Multiple sequence alignment - TraesCS2B01G288800

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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 TraesCS2B01G288800 chr2B 100.000 3137 0 0 1 3137 399355491 399352355 0.000000e+00 5794.0
1 TraesCS2B01G288800 chr2B 100.000 33 0 0 2164 2196 399353296 399353264 9.390000e-06 62.1
2 TraesCS2B01G288800 chr2B 100.000 33 0 0 2196 2228 399353328 399353296 9.390000e-06 62.1
3 TraesCS2B01G288800 chr2D 91.592 2676 78 59 1 2632 330753267 330750695 0.000000e+00 3559.0
4 TraesCS2B01G288800 chr2D 92.122 952 29 13 2196 3137 330751139 330750224 0.000000e+00 1301.0
5 TraesCS2B01G288800 chr2A 91.463 1757 56 30 495 2196 437977284 437975567 0.000000e+00 2327.0
6 TraesCS2B01G288800 chr2A 95.928 442 13 2 2196 2632 437975599 437975158 0.000000e+00 712.0
7 TraesCS2B01G288800 chr2A 91.903 494 28 6 2650 3137 437975165 437974678 0.000000e+00 680.0
8 TraesCS2B01G288800 chr2A 92.537 402 4 4 1 389 437977721 437977333 1.270000e-153 553.0


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 TraesCS2B01G288800 chr2B 399352355 399355491 3136 True 1972.733333 5794 100.00000 1 3137 3 chr2B.!!$R1 3136
1 TraesCS2B01G288800 chr2D 330750224 330753267 3043 True 2430.000000 3559 91.85700 1 3137 2 chr2D.!!$R1 3136
2 TraesCS2B01G288800 chr2A 437974678 437977721 3043 True 1068.000000 2327 92.95775 1 3137 4 chr2A.!!$R1 3136

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
337 351 0.037326 GACTGTGATGAAGTGGCGGA 60.037 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2195 2296 0.178767 CCAGGATTGGTCGATCAGCA 59.821 55.0 0.0 0.0 39.79 4.41 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
130 131 2.025863 GCATCTGGGCCACAATAGCTT 61.026 52.381 0.00 0.00 0.00 3.74
322 336 1.299850 TCGTTGCTGTCCGTGACTG 60.300 57.895 5.77 6.19 35.18 3.51
330 344 2.332104 CTGTCCGTGACTGTGATGAAG 58.668 52.381 5.77 0.00 33.15 3.02
331 345 1.686587 TGTCCGTGACTGTGATGAAGT 59.313 47.619 5.77 0.00 33.15 3.01
332 346 2.061773 GTCCGTGACTGTGATGAAGTG 58.938 52.381 0.00 0.00 0.00 3.16
333 347 1.000843 TCCGTGACTGTGATGAAGTGG 59.999 52.381 0.00 0.00 0.00 4.00
334 348 0.792640 CGTGACTGTGATGAAGTGGC 59.207 55.000 0.00 0.00 0.00 5.01
335 349 0.792640 GTGACTGTGATGAAGTGGCG 59.207 55.000 0.00 0.00 0.00 5.69
336 350 0.320683 TGACTGTGATGAAGTGGCGG 60.321 55.000 0.00 0.00 0.00 6.13
337 351 0.037326 GACTGTGATGAAGTGGCGGA 60.037 55.000 0.00 0.00 0.00 5.54
