Multiple sequence alignment - TraesCS7D01G409600

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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 TraesCS7D01G409600 chr7D 100.000 4426 0 0 1 4426 528129893 528134318 0.000000e+00 8174
1 TraesCS7D01G409600 chr7A 91.652 2348 85 29 699 2972 608394429 608396739 0.000000e+00 3147
2 TraesCS7D01G409600 chr7A 93.794 1434 48 16 2995 4426 608397381 608398775 0.000000e+00 2117
3 TraesCS7D01G409600 chr7A 87.866 478 35 10 240 705 608393764 608394230 1.400000e-149 540
4 TraesCS7D01G409600 chr7A 87.967 241 25 3 1 237 608392116 608392356 9.370000e-72 281
5 TraesCS7D01G409600 chr7B 89.360 1579 79 39 2920 4426 565907772 565909333 0.000000e+00 1903
6 TraesCS7D01G409600 chr7B 80.356 1573 205 54 722 2239 565905096 565906619 0.000000e+00 1098
7 TraesCS7D01G409600 chr7B 86.077 826 76 19 2118 2919 565906923 565907733 0.000000e+00 852
8 TraesCS7D01G409600 chr6D 77.824 239 38 6 18 241 470746881 470746643 2.780000e-27 134
9 TraesCS7D01G409600 chr3B 79.235 183 24 4 32 202 433779072 433778892 1.010000e-21 115
10 TraesCS7D01G409600 chr3B 85.714 98 11 3 1 95 138527611 138527708 2.820000e-17 100


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 TraesCS7D01G409600 chr7D 528129893 528134318 4425 False 8174.000000 8174 100.000000 1 4426 1 chr7D.!!$F1 4425
1 TraesCS7D01G409600 chr7A 608392116 608398775 6659 False 1521.250000 3147 90.319750 1 4426 4 chr7A.!!$F1 4425
2 TraesCS7D01G409600 chr7B 565905096 565909333 4237 False 1284.333333 1903 85.264333 722 4426 3 chr7B.!!$F1 3704

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
564 1986 0.105039 CGAGGGACAGGGTAGATTGC 59.895 60.000 0.00 0.00 0.00 3.56 F
1263 2964 0.318441 TTCACGGAACAGAGCAGAGG 59.682 55.000 0.00 0.00 0.00 3.69 F
1265 2966 0.668706 CACGGAACAGAGCAGAGGTG 60.669 60.000 0.00 0.00 0.00 4.00 F
2171 4345 1.535028 TCTGCTTTTACATGCGTGTGG 59.465 47.619 21.92 9.75 39.39 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 3847 0.770557 AGGGAACAGGGTACAGCCAA 60.771 55.0 0.00 0.0 39.65 4.52 R
2096 3848 0.770557 AAGGGAACAGGGTACAGCCA 60.771 55.0 0.00 0.0 39.65 4.75 R
2487 4681 1.349067 AGGGTGTAACTGGGACTCAC 58.651 55.0 0.00 0.0 36.74 3.51 R
3721 6633 0.663153 GGGATGTTAATGGCGCAGAC 59.337 55.0 10.83 0.0 0.00 3.51 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
30 33 6.949578 AAAAATCAACATATCCGCAAAGTG 57.050 33.333 0.00 0.00 0.00 3.16
39 44 6.166279 ACATATCCGCAAAGTGGTCATATAG 58.834 40.000 0.00 0.00 34.40 1.31
52 57 4.111375 GTCATATAGGACCGGCACTATG 57.889 50.000 22.21 13.09 32.51 2.23
