Multiple sequence alignment - TraesCS1B01G050800

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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 TraesCS1B01G050800 chr1B 100.000 2336 0 0 1 2336 30843359 30845694 0.000000e+00 4314
1 TraesCS1B01G050800 chr1B 82.851 863 115 18 1062 1912 24793141 24792300 0.000000e+00 743
2 TraesCS1B01G050800 chr1B 100.000 280 0 0 2660 2939 30846018 30846297 4.340000e-143 518
3 TraesCS1B01G050800 chr1B 91.176 102 7 1 2112 2213 24773001 24772902 1.420000e-28 137
4 TraesCS1B01G050800 chr1D 90.533 1933 124 25 3 1888 16979368 16977448 0.000000e+00 2501
5 TraesCS1B01G050800 chr1D 86.109 1483 140 36 784 2235 16894432 16895879 0.000000e+00 1537
6 TraesCS1B01G050800 chr1D 85.033 902 129 4 1002 1900 17021430 17020532 0.000000e+00 913
7 TraesCS1B01G050800 chr1D 82.785 912 124 12 989 1888 17052117 17051227 0.000000e+00 784
8 TraesCS1B01G050800 chr1D 81.789 928 131 15 1002 1913 17048256 17047351 0.000000e+00 743
9 TraesCS1B01G050800 chr1D 83.529 765 118 6 1141 1900 17061854 17061093 0.000000e+00 708
10 TraesCS1B01G050800 chr1D 88.218 348 29 7 1871 2209 16977434 16977090 3.530000e-109 405
11 TraesCS1B01G050800 chr1D 94.561 239 6 5 2660 2895 16896546 16896780 2.150000e-96 363
12 TraesCS1B01G050800 chr1D 75.195 512 118 7 1379 1884 90633085 90633593 1.760000e-57 233
13 TraesCS1B01G050800 chr1D 86.047 172 24 0 1002 1173 17042918 17042747 5.000000e-43 185
14 TraesCS1B01G050800 chr1D 91.011 89 8 0 2234 2322 16896075 16896163 1.430000e-23 121
15 TraesCS1B01G050800 chr1A 86.566 923 99 15 1307 2223 18082314 18083217 0.000000e+00 994
16 TraesCS1B01G050800 chr1A 82.170 1060 155 22 877 1911 18321204 18320154 0.000000e+00 880
17 TraesCS1B01G050800 chr1A 79.847 918 131 38 877 1777 18298984 18299864 3.220000e-174 621
18 TraesCS1B01G050800 chr1A 83.908 435 51 8 877 1310 18049152 18049568 5.900000e-107 398
19 TraesCS1B01G050800 chr1A 93.220 118 8 0 1772 1889 18300735 18300852 1.080000e-39 174
20 TraesCS1B01G050800 chr1A 83.750 160 14 5 2728 2886 18084158 18084306 1.100000e-29 141
21 TraesCS1B01G050800 chr1A 88.764 89 8 2 2808 2895 18102264 18102351 1.110000e-19 108


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 TraesCS1B01G050800 chr1B 30843359 30846297 2938 False 2416.000000 4314 100.000000 1 2939 2 chr1B.!!$F1 2938
1 TraesCS1B01G050800 chr1B 24792300 24793141 841 True 743.000000 743 82.851000 1062 1912 1 chr1B.!!$R2 850
2 TraesCS1B01G050800 chr1D 16977090 16979368 2278 True 1453.000000 2501 89.375500 3 2209 2 chr1D.!!$R4 2206
