Multiple sequence alignment - TraesCS6D01G320700

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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 TraesCS6D01G320700 chr6D 100.000 2702 0 0 1 2702 428651097 428648396 0.000000e+00 4990.0
1 TraesCS6D01G320700 chr6B 92.134 2657 130 43 81 2702 645360802 645358190 0.000000e+00 3675.0
2 TraesCS6D01G320700 chr6A 90.161 1677 85 42 319 1978 573414954 573413341 0.000000e+00 2109.0
3 TraesCS6D01G320700 chr6A 88.716 257 25 3 2447 2701 573413036 573412782 7.260000e-81 311.0
4 TraesCS6D01G320700 chr6A 86.782 174 12 6 2208 2381 573413343 573413181 1.650000e-42 183.0
5 TraesCS6D01G320700 chr7D 87.565 193 19 5 1986 2176 513211743 513211554 4.530000e-53 219.0
6 TraesCS6D01G320700 chr7D 85.789 190 23 4 1990 2179 51831081 51830896 5.900000e-47 198.0
7 TraesCS6D01G320700 chr7D 91.667 72 6 0 17 88 590814675 590814746 1.710000e-17 100.0
8 TraesCS6D01G320700 chr3D 87.766 188 20 2 1990 2177 83491889 83492073 1.630000e-52 217.0
9 TraesCS6D01G320700 chr4D 87.701 187 19 4 1986 2172 466669246 466669428 5.860000e-52 215.0
10 TraesCS6D01G320700 chr2D 87.368 190 21 3 1986 2175 533780298 533780112 5.860000e-52 215.0
11 TraesCS6D01G320700 chr2D 85.787 197 22 5 1991 2185 223550658 223550850 1.270000e-48 204.0
12 TraesCS6D01G320700 chr2D 77.679 112 23 2 1067 1177 396425467 396425357 1.740000e-07 67.6
13 TraesCS6D01G320700 chr7A 86.170 188 20 4 1990 2177 621568945 621569126 5.900000e-47 198.0
14 TraesCS6D01G320700 chr7A 96.000 75 3 0 17 91 604397862 604397788 3.650000e-24 122.0
15 TraesCS6D01G320700 chr7A 88.043 92 8 3 1 91 695813251 695813340 3.680000e-19 106.0
16 TraesCS6D01G320700 chr1B 85.864 191 20 6 1991 2178 94513422 94513236 2.120000e-46 196.0
17 TraesCS6D01G320700 chrUn 91.954 87 6 1 3 89 62218146 62218061 1.310000e-23 121.0
18 TraesCS6D01G320700 chr5D 93.243 74 4 1 16 89 565970147 565970219 1.020000e-19 108.0
19 TraesCS6D01G320700 chr4B 86.957 92 10 2 1 91 464216538 464216628 4.760000e-18 102.0
20 TraesCS6D01G320700 chr3B 90.667 75 6 1 18 91 513000003 512999929 6.160000e-17 99.0
21 TraesCS6D01G320700 chr2B 79.825 114 21 2 1065 1177 469613831 469613719 6.200000e-12 82.4
22 TraesCS6D01G320700 chr2A 78.947 114 22 2 1065 1177 534318608 534318496 2.880000e-10 76.8