338 352 0.615331 ACTGTGATGAAGTGGCGGAT 59.385 50.000 0.00 0.00 0.00 4.18
339 353 1.012086 CTGTGATGAAGTGGCGGATG 58.988 55.000 0.00 0.00 0.00 3.51
340 354 0.612744 TGTGATGAAGTGGCGGATGA 59.387 50.000 0.00 0.00 0.00 2.92
341 355 1.210234 TGTGATGAAGTGGCGGATGAT 59.790 47.619 0.00 0.00 0.00 2.45
342 356 1.600957 GTGATGAAGTGGCGGATGATG 59.399 52.381 0.00 0.00 0.00 3.07
376 390 1.544691 GCGGGTTTCTAGACAGACAGA 59.455 52.381 0.00 0.00 0.00 3.41
393 407 4.282195 AGACAGACATTCTTCGGTTCTTCT 59.718 41.667 0.00 0.00 0.00 2.85
395 409 4.991687 ACAGACATTCTTCGGTTCTTCTTC 59.008 41.667 0.00 0.00 0.00 2.87
396 410 4.390297 CAGACATTCTTCGGTTCTTCTTCC 59.610 45.833 0.00 0.00 0.00 3.46
397 411 4.284746 AGACATTCTTCGGTTCTTCTTCCT 59.715 41.667 0.00 0.00 0.00 3.36
398 412 4.974399 ACATTCTTCGGTTCTTCTTCCTT 58.026 39.130 0.00 0.00 0.00 3.36
399 413 5.377478 ACATTCTTCGGTTCTTCTTCCTTT 58.623 37.500 0.00 0.00 0.00 3.11
400 414 5.239525 ACATTCTTCGGTTCTTCTTCCTTTG 59.760 40.000 0.00 0.00 0.00 2.77
488 502 6.973229 ATCCTGCAGATTTTTATTTTGTGC 57.027 33.333 17.39 0.00 0.00 4.57
572 608 1.366111 TAACGGCAGCCATTTCTCGC 61.366 55.000 13.30 0.00 0.00 5.03
603 654 3.766051 ACGGACGGAGGTTTAGATTAGTT 59.234 43.478 0.00 0.00 0.00 2.24
608 659 6.146601 ACGGAGGTTTAGATTAGTTCTAGC 57.853 41.667 0.00 0.00 38.19 3.42
610 661 6.183360 ACGGAGGTTTAGATTAGTTCTAGCAG 60.183 42.308 0.00 0.00 38.19 4.24
870 923 7.805071 ACACATTTTCTTATTTTCTCAGCTTCG 59.195 33.333 0.00 0.00 0.00 3.79
946 999 2.639286 GTGCAAGCCCAACTCACG 59.361 61.111 0.00 0.00 0.00 4.35
962 1015 3.121030 CGGGTGCCGCTTCTTCTG 61.121 66.667 0.00 0.00 41.17 3.02
963 1016 3.435186 GGGTGCCGCTTCTTCTGC 61.435 66.667 0.00 0.00 0.00 4.26
964 1017 2.669569 GGTGCCGCTTCTTCTGCA 60.670 61.111 0.00 0.00 0.00 4.41
965 1018 2.684843 GGTGCCGCTTCTTCTGCAG 61.685 63.158 7.63 7.63 33.80 4.41
966 1019 3.052082 TGCCGCTTCTTCTGCAGC 61.052 61.111 9.47 0.00 34.72 5.25
1212 1274 0.908910 ACATGTGCCGTCCCTCATTA 59.091 50.000 0.00 0.00 0.00 1.90
1635 1721 3.170362 CCAAGGGGTGCTCCTCAA 58.830 61.111 7.57 0.00 36.47 3.02
1637 1723 0.178964 CCAAGGGGTGCTCCTCAAAA 60.179 55.000 7.57 0.00 36.47 2.44
1643 1729 0.538287 GGTGCTCCTCAAAAGGCAGT 60.538 55.000 0.00 0.00 43.02 4.40
1661 1747 3.739519 GCAGTGGAGCCATCTACTACAAG 60.740 52.174 0.00 0.00 44.71 3.16
1686 1772 0.457851 AGGAGAAAGATGACGAGCCG 59.542 55.000 0.00 0.00 0.00 5.52
1883 1984 0.107752 GAGCAGCCAGAGAAAGAGGG 60.108 60.000 0.00 0.00 0.00 4.30
1902 2003 3.880846 GCTGATGCCGGCGGAAAG 61.881 66.667 33.44 16.57 34.60 2.62
