Multiple sequence alignment - TraesCS5D01G369000

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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 TraesCS5D01G369000 chr5D 100.000 4173 0 0 1386 5558 444721847 444726019 0.000000e+00 7707.0
1 TraesCS5D01G369000 chr5D 100.000 1138 0 0 1 1138 444720462 444721599 0.000000e+00 2102.0
2 TraesCS5D01G369000 chr5A 93.469 3828 141 39 1411 5161 561654054 561657849 0.000000e+00 5583.0
3 TraesCS5D01G369000 chr5A 84.626 748 44 25 263 963 561652753 561653476 0.000000e+00 678.0
4 TraesCS5D01G369000 chr5A 88.616 448 25 5 5113 5558 561657853 561658276 6.380000e-144 521.0
5 TraesCS5D01G369000 chr5A 98.214 56 1 0 1080 1135 561653924 561653979 1.270000e-16 99.0
6 TraesCS5D01G369000 chr5B 96.310 3035 86 10 2129 5143 541610383 541613411 0.000000e+00 4961.0
7 TraesCS5D01G369000 chr5B 88.508 1166 69 26 1 1137 541608257 541609386 0.000000e+00 1351.0
8 TraesCS5D01G369000 chr5B 85.880 432 38 11 1386 1801 541609422 541609846 6.610000e-119 438.0
9 TraesCS5D01G369000 chr5B 90.074 272 23 3 5287 5558 541613566 541613833 3.190000e-92 350.0
10 TraesCS5D01G369000 chr5B 97.619 42 1 0 5324 5365 617167249 617167208 7.720000e-09 73.1
11 TraesCS5D01G369000 chr7D 75.888 676 101 23 3908 4543 602183515 602184168 7.040000e-74 289.0
12 TraesCS5D01G369000 chr6A 91.908 173 14 0 966 1138 162861688 162861516 5.560000e-60 243.0
13 TraesCS5D01G369000 chr2B 90.769 130 7 4 1676 1802 780647064 780647191 9.580000e-38 169.0
14 TraesCS5D01G369000 chr2B 97.619 42 1 0 5324 5365 476414769 476414728 7.720000e-09 73.1
15 TraesCS5D01G369000 chr2A 89.683 126 13 0 4433 4558 306014511 306014636 1.600000e-35 161.0
16 TraesCS5D01G369000 chr7A 87.069 116 12 2 4757 4871 679866887 679866774 1.630000e-25 128.0
17 TraesCS5D01G369000 chr7B 76.786 168 26 10 4925 5082 144720568 144720732 1.280000e-11 82.4
18 TraesCS5D01G369000 chr7B 89.796 49 5 0 5324 5372 498967205 498967157 4.650000e-06 63.9
19 TraesCS5D01G369000 chr7B 90.000 50 3 2 5324 5372 691261874 691261826 4.650000e-06 63.9
20 TraesCS5D01G369000 chr1A 97.619 42 1 0 5324 5365 20084213 20084254 7.720000e-09 73.1
21 TraesCS5D01G369000 chr1A 97.619 42 1 0 5324 5365 312722101 312722060 7.720000e-09 73.1
22 TraesCS5D01G369000 chr6B 89.796 49 5 0 5324 5372 157767106 157767058 4.650000e-06 63.9
23 TraesCS5D01G369000 chr1B 89.796 49 5 0 5324 5372 158539180 158539132 4.650000e-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 TraesCS5D01G369000 chr5D 444720462 444726019 5557 False 4904.50 7707 100.00000 1 5558 2 chr5D.!!$F1 5557
1 TraesCS5D01G369000 chr5A 561652753 561658276 5523 False 1720.25 5583 91.23125 263 5558 4 chr5A.!!$F1 5295
2 TraesCS5D01G369000 chr5B 541608257 541613833 5576 False 1775.00 4961 90.19300 1 5558 4 chr5B.!!$F1 5557
3 TraesCS5D01G369000 chr7D 602183515 602184168 653 False 289.00 289 75.88800 3908 4543 1 chr7D.!!$F1 635

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