53 58 3.510360 GTCATATAGGACCGGCACTATGT 59.490 47.826 22.21 15.76 32.51 2.29
59 64 1.687123 GGACCGGCACTATGTCTATGT 59.313 52.381 0.00 0.00 0.00 2.29
74 79 2.571653 TCTATGTCAAAGGAGGTGGTGG 59.428 50.000 0.00 0.00 0.00 4.61
95 100 6.383415 GTGGACCGATCTAGAGATTATGTTC 58.617 44.000 0.00 0.00 34.37 3.18
103 108 8.903723 CGATCTAGAGATTATGTTCGGTAAAAC 58.096 37.037 0.00 0.00 34.37 2.43
105 110 7.495055 TCTAGAGATTATGTTCGGTAAAACCC 58.505 38.462 0.00 0.00 33.75 4.11
136 141 2.173669 CGCTCCAACCGCATACAGG 61.174 63.158 0.00 0.00 0.00 4.00
144 149 3.576356 CGCATACAGGCCGCCTTG 61.576 66.667 9.99 7.25 0.00 3.61
151 156 2.978010 AGGCCGCCTTGAACAACG 60.978 61.111 5.94 0.00 0.00 4.10
158 163 0.248866 GCCTTGAACAACGGTTGGTG 60.249 55.000 23.51 7.62 37.36 4.17
168 173 2.317609 CGGTTGGTGCTCCGTTCAG 61.318 63.158 0.00 0.00 41.58 3.02
171 176 0.814010 GTTGGTGCTCCGTTCAGTGT 60.814 55.000 0.00 0.00 36.30 3.55
174 179 1.014564 GGTGCTCCGTTCAGTGTAGC 61.015 60.000 0.00 0.00 0.00 3.58
178 183 2.232696 TGCTCCGTTCAGTGTAGCATAA 59.767 45.455 0.00 0.00 38.22 1.90
238 243 9.847224 TTACCTACAAATGAGAAGAGTTTTTCT 57.153 29.630 0.00 0.00 40.02 2.52
258 1668 0.588252 CAAAGGGCGAAGACACACAG 59.412 55.000 0.00 0.00 37.00 3.66
268 1678 2.203337 ACACACAGCCACGCCATT 60.203 55.556 0.00 0.00 0.00 3.16
270 1680 1.372004 CACACAGCCACGCCATTTG 60.372 57.895 0.00 0.00 0.00 2.32
275 1685 2.180017 GCCACGCCATTTGCTCTG 59.820 61.111 0.00 0.00 38.05 3.35
286 1696 3.558505 CATTTGCTCTGTGTGTTAGCAC 58.441 45.455 2.25 2.25 45.41 4.40
291 1701 2.288825 GCTCTGTGTGTTAGCACCACTA 60.289 50.000 7.29 0.00 44.65 2.74
293 1703 3.990092 TCTGTGTGTTAGCACCACTAAG 58.010 45.455 7.29 1.57 44.65 2.18
306 1716 4.213482 GCACCACTAAGACAAACTTGTAGG 59.787 45.833 0.00 0.00 42.43 3.18
308 1718 6.053005 CACCACTAAGACAAACTTGTAGGAA 58.947 40.000 0.00 0.00 42.43 3.36
351 1762 1.374758 CACTCTTCACACGCCTCCC 60.375 63.158 0.00 0.00 0.00 4.30
354 1765 2.743928 CTTCACACGCCTCCCAGC 60.744 66.667 0.00 0.00 0.00 4.85
379 1790 0.384725 CAAAAAGCACACTCGCGAGG 60.385 55.000 36.93 27.29 36.85 4.63
380 1791 0.814010 AAAAAGCACACTCGCGAGGT 60.814 50.000 36.93 27.91 36.85 3.85
404 1816 2.405143 GGACTTATTCCAAGCCGGC 58.595 57.895 21.89 21.89 45.10 6.13
431 1843 1.645034 CAATTGTCTCGCCATCGACT 58.355 50.000 0.00 0.00 40.21 4.18
432 1844 1.325640 CAATTGTCTCGCCATCGACTG 59.674 52.381 0.00 0.00 40.21 3.51
449 1865 4.812626 TCGACTGAAGACCCAAAACTTAAC 59.187 41.667 0.00 0.00 0.00 2.01
459 1881 3.436761 CCCAAAACTTAACCCTACCACCA 60.437 47.826 0.00 0.00 0.00 4.17
