Multiple sequence alignment - TraesCS6D01G291400

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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 TraesCS6D01G291400 chr6D 100.000 5996 0 0 1 5996 402115455 402121450 0.000000e+00 11073
1 TraesCS6D01G291400 chr6B 90.357 4729 216 116 311 4918 602821066 602825675 0.000000e+00 5986
2 TraesCS6D01G291400 chr6B 95.788 1021 24 8 4975 5995 602825685 602826686 0.000000e+00 1629
3 TraesCS6D01G291400 chr6B 83.117 308 21 12 1 306 602820748 602821026 9.980000e-63 252
4 TraesCS6D01G291400 chr6A 95.918 2695 79 23 3329 5995 548403487 548406178 0.000000e+00 4338
5 TraesCS6D01G291400 chr6A 90.265 3061 142 73 320 3295 548400501 548403490 0.000000e+00 3858
6 TraesCS6D01G291400 chr6A 83.857 223 17 11 64 282 548398653 548398860 1.710000e-45 195
7 TraesCS6D01G291400 chr5D 87.234 94 9 1 2152 2242 189931081 189930988 2.960000e-18 104
8 TraesCS6D01G291400 chr2D 87.234 94 9 1 2152 2242 477222213 477222120 2.960000e-18 104


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 TraesCS6D01G291400 chr6D 402115455 402121450 5995 False 11073.000000 11073 100.000000 1 5996 1 chr6D.!!$F1 5995
1 TraesCS6D01G291400 chr6B 602820748 602826686 5938 False 2622.333333 5986 89.754000 1 5995 3 chr6B.!!$F1 5994
2 TraesCS6D01G291400 chr6A 548398653 548406178 7525 False 2797.000000 4338 90.013333 64 5995 3 chr6A.!!$F1 5931

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
217 223 0.034337 AAAGTAGCGGAAGTGCGGAA 59.966 50.000 0.00 0.00 40.67 4.30 F
540 2182 0.659417 CGCAGCACAAGAGCACAAAG 60.659 55.000 0.00 0.00 36.85 2.77 F
1091 2800 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71 F
1092 2801 1.150536 CTCCTCCTCCTCCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63 F
1267 2991 1.152839 CCTCCTCGTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71 F
2687 4476 1.213537 CCCTGAATGCGCAAAGGTG 59.786 57.895 26.25 17.71 0.00 4.00 F
3446 5288 0.317020 GACGTGTTTGCAGCTTGGAC 60.317 55.000 0.00 0.00 0.00 4.02 F
4505 6347 0.389817 TTGATCTGGTTCAGCGGACG 60.390 55.000 0.00 0.00 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 3820 0.910088 CTCCCTTCTTTCCTCCGGGT 60.910 60.000 0.0 0.0 36.30 5.28 R
2521 4281 0.323302 TTACTCGGTTCATGCCTGCA 59.677 50.000 0.0 0.0 0.00 4.41 R
2820 4621 0.186386 ACCGTGATTTGGGTTGGGAA 59.814 50.000 0.0 0.0 30.73 3.97 R
