.00 0.00 0.00 1.82
4292 4834 5.576384 GTCTCTCAAGAAACTAGCAGATGTG 59.424 44.000 0.00 0.00 31.93 3.21
4351 4893 9.681062 TTCCCGAAGAGAATTACTTTTTGATAT 57.319 29.630 0.00 0.00 0.00 1.63
4436 4978 6.912332 TGGCTGGTGGTACAGACCTTAGAT 62.912 50.000 13.03 0.00 46.17 1.98
4437 4979 5.680449 TGGCTGGTGGTACAGACCTTAGA 62.680 52.174 13.03 0.00 46.17 2.10
4438 4980 3.414684 TGGCTGGTGGTACAGACCTTAG 61.415 54.545 13.03 5.83 46.17 2.18
4439 4981 1.483496 TGGCTGGTGGTACAGACCTTA 60.483 52.381 13.03 0.00 46.17 2.69
4440 4982 0.766674 TGGCTGGTGGTACAGACCTT 60.767 55.000 13.03 0.00 46.17 3.50
4441 4983 0.766674 TTGGCTGGTGGTACAGACCT 60.767 55.000 13.03 0.00 46.17 3.85
4442 4984 0.109723 TTTGGCTGGTGGTACAGACC 59.890 55.000 6.39 6.39 46.17 3.85
4443 4985 1.607148 GTTTTGGCTGGTGGTACAGAC 59.393 52.381 0.00 0.00 46.91 3.51
4444 4986 1.213182 TGTTTTGGCTGGTGGTACAGA 59.787 47.619 0.00 0.00 41.80 3.41
4445 4987 1.608590 CTGTTTTGGCTGGTGGTACAG 59.391 52.381 0.00 0.00 41.80 2.74
4446 4988 1.213182 TCTGTTTTGGCTGGTGGTACA 59.787 47.619 0.00 0.00 0.00 2.90
4447 4989 1.880027 CTCTGTTTTGGCTGGTGGTAC 59.120 52.381 0.00 0.00 0.00 3.34
4448 4990 1.817740 GCTCTGTTTTGGCTGGTGGTA 60.818 52.381 0.00 0.00 0.00 3.25
4449 4991 1.109323 GCTCTGTTTTGGCTGGTGGT 61.109 55.000 0.00 0.00 0.00 4.16
4450 4992 1.108727 TGCTCTGTTTTGGCTGGTGG 61.109 55.000 0.00 0.00 0.00 4.61
4451 4993 0.313043 CTGCTCTGTTTTGGCTGGTG 59.687 55.000 0.00 0.00 0.00 4.17
4452 4994 0.106519 ACTGCTCTGTTTTGGCTGGT 60.107 50.000 0.00 0.00 0.00 4.00
4453 4995 1.896220 TACTGCTCTGTTTTGGCTGG 58.104 50.000 0.00 0.00 0.00 4.85
4454 4996 5.049818 GCTATATACTGCTCTGTTTTGGCTG 60.050 44.000 0.00 0.00 0.00 4.85
4455 4997 5.059833 GCTATATACTGCTCTGTTTTGGCT 58.940 41.667 0.00 0.00 0.00 4.75
4456 4998 5.059833 AGCTATATACTGCTCTGTTTTGGC 58.940 41.667 0.00 0.00 33.90 4.52
4466 5008 4.399219 TGGAAGTCGAGCTATATACTGCT 58.601 43.478 1.44 1.44 42.82 4.24
4467 5009 4.768130 TGGAAGTCGAGCTATATACTGC 57.232 45.455 0.00 0.00 0.00 4.40
4468 5010 6.072452 TGTCATGGAAGTCGAGCTATATACTG 60.072 42.308 0.00 0.00 0.00 2.74
4469 5011 6.004574 TGTCATGGAAGTCGAGCTATATACT 58.995 40.000 0.00 0.00 0.00 2.12
4470 5012 6.255596 TGTCATGGAAGTCGAGCTATATAC 57.744 41.667 0.00 0.00 0.00 1.47
4471 5013 6.715264 TCTTGTCATGGAAGTCGAGCTATATA 59.285 38.462 0.00 0.00 0.00 0.86
4472 5014 5.536538 TCTTGTCATGGAAGTCGAGCTATAT 59.463 40.000 0.00 0.00 0.00 0.86
4473 5015 4.887655 TCTTGTCATGGAAGTCGAGCTATA 59.112 41.667 0.00 0.00 0.00 1.31
4493 5037 5.417894 ACTGAATGATGATGTGCATTGTCTT 59.582 36.000 0.00 0.00 37.34 3.01
4534 5078 4.516323 TGTCACCACTTGGATGATATGTG 58.484 43.478 1.14 0.00 38.94 3.21
4689 5234 4.576463 CCCCTGACTGTTTGTATTAGATGC 59.424 45.833 0.00 0.00 0.00 3.91
