Multiple sequence alignment - TraesCS6D01G221300

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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 TraesCS6D01G221300 chr6D 100.000 2567 0 0 1 2567 312070573 312068007 0.000000e+00 4741
1 TraesCS6D01G221300 chr6B 92.599 1743 63 20 618 2338 514694739 514696437 0.000000e+00 2444
2 TraesCS6D01G221300 chr6B 92.814 334 17 6 294 620 514694080 514694413 6.430000e-131 477
3 TraesCS6D01G221300 chr6A 92.912 1679 50 17 691 2340 448651525 448649887 0.000000e+00 2377
4 TraesCS6D01G221300 chr6A 92.488 426 23 7 262 681 448652680 448652258 3.650000e-168 601
5 TraesCS6D01G221300 chr6A 80.702 228 24 6 40 247 448655170 448654943 2.640000e-35 159
6 TraesCS6D01G221300 chr6A 81.959 194 19 12 2388 2567 448646466 448646275 1.590000e-32 150


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 TraesCS6D01G221300 chr6D 312068007 312070573 2566 True 4741.00 4741 100.00000 1 2567 1 chr6D.!!$R1 2566
1 TraesCS6D01G221300 chr6B 514694080 514696437 2357 False 1460.50 2444 92.70650 294 2338 2 chr6B.!!$F1 2044
2 TraesCS6D01G221300 chr6A 448646275 448655170 8895 True 821.75 2377 87.01525 40 2567 4 chr6A.!!$R1 2527

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
188 209 0.036105 GGGAATTTGGACGTACGGGT 60.036 55.0 21.06 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1979 5344 0.110599 CTCGTATCCACTCTAGCGCG 60.111 60.0 0.0 0.0 0.0 6.86 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
21 22 3.291584 TGCATAAACAACCAGGAACACA 58.708 40.909 0.00 0.00 0.00 3.72
22 23 3.701542 TGCATAAACAACCAGGAACACAA 59.298 39.130 0.00 0.00 0.00 3.33
23 24 4.202101 TGCATAAACAACCAGGAACACAAG 60.202 41.667 0.00 0.00 0.00 3.16
24 25 4.202111 GCATAAACAACCAGGAACACAAGT 60.202 41.667 0.00 0.00 0.00 3.16
25 26 3.866883 AAACAACCAGGAACACAAGTG 57.133 42.857 0.00 0.00 0.00 3.16
27 28 3.637911 ACAACCAGGAACACAAGTGTA 57.362 42.857 6.24 0.00 44.13 2.90
28 29 4.164843 ACAACCAGGAACACAAGTGTAT 57.835 40.909 6.24 0.00 44.13 2.29
29 30 4.532834 ACAACCAGGAACACAAGTGTATT 58.467 39.130 6.24 0.00 44.13 1.89
30 31 4.953579 ACAACCAGGAACACAAGTGTATTT 59.046 37.500 6.24 0.00 44.13 1.40
31 32 5.420739 ACAACCAGGAACACAAGTGTATTTT 59.579 36.000 6.24 0.00 44.13 1.82
32 33 6.071051 ACAACCAGGAACACAAGTGTATTTTT 60.071 34.615 6.24 0.00 44.13 1.94
56 57 6.008696 TCCAATTCGGTTCCCTATTTATGT 57.991 37.500 0.00 0.00 35.57 2.29
59 60 3.202829 TCGGTTCCCTATTTATGTGCC 57.797 47.619 0.00 0.00 0.00 5.01