474 1896 4.729227 ACCACCACCAAACTAAAAACAG 57.271 40.909 0.00 0.00 0.00 3.16
478 1900 3.066203 ACCACCAAACTAAAAACAGCGAG 59.934 43.478 0.00 0.00 0.00 5.03
479 1901 3.550030 CCACCAAACTAAAAACAGCGAGG 60.550 47.826 0.00 0.00 0.00 4.63
480 1902 3.314080 CACCAAACTAAAAACAGCGAGGA 59.686 43.478 0.00 0.00 0.00 3.71
497 1919 3.358076 GACTTCGCCCCCTCTCGTG 62.358 68.421 0.00 0.00 0.00 4.35
498 1920 4.148825 CTTCGCCCCCTCTCGTGG 62.149 72.222 0.00 0.00 0.00 4.94
504 1926 2.266055 CCCCTCTCGTGGCTGAAC 59.734 66.667 0.00 0.00 0.00 3.18
554 1976 3.625897 TGGCCACACGAGGGACAG 61.626 66.667 0.00 0.00 38.94 3.51
564 1986 0.105039 CGAGGGACAGGGTAGATTGC 59.895 60.000 0.00 0.00 0.00 3.56
585 2007 4.750952 CGACTATCGCATTCTCTCCTAA 57.249 45.455 0.00 0.00 31.14 2.69
615 2037 1.068055 GGTGCAGAAAGATGGCTTGTG 60.068 52.381 0.00 0.00 33.79 3.33
622 2044 5.336690 GCAGAAAGATGGCTTGTGGAATAAA 60.337 40.000 0.00 0.00 33.79 1.40
686 2108 2.990066 AGGCACGGGAATAGAAGAAG 57.010 50.000 0.00 0.00 0.00 2.85
734 2359 9.679661 TCATTTTGCTAGGTAGAAAACATGATA 57.320 29.630 0.00 0.00 30.72 2.15
796 2421 5.627172 CATGGGTTATTTTCTACACACACG 58.373 41.667 0.00 0.00 29.02 4.49
797 2422 4.958509 TGGGTTATTTTCTACACACACGA 58.041 39.130 0.00 0.00 0.00 4.35
911 2558 1.372838 CGGTTGACAGCACACCACAA 61.373 55.000 0.00 0.00 0.00 3.33
1199 2900 2.435586 CTTGGTGGCTCCGCTCAG 60.436 66.667 0.53 0.00 39.52 3.35
1212 2913 2.690497 TCCGCTCAGTTATTCCTCTCTG 59.310 50.000 0.00 0.00 0.00 3.35
1225 2926 3.898509 CTCTGGCCTCCGCTCTCG 61.899 72.222 3.32 0.00 34.44 4.04
1261 2962 0.750249 TGTTCACGGAACAGAGCAGA 59.250 50.000 13.34 0.00 45.88 4.26
1262 2963 1.269778 TGTTCACGGAACAGAGCAGAG 60.270 52.381 13.34 0.00 45.88 3.35
1263 2964 0.318441 TTCACGGAACAGAGCAGAGG 59.682 55.000 0.00 0.00 0.00 3.69
1264 2965 0.827925 TCACGGAACAGAGCAGAGGT 60.828 55.000 0.00 0.00 0.00 3.85
1265 2966 0.668706 CACGGAACAGAGCAGAGGTG 60.669 60.000 0.00 0.00 0.00 4.00
1439 3146 8.638629 ATTCGTATGTAGATAGGAGCTTTAGT 57.361 34.615 2.96 0.00 32.05 2.24
1476 3185 6.377327 AATACACAAGAACAGTGGAAACTG 57.623 37.500 4.36 4.36 41.21 3.16
1490 3204 6.261826 CAGTGGAAACTGATAAATGGATCTCC 59.738 42.308 0.00 0.00 39.99 3.71
1529 3243 5.530915 TGGGAACTAACTTGTCTGACAAATG 59.469 40.000 22.25 14.74 37.69 2.32
1571 3285 8.552296 AGTAGTGAATTCAACTCTTAATGGGAT 58.448 33.333 10.35 0.00 0.00 3.85
1579 3293 7.228314 TCAACTCTTAATGGGATATCGGTAG 57.772 40.000 0.00 0.00 0.00 3.18
1581 3295 4.466726 ACTCTTAATGGGATATCGGTAGCC 59.533 45.833 0.00 0.00 35.59 3.93
1609 3323 7.712264 TTCCTTTGTAAAAATTGCACATCAG 57.288 32.000 0.00 0.00 0.00 2.90
