Multiple sequence alignment - TraesCS2A01G349000

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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 TraesCS2A01G349000 chr2A 100.000 4805 0 0 1 4805 587756175 587751371 0.000000e+00 8874.0
1 TraesCS2A01G349000 chr2A 97.577 2806 54 7 1454 4251 610714594 610711795 0.000000e+00 4793.0
2 TraesCS2A01G349000 chr2A 90.173 1384 109 14 97 1461 610716512 610715137 0.000000e+00 1777.0
3 TraesCS2A01G349000 chr2A 94.896 627 15 5 4190 4803 610711810 610711188 0.000000e+00 965.0
4 TraesCS2A01G349000 chr2A 82.967 182 26 5 1443 1623 70046380 70046557 4.980000e-35 159.0
5 TraesCS2A01G349000 chr2D 96.920 3182 75 8 1637 4803 445400130 445396957 0.000000e+00 5312.0
6 TraesCS2A01G349000 chr2D 91.243 1553 102 18 91 1623 445401651 445400113 0.000000e+00 2084.0
7 TraesCS2A01G349000 chr2D 83.060 183 28 2 1443 1623 588542992 588542811 3.850000e-36 163.0
8 TraesCS2A01G349000 chr2D 92.308 65 5 0 1639 1703 321240569 321240505 5.120000e-15 93.5
9 TraesCS2A01G349000 chr2D 88.571 70 7 1 1639 1708 126952415 126952483 3.080000e-12 84.2
10 TraesCS2A01G349000 chr2D 89.231 65 7 0 1442 1506 169639135 169639071 1.110000e-11 82.4
11 TraesCS2A01G349000 chr2B 93.602 3204 142 25 1637 4803 523764340 523761163 0.000000e+00 4723.0
12 TraesCS2A01G349000 chr2B 89.670 910 54 11 743 1623 523765221 523764323 0.000000e+00 1123.0
13 TraesCS2A01G349000 chr7A 84.153 183 27 1 1443 1623 40999098 40999280 4.940000e-40 176.0
14 TraesCS2A01G349000 chr7A 91.803 61 5 0 1441 1501 566530138 566530078 8.570000e-13 86.1
15 TraesCS2A01G349000 chr3B 87.970 133 16 0 1491 1623 413810065 413810197 1.790000e-34 158.0
16 TraesCS2A01G349000 chr3B 94.915 59 3 0 1645 1703 422155932 422155874 5.120000e-15 93.5
17 TraesCS2A01G349000 chr1D 89.516 124 13 0 1500 1623 182699830 182699707 1.790000e-34 158.0
18 TraesCS2A01G349000 chr5A 89.516 124 11 2 1500 1623 464197385 464197264 6.440000e-34 156.0
19 TraesCS2A01G349000 chr7D 91.304 69 6 0 1637 1705 480002925 480002857 1.420000e-15 95.3
20 TraesCS2A01G349000 chr1B 91.045 67 6 0 1636 1702 5176628 5176694 1.840000e-14 91.6
21 TraesCS2A01G349000 chr6A 93.220 59 4 0 1443 1501 387230616 387230674 2.380000e-13 87.9
22 TraesCS2A01G349000 chr5D 89.706 68 7 0 1639 1706 520641830 520641897 2.380000e-13 87.9