60 61 2.775384 TCGGTTCCCTATTTATGTGCCT 59.225 45.455 0.00 0.00 0.00 4.75
61 62 3.139077 CGGTTCCCTATTTATGTGCCTC 58.861 50.000 0.00 0.00 0.00 4.70
62 63 3.139077 GGTTCCCTATTTATGTGCCTCG 58.861 50.000 0.00 0.00 0.00 4.63
63 64 3.433173 GGTTCCCTATTTATGTGCCTCGT 60.433 47.826 0.00 0.00 0.00 4.18
70 71 2.902705 TTATGTGCCTCGTGGGATAC 57.097 50.000 5.54 2.65 35.69 2.24
72 73 0.465705 ATGTGCCTCGTGGGATACAG 59.534 55.000 5.54 0.00 37.22 2.74
75 76 0.535335 TGCCTCGTGGGATACAGAAC 59.465 55.000 5.54 0.00 37.23 3.01
77 78 1.100510 CCTCGTGGGATACAGAACGA 58.899 55.000 0.00 0.00 43.27 3.85
79 80 1.830279 TCGTGGGATACAGAACGAGT 58.170 50.000 0.00 0.00 41.51 4.18
80 81 1.471287 TCGTGGGATACAGAACGAGTG 59.529 52.381 0.00 0.00 41.51 3.51
81 82 1.469251 CGTGGGATACAGAACGAGTGG 60.469 57.143 0.00 0.00 40.54 4.00
87 91 2.005370 TACAGAACGAGTGGAAGGGT 57.995 50.000 0.00 0.00 0.00 4.34
92 96 1.550976 GAACGAGTGGAAGGGTCAGAT 59.449 52.381 0.00 0.00 0.00 2.90
96 100 2.417924 CGAGTGGAAGGGTCAGATTGAG 60.418 54.545 0.00 0.00 0.00 3.02
110 114 3.487574 CAGATTGAGAAATACGCGGACTC 59.512 47.826 12.47 5.67 0.00 3.36
112 116 2.846039 TGAGAAATACGCGGACTCTC 57.154 50.000 20.50 20.50 34.40 3.20
113 117 1.063616 TGAGAAATACGCGGACTCTCG 59.936 52.381 21.36 0.00 36.19 4.04
127 131 2.045340 CTCGGCGGGATTTTGGGT 60.045 61.111 0.00 0.00 0.00 4.51
139 143 0.820074 TTTTGGGTGCTACACGGTGG 60.820 55.000 13.48 0.00 34.83 4.61
157 178 1.013596 GGTGGCCAAAACTGTTTTGC 58.986 50.000 30.87 25.70 46.58 3.68
176 197 1.824852 GCATCCGGTTTGAGGGAATTT 59.175 47.619 0.00 0.00 35.60 1.82
181 202 1.199097 CGGTTTGAGGGAATTTGGACG 59.801 52.381 0.00 0.00 0.00 4.79
182 203 2.235891 GGTTTGAGGGAATTTGGACGT 58.764 47.619 0.00 0.00 0.00 4.34
186 207 1.066716 TGAGGGAATTTGGACGTACGG 60.067 52.381 21.06 1.43 0.00 4.02
187 208 0.251073 AGGGAATTTGGACGTACGGG 59.749 55.000 21.06 0.00 0.00 5.28
188 209 0.036105 GGGAATTTGGACGTACGGGT 60.036 55.000 21.06 0.00 0.00 5.28
192 213 2.368655 ATTTGGACGTACGGGTACAC 57.631 50.000 21.06 3.39 35.87 2.90
247 268 0.108377 TGTCCGAACATGATGGTCCG 60.108 55.000 4.66 0.00 27.88 4.79
258 316 0.390860 GATGGTCCGGTCCTCATCAG 59.609 60.000 18.85 0.00 36.82 2.90
277 2546 3.005684 TCAGGCTTATGTGGCAAACTTTG 59.994 43.478 0.00 0.00 34.73 2.77
306 2575 9.877178 AACAACCATAAAACAAGTGAAAATGTA 57.123 25.926 0.00 0.00 0.00 2.29
367 2643 4.753516 AACATGACAATGGTCTCCGATA 57.246 40.909 0.00 0.00 44.61 2.92
429 2706 5.677319 TTACTGCTGCACCTTAAGTAGAT 57.323 39.130 0.00 0.00 31.37 1.98