1622 3362 6.389830 TTGCACATCAGTTGTAAGTGAATT 57.610 33.333 6.26 0.00 41.34 2.17
1637 3377 6.409524 AAGTGAATTTTCAGGATTTCAGCA 57.590 33.333 0.00 0.00 37.98 4.41
1656 3396 8.438676 TTCAGCATAAGCCTAACTTCTTTATC 57.561 34.615 0.00 0.00 43.56 1.75
1731 3473 5.414454 CCATTCTAGGTTTTGGAATCGACAA 59.586 40.000 0.00 0.00 0.00 3.18
1869 3611 8.361139 CGTTACTCTAGTTCTCCATCCATATTT 58.639 37.037 0.00 0.00 0.00 1.40
1886 3628 9.936329 ATCCATATTTATTTACTTCCAGGTTGT 57.064 29.630 0.00 0.00 0.00 3.32
1887 3629 9.184523 TCCATATTTATTTACTTCCAGGTTGTG 57.815 33.333 0.00 0.00 0.00 3.33
1919 3661 7.876068 AGTTTTGACATCAGATGCAATTCATTT 59.124 29.630 10.59 0.00 35.05 2.32
2014 3764 7.028361 TGGAAAGGTTTGTTAACTGTTTTACG 58.972 34.615 7.22 0.00 34.59 3.18
2079 3831 9.787532 TCAGCATTTACAGATTTGTTAATAAGC 57.212 29.630 0.86 2.41 35.11 3.09
2143 4317 2.067013 CCGCTGTCATCAGAGCATATG 58.933 52.381 0.00 0.00 43.76 1.78
2148 4322 4.337555 GCTGTCATCAGAGCATATGGTTTT 59.662 41.667 9.14 0.00 43.76 2.43
2166 4340 4.382754 GGTTTTTCTCTGCTTTTACATGCG 59.617 41.667 0.00 0.00 0.00 4.73
2167 4341 4.829064 TTTTCTCTGCTTTTACATGCGT 57.171 36.364 0.00 0.00 0.00 5.24
2168 4342 3.811722 TTCTCTGCTTTTACATGCGTG 57.188 42.857 3.82 3.82 0.00 5.34
2171 4345 1.535028 TCTGCTTTTACATGCGTGTGG 59.465 47.619 21.92 9.75 39.39 4.17
2350 4533 4.937620 TGTGATCCAGCATTTACTCTTGTC 59.062 41.667 0.00 0.00 0.00 3.18
2372 4555 7.403421 TGTCACTAAATTTAGAAACACACACG 58.597 34.615 27.92 2.23 34.84 4.49
2487 4681 0.740149 TGCGGCCAATCATTTAGCTG 59.260 50.000 2.24 0.00 34.66 4.24
2660 4854 2.229792 TCAACTCAAGTGACCCATTGC 58.770 47.619 0.00 0.00 0.00 3.56
2834 5038 0.613777 ATTTCGAGGTGAGGGTGTCC 59.386 55.000 0.00 0.00 0.00 4.02
2972 5217 2.739292 TGAGTTCCGACAGAAGAAACG 58.261 47.619 0.00 0.00 34.29 3.60
2976 5221 2.163818 TCCGACAGAAGAAACGCAAT 57.836 45.000 0.00 0.00 0.00 3.56
3025 5890 3.928727 AATGACCACATTGAAGCACAG 57.071 42.857 0.00 0.00 43.90 3.66
3081 5946 2.656085 TGAAAGCAAATGTTAACGCCG 58.344 42.857 0.26 0.00 0.00 6.46
3134 6002 1.373435 CCCTTCGCAACTACCACCA 59.627 57.895 0.00 0.00 0.00 4.17
3210 6083 6.700020 CATTTACTCTGTGATAAACTGCTCG 58.300 40.000 0.00 0.00 0.00 5.03
3434 6343 4.158764 CAGGTCGAGAGTTGAGTTAGGATT 59.841 45.833 0.00 0.00 0.00 3.01
3435 6344 4.158764 AGGTCGAGAGTTGAGTTAGGATTG 59.841 45.833 0.00 0.00 0.00 2.67
3550 6459 7.449395 AGGATCATTCTCACTGAAACAAATTCA 59.551 33.333 0.00 0.00 45.71 2.57
3659 6568 7.940178 AATATGTGCTGTTAATGCATGATTG 57.060 32.000 0.00 0.00 42.69 2.67
3692 6601 7.865706 AAACGAAACCATCTTATATTCTGCT 57.134 32.000 0.00 0.00 0.00 4.24