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 TraesCS6D01G320700 chr6D 428648396 428651097 2701 True 4990.000000 4990 100.000 1 2702 1 chr6D.!!$R1 2701
1 TraesCS6D01G320700 chr6B 645358190 645360802 2612 True 3675.000000 3675 92.134 81 2702 1 chr6B.!!$R1 2621
2 TraesCS6D01G320700 chr6A 573412782 573414954 2172 True 867.666667 2109 88.553 319 2701 3 chr6A.!!$R1 2382

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
634 647 0.183731 GGCCCCAATTAGGACAGGAG 59.816 60.0 0.0 0.0 41.22 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2403 2548 0.31812 GGAACATTGTTGCCCTGTGG 59.682 55.0 6.8 0.0 0.0 4.17 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
17 18 2.436109 AGTGCCAACCCGAGCATT 59.564 55.556 0.00 0.00 41.86 3.56
18 19 1.973281 AGTGCCAACCCGAGCATTG 60.973 57.895 0.00 0.00 41.86 2.82
19 20 1.971167 GTGCCAACCCGAGCATTGA 60.971 57.895 0.00 0.00 41.86 2.57
20 21 1.675310 TGCCAACCCGAGCATTGAG 60.675 57.895 0.00 0.00 33.08 3.02
21 22 3.056313 GCCAACCCGAGCATTGAGC 62.056 63.158 0.00 0.00 46.19 4.26
30 31 4.157817 GCATTGAGCGTGCCTTTG 57.842 55.556 0.00 0.00 36.61 2.77
31 32 2.090524 GCATTGAGCGTGCCTTTGC 61.091 57.895 0.00 0.00 36.61 3.68
45 46 4.870363 TGCCTTTGCAAGATTGTAAGAAC 58.130 39.130 0.00 0.00 46.66 3.01
46 47 4.340666 TGCCTTTGCAAGATTGTAAGAACA 59.659 37.500 0.00 0.00 46.66 3.18
47 48 5.163468 TGCCTTTGCAAGATTGTAAGAACAA 60.163 36.000 0.00 0.00 46.61 2.83
48 49 5.928264 GCCTTTGCAAGATTGTAAGAACAAT 59.072 36.000 0.00 3.52 46.75 2.71
49 50 6.128742 GCCTTTGCAAGATTGTAAGAACAATG 60.129 38.462 8.39 0.00 45.45 2.82
152 153 5.588648 TGGAACAACTCTACCACTTTCTTTG 59.411 40.000 0.00 0.00 31.92 2.77
172 173 1.727335 GCGAAGGAACAACTCTAGCAC 59.273 52.381 0.00 0.00 0.00 4.40
174 175 3.654414 CGAAGGAACAACTCTAGCACTT 58.346 45.455 0.00 0.00 0.00 3.16
227 228 4.715534 TGGTGGGTTTTCTATCAAGTGA 57.284 40.909 0.00 0.00 0.00 3.41
228 229 4.651778 TGGTGGGTTTTCTATCAAGTGAG 58.348 43.478 0.00 0.00 0.00 3.51
229 230 4.349636 TGGTGGGTTTTCTATCAAGTGAGA 59.650 41.667 0.00 0.00 0.00 3.27
230 231 4.938226 GGTGGGTTTTCTATCAAGTGAGAG 59.062 45.833 0.00 0.00 34.87 3.20
231 232 5.513267 GGTGGGTTTTCTATCAAGTGAGAGT 60.513 44.000 3.07 0.00 35.10 3.24
232 233 6.295688 GGTGGGTTTTCTATCAAGTGAGAGTA 60.296 42.308 3.07 0.00 35.10 2.59
233 234 6.814146 GTGGGTTTTCTATCAAGTGAGAGTAG 59.186 42.308 3.07 0.00 35.10 2.57
234 235 6.724441 TGGGTTTTCTATCAAGTGAGAGTAGA 59.276 38.462 3.07 0.00 35.10 2.59
