Multiple sequence alignment - TraesCS1D01G276400

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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 TraesCS1D01G276400 chr1D 100.000 4659 0 0 1 4659 372859059 372863717 0.000000e+00 8604.0
1 TraesCS1D01G276400 chr1D 78.997 957 156 26 2178 3113 372836070 372837002 3.080000e-171 612.0
2 TraesCS1D01G276400 chr1D 78.133 814 122 41 1165 1941 372874623 372875417 2.540000e-127 466.0
3 TraesCS1D01G276400 chr1D 82.025 484 59 19 3338 3797 372837485 372837964 2.030000e-103 387.0
4 TraesCS1D01G276400 chr1D 80.769 494 68 17 3161 3631 372876849 372877338 1.230000e-95 361.0
5 TraesCS1D01G276400 chr1D 78.702 601 82 31 1398 1961 372835152 372835743 4.430000e-95 359.0
6 TraesCS1D01G276400 chr1D 82.609 299 34 6 2747 3044 372876319 372876600 1.000000e-61 248.0
7 TraesCS1D01G276400 chr1D 84.951 206 24 5 3128 3333 372837129 372837327 7.900000e-48 202.0
8 TraesCS1D01G276400 chr1B 93.867 2560 114 16 2131 4659 497780239 497782786 0.000000e+00 3818.0
9 TraesCS1D01G276400 chr1B 91.571 1222 65 17 492 1698 497778443 497779641 0.000000e+00 1652.0
10 TraesCS1D01G276400 chr1B 86.434 516 54 11 1 505 497777916 497778426 6.810000e-153 551.0
11 TraesCS1D01G276400 chr1B 77.868 863 148 30 2218 3062 497471869 497472706 3.240000e-136 496.0
12 TraesCS1D01G276400 chr1B 81.431 517 62 13 3342 3829 497473328 497473839 4.370000e-105 392.0
13 TraesCS1D01G276400 chr1B 79.754 568 94 18 1401 1961 497799607 497800160 4.370000e-105 392.0
14 TraesCS1D01G276400 chr1B 82.407 432 68 8 2178 2606 497820526 497820952 2.050000e-98 370.0
15 TraesCS1D01G276400 chr1B 80.273 512 69 18 3202 3690 497821522 497822024 1.590000e-94 357.0
16 TraesCS1D01G276400 chr1B 86.446 332 35 5 1728 2049 497779641 497779972 5.730000e-94 355.0
17 TraesCS1D01G276400 chr1B 81.535 417 58 13 1552 1961 497471192 497471596 4.500000e-85 326.0
18 TraesCS1D01G276400 chr1B 97.810 137 2 1 1914 2049 497780053 497780189 7.790000e-58 235.0
19 TraesCS1D01G276400 chr1A 93.352 2557 119 25 2131 4659 472141804 472144337 0.000000e+00 3733.0
20 TraesCS1D01G276400 chr1A 86.804 2084 193 43 1 2049 472139720 472141756 0.000000e+00 2250.0
21 TraesCS1D01G276400 chr1A 78.299 917 143 35 2221 3113 472080955 472081839 1.470000e-149 540.0
22 TraesCS1D01G276400 chr1A 81.594 527 63 19 3340 3837 472082331 472082852 5.610000e-109 405.0
23 TraesCS1D01G276400 chr1A 79.433 564 89 20 1404 1961 472164798 472165340 1.580000e-99 374.0
24 TraesCS1D01G276400 chr1A 80.562 427 65 13 2178 2600 472167492 472167904 3.500000e-81 313.0
25 TraesCS1D01G276400 chr1A 82.274 299 35 6 2747 3044 472168011 472168292 4.660000e-60 243.0
26 TraesCS1D01G276400 chr1A 85.811 148 13 6 1165 1308 472164522 472164665 2.900000e-32 150.0
27 TraesCS1D01G276400 chr5D 91.525 59 3 2 2061 2118 529528456 529528513 3.860000e-11 80.5
28 TraesCS1D01G276400 chr3D 91.525 59 3 2 2061 2118 610721899 610721956 3.860000e-11 80.5
29 TraesCS1D01G276400 chr3D 97.727 44 1 0 2075 2118 477910559 477910602 5.000000e-10 76.8