3715 6627 0.961753 GGTTGGTGGCCTTTCTTCTG 59.038 55.000 3.32 0.00 0.00 3.02
3721 6633 2.287608 GGTGGCCTTTCTTCTGTTTTCG 60.288 50.000 3.32 0.00 0.00 3.46
3727 6639 3.535860 CTTTCTTCTGTTTTCGTCTGCG 58.464 45.455 0.00 0.00 39.92 5.18
3746 6674 3.146066 GCGCCATTAACATCCCTATCAA 58.854 45.455 0.00 0.00 0.00 2.57
3912 6848 2.954318 CTCAAGGAATCGGCCATCAATT 59.046 45.455 2.24 0.00 0.00 2.32
3913 6849 4.136796 CTCAAGGAATCGGCCATCAATTA 58.863 43.478 2.24 0.00 0.00 1.40
3979 6915 0.261696 AGGTTGGGTTTTCTGCACCT 59.738 50.000 0.00 0.00 34.36 4.00
4110 7046 3.577805 ACTACCACAGAACTTGCCTTT 57.422 42.857 0.00 0.00 0.00 3.11
4123 7059 8.087750 CAGAACTTGCCTTTCCAATAATACAAA 58.912 33.333 0.00 0.00 0.00 2.83
4168 7104 7.180408 TCCAACTCTAGGTAAGCTTCATTTACT 59.820 37.037 0.00 0.00 32.81 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 44 1.687123 ACATAGACATAGTGCCGGTCC 59.313 52.381 1.90 0.00 31.99 4.46
45 50 5.053145 CCTCCTTTGACATAGACATAGTGC 58.947 45.833 0.00 0.00 0.00 4.40
52 57 3.600388 CACCACCTCCTTTGACATAGAC 58.400 50.000 0.00 0.00 0.00 2.59
53 58 2.571653 CCACCACCTCCTTTGACATAGA 59.428 50.000 0.00 0.00 0.00 1.98
59 64 1.764571 CGGTCCACCACCTCCTTTGA 61.765 60.000 0.00 0.00 44.21 2.69
74 79 5.181622 ACCGAACATAATCTCTAGATCGGTC 59.818 44.000 21.32 5.16 41.00 4.79
83 88 6.309389 AGGGTTTTACCGAACATAATCTCT 57.691 37.500 0.00 0.00 39.83 3.10
95 100 1.201424 AGCTAGGGAGGGTTTTACCG 58.799 55.000 0.00 0.00 39.83 4.02
103 108 2.918276 GCGGGTAGCTAGGGAGGG 60.918 72.222 0.00 0.00 44.04 4.30
144 149 1.652563 GGAGCACCAACCGTTGTTC 59.347 57.895 10.34 2.94 35.97 3.18
151 156 1.227853 ACTGAACGGAGCACCAACC 60.228 57.895 0.00 0.00 35.59 3.77
152 157 0.814010 ACACTGAACGGAGCACCAAC 60.814 55.000 0.00 0.00 35.59 3.77
158 163 2.579207 TATGCTACACTGAACGGAGC 57.421 50.000 0.00 0.00 0.00 4.70
163 168 5.880054 ACATGGTTTATGCTACACTGAAC 57.120 39.130 0.00 0.00 40.59 3.18
168 173 8.293867 TCACTTTTTACATGGTTTATGCTACAC 58.706 33.333 0.00 0.00 40.59 2.90
171 176 8.511321 CACTCACTTTTTACATGGTTTATGCTA 58.489 33.333 0.00 0.00 40.59 3.49
174 179 6.305399 CGCACTCACTTTTTACATGGTTTATG 59.695 38.462 0.00 0.00 42.68 1.90
178 183 3.630312 ACGCACTCACTTTTTACATGGTT 59.370 39.130 0.00 0.00 0.00 3.67
212 217 9.847224 AGAAAAACTCTTCTCATTTGTAGGTAA 57.153 29.630 0.00 0.00 29.31 2.85
237 242 0.868406 GTGTGTCTTCGCCCTTTGAG 59.132 55.000 0.00 0.00 0.00 3.02
238 243 0.179234 TGTGTGTCTTCGCCCTTTGA 59.821 50.000 0.00 0.00 0.00 2.69
275 1685 9.010431 AAGTTTGTCTTAGTGGTGCTAACACAC 62.010 40.741 7.01 0.00 37.97 3.82