235 236 7.036829 GGGTTTTCTATCAAGTGAGAGTAGAC 58.963 42.308 3.07 0.00 35.10 2.59
236 237 7.309867 GGGTTTTCTATCAAGTGAGAGTAGACA 60.310 40.741 3.07 0.00 35.10 3.41
237 238 7.542824 GGTTTTCTATCAAGTGAGAGTAGACAC 59.457 40.741 3.07 0.00 35.10 3.67
244 246 4.368565 AGTGAGAGTAGACACCACTACA 57.631 45.455 0.00 0.00 43.38 2.74
361 363 0.946221 GCGTCTTGCTATCGATGGGG 60.946 60.000 8.54 0.00 41.73 4.96
368 372 1.758440 GCTATCGATGGGGCCACTGA 61.758 60.000 6.53 1.27 0.00 3.41
374 378 2.876368 GATGGGGCCACTGACTTCCG 62.876 65.000 6.53 0.00 0.00 4.30
418 426 7.816031 ACATGTCATCAAATTTGGACTTTGATC 59.184 33.333 17.90 8.82 45.57 2.92
513 526 1.645034 CAATTGTCTCTCGGCGTCAT 58.355 50.000 6.85 0.00 0.00 3.06
520 533 1.683385 TCTCTCGGCGTCATCAATGAT 59.317 47.619 6.85 0.00 39.30 2.45
521 534 2.057316 CTCTCGGCGTCATCAATGATC 58.943 52.381 6.85 0.00 39.30 2.92
522 535 1.143305 CTCGGCGTCATCAATGATCC 58.857 55.000 6.85 0.95 39.30 3.36
523 536 0.752658 TCGGCGTCATCAATGATCCT 59.247 50.000 6.85 0.00 39.30 3.24
524 537 1.143305 CGGCGTCATCAATGATCCTC 58.857 55.000 0.00 0.00 39.30 3.71
525 538 1.517242 GGCGTCATCAATGATCCTCC 58.483 55.000 0.00 0.00 39.30 4.30
571 584 9.899661 AATTAGCTGGTACTGTATATGTCAAAA 57.100 29.630 0.00 0.00 0.00 2.44
572 585 9.899661 ATTAGCTGGTACTGTATATGTCAAAAA 57.100 29.630 0.00 0.00 0.00 1.94
633 646 0.253630 AGGCCCCAATTAGGACAGGA 60.254 55.000 0.00 0.00 41.22 3.86
634 647 0.183731 GGCCCCAATTAGGACAGGAG 59.816 60.000 0.00 0.00 41.22 3.69
635 648 1.213296 GCCCCAATTAGGACAGGAGA 58.787 55.000 0.00 0.00 41.22 3.71
636 649 1.141858 GCCCCAATTAGGACAGGAGAG 59.858 57.143 0.00 0.00 41.22 3.20
637 650 2.764269 CCCCAATTAGGACAGGAGAGA 58.236 52.381 0.00 0.00 41.22 3.10
638 651 3.321950 CCCCAATTAGGACAGGAGAGAT 58.678 50.000 0.00 0.00 41.22 2.75
639 652 3.326297 CCCCAATTAGGACAGGAGAGATC 59.674 52.174 0.00 0.00 41.22 2.75
640 653 3.326297 CCCAATTAGGACAGGAGAGATCC 59.674 52.174 0.00 0.00 41.22 3.36
641 654 4.230455 CCAATTAGGACAGGAGAGATCCT 58.770 47.826 0.00 0.00 45.12 3.24
684 697 4.624364 CACCGAGCAGCCACACCA 62.624 66.667 0.00 0.00 0.00 4.17
701 714 2.125512 AGGGATCTGCACGCGTTC 60.126 61.111 10.22 5.06 0.00 3.95
863 884 0.388294 CATCAGCTCAGCTCCATCGA 59.612 55.000 0.00 0.00 36.40 3.59
904 929 0.886490 AACCCTCGACGACGTACAGT 60.886 55.000 0.00 0.00 40.69 3.55