2920 4722 0.459585 GCCCATACGCAAGAGAACGA 60.460 55.000 0.0 0.0 43.62 3.85 R
3174 4988 0.404040 TTCAAGGTGTCCACATCCCC 59.596 55.000 0.0 0.0 0.00 4.81 R
4655 6497 0.238289 CCGTTGTTGGCTGTGATGAC 59.762 55.000 0.0 0.0 0.00 3.06 R
4716 6570 1.524621 CCGCCTTAGCACCATCAGG 60.525 63.158 0.0 0.0 39.83 3.86 R
5751 7606 1.000394 GGCGTAAAGGTTTGGCACATT 60.000 47.619 0.0 0.0 39.30 2.71 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
36 37 0.889994 TCTTGCTGCGGAAATGCATT 59.110 45.000 5.99 5.99 45.26 3.56
37 38 1.273048 TCTTGCTGCGGAAATGCATTT 59.727 42.857 24.33 24.33 45.26 2.32
38 39 1.392168 CTTGCTGCGGAAATGCATTTG 59.608 47.619 28.67 16.19 45.26 2.32
39 40 1.015085 TGCTGCGGAAATGCATTTGC 61.015 50.000 28.67 28.35 45.26 3.68
107 109 0.965866 AGTCCGCAGATTGAGACCGA 60.966 55.000 0.00 0.00 0.00 4.69
128 130 1.750399 GCATCCCCACGAGCAATGT 60.750 57.895 0.00 0.00 0.00 2.71
135 137 2.030412 ACGAGCAATGTCACCGCA 59.970 55.556 0.00 0.00 0.00 5.69
184 190 2.189594 ATGGCATACATACGCAGCAT 57.810 45.000 0.00 0.00 38.26 3.79
204 210 3.993376 TACGGCGCGCCCAAAGTAG 62.993 63.158 42.07 28.48 0.00 2.57
211 217 4.716003 GCCCAAAGTAGCGGAAGT 57.284 55.556 0.00 0.00 0.00 3.01
212 218 2.171635 GCCCAAAGTAGCGGAAGTG 58.828 57.895 0.00 0.00 0.00 3.16
213 219 1.923227 GCCCAAAGTAGCGGAAGTGC 61.923 60.000 0.00 0.00 0.00 4.40
214 220 1.635663 CCCAAAGTAGCGGAAGTGCG 61.636 60.000 0.00 0.00 40.67 5.34
215 221 1.635663 CCAAAGTAGCGGAAGTGCGG 61.636 60.000 0.00 0.00 40.67 5.69
216 222 0.669318 CAAAGTAGCGGAAGTGCGGA 60.669 55.000 0.00 0.00 40.67 5.54
217 223 0.034337 AAAGTAGCGGAAGTGCGGAA 59.966 50.000 0.00 0.00 40.67 4.30
238 244 3.368190 CTCTGGAGAGCACAGCGGG 62.368 68.421 0.00 0.00 35.94 6.13
300 1876 3.037549 ACCCCATTCGGTAATTACGGTA 58.962 45.455 19.17 12.50 33.04 4.02
457 2098 3.035727 CGTCCAAACCAAACCCCG 58.964 61.111 0.00 0.00 0.00 5.73
525 2167 1.883084 GCGTTCATACCCTCCGCAG 60.883 63.158 0.00 0.00 43.53 5.18
531 2173 1.091771 CATACCCTCCGCAGCACAAG 61.092 60.000 0.00 0.00 0.00 3.16
532 2174 1.264749 ATACCCTCCGCAGCACAAGA 61.265 55.000 0.00 0.00 0.00 3.02
533 2175 1.888436 TACCCTCCGCAGCACAAGAG 61.888 60.000 0.00 0.00 0.00 2.85
534 2176 3.123620 CCTCCGCAGCACAAGAGC 61.124 66.667 0.00 0.00 0.00 4.09
535 2177 2.357881 CTCCGCAGCACAAGAGCA 60.358 61.111 0.00 0.00 36.85 4.26
536 2178 2.666190 TCCGCAGCACAAGAGCAC 60.666 61.111 0.00 0.00 36.85 4.40
