Multiple sequence alignment - TraesCS4D01G188200

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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 TraesCS4D01G188200 chr4D 100.000 4428 0 0 1 4428 327440840 327436413 0.000000e+00 8178.0
1 TraesCS4D01G188200 chr4B 93.630 4364 162 54 1 4325 406894455 406890169 0.000000e+00 6412.0
2 TraesCS4D01G188200 chr4A 91.850 4466 188 80 1 4413 143432830 143437172 0.000000e+00 6069.0
3 TraesCS4D01G188200 chr1D 79.762 336 48 16 3938 4259 250148904 250149233 4.460000e-55 226.0
4 TraesCS4D01G188200 chr5D 86.538 208 18 6 1428 1634 378341989 378341791 2.070000e-53 220.0
5 TraesCS4D01G188200 chr7A 74.609 256 45 13 3965 4209 124082429 124082183 1.310000e-15 95.3
6 TraesCS4D01G188200 chr5A 97.778 45 1 0 1820 1864 564438220 564438176 1.320000e-10 78.7


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4D01G188200 chr4D 327436413 327440840 4427 True 8178 8178 100.00 1 4428 1 chr4D.!!$R1 4427
1 TraesCS4D01G188200 chr4B 406890169 406894455 4286 True 6412 6412 93.63 1 4325 1 chr4B.!!$R1 4324
2 TraesCS4D01G188200 chr4A 143432830 143437172 4342 False 6069 6069 91.85 1 4413 1 chr4A.!!$F1 4412

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
545 557 0.622738 ATCTCCAGCTCCACCACCAT 60.623 55.0 0.0 0.0 0.00 3.55 F
1171 1186 0.723981 GCTTGGTTCTGACGATGCTC 59.276 55.0 0.0 0.0 33.69 4.26 F
2858 2898 0.517316 GCAACGCAGAAGGTGGTTAG 59.483 55.0 0.0 0.0 0.00 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2185 2217 0.739112 CGAGCCTGAACTTCCTGCTC 60.739 60.000 15.05 15.05 43.79 4.26 R
2997 3037 0.676466 TTGAATTCCACGATGCGGCT 60.676 50.000 2.27 0.00 0.00 5.52 R
4012 4077 1.755395 CGGGACCGATGACCCTACA 60.755 63.158 4.40 0.00 43.47 2.74 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
45 46 4.437255 CCGAGCAATTCATCATTCGTTCAA 60.437 41.667 0.00 0.00 0.00 2.69
152 153 6.515832 ACAAAGTCCACTCCATTTCATTTTC 58.484 36.000 0.00 0.00 0.00 2.29
154 155 6.581171 AAGTCCACTCCATTTCATTTTCTC 57.419 37.500 0.00 0.00 0.00 2.87
155 156 5.885465 AGTCCACTCCATTTCATTTTCTCT 58.115 37.500 0.00 0.00 0.00 3.10
156 157 5.942826 AGTCCACTCCATTTCATTTTCTCTC 59.057 40.000 0.00 0.00 0.00 3.20
157 158 5.942826 GTCCACTCCATTTCATTTTCTCTCT 59.057 40.000 0.00 0.00 0.00 3.10
543 555 1.222936 CATCTCCAGCTCCACCACC 59.777 63.158 0.00 0.00 0.00 4.61
544 556 1.229625 ATCTCCAGCTCCACCACCA 60.230 57.895 0.00 0.00 0.00 4.17