267 274 0.694444 AGATACAATGTCCGGGCCCT 60.694 55.000 22.43 0.00 0.0 5.19 F
306 313 1.227704 AACACAACATCCGCACCGA 60.228 52.632 0.00 0.00 0.0 4.69 F
1500 1910 1.380403 CGCGGATCTCAGGACAGACT 61.380 60.000 0.00 0.00 0.0 3.24 F
2149 2786 0.250234 CCGGATCTGCCTCAACTGAA 59.750 55.000 0.00 0.00 0.0 3.02 F
2412 3064 0.751643 ACAGCGCTGAAAACCTTGGT 60.752 50.000 42.03 14.36 0.0 3.67 F
2696 3350 1.003223 GGTGTTGTCGCGCTTTACTTT 60.003 47.619 5.56 0.00 0.0 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1500 1910 0.038618 ATCAGCACTTGTGCGTACGA 60.039 50.000 21.65 13.98 40.27 3.43 R
1811 2230 0.249238 ACTCAATCAGCCGATCGAGC 60.249 55.000 18.66 17.93 36.32 5.03 R
2412 3064 0.895530 GATCACCACGGAGAACCTCA 59.104 55.000 0.00 0.00 31.08 3.86 R
4101 4770 0.983467 TCATGTACCAGGCTTGCTCA 59.017 50.000 0.00 0.00 0.00 4.26 R
4317 4986 1.971357 CTCCACCACCAGTTGTAGTCT 59.029 52.381 0.00 0.00 0.00 3.24 R
4899 5599 2.504367 ACTTACAAGCAGCAAACCGAT 58.496 42.857 0.00 0.00 0.00 4.18 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
57 58 4.008933 GGCACCACAGAGCCGTCT 62.009 66.667 0.00 0.00 40.09 4.18
71 72 1.438710 CGTCTCTGGCGCAAAAACG 60.439 57.895 10.83 8.49 0.00 3.60
140 141 4.853142 AGGAGTCCCGCCCGCATA 62.853 66.667 5.25 0.00 37.58 3.14
142 143 4.301027 GAGTCCCGCCCGCATAGG 62.301 72.222 0.00 0.00 40.63 2.57
170 177 2.583593 GTGCCTTCTAGCGCGAGG 60.584 66.667 17.79 16.17 32.88 4.63
191 198 1.493311 GCAACGAGCGTCAAGGAAG 59.507 57.895 0.00 0.00 0.00 3.46
193 200 1.004918 AACGAGCGTCAAGGAAGGG 60.005 57.895 0.00 0.00 0.00 3.95
194 201 2.815647 CGAGCGTCAAGGAAGGGC 60.816 66.667 0.00 0.00 0.00 5.19
222 229 1.126421 CACGTCGACGGTCAGAATCG 61.126 60.000 37.89 12.76 44.95 3.34
227 234 1.012086 CGACGGTCAGAATCGAGGTA 58.988 55.000 9.10 0.00 38.10 3.08
228 235 1.602851 CGACGGTCAGAATCGAGGTAT 59.397 52.381 9.10 0.00 38.10 2.73
234 241 3.385111 GGTCAGAATCGAGGTATGAGGTT 59.615 47.826 0.00 0.00 0.00 3.50
238 245 4.341235 CAGAATCGAGGTATGAGGTTACCA 59.659 45.833 3.51 0.00 43.51 3.25
246 253 1.335132 ATGAGGTTACCATCGCCGGT 61.335 55.000 1.90 1.07 43.46 5.28
254 261 1.040893 ACCATCGCCGGTCAGATACA 61.041 55.000 1.90 0.00 32.11 2.29
267 274 0.694444 AGATACAATGTCCGGGCCCT 60.694 55.000 22.43 0.00 0.00 5.19
276 283 4.820744 CCGGGCCCTTCCACCATG 62.821 72.222 22.43 0.00 36.21 3.66
294 301 4.340666 ACCATGTAATGTCTTGCAACACAA 59.659 37.500 11.69 0.00 44.81 3.33
297 304 5.512753 TGTAATGTCTTGCAACACAACAT 57.487 34.783 11.69 8.54 33.68 2.71
306 313 1.227704 AACACAACATCCGCACCGA 60.228 52.632 0.00 0.00 0.00 4.69
316 323 4.308458 CGCACCGAGACAACCCCA 62.308 66.667 0.00 0.00 0.00 4.96
381 388 2.291865 GGCAAAAGAAGGGAAGGGAGAT 60.292 50.000 0.00 0.00 0.00 2.75
536 544 1.860950 CTTGGACTCACGAGTGTGTTG 59.139 52.381 4.01 1.08 46.49 3.33
600 620 7.182817 ACATTGCCACTAGTTTCATCTACTA 57.817 36.000 0.00 0.00 0.00 1.82
601 621 7.042335 ACATTGCCACTAGTTTCATCTACTAC 58.958 38.462 0.00 0.00 0.00 2.73
602 622 6.852420 TTGCCACTAGTTTCATCTACTACT 57.148 37.500 0.00 0.00 0.00 2.57