537 2179 2.974148 CCGCAGCACAAGAGCACA 60.974 61.111 0.00 0.00 36.85 4.57
538 2180 2.545596 CCGCAGCACAAGAGCACAA 61.546 57.895 0.00 0.00 36.85 3.33
539 2181 1.356270 CGCAGCACAAGAGCACAAA 59.644 52.632 0.00 0.00 36.85 2.83
540 2182 0.659417 CGCAGCACAAGAGCACAAAG 60.659 55.000 0.00 0.00 36.85 2.77
757 2435 1.789576 TTGGTTGGCTCCCTCCCTTC 61.790 60.000 0.00 0.00 0.00 3.46
858 2549 2.026729 ACAAAACCCAACCAAACCCAAG 60.027 45.455 0.00 0.00 0.00 3.61
1029 2738 2.674754 GCGTTTCCATCCTCCCCA 59.325 61.111 0.00 0.00 0.00 4.96
1032 2741 1.562672 CGTTTCCATCCTCCCCACCT 61.563 60.000 0.00 0.00 0.00 4.00
1069 2778 3.315140 GGCTCCCTCGCCTATCCC 61.315 72.222 0.00 0.00 46.63 3.85
1072 2781 3.117648 TCCCTCGCCTATCCCCCT 61.118 66.667 0.00 0.00 0.00 4.79
1089 2798 1.541672 CTCCTCCTCCTCCTCCTCC 59.458 68.421 0.00 0.00 0.00 4.30
1090 2799 0.998945 CTCCTCCTCCTCCTCCTCCT 60.999 65.000 0.00 0.00 0.00 3.69
1091 2800 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1092 2801 1.150536 CTCCTCCTCCTCCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
1093 2802 2.520741 CCTCCTCCTCCTCCTCGC 60.521 72.222 0.00 0.00 0.00 5.03
1094 2803 2.520741 CTCCTCCTCCTCCTCGCC 60.521 72.222 0.00 0.00 0.00 5.54
1095 2804 4.507916 TCCTCCTCCTCCTCGCCG 62.508 72.222 0.00 0.00 0.00 6.46
1096 2805 4.824515 CCTCCTCCTCCTCGCCGT 62.825 72.222 0.00 0.00 0.00 5.68
1265 2989 2.835895 GCCTCCTCGTCCTCCTCC 60.836 72.222 0.00 0.00 0.00 4.30
1266 2990 3.011885 CCTCCTCGTCCTCCTCCT 58.988 66.667 0.00 0.00 0.00 3.69
1267 2991 1.152839 CCTCCTCGTCCTCCTCCTC 60.153 68.421 0.00 0.00 0.00 3.71
1390 3117 2.049063 GAAGGAGCTGACGCACGT 60.049 61.111 0.00 0.00 39.10 4.49
1721 3451 1.694169 GGGCTCCCTGGATTCCTCA 60.694 63.158 3.95 0.00 0.00 3.86
1898 3637 3.730761 GCATCGGCATCGGCATCC 61.731 66.667 0.00 0.00 43.71 3.51
2419 4166 4.212716 TCTCGTGCATTACTACTGGGTAT 58.787 43.478 0.00 0.00 0.00 2.73
2421 4168 5.472478 TCTCGTGCATTACTACTGGGTATAG 59.528 44.000 0.00 0.00 0.00 1.31
2422 4169 4.521639 TCGTGCATTACTACTGGGTATAGG 59.478 45.833 0.00 0.00 0.00 2.57
2423 4170 4.521639 CGTGCATTACTACTGGGTATAGGA 59.478 45.833 0.00 0.00 0.00 2.94
2424 4171 5.335740 CGTGCATTACTACTGGGTATAGGAG 60.336 48.000 0.00 0.00 34.65 3.69
2485 4241 1.649171 GTACGAACAGTGAGTCATGCG 59.351 52.381 0.00 0.00 0.00 4.73
2504 4264 1.271379 CGTGGAACCCTGAACCTTGAT 60.271 52.381 0.00 0.00 0.00 2.57