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 TraesCS2A01G349000 chr2A 587751371 587756175 4804 True 8874.000000 8874 100.000000 1 4805 1 chr2A.!!$R1 4804
1 TraesCS2A01G349000 chr2A 610711188 610716512 5324 True 2511.666667 4793 94.215333 97 4803 3 chr2A.!!$R2 4706
2 TraesCS2A01G349000 chr2D 445396957 445401651 4694 True 3698.000000 5312 94.081500 91 4803 2 chr2D.!!$R4 4712
3 TraesCS2A01G349000 chr2B 523761163 523765221 4058 True 2923.000000 4723 91.636000 743 4803 2 chr2B.!!$R1 4060

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
658 680 1.807742 GAGCGAGATATAGTCGGCAGT 59.192 52.381 8.59 0.0 37.91 4.40 F
1451 1517 1.689273 CGCTAGGCAAATACTCCCTCT 59.311 52.381 0.00 0.0 0.00 3.69 F
2178 2798 3.067106 ACTTTCACTTGACGTAGCATGG 58.933 45.455 0.00 0.0 0.00 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2810 2.621338 ACATGACAATACTGACCAGCG 58.379 47.619 0.00 0.0 0.00 5.18 R
3317 3944 0.250513 AAGGCCTCCAGCTAACTTCG 59.749 55.000 5.23 0.0 43.05 3.79 R
4175 4804 0.184451 ACAGCAGCCTGGGATAATGG 59.816 55.000 0.00 0.0 43.53 3.16 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
18 19 3.706055 AGCTCTCTTTTCGGTGCAA 57.294 47.368 0.00 0.00 0.00 4.08
19 20 1.967319 AGCTCTCTTTTCGGTGCAAA 58.033 45.000 0.00 0.00 0.00 3.68
20 21 2.297701 AGCTCTCTTTTCGGTGCAAAA 58.702 42.857 0.00 0.00 0.00 2.44
21 22 2.687935 AGCTCTCTTTTCGGTGCAAAAA 59.312 40.909 0.00 0.00 0.00 1.94
43 44 8.771920 AAAAAGAAAGACCCAAACAAAAGTAG 57.228 30.769 0.00 0.00 0.00 2.57
44 45 6.465439 AAGAAAGACCCAAACAAAAGTAGG 57.535 37.500 0.00 0.00 0.00 3.18
45 46 5.762279 AGAAAGACCCAAACAAAAGTAGGA 58.238 37.500 0.00 0.00 0.00 2.94
46 47 6.192044 AGAAAGACCCAAACAAAAGTAGGAA 58.808 36.000 0.00 0.00 0.00 3.36
47 48 6.321435 AGAAAGACCCAAACAAAAGTAGGAAG 59.679 38.462 0.00 0.00 0.00 3.46
48 49 5.382664 AGACCCAAACAAAAGTAGGAAGA 57.617 39.130 0.00 0.00 0.00 2.87
49 50 5.762279 AGACCCAAACAAAAGTAGGAAGAA 58.238 37.500 0.00 0.00 0.00 2.52
50 51 6.192044 AGACCCAAACAAAAGTAGGAAGAAA 58.808 36.000 0.00 0.00 0.00 2.52
51 52 6.096423 AGACCCAAACAAAAGTAGGAAGAAAC 59.904 38.462 0.00 0.00 0.00 2.78
52 53 5.717654 ACCCAAACAAAAGTAGGAAGAAACA 59.282 36.000 0.00 0.00 0.00 2.83
53 54 6.211785 ACCCAAACAAAAGTAGGAAGAAACAA 59.788 34.615 0.00 0.00 0.00 2.83
