Multiple sequence alignment - TraesCS4B01G376000

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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 TraesCS4B01G376000 chr4B 100.000 3632 0 0 428 4059 659667450 659663819 0.000000e+00 6708.0
1 TraesCS4B01G376000 chr4B 91.914 3203 179 32 899 4059 656814995 656818159 0.000000e+00 4407.0
2 TraesCS4B01G376000 chr4B 95.461 1322 44 3 467 1773 656811540 656812860 0.000000e+00 2095.0
3 TraesCS4B01G376000 chr4B 92.143 140 11 0 3920 4059 656804798 656804937 8.900000e-47 198.0
4 TraesCS4B01G376000 chr4B 85.714 189 17 6 626 812 661671025 661671205 1.490000e-44 191.0
5 TraesCS4B01G376000 chr4B 100.000 85 0 0 1 85 659667877 659667793 1.510000e-34 158.0
6 TraesCS4B01G376000 chr4B 98.333 60 1 0 1117 1176 659596342 659596283 5.550000e-19 106.0
7 TraesCS4B01G376000 chr4B 95.349 43 2 0 2774 2816 605953457 605953499 7.280000e-08 69.4
8 TraesCS4B01G376000 chr4B 95.349 43 2 0 2774 2816 612210216 612210258 7.280000e-08 69.4
9 TraesCS4B01G376000 chr4D 91.893 3244 200 37 843 4059 507965439 507968646 0.000000e+00 4475.0
10 TraesCS4B01G376000 chr7D 86.010 193 21 2 626 818 243807390 243807204 6.880000e-48 202.0
11 TraesCS4B01G376000 chr5B 83.957 187 19 7 630 813 508063799 508063621 6.980000e-38 169.0
12 TraesCS4B01G376000 chr5A 81.538 195 28 7 2110 2303 674572865 674573052 1.950000e-33 154.0
13 TraesCS4B01G376000 chr3B 81.967 183 27 2 628 810 739510745 739510569 2.530000e-32 150.0
14 TraesCS4B01G376000 chr3B 95.349 43 2 0 2774 2816 592527803 592527845 7.280000e-08 69.4
15 TraesCS4B01G376000 chr7B 81.218 197 26 4 628 814 44327407 44327212 9.090000e-32 148.0
16 TraesCS4B01G376000 chr2D 80.000 200 32 6 2107 2304 75397917 75397724 1.520000e-29 141.0
17 TraesCS4B01G376000 chr6A 79.512 205 32 9 2107 2308 606719822 606719625 1.970000e-28 137.0
18 TraesCS4B01G376000 chr3D 79.310 203 36 4 2107 2308 148250997 148251194 1.970000e-28 137.0
19 TraesCS4B01G376000 chr3D 78.818 203 37 4 2107 2308 481916221 481916418 9.150000e-27 132.0
20 TraesCS4B01G376000 chr4A 79.310 203 35 5 2107 2308 737235921 737236117 7.080000e-28 135.0
21 TraesCS4B01G376000 chr1A 78.922 204 35 7 2107 2308 91044847 91044650 9.150000e-27 132.0
22 TraesCS4B01G376000 chr6B 97.727 44 1 0 2773 2816 192931471 192931428 4.350000e-10 76.8
23 TraesCS4B01G376000 chr6B 95.349 43 2 0 2774 2816 212971205 212971163 7.280000e-08 69.4
24 TraesCS4B01G376000 chr3A 97.674 43 1 0 2774 2816 111563312 111563354 1.560000e-09 75.0
25 TraesCS4B01G376000 chr3A 95.238 42 1 1 3303 3344 1506374 1506414 9.420000e-07 65.8