2510 4270 3.884037 ACCCTGAACCTTGATGAAAGT 57.116 42.857 0.00 0.00 33.66 2.66
2521 4281 5.192522 ACCTTGATGAAAGTAGGACCATCAT 59.807 40.000 0.00 0.00 43.10 2.45
2596 4385 6.247727 CTCGATTAGCATTCTAGTAGCTGA 57.752 41.667 13.82 8.14 39.30 4.26
2597 4386 6.247727 TCGATTAGCATTCTAGTAGCTGAG 57.752 41.667 13.82 0.00 39.30 3.35
2598 4387 5.765677 TCGATTAGCATTCTAGTAGCTGAGT 59.234 40.000 13.82 3.31 39.30 3.41
2600 4389 6.362016 CGATTAGCATTCTAGTAGCTGAGTTG 59.638 42.308 13.82 0.00 39.30 3.16
2657 4446 2.193447 GAAGATGATGCGCGTAGTGAA 58.807 47.619 8.43 0.00 43.07 3.18
2681 4470 1.876497 GAAAAGGCCCTGAATGCGCA 61.876 55.000 14.96 14.96 0.00 6.09
2682 4471 1.470996 AAAAGGCCCTGAATGCGCAA 61.471 50.000 17.11 0.00 0.00 4.85
2683 4472 1.470996 AAAGGCCCTGAATGCGCAAA 61.471 50.000 17.11 1.70 0.00 3.68
2684 4473 1.880819 AAGGCCCTGAATGCGCAAAG 61.881 55.000 17.11 12.80 0.00 2.77
2685 4474 2.182537 GCCCTGAATGCGCAAAGG 59.817 61.111 23.37 23.37 0.00 3.11
2686 4475 2.639327 GCCCTGAATGCGCAAAGGT 61.639 57.895 26.25 10.38 0.00 3.50
2687 4476 1.213537 CCCTGAATGCGCAAAGGTG 59.786 57.895 26.25 17.71 0.00 4.00
2920 4722 2.113139 CAGACGGCCACCTTTGGT 59.887 61.111 2.24 0.00 45.98 3.67
3042 4854 6.154445 AGTTCATTCACATTTGCTTTGCTAG 58.846 36.000 0.00 0.00 0.00 3.42
3117 4931 2.509052 TGATCGCGTAAGAATCTGGG 57.491 50.000 5.77 0.00 43.02 4.45
3123 4937 1.884235 CGTAAGAATCTGGGATGGGC 58.116 55.000 0.00 0.00 43.02 5.36
3127 4941 1.224592 GAATCTGGGATGGGCACGT 59.775 57.895 0.00 0.00 0.00 4.49
3130 4944 1.852157 ATCTGGGATGGGCACGTGTT 61.852 55.000 18.38 0.00 0.00 3.32
3174 4988 4.522022 GCAATGATGGGAGGATTTAGGAAG 59.478 45.833 0.00 0.00 0.00 3.46
3175 4989 5.075493 CAATGATGGGAGGATTTAGGAAGG 58.925 45.833 0.00 0.00 0.00 3.46
3186 5000 2.352561 TTAGGAAGGGGATGTGGACA 57.647 50.000 0.00 0.00 0.00 4.02
3231 5045 2.224314 CCCACTTTTCTTCGTCAGCTTC 59.776 50.000 0.00 0.00 0.00 3.86
3289 5103 3.126831 CGGTGACAAGAGAATCATAGCC 58.873 50.000 0.00 0.00 37.82 3.93
3296 5110 5.366460 ACAAGAGAATCATAGCCAGTGATG 58.634 41.667 0.00 0.00 36.49 3.07
3322 5136 4.749976 AGAGAATCGTAGCTGAAAGAACC 58.250 43.478 0.00 0.00 42.67 3.62
3334 5148 2.692273 AAAGAACCCGGCTGTGACCC 62.692 60.000 0.00 0.00 0.00 4.46
3366 5180 5.711976 ACATGATTGGCAACTATATTAGGCC 59.288 40.000 0.00 0.00 44.82 5.19
3385 5203 2.781945 CAGTGTTTCAGAAACTGGGC 57.218 50.000 23.57 12.73 41.90 5.36
3446 5288 0.317020 GACGTGTTTGCAGCTTGGAC 60.317 55.000 0.00 0.00 0.00 4.02