603 623 7.949690 TTGCCACTAGTTTCATCTACTACTA 57.050 36.000 0.00 0.00 0.00 1.82
604 624 8.534954 TTGCCACTAGTTTCATCTACTACTAT 57.465 34.615 0.00 0.00 0.00 2.12
605 625 8.534954 TGCCACTAGTTTCATCTACTACTATT 57.465 34.615 0.00 0.00 0.00 1.73
606 626 9.636789 TGCCACTAGTTTCATCTACTACTATTA 57.363 33.333 0.00 0.00 0.00 0.98
625 645 4.666412 TTATGATTCAAGTCCCCAACCA 57.334 40.909 0.00 0.00 0.00 3.67
626 646 3.541242 ATGATTCAAGTCCCCAACCAA 57.459 42.857 0.00 0.00 0.00 3.67
653 673 4.038402 ACCTTTGCCTGAAAATGACAAGAG 59.962 41.667 0.00 0.00 0.00 2.85
654 674 4.553323 CTTTGCCTGAAAATGACAAGAGG 58.447 43.478 0.00 0.00 0.00 3.69
664 684 3.334054 ACAAGAGGGGCCTGCCTC 61.334 66.667 17.92 17.92 36.66 4.70
682 702 4.748679 GCTGCTTCCGCACGCAAG 62.749 66.667 0.00 0.00 42.25 4.01
683 703 4.748679 CTGCTTCCGCACGCAAGC 62.749 66.667 11.64 11.64 42.25 4.01
791 840 1.518774 GACACCCTCCGCCGAATTA 59.481 57.895 0.00 0.00 0.00 1.40
793 842 1.881252 CACCCTCCGCCGAATTACG 60.881 63.158 0.00 0.00 42.18 3.18
942 1009 3.519930 GGTCGTCGCCTCCTCCTC 61.520 72.222 0.00 0.00 0.00 3.71
943 1010 3.519930 GTCGTCGCCTCCTCCTCC 61.520 72.222 0.00 0.00 0.00 4.30
944 1011 3.729489 TCGTCGCCTCCTCCTCCT 61.729 66.667 0.00 0.00 0.00 3.69
1498 1908 2.121538 CCGCGGATCTCAGGACAGA 61.122 63.158 24.07 0.00 0.00 3.41
1500 1910 1.380403 CGCGGATCTCAGGACAGACT 61.380 60.000 0.00 0.00 0.00 3.24
1609 2019 4.222589 CGCCATGATTCGCGCGTT 62.223 61.111 30.98 18.81 42.17 4.84
1614 2024 1.520564 ATGATTCGCGCGTTGCCTA 60.521 52.632 30.98 12.81 42.08 3.93
1617 2027 2.348140 GATTCGCGCGTTGCCTACTG 62.348 60.000 30.98 0.00 42.08 2.74
1655 2065 1.519455 CTGATCCCGAACGTGCTCC 60.519 63.158 0.00 0.00 0.00 4.70
1656 2066 1.949847 CTGATCCCGAACGTGCTCCT 61.950 60.000 0.00 0.00 0.00 3.69
1666 2076 2.674796 ACGTGCTCCTTAGATTCACC 57.325 50.000 0.00 0.00 0.00 4.02
1696 2112 3.357203 TGGCTCACAGTTGGTTTTGTTA 58.643 40.909 0.00 0.00 0.00 2.41
1738 2154 5.773680 ACTTGTAGTGCTAGTGGTTCTAAGA 59.226 40.000 0.00 0.00 32.18 2.10
1756 2172 3.777106 AGACACTGAGAATTGGAAGCA 57.223 42.857 0.00 0.00 0.00 3.91
1758 2174 3.326006 AGACACTGAGAATTGGAAGCAGA 59.674 43.478 0.00 0.00 0.00 4.26
1801 2220 8.729805 ATCTCATCTTGTTCTTAGTTTGATCC 57.270 34.615 0.00 0.00 0.00 3.36
1802 2221 7.679783 TCTCATCTTGTTCTTAGTTTGATCCA 58.320 34.615 0.00 0.00 0.00 3.41
1803 2222 7.604164 TCTCATCTTGTTCTTAGTTTGATCCAC 59.396 37.037 0.00 0.00 0.00 4.02
1804 2223 7.223584 TCATCTTGTTCTTAGTTTGATCCACA 58.776 34.615 0.00 0.00 0.00 4.17
1805 2224 7.388776 TCATCTTGTTCTTAGTTTGATCCACAG 59.611 37.037 0.00 0.00 0.00 3.66
1806 2225 5.470098 TCTTGTTCTTAGTTTGATCCACAGC 59.530 40.000 0.00 0.00 0.00 4.40
1808 2227 6.109156 TGTTCTTAGTTTGATCCACAGCTA 57.891 37.500 0.00 0.00 0.00 3.32
1809 2228 6.166279 TGTTCTTAGTTTGATCCACAGCTAG 58.834 40.000 0.00 0.00 0.00 3.42
1810 2229 5.344743 TCTTAGTTTGATCCACAGCTAGG 57.655 43.478 0.00 0.00 0.00 3.02
1811 2230 4.162320 TCTTAGTTTGATCCACAGCTAGGG 59.838 45.833 4.68 0.64 0.00 3.53