26 TraesCS4B01G376000 chrUn 97.619 42 1 0 2774 2815 351401975 351402016 5.630000e-09 73.1
27 TraesCS4B01G376000 chr7A 93.182 44 2 1 3303 3345 90686003 90685960 3.390000e-06 63.9


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 TraesCS4B01G376000 chr4B 659663819 659667877 4058 True 3433 6708 100.0000 1 4059 2 chr4B.!!$R2 4058
1 TraesCS4B01G376000 chr4B 656811540 656818159 6619 False 3251 4407 93.6875 467 4059 2 chr4B.!!$F5 3592
2 TraesCS4B01G376000 chr4D 507965439 507968646 3207 False 4475 4475 91.8930 843 4059 1 chr4D.!!$F1 3216

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
448 449 0.175760 GATAAGCTGACGTGGGCAGA 59.824 55.0 1.91 0.0 35.39 4.26 F
449 450 0.176680 ATAAGCTGACGTGGGCAGAG 59.823 55.0 1.91 0.0 35.39 3.35 F
1623 1654 0.253044 GGATCAGCCTGCACACCTTA 59.747 55.0 0.00 0.0 0.00 2.69 F
2497 5564 0.601558 TACCAGTGGAAGACGACAGC 59.398 55.0 18.40 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 1697 0.039618 ATCCCTTCGTTGTTGGGCAT 59.960 50.000 0.0 0.0 40.69 4.40 R
1671 1702 0.796312 CGACCATCCCTTCGTTGTTG 59.204 55.000 0.0 0.0 0.00 3.33 R
2654 5721 1.135139 CTCGACGGTGATGTTGAGGAT 59.865 52.381 0.0 0.0 43.70 3.24 R
3792 6862 0.316204 GCAACAACAATCTGCCAGCT 59.684 50.000 0.0 0.0 0.00 4.24 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
24 25 5.211266 TGCTACATCCACGAAAATAAACG 57.789 39.130 0.00 0.00 0.00 3.60
25 26 4.691685 TGCTACATCCACGAAAATAAACGT 59.308 37.500 0.00 0.00 43.50 3.99
26 27 5.868258 TGCTACATCCACGAAAATAAACGTA 59.132 36.000 0.00 0.00 40.76 3.57
27 28 6.368243 TGCTACATCCACGAAAATAAACGTAA 59.632 34.615 0.00 0.00 40.76 3.18
28 29 7.095313 TGCTACATCCACGAAAATAAACGTAAA 60.095 33.333 0.00 0.00 40.76 2.01
29 30 7.906527 GCTACATCCACGAAAATAAACGTAAAT 59.093 33.333 0.00 0.00 40.76 1.40
30 31 9.417284 CTACATCCACGAAAATAAACGTAAATC 57.583 33.333 0.00 0.00 40.76 2.17
31 32 8.036273 ACATCCACGAAAATAAACGTAAATCT 57.964 30.769 0.00 0.00 40.76 2.40
32 33 8.508875 ACATCCACGAAAATAAACGTAAATCTT 58.491 29.630 0.00 0.00 40.76 2.40
33 34 9.337091 CATCCACGAAAATAAACGTAAATCTTT 57.663 29.630 0.00 0.00 40.76 2.52
61 62 9.990360 TGTAATTAGTCACTTGTGAAGTTATGA 57.010 29.630 4.93 0.00 40.46 2.15
65 66 6.808008 AGTCACTTGTGAAGTTATGATTGG 57.192 37.500 4.93 0.00 40.46 3.16
66 67 6.533730 AGTCACTTGTGAAGTTATGATTGGA 58.466 36.000 4.93 0.00 40.46 3.53
67 68 6.998074 AGTCACTTGTGAAGTTATGATTGGAA 59.002 34.615 4.93 0.00 40.46 3.53
68 69 7.502226 AGTCACTTGTGAAGTTATGATTGGAAA 59.498 33.333 4.93 0.00 40.46 3.13
69 70 8.299570 GTCACTTGTGAAGTTATGATTGGAAAT 58.700 33.333 4.93 0.00 40.46 2.17