54 55 7.100409 CCCAAACAAAAGTAGGAAGAAACAAA 58.900 34.615 0.00 0.00 0.00 2.83
55 56 7.277760 CCCAAACAAAAGTAGGAAGAAACAAAG 59.722 37.037 0.00 0.00 0.00 2.77
56 57 7.277760 CCAAACAAAAGTAGGAAGAAACAAAGG 59.722 37.037 0.00 0.00 0.00 3.11
57 58 7.712204 AACAAAAGTAGGAAGAAACAAAGGA 57.288 32.000 0.00 0.00 0.00 3.36
58 59 7.712204 ACAAAAGTAGGAAGAAACAAAGGAA 57.288 32.000 0.00 0.00 0.00 3.36
59 60 8.129496 ACAAAAGTAGGAAGAAACAAAGGAAA 57.871 30.769 0.00 0.00 0.00 3.13
60 61 8.033038 ACAAAAGTAGGAAGAAACAAAGGAAAC 58.967 33.333 0.00 0.00 0.00 2.78
61 62 6.710597 AAGTAGGAAGAAACAAAGGAAACC 57.289 37.500 0.00 0.00 0.00 3.27
62 63 4.820173 AGTAGGAAGAAACAAAGGAAACCG 59.180 41.667 0.00 0.00 0.00 4.44
63 64 3.893521 AGGAAGAAACAAAGGAAACCGA 58.106 40.909 0.00 0.00 0.00 4.69
64 65 4.470602 AGGAAGAAACAAAGGAAACCGAT 58.529 39.130 0.00 0.00 0.00 4.18
65 66 4.519350 AGGAAGAAACAAAGGAAACCGATC 59.481 41.667 0.00 0.00 0.00 3.69
66 67 4.519350 GGAAGAAACAAAGGAAACCGATCT 59.481 41.667 0.00 0.00 0.00 2.75
67 68 5.704053 GGAAGAAACAAAGGAAACCGATCTA 59.296 40.000 0.00 0.00 0.00 1.98
68 69 6.374613 GGAAGAAACAAAGGAAACCGATCTAT 59.625 38.462 0.00 0.00 0.00 1.98
69 70 6.743575 AGAAACAAAGGAAACCGATCTATG 57.256 37.500 0.00 0.00 0.00 2.23
70 71 6.472887 AGAAACAAAGGAAACCGATCTATGA 58.527 36.000 0.00 0.00 0.00 2.15
71 72 6.940298 AGAAACAAAGGAAACCGATCTATGAA 59.060 34.615 0.00 0.00 0.00 2.57
72 73 7.447238 AGAAACAAAGGAAACCGATCTATGAAA 59.553 33.333 0.00 0.00 0.00 2.69
73 74 7.519032 AACAAAGGAAACCGATCTATGAAAA 57.481 32.000 0.00 0.00 0.00 2.29
74 75 7.145932 ACAAAGGAAACCGATCTATGAAAAG 57.854 36.000 0.00 0.00 0.00 2.27
75 76 6.151144 ACAAAGGAAACCGATCTATGAAAAGG 59.849 38.462 0.00 0.00 0.00 3.11
76 77 5.693769 AGGAAACCGATCTATGAAAAGGA 57.306 39.130 0.00 0.00 0.00 3.36
77 78 6.062258 AGGAAACCGATCTATGAAAAGGAA 57.938 37.500 0.00 0.00 0.00 3.36
78 79 6.481643 AGGAAACCGATCTATGAAAAGGAAA 58.518 36.000 0.00 0.00 0.00 3.13
79 80 6.946009 AGGAAACCGATCTATGAAAAGGAAAA 59.054 34.615 0.00 0.00 0.00 2.29
80 81 7.121315 AGGAAACCGATCTATGAAAAGGAAAAG 59.879 37.037 0.00 0.00 0.00 2.27
81 82 7.094334 GGAAACCGATCTATGAAAAGGAAAAGT 60.094 37.037 0.00 0.00 0.00 2.66
82 83 8.857694 AAACCGATCTATGAAAAGGAAAAGTA 57.142 30.769 0.00 0.00 0.00 2.24
83 84 8.857694 AACCGATCTATGAAAAGGAAAAGTAA 57.142 30.769 0.00 0.00 0.00 2.24