286 1696 7.562454 TTTTCCTACAAGTTTGTCTTAGTGG 57.438 36.000 0.00 0.00 42.35 4.00
314 1724 1.073763 TGGTGTGTCCCCAGATTTGAG 59.926 52.381 0.00 0.00 34.77 3.02
321 1731 0.035458 GAAGAGTGGTGTGTCCCCAG 59.965 60.000 0.00 0.00 34.77 4.45
322 1732 0.692756 TGAAGAGTGGTGTGTCCCCA 60.693 55.000 0.00 0.00 34.77 4.96
351 1762 0.318869 TGTGCTTTTTGGCATCGCTG 60.319 50.000 0.00 0.00 44.34 5.18
354 1765 1.689959 GAGTGTGCTTTTTGGCATCG 58.310 50.000 0.00 0.00 44.34 3.84
369 1780 1.734477 CCAACTCACCTCGCGAGTG 60.734 63.158 32.41 27.52 42.90 3.51
371 1782 1.444553 GTCCAACTCACCTCGCGAG 60.445 63.158 29.06 29.06 36.53 5.03
431 1843 4.529716 AGGGTTAAGTTTTGGGTCTTCA 57.470 40.909 0.00 0.00 0.00 3.02
432 1844 4.763793 GGTAGGGTTAAGTTTTGGGTCTTC 59.236 45.833 0.00 0.00 0.00 2.87
449 1865 3.512219 TTTAGTTTGGTGGTGGTAGGG 57.488 47.619 0.00 0.00 0.00 3.53
459 1881 3.314357 GTCCTCGCTGTTTTTAGTTTGGT 59.686 43.478 0.00 0.00 0.00 3.67
479 1901 3.069318 ACGAGAGGGGGCGAAGTC 61.069 66.667 0.00 0.00 0.00 3.01
480 1902 3.382832 CACGAGAGGGGGCGAAGT 61.383 66.667 0.00 0.00 0.00 3.01
500 1922 2.359169 CCCTCCGCCTGCTAGTTCA 61.359 63.158 0.00 0.00 0.00 3.18
504 1926 2.123683 TCTCCCTCCGCCTGCTAG 60.124 66.667 0.00 0.00 0.00 3.42
536 1958 3.883744 CTGTCCCTCGTGTGGCCAC 62.884 68.421 29.67 29.67 38.27 5.01
537 1959 3.625897 CTGTCCCTCGTGTGGCCA 61.626 66.667 0.00 0.00 0.00 5.36
538 1960 4.394712 CCTGTCCCTCGTGTGGCC 62.395 72.222 0.00 0.00 0.00 5.36
539 1961 4.394712 CCCTGTCCCTCGTGTGGC 62.395 72.222 0.00 0.00 0.00 5.01
540 1962 1.605058 CTACCCTGTCCCTCGTGTGG 61.605 65.000 0.00 0.00 0.00 4.17
541 1963 0.611062 TCTACCCTGTCCCTCGTGTG 60.611 60.000 0.00 0.00 0.00 3.82
542 1964 0.335361 ATCTACCCTGTCCCTCGTGT 59.665 55.000 0.00 0.00 0.00 4.49
564 1986 4.378978 CCTTAGGAGAGAATGCGATAGTCG 60.379 50.000 0.00 0.00 43.89 4.18
585 2007 1.895020 TTTCTGCACCCGCGATACCT 61.895 55.000 8.23 0.00 42.97 3.08
694 2116 0.250513 AAATGAGAGGCCTCGTGGTC 59.749 55.000 26.95 18.80 42.33 4.02
695 2117 0.693049 AAAATGAGAGGCCTCGTGGT 59.307 50.000 26.95 9.79 42.33 4.16
696 2118 1.089920 CAAAATGAGAGGCCTCGTGG 58.910 55.000 26.95 9.80 42.33 4.94
706 2331 7.882791 TCATGTTTTCTACCTAGCAAAATGAGA 59.117 33.333 0.00 0.00 0.00 3.27
734 2359 7.336427 GTGAAAGTTTCTGATCAGAGGATTGAT 59.664 37.037 23.92 9.76 40.40 2.57
770 2395 5.714333 TGTGTGTAGAAAATAACCCATGCAT 59.286 36.000 0.00 0.00 0.00 3.96
804 2444 7.178983 TGCTCTGGATGGAATAATTTTCAAAGT 59.821 33.333 0.00 0.00 0.00 2.66
911 2558 2.396955 CGTACGACCGAGCTCAGGT 61.397 63.158 24.15 24.15 46.16 4.00