470 2752 4.129380 CACACAGAGGATTGAACACTTGA 58.871 43.478 0.00 0.00 0.00 3.02
536 2818 4.207224 CGTCTTTTTGATACGCTCGATGAT 59.793 41.667 0.00 0.00 0.00 2.45
537 2819 5.398416 CGTCTTTTTGATACGCTCGATGATA 59.602 40.000 0.00 0.00 0.00 2.15
550 2832 1.403382 CGATGATATGACGAGGGGCAG 60.403 57.143 0.00 0.00 0.00 4.85
565 2847 2.632996 GGGGCAGGAAACTTTAAAAGCT 59.367 45.455 0.00 0.00 40.21 3.74
636 3246 4.481368 AGTAAGTAACGGCATCCATCAA 57.519 40.909 0.00 0.00 0.00 2.57
675 3285 5.313772 AGGGCATGGTACTACTCTACTCTAT 59.686 44.000 0.00 0.00 0.00 1.98
854 4187 4.069232 CAGCCCGTCAGCTCCGAA 62.069 66.667 3.94 0.00 42.61 4.30
865 4198 3.187432 GTCAGCTCCGAAGAAAGAAAAGG 59.813 47.826 0.00 0.00 0.00 3.11
878 4211 7.526142 AGAAAGAAAAGGAAGAAACCATACC 57.474 36.000 0.00 0.00 0.00 2.73
889 4222 4.479158 AGAAACCATACCAAAAGCCAAGA 58.521 39.130 0.00 0.00 0.00 3.02
997 4330 0.667993 GCACTCTCCAGAGATCGAGG 59.332 60.000 10.68 0.00 44.74 4.63
998 4331 0.667993 CACTCTCCAGAGATCGAGGC 59.332 60.000 10.68 0.00 44.74 4.70
999 4332 0.467290 ACTCTCCAGAGATCGAGGCC 60.467 60.000 10.68 0.00 44.74 5.19
1000 4333 0.467106 CTCTCCAGAGATCGAGGCCA 60.467 60.000 5.01 0.00 44.74 5.36
1001 4334 0.187117 TCTCCAGAGATCGAGGCCAT 59.813 55.000 5.01 0.00 31.41 4.40
1170 4503 1.195442 TCTCCAACGTGGCCACCATA 61.195 55.000 29.95 10.28 37.47 2.74
1636 4981 0.882474 GTCACTCTGTCTGTACCGCT 59.118 55.000 0.00 0.00 0.00 5.52
1792 5137 0.660595 AGCTCGGATCGTAATTCGCG 60.661 55.000 0.00 0.00 39.67 5.87
1807 5152 1.227350 CGCGATCATCCCTCTTGCA 60.227 57.895 0.00 0.00 0.00 4.08
1822 5167 5.454329 CCCTCTTGCATTCTCATCTCATGTA 60.454 44.000 0.00 0.00 0.00 2.29
1839 5184 4.858140 TCATGTAAAACTTGCATTGCATCG 59.142 37.500 12.95 9.34 38.76 3.84
1845 5190 1.135972 ACTTGCATTGCATCGTTCGAC 60.136 47.619 12.95 0.00 38.76 4.20
1854 5199 1.909376 CATCGTTCGACTCATCCGTT 58.091 50.000 0.00 0.00 0.00 4.44
1868 5213 1.135315 CCGTTGGATTCTTGCGCAG 59.865 57.895 11.31 5.25 0.00 5.18
1890 5255 2.016318 CGTTGATGAAGGCCTGCATTA 58.984 47.619 27.81 21.11 0.00 1.90
1906 5271 1.603802 CATTATTTGGCGTCCGAGCAT 59.396 47.619 0.00 0.00 39.27 3.79
1933 5298 2.603892 GCTCGTCGTCAGTGACAAACTA 60.604 50.000 22.66 10.98 36.83 2.24
1977 5342 2.819550 GGATTCCTTCCGGCGCTA 59.180 61.111 7.64 0.00 33.93 4.26
1978 5343 1.594564 GGATTCCTTCCGGCGCTAC 60.595 63.158 7.64 0.00 33.93 3.58
1979 5344 1.594564 GATTCCTTCCGGCGCTACC 60.595 63.158 7.64 0.00 0.00 3.18