70 71 9.513906 TCACTTGTGAAGTTATGATTGGAAATA 57.486 29.630 0.44 0.00 40.46 1.40
71 72 9.778993 CACTTGTGAAGTTATGATTGGAAATAG 57.221 33.333 0.00 0.00 40.46 1.73
72 73 9.739276 ACTTGTGAAGTTATGATTGGAAATAGA 57.261 29.630 0.00 0.00 39.04 1.98
74 75 8.737168 TGTGAAGTTATGATTGGAAATAGAGG 57.263 34.615 0.00 0.00 0.00 3.69
75 76 7.775093 TGTGAAGTTATGATTGGAAATAGAGGG 59.225 37.037 0.00 0.00 0.00 4.30
76 77 7.993183 GTGAAGTTATGATTGGAAATAGAGGGA 59.007 37.037 0.00 0.00 0.00 4.20
77 78 8.556589 TGAAGTTATGATTGGAAATAGAGGGAA 58.443 33.333 0.00 0.00 0.00 3.97
78 79 8.986929 AAGTTATGATTGGAAATAGAGGGAAG 57.013 34.615 0.00 0.00 0.00 3.46
79 80 7.521669 AGTTATGATTGGAAATAGAGGGAAGG 58.478 38.462 0.00 0.00 0.00 3.46
80 81 4.796110 TGATTGGAAATAGAGGGAAGGG 57.204 45.455 0.00 0.00 0.00 3.95
81 82 3.463329 TGATTGGAAATAGAGGGAAGGGG 59.537 47.826 0.00 0.00 0.00 4.79
82 83 1.907240 TGGAAATAGAGGGAAGGGGG 58.093 55.000 0.00 0.00 0.00 5.40
444 445 4.857251 GGGATAAGCTGACGTGGG 57.143 61.111 0.00 0.00 0.00 4.61
445 446 1.523938 GGGATAAGCTGACGTGGGC 60.524 63.158 0.00 0.00 0.00 5.36
446 447 1.220749 GGATAAGCTGACGTGGGCA 59.779 57.895 11.15 0.00 0.00 5.36
447 448 0.811616 GGATAAGCTGACGTGGGCAG 60.812 60.000 11.15 5.39 36.47 4.85
448 449 0.175760 GATAAGCTGACGTGGGCAGA 59.824 55.000 1.91 0.00 35.39 4.26
449 450 0.176680 ATAAGCTGACGTGGGCAGAG 59.823 55.000 1.91 0.00 35.39 3.35
450 451 0.898326 TAAGCTGACGTGGGCAGAGA 60.898 55.000 1.91 0.00 35.39 3.10
451 452 1.758440 AAGCTGACGTGGGCAGAGAA 61.758 55.000 1.91 0.00 35.39 2.87
452 453 1.078848 GCTGACGTGGGCAGAGAAT 60.079 57.895 1.91 0.00 35.39 2.40
453 454 0.674895 GCTGACGTGGGCAGAGAATT 60.675 55.000 1.91 0.00 35.39 2.17
454 455 1.405526 GCTGACGTGGGCAGAGAATTA 60.406 52.381 1.91 0.00 35.39 1.40
455 456 2.935238 GCTGACGTGGGCAGAGAATTAA 60.935 50.000 1.91 0.00 35.39 1.40
456 457 2.932614 CTGACGTGGGCAGAGAATTAAG 59.067 50.000 0.00 0.00 35.39 1.85
457 458 2.280628 GACGTGGGCAGAGAATTAAGG 58.719 52.381 0.00 0.00 0.00 2.69
458 459 1.065418 ACGTGGGCAGAGAATTAAGGG 60.065 52.381 0.00 0.00 0.00 3.95
459 460 1.209504 CGTGGGCAGAGAATTAAGGGA 59.790 52.381 0.00 0.00 0.00 4.20
460 461 2.355716 CGTGGGCAGAGAATTAAGGGAA 60.356 50.000 0.00 0.00 0.00 3.97
461 462 3.697166 GTGGGCAGAGAATTAAGGGAAA 58.303 45.455 0.00 0.00 0.00 3.13
462 463 4.281657 GTGGGCAGAGAATTAAGGGAAAT 58.718 43.478 0.00 0.00 0.00 2.17
463 464 4.711846 GTGGGCAGAGAATTAAGGGAAATT 59.288 41.667 0.00 0.00 0.00 1.82
464 465 5.187772 GTGGGCAGAGAATTAAGGGAAATTT 59.812 40.000 0.00 0.00 0.00 1.82
465 466 6.379988 GTGGGCAGAGAATTAAGGGAAATTTA 59.620 38.462 0.00 0.00 0.00 1.40
