Multiple sequence alignment - TraesCS5D01G292200

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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 TraesCS5D01G292200 chr5D 100.000 4400 0 0 1 4400 389599251 389594852 0.000000e+00 8126.0
1 TraesCS5D01G292200 chr5A 94.159 4434 171 40 1 4400 492906243 492901864 0.000000e+00 6673.0
2 TraesCS5D01G292200 chr5B 93.228 4474 182 46 1 4400 469832745 469828319 0.000000e+00 6471.0
3 TraesCS5D01G292200 chr3D 82.812 128 14 3 1767 1886 585936980 585936853 1.670000e-19 108.0
4 TraesCS5D01G292200 chr3B 83.636 110 10 2 1785 1886 782656147 782656038 3.620000e-16 97.1


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 TraesCS5D01G292200 chr5D 389594852 389599251 4399 True 8126 8126 100.000 1 4400 1 chr5D.!!$R1 4399
1 TraesCS5D01G292200 chr5A 492901864 492906243 4379 True 6673 6673 94.159 1 4400 1 chr5A.!!$R1 4399
2 TraesCS5D01G292200 chr5B 469828319 469832745 4426 True 6471 6471 93.228 1 4400 1 chr5B.!!$R1 4399

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
510 522 0.179073 GCTACCATGACACGCCAGAT 60.179 55.0 0.0 0.0 0.00 2.90 F
1037 1065 0.033011 TCTTCTTCCTCCTCCTCCGG 60.033 60.0 0.0 0.0 0.00 5.14 F
1542 1582 0.036199 CTTCTGCTTCTGCTCCTGCT 60.036 55.0 0.0 0.0 40.48 4.24 F
1543 1583 0.036577 TTCTGCTTCTGCTCCTGCTC 60.037 55.0 0.0 0.0 40.48 4.26 F
2755 2802 1.342555 CATGCAAACATTGACGCCAG 58.657 50.0 0.0 0.0 32.87 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1546 1586 0.033920 CTTTTTGGGGGTGCAGAAGC 59.966 55.0 0.00 0.0 42.57 3.86 R
2171 2218 0.179000 AATCTGCGCCCAAGGACTAG 59.821 55.0 4.18 0.0 0.00 2.57 R
3304 3353 0.401738 TCTTTCTTCTGGGGTGCAGG 59.598 55.0 0.00 0.0 0.00 4.85 R
3385 3434 1.006832 GAGCATTACCGCACGAACAT 58.993 50.0 0.00 0.0 0.00 2.71 R
3767 3827 0.399949 TCCGGTGGCTGGATAGGATT 60.400 55.0 0.00 0.0 33.41 3.01 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
84 85 0.611618 AATGGCGCATCAACCTCCAA 60.612 50.000 10.83 0.00 0.00 3.53
153 154 2.284288 GCGTGACTGCTACGTAATTTCG 60.284 50.000 2.65 2.65 43.09 3.46
157 158 5.059587 CGTGACTGCTACGTAATTTCGTTTA 59.940 40.000 15.39 0.00 43.80 2.01
160 161 6.129115 TGACTGCTACGTAATTTCGTTTACAC 60.129 38.462 15.39 4.88 43.80 2.90
169 170 6.628461 CGTAATTTCGTTTACACCGTTCTTTT 59.372 34.615 0.00 0.00 32.69 2.27
200 201 4.282703 GGTTGGTGAGTAGTAGTTCCTTCA 59.717 45.833 0.00 0.00 0.00 3.02
292 293 1.338765 TTAATACACGACACGCACGG 58.661 50.000 0.00 0.00 34.93 4.94