932 957 0.737367 CACGAGCAAGCTTCCATCGA 60.737 55.000 23.73 0.00 37.16 3.59
933 958 0.737715 ACGAGCAAGCTTCCATCGAC 60.738 55.000 23.73 2.16 37.16 4.20
934 959 1.746727 CGAGCAAGCTTCCATCGACG 61.747 60.000 15.80 0.00 35.47 5.12
970 995 0.825840 CTAGCTAGCTTCTCCCGGCT 60.826 60.000 24.88 0.00 41.92 5.52
1420 1445 1.533469 GCTGTCTACGGACCAGTGGT 61.533 60.000 16.70 16.70 41.47 4.16
1782 1810 4.274950 GTCACTGCTGCAGTTAACCTAAAA 59.725 41.667 31.20 6.96 42.59 1.52
1789 1817 3.242804 TGCAGTTAACCTAAAACGTGCAC 60.243 43.478 6.82 6.82 36.73 4.57
1936 1965 5.867174 AGAAAATTTGTATGGCCGCTTAAAC 59.133 36.000 0.00 0.00 0.00 2.01
1947 1978 3.981416 GGCCGCTTAAACAAAAGAAGAAG 59.019 43.478 0.00 0.00 0.00 2.85
1995 2026 9.744468 GGTTACAGTTCATTTCAAATACAGTTT 57.256 29.630 0.00 0.00 0.00 2.66
2008 2039 8.087982 TCAAATACAGTTTTGCTAAGTCTCAG 57.912 34.615 0.00 0.00 36.69 3.35
2014 2045 3.299340 TTTGCTAAGTCTCAGTCGACC 57.701 47.619 13.01 0.00 34.46 4.79
2055 2086 9.794685 TCTCTATCGATGCTATATTCATTTGAC 57.205 33.333 8.54 0.00 0.00 3.18
2056 2087 9.800433 CTCTATCGATGCTATATTCATTTGACT 57.200 33.333 8.54 0.00 0.00 3.41
2060 2091 9.888878 ATCGATGCTATATTCATTTGACTTTTG 57.111 29.630 0.00 0.00 0.00 2.44
2061 2092 7.857389 TCGATGCTATATTCATTTGACTTTTGC 59.143 33.333 0.00 0.00 0.00 3.68
2062 2093 7.644945 CGATGCTATATTCATTTGACTTTTGCA 59.355 33.333 0.00 0.00 0.00 4.08
2063 2094 9.472361 GATGCTATATTCATTTGACTTTTGCAT 57.528 29.630 8.81 8.81 33.38 3.96
2065 2096 7.707464 TGCTATATTCATTTGACTTTTGCATGG 59.293 33.333 0.00 0.00 0.00 3.66
2066 2097 7.922278 GCTATATTCATTTGACTTTTGCATGGA 59.078 33.333 0.00 0.00 0.00 3.41
2067 2098 9.459640 CTATATTCATTTGACTTTTGCATGGAG 57.540 33.333 0.00 0.00 0.00 3.86
2068 2099 5.787953 TTCATTTGACTTTTGCATGGAGA 57.212 34.783 0.00 0.00 0.00 3.71
2085 2117 8.181573 TGCATGGAGATTCGTACTAAATTTTTC 58.818 33.333 0.00 0.00 0.00 2.29
2100 2132 9.438228 ACTAAATTTTTCTTTTCGGTTTTTCCA 57.562 25.926 0.00 0.00 35.57 3.53
2105 2137 8.956617 TTTTTCTTTTCGGTTTTTCCATTTTG 57.043 26.923 0.00 0.00 35.57 2.44
2157 2192 3.005578 ACTTGGTTAAGTCTCAGTCGACC 59.994 47.826 13.01 0.00 43.53 4.79
2160 2195 2.159544 GGTTAAGTCTCAGTCGACCGAG 60.160 54.545 20.59 20.59 34.46 4.63
2193 2228 5.920273 ACAACCTTTCAAATATCGCAAACAG 59.080 36.000 0.00 0.00 0.00 3.16
2218 2253 2.893637 CTACATCCAAGTCCCTTGTCG 58.106 52.381 3.53 0.00 39.58 4.35