1080 2758 4.057428 GCGCTGACCACCTCGTCT 62.057 66.667 0.00 0.00 33.70 4.18
1199 2900 1.069358 CGGAGGCCAGAGAGGAATAAC 59.931 57.143 5.01 0.00 41.22 1.89
1225 2926 3.000523 TGAACAAACGTAACACGAGAAGC 59.999 43.478 5.61 0.00 46.05 3.86
1258 2959 1.242076 CCAACTCCAAAGCACCTCTG 58.758 55.000 0.00 0.00 0.00 3.35
1259 2960 0.846693 ACCAACTCCAAAGCACCTCT 59.153 50.000 0.00 0.00 0.00 3.69
1261 2962 0.468029 CCACCAACTCCAAAGCACCT 60.468 55.000 0.00 0.00 0.00 4.00
1262 2963 2.041153 CCACCAACTCCAAAGCACC 58.959 57.895 0.00 0.00 0.00 5.01
1263 2964 1.363807 GCCACCAACTCCAAAGCAC 59.636 57.895 0.00 0.00 0.00 4.40
1264 2965 2.192861 CGCCACCAACTCCAAAGCA 61.193 57.895 0.00 0.00 0.00 3.91
1265 2966 1.856265 CTCGCCACCAACTCCAAAGC 61.856 60.000 0.00 0.00 0.00 3.51
1266 2967 1.237285 CCTCGCCACCAACTCCAAAG 61.237 60.000 0.00 0.00 0.00 2.77
1267 2968 1.228124 CCTCGCCACCAACTCCAAA 60.228 57.895 0.00 0.00 0.00 3.28
1364 3065 6.491476 ATCCAATGGATTGCGATCATTCGAA 61.491 40.000 9.36 0.00 43.07 3.71
1490 3204 7.824779 AGTTAGTTCCCAAGTTTAAGAGCTATG 59.175 37.037 0.00 0.00 0.00 2.23
1500 3214 5.589050 GTCAGACAAGTTAGTTCCCAAGTTT 59.411 40.000 0.00 0.00 0.00 2.66
1579 3293 5.178438 TGCAATTTTTACAAAGGAAATCGGC 59.822 36.000 0.00 0.00 0.00 5.54
1581 3295 7.171447 TGTGCAATTTTTACAAAGGAAATCG 57.829 32.000 0.00 0.00 0.00 3.34
1593 3307 8.409371 TCACTTACAACTGATGTGCAATTTTTA 58.591 29.630 0.34 0.00 43.77 1.52
1609 3323 9.185192 CTGAAATCCTGAAAATTCACTTACAAC 57.815 33.333 0.00 0.00 32.90 3.32
1622 3362 4.603131 AGGCTTATGCTGAAATCCTGAAA 58.397 39.130 0.13 0.00 39.59 2.69
1731 3473 2.548067 CCAGTACGAGCACAAGAAACCT 60.548 50.000 0.00 0.00 0.00 3.50
1869 3611 8.434392 ACTTAACTCACAACCTGGAAGTAAATA 58.566 33.333 0.00 0.00 0.00 1.40
1881 3623 6.791303 TGATGTCAAAACTTAACTCACAACC 58.209 36.000 0.00 0.00 0.00 3.77
1886 3628 6.486320 TGCATCTGATGTCAAAACTTAACTCA 59.514 34.615 18.19 0.89 0.00 3.41
1887 3629 6.902341 TGCATCTGATGTCAAAACTTAACTC 58.098 36.000 18.19 0.00 0.00 3.01
1919 3661 3.965379 TGACGTTAAACCTATGGCTGA 57.035 42.857 0.00 0.00 0.00 4.26
2055 3807 8.971073 AGGCTTATTAACAAATCTGTAAATGCT 58.029 29.630 0.00 0.00 33.45 3.79
2077 3829 5.760131 AGCCAACTGAGAAAATTATAGGCT 58.240 37.500 0.00 0.00 43.38 4.58
2095 3847 0.770557 AGGGAACAGGGTACAGCCAA 60.771 55.000 0.00 0.00 39.65 4.52
2096 3848 0.770557 AAGGGAACAGGGTACAGCCA 60.771 55.000 0.00 0.00 39.65 4.75
2143 4317 4.382754 CGCATGTAAAAGCAGAGAAAAACC 59.617 41.667 0.00 0.00 0.00 3.27
2148 4322 3.058983 CACACGCATGTAAAAGCAGAGAA 60.059 43.478 0.00 0.00 36.72 2.87
2166 4340 2.687935 TGAAAAGCCTGAGAAACCACAC 59.312 45.455 0.00 0.00 0.00 3.82