1812 2231 1.065126 AGTTTGATCCACAGCTAGGGC 60.065 52.381 4.68 0.00 39.06 5.19
1834 2279 2.949644 TCGATCGGCTGATTGAGTAGAA 59.050 45.455 19.87 0.00 39.60 2.10
1837 2282 5.092105 CGATCGGCTGATTGAGTAGAATAG 58.908 45.833 16.81 0.00 38.12 1.73
1838 2283 5.106515 CGATCGGCTGATTGAGTAGAATAGA 60.107 44.000 16.81 0.00 38.12 1.98
1840 2285 4.023963 TCGGCTGATTGAGTAGAATAGACG 60.024 45.833 0.00 0.00 36.60 4.18
1865 2310 2.753452 CAGCCAAGCACAAATCTGATCT 59.247 45.455 0.00 0.00 0.00 2.75
1866 2311 3.015327 AGCCAAGCACAAATCTGATCTC 58.985 45.455 0.00 0.00 0.00 2.75
1867 2312 2.751259 GCCAAGCACAAATCTGATCTCA 59.249 45.455 0.00 0.00 0.00 3.27
1868 2313 3.380637 GCCAAGCACAAATCTGATCTCAT 59.619 43.478 0.00 0.00 0.00 2.90
1869 2314 4.577693 GCCAAGCACAAATCTGATCTCATA 59.422 41.667 0.00 0.00 0.00 2.15
1875 2320 9.453572 AAGCACAAATCTGATCTCATAGTTTTA 57.546 29.630 0.00 0.00 0.00 1.52
1888 2333 9.822185 ATCTCATAGTTTTAAAATGCCCAATTC 57.178 29.630 3.52 0.00 0.00 2.17
1954 2402 9.562583 TTTATTATTACTGTTTAAAAGGCTGCG 57.437 29.630 0.00 0.00 0.00 5.18
1965 2413 3.959975 GGCTGCGCCGTTTGTCAA 61.960 61.111 4.18 0.00 39.62 3.18
1967 2415 2.010817 GCTGCGCCGTTTGTCAAAG 61.011 57.895 4.18 0.00 0.00 2.77
1971 2419 1.463056 TGCGCCGTTTGTCAAAGATAG 59.537 47.619 4.18 0.00 0.00 2.08
1973 2421 2.095919 GCGCCGTTTGTCAAAGATAGTT 60.096 45.455 0.00 0.00 0.00 2.24
1976 2424 4.611366 CGCCGTTTGTCAAAGATAGTTTTC 59.389 41.667 0.00 0.00 0.00 2.29
2059 2517 9.933723 GTTTAGTACATGTTCCTAGGAAACTAA 57.066 33.333 27.28 27.28 43.83 2.24
2068 2526 6.013725 TGTTCCTAGGAAACTAAATGCTCTGA 60.014 38.462 25.89 0.00 43.83 3.27
2091 2549 8.877808 TGAAGAGCAGTATAGAATATTGTGTG 57.122 34.615 0.00 0.00 0.00 3.82
2149 2786 0.250234 CCGGATCTGCCTCAACTGAA 59.750 55.000 0.00 0.00 0.00 3.02
2178 2815 3.631250 TGGTTGGGCCAGATATCTTTTC 58.369 45.455 6.23 0.00 43.61 2.29
2182 2819 2.511218 TGGGCCAGATATCTTTTCTGCT 59.489 45.455 0.00 0.00 39.42 4.24
2245 2891 7.605449 TCTGCATATAGCTTTTCTTTTTGCTT 58.395 30.769 0.00 0.00 45.94 3.91
2261 2907 9.912634 TCTTTTTGCTTCTAAAATATGTCCTTG 57.087 29.630 0.00 0.00 30.39 3.61
2281 2933 7.385478 GTCCTTGATTTATCTCTCGGTTTATCC 59.615 40.741 0.00 0.00 0.00 2.59
2352 3004 2.901338 AGACTCAGCTACCCTACACA 57.099 50.000 0.00 0.00 0.00 3.72
2358 3010 7.242359 AGACTCAGCTACCCTACACATATTAT 58.758 38.462 0.00 0.00 0.00 1.28
2412 3064 0.751643 ACAGCGCTGAAAACCTTGGT 60.752 50.000 42.03 14.36 0.00 3.67
2501 3153 7.699709 TCAATAATTTATGTACCTGGGAGGA 57.300 36.000 0.00 0.00 37.67 3.71
2512 3164 1.180029 CTGGGAGGAAAATGTGCCTG 58.820 55.000 0.00 0.00 33.84 4.85
2529 3183 6.276847 TGTGCCTGGTTTTTAGTTTAACATG 58.723 36.000 0.00 0.00 0.00 3.21
2665 3319 5.815222 TGAATATCGTGTGAACATGTAAGGG 59.185 40.000 0.00 0.00 34.59 3.95
2693 3347 1.125566 GTAGGTGTTGTCGCGCTTTAC 59.874 52.381 5.56 1.15 0.00 2.01
2696 3350 1.003223 GGTGTTGTCGCGCTTTACTTT 60.003 47.619 5.56 0.00 0.00 2.66
2910 3566 4.928601 TGATCGGGACTAACTAATTCACG 58.071 43.478 0.00 0.00 37.52 4.35