3 TraesCS1B01G050800 chr1D 17020532 17021430 898 True 913.000000 913 85.033000 1002 1900 1 chr1D.!!$R1 898
4 TraesCS1B01G050800 chr1D 17047351 17052117 4766 True 763.500000 784 82.287000 989 1913 2 chr1D.!!$R5 924
5 TraesCS1B01G050800 chr1D 17061093 17061854 761 True 708.000000 708 83.529000 1141 1900 1 chr1D.!!$R3 759
6 TraesCS1B01G050800 chr1D 16894432 16896780 2348 False 673.666667 1537 90.560333 784 2895 3 chr1D.!!$F2 2111
7 TraesCS1B01G050800 chr1D 90633085 90633593 508 False 233.000000 233 75.195000 1379 1884 1 chr1D.!!$F1 505
8 TraesCS1B01G050800 chr1A 18320154 18321204 1050 True 880.000000 880 82.170000 877 1911 1 chr1A.!!$R1 1034
9 TraesCS1B01G050800 chr1A 18082314 18084306 1992 False 567.500000 994 85.158000 1307 2886 2 chr1A.!!$F3 1579
10 TraesCS1B01G050800 chr1A 18298984 18300852 1868 False 397.500000 621 86.533500 877 1889 2 chr1A.!!$F4 1012

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
335 337 0.102300 GGCGTCATATTTGGTTGGGC 59.898 55.0 0.0 0.0 0.0 5.36 F
463 465 0.183971 TTTTTCTTGGAGGGGTCGCA 59.816 50.0 0.0 0.0 0.0 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1691 1822 0.391966 GGAGGGGTTATCCTGCGTAC 59.608 60.000 0.0 0.0 37.25 3.67 R
2280 8063 2.227194 ACGTGCCCCTTCAGTTTAAAG 58.773 47.619 0.0 0.0 0.00 1.85 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
43 44 0.589708 GTCGGAAGTTGTTTTCGGGG 59.410 55.000 0.00 0.00 0.00 5.73
51 52 4.370094 AGTTGTTTTCGGGGGTATAACA 57.630 40.909 0.00 0.00 0.00 2.41
76 78 4.229582 ACCCAACCATACTGGAACATATGT 59.770 41.667 1.41 1.41 40.96 2.29
82 84 4.686091 CCATACTGGAACATATGTAGCACG 59.314 45.833 9.21 0.04 40.96 5.34
117 119 2.333069 TGGCTGGGGATCTTGATCTAG 58.667 52.381 10.03 0.00 0.00 2.43
127 129 6.463755 GGGGATCTTGATCTAGAAAGACTTCC 60.464 46.154 10.93 13.83 35.34 3.46
139 141 1.760192 AGACTTCCCATTGCATCAGC 58.240 50.000 0.00 0.00 42.57 4.26
142 144 1.822990 ACTTCCCATTGCATCAGCTTG 59.177 47.619 0.00 0.00 42.74 4.01
158 160 1.823250 GCTTGTGAAGGGGTGGTGAAT 60.823 52.381 0.00 0.00 0.00 2.57
163 165 1.073763 TGAAGGGGTGGTGAATGACAG 59.926 52.381 0.00 0.00 0.00 3.51
182 184 0.538287 GAAAGCAAGGCTCTGGTGGT 60.538 55.000 0.00 0.00 38.25 4.16
193 195 1.137872 CTCTGGTGGTAGACATGGAGC 59.862 57.143 0.00 0.00 0.00 4.70
229 231 6.430007 AGATCATTGATAGAAAGGGTGCTTT 58.570 36.000 0.00 0.00 0.00 3.51
239 241 5.385198 AGAAAGGGTGCTTTTAGTTCATGA 58.615 37.500 0.00 0.00 0.00 3.07
266 268 9.233232 AGTTTTATTCATGAACGTTGAGTTTTC 57.767 29.630 11.07 0.00 44.35 2.29