535 536 5.168569 CAGAGTAAAGCTACATCAACGGAA 58.831 41.667 0.00 0.00 0.00 4.30
537 538 6.313905 CAGAGTAAAGCTACATCAACGGAAAT 59.686 38.462 0.00 0.00 0.00 2.17
538 539 6.879458 AGAGTAAAGCTACATCAACGGAAATT 59.121 34.615 0.00 0.00 0.00 1.82
567 568 2.024369 AGACCTCCCCCGCAAAAATATT 60.024 45.455 0.00 0.00 0.00 1.28
625 626 9.521503 GGCAGATCTAATAATTGGAAAAAGAAC 57.478 33.333 0.00 0.00 0.00 3.01
660 661 2.490903 TCACGGACTCTTACAGGCTAAC 59.509 50.000 0.00 0.00 0.00 2.34
778 779 2.266055 CAGCCTCTCCGTGAACCC 59.734 66.667 0.00 0.00 0.00 4.11
793 794 3.192633 GTGAACCCCGTAAAATTGATGCT 59.807 43.478 0.00 0.00 0.00 3.79
823 824 3.467374 AGCATTGCCCGAAAAAGAAAA 57.533 38.095 4.70 0.00 0.00 2.29
828 829 1.684450 TGCCCGAAAAAGAAAAGGGAC 59.316 47.619 2.59 0.00 44.70 4.46
855 856 4.338879 CCACCCAGTGAAATTCAGAGATT 58.661 43.478 0.00 0.00 35.23 2.40
890 891 2.263077 GTCCGTCTGTCTAGCATGTTG 58.737 52.381 0.00 0.00 0.00 3.33
891 892 1.002366 CCGTCTGTCTAGCATGTTGC 58.998 55.000 0.00 0.00 45.46 4.17
1104 1126 2.365617 TGTATCCATCTCCTTCTTCGGC 59.634 50.000 0.00 0.00 0.00 5.54
1173 1204 1.546029 CTGGACCTGATCTTCACGTCA 59.454 52.381 8.28 0.00 35.19 4.35
1325 1356 2.897969 TCACCTACCTCAAGTCCAAGAC 59.102 50.000 0.00 0.00 0.00 3.01
1495 1526 0.689623 CTTCCTCACCAGGTTGCTCT 59.310 55.000 0.00 0.00 41.28 4.09
1623 1654 0.253044 GGATCAGCCTGCACACCTTA 59.747 55.000 0.00 0.00 0.00 2.69
1695 4758 1.078426 CGAAGGGATGGTCGCCTTT 60.078 57.895 0.00 0.00 30.59 3.11
1737 4800 2.202557 CTCGTCATGCCGCACGTA 60.203 61.111 0.00 0.00 37.30 3.57
1887 4950 1.133668 ACCTGCTTCTTGGCTTTCACT 60.134 47.619 0.00 0.00 0.00 3.41
1895 4958 4.102113 GGCTTTCACTGTGGCCAT 57.898 55.556 9.72 0.00 43.59 4.40
2096 5159 4.098044 CGTGGTCATGATGTAAGTAGTCCT 59.902 45.833 0.00 0.00 0.00 3.85
2138 5201 7.047891 TCCGCATATAAGATTTGTCTGAAGTT 58.952 34.615 0.00 0.00 0.00 2.66
2217 5280 5.538118 ACGAAATCATACCATTAGATGCGA 58.462 37.500 0.00 0.00 0.00 5.10
2230 5293 7.439955 ACCATTAGATGCGACGTGAATTAAATA 59.560 33.333 0.00 0.00 0.00 1.40
2388 5455 6.045072 ACGTTAAATACCTTCACTCCATCA 57.955 37.500 0.00 0.00 0.00 3.07
2497 5564 0.601558 TACCAGTGGAAGACGACAGC 59.398 55.000 18.40 0.00 0.00 4.40
2569 5636 4.604114 CGGAAGCTGCTCATGTCA 57.396 55.556 1.00 0.00 0.00 3.58
2599 5666 1.099879 GCTTGGCCATCTTCATCGCT 61.100 55.000 6.09 0.00 0.00 4.93
2654 5721 1.217916 TGACCCCCTCAACTTCAACA 58.782 50.000 0.00 0.00 0.00 3.33
2770 5838 9.599866 TGATCGATACCATTATACATGAAATCC 57.400 33.333 0.00 0.00 0.00 3.01
2833 5901 3.058016 GCTATCGCCACCACTATAACGTA 60.058 47.826 0.00 0.00 0.00 3.57