3076 3735 8.401046 TCAACTTTGCTTGTTGTGTTAATAAC 57.599 30.769 13.57 0.00 43.54 1.89
3181 3840 2.455557 TGGGAATTGGAATGACGCAAT 58.544 42.857 0.00 0.00 0.00 3.56
4101 4770 2.123251 ATCCCGCGTCAGATCCCT 60.123 61.111 4.92 0.00 0.00 4.20
4497 5196 0.179004 TTGTGCTCACCGGAACCATT 60.179 50.000 9.46 0.00 0.00 3.16
4899 5599 3.076621 CTGTAATTCTTGTGCTGCTGGA 58.923 45.455 0.00 0.00 0.00 3.86
4923 5623 3.242712 CGGTTTGCTGCTTGTAAGTTTTG 59.757 43.478 0.00 0.00 0.00 2.44
4943 5645 5.845391 TTGTTTTCTTTCGAATTGGAGGT 57.155 34.783 0.00 0.00 0.00 3.85
5030 5732 2.159787 GCATGACAACTACTCGTGCAAG 60.160 50.000 0.00 0.00 46.03 4.01
5166 5882 5.649557 TCTCTTGTTTCAAATTGTGGTGTG 58.350 37.500 0.00 0.00 0.00 3.82
5237 6003 2.418609 GCATCTATTGGGGGTTTTGCAC 60.419 50.000 0.00 0.00 0.00 4.57
5396 6188 3.530910 AACCGACCGGCAGTCCAAG 62.531 63.158 8.55 0.00 43.08 3.61
5399 6191 2.932234 CGACCGGCAGTCCAAGTCT 61.932 63.158 0.00 0.00 43.08 3.24
5400 6192 1.592400 CGACCGGCAGTCCAAGTCTA 61.592 60.000 0.00 0.00 43.08 2.59
5403 6195 0.608640 CCGGCAGTCCAAGTCTAACT 59.391 55.000 0.00 0.00 0.00 2.24
5496 6288 7.819900 AGCGTAAATTCCATCCATAGAATACTC 59.180 37.037 0.00 0.00 32.46 2.59
5515 6307 4.728772 ACTCCCAAACAATGTCATCTTCA 58.271 39.130 0.00 0.00 0.00 3.02
5528 6320 7.621428 ATGTCATCTTCATTTTCTTCGTCAT 57.379 32.000 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 1.669115 CTCTGTGGTGCCTTGTCGG 60.669 63.158 0.00 0.00 0.00 4.79
35 36 1.968540 GGCTCTGTGGTGCCTTGTC 60.969 63.158 0.00 0.00 45.53 3.18
55 56 2.087501 TATCGTTTTTGCGCCAGAGA 57.912 45.000 4.18 0.00 0.00 3.10
57 58 1.198178 GGTTATCGTTTTTGCGCCAGA 59.802 47.619 4.18 0.00 0.00 3.86
59 60 0.952280 TGGTTATCGTTTTTGCGCCA 59.048 45.000 4.18 0.00 0.00 5.69
60 61 1.982913 CTTGGTTATCGTTTTTGCGCC 59.017 47.619 4.18 0.00 0.00 6.53
63 64 2.029380 AGGCCTTGGTTATCGTTTTTGC 60.029 45.455 0.00 0.00 0.00 3.68
71 72 2.897969 TCGATAGGAGGCCTTGGTTATC 59.102 50.000 6.77 11.10 34.61 1.75
110 111 0.462759 GACTCCTCCAATTCCAGGCG 60.463 60.000 0.00 0.00 0.00 5.52
170 177 2.383527 CCTTGACGCTCGTTGCCTC 61.384 63.158 0.00 0.00 38.78 4.70
183 190 1.072505 GTCAACGGCCCTTCCTTGA 59.927 57.895 0.00 0.00 32.97 3.02
207 214 0.675837 ACCTCGATTCTGACCGTCGA 60.676 55.000 0.00 8.19 41.53 4.20
222 229 2.288886 GGCGATGGTAACCTCATACCTC 60.289 54.545 5.22 0.68 44.72 3.85
227 234 1.335132 ACCGGCGATGGTAACCTCAT 61.335 55.000 9.30 0.00 41.55 2.90
228 235 1.952102 GACCGGCGATGGTAACCTCA 61.952 60.000 9.30 0.00 44.01 3.86
234 241 0.956633 GTATCTGACCGGCGATGGTA 59.043 55.000 9.30 0.00 44.01 3.25
238 245 1.412710 ACATTGTATCTGACCGGCGAT 59.587 47.619 9.30 3.82 0.00 4.58
246 253 0.468226 GGCCCGGACATTGTATCTGA 59.532 55.000 0.73 0.00 0.00 3.27
254 261 2.938798 TGGAAGGGCCCGGACATT 60.939 61.111 18.44 4.05 34.97 2.71
267 274 3.760738 TGCAAGACATTACATGGTGGAA 58.239 40.909 0.00 0.00 33.60 3.53
276 283 4.917415 GGATGTTGTGTTGCAAGACATTAC 59.083 41.667 27.70 23.09 37.83 1.89