298 300 4.334759 AGCTCATCATCTCGTCAAATTTGG 59.665 41.667 17.90 3.33 0.00 3.28
334 336 0.744281 GGGCGTCATATTTGGTTGGG 59.256 55.000 0.00 0.00 0.00 4.12
335 337 0.102300 GGCGTCATATTTGGTTGGGC 59.898 55.000 0.00 0.00 0.00 5.36
360 362 3.181412 ACCCCATGACCAAAACCTTGTAT 60.181 43.478 0.00 0.00 0.00 2.29
361 363 3.837731 CCCCATGACCAAAACCTTGTATT 59.162 43.478 0.00 0.00 0.00 1.89
378 380 8.698210 ACCTTGTATTGATGAACATTATTGCAT 58.302 29.630 0.00 0.00 0.00 3.96
391 393 4.566545 TTATTGCATATCAAAGTGGGCG 57.433 40.909 0.00 0.00 38.34 6.13
442 444 2.562738 AGCGCATAGGCTTTTCCTTTTT 59.437 40.909 11.47 0.00 44.75 1.94
463 465 0.183971 TTTTTCTTGGAGGGGTCGCA 59.816 50.000 0.00 0.00 0.00 5.10
473 475 2.282783 GGGGTCGCATGGGCTTTTT 61.283 57.895 4.59 0.00 38.10 1.94
493 495 3.308438 TTCTACTTGACACCCGTTAGC 57.692 47.619 0.00 0.00 0.00 3.09
496 498 4.081406 TCTACTTGACACCCGTTAGCTTA 58.919 43.478 0.00 0.00 0.00 3.09
497 499 3.756933 ACTTGACACCCGTTAGCTTAA 57.243 42.857 0.00 0.00 0.00 1.85
498 500 3.660865 ACTTGACACCCGTTAGCTTAAG 58.339 45.455 0.00 0.00 0.00 1.85
501 503 3.921677 TGACACCCGTTAGCTTAAGAAG 58.078 45.455 6.67 0.00 0.00 2.85
506 508 5.824097 ACACCCGTTAGCTTAAGAAGAAAAA 59.176 36.000 6.67 0.00 0.00 1.94
509 511 7.326063 CACCCGTTAGCTTAAGAAGAAAAATTG 59.674 37.037 6.67 0.00 0.00 2.32
519 521 4.646572 AGAAGAAAAATTGAGTCTCCGCT 58.353 39.130 0.00 0.00 0.00 5.52
525 527 2.301577 ATTGAGTCTCCGCTTACAGC 57.698 50.000 0.00 0.00 38.02 4.40
535 537 2.668632 CTTACAGCCCCCGCAGAA 59.331 61.111 0.00 0.00 37.52 3.02
555 572 3.341857 AAAAACATACAGCGACGCAAA 57.658 38.095 23.70 6.94 0.00 3.68
562 579 3.747976 AGCGACGCAAAATGGGCC 61.748 61.111 23.70 0.00 33.10 5.80
564 581 4.474846 CGACGCAAAATGGGCCGG 62.475 66.667 0.00 0.00 33.01 6.13
565 582 4.794439 GACGCAAAATGGGCCGGC 62.794 66.667 21.18 21.18 33.10 6.13
568 585 4.014108 GCAAAATGGGCCGGCCAA 62.014 61.111 44.46 37.76 37.98 4.52
569 586 2.746359 CAAAATGGGCCGGCCAAA 59.254 55.556 44.46 32.79 37.98 3.28
570 587 1.299321 CAAAATGGGCCGGCCAAAT 59.701 52.632 44.46 33.46 37.98 2.32
571 588 0.322366 CAAAATGGGCCGGCCAAATT 60.322 50.000 44.46 36.48 37.98 1.82
572 589 1.065854 CAAAATGGGCCGGCCAAATTA 60.066 47.619 44.46 25.32 37.98 1.40
573 590 0.829990 AAATGGGCCGGCCAAATTAG 59.170 50.000 44.46 0.00 37.98 1.73
581 598 1.680735 CCGGCCAAATTAGCATTAGCA 59.319 47.619 2.24 0.00 45.49 3.49
607 624 2.335712 GGCCGGCCAAAAGAGTCTG 61.336 63.158 40.73 0.00 35.81 3.51
657 674 7.023575 CCCAGAAAAATCTTAACGACAATCAG 58.976 38.462 0.00 0.00 0.00 2.90