3785 5627 1.298014 CGCAGAGGCCTTCCTTCTT 59.702 57.895 6.77 0.00 44.46 2.52
3788 5630 0.898320 CAGAGGCCTTCCTTCTTCGA 59.102 55.000 6.77 0.00 44.46 3.71
3845 5687 1.019673 ATGCGCTGCTATTCAAGGTG 58.980 50.000 9.73 0.00 0.00 4.00
3956 5798 2.265739 CTGCTTGAGGCGGTGCTA 59.734 61.111 0.00 0.00 45.43 3.49
4052 5894 0.596600 TCAACGACGTGAAGAGCACC 60.597 55.000 0.00 0.00 44.85 5.01
4238 6080 2.185350 CGCGAGGACAGGCAGAAT 59.815 61.111 0.00 0.00 0.00 2.40
4310 6152 1.250328 CCAATGTGAAGAAGGCTGCA 58.750 50.000 0.50 0.00 0.00 4.41
4344 6186 1.618487 TGTGACTGCCAATGAATGCA 58.382 45.000 0.00 0.00 35.86 3.96
4505 6347 0.389817 TTGATCTGGTTCAGCGGACG 60.390 55.000 0.00 0.00 0.00 4.79
4580 6422 3.074412 GTTGTTCGTCATTGTGAGGGAT 58.926 45.455 0.51 0.00 33.45 3.85
4655 6497 1.112916 AAAAGAAGCCAACACCCCCG 61.113 55.000 0.00 0.00 0.00 5.73
4745 6599 2.925162 CTAAGGCGGTAGCTGGTGGC 62.925 65.000 0.00 0.00 44.37 5.01
4775 6629 1.076632 ACCACCGGCTCAAAAACCA 60.077 52.632 0.00 0.00 0.00 3.67
4899 6753 7.013823 AGTGATGAGGAATAGAATGTATGGG 57.986 40.000 0.00 0.00 0.00 4.00
5019 6873 8.215050 TGGTTCTTTTCTCCAGTTCTTTACATA 58.785 33.333 0.00 0.00 0.00 2.29
5085 6939 9.529325 CAGAAATTGAATTTGATGTGCAGATAT 57.471 29.630 8.03 0.00 31.47 1.63
5095 6949 4.094739 TGATGTGCAGATATCAACAAACCG 59.905 41.667 5.32 0.00 30.84 4.44
5495 7350 6.031471 ACAAAATTAACAACACGTTGGAGAC 58.969 36.000 14.07 0.00 44.45 3.36
5543 7398 7.380423 ACATACCTGAGCTAGTAAATCCATT 57.620 36.000 0.00 0.00 0.00 3.16
5621 7476 0.254178 CCCTCCATGTCAACCCTGAG 59.746 60.000 0.00 0.00 30.14 3.35
5668 7523 4.755266 ACTGGGTATCTATTTCGCAAGT 57.245 40.909 0.00 0.00 39.48 3.16
5690 7545 1.795768 TCTGTACGCCAAGAAGCAAG 58.204 50.000 0.00 0.00 0.00 4.01
5694 7549 2.224329 TGTACGCCAAGAAGCAAGGTAA 60.224 45.455 0.00 0.00 0.00 2.85
5700 7555 3.119352 GCCAAGAAGCAAGGTAAATGAGG 60.119 47.826 0.00 0.00 0.00 3.86
5751 7606 7.496346 AAAGACACAGGAGAATAGGAACATA 57.504 36.000 0.00 0.00 0.00 2.29
5805 7660 3.445805 GGAGATCGAGGAGTGAGTTTCTT 59.554 47.826 0.00 0.00 0.00 2.52
5909 7764 3.126858 TGATGCCTAAGAAAACGCATGAC 59.873 43.478 0.00 0.00 41.85 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.739035 CGCAGCAAGATTTCCCGAGTA 60.739 52.381 0.00 0.00 0.00 2.59
107 109 0.767375 ATTGCTCGTGGGGATGCTAT 59.233 50.000 0.00 0.00 0.00 2.97
238 244 1.597854 GGCTGTTTTTGCCCTTGCC 60.598 57.895 0.00 0.00 44.32 4.52