294 301 1.374252 GTTGTCTCGGTGCGGATGT 60.374 57.895 0.00 0.00 0.00 3.06
297 304 3.998672 GGGTTGTCTCGGTGCGGA 61.999 66.667 0.00 0.00 0.00 5.54
306 313 1.286553 TGAAGGTTTGTGGGGTTGTCT 59.713 47.619 0.00 0.00 0.00 3.41
316 323 1.734388 GCCCGCTGTTGAAGGTTTGT 61.734 55.000 0.00 0.00 0.00 2.83
536 544 4.022329 CACTGAGGTGTTGGGATTTTAACC 60.022 45.833 0.00 0.00 38.54 2.85
570 578 6.403866 TGAAACTAGTGGCAATGTTTGATT 57.596 33.333 16.12 0.00 33.49 2.57
573 581 6.017400 AGATGAAACTAGTGGCAATGTTTG 57.983 37.500 16.12 0.44 33.49 2.93
600 620 6.069088 TGGTTGGGGACTTGAATCATAATAGT 60.069 38.462 0.00 0.00 0.00 2.12
601 621 6.364701 TGGTTGGGGACTTGAATCATAATAG 58.635 40.000 0.00 0.00 0.00 1.73
602 622 6.334378 TGGTTGGGGACTTGAATCATAATA 57.666 37.500 0.00 0.00 0.00 0.98
603 623 5.205517 TGGTTGGGGACTTGAATCATAAT 57.794 39.130 0.00 0.00 0.00 1.28
604 624 4.666412 TGGTTGGGGACTTGAATCATAA 57.334 40.909 0.00 0.00 0.00 1.90
605 625 4.666412 TTGGTTGGGGACTTGAATCATA 57.334 40.909 0.00 0.00 0.00 2.15
606 626 3.541242 TTGGTTGGGGACTTGAATCAT 57.459 42.857 0.00 0.00 0.00 2.45
618 638 1.824852 GGCAAAGGTAGATTGGTTGGG 59.175 52.381 0.00 0.00 0.00 4.12
625 645 5.774690 TGTCATTTTCAGGCAAAGGTAGATT 59.225 36.000 0.00 0.00 0.00 2.40
626 646 5.324409 TGTCATTTTCAGGCAAAGGTAGAT 58.676 37.500 0.00 0.00 0.00 1.98
682 702 3.344215 CGATGCTGCTGATCCGGC 61.344 66.667 0.00 0.00 37.61 6.13
683 703 1.005275 ATCGATGCTGCTGATCCGG 60.005 57.895 0.00 0.00 0.00 5.14
685 705 1.624865 GCGATCGATGCTGCTGATCC 61.625 60.000 21.57 10.88 36.08 3.36
688 708 2.279717 GGCGATCGATGCTGCTGA 60.280 61.111 21.57 0.00 0.00 4.26
778 827 1.157870 AATGCGTAATTCGGCGGAGG 61.158 55.000 7.21 0.00 40.26 4.30
785 834 1.333619 CCCCAGGAAATGCGTAATTCG 59.666 52.381 0.00 0.00 43.12 3.34
964 1031 3.866582 CGTGGATCTGGGAGGGGC 61.867 72.222 0.00 0.00 0.00 5.80
965 1032 3.866582 GCGTGGATCTGGGAGGGG 61.867 72.222 0.00 0.00 0.00 4.79
966 1033 3.866582 GGCGTGGATCTGGGAGGG 61.867 72.222 0.00 0.00 0.00 4.30
967 1034 3.083349 TGGCGTGGATCTGGGAGG 61.083 66.667 0.00 0.00 0.00 4.30
968 1035 2.187946 GTGGCGTGGATCTGGGAG 59.812 66.667 0.00 0.00 0.00 4.30
969 1036 3.399181 GGTGGCGTGGATCTGGGA 61.399 66.667 0.00 0.00 0.00 4.37
970 1037 4.838152 CGGTGGCGTGGATCTGGG 62.838 72.222 0.00 0.00 0.00 4.45
1491 1901 0.887836 TGTGCGTACGAGTCTGTCCT 60.888 55.000 21.65 0.00 0.00 3.85
1500 1910 0.038618 ATCAGCACTTGTGCGTACGA 60.039 50.000 21.65 13.98 40.27 3.43
1515 1925 2.614057 GCGAAGGTAATTGGACCATCAG 59.386 50.000 0.00 0.00 42.47 2.90
1519 1929 0.391927 CGGCGAAGGTAATTGGACCA 60.392 55.000 0.00 0.00 42.47 4.02
1520 1930 1.712018 GCGGCGAAGGTAATTGGACC 61.712 60.000 12.98 0.00 40.08 4.46
1548 1958 3.164269 ATCCTAGTGCGCCCCTGG 61.164 66.667 4.18 2.35 0.00 4.45
1631 2041 4.515404 GTTCGGGATCAGAACGGG 57.485 61.111 14.67 0.00 38.59 5.28
1634 2044 0.389948 AGCACGTTCGGGATCAGAAC 60.390 55.000 18.01 18.01 43.16 3.01
1644 2054 2.599082 GTGAATCTAAGGAGCACGTTCG 59.401 50.000 0.00 0.00 0.00 3.95