1903 2004 2.125147 CTGATGCCGGCGGAAAGA 60.125 61.111 33.44 9.37 0.00 2.52
1904 2005 1.745115 CTGATGCCGGCGGAAAGAA 60.745 57.895 33.44 8.39 0.00 2.52
1905 2006 1.982073 CTGATGCCGGCGGAAAGAAC 61.982 60.000 33.44 11.52 0.00 3.01
1906 2007 2.033448 ATGCCGGCGGAAAGAACA 59.967 55.556 33.44 17.64 0.00 3.18
1907 2008 1.582610 GATGCCGGCGGAAAGAACAA 61.583 55.000 33.44 0.00 0.00 2.83
1908 2009 1.862602 ATGCCGGCGGAAAGAACAAC 61.863 55.000 33.44 8.98 0.00 3.32
1909 2010 2.548295 GCCGGCGGAAAGAACAACA 61.548 57.895 33.44 0.00 0.00 3.33
1910 2011 2.026522 CCGGCGGAAAGAACAACAA 58.973 52.632 24.41 0.00 0.00 2.83
1911 2012 0.382515 CCGGCGGAAAGAACAACAAA 59.617 50.000 24.41 0.00 0.00 2.83
1912 2013 1.472990 CGGCGGAAAGAACAACAAAC 58.527 50.000 0.00 0.00 0.00 2.93
1913 2014 1.847818 GGCGGAAAGAACAACAAACC 58.152 50.000 0.00 0.00 0.00 3.27
1914 2015 1.407618 GGCGGAAAGAACAACAAACCT 59.592 47.619 0.00 0.00 0.00 3.50
1949 2050 1.412343 TGCCGATGAATTGGATCGAGA 59.588 47.619 15.03 2.28 44.46 4.04
2117 2218 3.292481 TAGGGGCCTTCGAGACGGT 62.292 63.158 0.84 0.00 0.00 4.83
2131 2232 1.276421 AGACGGTCATGTCCTTCAAGG 59.724 52.381 15.84 0.00 39.77 3.61
2132 2233 1.275291 GACGGTCATGTCCTTCAAGGA 59.725 52.381 0.34 0.34 43.43 3.36
2133 2234 1.276421 ACGGTCATGTCCTTCAAGGAG 59.724 52.381 6.31 0.00 46.90 3.69
2134 2235 1.276421 CGGTCATGTCCTTCAAGGAGT 59.724 52.381 6.31 0.00 46.90 3.85
2191 2292 1.616921 CCAATCCTGGGTGCATCCT 59.383 57.895 18.94 0.00 39.30 3.24
2192 2293 0.754217 CCAATCCTGGGTGCATCCTG 60.754 60.000 18.94 17.20 39.30 3.86
2193 2294 1.076485 AATCCTGGGTGCATCCTGC 60.076 57.895 18.94 0.00 45.29 4.85
2204 2305 3.300711 CATCCTGCATGCTGATCGA 57.699 52.632 24.53 14.08 0.00 3.59
2205 2306 0.866427 CATCCTGCATGCTGATCGAC 59.134 55.000 24.53 0.00 0.00 4.20
2206 2307 0.250209 ATCCTGCATGCTGATCGACC 60.250 55.000 24.53 0.00 0.00 4.79
2207 2308 1.153309 CCTGCATGCTGATCGACCA 60.153 57.895 24.53 0.00 0.00 4.02
2208 2309 0.745486 CCTGCATGCTGATCGACCAA 60.745 55.000 24.53 0.00 0.00 3.67
2209 2310 1.306148 CTGCATGCTGATCGACCAAT 58.694 50.000 20.33 0.00 0.00 3.16
2210 2311 1.263484 CTGCATGCTGATCGACCAATC 59.737 52.381 20.33 0.00 0.00 2.67
2211 2312 0.590195 GCATGCTGATCGACCAATCC 59.410 55.000 11.37 0.00 0.00 3.01
2212 2313 1.813092 GCATGCTGATCGACCAATCCT 60.813 52.381 11.37 0.00 0.00 3.24
2213 2314 1.871676 CATGCTGATCGACCAATCCTG 59.128 52.381 0.00 0.00 0.00 3.86
2222 2323 4.265206 CCAATCCTGGGTGCATCC 57.735 61.111 9.82 9.82 39.30 3.51