30 TraesCS1D01G276400 chr4B 90.164 61 5 1 2058 2118 362839842 362839901 1.390000e-10 78.7
31 TraesCS1D01G276400 chr4A 92.727 55 3 1 2065 2118 581333725 581333671 1.390000e-10 78.7
32 TraesCS1D01G276400 chr7A 94.118 51 2 1 2069 2118 17334981 17334931 5.000000e-10 76.8
33 TraesCS1D01G276400 chr6D 95.745 47 2 0 2072 2118 302113753 302113707 5.000000e-10 76.8
34 TraesCS1D01G276400 chr7B 93.878 49 3 0 2063 2111 538878472 538878520 1.800000e-09 75.0
35 TraesCS1D01G276400 chr2D 89.655 58 3 1 2075 2129 472943994 472944051 2.330000e-08 71.3


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 TraesCS1D01G276400 chr1D 372859059 372863717 4658 False 8604.000000 8604 100.000000 1 4659 1 chr1D.!!$F1 4658
1 TraesCS1D01G276400 chr1D 372835152 372837964 2812 False 390.000000 612 81.168750 1398 3797 4 chr1D.!!$F2 2399
2 TraesCS1D01G276400 chr1D 372874623 372877338 2715 False 358.333333 466 80.503667 1165 3631 3 chr1D.!!$F3 2466
3 TraesCS1D01G276400 chr1B 497777916 497782786 4870 False 1322.200000 3818 91.225600 1 4659 5 chr1B.!!$F3 4658
4 TraesCS1D01G276400 chr1B 497471192 497473839 2647 False 404.666667 496 80.278000 1552 3829 3 chr1B.!!$F2 2277
5 TraesCS1D01G276400 chr1B 497799607 497800160 553 False 392.000000 392 79.754000 1401 1961 1 chr1B.!!$F1 560
6 TraesCS1D01G276400 chr1B 497820526 497822024 1498 False 363.500000 370 81.340000 2178 3690 2 chr1B.!!$F4 1512
7 TraesCS1D01G276400 chr1A 472139720 472144337 4617 False 2991.500000 3733 90.078000 1 4659 2 chr1A.!!$F2 4658
8 TraesCS1D01G276400 chr1A 472080955 472082852 1897 False 472.500000 540 79.946500 2221 3837 2 chr1A.!!$F1 1616
9 TraesCS1D01G276400 chr1A 472164522 472168292 3770 False 270.000000 374 82.020000 1165 3044 4 chr1A.!!$F3 1879

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
229 236 0.459585 TTCTTCTCGGTGGTATGCGC 60.460 55.0 0.00 0.0 0.00 6.09 F
642 710 0.870393 CGCAACAACAGACTGCATCT 59.130 50.0 1.25 0.0 38.66 2.90 F
1166 1259 0.321122 GAGGCTTGGTGGTCAGACAG 60.321 60.0 2.17 0.0 0.00 3.51 F
1717 1917 0.250234 TTCCTTGATCCCAGTGAGCG 59.750 55.0 0.00 0.0 29.76 5.03 F
1803 2005 0.719465 CGTCCATCACAAGCGTAACC 59.281 55.0 0.00 0.0 0.00 2.85 F
3192 6110 0.899717 TTGCCCTTCCTGATTGCCAC 60.900 55.0 0.00 0.0 0.00 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1065 1144 0.106819 GGAGACTGGACGGGTAGCTA 60.107 60.0 0.00 0.00 0.00 3.32 R
1500 1642 0.396435 AGTTTCATGCTCACCCGTGA 59.604 50.0 0.00 0.00 38.06 4.35 R
2107 4645 0.772384 ACTCCCTCCGATAGATCCGT 59.228 55.0 0.00 0.00 39.76 4.69 R
3391 6482 0.178995 TGGCCACAACTGAGAATGCA 60.179 50.0 0.00 0.00 0.00 3.96 R
3524 6638 1.115467 CCTGTAGCTCTTCCATCGGT 58.885 55.0 0.00 0.00 0.00 4.69 R
4110 7252 1.831580 AGCTGAAGGCCAATCAGAAC 58.168 50.0 31.66 19.56 45.74 3.01 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
67 68 6.539324 CGTTGCTAAAACAATAATTCGGAGA 58.461 36.000 0.00 0.00 0.00 3.71
73 74 6.911250 AAAACAATAATTCGGAGAACCCTT 57.089 33.333 0.00 0.00 45.90 3.95
75 76 6.911250 AACAATAATTCGGAGAACCCTTTT 57.089 33.333 0.00 0.00 45.90 2.27