1666 2076 2.034532 TGTGAGCCAGCACCATGG 59.965 61.111 11.19 11.19 43.72 3.66
1678 2094 4.739716 GCATGTAACAAAACCAACTGTGAG 59.260 41.667 0.00 0.00 0.00 3.51
1691 2107 2.566913 ACAAGGACACGCATGTAACAA 58.433 42.857 0.00 0.00 39.95 2.83
1696 2112 1.508632 GTGTACAAGGACACGCATGT 58.491 50.000 0.00 0.00 40.33 3.21
1726 2142 6.226787 CAATTCTCAGTGTCTTAGAACCACT 58.773 40.000 0.39 0.39 39.93 4.00
1733 2149 5.240891 TGCTTCCAATTCTCAGTGTCTTAG 58.759 41.667 0.00 0.00 0.00 2.18
1738 2154 3.406764 GTCTGCTTCCAATTCTCAGTGT 58.593 45.455 0.00 0.00 0.00 3.55
1758 2174 7.957676 AGATGAGATCTAAATTGCCATAAGCGT 60.958 37.037 0.00 0.00 40.77 5.07
1764 2180 7.778853 AGAACAAGATGAGATCTAAATTGCCAT 59.221 33.333 0.00 0.00 39.08 4.40
1766 2182 7.565323 AGAACAAGATGAGATCTAAATTGCC 57.435 36.000 0.00 0.00 39.08 4.52
1805 2224 3.299190 AGCCGATCGAGCCCTAGC 61.299 66.667 18.66 9.51 40.32 3.42
1806 2225 1.247419 ATCAGCCGATCGAGCCCTAG 61.247 60.000 18.66 8.71 0.00 3.02
1808 2227 2.136878 AATCAGCCGATCGAGCCCT 61.137 57.895 18.66 4.21 0.00 5.19
1809 2228 1.958205 CAATCAGCCGATCGAGCCC 60.958 63.158 18.66 1.72 0.00 5.19
1810 2229 0.943359 CTCAATCAGCCGATCGAGCC 60.943 60.000 18.66 4.42 26.21 4.70
1811 2230 0.249238 ACTCAATCAGCCGATCGAGC 60.249 55.000 18.66 17.93 36.32 5.03
1812 2231 2.550180 TCTACTCAATCAGCCGATCGAG 59.450 50.000 18.66 8.00 38.46 4.04
1813 2232 2.572290 TCTACTCAATCAGCCGATCGA 58.428 47.619 18.66 0.00 0.00 3.59
1815 2234 6.090129 GTCTATTCTACTCAATCAGCCGATC 58.910 44.000 0.00 0.00 0.00 3.69
1818 2237 4.222886 CGTCTATTCTACTCAATCAGCCG 58.777 47.826 0.00 0.00 0.00 5.52
1819 2238 5.009210 AGACGTCTATTCTACTCAATCAGCC 59.991 44.000 18.46 0.00 0.00 4.85
1820 2239 6.067263 AGACGTCTATTCTACTCAATCAGC 57.933 41.667 18.46 0.00 0.00 4.26
1831 2276 2.159170 GCTTGGCTGAGACGTCTATTCT 60.159 50.000 20.09 0.00 0.00 2.40
1834 2279 1.134965 GTGCTTGGCTGAGACGTCTAT 60.135 52.381 20.09 0.00 0.00 1.98
1837 2282 0.880278 TTGTGCTTGGCTGAGACGTC 60.880 55.000 7.70 7.70 0.00 4.34
1838 2283 0.463654 TTTGTGCTTGGCTGAGACGT 60.464 50.000 0.00 0.00 0.00 4.34
1840 2285 2.095364 CAGATTTGTGCTTGGCTGAGAC 60.095 50.000 0.00 0.00 0.00 3.36
1865 2310 6.533367 GCGAATTGGGCATTTTAAAACTATGA 59.467 34.615 1.97 0.00 0.00 2.15
1866 2311 6.312426 TGCGAATTGGGCATTTTAAAACTATG 59.688 34.615 1.97 0.00 35.04 2.23
1867 2312 6.402222 TGCGAATTGGGCATTTTAAAACTAT 58.598 32.000 1.97 0.00 35.04 2.12
1868 2313 5.784177 TGCGAATTGGGCATTTTAAAACTA 58.216 33.333 1.97 0.00 35.04 2.24
1869 2314 4.636249 TGCGAATTGGGCATTTTAAAACT 58.364 34.783 1.97 0.00 35.04 2.66
1875 2320 3.951775 TTACTGCGAATTGGGCATTTT 57.048 38.095 1.58 0.00 40.09 1.82
1954 2402 5.758924 AGAAAACTATCTTTGACAAACGGC 58.241 37.500 0.00 0.00 0.00 5.68
1961 2409 9.399403 GATCCAAACAAGAAAACTATCTTTGAC 57.601 33.333 0.00 0.00 37.56 3.18
1971 2419 9.528018 TGACATAAAAGATCCAAACAAGAAAAC 57.472 29.630 0.00 0.00 0.00 2.43
2013 2467 2.081462 CCCCGGTGTATCAAACAGAAC 58.919 52.381 0.00 0.00 39.29 3.01