3048 6116 0.477204 CATGGTGGAGAGGCATGGAT 59.523 55.000 0.00 0.00 0.00 3.41
3053 6121 2.373169 GGTGGAGAGGCATGGATGATAA 59.627 50.000 0.00 0.00 0.00 1.75
3129 6197 3.201353 AGCTACATCTCGCTCTAGTCA 57.799 47.619 0.00 0.00 0.00 3.41
3202 6271 4.790878 CATATCGATGGCCTGAACAATTG 58.209 43.478 8.54 3.24 0.00 2.32
3203 6272 1.462616 TCGATGGCCTGAACAATTGG 58.537 50.000 10.83 0.00 0.00 3.16
3206 6275 2.752354 CGATGGCCTGAACAATTGGTTA 59.248 45.455 10.83 0.00 40.63 2.85
3208 6277 4.578516 CGATGGCCTGAACAATTGGTTATA 59.421 41.667 10.83 0.00 40.63 0.98
3354 6424 6.855914 GCGCTTTATCGAAAAATAATCCATCA 59.144 34.615 0.00 0.00 0.00 3.07
3447 6517 9.093458 ACAGAGGAATTAATTTGGTTTCTCAAT 57.907 29.630 1.43 0.00 0.00 2.57
3573 6643 3.686241 CGTCAAAGCCAATGAGATTCTCA 59.314 43.478 18.29 18.29 44.99 3.27
3671 6741 1.620819 ACCTTGTGGTCTGCTGTAGAG 59.379 52.381 0.00 0.00 44.78 2.43
3672 6742 1.620819 CCTTGTGGTCTGCTGTAGAGT 59.379 52.381 0.00 0.00 35.70 3.24
3731 6801 2.951457 TCGAATATGCCAACGAGACA 57.049 45.000 0.00 0.00 0.00 3.41
3739 6809 1.412710 TGCCAACGAGACAAAGAGACT 59.587 47.619 0.00 0.00 0.00 3.24
3749 6819 3.388024 AGACAAAGAGACTGGTAAGTGCA 59.612 43.478 0.00 0.00 36.52 4.57
3792 6862 1.078988 GTAACGCCGGTCCCATTGA 60.079 57.895 1.90 0.00 0.00 2.57
3875 6945 3.932580 CTAGCCGAGGCACGCACAA 62.933 63.158 17.18 0.00 44.88 3.33
3882 6954 2.353839 GGCACGCACAAGCACAAG 60.354 61.111 0.00 0.00 42.27 3.16
3951 7023 2.113139 CAACAAGGAGGTGGCGGT 59.887 61.111 0.00 0.00 0.00 5.68
3966 7038 3.684788 GTGGCGGTATAATGCTGGATAAG 59.315 47.826 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.128117 ACGTTTATTTTCGTGGATGTAGCATT 60.128 34.615 0.00 0.00 38.85 3.56
1 2 5.353123 ACGTTTATTTTCGTGGATGTAGCAT 59.647 36.000 0.00 0.00 38.85 3.79
2 3 4.691685 ACGTTTATTTTCGTGGATGTAGCA 59.308 37.500 0.00 0.00 38.85 3.49
3 4 5.212589 ACGTTTATTTTCGTGGATGTAGC 57.787 39.130 0.00 0.00 38.85 3.58
4 5 9.417284 GATTTACGTTTATTTTCGTGGATGTAG 57.583 33.333 0.00 0.00 40.50 2.74
5 6 9.153721 AGATTTACGTTTATTTTCGTGGATGTA 57.846 29.630 0.00 0.00 40.50 2.29
6 7 8.036273 AGATTTACGTTTATTTTCGTGGATGT 57.964 30.769 0.00 0.00 40.50 3.06
7 8 8.889849 AAGATTTACGTTTATTTTCGTGGATG 57.110 30.769 0.00 0.00 40.50 3.51
35 36 9.990360 TCATAACTTCACAAGTGACTAATTACA 57.010 29.630 1.73 0.00 41.91 2.41
39 40 8.950210 CCAATCATAACTTCACAAGTGACTAAT 58.050 33.333 1.73 0.00 41.91 1.73
40 41 8.154203 TCCAATCATAACTTCACAAGTGACTAA 58.846 33.333 1.73 0.00 41.91 2.24
41 42 7.676004 TCCAATCATAACTTCACAAGTGACTA 58.324 34.615 1.73 0.00 41.91 2.59
42 43 6.533730 TCCAATCATAACTTCACAAGTGACT 58.466 36.000 1.73 0.00 41.91 3.41