84 91 1.001706 GAGAACCCTTTTTGCCACGAC 60.002 52.381 0.00 0.00 0.00 4.34
118 125 1.078709 CATCCATGTGTCGCTCGTTT 58.921 50.000 0.00 0.00 0.00 3.60
120 127 0.865111 TCCATGTGTCGCTCGTTTTG 59.135 50.000 0.00 0.00 0.00 2.44
137 144 4.614993 CGTTTTGCGATATCTTGGTTGGTT 60.615 41.667 0.34 0.00 44.77 3.67
140 147 3.006940 TGCGATATCTTGGTTGGTTGTC 58.993 45.455 0.34 0.00 0.00 3.18
142 149 4.081365 TGCGATATCTTGGTTGGTTGTCTA 60.081 41.667 0.34 0.00 0.00 2.59
144 151 5.416083 CGATATCTTGGTTGGTTGTCTACA 58.584 41.667 0.34 0.00 0.00 2.74
145 152 5.872617 CGATATCTTGGTTGGTTGTCTACAA 59.127 40.000 0.34 0.00 0.00 2.41
181 188 1.521681 GCTCGGGGAGAAACGATGG 60.522 63.158 0.00 0.00 38.56 3.51
229 236 0.459585 TTCTTCTCGGTGGTATGCGC 60.460 55.000 0.00 0.00 0.00 6.09
239 246 2.125269 GTATGCGCGGGTCTTGGT 60.125 61.111 8.83 0.00 0.00 3.67
295 302 3.419596 GGACGTGTTGTAACATTTTTCGC 59.580 43.478 0.00 0.00 41.59 4.70
297 304 3.065648 ACGTGTTGTAACATTTTTCGCCT 59.934 39.130 0.26 0.00 41.59 5.52
315 323 6.827586 TCGCCTAGGTTTTTGTCAATTAAT 57.172 33.333 11.31 0.00 0.00 1.40
317 325 6.657541 TCGCCTAGGTTTTTGTCAATTAATCT 59.342 34.615 11.31 0.00 0.00 2.40
336 344 4.214986 TCTGGCAATTTTCGTCTATCCA 57.785 40.909 0.00 0.00 0.00 3.41
340 348 5.890334 TGGCAATTTTCGTCTATCCATTTC 58.110 37.500 0.00 0.00 0.00 2.17
378 387 5.123502 CCAAGGACATCATGACTTGAGAAAG 59.876 44.000 19.93 4.71 37.75 2.62
402 411 5.706369 GGAAAATCTCTCTCATCCATCATGG 59.294 44.000 0.00 0.00 39.43 3.66
430 439 2.300967 ATGTGATGAGCCCACCGGT 61.301 57.895 0.00 0.00 33.80 5.28
444 453 0.893727 ACCGGTCCCAAGCATCAAAC 60.894 55.000 0.00 0.00 0.00 2.93
514 556 9.132521 GTAGGAATTTTGTTTCTGAACATGATG 57.867 33.333 0.00 0.00 44.71 3.07
624 692 4.024893 GCTATAAATCCACACCACACATCG 60.025 45.833 0.00 0.00 0.00 3.84
642 710 0.870393 CGCAACAACAGACTGCATCT 59.130 50.000 1.25 0.00 38.66 2.90
665 733 2.722201 CCGGTCCTCTCCCTTTCCG 61.722 68.421 0.00 0.00 38.05 4.30
667 735 1.542187 CGGTCCTCTCCCTTTCCGTT 61.542 60.000 0.00 0.00 34.38 4.44
677 745 1.600636 CTTTCCGTTCTGCCTGCCA 60.601 57.895 0.00 0.00 0.00 4.92
680 748 3.052082 CCGTTCTGCCTGCCACAG 61.052 66.667 0.00 0.00 36.44 3.66
686 754 1.071987 CTGCCTGCCACAGAAGTCA 59.928 57.895 0.00 0.00 37.32 3.41
740 808 2.343758 GCACGGAGCAGAGGTGAA 59.656 61.111 0.00 0.00 44.79 3.18
766 834 1.458777 ATGGGCTGCCATGATTGGG 60.459 57.895 22.05 0.00 43.84 4.12
896 972 3.036429 AAGAGGCAGATCCGCACCC 62.036 63.158 2.82 0.00 40.77 4.61
1166 1259 0.321122 GAGGCTTGGTGGTCAGACAG 60.321 60.000 2.17 0.00 0.00 3.51
1167 1260 0.764369 AGGCTTGGTGGTCAGACAGA 60.764 55.000 2.17 0.00 0.00 3.41
1168 1261 0.603975 GGCTTGGTGGTCAGACAGAC 60.604 60.000 2.17 0.00 46.83 3.51
1185 1278 1.360852 AGACAGAGACCCATGGAGACT 59.639 52.381 15.22 9.10 0.00 3.24
1315 1411 0.907486 CCATCCTTCTCACTGCCTCA 59.093 55.000 0.00 0.00 0.00 3.86
1400 1501 1.519758 GAATTACCCGTCGCATGTACG 59.480 52.381 13.68 13.68 40.01 3.67
1433 1575 4.929808 GGAGTTAATACACCACTCACACAG 59.070 45.833 0.00 0.00 39.02 3.66
1480 1622 3.134623 ACTCTGATTTATGTGCCGATCCA 59.865 43.478 0.00 0.00 0.00 3.41