545 557 0.622738 ATCTCCAGCTCCACCACCAT 60.623 55.000 0.00 0.00 0.00 3.55
839 851 1.627019 GGGAGGGGGAGAGAAGCTA 59.373 63.158 0.00 0.00 0.00 3.32
860 872 2.511145 CGCTGCTTCCTCTGCTCC 60.511 66.667 0.00 0.00 0.00 4.70
1136 1151 5.489792 TCTTGCTTCTCTACAGAATGGTT 57.510 39.130 0.00 0.00 43.62 3.67
1171 1186 0.723981 GCTTGGTTCTGACGATGCTC 59.276 55.000 0.00 0.00 33.69 4.26
1295 1310 7.118971 AGAGTTGTAAGCACATTTCTCTTCATC 59.881 37.037 0.00 0.00 35.77 2.92
1310 1329 7.180322 TCTCTTCATCTTTACTCTGCAGAAT 57.820 36.000 18.85 10.98 0.00 2.40
1313 1332 6.533012 TCTTCATCTTTACTCTGCAGAATTCG 59.467 38.462 18.85 8.55 0.00 3.34
1333 1352 1.086696 GCTTCTTCGGTAGCAATGCA 58.913 50.000 8.35 0.00 38.09 3.96
1487 1509 7.120432 TGTGCAGTTACATGCTTCATTAACATA 59.880 33.333 0.00 0.00 46.63 2.29
1488 1510 7.429340 GTGCAGTTACATGCTTCATTAACATAC 59.571 37.037 0.00 0.00 46.63 2.39
1489 1511 7.336679 TGCAGTTACATGCTTCATTAACATACT 59.663 33.333 0.00 0.00 46.63 2.12
1490 1512 8.826710 GCAGTTACATGCTTCATTAACATACTA 58.173 33.333 0.00 0.00 43.07 1.82
1549 1571 9.219603 GTAGCAACAATAATATGGAGCAGATAA 57.780 33.333 0.00 0.00 0.00 1.75
1552 1574 9.748708 GCAACAATAATATGGAGCAGATAAAAA 57.251 29.630 0.00 0.00 0.00 1.94
1597 1623 6.143758 GCTGAATTTGCAATTTTGAAGTCGTA 59.856 34.615 0.00 0.00 0.00 3.43
1619 1645 6.966632 CGTAACAAACAATATGGACCTGAATG 59.033 38.462 0.00 0.00 0.00 2.67
1661 1687 3.417069 AAACCCTTTAAATTGCCAGCC 57.583 42.857 0.00 0.00 0.00 4.85
1683 1709 6.033966 GCCTATGGTTGTTACAAACATTAGC 58.966 40.000 29.82 26.44 41.79 3.09
1689 1715 5.221165 GGTTGTTACAAACATTAGCCAGTGT 60.221 40.000 8.41 0.00 41.79 3.55
1733 1765 9.384764 CTTTATTATAGGGCTGCTAATTCTACC 57.615 37.037 0.00 0.00 0.00 3.18
1750 1782 1.601166 ACCTTGGCCGAAAGTGTTAC 58.399 50.000 0.00 0.00 0.00 2.50
1755 1787 3.042871 TGGCCGAAAGTGTTACGTTAT 57.957 42.857 0.00 0.00 0.00 1.89
1756 1788 4.185467 TGGCCGAAAGTGTTACGTTATA 57.815 40.909 0.00 0.00 0.00 0.98
1757 1789 3.925913 TGGCCGAAAGTGTTACGTTATAC 59.074 43.478 0.00 0.00 0.00 1.47
1900 1932 1.079127 CACGGGCAACAGGGTAGAG 60.079 63.158 0.00 0.00 39.74 2.43
2005 2037 2.716017 GGTGGAGCTCCTCGTCCTG 61.716 68.421 32.28 0.00 36.82 3.86
2185 2217 0.617413 ACAACTCCAGCTGGATCAGG 59.383 55.000 35.11 24.85 44.46 3.86
2308 2340 5.413213 CCGTGGTGAAGGTTTGTGATTATTA 59.587 40.000 0.00 0.00 0.00 0.98
2313 2345 9.521841 TGGTGAAGGTTTGTGATTATTAATACA 57.478 29.630 0.00 0.00 0.00 2.29