2267 2370 2.395654 GTTCCTCGAGTGTCAGTGTTC 58.604 52.381 12.31 0.00 0.00 3.18
2401 2509 2.224018 TGAATGAAACCTTGGTGCTTGC 60.224 45.455 0.00 0.00 0.00 4.01
2538 2646 1.541147 CCAATGCGTCACCAAATGTCT 59.459 47.619 0.00 0.00 0.00 3.41
2545 2653 4.390603 TGCGTCACCAAATGTCTAATACAC 59.609 41.667 0.00 0.00 42.09 2.90
2624 2738 5.512232 GGGTATTTTGGCCACATTCAAAAGA 60.512 40.000 3.88 0.00 43.28 2.52
2625 2739 5.994668 GGTATTTTGGCCACATTCAAAAGAA 59.005 36.000 3.88 0.00 43.28 2.52
2626 2740 6.484977 GGTATTTTGGCCACATTCAAAAGAAA 59.515 34.615 3.88 0.00 43.28 2.52
2627 2741 6.622833 ATTTTGGCCACATTCAAAAGAAAG 57.377 33.333 3.88 0.00 43.28 2.62
2628 2742 3.749665 TGGCCACATTCAAAAGAAAGG 57.250 42.857 0.00 0.00 0.00 3.11
2629 2743 2.224257 TGGCCACATTCAAAAGAAAGGC 60.224 45.455 0.00 0.00 40.08 4.35
2630 2744 2.416747 GCCACATTCAAAAGAAAGGCC 58.583 47.619 0.00 0.00 34.94 5.19
2631 2745 2.871637 GCCACATTCAAAAGAAAGGCCC 60.872 50.000 0.00 0.00 34.94 5.80
2632 2746 2.610232 CCACATTCAAAAGAAAGGCCCG 60.610 50.000 0.00 0.00 0.00 6.13
2633 2747 1.000843 ACATTCAAAAGAAAGGCCCGC 59.999 47.619 0.00 0.00 0.00 6.13
2634 2748 0.243636 ATTCAAAAGAAAGGCCCGCG 59.756 50.000 0.00 0.00 0.00 6.46
2635 2749 1.104577 TTCAAAAGAAAGGCCCGCGT 61.105 50.000 4.92 0.00 0.00 6.01
2636 2750 1.081442 CAAAAGAAAGGCCCGCGTC 60.081 57.895 4.92 0.00 0.00 5.19
2637 2751 1.228154 AAAAGAAAGGCCCGCGTCT 60.228 52.632 4.92 0.00 0.00 4.18
2638 2752 0.822121 AAAAGAAAGGCCCGCGTCTT 60.822 50.000 4.92 3.15 31.69 3.01
2639 2753 0.035739 AAAGAAAGGCCCGCGTCTTA 59.964 50.000 4.92 0.00 30.24 2.10
2640 2754 0.035739 AAGAAAGGCCCGCGTCTTAA 59.964 50.000 4.92 0.00 0.00 1.85
2641 2755 0.035739 AGAAAGGCCCGCGTCTTAAA 59.964 50.000 4.92 0.00 0.00 1.52
2642 2756 0.876399 GAAAGGCCCGCGTCTTAAAA 59.124 50.000 4.92 0.00 0.00 1.52
2643 2757 1.267533 GAAAGGCCCGCGTCTTAAAAA 59.732 47.619 4.92 0.00 0.00 1.94
2800 2916 2.092212 AGTCCAACATTATCCAGCTGGG 60.092 50.000 32.23 18.05 35.41 4.45
2820 2936 2.614057 GGGCCTCAATAATTGACACTCG 59.386 50.000 0.84 0.00 35.46 4.18
2832 2948 1.335597 TGACACTCGACGACAACATCC 60.336 52.381 0.00 0.00 0.00 3.51
2851 2967 4.314522 TCCATCCATCCAAGCAAAAGTA 57.685 40.909 0.00 0.00 0.00 2.24
2928 3044 2.517959 CTGGGGAAACTTGCATCTTCA 58.482 47.619 0.00 0.00 0.00 3.02
2941 3057 1.839994 CATCTTCAGCCCAACCTCCTA 59.160 52.381 0.00 0.00 0.00 2.94
2974 3090 6.481976 TGAAACACTACGTCTCATCACATTTT 59.518 34.615 0.00 0.00 0.00 1.82