325 334 7.765695 ACTTCAGAAGAAAAAGATTATGCCA 57.234 32.000 17.56 0.00 32.35 4.92
351 360 5.298527 GGCACACTTACCTAAAAAGAACTGT 59.701 40.000 0.00 0.00 0.00 3.55
352 361 6.427974 GCACACTTACCTAAAAAGAACTGTC 58.572 40.000 0.00 0.00 0.00 3.51
472 481 1.903404 CCTTGTTGCCCTCGCCTTT 60.903 57.895 0.00 0.00 0.00 3.11
484 493 2.349532 CCTCGCCTTTTCTCGTTTTCAC 60.350 50.000 0.00 0.00 0.00 3.18
505 517 2.125673 ACGGCTACCATGACACGC 60.126 61.111 0.00 0.00 0.00 5.34
506 518 2.890474 CGGCTACCATGACACGCC 60.890 66.667 0.00 0.00 37.40 5.68
507 519 2.267642 GGCTACCATGACACGCCA 59.732 61.111 0.00 0.00 40.41 5.69
508 520 1.815421 GGCTACCATGACACGCCAG 60.815 63.158 0.00 0.00 40.41 4.85
509 521 1.218047 GCTACCATGACACGCCAGA 59.782 57.895 0.00 0.00 0.00 3.86
510 522 0.179073 GCTACCATGACACGCCAGAT 60.179 55.000 0.00 0.00 0.00 2.90
511 523 1.858091 CTACCATGACACGCCAGATC 58.142 55.000 0.00 0.00 0.00 2.75
513 525 0.615331 ACCATGACACGCCAGATCTT 59.385 50.000 0.00 0.00 0.00 2.40
514 526 1.831106 ACCATGACACGCCAGATCTTA 59.169 47.619 0.00 0.00 0.00 2.10
573 586 2.556114 CCCCAGAGGAAGAGCAATTTGT 60.556 50.000 0.00 0.00 38.24 2.83
578 591 5.649395 CCAGAGGAAGAGCAATTTGTGATAA 59.351 40.000 0.00 0.00 0.00 1.75
592 605 0.692756 TGATAATCTCCCCGTGGCCA 60.693 55.000 0.00 0.00 0.00 5.36
629 642 3.181521 CGTGCGCATATTTCACAGAAAGA 60.182 43.478 15.91 0.00 0.00 2.52
701 717 0.554792 ATTCCCAGCCCAGGATTCTG 59.445 55.000 0.00 0.00 40.59 3.02
911 931 3.682377 CCCGAGAAAGAAGAAGAAGAAGC 59.318 47.826 0.00 0.00 0.00 3.86
939 959 1.484038 CAGAGGAACAGAGAGGGAGG 58.516 60.000 0.00 0.00 0.00 4.30
951 973 0.179936 GAGGGAGGGAGCAATCACTG 59.820 60.000 0.00 0.00 0.00 3.66
1017 1042 1.618345 GCCATGTCCATTGGTAACCCA 60.618 52.381 1.86 0.00 39.65 4.51
1033 1061 1.367848 ACCCATCTTCTTCCTCCTCCT 59.632 52.381 0.00 0.00 0.00 3.69
1037 1065 0.033011 TCTTCTTCCTCCTCCTCCGG 60.033 60.000 0.00 0.00 0.00 5.14
1537 1577 1.067000 TCTCTGCTTCTGCTTCTGCTC 60.067 52.381 0.00 0.00 40.48 4.26
1542 1582 0.036199 CTTCTGCTTCTGCTCCTGCT 60.036 55.000 0.00 0.00 40.48 4.24
1543 1583 0.036577 TTCTGCTTCTGCTCCTGCTC 60.037 55.000 0.00 0.00 40.48 4.26
1544 1584 1.449956 CTGCTTCTGCTCCTGCTCC 60.450 63.158 0.00 0.00 40.48 4.70
1545 1585 1.901654 CTGCTTCTGCTCCTGCTCCT 61.902 60.000 0.00 0.00 40.48 3.69
1546 1586 1.449956 GCTTCTGCTCCTGCTCCTG 60.450 63.158 0.00 0.00 40.48 3.86
1547 1587 1.449956 CTTCTGCTCCTGCTCCTGC 60.450 63.158 0.00 0.00 40.48 4.85