664 681 8.589335 AAATCTTAACGACAATCAGCGTATAT 57.411 30.769 0.00 0.00 40.23 0.86
665 682 9.687210 AAATCTTAACGACAATCAGCGTATATA 57.313 29.630 0.00 0.00 40.23 0.86
666 683 9.856488 AATCTTAACGACAATCAGCGTATATAT 57.144 29.630 0.00 0.00 40.23 0.86
668 685 9.983804 TCTTAACGACAATCAGCGTATATATAG 57.016 33.333 0.00 0.00 40.23 1.31
669 686 9.770503 CTTAACGACAATCAGCGTATATATAGT 57.229 33.333 0.00 0.00 40.23 2.12
714 731 2.093973 AGAGCAATACGTTGGAGGTCAG 60.094 50.000 0.00 0.00 35.83 3.51
715 732 1.623811 AGCAATACGTTGGAGGTCAGT 59.376 47.619 0.00 0.00 35.83 3.41
717 734 3.119101 AGCAATACGTTGGAGGTCAGTAG 60.119 47.826 0.00 0.00 35.83 2.57
778 795 1.745489 GATCAGGCGACCCAACACC 60.745 63.158 0.00 0.00 0.00 4.16
897 971 5.163591 ACGTTTCTTTGGATCTTTCGGTTTT 60.164 36.000 0.00 0.00 0.00 2.43
935 1011 6.421801 ACTTAACTGTTGCTTGATTTGATTGC 59.578 34.615 2.69 0.00 0.00 3.56
1011 1090 0.598680 CGACTCCGATGGATTCTGCC 60.599 60.000 2.33 0.00 38.22 4.85
1173 1267 4.969484 AGGACACTGGAAATTACGTTTCT 58.031 39.130 0.00 0.00 44.54 2.52
1227 1321 2.354196 GTAAATGCAATCTTCGACGCG 58.646 47.619 3.53 3.53 0.00 6.01
1240 1334 1.702299 GACGCGTTCTTGATGGACG 59.298 57.895 15.53 0.00 0.00 4.79
1245 1339 1.136057 GCGTTCTTGATGGACGGAAAC 60.136 52.381 1.23 0.00 0.00 2.78
1686 1817 5.209818 TCATATACACGGATGAGTTTCCC 57.790 43.478 0.00 0.00 31.61 3.97
1691 1822 2.233922 ACACGGATGAGTTTCCCACTAG 59.766 50.000 0.00 0.00 35.01 2.57
1770 1913 1.517694 CGCGCTAGACCGGCTAAAA 60.518 57.895 5.56 0.00 0.00 1.52
1857 6727 2.648059 GCTGAGATGTACAATTGCCCT 58.352 47.619 5.05 0.00 0.00 5.19
1889 6790 5.536161 AGGACAAGTGCATTGACTTTATTGT 59.464 36.000 13.53 0.00 41.83 2.71
1934 6835 1.479709 CTGGAGGAGTCTTCATCGGT 58.520 55.000 4.48 0.00 35.01 4.69
1973 6878 9.683069 CAAACTTCATGGATTATTATAGTTGGC 57.317 33.333 0.00 0.00 0.00 4.52
1984 6889 9.472361 GATTATTATAGTTGGCGAGTTTAGACA 57.528 33.333 0.00 0.00 0.00 3.41
1988 6893 9.826574 ATTATAGTTGGCGAGTTTAGACATTAA 57.173 29.630 0.00 0.00 0.00 1.40
1995 6900 5.005875 GGCGAGTTTAGACATTAAAGAGAGC 59.994 44.000 0.00 0.00 0.00 4.09
2063 6978 9.577110 CATATTCACTATTTGTGCTTTGACAAT 57.423 29.630 0.00 0.00 45.81 2.71
2101 7016 7.450124 TTGTGTTTAACAAGTACCTTCACAA 57.550 32.000 0.00 0.00 43.96 3.33
2179 7094 8.764524 ACTGTGTTTTGTTGTTGCTAAATTTA 57.235 26.923 0.00 0.00 0.00 1.40
2275 8058 6.692681 CAGATTAGTTGTTAATTTGCCCATCG 59.307 38.462 0.00 0.00 32.09 3.84
2280 8063 0.820871 TTAATTTGCCCATCGTGCCC 59.179 50.000 0.00 0.00 0.00 5.36
2282 8065 0.904394 AATTTGCCCATCGTGCCCTT 60.904 50.000 0.00 0.00 0.00 3.95