2975 3091 5.845985 ACACTACGTCTCATCACATTTTG 57.154 39.130 0.00 0.00 0.00 2.44
2976 3092 5.538118 ACACTACGTCTCATCACATTTTGA 58.462 37.500 0.00 0.00 39.11 2.69
2977 3093 5.635280 ACACTACGTCTCATCACATTTTGAG 59.365 40.000 0.00 0.00 37.77 3.02
2978 3094 5.863935 CACTACGTCTCATCACATTTTGAGA 59.136 40.000 0.00 0.00 44.55 3.27
2979 3095 6.034363 CACTACGTCTCATCACATTTTGAGAG 59.966 42.308 0.00 0.00 46.63 3.20
2980 3096 4.854361 CGTCTCATCACATTTTGAGAGG 57.146 45.455 3.02 5.71 46.63 3.69
2981 3097 3.063180 CGTCTCATCACATTTTGAGAGGC 59.937 47.826 8.99 0.00 46.63 4.70
2982 3098 4.005650 GTCTCATCACATTTTGAGAGGCA 58.994 43.478 3.02 0.00 46.63 4.75
2983 3099 4.639310 GTCTCATCACATTTTGAGAGGCAT 59.361 41.667 3.02 0.00 46.63 4.40
2984 3100 4.638865 TCTCATCACATTTTGAGAGGCATG 59.361 41.667 0.00 0.00 42.52 4.06
2985 3101 4.591929 TCATCACATTTTGAGAGGCATGA 58.408 39.130 0.00 0.00 37.77 3.07
2986 3102 5.198207 TCATCACATTTTGAGAGGCATGAT 58.802 37.500 0.00 0.00 37.77 2.45
2987 3103 5.298527 TCATCACATTTTGAGAGGCATGATC 59.701 40.000 0.00 0.00 37.77 2.92
2990 3106 4.157105 CACATTTTGAGAGGCATGATCACA 59.843 41.667 0.00 0.00 0.00 3.58
3040 3167 3.253188 ACAACTGATGCCACACATGTTAC 59.747 43.478 0.00 0.00 39.84 2.50
3062 3189 4.202101 ACATTTGTGAAATTTCCGCACTCA 60.202 37.500 15.48 3.20 33.83 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
322 336 1.600957 CATCATCCGCCACTTCATCAC 59.399 52.381 0.00 0.00 0.00 3.06
330 344 1.601759 CCCATCCATCATCCGCCAC 60.602 63.158 0.00 0.00 0.00 5.01
331 345 2.078044 ACCCATCCATCATCCGCCA 61.078 57.895 0.00 0.00 0.00 5.69
332 346 1.601759 CACCCATCCATCATCCGCC 60.602 63.158 0.00 0.00 0.00 6.13
333 347 1.601759 CCACCCATCCATCATCCGC 60.602 63.158 0.00 0.00 0.00 5.54
334 348 1.073722 CCCACCCATCCATCATCCG 59.926 63.158 0.00 0.00 0.00 4.18
335 349 0.178981 CACCCACCCATCCATCATCC 60.179 60.000 0.00 0.00 0.00 3.51
336 350 0.846015 TCACCCACCCATCCATCATC 59.154 55.000 0.00 0.00 0.00 2.92
337 351 0.848735 CTCACCCACCCATCCATCAT 59.151 55.000 0.00 0.00 0.00 2.45
338 352 1.925285 GCTCACCCACCCATCCATCA 61.925 60.000 0.00 0.00 0.00 3.07
339 353 1.152881 GCTCACCCACCCATCCATC 60.153 63.158 0.00 0.00 0.00 3.51
340 354 3.010144 GCTCACCCACCCATCCAT 58.990 61.111 0.00 0.00 0.00 3.41
341 355 3.716195 CGCTCACCCACCCATCCA 61.716 66.667 0.00 0.00 0.00 3.41
342 356 4.489771 CCGCTCACCCACCCATCC 62.490 72.222 0.00 0.00 0.00 3.51
376 390 4.625607 AGGAAGAAGAACCGAAGAATGT 57.374 40.909 0.00 0.00 0.00 2.71
400 414 0.675633 AATTATTCCCTGCGGCATGC 59.324 50.000 9.90 9.90 46.70 4.06