2221 2256 2.105821 ACATCCAAGTCCCTTGTCGAAA 59.894 45.455 3.53 0.00 39.58 3.46
2257 2292 2.156117 CGTCCTATGTTTTCGCGTTGAA 59.844 45.455 5.77 0.00 33.85 2.69
2258 2293 3.720920 CGTCCTATGTTTTCGCGTTGAAG 60.721 47.826 5.77 0.00 37.99 3.02
2263 2304 2.510874 TGTTTTCGCGTTGAAGTTGTG 58.489 42.857 5.77 0.00 37.99 3.33
2285 2326 1.273886 AGAGAAGAAGGCAACCGAGAC 59.726 52.381 0.00 0.00 37.17 3.36
2324 2365 7.368059 TGCTAGTACCATTTACATAGACATCG 58.632 38.462 0.00 0.00 0.00 3.84
2346 2387 1.713297 ATAGATGGACCCACGTACCC 58.287 55.000 0.00 0.00 0.00 3.69
2425 2570 0.523072 CAGGGCAACAATGTTCCGAG 59.477 55.000 0.00 0.00 39.74 4.63
2449 2594 7.187676 AGGGTTTACACAAGTAGTACTCCTAT 58.812 38.462 2.58 0.00 0.00 2.57
2489 2638 9.700831 AAACAATTACTAGGCTGGAAGAAATAT 57.299 29.630 4.33 0.00 34.07 1.28
2535 2685 6.879458 AGGCAGAATAAACGTTACAATCTCTT 59.121 34.615 0.00 0.00 0.00 2.85
2574 2725 0.247460 TACTAGTGCACTGCTGCCTG 59.753 55.000 29.57 11.90 43.51 4.85
2597 2748 4.677584 CTTTTCTTCAGAGGATCGACGAT 58.322 43.478 10.78 10.78 42.67 3.73
2637 2788 2.746362 GTCAAGGATGCTTTGTCTGGAG 59.254 50.000 0.00 0.00 0.00 3.86
2643 2794 2.574006 TGCTTTGTCTGGAGCAGAAT 57.426 45.000 0.00 0.00 43.46 2.40
2644 2795 2.867624 TGCTTTGTCTGGAGCAGAATT 58.132 42.857 0.00 0.00 43.46 2.17
2647 2798 4.233005 GCTTTGTCTGGAGCAGAATTTTC 58.767 43.478 0.00 0.00 42.46 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.973281 CAATGCTCGGGTTGGCACT 60.973 57.895 0.00 0.00 41.39 4.40
1 2 1.926511 CTCAATGCTCGGGTTGGCAC 61.927 60.000 0.00 0.00 41.39 5.01
2 3 1.675310 CTCAATGCTCGGGTTGGCA 60.675 57.895 0.00 0.00 42.80 4.92
3 4 3.056313 GCTCAATGCTCGGGTTGGC 62.056 63.158 0.00 0.00 38.95 4.52
4 5 2.753966 CGCTCAATGCTCGGGTTGG 61.754 63.158 0.00 0.00 40.11 3.77
5 6 2.034879 ACGCTCAATGCTCGGGTTG 61.035 57.895 0.00 0.00 40.11 3.77
6 7 2.034879 CACGCTCAATGCTCGGGTT 61.035 57.895 0.00 0.00 40.11 4.11
7 8 2.434884 CACGCTCAATGCTCGGGT 60.435 61.111 0.00 0.00 40.11 5.28
8 9 3.869272 GCACGCTCAATGCTCGGG 61.869 66.667 0.00 0.00 40.08 5.14
9 10 3.869272 GGCACGCTCAATGCTCGG 61.869 66.667 0.00 0.00 42.93 4.63
10 11 1.915614 AAAGGCACGCTCAATGCTCG 61.916 55.000 0.00 0.00 42.93 5.03
11 12 0.455633 CAAAGGCACGCTCAATGCTC 60.456 55.000 0.00 0.00 42.93 4.26
12 13 1.582968 CAAAGGCACGCTCAATGCT 59.417 52.632 0.00 0.00 42.93 3.79
13 14 2.090524 GCAAAGGCACGCTCAATGC 61.091 57.895 0.00 0.00 42.62 3.56