84 85 8.857694 ACCGATCTATGAAAAGGAAAAGTAAA 57.142 30.769 0.00 0.00 0.00 2.01
85 86 9.292195 ACCGATCTATGAAAAGGAAAAGTAAAA 57.708 29.630 0.00 0.00 0.00 1.52
221 222 7.361542 CCCAATGTTTGTGAAGATCTAGAACAG 60.362 40.741 0.00 0.00 0.00 3.16
367 372 6.223138 ACTGTACAATGTGTATGACAAACG 57.777 37.500 0.00 0.00 38.36 3.60
368 373 5.756347 ACTGTACAATGTGTATGACAAACGT 59.244 36.000 0.00 0.00 38.36 3.99
409 414 8.365938 GTTTTGTAAATTCTAATCAAGCGCTTC 58.634 33.333 22.21 4.59 0.00 3.86
422 427 5.531634 TCAAGCGCTTCAAAAATCTGAAAT 58.468 33.333 22.21 0.00 34.96 2.17
427 432 8.792831 AGCGCTTCAAAAATCTGAAATATATG 57.207 30.769 2.64 0.00 34.96 1.78
473 478 8.806634 CAACTCATGAACGAAGAAAAATGAAAA 58.193 29.630 0.00 0.00 0.00 2.29
474 479 8.566008 ACTCATGAACGAAGAAAAATGAAAAG 57.434 30.769 0.00 0.00 0.00 2.27
477 482 5.047188 TGAACGAAGAAAAATGAAAAGCCC 58.953 37.500 0.00 0.00 0.00 5.19
478 483 4.937201 ACGAAGAAAAATGAAAAGCCCT 57.063 36.364 0.00 0.00 0.00 5.19
479 484 4.620982 ACGAAGAAAAATGAAAAGCCCTG 58.379 39.130 0.00 0.00 0.00 4.45
634 656 2.097791 GCGAGACTATCTTTGGACTCGT 59.902 50.000 0.00 0.00 45.45 4.18
658 680 1.807742 GAGCGAGATATAGTCGGCAGT 59.192 52.381 8.59 0.00 37.91 4.40
681 703 3.318017 GCAGTAAGCGTCATATAGGGTG 58.682 50.000 0.00 0.00 0.00 4.61
682 704 3.861131 GCAGTAAGCGTCATATAGGGTGG 60.861 52.174 0.00 0.00 0.00 4.61
718 741 3.259314 TCCAGTGGGCCAGTGCAT 61.259 61.111 31.84 2.60 40.13 3.96
784 807 2.126189 CGTCGTCCCCGTTCTTCC 60.126 66.667 0.00 0.00 35.01 3.46
899 926 3.536917 CCACGCCGGCTCTCCATA 61.537 66.667 26.68 0.00 0.00 2.74
1197 1235 3.945285 TCTTGCCCGTTGATTCTTATTCC 59.055 43.478 0.00 0.00 0.00 3.01
1243 1281 2.095415 CGATTTTCGGGAGGTTTTGGTC 60.095 50.000 0.00 0.00 36.00 4.02
1379 1445 6.237728 GCTTTTGCTTTTGTGGTTTAGTGTAC 60.238 38.462 0.00 0.00 43.35 2.90
1451 1517 1.689273 CGCTAGGCAAATACTCCCTCT 59.311 52.381 0.00 0.00 0.00 3.69
1715 2331 9.772973 AACAGAGAGTGTACAATAATGTAACAA 57.227 29.630 0.00 0.00 43.41 2.83
2178 2798 3.067106 ACTTTCACTTGACGTAGCATGG 58.933 45.455 0.00 0.00 0.00 3.66
2190 2810 5.813672 TGACGTAGCATGGTTTTCTAATACC 59.186 40.000 1.12 0.00 34.93 2.73
2331 2951 8.610248 TGAATCTACGTGTTTCCTTTTTATGA 57.390 30.769 0.00 0.00 0.00 2.15
2908 3528 4.833469 AAAAACACGCACAAAAACTAGC 57.167 36.364 0.00 0.00 0.00 3.42