2533 2572 2.616510 CCTCAGGAACTTGGTGATGGAC 60.617 54.545 0.00 0.00 34.60 4.02
2586 2626 4.646572 CCTGCCTCTTTCTACAGAGTTTT 58.353 43.478 0.00 0.00 39.04 2.43
2587 2627 4.693095 CCTGCCTCTTTCTACAGAGTTTTC 59.307 45.833 0.00 0.00 39.04 2.29
2588 2628 5.512232 CCTGCCTCTTTCTACAGAGTTTTCT 60.512 44.000 0.00 0.00 39.04 2.52
2604 2644 9.877178 CAGAGTTTTCTGTATTATAGGTTCACT 57.123 33.333 0.00 0.00 44.74 3.41
2605 2645 9.877178 AGAGTTTTCTGTATTATAGGTTCACTG 57.123 33.333 0.00 0.00 30.72 3.66
2606 2646 8.494016 AGTTTTCTGTATTATAGGTTCACTGC 57.506 34.615 0.00 0.00 0.00 4.40
2607 2647 8.322091 AGTTTTCTGTATTATAGGTTCACTGCT 58.678 33.333 0.00 0.00 0.00 4.24
2608 2648 8.947115 GTTTTCTGTATTATAGGTTCACTGCTT 58.053 33.333 0.00 0.00 0.00 3.91
2609 2649 8.718102 TTTCTGTATTATAGGTTCACTGCTTC 57.282 34.615 0.00 0.00 0.00 3.86
2610 2650 6.504398 TCTGTATTATAGGTTCACTGCTTCG 58.496 40.000 0.00 0.00 0.00 3.79
2611 2651 5.047847 TGTATTATAGGTTCACTGCTTCGC 58.952 41.667 0.00 0.00 0.00 4.70
2612 2652 3.603158 TTATAGGTTCACTGCTTCGCA 57.397 42.857 0.00 0.00 36.92 5.10
2613 2653 1.726853 ATAGGTTCACTGCTTCGCAC 58.273 50.000 0.00 0.00 33.79 5.34
2614 2654 0.666274 TAGGTTCACTGCTTCGCACG 60.666 55.000 0.00 0.00 33.79 5.34
2799 2839 2.638480 TCCATGAAATCATCGGGGTC 57.362 50.000 0.00 0.00 33.61 4.46
2829 2869 3.368531 GGAGTAACTGCTTCTCCGTGAAT 60.369 47.826 0.00 0.00 38.37 2.57
2858 2898 0.517316 GCAACGCAGAAGGTGGTTAG 59.483 55.000 0.00 0.00 0.00 2.34
2911 2951 3.643763 ACGTCTCTGTCTCATGAACAAC 58.356 45.455 0.00 0.00 0.00 3.32
2913 2953 2.989840 GTCTCTGTCTCATGAACAACGG 59.010 50.000 0.00 1.09 0.00 4.44
2942 2982 4.327898 TCGTTCGTAAACATAACAGCATCC 59.672 41.667 0.00 0.00 34.93 3.51
2996 3036 2.090524 GGACGCGTACAAGTTCCCG 61.091 63.158 18.68 0.00 0.00 5.14
2997 3037 1.081242 GACGCGTACAAGTTCCCGA 60.081 57.895 13.97 0.00 0.00 5.14
3326 3378 4.899239 GCGAGCCCTGGATCACCG 62.899 72.222 1.97 0.00 39.42 4.94
3376 3428 1.211969 CATGCTGCAGTTCAGTGGC 59.788 57.895 16.64 0.00 44.66 5.01
3377 3429 1.074423 ATGCTGCAGTTCAGTGGCT 59.926 52.632 16.64 0.00 44.66 4.75
3440 3492 1.202371 GGTTGTGATCCATGCATGCAG 60.202 52.381 26.69 16.97 0.00 4.41
3476 3528 5.715070 ACTAACTGTCTGCTAAGTGCTAAG 58.285 41.667 0.00 0.00 43.37 2.18
3477 3529 4.608948 AACTGTCTGCTAAGTGCTAAGT 57.391 40.909 0.00 0.00 43.37 2.24
3478 3530 4.608948 ACTGTCTGCTAAGTGCTAAGTT 57.391 40.909 0.00 0.00 43.37 2.66
3480 3532 3.067106 TGTCTGCTAAGTGCTAAGTTGC 58.933 45.455 0.00 0.00 43.37 4.17