43 44 6.801539 TCCAATCATAACTTCACAAGTGAC 57.198 37.500 1.73 0.00 41.91 3.67
44 45 7.815840 TTTCCAATCATAACTTCACAAGTGA 57.184 32.000 0.00 0.00 41.91 3.41
45 46 9.778993 CTATTTCCAATCATAACTTCACAAGTG 57.221 33.333 0.00 0.00 41.91 3.16
46 47 9.739276 TCTATTTCCAATCATAACTTCACAAGT 57.261 29.630 0.00 0.00 45.46 3.16
48 49 9.177608 CCTCTATTTCCAATCATAACTTCACAA 57.822 33.333 0.00 0.00 0.00 3.33
49 50 7.775093 CCCTCTATTTCCAATCATAACTTCACA 59.225 37.037 0.00 0.00 0.00 3.58
50 51 7.993183 TCCCTCTATTTCCAATCATAACTTCAC 59.007 37.037 0.00 0.00 0.00 3.18
51 52 8.101309 TCCCTCTATTTCCAATCATAACTTCA 57.899 34.615 0.00 0.00 0.00 3.02
52 53 8.980481 TTCCCTCTATTTCCAATCATAACTTC 57.020 34.615 0.00 0.00 0.00 3.01
53 54 8.001292 CCTTCCCTCTATTTCCAATCATAACTT 58.999 37.037 0.00 0.00 0.00 2.66
54 55 7.421853 CCCTTCCCTCTATTTCCAATCATAACT 60.422 40.741 0.00 0.00 0.00 2.24
55 56 6.717084 CCCTTCCCTCTATTTCCAATCATAAC 59.283 42.308 0.00 0.00 0.00 1.89
56 57 6.183361 CCCCTTCCCTCTATTTCCAATCATAA 60.183 42.308 0.00 0.00 0.00 1.90
57 58 5.313240 CCCCTTCCCTCTATTTCCAATCATA 59.687 44.000 0.00 0.00 0.00 2.15
58 59 4.106987 CCCCTTCCCTCTATTTCCAATCAT 59.893 45.833 0.00 0.00 0.00 2.45
59 60 3.463329 CCCCTTCCCTCTATTTCCAATCA 59.537 47.826 0.00 0.00 0.00 2.57
60 61 3.181428 CCCCCTTCCCTCTATTTCCAATC 60.181 52.174 0.00 0.00 0.00 2.67
61 62 2.791774 CCCCCTTCCCTCTATTTCCAAT 59.208 50.000 0.00 0.00 0.00 3.16
62 63 2.214201 CCCCCTTCCCTCTATTTCCAA 58.786 52.381 0.00 0.00 0.00 3.53
63 64 1.907240 CCCCCTTCCCTCTATTTCCA 58.093 55.000 0.00 0.00 0.00 3.53
427 428 1.523938 GCCCACGTCAGCTTATCCC 60.524 63.158 0.00 0.00 0.00 3.85
428 429 0.811616 CTGCCCACGTCAGCTTATCC 60.812 60.000 7.76 0.00 0.00 2.59
429 430 0.175760 TCTGCCCACGTCAGCTTATC 59.824 55.000 7.76 0.00 0.00 1.75
430 431 0.176680 CTCTGCCCACGTCAGCTTAT 59.823 55.000 7.76 0.00 0.00 1.73
431 432 0.898326 TCTCTGCCCACGTCAGCTTA 60.898 55.000 7.76 0.00 0.00 3.09
432 433 1.758440 TTCTCTGCCCACGTCAGCTT 61.758 55.000 7.76 0.00 0.00 3.74
433 434 1.548357 ATTCTCTGCCCACGTCAGCT 61.548 55.000 7.76 0.00 0.00 4.24
434 435 0.674895 AATTCTCTGCCCACGTCAGC 60.675 55.000 0.00 0.00 0.00 4.26
435 436 2.672961 TAATTCTCTGCCCACGTCAG 57.327 50.000 0.00 0.00 0.00 3.51
436 437 2.354704 CCTTAATTCTCTGCCCACGTCA 60.355 50.000 0.00 0.00 0.00 4.35
437 438 2.280628 CCTTAATTCTCTGCCCACGTC 58.719 52.381 0.00 0.00 0.00 4.34
438 439 1.065418 CCCTTAATTCTCTGCCCACGT 60.065 52.381 0.00 0.00 0.00 4.49
439 440 1.209504 TCCCTTAATTCTCTGCCCACG 59.790 52.381 0.00 0.00 0.00 4.94
440 441 3.366052 TTCCCTTAATTCTCTGCCCAC 57.634 47.619 0.00 0.00 0.00 4.61