1500 1642 3.454587 TTGCACCGACGGCAGAAGT 62.455 57.895 15.39 0.00 43.05 3.01
1709 1909 4.248691 GCTAAATGCATTCCTTGATCCC 57.751 45.455 13.38 0.00 42.31 3.85
1710 1910 3.638160 GCTAAATGCATTCCTTGATCCCA 59.362 43.478 13.38 0.00 42.31 4.37
1715 1915 2.295885 GCATTCCTTGATCCCAGTGAG 58.704 52.381 0.00 0.00 0.00 3.51
1716 1916 2.295885 CATTCCTTGATCCCAGTGAGC 58.704 52.381 0.00 0.00 0.00 4.26
1717 1917 0.250234 TTCCTTGATCCCAGTGAGCG 59.750 55.000 0.00 0.00 29.76 5.03
1718 1918 0.904865 TCCTTGATCCCAGTGAGCGT 60.905 55.000 0.00 0.00 29.76 5.07
1719 1919 0.824109 CCTTGATCCCAGTGAGCGTA 59.176 55.000 0.00 0.00 29.76 4.42
1720 1920 1.202463 CCTTGATCCCAGTGAGCGTAG 60.202 57.143 0.00 0.00 29.76 3.51
1776 1978 4.817464 TGTGTTTCAGTTGTTAAGGCGTAT 59.183 37.500 0.00 0.00 0.00 3.06
1794 1996 3.311596 CGTATCAGTACTCGTCCATCACA 59.688 47.826 0.00 0.00 0.00 3.58
1803 2005 0.719465 CGTCCATCACAAGCGTAACC 59.281 55.000 0.00 0.00 0.00 2.85
1944 2146 3.194116 TGCTCCTTTCAGATGCAAAATCC 59.806 43.478 0.00 0.00 0.00 3.01
1950 2152 3.454719 TCAGATGCAAAATCCCCAGAA 57.545 42.857 0.00 0.00 0.00 3.02
1951 2153 3.091545 TCAGATGCAAAATCCCCAGAAC 58.908 45.455 0.00 0.00 0.00 3.01
1963 2165 1.281867 CCCCAGAACAGCAAGGTATGA 59.718 52.381 0.00 0.00 0.00 2.15
1966 2168 3.265791 CCAGAACAGCAAGGTATGAGTC 58.734 50.000 0.00 0.00 0.00 3.36
1980 2189 7.549147 AGGTATGAGTCCTAACAACAAGTTA 57.451 36.000 0.00 0.00 41.64 2.24
1991 4256 9.841295 TCCTAACAACAAGTTAAATTAGAGTGT 57.159 29.630 10.18 0.00 41.89 3.55
1999 4264 8.975439 ACAAGTTAAATTAGAGTGTCAGTTACG 58.025 33.333 0.00 0.00 0.00 3.18
2081 4619 9.847224 TCTTTACAAGAAATCATAATACTCCCC 57.153 33.333 0.00 0.00 33.83 4.81
2104 4642 3.921021 CCGATCCATATTACTTGTCGCTC 59.079 47.826 0.00 0.00 0.00 5.03
2106 4644 4.982295 CGATCCATATTACTTGTCGCTCAA 59.018 41.667 0.00 0.00 34.61 3.02
2107 4645 5.462068 CGATCCATATTACTTGTCGCTCAAA 59.538 40.000 0.00 0.00 35.48 2.69
2108 4646 6.562270 CGATCCATATTACTTGTCGCTCAAAC 60.562 42.308 0.00 0.00 35.48 2.93
2109 4647 4.565166 TCCATATTACTTGTCGCTCAAACG 59.435 41.667 0.00 0.00 35.48 3.60
2111 4649 2.512485 TTACTTGTCGCTCAAACGGA 57.488 45.000 0.00 0.00 35.48 4.69
2112 4650 2.736144 TACTTGTCGCTCAAACGGAT 57.264 45.000 0.00 0.00 35.48 4.18
2114 4652 1.000955 ACTTGTCGCTCAAACGGATCT 59.999 47.619 0.00 0.00 35.48 2.75
2129 4698 2.371306 GGATCTATCGGAGGGAGTAGC 58.629 57.143 0.00 0.00 0.00 3.58
2173 4742 6.585695 ATTCACTGCTGAATCTTGTTCAAT 57.414 33.333 0.00 0.00 42.54 2.57
2174 4743 6.395426 TTCACTGCTGAATCTTGTTCAATT 57.605 33.333 0.00 0.00 31.00 2.32
2175 4744 6.395426 TCACTGCTGAATCTTGTTCAATTT 57.605 33.333 0.00 0.00 0.00 1.82
2176 4745 6.808829 TCACTGCTGAATCTTGTTCAATTTT 58.191 32.000 0.00 0.00 0.00 1.82
2307 4876 1.115467 AGCGTGGATAAGTGCTAGCT 58.885 50.000 17.23 0.00 35.56 3.32
2566 5149 1.106285 GCTTGGACTATTTGGGCTGG 58.894 55.000 0.00 0.00 0.00 4.85
2613 5197 7.807977 TCCTCTCCACAATTCATTATTAAGC 57.192 36.000 0.00 0.00 0.00 3.09
2614 5198 7.345691 TCCTCTCCACAATTCATTATTAAGCA 58.654 34.615 0.00 0.00 0.00 3.91