3481 3533 3.244215 TGTCTGCTAAGTGCTAAGTTGCT 60.244 43.478 0.00 0.00 43.37 3.91
3482 3534 4.021456 TGTCTGCTAAGTGCTAAGTTGCTA 60.021 41.667 0.00 0.00 43.37 3.49
3483 3535 4.929808 GTCTGCTAAGTGCTAAGTTGCTAA 59.070 41.667 0.00 0.00 43.37 3.09
3484 3536 4.929808 TCTGCTAAGTGCTAAGTTGCTAAC 59.070 41.667 0.00 0.00 43.37 2.34
3485 3537 4.637276 TGCTAAGTGCTAAGTTGCTAACA 58.363 39.130 0.00 0.00 43.37 2.41
3486 3538 4.451096 TGCTAAGTGCTAAGTTGCTAACAC 59.549 41.667 0.00 0.00 43.37 3.32
3487 3539 4.434330 GCTAAGTGCTAAGTTGCTAACACG 60.434 45.833 0.00 0.00 38.95 4.49
3488 3540 3.107642 AGTGCTAAGTTGCTAACACGT 57.892 42.857 0.00 0.00 33.36 4.49
3489 3541 4.247267 AGTGCTAAGTTGCTAACACGTA 57.753 40.909 0.00 0.00 33.36 3.57
3490 3542 3.985925 AGTGCTAAGTTGCTAACACGTAC 59.014 43.478 0.00 0.00 33.36 3.67
3535 3587 1.983481 GGTTGGGGTGATGCATGCA 60.983 57.895 25.04 25.04 0.00 3.96
3536 3588 1.514087 GTTGGGGTGATGCATGCAG 59.486 57.895 26.69 0.00 0.00 4.41
3578 3634 3.988517 GGTAGCGTGATAGGATTTGTAGC 59.011 47.826 0.00 0.00 0.00 3.58
3648 3704 4.302622 TCCATGCTAGGAGCCTCC 57.697 61.111 1.26 1.26 41.51 4.30
3669 3727 4.841813 TCCATCTCCTGTGTGTAAAAGGTA 59.158 41.667 0.00 0.00 32.59 3.08
3780 3838 3.057315 CCGCAAAGGACAGTGAAATGAAT 60.057 43.478 0.00 0.00 45.00 2.57
3781 3839 3.916172 CGCAAAGGACAGTGAAATGAATG 59.084 43.478 0.00 0.00 0.00 2.67
3802 3861 7.283127 TGAATGAACTTGTAAACTTTCTCTGCT 59.717 33.333 0.00 0.00 0.00 4.24
3803 3862 6.363577 TGAACTTGTAAACTTTCTCTGCTG 57.636 37.500 0.00 0.00 0.00 4.41
3806 3865 5.428253 ACTTGTAAACTTTCTCTGCTGACA 58.572 37.500 0.00 0.00 0.00 3.58
3868 3929 4.164087 ACCACAACGGACGTGCCA 62.164 61.111 0.00 0.00 38.63 4.92
3946 4011 3.821421 ATCCTTACAGTTAAGCTCCCG 57.179 47.619 0.00 0.00 34.36 5.14
3963 4028 1.323412 CCGAGCAGTAGAGGCATAGT 58.677 55.000 0.00 0.00 0.00 2.12
3977 4042 3.777522 AGGCATAGTAGAGCTCCAAAGTT 59.222 43.478 10.93 0.00 0.00 2.66
4038 4103 1.449423 CATCGGTCCCGCATGACAA 60.449 57.895 0.00 0.00 39.59 3.18
4394 4472 8.750515 ATGTTCCCAAAATTGAAAAACATTCT 57.249 26.923 11.52 0.00 34.14 2.40
4396 4474 8.457261 TGTTCCCAAAATTGAAAAACATTCTTG 58.543 29.630 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 3.872630 GCTGAAAGGACTTTCCCGGTTAT 60.873 47.826 18.99 0.00 46.15 1.89
148 149 3.930229 CGAGACGAGAGAGAGAGAGAAAA 59.070 47.826 0.00 0.00 0.00 2.29
152 153 2.099263 AGACGAGACGAGAGAGAGAGAG 59.901 54.545 0.00 0.00 0.00 3.20