4697 5250 1.347707 CTCAGCCCCTGACTGTTTGTA 59.652 52.381 0.00 0.00 35.39 2.41
4767 5324 3.069872 TGGTACGTATTCTTGTGTGGTGT 59.930 43.478 0.00 0.00 0.00 4.16
4863 5420 6.678900 GCCCATTGTTTCTAGCTCAAACATAG 60.679 42.308 19.46 15.39 42.04 2.23
4864 5421 5.125417 GCCCATTGTTTCTAGCTCAAACATA 59.875 40.000 19.46 13.01 42.04 2.29
4865 5422 4.082026 GCCCATTGTTTCTAGCTCAAACAT 60.082 41.667 19.46 10.48 42.04 2.71
4866 5423 3.255642 GCCCATTGTTTCTAGCTCAAACA 59.744 43.478 16.34 16.34 41.05 2.83
4867 5424 3.507622 AGCCCATTGTTTCTAGCTCAAAC 59.492 43.478 12.35 12.35 34.79 2.93
4868 5425 3.766545 AGCCCATTGTTTCTAGCTCAAA 58.233 40.909 0.00 0.00 0.00 2.69
4869 5426 3.439857 AGCCCATTGTTTCTAGCTCAA 57.560 42.857 0.00 0.00 0.00 3.02
4870 5427 3.084039 CAAGCCCATTGTTTCTAGCTCA 58.916 45.455 0.00 0.00 33.95 4.26
4871 5428 3.347216 TCAAGCCCATTGTTTCTAGCTC 58.653 45.455 0.00 0.00 40.05 4.09
4872 5429 3.439857 TCAAGCCCATTGTTTCTAGCT 57.560 42.857 0.00 0.00 40.05 3.32
4873 5430 4.237724 GTTTCAAGCCCATTGTTTCTAGC 58.762 43.478 0.00 0.00 40.05 3.42
4874 5431 5.222631 GTGTTTCAAGCCCATTGTTTCTAG 58.777 41.667 0.00 0.00 40.05 2.43
4875 5432 4.261405 CGTGTTTCAAGCCCATTGTTTCTA 60.261 41.667 0.00 0.00 40.05 2.10
4876 5433 3.490761 CGTGTTTCAAGCCCATTGTTTCT 60.491 43.478 0.00 0.00 40.05 2.52
4877 5434 2.794350 CGTGTTTCAAGCCCATTGTTTC 59.206 45.455 0.00 0.00 40.05 2.78
4878 5435 2.428890 TCGTGTTTCAAGCCCATTGTTT 59.571 40.909 0.00 0.00 40.05 2.83
4879 5436 2.028130 TCGTGTTTCAAGCCCATTGTT 58.972 42.857 0.00 0.00 40.05 2.83
4880 5437 1.608590 CTCGTGTTTCAAGCCCATTGT 59.391 47.619 0.00 0.00 40.05 2.71
4910 5467 7.106239 TGAAGGATGGAGAGAAAGAATACAAC 58.894 38.462 0.00 0.00 0.00 3.32
4920 5477 7.211897 TCCAATTATTGAAGGATGGAGAGAA 57.788 36.000 6.50 0.00 33.30 2.87
4921 5478 6.829985 TCCAATTATTGAAGGATGGAGAGA 57.170 37.500 6.50 0.00 33.30 3.10
4938 5495 9.791801 AATTTTGCCTACTTTAATGTTCCAATT 57.208 25.926 0.00 0.00 0.00 2.32
4982 5541 6.715464 AATTTACTAATTTGACGAGGCATCG 58.285 36.000 20.58 20.58 41.68 3.84
5025 5584 9.442047 GCACTGCTATATAGAAATACAATTCCT 57.558 33.333 14.16 0.00 0.00 3.36
5033 5592 6.662234 AGGTACGGCACTGCTATATAGAAATA 59.338 38.462 14.16 0.00 0.00 1.40
5035 5594 4.831155 AGGTACGGCACTGCTATATAGAAA 59.169 41.667 14.16 0.00 0.00 2.52
5050 5611 2.396590 TCAAGGAATCAAGGTACGGC 57.603 50.000 0.00 0.00 0.00 5.68
5070 5631 7.971168 CACCGGCATTTTATATCAACTTTAACA 59.029 33.333 0.00 0.00 0.00 2.41
5074 5635 6.767524 TCACCGGCATTTTATATCAACTTT 57.232 33.333 0.00 0.00 0.00 2.66
5083 5646 2.094752 GTGTGCTTCACCGGCATTTTAT 60.095 45.455 0.00 0.00 41.86 1.40
5086 5649 1.106351 TGTGTGCTTCACCGGCATTT 61.106 50.000 0.00 0.00 45.61 2.32
5136 5699 2.925170 AGCACTTCACTCCCGGCT 60.925 61.111 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.