2621 5205 7.221452 CCACAATTCATTATTAAGCAAGCAGAC 59.779 37.037 0.00 0.00 0.00 3.51
2624 5208 6.832520 TTCATTATTAAGCAAGCAGACCAA 57.167 33.333 0.00 0.00 0.00 3.67
2722 5312 5.180492 TCACTACGCTTTTTATTGGAACAGG 59.820 40.000 0.00 0.00 42.39 4.00
2728 5318 5.925969 CGCTTTTTATTGGAACAGGAATGTT 59.074 36.000 0.00 0.00 42.39 2.71
2897 5502 7.086376 ACACATTATTCAATTGTCTTGACAGC 58.914 34.615 5.13 0.00 0.00 4.40
3192 6110 0.899717 TTGCCCTTCCTGATTGCCAC 60.900 55.000 0.00 0.00 0.00 5.01
3283 6201 3.106672 CGCCATTCGACTACTGTTCTAC 58.893 50.000 0.00 0.00 41.67 2.59
3786 6921 8.082242 AGAACCATTATTTTTCAACCGAAAGAG 58.918 33.333 0.00 0.00 42.00 2.85
3881 7021 9.649167 AGGAATGAAAAAGAAATTCATCATCAC 57.351 29.630 2.56 0.00 44.53 3.06
3906 7046 8.516811 CTTACAGTGGTTTGTGTAAGTACTAG 57.483 38.462 12.17 0.00 45.89 2.57
3907 7047 6.475596 ACAGTGGTTTGTGTAAGTACTAGT 57.524 37.500 0.00 0.00 0.00 2.57
3908 7048 7.587037 ACAGTGGTTTGTGTAAGTACTAGTA 57.413 36.000 0.00 0.00 0.00 1.82
3909 7049 7.428826 ACAGTGGTTTGTGTAAGTACTAGTAC 58.571 38.462 23.03 23.03 36.35 2.73
3950 7091 2.959030 GGCAAAATATGGAGAGGGGAAC 59.041 50.000 0.00 0.00 0.00 3.62
3973 7114 5.422012 ACAACAGGTGAAAGTTCCAAGATTT 59.578 36.000 0.00 0.00 0.00 2.17
3995 7136 8.970859 ATTTACTTACCTCCTTCATGAATCAG 57.029 34.615 8.96 7.62 0.00 2.90
4050 7192 8.397018 CCTATTGGGAATCATTACAGCATGGAA 61.397 40.741 0.00 0.00 39.96 3.53
4057 7199 7.414222 AATCATTACAGCATGGAACAAGATT 57.586 32.000 0.00 0.00 45.30 2.40
4104 7246 7.531871 CACAGACTGAAAATAATCTGAACAACG 59.468 37.037 10.08 0.00 40.92 4.10
4110 7252 7.359595 TGAAAATAATCTGAACAACGGTGAAG 58.640 34.615 7.88 1.31 0.00 3.02
4125 7267 2.489722 GGTGAAGTTCTGATTGGCCTTC 59.510 50.000 3.32 1.19 33.74 3.46
4126 7268 3.149196 GTGAAGTTCTGATTGGCCTTCA 58.851 45.455 3.32 6.54 39.21 3.02
4137 7279 0.991146 TGGCCTTCAGCTTCCACATA 59.009 50.000 3.32 0.00 43.05 2.29
4223 7374 5.261216 TCATAAAGGGTCCTTTTCCATCAC 58.739 41.667 18.71 0.00 42.93 3.06
4325 7476 3.515602 ATTCAGTCAAGCAAACTCCCT 57.484 42.857 0.00 0.00 0.00 4.20
4473 7644 1.135915 AGCATTGAGTAGGAGCTCACG 59.864 52.381 17.19 0.00 44.23 4.35
4559 7730 6.911250 ATTGTGTGCATCATGGATGAATAT 57.089 33.333 10.24 0.00 42.09 1.28
4579 7750 2.204491 CGACAGTAATAGCGCACCG 58.796 57.895 11.47 0.00 0.00 4.94
4623 7794 2.094957 CCGACAGTTCTTCCTCACTCTC 60.095 54.545 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 1.731093 CGTCGTGGCAAAAAGGGTT 59.269 52.632 0.00 0.00 0.00 4.11
84 91 1.625315 TGGATGGGAGATATTGAGGCG 59.375 52.381 0.00 0.00 0.00 5.52
118 125 3.417101 ACAACCAACCAAGATATCGCAA 58.583 40.909 0.00 0.00 0.00 4.85
120 127 3.270877 AGACAACCAACCAAGATATCGC 58.729 45.455 0.00 0.00 0.00 4.58
123 130 6.603201 CCATTGTAGACAACCAACCAAGATAT 59.397 38.462 0.00 0.00 38.86 1.63
133 140 3.392947 TCCAACTCCATTGTAGACAACCA 59.607 43.478 0.00 0.00 38.86 3.67
137 144 3.901222 TGACTCCAACTCCATTGTAGACA 59.099 43.478 0.00 0.00 36.47 3.41
140 147 4.543590 AGTGACTCCAACTCCATTGTAG 57.456 45.455 0.00 0.00 36.47 2.74
142 149 3.480470 CAAGTGACTCCAACTCCATTGT 58.520 45.455 0.00 0.00 36.47 2.71