154 155 2.460918 GAGACGAGACGAGAGAGAGAG 58.539 57.143 0.00 0.00 0.00 3.20
155 156 1.135527 GGAGACGAGACGAGAGAGAGA 59.864 57.143 0.00 0.00 0.00 3.10
156 157 1.567504 GGAGACGAGACGAGAGAGAG 58.432 60.000 0.00 0.00 0.00 3.20
157 158 0.176219 GGGAGACGAGACGAGAGAGA 59.824 60.000 0.00 0.00 0.00 3.10
380 381 2.447379 ATGGCGATGGGAGAGGCT 60.447 61.111 0.00 0.00 0.00 4.58
839 851 4.749310 CAGAGGAAGCAGCGCCGT 62.749 66.667 2.29 0.00 0.00 5.68
860 872 1.128692 GCTATAAATAGCGGCGGCAAG 59.871 52.381 19.21 5.09 45.30 4.01
1136 1151 2.101249 CCAAGCAAACTCAAAGCCTGAA 59.899 45.455 0.00 0.00 32.17 3.02
1171 1186 0.517316 GCACAGAGCAAAAGGTACCG 59.483 55.000 6.18 0.00 44.79 4.02
1295 1310 3.265791 AGCCGAATTCTGCAGAGTAAAG 58.734 45.455 21.79 8.49 0.00 1.85
1310 1329 0.319083 TTGCTACCGAAGAAGCCGAA 59.681 50.000 0.00 0.00 35.86 4.30
1313 1332 0.378610 GCATTGCTACCGAAGAAGCC 59.621 55.000 0.16 0.00 35.86 4.35
1333 1352 3.062763 CTGAATTCGCAACAGAGTCAGT 58.937 45.455 0.04 0.00 33.28 3.41
1490 1512 9.086758 AGTGTTTCAGTAGTAACCTTGTATAGT 57.913 33.333 0.00 0.00 0.00 2.12
1549 1571 5.221322 GCAGTGAAAAGGACCTTCAGATTTT 60.221 40.000 7.34 0.00 33.56 1.82
1552 1574 3.073650 AGCAGTGAAAAGGACCTTCAGAT 59.926 43.478 7.34 0.00 33.56 2.90
1560 1582 3.737774 GCAAATTCAGCAGTGAAAAGGAC 59.262 43.478 0.00 0.00 45.88 3.85
1597 1623 6.916360 ACATTCAGGTCCATATTGTTTGTT 57.084 33.333 0.00 0.00 0.00 2.83
1619 1645 6.939551 TTTCAACAGCATTACGAGTAGTAC 57.060 37.500 0.00 0.00 34.56 2.73
1661 1687 7.094377 ACTGGCTAATGTTTGTAACAACCATAG 60.094 37.037 0.00 0.00 45.86 2.23
1709 1741 8.680820 AGGTAGAATTAGCAGCCCTATAATAA 57.319 34.615 0.00 0.00 0.00 1.40
1710 1742 8.540388 CAAGGTAGAATTAGCAGCCCTATAATA 58.460 37.037 0.00 0.00 0.00 0.98
1711 1743 7.398024 CAAGGTAGAATTAGCAGCCCTATAAT 58.602 38.462 0.00 0.00 0.00 1.28
1733 1765 1.223187 ACGTAACACTTTCGGCCAAG 58.777 50.000 2.24 1.69 0.00 3.61
1750 1782 5.848833 ACAGGAAGGAACCTAGTATAACG 57.151 43.478 0.00 0.00 38.32 3.18
1755 1787 6.328148 TCAGAAAAACAGGAAGGAACCTAGTA 59.672 38.462 0.00 0.00 38.32 1.82
1756 1788 5.132144 TCAGAAAAACAGGAAGGAACCTAGT 59.868 40.000 0.00 0.00 38.32 2.57
1757 1789 5.470437 GTCAGAAAAACAGGAAGGAACCTAG 59.530 44.000 0.00 0.00 38.32 3.02
1900 1932 1.601759 TGGCTGCTTGTTCTCTGCC 60.602 57.895 0.00 0.00 44.44 4.85
2005 2037 3.774702 GCGTTGAAGTCGCCGTCC 61.775 66.667 0.00 0.00 46.61 4.79
2023 2055 3.989787 TGCTCAAGGCGCTCGTCA 61.990 61.111 7.64 0.00 45.43 4.35