333 1951 0.036952 CAGTGAGCTGGTGGATCGTT 60.037 55.000 0.00 0.00 39.01 3.85
525 2167 3.259207 CACTACTTTGTGCTCTTGTGC 57.741 47.619 0.00 0.00 0.00 4.57
534 2176 3.568538 GCTCCAAATGCACTACTTTGTG 58.431 45.455 9.10 4.02 40.62 3.33
535 2177 2.226437 CGCTCCAAATGCACTACTTTGT 59.774 45.455 9.10 0.00 31.83 2.83
536 2178 2.855180 CGCTCCAAATGCACTACTTTG 58.145 47.619 3.93 3.93 33.20 2.77
537 2179 1.200020 GCGCTCCAAATGCACTACTTT 59.800 47.619 0.00 0.00 0.00 2.66
538 2180 0.804989 GCGCTCCAAATGCACTACTT 59.195 50.000 0.00 0.00 0.00 2.24
539 2181 1.361668 CGCGCTCCAAATGCACTACT 61.362 55.000 5.56 0.00 0.00 2.57
540 2182 1.060937 CGCGCTCCAAATGCACTAC 59.939 57.895 5.56 0.00 0.00 2.73
757 2435 2.027625 GAAGACGCGTTGAGTGGGG 61.028 63.158 15.53 0.00 33.90 4.96
858 2549 0.248296 TGCGTTTTGACTTGTTCGGC 60.248 50.000 0.00 0.00 0.00 5.54
1058 2767 1.608046 GAGGAGGGGGATAGGCGAG 60.608 68.421 0.00 0.00 0.00 5.03
1061 2770 1.229368 GAGGAGGAGGGGGATAGGC 60.229 68.421 0.00 0.00 0.00 3.93
1065 2774 2.416923 GGAGGAGGAGGAGGGGGAT 61.417 68.421 0.00 0.00 0.00 3.85
1069 2778 2.018086 AGGAGGAGGAGGAGGAGGG 61.018 68.421 0.00 0.00 0.00 4.30
1072 2781 0.996762 GAGGAGGAGGAGGAGGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
1265 2989 2.507992 CTGCGCTTCGTGGAGGAG 60.508 66.667 9.73 0.00 0.00 3.69
1266 2990 4.742201 GCTGCGCTTCGTGGAGGA 62.742 66.667 9.73 0.00 32.26 3.71
1715 3445 1.079405 GAACACGGCGGATGAGGAA 60.079 57.895 13.24 0.00 0.00 3.36
1880 3619 3.730761 GATGCCGATGCCGATGCC 61.731 66.667 0.00 0.00 38.22 4.40
1881 3620 3.730761 GGATGCCGATGCCGATGC 61.731 66.667 0.00 0.00 38.22 3.91
1882 3621 3.052082 GGGATGCCGATGCCGATG 61.052 66.667 0.00 0.00 38.22 3.84
1883 3622 3.244580 AGGGATGCCGATGCCGAT 61.245 61.111 0.00 0.00 44.79 4.18
1884 3623 4.240103 CAGGGATGCCGATGCCGA 62.240 66.667 0.00 0.00 44.79 5.54
2036 3781 2.930019 CTGGGTGCTGGTGGAGGA 60.930 66.667 0.00 0.00 0.00 3.71
2039 3784 2.930019 CCTCTGGGTGCTGGTGGA 60.930 66.667 0.00 0.00 0.00 4.02
2075 3820 0.910088 CTCCCTTCTTTCCTCCGGGT 60.910 60.000 0.00 0.00 36.30 5.28
2114 3859 3.646715 CCCTTCTTGCCACCGGGA 61.647 66.667 6.32 0.00 37.05 5.14
2204 3949 4.070552 AGCTTCGCCAGGTCGTCC 62.071 66.667 3.62 0.00 0.00 4.79
2340 4086 2.671914 CGGCAATGGTGAACTGAAATGG 60.672 50.000 0.00 0.00 0.00 3.16
2419 4166 3.492656 GCAATCAGTAATGACCGCTCCTA 60.493 47.826 8.06 0.00 0.00 2.94