14 15 4.157817 GCAAAGGCACGCTCAATG 57.842 55.556 0.00 0.00 40.72 2.82
22 23 7.174440 TTGTTCTTACAATCTTGCAAAGGCAC 61.174 38.462 0.00 0.00 43.77 5.01
23 24 5.163468 TTGTTCTTACAATCTTGCAAAGGCA 60.163 36.000 0.00 0.00 43.03 4.75
24 25 4.870363 TGTTCTTACAATCTTGCAAAGGC 58.130 39.130 0.00 0.00 46.24 4.35
118 119 7.174253 GTGGTAGAGTTGTTCCAAATTATGTCA 59.826 37.037 0.00 0.00 0.00 3.58
121 122 7.687941 AGTGGTAGAGTTGTTCCAAATTATG 57.312 36.000 0.00 0.00 0.00 1.90
143 144 3.694566 AGTTGTTCCTTCGCAAAGAAAGT 59.305 39.130 0.00 0.00 38.57 2.66
144 145 4.035675 AGAGTTGTTCCTTCGCAAAGAAAG 59.964 41.667 0.00 0.00 38.57 2.62
152 153 1.727335 GTGCTAGAGTTGTTCCTTCGC 59.273 52.381 0.00 0.00 0.00 4.70
227 228 9.642343 TTATTATCATGTAGTGGTGTCTACTCT 57.358 33.333 0.00 0.00 40.39 3.24
230 231 9.982651 ACATTATTATCATGTAGTGGTGTCTAC 57.017 33.333 0.00 0.00 40.22 2.59
232 233 9.982651 GTACATTATTATCATGTAGTGGTGTCT 57.017 33.333 0.02 0.00 37.71 3.41
233 234 9.982651 AGTACATTATTATCATGTAGTGGTGTC 57.017 33.333 6.19 0.00 38.71 3.67
234 235 9.764363 CAGTACATTATTATCATGTAGTGGTGT 57.236 33.333 19.16 0.00 46.23 4.16
286 288 3.948196 TTACTCGGTGTTTCCAAAACG 57.052 42.857 0.00 0.00 35.57 3.60
297 299 5.337554 TGAAACTCATCGTATTACTCGGTG 58.662 41.667 0.00 0.00 40.24 4.94
301 303 9.784680 TTACTCTTGAAACTCATCGTATTACTC 57.215 33.333 0.00 0.00 0.00 2.59
343 345 0.946221 GCCCCATCGATAGCAAGACG 60.946 60.000 0.00 0.00 0.00 4.18
361 363 1.519408 TTTAAGCGGAAGTCAGTGGC 58.481 50.000 0.00 0.00 0.00 5.01
368 372 8.952278 TGTGTGAATATATTTTTAAGCGGAAGT 58.048 29.630 0.00 0.00 0.00 3.01
479 489 4.525487 AGACAATTGGGTTGACTCTACGTA 59.475 41.667 10.83 0.00 38.18 3.57
513 526 1.582624 AGGGAGGAGGAGGATCATTGA 59.417 52.381 0.00 0.00 36.25 2.57
520 533 1.405243 AGGTTTAGGGAGGAGGAGGA 58.595 55.000 0.00 0.00 0.00 3.71
521 534 2.120312 GAAGGTTTAGGGAGGAGGAGG 58.880 57.143 0.00 0.00 0.00 4.30
522 535 2.834113 TGAAGGTTTAGGGAGGAGGAG 58.166 52.381 0.00 0.00 0.00 3.69
523 536 3.285290 TTGAAGGTTTAGGGAGGAGGA 57.715 47.619 0.00 0.00 0.00 3.71
524 537 5.710409 TTATTGAAGGTTTAGGGAGGAGG 57.290 43.478 0.00 0.00 0.00 4.30
525 538 7.445707 GCTAATTATTGAAGGTTTAGGGAGGAG 59.554 40.741 0.00 0.00 0.00 3.69
639 652 2.125912 CGGTCGTCCTCTTGCAGG 60.126 66.667 0.00 0.00 45.15 4.85
640 653 1.444553 GTCGGTCGTCCTCTTGCAG 60.445 63.158 0.00 0.00 0.00 4.41