488 502 7.227314 TGCAAGGAAGCTATAACAAGATACATG 59.773 37.037 0.00 0.00 34.99 3.21
497 513 4.706476 AGCAAATGCAAGGAAGCTATAACA 59.294 37.500 8.28 0.00 45.16 2.41
498 514 5.039333 CAGCAAATGCAAGGAAGCTATAAC 58.961 41.667 8.28 0.00 45.16 1.89
500 516 3.633525 CCAGCAAATGCAAGGAAGCTATA 59.366 43.478 8.28 0.00 45.16 1.31
572 608 1.664321 CCTCCGTCCGTACCAGGAAG 61.664 65.000 0.00 0.00 42.77 3.46
603 654 4.766373 TGAAAAACATTGCCATCTGCTAGA 59.234 37.500 0.00 0.00 42.00 2.43
608 659 7.837202 AATACATGAAAAACATTGCCATCTG 57.163 32.000 0.00 0.00 37.07 2.90
870 923 3.307782 CCCCATTATTGTACGAACACGAC 59.692 47.826 0.00 0.00 34.61 4.34
946 999 3.435186 GCAGAAGAAGCGGCACCC 61.435 66.667 1.45 0.00 0.00 4.61
1212 1274 4.760047 GACCGGCCAGCGTGTGAT 62.760 66.667 0.00 0.00 0.00 3.06
1444 1524 4.660938 GGACGCCACCCCTTTGCT 62.661 66.667 0.00 0.00 0.00 3.91
1563 1649 1.528129 CTTCTCTTTTCTTGGCCGCT 58.472 50.000 0.00 0.00 0.00 5.52
1569 1655 2.292569 TGCTGCTGCTTCTCTTTTCTTG 59.707 45.455 17.00 0.00 40.48 3.02
1610 1696 3.170362 CACCCCTTGGCCTTGAGA 58.830 61.111 3.32 0.00 33.59 3.27
1643 1729 2.432146 CTGCTTGTAGTAGATGGCTCCA 59.568 50.000 0.00 0.00 28.61 3.86
1653 1739 5.084519 TCTTTCTCCTTCCTGCTTGTAGTA 58.915 41.667 0.00 0.00 0.00 1.82
1661 1747 2.093973 TCGTCATCTTTCTCCTTCCTGC 60.094 50.000 0.00 0.00 0.00 4.85
1686 1772 2.352960 GGATTCCTCAAACTGCATCGAC 59.647 50.000 0.00 0.00 0.00 4.20
1694 1780 1.208293 GGCTCTCGGATTCCTCAAACT 59.792 52.381 0.30 0.00 0.00 2.66
1902 2003 3.779759 TGCAATGTCAGGTTTGTTGTTC 58.220 40.909 0.00 0.00 0.00 3.18
1903 2004 3.883830 TGCAATGTCAGGTTTGTTGTT 57.116 38.095 0.00 0.00 0.00 2.83
1904 2005 3.883830 TTGCAATGTCAGGTTTGTTGT 57.116 38.095 0.00 0.00 0.00 3.32
1905 2006 3.556775 CCTTTGCAATGTCAGGTTTGTTG 59.443 43.478 0.00 0.00 0.00 3.33
1906 2007 3.197549 ACCTTTGCAATGTCAGGTTTGTT 59.802 39.130 13.69 0.00 36.09 2.83
1907 2008 2.765699 ACCTTTGCAATGTCAGGTTTGT 59.234 40.909 13.69 0.00 36.09 2.83
1908 2009 3.457610 ACCTTTGCAATGTCAGGTTTG 57.542 42.857 13.69 0.00 36.09 2.93
1909 2010 3.795877 CAACCTTTGCAATGTCAGGTTT 58.204 40.909 24.34 11.69 45.63 3.27
1949 2050 0.252193 AGCCTCTTCTGTCTCTGCCT 60.252 55.000 0.00 0.00 0.00 4.75
1990 2091 0.727970 CATGACTGAGCAGCTTCAGC 59.272 55.000 14.15 8.53 46.77 4.26
2050 2151 1.211190 CCAGGAGCTTGCTTTTCGC 59.789 57.895 0.00 0.00 39.77 4.70
2117 2218 3.242867 ACTCACTCCTTGAAGGACATGA 58.757 45.455 10.46 15.21 40.06 3.07