2014 2468 1.700739 ACCCCGGTGTATCAAACAGAA 59.299 47.619 0.00 0.00 39.29 3.02
2015 2469 1.354101 ACCCCGGTGTATCAAACAGA 58.646 50.000 0.00 0.00 39.29 3.41
2068 2526 7.071196 TCCCACACAATATTCTATACTGCTCTT 59.929 37.037 0.00 0.00 0.00 2.85
2091 2549 4.698304 TCGAAACTATGTTTCAACCATCCC 59.302 41.667 19.02 0.00 0.00 3.85
2140 2777 5.278463 CCCAACCAGTACAATTTCAGTTGAG 60.278 44.000 0.00 0.00 36.16 3.02
2178 2815 6.141560 TCAGATACAGTCATAACTCAGCAG 57.858 41.667 0.00 0.00 31.71 4.24
2236 2882 9.912634 TCAAGGACATATTTTAGAAGCAAAAAG 57.087 29.630 0.00 0.00 31.54 2.27
2252 2898 6.978674 ACCGAGAGATAAATCAAGGACATA 57.021 37.500 0.00 0.00 0.00 2.29
2256 2902 7.442656 GGATAAACCGAGAGATAAATCAAGGA 58.557 38.462 0.00 0.00 0.00 3.36
2281 2933 2.755655 ACAGTTCATCTCCCTGTAGACG 59.244 50.000 0.00 0.00 37.66 4.18
2352 3004 6.266330 GCTTGCAGAAAGGAAGGGAATAATAT 59.734 38.462 0.00 0.00 44.95 1.28
2358 3010 1.620822 GCTTGCAGAAAGGAAGGGAA 58.379 50.000 0.00 0.00 44.95 3.97
2412 3064 0.895530 GATCACCACGGAGAACCTCA 59.104 55.000 0.00 0.00 31.08 3.86
2481 3133 8.340757 ACATTTTCCTCCCAGGTACATAAATTA 58.659 33.333 0.00 0.00 36.53 1.40
2501 3153 7.824779 TGTTAAACTAAAAACCAGGCACATTTT 59.175 29.630 0.00 0.00 0.00 1.82
2512 3164 7.207383 ACAAGGAGCATGTTAAACTAAAAACC 58.793 34.615 0.00 0.00 0.00 3.27
2529 3183 1.155042 CTGCAGTTCAGACAAGGAGC 58.845 55.000 5.25 0.00 45.72 4.70
2665 3319 3.181774 CGCGACAACACCTACTATATTGC 59.818 47.826 0.00 0.00 0.00 3.56
2720 3375 1.760029 GAACCCTGCAAAGAAAACCCA 59.240 47.619 0.00 0.00 0.00 4.51
2727 3382 2.727123 TGTCAAGAACCCTGCAAAGA 57.273 45.000 0.00 0.00 0.00 2.52
3076 3735 6.877236 ACATTCCATTTAGGTATGGCAAAAG 58.123 36.000 0.00 0.00 46.33 2.27
3099 3758 7.854534 ACAGAACACAAAAATTAGGTACGTAC 58.145 34.615 17.56 17.56 0.00 3.67
3100 3759 7.927629 AGACAGAACACAAAAATTAGGTACGTA 59.072 33.333 0.00 0.00 0.00 3.57
3101 3760 6.764560 AGACAGAACACAAAAATTAGGTACGT 59.235 34.615 0.00 0.00 0.00 3.57
3102 3761 7.186021 AGACAGAACACAAAAATTAGGTACG 57.814 36.000 0.00 0.00 0.00 3.67
3181 3840 2.159028 TCACATGTGGTCAAACGAGTGA 60.159 45.455 25.16 0.00 35.44 3.41
4101 4770 0.983467 TCATGTACCAGGCTTGCTCA 59.017 50.000 0.00 0.00 0.00 4.26
4317 4986 1.971357 CTCCACCACCAGTTGTAGTCT 59.029 52.381 0.00 0.00 0.00 3.24
4899 5599 2.504367 ACTTACAAGCAGCAAACCGAT 58.496 42.857 0.00 0.00 0.00 4.18
5030 5732 6.017852 GTGCTAAGAAACTAGGGCATATTGTC 60.018 42.308 0.00 0.00 32.38 3.18
5237 6003 1.202382 GGTGGGATAAGAGAACCGACG 60.202 57.143 0.00 0.00 34.18 5.12
5272 6038 5.552870 AAGTTTGAGCTTCACTTAGAGGA 57.447 39.130 4.73 0.00 0.00 3.71
5418 6210 3.265489 TGGACCCCTCCAAAAGTTAGAT 58.735 45.455 0.00 0.00 44.26 1.98
5496 6288 7.156673 AGAAAATGAAGATGACATTGTTTGGG 58.843 34.615 0.00 0.00 37.89 4.12
5515 6307 4.906618 ACTACCACCATGACGAAGAAAAT 58.093 39.130 0.00 0.00 0.00 1.82
5528 6320 1.881925 GCTTGTGCATGACTACCACCA 60.882 52.381 0.00 0.00 39.41 4.17


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

AutoCloner maintained by Alex Coulton.