2971 3591 6.994496 CAGTAAGATCCTCCTGATTTATGCAA 59.006 38.462 0.00 0.00 32.41 4.08
3071 3691 5.853572 ATTTTCAGTTGGTAGGAAGGGTA 57.146 39.130 0.00 0.00 0.00 3.69
3150 3776 7.748677 TGCAGGATGAGAATGAATAAAGGATA 58.251 34.615 0.00 0.00 39.69 2.59
3317 3944 1.221414 GAATATCAGCACGCCCTGAC 58.779 55.000 7.66 0.00 44.00 3.51
3429 4056 8.541133 AAGATTCTTCTAGCTCAGTTTACAAC 57.459 34.615 0.00 0.00 0.00 3.32
3666 4293 8.834465 CCAGAAAAAGTCGATAATGAATCAGAT 58.166 33.333 0.00 0.00 33.87 2.90
3864 4491 5.973899 TCTAGCCAAACATTTATGTGCAA 57.026 34.783 0.00 0.00 41.61 4.08
3868 4495 6.243811 AGCCAAACATTTATGTGCAATTTG 57.756 33.333 0.00 0.00 41.61 2.32
4006 4634 0.103937 ACTGCAATCTAGCGAGCTCC 59.896 55.000 8.47 0.68 37.31 4.70
4048 4676 7.251704 AGTAACCTGAAATATCGCAATCAAG 57.748 36.000 0.00 0.00 0.00 3.02
4129 4757 4.408921 TGTTAAGCAGTAGCCATCCTATGT 59.591 41.667 0.00 0.00 43.56 2.29
4130 4758 5.600898 TGTTAAGCAGTAGCCATCCTATGTA 59.399 40.000 0.00 0.00 43.56 2.29
4131 4759 4.881019 AAGCAGTAGCCATCCTATGTAG 57.119 45.455 0.00 0.00 43.56 2.74
4175 4804 6.902341 TGTTCATTCATTGTTGTAGAAGAGC 58.098 36.000 0.00 0.00 0.00 4.09
4185 4814 4.473196 TGTTGTAGAAGAGCCATTATCCCA 59.527 41.667 0.00 0.00 0.00 4.37
4214 4889 3.506844 TGTGCACGGTGATTACAGTACTA 59.493 43.478 13.29 0.00 33.35 1.82
4217 4892 6.040054 TGTGCACGGTGATTACAGTACTATAT 59.960 38.462 13.29 0.00 33.35 0.86
4584 5297 4.471726 GTCGTCGTCGTCGGGCAT 62.472 66.667 11.74 0.00 38.33 4.40
4638 5351 1.296715 CTGCCTTGTAGAAGCCGGT 59.703 57.895 1.90 0.00 0.00 5.28
4803 5522 0.032540 CCCTTCTGCAACAGCAAACC 59.967 55.000 0.00 0.00 37.91 3.27
4804 5523 0.318107 CCTTCTGCAACAGCAAACCG 60.318 55.000 0.00 0.00 37.91 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.967319 TTTGCACCGAAAAGAGAGCT 58.033 45.000 0.00 0.00 0.00 4.09
1 2 2.774439 TTTTGCACCGAAAAGAGAGC 57.226 45.000 0.00 0.00 0.00 4.09
18 19 7.822334 CCTACTTTTGTTTGGGTCTTTCTTTTT 59.178 33.333 0.00 0.00 0.00 1.94
19 20 7.179516 TCCTACTTTTGTTTGGGTCTTTCTTTT 59.820 33.333 0.00 0.00 0.00 2.27
20 21 6.666113 TCCTACTTTTGTTTGGGTCTTTCTTT 59.334 34.615 0.00 0.00 0.00 2.52
21 22 6.192044 TCCTACTTTTGTTTGGGTCTTTCTT 58.808 36.000 0.00 0.00 0.00 2.52
22 23 5.762279 TCCTACTTTTGTTTGGGTCTTTCT 58.238 37.500 0.00 0.00 0.00 2.52