144 151 2.107204 AGCAAGTGACTCCAACTCCATT 59.893 45.455 0.00 0.00 0.00 3.16
145 152 1.701847 AGCAAGTGACTCCAACTCCAT 59.298 47.619 0.00 0.00 0.00 3.41
181 188 1.638467 GTCGCCTCAATGTCATCGC 59.362 57.895 0.00 0.00 0.00 4.58
206 213 4.116961 CGCATACCACCGAGAAGAAATTA 58.883 43.478 0.00 0.00 0.00 1.40
229 236 0.673644 CTTGCTACCACCAAGACCCG 60.674 60.000 0.00 0.00 41.64 5.28
239 246 0.251916 CCCGGTCAATCTTGCTACCA 59.748 55.000 0.00 0.00 32.04 3.25
295 302 7.035612 GCCAGATTAATTGACAAAAACCTAGG 58.964 38.462 7.41 7.41 0.00 3.02
297 304 7.531857 TGCCAGATTAATTGACAAAAACCTA 57.468 32.000 0.00 0.00 0.00 3.08
315 323 4.214986 TGGATAGACGAAAATTGCCAGA 57.785 40.909 0.00 0.00 0.00 3.86
317 325 5.417266 TGAAATGGATAGACGAAAATTGCCA 59.583 36.000 0.00 0.00 0.00 4.92
336 344 7.890127 TGTCCTTGGAACTCTGATTTATGAAAT 59.110 33.333 0.00 0.00 0.00 2.17
340 348 6.825213 TGATGTCCTTGGAACTCTGATTTATG 59.175 38.462 0.00 0.00 0.00 1.90
378 387 5.706369 CCATGATGGATGAGAGAGATTTTCC 59.294 44.000 5.27 0.00 40.96 3.13
430 439 0.178967 TGCCAGTTTGATGCTTGGGA 60.179 50.000 0.00 0.00 0.00 4.37
514 556 2.365617 TGAAATGGGTATCTCGGCTCTC 59.634 50.000 0.00 0.00 0.00 3.20
574 617 2.235016 CGGCGTGGCACGGTTATAG 61.235 63.158 37.33 11.88 42.82 1.31
642 710 2.764128 GGGAGAGGACCGGATGCA 60.764 66.667 9.46 0.00 0.00 3.96
643 711 1.627297 AAAGGGAGAGGACCGGATGC 61.627 60.000 9.46 0.00 0.00 3.91
644 712 0.466124 GAAAGGGAGAGGACCGGATG 59.534 60.000 9.46 0.00 0.00 3.51
645 713 0.691413 GGAAAGGGAGAGGACCGGAT 60.691 60.000 9.46 0.00 0.00 4.18
646 714 1.305887 GGAAAGGGAGAGGACCGGA 60.306 63.158 9.46 0.00 0.00 5.14
647 715 2.722201 CGGAAAGGGAGAGGACCGG 61.722 68.421 0.00 0.00 37.28 5.28
665 733 0.536006 ACTTCTGTGGCAGGCAGAAC 60.536 55.000 14.49 0.00 44.90 3.01
667 735 1.372683 GACTTCTGTGGCAGGCAGA 59.627 57.895 0.00 3.86 40.76 4.26
677 745 3.795688 AATGGACATGGTGACTTCTGT 57.204 42.857 0.00 0.00 0.00 3.41
680 748 2.420022 CGGAAATGGACATGGTGACTTC 59.580 50.000 0.00 0.00 0.00 3.01
686 754 1.748879 CCGCGGAAATGGACATGGT 60.749 57.895 24.07 0.00 0.00 3.55
740 808 2.042639 GGCAGCCCATGTCCCATT 60.043 61.111 0.00 0.00 0.00 3.16
769 837 0.671781 CTGTCAGAGAAGGCCCAACG 60.672 60.000 0.00 0.00 0.00 4.10
896 972 3.558829 CGTCTGGATCTGACCATTGATTG 59.441 47.826 11.70 0.00 39.34 2.67
905 981 0.798771 GTCACGCGTCTGGATCTGAC 60.799 60.000 9.86 7.72 0.00 3.51
1065 1144 0.106819 GGAGACTGGACGGGTAGCTA 60.107 60.000 0.00 0.00 0.00 3.32
1115 1203 1.433121 GGAGATGCAGGGGAGAGATT 58.567 55.000 0.00 0.00 0.00 2.40
1166 1259 1.859302 AGTCTCCATGGGTCTCTGTC 58.141 55.000 13.02 0.00 0.00 3.51
1167 1260 3.370104 CTTAGTCTCCATGGGTCTCTGT 58.630 50.000 13.02 0.00 0.00 3.41
1168 1261 2.697751 CCTTAGTCTCCATGGGTCTCTG 59.302 54.545 13.02 4.85 0.00 3.35
1169 1262 2.957312 GCCTTAGTCTCCATGGGTCTCT 60.957 54.545 13.02 8.22 0.00 3.10
1185 1278 1.077787 CCATGCGTCCTTGGCCTTA 60.078 57.895 3.32 0.00 30.57 2.69
1315 1411 9.646522 AATGATAATTTGGATTGTTAGGCTACT 57.353 29.630 0.00 0.00 0.00 2.57
1365 1464 5.694910 CGGGTAATTCGCAATTGAGTAGTAT 59.305 40.000 10.34 0.00 32.38 2.12