2421 4168 1.599542 GCAATCAGTAATGACCGCTCC 59.400 52.381 8.06 0.00 0.00 4.70
2422 4169 2.279741 TGCAATCAGTAATGACCGCTC 58.720 47.619 14.46 0.00 0.00 5.03
2423 4170 2.401583 TGCAATCAGTAATGACCGCT 57.598 45.000 14.46 0.00 0.00 5.52
2424 4171 3.187227 CCTATGCAATCAGTAATGACCGC 59.813 47.826 8.32 8.32 0.00 5.68
2485 4241 2.162681 CATCAAGGTTCAGGGTTCCAC 58.837 52.381 0.00 0.00 0.00 4.02
2504 4264 3.370846 CCTGCATGATGGTCCTACTTTCA 60.371 47.826 0.00 0.00 0.00 2.69
2510 4270 1.142936 ATGCCTGCATGATGGTCCTA 58.857 50.000 3.36 0.00 35.03 2.94
2521 4281 0.323302 TTACTCGGTTCATGCCTGCA 59.677 50.000 0.00 0.00 0.00 4.41
2612 4401 7.022384 CAGTTTCTACACACTACAGCTACTAC 58.978 42.308 0.00 0.00 0.00 2.73
2614 4403 5.768662 TCAGTTTCTACACACTACAGCTACT 59.231 40.000 0.00 0.00 0.00 2.57
2657 4446 2.037641 GCATTCAGGGCCTTTTCAGTTT 59.962 45.455 1.32 0.00 0.00 2.66
2681 4470 6.976934 TTTTTCCTCTTCTAATGCACCTTT 57.023 33.333 0.00 0.00 0.00 3.11
2819 4620 0.601057 CCGTGATTTGGGTTGGGAAC 59.399 55.000 0.00 0.00 0.00 3.62
2820 4621 0.186386 ACCGTGATTTGGGTTGGGAA 59.814 50.000 0.00 0.00 30.73 3.97
2821 4622 0.538516 CACCGTGATTTGGGTTGGGA 60.539 55.000 0.00 0.00 33.23 4.37
2920 4722 0.459585 GCCCATACGCAAGAGAACGA 60.460 55.000 0.00 0.00 43.62 3.85
3042 4854 2.350772 CGGTTGATTCTGTCAAGGTTGC 60.351 50.000 0.00 0.00 46.99 4.17
3044 4856 3.208747 ACGGTTGATTCTGTCAAGGTT 57.791 42.857 0.00 0.00 46.99 3.50
3123 4937 0.599991 TGGAGCTACAGCAACACGTG 60.600 55.000 15.48 15.48 45.16 4.49
3127 4941 1.270839 GGAACTGGAGCTACAGCAACA 60.271 52.381 26.52 1.16 45.16 3.33
3130 4944 1.055849 TTGGAACTGGAGCTACAGCA 58.944 50.000 26.52 13.19 45.16 4.41
3139 4953 2.827322 CCATCATTGCTTTGGAACTGGA 59.173 45.455 0.00 0.00 31.94 3.86
3174 4988 0.404040 TTCAAGGTGTCCACATCCCC 59.596 55.000 0.00 0.00 0.00 4.81
3175 4989 1.073923 AGTTCAAGGTGTCCACATCCC 59.926 52.381 0.00 0.00 0.00 3.85
3231 5045 3.062763 CAGAGCTAATAATGTCCAGCGG 58.937 50.000 0.00 0.00 39.04 5.52
3264 5078 1.066858 TGATTCTCTTGTCACCGGAGC 60.067 52.381 9.46 0.00 0.00 4.70
3269 5083 4.125703 CTGGCTATGATTCTCTTGTCACC 58.874 47.826 0.00 0.00 0.00 4.02
3272 5086 5.016051 TCACTGGCTATGATTCTCTTGTC 57.984 43.478 0.00 0.00 0.00 3.18
3274 5088 5.608449 TCATCACTGGCTATGATTCTCTTG 58.392 41.667 1.87 0.00 34.49 3.02
3289 5103 6.581919 CAGCTACGATTCTCTTATCATCACTG 59.418 42.308 0.00 0.00 0.00 3.66