23 24 6.320418 TCTTCCTACTTTTGTTTGGGTCTTTC 59.680 38.462 0.00 0.00 0.00 2.62
24 25 6.192044 TCTTCCTACTTTTGTTTGGGTCTTT 58.808 36.000 0.00 0.00 0.00 2.52
25 26 5.762279 TCTTCCTACTTTTGTTTGGGTCTT 58.238 37.500 0.00 0.00 0.00 3.01
26 27 5.382664 TCTTCCTACTTTTGTTTGGGTCT 57.617 39.130 0.00 0.00 0.00 3.85
27 28 6.127563 TGTTTCTTCCTACTTTTGTTTGGGTC 60.128 38.462 0.00 0.00 0.00 4.46
28 29 5.717654 TGTTTCTTCCTACTTTTGTTTGGGT 59.282 36.000 0.00 0.00 0.00 4.51
29 30 6.215495 TGTTTCTTCCTACTTTTGTTTGGG 57.785 37.500 0.00 0.00 0.00 4.12
30 31 7.277760 CCTTTGTTTCTTCCTACTTTTGTTTGG 59.722 37.037 0.00 0.00 0.00 3.28
31 32 8.032451 TCCTTTGTTTCTTCCTACTTTTGTTTG 58.968 33.333 0.00 0.00 0.00 2.93
32 33 8.129496 TCCTTTGTTTCTTCCTACTTTTGTTT 57.871 30.769 0.00 0.00 0.00 2.83
33 34 7.712204 TCCTTTGTTTCTTCCTACTTTTGTT 57.288 32.000 0.00 0.00 0.00 2.83
34 35 7.712204 TTCCTTTGTTTCTTCCTACTTTTGT 57.288 32.000 0.00 0.00 0.00 2.83
35 36 7.491372 GGTTTCCTTTGTTTCTTCCTACTTTTG 59.509 37.037 0.00 0.00 0.00 2.44
36 37 7.553334 GGTTTCCTTTGTTTCTTCCTACTTTT 58.447 34.615 0.00 0.00 0.00 2.27
37 38 6.183360 CGGTTTCCTTTGTTTCTTCCTACTTT 60.183 38.462 0.00 0.00 0.00 2.66
38 39 5.298527 CGGTTTCCTTTGTTTCTTCCTACTT 59.701 40.000 0.00 0.00 0.00 2.24
39 40 4.820173 CGGTTTCCTTTGTTTCTTCCTACT 59.180 41.667 0.00 0.00 0.00 2.57
40 41 4.818005 TCGGTTTCCTTTGTTTCTTCCTAC 59.182 41.667 0.00 0.00 0.00 3.18
41 42 5.038651 TCGGTTTCCTTTGTTTCTTCCTA 57.961 39.130 0.00 0.00 0.00 2.94
42 43 3.893521 TCGGTTTCCTTTGTTTCTTCCT 58.106 40.909 0.00 0.00 0.00 3.36
43 44 4.519350 AGATCGGTTTCCTTTGTTTCTTCC 59.481 41.667 0.00 0.00 0.00 3.46
44 45 5.690997 AGATCGGTTTCCTTTGTTTCTTC 57.309 39.130 0.00 0.00 0.00 2.87
45 46 6.940298 TCATAGATCGGTTTCCTTTGTTTCTT 59.060 34.615 0.00 0.00 0.00 2.52
46 47 6.472887 TCATAGATCGGTTTCCTTTGTTTCT 58.527 36.000 0.00 0.00 0.00 2.52
47 48 6.737254 TCATAGATCGGTTTCCTTTGTTTC 57.263 37.500 0.00 0.00 0.00 2.78
48 49 7.519032 TTTCATAGATCGGTTTCCTTTGTTT 57.481 32.000 0.00 0.00 0.00 2.83
49 50 7.309194 CCTTTTCATAGATCGGTTTCCTTTGTT 60.309 37.037 0.00 0.00 0.00 2.83
50 51 6.151144 CCTTTTCATAGATCGGTTTCCTTTGT 59.849 38.462 0.00 0.00 0.00 2.83
51 52 6.374333 TCCTTTTCATAGATCGGTTTCCTTTG 59.626 38.462 0.00 0.00 0.00 2.77
52 53 6.481643 TCCTTTTCATAGATCGGTTTCCTTT 58.518 36.000 0.00 0.00 0.00 3.11