2288 8071 1.834188 CCCATCGTGCCCTTTAAACT 58.166 50.000 0.00 0.00 0.00 2.66
2313 8096 6.042781 TGAAGGGGCACGTTTATTATCTCTAT 59.957 38.462 0.00 0.00 0.00 1.98
2783 8612 4.362932 TCGAGAAAAACAACAATGTGCA 57.637 36.364 0.00 0.00 40.46 4.57
2784 8613 4.101942 TCGAGAAAAACAACAATGTGCAC 58.898 39.130 10.75 10.75 40.46 4.57
2785 8614 3.856521 CGAGAAAAACAACAATGTGCACA 59.143 39.130 24.08 24.08 40.46 4.57
2801 8630 1.748879 ACACACACACACACAGGGC 60.749 57.895 0.00 0.00 0.00 5.19
2891 8720 2.867472 GCACGGCGCAACTGTAAT 59.133 55.556 10.83 0.00 41.79 1.89
2892 8721 1.209127 GCACGGCGCAACTGTAATT 59.791 52.632 10.83 0.00 41.79 1.40
2894 8723 1.135916 GCACGGCGCAACTGTAATTTA 60.136 47.619 10.83 0.00 41.79 1.40
2896 8725 3.753842 CACGGCGCAACTGTAATTTATT 58.246 40.909 10.83 0.00 35.54 1.40
2897 8726 3.541916 CACGGCGCAACTGTAATTTATTG 59.458 43.478 10.83 0.00 35.54 1.90
2898 8727 3.105203 CGGCGCAACTGTAATTTATTGG 58.895 45.455 10.83 0.00 0.00 3.16
2899 8728 3.426963 CGGCGCAACTGTAATTTATTGGT 60.427 43.478 10.83 0.00 0.00 3.67
2900 8729 4.102649 GGCGCAACTGTAATTTATTGGTC 58.897 43.478 10.83 0.00 0.00 4.02
2901 8730 4.102649 GCGCAACTGTAATTTATTGGTCC 58.897 43.478 0.30 0.00 0.00 4.46
2902 8731 4.380023 GCGCAACTGTAATTTATTGGTCCA 60.380 41.667 0.30 0.00 0.00 4.02
2903 8732 5.678616 GCGCAACTGTAATTTATTGGTCCAT 60.679 40.000 0.30 0.00 0.00 3.41
2904 8733 6.459024 GCGCAACTGTAATTTATTGGTCCATA 60.459 38.462 0.30 0.00 0.00 2.74
2905 8734 7.648142 CGCAACTGTAATTTATTGGTCCATAT 58.352 34.615 0.00 0.00 0.00 1.78
2906 8735 8.779303 CGCAACTGTAATTTATTGGTCCATATA 58.221 33.333 0.00 0.00 0.00 0.86
2936 8765 9.563593 AGTAGTAGATATATGTAGGGTCTCTGA 57.436 37.037 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.364889 TTTGATCTCTACATACCGCCG 57.635 47.619 0.00 0.00 0.00 6.46
2 3 3.489785 CGTTTTGATCTCTACATACCGCC 59.510 47.826 0.00 0.00 0.00 6.13
3 4 4.110482 ACGTTTTGATCTCTACATACCGC 58.890 43.478 0.00 0.00 0.00 5.68
4 5 4.436847 CGACGTTTTGATCTCTACATACCG 59.563 45.833 0.00 0.00 0.00 4.02
5 6 4.738740 CCGACGTTTTGATCTCTACATACC 59.261 45.833 0.00 0.00 0.00 2.73
43 44 6.445357 CAGTATGGTTGGGTTTGTTATACC 57.555 41.667 0.00 0.00 34.82 2.73
76 78 3.019003 GCCAGGGCTTCTCGTGCTA 62.019 63.158 2.30 0.00 38.26 3.49
82 84 2.421399 GCCAATGCCAGGGCTTCTC 61.421 63.158 12.19 0.00 46.74 2.87
104 106 6.098982 TGGGAAGTCTTTCTAGATCAAGATCC 59.901 42.308 13.83 13.83 34.75 3.36
117 119 3.428589 GCTGATGCAATGGGAAGTCTTTC 60.429 47.826 0.00 0.00 39.41 2.62