2185 2217 0.739112 CGAGCCTGAACTTCCTGCTC 60.739 60.000 15.05 15.05 43.79 4.26
2308 2340 9.777575 GCGTTTGGTTAAAATATGTACTGTATT 57.222 29.630 0.00 0.00 0.00 1.89
2313 2345 8.301002 ACATTGCGTTTGGTTAAAATATGTACT 58.699 29.630 0.00 0.00 0.00 2.73
2314 2346 8.455598 ACATTGCGTTTGGTTAAAATATGTAC 57.544 30.769 0.00 0.00 0.00 2.90
2365 2404 8.749354 ACTGAAGAATAAAAAGTTCAACCAGTT 58.251 29.630 0.00 0.00 32.86 3.16
2385 2424 5.335191 GGGTGATGCTTCTTGTAAACTGAAG 60.335 44.000 0.88 10.12 39.88 3.02
2533 2572 2.896801 GCCGCGCAGTCCATATTGG 61.897 63.158 8.75 0.00 39.43 3.16
2586 2626 6.504398 CGAAGCAGTGAACCTATAATACAGA 58.496 40.000 0.00 0.00 0.00 3.41
2587 2627 6.755461 CGAAGCAGTGAACCTATAATACAG 57.245 41.667 0.00 0.00 0.00 2.74
2606 2646 8.503486 AGAATATATAGTTTGTACGTGCGAAG 57.497 34.615 6.56 0.00 0.00 3.79
2607 2647 8.130469 TGAGAATATATAGTTTGTACGTGCGAA 58.870 33.333 1.73 1.73 0.00 4.70
2608 2648 7.641760 TGAGAATATATAGTTTGTACGTGCGA 58.358 34.615 0.00 0.00 0.00 5.10
2609 2649 7.847166 TGAGAATATATAGTTTGTACGTGCG 57.153 36.000 0.00 0.00 0.00 5.34
2610 2650 9.406828 TGATGAGAATATATAGTTTGTACGTGC 57.593 33.333 0.00 0.00 0.00 5.34
2612 2652 9.608617 CGTGATGAGAATATATAGTTTGTACGT 57.391 33.333 0.00 0.00 0.00 3.57
2613 2653 9.608617 ACGTGATGAGAATATATAGTTTGTACG 57.391 33.333 0.00 0.00 0.00 3.67
2799 2839 1.445582 GCAGTTACTCCCGACCACG 60.446 63.158 0.00 0.00 39.43 4.94
2858 2898 5.909610 CGAAATGAAGTGTTTTCAGAGGTTC 59.090 40.000 0.00 0.00 32.57 3.62
2862 2902 5.007626 TGTCCGAAATGAAGTGTTTTCAGAG 59.992 40.000 0.00 0.00 32.57 3.35
2911 2951 0.994263 GTTTACGAACGATCCACCCG 59.006 55.000 0.14 0.00 0.00 5.28
2913 2953 4.626604 TGTTATGTTTACGAACGATCCACC 59.373 41.667 0.14 0.00 38.65 4.61
2984 3024 2.098831 GCGGCTCGGGAACTTGTAC 61.099 63.158 0.00 0.00 0.00 2.90
2996 3036 1.089481 TGAATTCCACGATGCGGCTC 61.089 55.000 2.27 0.00 0.00 4.70
2997 3037 0.676466 TTGAATTCCACGATGCGGCT 60.676 50.000 2.27 0.00 0.00 5.52
3300 3352 3.866582 AGGGCTCGCTATGGTGGC 61.867 66.667 0.00 0.00 0.00 5.01
3326 3378 3.607987 CGTCGCGTCGAAGCCATC 61.608 66.667 20.81 7.28 37.72 3.51
3440 3492 0.038159 AGTTAGTCACAGCGAGGCAC 60.038 55.000 0.00 0.00 0.00 5.01
3476 3528 4.539870 TGTGAGTAGTACGTGTTAGCAAC 58.460 43.478 0.00 0.00 0.00 4.17
3477 3529 4.834357 TGTGAGTAGTACGTGTTAGCAA 57.166 40.909 0.00 0.00 0.00 3.91
3478 3530 4.216902 ACATGTGAGTAGTACGTGTTAGCA 59.783 41.667 0.00 0.00 43.66 3.49