3296 5110 7.168469 GGTTCTTTCAGCTACGATTCTCTTATC 59.832 40.741 0.00 0.00 0.00 1.75
3322 5136 2.556840 ATCCAATGGGTCACAGCCGG 62.557 60.000 0.00 0.00 38.98 6.13
3334 5148 5.524971 AGTTGCCAATCATGTATCCAATG 57.475 39.130 0.00 0.00 0.00 2.82
3352 5166 7.047891 TCTGAAACACTGGCCTAATATAGTTG 58.952 38.462 3.32 0.00 0.00 3.16
3366 5180 2.301346 AGCCCAGTTTCTGAAACACTG 58.699 47.619 28.99 20.88 43.79 3.66
3446 5288 2.892425 GCCTCGATGGTGCCTTCG 60.892 66.667 17.10 17.10 42.48 3.79
3785 5627 2.358369 ACGTCGAGCAGGAGTCGA 60.358 61.111 0.00 0.00 43.97 4.20
3788 5630 4.057428 GGCACGTCGAGCAGGAGT 62.057 66.667 16.44 0.00 0.00 3.85
4037 5879 1.154016 ATCGGTGCTCTTCACGTCG 60.154 57.895 0.00 0.00 46.56 5.12
4067 5909 1.344438 TCGATGACAAAGTGGAGCAGT 59.656 47.619 0.00 0.00 0.00 4.40
4238 6080 4.081087 GGCAATCCTAGGTTCAAGTACTCA 60.081 45.833 9.08 0.00 0.00 3.41
4310 6152 2.891580 AGTCACATCGTAGTCCACAGTT 59.108 45.455 0.00 0.00 0.00 3.16
4344 6186 2.674177 CGAGTCGGTTGCCTAAGATTGT 60.674 50.000 4.10 0.00 0.00 2.71
4505 6347 1.067212 CCTGCATGGTAGTACTCCGTC 59.933 57.143 0.00 0.00 0.00 4.79
4580 6422 1.506028 GGTCCACCATCCCCAGGAAA 61.506 60.000 0.00 0.00 34.34 3.13
4655 6497 0.238289 CCGTTGTTGGCTGTGATGAC 59.762 55.000 0.00 0.00 0.00 3.06
4682 6524 2.202236 CTTCAGCTGGCCCCTTAGCA 62.202 60.000 15.13 0.00 42.29 3.49
4716 6570 1.524621 CCGCCTTAGCACCATCAGG 60.525 63.158 0.00 0.00 39.83 3.86
4769 6623 2.031870 GCTTCTTCTGGTGGTGGTTTT 58.968 47.619 0.00 0.00 0.00 2.43
4775 6629 2.093235 GCTATCTGCTTCTTCTGGTGGT 60.093 50.000 0.00 0.00 38.95 4.16
4899 6753 5.622233 GCAAACAATCTCCATTTACACCTCC 60.622 44.000 0.00 0.00 0.00 4.30
5019 6873 3.685139 ACTGTTGTCGACATGGATCTT 57.315 42.857 20.80 0.00 37.69 2.40
5495 7350 2.989909 TGGGTGTGCAGATTCTGTATG 58.010 47.619 14.90 0.00 33.43 2.39
5621 7476 1.607801 GAATGGTTGAAGCCTGGGCC 61.608 60.000 8.11 0.00 43.17 5.80
5668 7523 3.603158 TGCTTCTTGGCGTACAGATAA 57.397 42.857 0.00 0.00 34.52 1.75
5690 7545 5.105877 GCCCTTGTTACTTTCCTCATTTACC 60.106 44.000 0.00 0.00 0.00 2.85
5694 7549 4.112634 TGCCCTTGTTACTTTCCTCATT 57.887 40.909 0.00 0.00 0.00 2.57
5700 7555 6.569179 TCAATAGTTGCCCTTGTTACTTTC 57.431 37.500 0.00 0.00 0.00 2.62
5751 7606 1.000394 GGCGTAAAGGTTTGGCACATT 60.000 47.619 0.00 0.00 39.30 2.71
5805 7660 9.162764 GGTGTCATAAACTATTTAGAAGAGCAA 57.837 33.333 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.