1400 1501 7.931948 AGTGGTGTATTAACTCCTGCATAATAC 59.068 37.037 15.57 15.57 40.45 1.89
1433 1575 0.460722 GGAGGTAGGCGAAGAAGGAC 59.539 60.000 0.00 0.00 0.00 3.85
1480 1622 3.454587 TTCTGCCGTCGGTGCAAGT 62.455 57.895 13.94 0.00 38.46 3.16
1500 1642 0.396435 AGTTTCATGCTCACCCGTGA 59.604 50.000 0.00 0.00 38.06 4.35
1705 1905 0.750546 TACGCTACGCTCACTGGGAT 60.751 55.000 0.00 0.00 0.00 3.85
1709 1909 6.417044 AGTTTATTTATACGCTACGCTCACTG 59.583 38.462 0.00 0.00 0.00 3.66
1710 1910 6.501781 AGTTTATTTATACGCTACGCTCACT 58.498 36.000 0.00 0.00 0.00 3.41
1715 1915 8.499514 AGAACTAGTTTATTTATACGCTACGC 57.500 34.615 10.02 0.00 0.00 4.42
1734 1936 8.974060 AAACACAGGTTTCAGAATTAGAACTA 57.026 30.769 0.00 0.00 43.60 2.24
1735 1937 7.881775 AAACACAGGTTTCAGAATTAGAACT 57.118 32.000 0.00 0.00 43.60 3.01
1776 1978 2.094700 GCTTGTGATGGACGAGTACTGA 60.095 50.000 0.00 0.00 38.27 3.41
1794 1996 2.218603 CAGTCCAACAAGGTTACGCTT 58.781 47.619 0.00 0.00 39.02 4.68
1803 2005 1.230635 CGGTCCAGCAGTCCAACAAG 61.231 60.000 0.00 0.00 0.00 3.16
1866 2068 3.691609 CCAGAAATTGCCAGAAGGAGTAC 59.308 47.826 0.00 0.00 36.89 2.73
1944 2146 2.026822 ACTCATACCTTGCTGTTCTGGG 60.027 50.000 0.00 0.00 0.00 4.45
1950 2152 3.838317 TGTTAGGACTCATACCTTGCTGT 59.162 43.478 0.00 0.00 38.76 4.40
1951 2153 4.471904 TGTTAGGACTCATACCTTGCTG 57.528 45.455 0.00 0.00 38.76 4.41
1988 4253 5.374898 GCAGAGAATTTTCGTAACTGACAC 58.625 41.667 0.00 0.00 0.00 3.67
1991 4256 4.384846 GTCGCAGAGAATTTTCGTAACTGA 59.615 41.667 0.00 0.00 36.95 3.41
1999 4264 3.330267 AGGTCTGTCGCAGAGAATTTTC 58.670 45.455 9.38 0.00 41.46 2.29
2081 4619 2.993899 GCGACAAGTAATATGGATCGGG 59.006 50.000 0.00 0.00 0.00 5.14
2095 4633 1.714794 AGATCCGTTTGAGCGACAAG 58.285 50.000 0.00 0.00 39.77 3.16
2104 4642 1.961394 TCCCTCCGATAGATCCGTTTG 59.039 52.381 0.00 0.00 39.76 2.93
2106 4644 1.145325 ACTCCCTCCGATAGATCCGTT 59.855 52.381 0.00 0.00 39.76 4.44
2107 4645 0.772384 ACTCCCTCCGATAGATCCGT 59.228 55.000 0.00 0.00 39.76 4.69
2108 4646 2.634600 CTACTCCCTCCGATAGATCCG 58.365 57.143 0.00 0.00 39.76 4.18
2109 4647 2.291024 TGCTACTCCCTCCGATAGATCC 60.291 54.545 0.00 0.00 39.76 3.36
2111 4649 2.108425 TGTGCTACTCCCTCCGATAGAT 59.892 50.000 0.00 0.00 39.76 1.98
2112 4650 1.493446 TGTGCTACTCCCTCCGATAGA 59.507 52.381 0.00 0.00 39.76 1.98
2114 4652 1.214673 ACTGTGCTACTCCCTCCGATA 59.785 52.381 0.00 0.00 0.00 2.92
2129 4698 6.266330 TGAATATGATCTCCTGGACTACTGTG 59.734 42.308 0.00 0.00 0.00 3.66
2175 4744 9.405587 GTTTGCTATGTTATTCAGCTGTAAAAA 57.594 29.630 14.67 0.06 36.26 1.94
2176 4745 8.792633 AGTTTGCTATGTTATTCAGCTGTAAAA 58.207 29.630 14.67 0.48 36.26 1.52
2307 4876 5.738783 GCAGAAAATGAAGGGTTTGTAAGCA 60.739 40.000 0.00 0.00 0.00 3.91
2486 5068 5.940470 CAGTATTCCTACATATTCAAGGGGC 59.060 44.000 0.00 0.00 0.00 5.80
2487 5069 6.936900 CACAGTATTCCTACATATTCAAGGGG 59.063 42.308 0.00 0.00 0.00 4.79
2566 5149 4.494350 ACATCTGAATTGCACTGACAAC 57.506 40.909 0.00 0.00 31.03 3.32
2612 5196 1.597742 TTCTCTGTTGGTCTGCTTGC 58.402 50.000 0.00 0.00 0.00 4.01
2613 5197 4.637483 TTTTTCTCTGTTGGTCTGCTTG 57.363 40.909 0.00 0.00 0.00 4.01