1548 1588 1.901654 CTTCTGCTCCTGCTCCTGCT 61.902 60.000 0.00 0.00 40.48 4.24
1549 1589 1.486997 TTCTGCTCCTGCTCCTGCTT 61.487 55.000 0.00 0.00 40.48 3.91
1550 1590 1.449956 CTGCTCCTGCTCCTGCTTC 60.450 63.158 0.00 0.00 40.48 3.86
1551 1591 1.901654 CTGCTCCTGCTCCTGCTTCT 61.902 60.000 0.00 0.00 40.48 2.85
1552 1592 1.449956 GCTCCTGCTCCTGCTTCTG 60.450 63.158 0.00 0.00 40.48 3.02
1553 1593 1.449956 CTCCTGCTCCTGCTTCTGC 60.450 63.158 0.00 0.00 40.48 4.26
1555 1595 2.039405 CCTGCTCCTGCTTCTGCAC 61.039 63.158 0.00 0.00 45.31 4.57
1723 1764 5.380043 AGTTCATGGTTTTCTGTGACAGAT 58.620 37.500 16.98 0.00 40.39 2.90
1736 1777 3.686241 TGTGACAGATATTGCAGTCAAGC 59.314 43.478 5.85 0.00 42.03 4.01
1756 1797 4.881920 AGCGTGCTGGTTTGATTTATTTT 58.118 34.783 0.00 0.00 0.00 1.82
1758 1799 5.405269 AGCGTGCTGGTTTGATTTATTTTTC 59.595 36.000 0.00 0.00 0.00 2.29
1759 1800 5.389411 GCGTGCTGGTTTGATTTATTTTTCC 60.389 40.000 0.00 0.00 0.00 3.13
1760 1801 5.925969 CGTGCTGGTTTGATTTATTTTTCCT 59.074 36.000 0.00 0.00 0.00 3.36
1763 1804 9.267084 GTGCTGGTTTGATTTATTTTTCCTTTA 57.733 29.630 0.00 0.00 0.00 1.85
2125 2172 5.664457 TCAGTTCACCAGTCATGTATGATC 58.336 41.667 0.00 0.00 39.30 2.92
2141 2188 2.291365 TGATCATCCAACATTCCAGCG 58.709 47.619 0.00 0.00 0.00 5.18
2164 2211 5.116074 CGCACTGACAATTGAAACATTCTTC 59.884 40.000 13.59 0.00 0.00 2.87
2171 2218 7.591057 TGACAATTGAAACATTCTTCGAATGTC 59.409 33.333 19.07 12.54 43.76 3.06
2240 2287 4.072088 GGTGTCGCCGCTTCAACG 62.072 66.667 0.00 0.00 0.00 4.10
2387 2434 3.188786 GCCGTGATGCGAGTCACC 61.189 66.667 12.97 0.00 44.37 4.02
2417 2464 1.878522 CATGCTAGCCGTCACCGAC 60.879 63.158 13.29 0.00 35.63 4.79
2523 2570 1.488705 ATCGGGGACTTCTGCCACAA 61.489 55.000 0.00 0.00 0.00 3.33
2702 2749 1.858091 AGCTTCTGTTCGACACTGTG 58.142 50.000 6.19 6.19 0.00 3.66
2755 2802 1.342555 CATGCAAACATTGACGCCAG 58.657 50.000 0.00 0.00 32.87 4.85
2874 2923 3.189287 GGAAATGTGTGACCTTGCTACTG 59.811 47.826 0.00 0.00 0.00 2.74
3223 3272 3.706373 GCAGTTCTGCGGGGGAGA 61.706 66.667 9.04 0.00 0.00 3.71
3273 3322 4.242811 TCAGGGAAGCCATAGGACATAAT 58.757 43.478 0.00 0.00 0.00 1.28
3305 3354 4.351054 CCACCCTGAGGCACCACC 62.351 72.222 0.00 0.00 36.11 4.61
3385 3434 2.655407 AGGTCTCTCCCTAGTCTTGGAA 59.345 50.000 1.39 0.00 36.75 3.53
3416 3465 3.385577 GGTAATGCTCTCATCGAACTCC 58.614 50.000 0.00 0.00 31.27 3.85
3418 3467 0.387202 ATGCTCTCATCGAACTCCGG 59.613 55.000 0.00 0.00 39.14 5.14