2131 2232 1.548269 AGGCTGAGCAACTACTCACTC 59.452 52.381 6.82 0.00 41.72 3.51
2132 2233 1.548269 GAGGCTGAGCAACTACTCACT 59.452 52.381 6.82 0.00 41.72 3.41
2133 2234 1.734047 CGAGGCTGAGCAACTACTCAC 60.734 57.143 6.82 0.00 41.72 3.51
2134 2235 0.528017 CGAGGCTGAGCAACTACTCA 59.472 55.000 6.82 0.00 44.32 3.41
2191 2292 1.302366 GATTGGTCGATCAGCATGCA 58.698 50.000 21.98 0.00 34.76 3.96
2192 2293 0.590195 GGATTGGTCGATCAGCATGC 59.410 55.000 10.51 10.51 34.76 4.06
2193 2294 1.871676 CAGGATTGGTCGATCAGCATG 59.128 52.381 0.00 0.00 30.77 4.06
2194 2295 1.202734 CCAGGATTGGTCGATCAGCAT 60.203 52.381 0.00 0.00 39.79 3.79
2195 2296 0.178767 CCAGGATTGGTCGATCAGCA 59.821 55.000 0.00 0.00 39.79 4.41
2196 2297 0.533755 CCCAGGATTGGTCGATCAGC 60.534 60.000 0.00 0.00 43.40 4.26
2197 2298 0.833287 ACCCAGGATTGGTCGATCAG 59.167 55.000 0.00 0.00 43.40 2.90
2198 2299 0.541392 CACCCAGGATTGGTCGATCA 59.459 55.000 0.00 0.00 43.40 2.92
2199 2300 0.815615 GCACCCAGGATTGGTCGATC 60.816 60.000 0.00 0.00 43.40 3.69
2200 2301 1.224592 GCACCCAGGATTGGTCGAT 59.775 57.895 0.00 0.00 43.40 3.59
2201 2302 1.561769 ATGCACCCAGGATTGGTCGA 61.562 55.000 0.00 0.00 43.40 4.20
2202 2303 1.077501 ATGCACCCAGGATTGGTCG 60.078 57.895 0.00 0.00 43.40 4.79
2203 2304 0.753111 GGATGCACCCAGGATTGGTC 60.753 60.000 0.00 0.00 43.40 4.02
2204 2305 1.217057 AGGATGCACCCAGGATTGGT 61.217 55.000 0.00 0.00 43.40 3.67
2205 2306 0.754217 CAGGATGCACCCAGGATTGG 60.754 60.000 0.00 0.00 44.60 3.16
2206 2307 2.803203 CAGGATGCACCCAGGATTG 58.197 57.895 0.00 0.00 40.05 2.67
2218 2319 4.277423 TCACAGCATATTCAATGCAGGATG 59.723 41.667 12.12 4.48 46.77 3.51
2219 2320 4.466827 TCACAGCATATTCAATGCAGGAT 58.533 39.130 12.12 0.00 46.77 3.24
2220 2321 3.888583 TCACAGCATATTCAATGCAGGA 58.111 40.909 12.12 4.01 46.77 3.86
2221 2322 4.277423 TGATCACAGCATATTCAATGCAGG 59.723 41.667 12.12 6.46 46.77 4.85
2222 2323 5.432885 TGATCACAGCATATTCAATGCAG 57.567 39.130 12.12 6.77 46.77 4.41
2267 2370 2.943033 GGACCAAGGAAACCATCGTATG 59.057 50.000 0.00 0.00 0.00 2.39
2401 2509 0.040204 AGGATTTCCCAGCCAACCAG 59.960 55.000 0.00 0.00 37.41 4.00
2545 2653 9.890085 CATTCAAACATTTTTGTTATAGCATCG 57.110 29.630 4.35 0.00 42.51 3.84
2624 2738 1.320507 TTTTTAAGACGCGGGCCTTT 58.679 45.000 12.47 0.00 0.00 3.11
2625 2739 3.024431 TTTTTAAGACGCGGGCCTT 57.976 47.368 12.47 13.15 0.00 4.35
2626 2740 4.804806 TTTTTAAGACGCGGGCCT 57.195 50.000 12.47 0.83 0.00 5.19
2642 2756 5.478332 CCTGCTCTCTGGTCCTTTAATTTTT 59.522 40.000 0.00 0.00 0.00 1.94