2167 4341 2.687935 GTGAAAAGCCTGAGAAACCACA 59.312 45.455 0.00 0.00 0.00 4.17
2168 4342 2.034685 GGTGAAAAGCCTGAGAAACCAC 59.965 50.000 0.00 0.00 0.00 4.16
2171 4345 1.613925 GGGGTGAAAAGCCTGAGAAAC 59.386 52.381 0.00 0.00 0.00 2.78
2350 4533 9.445786 AAATCGTGTGTGTTTCTAAATTTAGTG 57.554 29.630 21.69 2.04 32.61 2.74
2379 4562 7.326063 GCAGTTACTACAACAATTTCATGGTTC 59.674 37.037 0.00 0.00 0.00 3.62
2470 4664 2.016318 TCACAGCTAAATGATTGGCCG 58.984 47.619 0.00 0.00 43.48 6.13
2487 4681 1.349067 AGGGTGTAACTGGGACTCAC 58.651 55.000 0.00 0.00 36.74 3.51
2660 4854 8.571336 AGTTTCTGATAAAAACAAGACCATGAG 58.429 33.333 0.00 0.00 38.73 2.90
2672 4866 9.567848 GACAAGTCAAACAGTTTCTGATAAAAA 57.432 29.630 0.00 0.00 35.18 1.94
2834 5038 8.385111 GCATCAATAGACCACAATGAAAAATTG 58.615 33.333 0.00 0.00 35.29 2.32
2972 5217 6.597280 TCTTATGGGGCAAACATTTTTATTGC 59.403 34.615 1.29 1.29 46.60 3.56
2976 5221 8.040132 CAGAATCTTATGGGGCAAACATTTTTA 58.960 33.333 0.00 0.00 0.00 1.52
3067 5932 5.164138 CCAACATAAACGGCGTTAACATTTG 60.164 40.000 27.05 21.90 0.00 2.32
3081 5946 6.037610 CCTCTCTGCTGAATACCAACATAAAC 59.962 42.308 0.00 0.00 0.00 2.01
3134 6002 2.158475 TGTTCTCAAATGGGCAGAAGGT 60.158 45.455 0.00 0.00 0.00 3.50
3550 6459 6.410540 GGGTCTCACAGAAGAGATTGTATTT 58.589 40.000 0.00 0.00 45.61 1.40
3611 6520 8.627208 TTTCATCTTGATTCTAGCAGAAAAGT 57.373 30.769 10.10 0.00 37.82 2.66
3627 6536 7.703197 TGCATTAACAGCACATATTTCATCTTG 59.297 33.333 0.57 0.00 37.02 3.02
3628 6537 7.774134 TGCATTAACAGCACATATTTCATCTT 58.226 30.769 0.57 0.00 37.02 2.40
3659 6568 4.855531 AGATGGTTTCGTTTTGCTTGTAC 58.144 39.130 0.00 0.00 0.00 2.90
3692 6601 2.990740 AGAAAGGCCACCAACCAATA 57.009 45.000 5.01 0.00 0.00 1.90
3715 6627 2.239201 GTTAATGGCGCAGACGAAAAC 58.761 47.619 10.83 0.00 41.59 2.43
3721 6633 0.663153 GGGATGTTAATGGCGCAGAC 59.337 55.000 10.83 0.00 0.00 3.51
3727 6639 6.265196 TCAATGTTGATAGGGATGTTAATGGC 59.735 38.462 0.00 0.00 31.01 4.40
3746 6674 6.757947 CACAATCTCAAACTTTGGTTCAATGT 59.242 34.615 1.62 0.00 34.07 2.71
3898 6834 7.053316 TCATTCAAATAATTGATGGCCGATT 57.947 32.000 0.00 0.00 44.70 3.34
3979 6915 1.550072 TGTCTGATGCCATCTGAACGA 59.450 47.619 14.85 1.47 38.67 3.85
4123 7059 3.049778 TGGAGAGGGTTAGGGGGAATATT 60.050 47.826 0.00 0.00 0.00 1.28
4168 7104 4.640771 ACAAGAAAGGAAGTAGGCATGA 57.359 40.909 0.00 0.00 0.00 3.07
4368 7305 3.343617 CACCGGTTCATATGACCAGTTT 58.656 45.455 2.97 0.00 0.00 2.66


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

AutoCloner maintained by Alex Coulton.