3502 3551 1.002544 GGCTCCAGTAGTGCAGAGTTT 59.997 52.381 0.00 0.00 36.68 2.66
3594 3643 9.351570 GAGTGTAAATACAACTGTAGGAAGTAC 57.648 37.037 0.00 0.00 38.04 2.73
3697 3747 2.009774 CATGGAATTTCGCCGTCTTCT 58.990 47.619 0.00 0.00 0.00 2.85
3767 3827 3.772387 TGGTTCTGGAATTATTGTGGCA 58.228 40.909 0.00 0.00 0.00 4.92
3869 3929 3.254166 CCAAAAAGCATCATCCCCTATCG 59.746 47.826 0.00 0.00 0.00 2.92
3886 3956 1.733041 CGTCTTCTTCGCCGAAGCA 60.733 57.895 21.58 10.61 40.11 3.91
3914 3984 4.273235 TGATAAGGACATGTTGCATTAGCG 59.727 41.667 0.00 0.00 46.23 4.26
4123 4207 1.340697 GGCCGGAACCAAGAAATAGGT 60.341 52.381 5.05 0.00 40.61 3.08
4126 4210 3.564225 GCCGGAACCAAGAAATAGGTATG 59.436 47.826 5.05 0.00 37.07 2.39
4151 4235 1.001974 TGGTAGCACGCAATGAGAGTT 59.998 47.619 0.00 0.00 0.00 3.01
4152 4236 2.232696 TGGTAGCACGCAATGAGAGTTA 59.767 45.455 0.00 0.00 0.00 2.24
4153 4237 2.860735 GGTAGCACGCAATGAGAGTTAG 59.139 50.000 0.00 0.00 0.00 2.34
4154 4238 2.751166 AGCACGCAATGAGAGTTAGT 57.249 45.000 0.00 0.00 0.00 2.24
4167 4251 6.681729 TGAGAGTTAGTAGTTTGGGATGTT 57.318 37.500 0.00 0.00 0.00 2.71
4196 4280 4.192317 CCTTTTAGGTCCTCATGTGTAGC 58.808 47.826 0.00 0.00 0.00 3.58
4232 4316 1.378911 TTGCGATGGCTGATTGGCT 60.379 52.632 0.15 0.00 42.34 4.75
4278 4362 2.103432 TGACGTCTGACCTAAAAAGGCA 59.897 45.455 17.92 0.00 0.00 4.75
4279 4363 3.244422 TGACGTCTGACCTAAAAAGGCAT 60.244 43.478 17.92 0.00 0.00 4.40
4340 4426 0.034756 TAATGCACGCTGTGGTGAGT 59.965 50.000 10.02 0.00 40.38 3.41
4377 4463 0.886563 ATTGCTGAGCAGTGAAAGCC 59.113 50.000 7.39 0.00 40.61 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 7.917505 CCATTAAAGACAAAGTCATTCCTATGC 59.082 37.037 0.00 0.00 34.60 3.14
84 85 2.353208 GCACTTTCTCGAGGACATGAGT 60.353 50.000 13.56 0.66 33.88 3.41
160 161 0.816421 ACCGTCCACCAAAAGAACGG 60.816 55.000 10.42 10.42 43.88 4.44
169 170 0.759812 TACTCACCAACCGTCCACCA 60.760 55.000 0.00 0.00 0.00 4.17
240 241 0.618458 AAAGAGCCCGTCCATGCTAA 59.382 50.000 0.00 0.00 38.11 3.09
292 293 0.388134 TCTTCTGAAGTACGCGCACC 60.388 55.000 16.43 0.00 0.00 5.01
304 313 6.406177 GCCATGGCATAATCTTTTTCTTCTGA 60.406 38.462 32.08 0.00 41.49 3.27
325 334 6.016276 CAGTTCTTTTTAGGTAAGTGTGCCAT 60.016 38.462 0.00 0.00 30.37 4.40
337 346 3.127030 GCCGATGGACAGTTCTTTTTAGG 59.873 47.826 0.00 0.00 0.00 2.69
472 481 1.595794 GCCGTGAAGTGAAAACGAGAA 59.404 47.619 0.00 0.00 39.64 2.87
505 517 0.931005 GTTTCCGCGCTAAGATCTGG 59.069 55.000 5.56 0.00 0.00 3.86