127 129 2.416836 CCTTCACAAGCTGATGCAATGG 60.417 50.000 0.00 0.00 42.74 3.16
139 141 1.888512 CATTCACCACCCCTTCACAAG 59.111 52.381 0.00 0.00 0.00 3.16
142 144 1.202879 TGTCATTCACCACCCCTTCAC 60.203 52.381 0.00 0.00 0.00 3.18
158 160 1.544093 CCAGAGCCTTGCTTTCTGTCA 60.544 52.381 5.10 0.00 39.88 3.58
163 165 0.538287 ACCACCAGAGCCTTGCTTTC 60.538 55.000 0.00 0.00 39.88 2.62
182 184 4.023980 CCCGGATAATAGCTCCATGTCTA 58.976 47.826 0.73 0.00 32.72 2.59
193 195 8.470657 TCTATCAATGATCTCCCGGATAATAG 57.529 38.462 0.73 0.00 34.33 1.73
239 241 9.581099 AAAACTCAACGTTCATGAATAAAACTT 57.419 25.926 12.12 0.00 33.90 2.66
266 268 5.877031 ACGAGATGATGAGCTTCAAAATTG 58.123 37.500 0.00 0.00 0.00 2.32
298 300 4.700700 ACGCCCAATACCTAGATTACAAC 58.299 43.478 0.00 0.00 0.00 3.32
334 336 1.480545 GGTTTTGGTCATGGGGTATGC 59.519 52.381 0.00 0.00 36.70 3.14
335 337 3.100207 AGGTTTTGGTCATGGGGTATG 57.900 47.619 0.00 0.00 38.17 2.39
361 363 9.738832 CACTTTGATATGCAATAATGTTCATCA 57.261 29.630 0.00 0.00 36.15 3.07
378 380 4.081142 TGAGAAATCTCGCCCACTTTGATA 60.081 41.667 5.99 0.00 45.72 2.15
410 412 1.069823 CCTATGCGCTCCATGTCTCTT 59.930 52.381 9.73 0.00 35.34 2.85
412 414 0.948141 GCCTATGCGCTCCATGTCTC 60.948 60.000 9.73 0.00 35.34 3.36
449 451 2.124570 CCATGCGACCCCTCCAAG 60.125 66.667 0.00 0.00 0.00 3.61
450 452 3.727258 CCCATGCGACCCCTCCAA 61.727 66.667 0.00 0.00 0.00 3.53
473 475 2.895404 AGCTAACGGGTGTCAAGTAGAA 59.105 45.455 0.00 0.00 0.00 2.10
474 476 2.522185 AGCTAACGGGTGTCAAGTAGA 58.478 47.619 0.00 0.00 0.00 2.59
485 487 7.590279 TCAATTTTTCTTCTTAAGCTAACGGG 58.410 34.615 0.00 0.00 0.00 5.28
492 494 7.018235 CGGAGACTCAATTTTTCTTCTTAAGC 58.982 38.462 4.53 0.00 0.00 3.09
493 495 7.018235 GCGGAGACTCAATTTTTCTTCTTAAG 58.982 38.462 4.53 0.00 0.00 1.85
496 498 5.066593 AGCGGAGACTCAATTTTTCTTCTT 58.933 37.500 4.53 0.00 0.00 2.52
497 499 4.646572 AGCGGAGACTCAATTTTTCTTCT 58.353 39.130 4.53 0.00 0.00 2.85
498 500 5.363979 AAGCGGAGACTCAATTTTTCTTC 57.636 39.130 4.53 0.00 0.00 2.87
501 503 5.607119 TGTAAGCGGAGACTCAATTTTTC 57.393 39.130 4.53 0.00 0.00 2.29
519 521 0.178987 TTTTTCTGCGGGGGCTGTAA 60.179 50.000 0.00 0.00 0.00 2.41
535 537 3.341857 TTTGCGTCGCTGTATGTTTTT 57.658 38.095 19.50 0.00 0.00 1.94
541 558 0.732571 CCCATTTTGCGTCGCTGTAT 59.267 50.000 19.50 5.79 0.00 2.29
555 572 1.685355 GCTAATTTGGCCGGCCCATT 61.685 55.000 41.75 35.98 44.89 3.16
562 579 3.648339 ATGCTAATGCTAATTTGGCCG 57.352 42.857 0.00 0.00 40.48 6.13
563 580 5.358922 TCAAATGCTAATGCTAATTTGGCC 58.641 37.500 0.00 0.00 40.23 5.36