641 654 1.901948 AGTCGGTCGTCCTCTTGCA 60.902 57.895 0.00 0.00 0.00 4.08
642 655 1.444553 CAGTCGGTCGTCCTCTTGC 60.445 63.158 0.00 0.00 0.00 4.01
643 656 1.444553 GCAGTCGGTCGTCCTCTTG 60.445 63.158 0.00 0.00 0.00 3.02
684 697 2.125512 GAACGCGTGCAGATCCCT 60.126 61.111 14.98 0.00 0.00 4.20
884 905 0.453950 CTGTACGTCGTCGAGGGTTG 60.454 60.000 18.29 3.20 40.62 3.77
886 907 1.302033 ACTGTACGTCGTCGAGGGT 60.302 57.895 18.29 11.25 40.62 4.34
887 908 1.134075 CACTGTACGTCGTCGAGGG 59.866 63.158 18.29 5.85 40.62 4.30
888 909 1.134075 CCACTGTACGTCGTCGAGG 59.866 63.158 13.12 13.12 40.62 4.63
904 929 4.933563 TTGCTCGTGCTGCTGCCA 62.934 61.111 13.47 0.10 40.48 4.92
932 957 2.424157 CGTTGTCGTCGTCGTCGT 60.424 61.111 11.41 0.00 38.33 4.34
933 958 2.128017 TCGTTGTCGTCGTCGTCG 60.128 61.111 5.50 5.50 38.33 5.12
934 959 0.161658 TAGTCGTTGTCGTCGTCGTC 59.838 55.000 1.33 0.00 38.33 4.20
946 971 2.025898 GGGAGAAGCTAGCTAGTCGTT 58.974 52.381 19.70 12.73 0.00 3.85
1413 1438 4.293648 TGCGTCACGGACCACTGG 62.294 66.667 0.00 0.00 0.00 4.00
1782 1810 2.030893 CACCTGATGAAATTGTGCACGT 60.031 45.455 13.13 0.00 0.00 4.49
1789 1817 3.591023 TGCAATGCACCTGATGAAATTG 58.409 40.909 2.72 0.00 37.14 2.32
1866 1895 7.360861 CGTTTGCAAGATACAAATAAGACAGGA 60.361 37.037 0.00 0.00 39.09 3.86
1995 2026 1.199327 CGGTCGACTGAGACTTAGCAA 59.801 52.381 20.01 0.00 40.76 3.91
2008 2039 2.159599 ACATAACGAAGTCTCGGTCGAC 60.160 50.000 7.13 7.13 42.92 4.20
2034 2065 9.888878 CAAAAGTCAAATGAATATAGCATCGAT 57.111 29.630 0.00 0.00 0.00 3.59
2049 2080 5.047802 ACGAATCTCCATGCAAAAGTCAAAT 60.048 36.000 0.00 0.00 0.00 2.32
2055 2086 6.662414 TTAGTACGAATCTCCATGCAAAAG 57.338 37.500 0.00 0.00 0.00 2.27
2056 2087 7.624360 ATTTAGTACGAATCTCCATGCAAAA 57.376 32.000 0.00 0.00 0.00 2.44
2059 2090 7.624360 AAAATTTAGTACGAATCTCCATGCA 57.376 32.000 0.00 0.00 0.00 3.96
2060 2091 8.398665 AGAAAAATTTAGTACGAATCTCCATGC 58.601 33.333 0.00 0.00 0.00 4.06
2066 2097 9.821662 CCGAAAAGAAAAATTTAGTACGAATCT 57.178 29.630 0.00 0.00 0.00 2.40
2067 2098 9.603298 ACCGAAAAGAAAAATTTAGTACGAATC 57.397 29.630 0.00 0.00 0.00 2.52
2068 2099 9.955208 AACCGAAAAGAAAAATTTAGTACGAAT 57.045 25.926 0.00 0.00 0.00 3.34
2085 2117 5.733226 AGCAAAATGGAAAAACCGAAAAG 57.267 34.783 0.00 0.00 42.61 2.27
2089 2121 4.664150 AGAAGCAAAATGGAAAAACCGA 57.336 36.364 0.00 0.00 42.61 4.69