441 442 4.608170 ATTTCCCTTAATTCTCTGCCCA 57.392 40.909 0.00 0.00 0.00 5.36
442 443 5.939764 AAATTTCCCTTAATTCTCTGCCC 57.060 39.130 0.00 0.00 0.00 5.36
443 444 6.607600 ACCTAAATTTCCCTTAATTCTCTGCC 59.392 38.462 0.00 0.00 0.00 4.85
444 445 7.646548 ACCTAAATTTCCCTTAATTCTCTGC 57.353 36.000 0.00 0.00 0.00 4.26
446 447 9.922477 CCTAACCTAAATTTCCCTTAATTCTCT 57.078 33.333 0.00 0.00 0.00 3.10
447 448 9.696572 ACCTAACCTAAATTTCCCTTAATTCTC 57.303 33.333 0.00 0.00 0.00 2.87
453 454 9.287818 ACATCTACCTAACCTAAATTTCCCTTA 57.712 33.333 0.00 0.00 0.00 2.69
454 455 8.171337 ACATCTACCTAACCTAAATTTCCCTT 57.829 34.615 0.00 0.00 0.00 3.95
455 456 7.766736 ACATCTACCTAACCTAAATTTCCCT 57.233 36.000 0.00 0.00 0.00 4.20
456 457 8.712103 ACTACATCTACCTAACCTAAATTTCCC 58.288 37.037 0.00 0.00 0.00 3.97
464 465 9.705103 ACAACAATACTACATCTACCTAACCTA 57.295 33.333 0.00 0.00 0.00 3.08
465 466 8.605325 ACAACAATACTACATCTACCTAACCT 57.395 34.615 0.00 0.00 0.00 3.50
503 504 5.470368 TGTAGCTTTACTCTGTGTGATGAC 58.530 41.667 0.00 0.00 0.00 3.06
508 509 5.164051 CGTTGATGTAGCTTTACTCTGTGTG 60.164 44.000 0.00 0.00 0.00 3.82
582 583 1.227263 CCCACGTCAGCTTATCCCG 60.227 63.158 0.00 0.00 0.00 5.14
625 626 2.921754 GTCCGTGAGTCTACCATTTTCG 59.078 50.000 0.00 0.00 0.00 3.46
660 661 6.817765 TTAATTAGTTGGAAAGAGCCTGTG 57.182 37.500 0.00 0.00 0.00 3.66
728 729 4.888326 TTTGATTGGGTGAAAATCAGGG 57.112 40.909 0.00 0.00 43.10 4.45
778 779 3.057596 ACACACCAGCATCAATTTTACGG 60.058 43.478 0.00 0.00 0.00 4.02
793 794 0.893270 GGGCAATGCTACACACACCA 60.893 55.000 4.82 0.00 0.00 4.17
828 829 0.609131 AATTTCACTGGGTGGGCTCG 60.609 55.000 0.00 0.00 33.87 5.03
876 877 1.020861 TGGCGCAACATGCTAGACAG 61.021 55.000 10.83 0.00 42.25 3.51
890 891 1.172812 ACCAGAGAAAAAGGTGGCGC 61.173 55.000 0.00 0.00 33.57 6.53
891 892 0.593128 CACCAGAGAAAAAGGTGGCG 59.407 55.000 0.00 0.00 46.98 5.69
1173 1204 2.821366 ACCGTCGTCGCCGATACT 60.821 61.111 0.00 0.00 46.30 2.12
1325 1356 1.581447 GGGGCTTGTGCTTCTTTCG 59.419 57.895 0.00 0.00 39.59 3.46
1357 1388 1.068895 TGGTTTGCCTTTGTCAGCATG 59.931 47.619 0.00 0.00 39.11 4.06
1409 1440 0.391661 GACGTCATCCATGCAGGTGT 60.392 55.000 11.55 0.00 39.02 4.16
1495 1526 3.199727 TGATAGCCCAGCACTATGAACAA 59.800 43.478 0.00 0.00 30.46 2.83
1546 1577 1.202510 GCTCAGGTAGACCAGCATCAG 60.203 57.143 0.66 0.00 35.71 2.90
1623 1654 0.959372 AGACGACGGTGAAGACGGAT 60.959 55.000 0.00 0.00 33.94 4.18
1666 1697 0.039618 ATCCCTTCGTTGTTGGGCAT 59.960 50.000 0.00 0.00 40.69 4.40
1671 1702 0.796312 CGACCATCCCTTCGTTGTTG 59.204 55.000 0.00 0.00 0.00 3.33
1887 4950 2.112928 AGCACGAACATGGCCACA 59.887 55.556 8.16 0.00 0.00 4.17