564 581 6.073440 CCATCAAATGCTAATGCTAATTTGGC 60.073 38.462 11.27 0.00 40.23 4.52
565 582 6.425721 CCCATCAAATGCTAATGCTAATTTGG 59.574 38.462 11.27 0.00 40.23 3.28
566 583 6.073440 GCCCATCAAATGCTAATGCTAATTTG 60.073 38.462 0.00 0.00 40.71 2.32
567 584 5.993441 GCCCATCAAATGCTAATGCTAATTT 59.007 36.000 0.00 0.00 40.48 1.82
568 585 5.511888 GGCCCATCAAATGCTAATGCTAATT 60.512 40.000 0.00 0.00 40.48 1.40
569 586 4.020839 GGCCCATCAAATGCTAATGCTAAT 60.021 41.667 0.00 0.00 40.48 1.73
570 587 3.321682 GGCCCATCAAATGCTAATGCTAA 59.678 43.478 0.00 0.00 40.48 3.09
571 588 2.892852 GGCCCATCAAATGCTAATGCTA 59.107 45.455 0.00 0.00 40.48 3.49
572 589 1.690352 GGCCCATCAAATGCTAATGCT 59.310 47.619 0.00 0.00 40.48 3.79
573 590 1.603678 CGGCCCATCAAATGCTAATGC 60.604 52.381 0.00 0.00 40.20 3.56
581 598 1.197430 TTTTGGCCGGCCCATCAAAT 61.197 50.000 41.75 0.00 44.89 2.32
607 624 0.460635 TCCCATGTACGTTTAGGCGC 60.461 55.000 0.00 0.00 34.88 6.53
664 681 7.885922 GTCTCCAGAGTCCTGATGATAACTATA 59.114 40.741 0.00 0.00 43.02 1.31
665 682 6.719370 GTCTCCAGAGTCCTGATGATAACTAT 59.281 42.308 0.00 0.00 43.02 2.12
666 683 6.065374 GTCTCCAGAGTCCTGATGATAACTA 58.935 44.000 0.00 0.00 43.02 2.24
667 684 4.892934 GTCTCCAGAGTCCTGATGATAACT 59.107 45.833 0.00 0.00 43.02 2.24
668 685 4.038642 GGTCTCCAGAGTCCTGATGATAAC 59.961 50.000 3.98 0.00 43.02 1.89
669 686 4.219115 GGTCTCCAGAGTCCTGATGATAA 58.781 47.826 3.98 0.00 43.02 1.75
714 731 0.248289 TGGCTAGGGTTTCGTGCTAC 59.752 55.000 0.00 0.00 0.00 3.58
715 732 0.248289 GTGGCTAGGGTTTCGTGCTA 59.752 55.000 0.00 0.00 0.00 3.49
717 734 2.038837 GGTGGCTAGGGTTTCGTGC 61.039 63.158 0.00 0.00 0.00 5.34
758 775 3.195698 GTTGGGTCGCCTGATCGC 61.196 66.667 0.00 0.00 0.00 4.58
762 779 3.164977 TGGTGTTGGGTCGCCTGA 61.165 61.111 0.00 0.00 38.63 3.86
812 850 2.016393 GCGATCGGTGGTGAGGATGA 62.016 60.000 18.30 0.00 0.00 2.92
813 851 1.592669 GCGATCGGTGGTGAGGATG 60.593 63.158 18.30 0.00 0.00 3.51
815 853 3.458163 GGCGATCGGTGGTGAGGA 61.458 66.667 18.30 0.00 0.00 3.71
869 919 4.377431 CGAAAGATCCAAAGAAACGTGAGG 60.377 45.833 0.00 0.00 0.00 3.86
897 971 7.230913 AGCAACAGTTAAGTAGACTAGTTCTCA 59.769 37.037 5.82 0.00 35.55 3.27
935 1011 2.613977 CCTCCCTTGCTCACTGTAGTTG 60.614 54.545 0.00 0.00 0.00 3.16
987 1066 0.100682 AATCCATCGGAGTCGTCGTG 59.899 55.000 0.00 0.00 34.05 4.35
1011 1090 0.818296 CTACCCTGAACTGGAGGACG 59.182 60.000 0.00 0.00 31.48 4.79
1157 1251 6.164176 AGGTACAGAGAAACGTAATTTCCAG 58.836 40.000 0.00 0.00 46.94 3.86
1227 1321 2.157085 GTCGTTTCCGTCCATCAAGAAC 59.843 50.000 0.00 0.00 35.01 3.01