506 518 0.931005 GGTTTCCGCGCTAAGATCTG 59.069 55.000 5.56 0.00 0.00 2.90
507 519 0.179081 GGGTTTCCGCGCTAAGATCT 60.179 55.000 5.56 0.00 0.00 2.75
508 520 0.461339 TGGGTTTCCGCGCTAAGATC 60.461 55.000 5.56 0.00 35.24 2.75
509 521 0.180406 ATGGGTTTCCGCGCTAAGAT 59.820 50.000 5.56 0.00 35.24 2.40
510 522 0.825410 TATGGGTTTCCGCGCTAAGA 59.175 50.000 5.56 0.00 35.24 2.10
511 523 1.202486 TCTATGGGTTTCCGCGCTAAG 60.202 52.381 5.56 0.00 35.24 2.18
513 525 0.103572 GTCTATGGGTTTCCGCGCTA 59.896 55.000 5.56 0.00 35.24 4.26
514 526 1.153429 GTCTATGGGTTTCCGCGCT 60.153 57.895 5.56 0.00 35.24 5.92
555 568 6.748333 TTATCACAAATTGCTCTTCCTCTG 57.252 37.500 0.00 0.00 0.00 3.35
563 576 4.023707 CGGGGAGATTATCACAAATTGCTC 60.024 45.833 0.00 0.00 30.31 4.26
573 586 0.692756 TGGCCACGGGGAGATTATCA 60.693 55.000 8.67 0.00 35.59 2.15
609 622 3.750652 TGTCTTTCTGTGAAATATGCGCA 59.249 39.130 14.96 14.96 0.00 6.09
889 907 3.682377 GCTTCTTCTTCTTCTTTCTCGGG 59.318 47.826 0.00 0.00 0.00 5.14
890 908 4.310769 TGCTTCTTCTTCTTCTTTCTCGG 58.689 43.478 0.00 0.00 0.00 4.63
892 910 6.928492 TCTTCTGCTTCTTCTTCTTCTTTCTC 59.072 38.462 0.00 0.00 0.00 2.87
893 911 6.825610 TCTTCTGCTTCTTCTTCTTCTTTCT 58.174 36.000 0.00 0.00 0.00 2.52
894 912 7.489574 TTCTTCTGCTTCTTCTTCTTCTTTC 57.510 36.000 0.00 0.00 0.00 2.62
895 913 6.017192 GCTTCTTCTGCTTCTTCTTCTTCTTT 60.017 38.462 0.00 0.00 0.00 2.52
896 914 5.469760 GCTTCTTCTGCTTCTTCTTCTTCTT 59.530 40.000 0.00 0.00 0.00 2.52
897 915 4.996758 GCTTCTTCTGCTTCTTCTTCTTCT 59.003 41.667 0.00 0.00 0.00 2.85
898 916 4.754114 TGCTTCTTCTGCTTCTTCTTCTTC 59.246 41.667 0.00 0.00 0.00 2.87
899 917 4.712476 TGCTTCTTCTGCTTCTTCTTCTT 58.288 39.130 0.00 0.00 0.00 2.52
900 918 4.040217 TCTGCTTCTTCTGCTTCTTCTTCT 59.960 41.667 0.00 0.00 0.00 2.85
901 919 4.314121 TCTGCTTCTTCTGCTTCTTCTTC 58.686 43.478 0.00 0.00 0.00 2.87
911 931 3.257873 TCTCTGTTCCTCTGCTTCTTCTG 59.742 47.826 0.00 0.00 0.00 3.02
939 959 1.808411 TTTCGACCAGTGATTGCTCC 58.192 50.000 0.00 0.00 0.00 4.70
951 973 4.351131 AACACTTGTTCACTTTTCGACC 57.649 40.909 0.00 0.00 31.64 4.79
1017 1042 2.080654 CGGAGGAGGAGGAAGAAGAT 57.919 55.000 0.00 0.00 0.00 2.40
1037 1065 2.514505 GAAAGCAGTTTCGAGGCGGC 62.515 60.000 0.00 0.00 33.03 6.53
1201 1240 7.487189 CAGCTGAATATGTTCCAAGAATGTTTC 59.513 37.037 8.42 0.00 33.26 2.78
1546 1586 0.033920 CTTTTTGGGGGTGCAGAAGC 59.966 55.000 0.00 0.00 42.57 3.86