3480 3532 5.020128 CGACATGTGAGTAGTACGTGTTAG 58.980 45.833 1.15 0.24 45.48 2.34
3481 3533 4.452114 ACGACATGTGAGTAGTACGTGTTA 59.548 41.667 1.15 0.00 45.48 2.41
3482 3534 3.251729 ACGACATGTGAGTAGTACGTGTT 59.748 43.478 1.15 0.00 45.48 3.32
3484 3536 3.466712 ACGACATGTGAGTAGTACGTG 57.533 47.619 1.15 0.00 40.13 4.49
3485 3537 3.251729 ACAACGACATGTGAGTAGTACGT 59.748 43.478 1.15 0.26 30.82 3.57
3486 3538 3.818387 ACAACGACATGTGAGTAGTACG 58.182 45.455 1.15 0.00 30.82 3.67
3487 3539 4.980434 ACAACAACGACATGTGAGTAGTAC 59.020 41.667 1.15 0.00 32.81 2.73
3488 3540 5.190992 ACAACAACGACATGTGAGTAGTA 57.809 39.130 1.15 0.00 32.81 1.82
3489 3541 4.054780 ACAACAACGACATGTGAGTAGT 57.945 40.909 1.15 0.00 32.81 2.73
3490 3542 5.403897 AAACAACAACGACATGTGAGTAG 57.596 39.130 1.15 0.00 32.81 2.57
3535 3587 6.628644 ACCTACTTTTATTGCCTTCTCTCT 57.371 37.500 0.00 0.00 0.00 3.10
3536 3588 6.480651 GCTACCTACTTTTATTGCCTTCTCTC 59.519 42.308 0.00 0.00 0.00 3.20
3578 3634 3.831911 ACATTTTACAAGACCCCCATGTG 59.168 43.478 0.00 0.00 0.00 3.21
3648 3704 5.794894 AGTACCTTTTACACACAGGAGATG 58.205 41.667 0.00 0.00 0.00 2.90
3669 3727 6.531948 CGAATAAAGTCTACTAAGCAGCAAGT 59.468 38.462 5.79 5.79 0.00 3.16
3679 3737 6.985117 ACACACAACCGAATAAAGTCTACTA 58.015 36.000 0.00 0.00 0.00 1.82
3680 3738 5.850614 ACACACAACCGAATAAAGTCTACT 58.149 37.500 0.00 0.00 0.00 2.57
3681 3739 5.693104 TGACACACAACCGAATAAAGTCTAC 59.307 40.000 0.00 0.00 0.00 2.59
3780 3838 6.037172 GTCAGCAGAGAAAGTTTACAAGTTCA 59.963 38.462 0.00 0.00 0.00 3.18
3781 3839 6.037172 TGTCAGCAGAGAAAGTTTACAAGTTC 59.963 38.462 0.00 0.00 0.00 3.01
3799 3858 6.096673 TCATTTAAGTGTACTCTGTCAGCA 57.903 37.500 0.00 0.00 0.00 4.41
3833 3894 5.369833 TGTGGTCGTTTCCAAGAAAGATTA 58.630 37.500 0.00 0.00 39.34 1.75
3868 3929 2.199236 GCCGTACGCTAAAGCAGTATT 58.801 47.619 10.49 0.00 42.21 1.89
3946 4011 3.190535 GCTCTACTATGCCTCTACTGCTC 59.809 52.174 0.00 0.00 0.00 4.26
3977 4042 3.680777 AGGGTCCACTTTGAGGAAAAA 57.319 42.857 0.00 0.00 36.80 1.94
3986 4051 3.265995 CCCTTACATGTAGGGTCCACTTT 59.734 47.826 27.06 0.00 38.06 2.66
4012 4077 1.755395 CGGGACCGATGACCCTACA 60.755 63.158 4.40 0.00 43.47 2.74
4038 4103 1.814429 TGGGATGTGGGTTCCGATAT 58.186 50.000 0.00 0.00 33.82 1.63
4352 4430 9.487790 TTGGGAACATAATTCAAAATCTTGAAC 57.512 29.630 0.00 0.00 46.55 3.18


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

AutoCloner maintained by Alex Coulton.