1254 1348 3.422546 CAGTCGTCTTTCGTTCTTCTGAC 59.577 47.826 0.00 0.00 40.80 3.51
1262 1356 2.100252 TGAAGTCCAGTCGTCTTTCGTT 59.900 45.455 0.00 0.00 40.80 3.85
1316 1410 2.493675 CGATGATATCCCCAGTCGTCAT 59.506 50.000 0.00 0.00 0.00 3.06
1686 1817 2.035576 GGGGTTATCCTGCGTACTAGTG 59.964 54.545 5.39 0.00 35.33 2.74
1691 1822 0.391966 GGAGGGGTTATCCTGCGTAC 59.608 60.000 0.00 0.00 37.25 3.67
1770 1913 6.208599 CCCATAACTTTTGGACACACATAAGT 59.791 38.462 0.05 0.00 42.01 2.24
1831 6701 4.665212 CAATTGTACATCTCAGCGCAAAT 58.335 39.130 11.47 0.00 0.00 2.32
1832 6702 3.670359 GCAATTGTACATCTCAGCGCAAA 60.670 43.478 11.47 0.00 0.00 3.68
1857 6727 2.708216 TGCACTTGTCCTTCAACTCA 57.292 45.000 0.00 0.00 32.18 3.41
1889 6790 7.595819 TGCTTCTTGGATCCTTTCTTTTTAA 57.404 32.000 14.23 0.00 0.00 1.52
1934 6835 2.903784 TGAAGTTTGTGCCCTAGCTAGA 59.096 45.455 22.70 0.00 40.80 2.43
1973 6878 5.275974 GCGCTCTCTTTAATGTCTAAACTCG 60.276 44.000 0.00 0.00 0.00 4.18
1984 6889 3.334583 TGTTCCAGCGCTCTCTTTAAT 57.665 42.857 7.13 0.00 0.00 1.40
1988 6893 3.550437 ATTATGTTCCAGCGCTCTCTT 57.450 42.857 7.13 0.00 0.00 2.85
1995 6900 5.784177 ACTCCAGTATATTATGTTCCAGCG 58.216 41.667 0.00 0.00 0.00 5.18
2029 6935 4.574828 ACAAATAGTGAATATGCACCGACC 59.425 41.667 10.44 0.00 39.59 4.79
2030 6936 5.734855 ACAAATAGTGAATATGCACCGAC 57.265 39.130 10.44 0.00 39.59 4.79
2123 7038 7.013846 CCCAGTTGATACACCTTTTGTAAGAAA 59.986 37.037 0.00 0.00 44.11 2.52
2130 7045 5.982890 AATCCCAGTTGATACACCTTTTG 57.017 39.130 0.00 0.00 0.00 2.44
2146 7061 5.923733 ACAACAAAACACAGTAAATCCCA 57.076 34.783 0.00 0.00 0.00 4.37
2179 7094 9.959721 ACAAACTTGAAACCATATCTAGTACAT 57.040 29.630 0.00 0.00 32.88 2.29
2280 8063 2.227194 ACGTGCCCCTTCAGTTTAAAG 58.773 47.619 0.00 0.00 0.00 1.85
2282 8065 2.351706 AACGTGCCCCTTCAGTTTAA 57.648 45.000 0.00 0.00 0.00 1.52
2288 8071 4.163458 AGAGATAATAAACGTGCCCCTTCA 59.837 41.667 0.00 0.00 0.00 3.02
2707 8535 9.027202 TGTGAATGTATTATACCGCCTCTTATA 57.973 33.333 0.00 0.00 0.00 0.98
2708 8536 7.903145 TGTGAATGTATTATACCGCCTCTTAT 58.097 34.615 0.00 0.00 0.00 1.73
2783 8612 1.748879 GCCCTGTGTGTGTGTGTGT 60.749 57.895 0.00 0.00 0.00 3.72
2784 8613 2.480610 GGCCCTGTGTGTGTGTGTG 61.481 63.158 0.00 0.00 0.00 3.82
2785 8614 2.124320 GGCCCTGTGTGTGTGTGT 60.124 61.111 0.00 0.00 0.00 3.72
2801 8630 4.112634 CGTGAGTGACATAATAGTGGTGG 58.887 47.826 0.00 0.00 0.00 4.61
2910 8739 9.563593 TCAGAGACCCTACATATATCTACTACT 57.436 37.037 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.