53 54 6.062258 TCCTTTTCATAGATCGGTTTCCTT 57.938 37.500 0.00 0.00 0.00 3.36
54 55 5.693769 TCCTTTTCATAGATCGGTTTCCT 57.306 39.130 0.00 0.00 0.00 3.36
55 56 6.753107 TTTCCTTTTCATAGATCGGTTTCC 57.247 37.500 0.00 0.00 0.00 3.13
56 57 7.817641 ACTTTTCCTTTTCATAGATCGGTTTC 58.182 34.615 0.00 0.00 0.00 2.78
57 58 7.761038 ACTTTTCCTTTTCATAGATCGGTTT 57.239 32.000 0.00 0.00 0.00 3.27
58 59 8.857694 TTACTTTTCCTTTTCATAGATCGGTT 57.142 30.769 0.00 0.00 0.00 4.44
59 60 8.857694 TTTACTTTTCCTTTTCATAGATCGGT 57.142 30.769 0.00 0.00 0.00 4.69
83 84 7.708998 ACAGTTTGTACATTACCGACATTTTT 58.291 30.769 0.00 0.00 0.00 1.94
84 85 7.266922 ACAGTTTGTACATTACCGACATTTT 57.733 32.000 0.00 0.00 0.00 1.82
85 86 6.870971 ACAGTTTGTACATTACCGACATTT 57.129 33.333 0.00 0.00 0.00 2.32
86 87 8.556213 AATACAGTTTGTACATTACCGACATT 57.444 30.769 0.00 0.00 35.42 2.71
87 88 9.656040 TTAATACAGTTTGTACATTACCGACAT 57.344 29.630 0.00 0.00 35.42 3.06
88 89 9.486497 TTTAATACAGTTTGTACATTACCGACA 57.514 29.630 0.00 0.00 35.42 4.35
228 229 9.448294 AACTTATGTTTTCGCGTTAAAATGTTA 57.552 25.926 5.77 0.00 31.37 2.41
383 388 7.796958 AGCGCTTGATTAGAATTTACAAAAC 57.203 32.000 2.64 0.00 0.00 2.43
449 454 7.168135 GCTTTTCATTTTTCTTCGTTCATGAGT 59.832 33.333 0.00 0.00 0.00 3.41
524 541 8.263940 TCTTAGTTTTGTTCATATTCTTCGGG 57.736 34.615 0.00 0.00 0.00 5.14
580 602 9.863845 CTTTTTGTTCCCCACGTATTATTATTT 57.136 29.630 0.00 0.00 0.00 1.40
581 603 7.977293 GCTTTTTGTTCCCCACGTATTATTATT 59.023 33.333 0.00 0.00 0.00 1.40
582 604 7.340999 AGCTTTTTGTTCCCCACGTATTATTAT 59.659 33.333 0.00 0.00 0.00 1.28
583 605 6.660094 AGCTTTTTGTTCCCCACGTATTATTA 59.340 34.615 0.00 0.00 0.00 0.98
584 606 5.479027 AGCTTTTTGTTCCCCACGTATTATT 59.521 36.000 0.00 0.00 0.00 1.40
585 607 5.014202 AGCTTTTTGTTCCCCACGTATTAT 58.986 37.500 0.00 0.00 0.00 1.28
586 608 4.400120 AGCTTTTTGTTCCCCACGTATTA 58.600 39.130 0.00 0.00 0.00 0.98
634 656 2.031069 GCCGACTATATCTCGCTCAACA 60.031 50.000 0.00 0.00 0.00 3.33
681 703 0.611896 CTGGGATGTTGTTGGGGTCC 60.612 60.000 0.00 0.00 0.00 4.46
682 704 0.112412 ACTGGGATGTTGTTGGGGTC 59.888 55.000 0.00 0.00 0.00 4.46
713 736 0.517316 AGCGGAGAAACGAAATGCAC 59.483 50.000 0.00 0.00 35.47 4.57
718 741 3.687200 GAAACAAAGCGGAGAAACGAAA 58.313 40.909 0.00 0.00 35.47 3.46