1916 4979 2.437180 CCATGGCGCAGAAGAGCA 60.437 61.111 10.83 0.00 42.88 4.26
1983 5046 1.492873 CGACATGAACAGTGCCGTG 59.507 57.895 0.00 0.00 0.00 4.94
1984 5047 1.667830 CCGACATGAACAGTGCCGT 60.668 57.895 0.00 0.00 0.00 5.68
2171 5234 7.389330 TCGTACTGTGTGAATGGTGATATTTTT 59.611 33.333 0.00 0.00 0.00 1.94
2175 5238 5.592104 TCGTACTGTGTGAATGGTGATAT 57.408 39.130 0.00 0.00 0.00 1.63
2176 5239 5.394224 TTCGTACTGTGTGAATGGTGATA 57.606 39.130 0.00 0.00 0.00 2.15
2311 5376 4.785173 AATCTATATGGAGTGGAGGGGA 57.215 45.455 0.00 0.00 0.00 4.81
2312 5377 5.850046 AAAATCTATATGGAGTGGAGGGG 57.150 43.478 0.00 0.00 0.00 4.79
2497 5564 1.227823 TGCTCCCACTTGTTGGTCG 60.228 57.895 0.00 0.00 45.25 4.79
2654 5721 1.135139 CTCGACGGTGATGTTGAGGAT 59.865 52.381 0.00 0.00 43.70 3.24
2770 5838 4.497473 TTTGCAATTTGGGTAAGTCTCG 57.503 40.909 0.00 0.00 0.00 4.04
2833 5901 3.216800 AGCACAGTTCACACAATGTCAT 58.783 40.909 0.00 0.00 0.00 3.06
3037 6105 7.761981 AGGTTATATTATCATCCATGCCTCT 57.238 36.000 0.00 0.00 0.00 3.69
3048 6116 8.740906 GCAGTCTGCTACTAGGTTATATTATCA 58.259 37.037 17.89 0.00 40.96 2.15
3053 6121 8.830915 ATATGCAGTCTGCTACTAGGTTATAT 57.169 34.615 24.76 13.01 45.31 0.86
3171 6240 2.349590 GCCATCGATATGCATGCAGTA 58.650 47.619 26.69 17.52 0.00 2.74
3354 6424 5.134202 TGTTGTTCAGTCACATATCGACT 57.866 39.130 0.00 0.00 44.55 4.18
3405 6475 4.225717 TCCTCTGTGTTGATGATGATGGAA 59.774 41.667 0.00 0.00 0.00 3.53
3447 6517 1.408683 GGCAAGATATGACAGGGCACA 60.409 52.381 0.00 0.00 36.87 4.57
3573 6643 3.991773 ACATACTTGTTGAATACACGCGT 59.008 39.130 5.58 5.58 36.21 6.01
3671 6741 1.662629 TCGAATCGTACCGTCTCTCAC 59.337 52.381 1.52 0.00 0.00 3.51
3672 6742 1.662629 GTCGAATCGTACCGTCTCTCA 59.337 52.381 1.52 0.00 0.00 3.27
3708 6778 3.990469 GTCTCGTTGGCATATTCGATGAT 59.010 43.478 0.00 0.00 0.00 2.45
3723 6793 4.341520 ACTTACCAGTCTCTTTGTCTCGTT 59.658 41.667 0.00 0.00 0.00 3.85
3731 6801 5.437060 TCTTTTGCACTTACCAGTCTCTTT 58.563 37.500 0.00 0.00 0.00 2.52
3739 6809 4.707448 TGTTCCTTTCTTTTGCACTTACCA 59.293 37.500 0.00 0.00 0.00 3.25
3749 6819 2.484264 CTCGCCGATGTTCCTTTCTTTT 59.516 45.455 0.00 0.00 0.00 2.27
3792 6862 0.316204 GCAACAACAATCTGCCAGCT 59.684 50.000 0.00 0.00 0.00 4.24
3875 6945 1.227853 GTTCACGGGGACTTGTGCT 60.228 57.895 0.00 0.00 35.36 4.40
3951 7023 6.010850 AGAGGACGACTTATCCAGCATTATA 58.989 40.000 0.00 0.00 38.86 0.98
3966 7038 1.390463 CGCTTTTGCTTAGAGGACGAC 59.610 52.381 0.00 0.00 44.80 4.34
4009 7081 2.722487 CGTCGGGGAGGAGATTCG 59.278 66.667 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.