1547 1587 1.703411 TCTTTTTGGGGGTGCAGAAG 58.297 50.000 0.00 0.00 0.00 2.85
1548 1588 2.397044 ATCTTTTTGGGGGTGCAGAA 57.603 45.000 0.00 0.00 0.00 3.02
1549 1589 2.397044 AATCTTTTTGGGGGTGCAGA 57.603 45.000 0.00 0.00 0.00 4.26
1550 1590 2.233676 GGTAATCTTTTTGGGGGTGCAG 59.766 50.000 0.00 0.00 0.00 4.41
1551 1591 2.252714 GGTAATCTTTTTGGGGGTGCA 58.747 47.619 0.00 0.00 0.00 4.57
1552 1592 1.553248 GGGTAATCTTTTTGGGGGTGC 59.447 52.381 0.00 0.00 0.00 5.01
1553 1593 3.096852 GAGGGTAATCTTTTTGGGGGTG 58.903 50.000 0.00 0.00 0.00 4.61
1554 1594 2.043939 GGAGGGTAATCTTTTTGGGGGT 59.956 50.000 0.00 0.00 0.00 4.95
1555 1595 2.043801 TGGAGGGTAATCTTTTTGGGGG 59.956 50.000 0.00 0.00 0.00 5.40
1583 1624 5.534207 TTAAGAAACAAGACCTGACGGTA 57.466 39.130 0.00 0.00 45.73 4.02
1587 1628 4.392138 CGGGATTAAGAAACAAGACCTGAC 59.608 45.833 0.00 0.00 0.00 3.51
1661 1702 1.006825 CTTGACAATCGTCGCGTCCA 61.007 55.000 5.77 0.00 45.80 4.02
1723 1764 0.798159 CAGCACGCTTGACTGCAATA 59.202 50.000 0.00 0.00 35.73 1.90
1736 1777 5.925969 AGGAAAAATAAATCAAACCAGCACG 59.074 36.000 0.00 0.00 0.00 5.34
1756 1797 9.984190 GTAATTGTAACCACCAAAATAAAGGAA 57.016 29.630 0.00 0.00 0.00 3.36
1758 1799 9.418045 CTGTAATTGTAACCACCAAAATAAAGG 57.582 33.333 0.00 0.00 0.00 3.11
1759 1800 9.418045 CCTGTAATTGTAACCACCAAAATAAAG 57.582 33.333 0.00 0.00 0.00 1.85
1760 1801 8.925338 ACCTGTAATTGTAACCACCAAAATAAA 58.075 29.630 0.00 0.00 0.00 1.40
1763 1804 6.987403 ACCTGTAATTGTAACCACCAAAAT 57.013 33.333 0.00 0.00 0.00 1.82
1764 1805 6.407074 CCAACCTGTAATTGTAACCACCAAAA 60.407 38.462 0.00 0.00 0.00 2.44
1765 1806 5.069251 CCAACCTGTAATTGTAACCACCAAA 59.931 40.000 0.00 0.00 0.00 3.28
1775 1816 4.093472 TGCACTACCAACCTGTAATTGT 57.907 40.909 0.00 0.00 0.00 2.71
1934 1975 3.438183 AGAGCAAGGAAATCAAAGGCAT 58.562 40.909 0.00 0.00 0.00 4.40
1939 1980 7.102346 TCAACAAAAAGAGCAAGGAAATCAAA 58.898 30.769 0.00 0.00 0.00 2.69
1941 1982 6.219417 TCAACAAAAAGAGCAAGGAAATCA 57.781 33.333 0.00 0.00 0.00 2.57
2125 2172 0.179156 GTGCGCTGGAATGTTGGATG 60.179 55.000 9.73 0.00 0.00 3.51
2141 2188 5.116074 CGAAGAATGTTTCAATTGTCAGTGC 59.884 40.000 5.13 0.00 0.00 4.40
2164 2211 1.802880 CGCCCAAGGACTAGACATTCG 60.803 57.143 0.00 0.00 0.00 3.34
2171 2218 0.179000 AATCTGCGCCCAAGGACTAG 59.821 55.000 4.18 0.00 0.00 2.57
2240 2287 2.163010 CAGCTCAATGACATTGTGGTCC 59.837 50.000 24.53 12.60 40.97 4.46
2309 2356 1.338389 ACATTGCATTTGAGGCTTGCC 60.338 47.619 2.97 2.97 35.51 4.52