805 828 2.433318 GGCGAGTGGACACTGAGC 60.433 66.667 10.08 14.03 42.66 4.26
1055 1092 4.091939 GGGGCGGAGGTGGTGTAC 62.092 72.222 0.00 0.00 0.00 2.90
1086 1123 2.202743 GTCGCATCTACGCTGCCA 60.203 61.111 0.00 0.00 36.24 4.92
1197 1235 6.401153 GCTCACTAAACCTCATTTACAACTCG 60.401 42.308 0.00 0.00 0.00 4.18
1243 1281 1.975407 CAAGCCTGAAGCCCTGGTG 60.975 63.158 0.00 0.00 45.47 4.17
1467 2083 5.986004 GACTTCGGTCAAACCTAATATGG 57.014 43.478 0.00 0.00 43.91 2.74
2100 2718 4.335315 TGACACGGATCATTCTTTTATGGC 59.665 41.667 0.00 0.00 0.00 4.40
2178 2798 4.251268 ACTGACCAGCGGTATTAGAAAAC 58.749 43.478 0.09 0.00 35.25 2.43
2190 2810 2.621338 ACATGACAATACTGACCAGCG 58.379 47.619 0.00 0.00 0.00 5.18
2283 2903 3.926527 TCGTAATGTGAGAGCAACATCAC 59.073 43.478 0.00 0.00 44.88 3.06
2331 2951 9.921637 TTACAAGAAAATTTTCACAACAGAGTT 57.078 25.926 28.00 10.97 39.61 3.01
2908 3528 3.923017 AATCTTGAAGCCGGTCTTTTG 57.077 42.857 1.90 2.38 34.56 2.44
3071 3691 7.069331 CCTGACTTCCTGACTAGAATACAGAAT 59.931 40.741 0.00 0.00 32.77 2.40
3150 3776 8.605325 AGGTATAACAGGACAGTGTATTAGTT 57.395 34.615 0.00 2.06 0.00 2.24
3240 3867 1.399089 GCTCGGAGGCGATCTCTATAC 59.601 57.143 7.20 0.00 42.10 1.47
3317 3944 0.250513 AAGGCCTCCAGCTAACTTCG 59.749 55.000 5.23 0.00 43.05 3.79
3429 4056 3.193691 ACAGGAGTTCGGATACAGTTCTG 59.806 47.826 0.00 0.00 0.00 3.02
3606 4233 5.087323 TCCAGCCTATCTAGATACAAAGGG 58.913 45.833 17.38 13.53 0.00 3.95
3666 4293 2.011947 CGCAGATGCTCCTCAAAATCA 58.988 47.619 2.95 0.00 39.32 2.57
4006 4634 8.124823 CAGGTTACTAATTATGCAACATCACAG 58.875 37.037 0.00 0.00 0.00 3.66
4048 4676 2.675844 TCATGTAAGCACGCACCATAAC 59.324 45.455 0.00 0.00 0.00 1.89
4130 4758 8.527810 TGAACAAAAAGGAAATCAACAAGTACT 58.472 29.630 0.00 0.00 0.00 2.73
4131 4759 8.696410 TGAACAAAAAGGAAATCAACAAGTAC 57.304 30.769 0.00 0.00 0.00 2.73
4175 4804 0.184451 ACAGCAGCCTGGGATAATGG 59.816 55.000 0.00 0.00 43.53 3.16
4214 4889 4.037208 GCATGCTTGAACTACAGCCAATAT 59.963 41.667 11.37 0.00 0.00 1.28
4217 4892 1.541147 GCATGCTTGAACTACAGCCAA 59.459 47.619 11.37 0.00 0.00 4.52
4584 5297 1.229209 AAGAAGGCGAGGGTGGAGA 60.229 57.895 0.00 0.00 0.00 3.71
4615 5328 2.046314 TTCTACAAGGCAGCCGGC 60.046 61.111 21.89 21.89 43.74 6.13
4623 5336 1.156736 CAACACCGGCTTCTACAAGG 58.843 55.000 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.