2120 2152 8.867097 ACTTAACCAAGTCTCAGTCAAGTAATA 58.133 33.333 0.00 0.00 41.25 0.98
2121 2153 7.736893 ACTTAACCAAGTCTCAGTCAAGTAAT 58.263 34.615 0.00 0.00 41.25 1.89
2122 2154 7.120923 ACTTAACCAAGTCTCAGTCAAGTAA 57.879 36.000 0.00 0.00 41.25 2.24
2123 2155 6.726490 ACTTAACCAAGTCTCAGTCAAGTA 57.274 37.500 0.00 0.00 41.25 2.24
2149 2184 0.945813 GGATAGGTCTCGGTCGACTG 59.054 60.000 18.66 18.66 34.38 3.51
2151 2186 0.662085 GTGGATAGGTCTCGGTCGAC 59.338 60.000 7.13 7.13 0.00 4.20
2153 2188 1.100510 TTGTGGATAGGTCTCGGTCG 58.899 55.000 0.00 0.00 0.00 4.79
2157 2192 3.056107 TGAAAGGTTGTGGATAGGTCTCG 60.056 47.826 0.00 0.00 0.00 4.04
2160 2195 7.254795 CGATATTTGAAAGGTTGTGGATAGGTC 60.255 40.741 0.00 0.00 0.00 3.85
2193 2228 0.530870 GGGACTTGGATGTAGCGAGC 60.531 60.000 0.00 0.00 0.00 5.03
2218 2253 3.242870 GGACGGCTCATGATGTTGATTTC 60.243 47.826 0.00 0.00 0.00 2.17
2221 2256 1.487976 AGGACGGCTCATGATGTTGAT 59.512 47.619 0.00 0.00 0.00 2.57
2257 2292 4.381411 GTTGCCTTCTTCTCTACACAACT 58.619 43.478 0.00 0.00 34.72 3.16
2258 2293 3.498777 GGTTGCCTTCTTCTCTACACAAC 59.501 47.826 0.00 0.00 36.34 3.32
2263 2304 2.492484 TCTCGGTTGCCTTCTTCTCTAC 59.508 50.000 0.00 0.00 0.00 2.59
2285 2326 4.215399 GGTACTAGCAGCAGTCTGATCTAG 59.785 50.000 16.46 16.46 42.95 2.43
2324 2365 3.493873 GGGTACGTGGGTCCATCTATTTC 60.494 52.174 0.00 0.00 0.00 2.17
2346 2387 1.854126 CGTGCTGTTTGAAAAGCTTGG 59.146 47.619 0.00 0.00 40.21 3.61
2403 2548 0.318120 GGAACATTGTTGCCCTGTGG 59.682 55.000 6.80 0.00 0.00 4.17
2425 2570 5.735285 AGGAGTACTACTTGTGTAAACCC 57.265 43.478 0.17 0.00 0.00 4.11
2449 2594 7.086685 AGTAATTGTTTCTTCCCTCCTTGTA 57.913 36.000 0.00 0.00 0.00 2.41
2489 2638 4.402829 CTTATCTAGCTAGCTCAGGGTGA 58.597 47.826 23.26 11.15 0.00 4.02
2535 2685 0.682532 TGTTGTTTCACCTGGCTGCA 60.683 50.000 0.50 0.00 0.00 4.41
2574 2725 2.600867 CGTCGATCCTCTGAAGAAAAGC 59.399 50.000 0.00 0.00 0.00 3.51
2597 2748 4.055360 TGACTTTTCTTTTCGCGAGATCA 58.945 39.130 9.59 0.36 41.60 2.92
2640 2791 5.490139 TCATCAATCAGAGCGGAAAATTC 57.510 39.130 0.00 0.00 0.00 2.17
2643 2794 4.071423 TGTTCATCAATCAGAGCGGAAAA 58.929 39.130 0.00 0.00 0.00 2.29
2644 2795 3.673902 TGTTCATCAATCAGAGCGGAAA 58.326 40.909 0.00 0.00 0.00 3.13
2647 2798 6.456584 GCATATATGTTCATCAATCAGAGCGG 60.457 42.308 14.14 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.