2312 2359 1.972795 ACCACATTGCATTTGAGGCTT 59.027 42.857 11.80 0.00 0.00 4.35
2387 2434 1.871408 GCTAGCATGGTGTCCTCATCG 60.871 57.143 10.63 0.00 0.00 3.84
2417 2464 1.522668 TCATTTCAAGCCTCACGGTG 58.477 50.000 0.56 0.56 0.00 4.94
2523 2570 1.134670 GTGCAGCCTTCTCTCGGTATT 60.135 52.381 0.00 0.00 0.00 1.89
2702 2749 1.510480 GCAGGTCTGTCAAGGTGCAC 61.510 60.000 8.80 8.80 0.00 4.57
2755 2802 2.943033 ACCTGGTACGCTTGATTATTGC 59.057 45.455 0.00 0.00 0.00 3.56
2821 2868 8.250143 TGAAATCTTATGAGCCTACTACATGA 57.750 34.615 0.00 0.00 0.00 3.07
2869 2916 7.383102 ACATAGAATTCCTGCAAAACAGTAG 57.617 36.000 0.65 0.00 45.68 2.57
2874 2923 7.816640 TGTCTTACATAGAATTCCTGCAAAAC 58.183 34.615 0.65 0.00 33.81 2.43
3223 3272 5.762179 TCAATGGTCTTCTGGTCAACTAT 57.238 39.130 0.00 0.00 0.00 2.12
3304 3353 0.401738 TCTTTCTTCTGGGGTGCAGG 59.598 55.000 0.00 0.00 0.00 4.85
3305 3354 1.072965 ACTCTTTCTTCTGGGGTGCAG 59.927 52.381 0.00 0.00 0.00 4.41
3306 3355 1.072331 GACTCTTTCTTCTGGGGTGCA 59.928 52.381 0.00 0.00 0.00 4.57
3312 3361 1.066787 GTCGGGGACTCTTTCTTCTGG 60.067 57.143 0.00 0.00 0.00 3.86
3385 3434 1.006832 GAGCATTACCGCACGAACAT 58.993 50.000 0.00 0.00 0.00 2.71
3416 3465 3.319137 TGATTGACAGAGAAGTTCCCG 57.681 47.619 0.00 0.00 0.00 5.14
3418 3467 3.438434 GGCTTGATTGACAGAGAAGTTCC 59.562 47.826 0.00 0.00 0.00 3.62
3594 3643 4.386711 GGTTCCGGATTCCTTATTGGTAG 58.613 47.826 4.15 0.00 37.07 3.18
3670 3719 2.477863 CGGCGAAATTCCATGACCTTTC 60.478 50.000 0.00 0.00 0.00 2.62
3697 3747 2.703416 GCATCATCGCCATGGAAGATA 58.297 47.619 18.40 8.66 0.00 1.98
3767 3827 0.399949 TCCGGTGGCTGGATAGGATT 60.400 55.000 0.00 0.00 33.41 3.01
3886 3956 4.018490 TGCAACATGTCCTTATCAGCAAT 58.982 39.130 0.00 0.00 0.00 3.56
3914 3984 5.347907 CGGTCTTGTTAGGATACAGACAAAC 59.652 44.000 0.00 1.22 41.19 2.93
4123 4207 1.476477 TGCGTGCTACCACTACCATA 58.524 50.000 0.00 0.00 39.86 2.74
4126 4210 1.006832 CATTGCGTGCTACCACTACC 58.993 55.000 0.00 0.00 39.86 3.18
4152 4236 9.596308 AAAGGTAAATAAACATCCCAAACTACT 57.404 29.630 0.00 0.00 0.00 2.57
4196 4280 4.404654 GACGGCCCAAAAGCAGCG 62.405 66.667 0.00 0.00 0.00 5.18
4278 4362 3.969312 CCATGCCTTTCCTTTTCCCATAT 59.031 43.478 0.00 0.00 0.00 1.78
4279 4363 3.012274 TCCATGCCTTTCCTTTTCCCATA 59.988 43.478 0.00 0.00 0.00 2.74
4340 4426 3.079578 CAATGCCTTGAGCTCTTCTGAA 58.920 45.455 16.19 0.00 44.23 3.02


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

AutoCloner maintained by Alex Coulton.