2636 5220 8.603898 ATGGCAATATCAATGGATTATGACAT 57.396 30.769 9.36 9.36 39.69 3.06
2706 5295 9.323985 TCAAAACATTCCTGTTCCAATAAAAAG 57.676 29.630 0.00 0.00 44.83 2.27
2712 5302 5.867903 TGTCAAAACATTCCTGTTCCAAT 57.132 34.783 0.00 0.00 44.83 3.16
2713 5303 5.667539 TTGTCAAAACATTCCTGTTCCAA 57.332 34.783 0.00 0.00 44.83 3.53
2722 5312 9.387123 GAACAGAAGAGTATTGTCAAAACATTC 57.613 33.333 0.00 0.00 34.73 2.67
2728 5318 7.714813 TCACATGAACAGAAGAGTATTGTCAAA 59.285 33.333 0.00 0.00 0.00 2.69
3164 6082 6.350949 GCAATCAGGAAGGGCAAAACTATTAA 60.351 38.462 0.00 0.00 0.00 1.40
3174 6092 1.304381 GTGGCAATCAGGAAGGGCA 60.304 57.895 0.00 0.00 0.00 5.36
3192 6110 2.161808 CCACTCATCTGCAAAAGAGCTG 59.838 50.000 0.00 6.67 38.67 4.24
3283 6201 6.438763 GTCAGAAATCTTAACCTGTTGTTGG 58.561 40.000 0.00 0.00 37.83 3.77
3297 6215 3.274288 GCAAAGGATCGGTCAGAAATCT 58.726 45.455 0.00 0.00 0.00 2.40
3391 6482 0.178995 TGGCCACAACTGAGAATGCA 60.179 50.000 0.00 0.00 0.00 3.96
3478 6575 8.434392 ACATTACAAGGAAAGTGTTAGGTTCTA 58.566 33.333 0.00 0.00 0.00 2.10
3524 6638 1.115467 CCTGTAGCTCTTCCATCGGT 58.885 55.000 0.00 0.00 0.00 4.69
3786 6921 9.391006 TCTGATAACCATCCTAACACAAAATAC 57.609 33.333 0.00 0.00 0.00 1.89
3906 7046 8.253113 TGCCTGTATTACCTTACTACAAAGTAC 58.747 37.037 0.00 0.00 37.94 2.73
3907 7047 8.365060 TGCCTGTATTACCTTACTACAAAGTA 57.635 34.615 0.00 0.00 37.15 2.24
3908 7048 7.248743 TGCCTGTATTACCTTACTACAAAGT 57.751 36.000 0.00 0.00 39.91 2.66
3909 7049 8.556213 TTTGCCTGTATTACCTTACTACAAAG 57.444 34.615 0.00 0.00 0.00 2.77
3910 7050 8.921353 TTTTGCCTGTATTACCTTACTACAAA 57.079 30.769 0.00 0.00 0.00 2.83
3930 7070 3.631250 TGTTCCCCTCTCCATATTTTGC 58.369 45.455 0.00 0.00 0.00 3.68
3950 7091 5.520376 AATCTTGGAACTTTCACCTGTTG 57.480 39.130 0.00 0.00 0.00 3.33
3973 7114 7.839705 ACTACTGATTCATGAAGGAGGTAAGTA 59.160 37.037 14.54 8.36 0.00 2.24
3995 7136 6.312426 CAGTGATGAATTTCTGTGGAGACTAC 59.688 42.308 0.00 0.00 0.00 2.73
4050 7192 9.045223 GCAGTTTCCTATTTTCAAAAATCTTGT 57.955 29.630 4.07 0.00 39.24 3.16
4057 7199 5.129485 TGTGGGCAGTTTCCTATTTTCAAAA 59.871 36.000 0.00 0.00 0.00 2.44
4083 7225 6.485313 TCACCGTTGTTCAGATTATTTTCAGT 59.515 34.615 0.00 0.00 0.00 3.41
4093 7235 3.809832 CAGAACTTCACCGTTGTTCAGAT 59.190 43.478 0.00 0.00 41.56 2.90
4104 7246 2.206576 AGGCCAATCAGAACTTCACC 57.793 50.000 5.01 0.00 0.00 4.02
4110 7252 1.831580 AGCTGAAGGCCAATCAGAAC 58.168 50.000 31.66 19.56 45.74 3.01
4137 7279 6.705825 GGTGTTGCATTTTCTTAATTCCAAGT 59.294 34.615 0.00 0.00 0.00 3.16
4223 7374 2.674852 CGATGGAGATGACCAGTTTGTG 59.325 50.000 0.00 0.00 43.49 3.33
4350 7503 7.872061 TCTCCCCTAATATAATGAAAGCAGA 57.128 36.000 0.00 0.00 0.00 4.26
4368 7539 5.422214 TCTCTGTAACATTTCTTCTCCCC 57.578 43.478 0.00 0.00 0.00 4.81
4439 7610 6.115448 ACTCAATGCTACTAGTGTTTCCTT 57.885 37.500 5.39 0.00 0.00 3.36
4473 7644 2.904434 TCAGAGTTAGGTGGAAACCTCC 59.096 50.000 0.00 0.00 41.12 4.30
4623 7794 2.813179 GCTGCTCGGGTAATGTGCG 61.813 63.158 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.