2643 2757 5.012893 CCTGCTCTCTGGTCCTTTAATTTT 58.987 41.667 0.00 0.00 0.00 1.82
2644 2758 4.043435 ACCTGCTCTCTGGTCCTTTAATTT 59.957 41.667 0.00 0.00 40.00 1.82
2645 2759 3.589288 ACCTGCTCTCTGGTCCTTTAATT 59.411 43.478 0.00 0.00 40.00 1.40
2646 2760 3.185455 ACCTGCTCTCTGGTCCTTTAAT 58.815 45.455 0.00 0.00 40.00 1.40
2647 2761 2.621070 ACCTGCTCTCTGGTCCTTTAA 58.379 47.619 0.00 0.00 40.00 1.52
2648 2762 2.327325 ACCTGCTCTCTGGTCCTTTA 57.673 50.000 0.00 0.00 40.00 1.85
2800 2916 3.309954 GTCGAGTGTCAATTATTGAGGCC 59.690 47.826 8.00 0.00 41.01 5.19
2820 2936 2.213499 GGATGGATGGATGTTGTCGTC 58.787 52.381 0.00 0.00 0.00 4.20
2832 2948 5.277683 CGATCTACTTTTGCTTGGATGGATG 60.278 44.000 0.00 0.00 0.00 3.51
2851 2967 3.474570 GCCTCACCCCTGCGATCT 61.475 66.667 0.00 0.00 0.00 2.75
2928 3044 1.501582 GATCACTAGGAGGTTGGGCT 58.498 55.000 0.00 0.00 0.00 5.19
2941 3057 3.637998 ACGTAGTGTTTCACGATCACT 57.362 42.857 0.62 0.00 42.51 3.41
2974 3090 2.568509 TCAGTTGTGATCATGCCTCTCA 59.431 45.455 0.00 0.00 0.00 3.27
2975 3091 3.118847 TCTCAGTTGTGATCATGCCTCTC 60.119 47.826 0.00 0.00 30.18 3.20
2976 3092 2.836372 TCTCAGTTGTGATCATGCCTCT 59.164 45.455 0.00 0.00 30.18 3.69
2977 3093 3.196463 CTCTCAGTTGTGATCATGCCTC 58.804 50.000 0.00 0.00 30.18 4.70
2978 3094 2.680221 GCTCTCAGTTGTGATCATGCCT 60.680 50.000 0.00 0.00 30.18 4.75
2979 3095 1.669779 GCTCTCAGTTGTGATCATGCC 59.330 52.381 0.00 0.00 30.18 4.40
2980 3096 1.669779 GGCTCTCAGTTGTGATCATGC 59.330 52.381 0.00 0.00 30.18 4.06
2981 3097 1.931841 CGGCTCTCAGTTGTGATCATG 59.068 52.381 0.00 0.00 30.18 3.07
2982 3098 1.552337 ACGGCTCTCAGTTGTGATCAT 59.448 47.619 0.00 0.00 30.18 2.45
2983 3099 0.969149 ACGGCTCTCAGTTGTGATCA 59.031 50.000 0.00 0.00 30.18 2.92
2984 3100 2.086054 AACGGCTCTCAGTTGTGATC 57.914 50.000 0.00 0.00 30.18 2.92
2985 3101 2.146342 CAAACGGCTCTCAGTTGTGAT 58.854 47.619 0.00 0.00 30.18 3.06
2986 3102 1.138069 TCAAACGGCTCTCAGTTGTGA 59.862 47.619 0.00 0.00 0.00 3.58
2987 3103 1.528586 CTCAAACGGCTCTCAGTTGTG 59.471 52.381 0.00 0.00 0.00 3.33
2990 3106 1.001406 CCTCTCAAACGGCTCTCAGTT 59.999 52.381 0.00 0.00 0.00 3.16
3040 3167 4.297510 TGAGTGCGGAAATTTCACAAATG 58.702 39.130 19.49 3.54 33.44 2.32
3062 3189 0.452987 GTCATGACCATGCGCAACAT 59.547 50.000 17.11 14.96 40.66 2.71
3085 3212 1.547292 CGGTGCAAAAATGTGTGCCG 61.547 55.000 0.00 0.00 40.14 5.69


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

AutoCloner maintained by Alex Coulton.