2344 5714 2.464865 CTGACGAAGCTAGTATGTGGC 58.535 52.381 0.00 0.00 0.00 5.01
2345 5715 2.099921 CTGACGAAGCTAGTATGTGGCT 59.900 50.000 0.00 0.00 37.99 4.75
2346 5716 2.099263 TGACGAAGCTAGTATGTGGCTC 59.901 50.000 0.00 0.00 35.06 4.70
2349 5719 2.544694 CGAAGCTAGTATGTGGCTCAGG 60.545 54.545 0.00 0.00 35.06 3.86
2350 5720 0.755686 AGCTAGTATGTGGCTCAGGC 59.244 55.000 0.00 0.00 37.82 4.85
2351 5721 0.755686 GCTAGTATGTGGCTCAGGCT 59.244 55.000 0.00 0.00 38.73 4.58
2352 5722 1.964223 GCTAGTATGTGGCTCAGGCTA 59.036 52.381 0.00 0.00 38.73 3.93
2358 5728 3.935993 GTGGCTCAGGCTACTCAAA 57.064 52.632 0.00 0.00 44.80 2.69
2359 5729 2.409948 GTGGCTCAGGCTACTCAAAT 57.590 50.000 0.00 0.00 44.80 2.32
2360 5730 3.543680 GTGGCTCAGGCTACTCAAATA 57.456 47.619 0.00 0.00 44.80 1.40
2361 5731 3.873910 GTGGCTCAGGCTACTCAAATAA 58.126 45.455 0.00 0.00 44.80 1.40
2362 5732 3.873952 GTGGCTCAGGCTACTCAAATAAG 59.126 47.826 0.00 0.00 44.80 1.73
2365 5735 4.133078 GCTCAGGCTACTCAAATAAGCAT 58.867 43.478 0.00 0.00 38.01 3.79
2366 5736 5.300752 GCTCAGGCTACTCAAATAAGCATA 58.699 41.667 0.00 0.00 38.01 3.14
2367 5737 5.936956 GCTCAGGCTACTCAAATAAGCATAT 59.063 40.000 0.00 0.00 38.01 1.78
2369 5739 7.066307 TCAGGCTACTCAAATAAGCATATCA 57.934 36.000 0.00 0.00 38.01 2.15
2371 5741 8.815912 TCAGGCTACTCAAATAAGCATATCATA 58.184 33.333 0.00 0.00 38.01 2.15
2372 5742 8.877779 CAGGCTACTCAAATAAGCATATCATAC 58.122 37.037 0.00 0.00 38.01 2.39
2373 5743 8.820831 AGGCTACTCAAATAAGCATATCATACT 58.179 33.333 0.00 0.00 38.01 2.12
2391 5761 8.686397 ATCATACTACTAGTATACGACAGTCG 57.314 38.462 21.62 21.62 41.47 4.18
2392 5762 6.584184 TCATACTACTAGTATACGACAGTCGC 59.416 42.308 23.09 6.53 40.34 5.19
2394 5764 4.981674 ACTACTAGTATACGACAGTCGCTC 59.018 45.833 23.09 10.45 45.12 5.03
2396 5766 2.034104 AGTATACGACAGTCGCTCCA 57.966 50.000 23.09 6.26 45.12 3.86
2397 5767 2.573369 AGTATACGACAGTCGCTCCAT 58.427 47.619 23.09 12.88 45.12 3.41
2400 9142 2.273370 TACGACAGTCGCTCCATTTC 57.727 50.000 23.09 0.00 45.12 2.17
2412 9154 8.031864 CAGTCGCTCCATTTCTATATACAAGAT 58.968 37.037 0.00 0.00 0.00 2.40
2415 9157 8.246871 TCGCTCCATTTCTATATACAAGATCAG 58.753 37.037 0.00 0.00 0.00 2.90
2417 9159 9.364989 GCTCCATTTCTATATACAAGATCAGAC 57.635 37.037 0.00 0.00 0.00 3.51
2457 9204 7.352739 AGATAAAATTTAATAACGGCTCTGCG 58.647 34.615 0.00 0.00 0.00 5.18
2459 9206 5.554822 AAATTTAATAACGGCTCTGCGAA 57.445 34.783 0.00 0.00 0.00 4.70
2465 9212 1.878656 AACGGCTCTGCGAACTAGCT 61.879 55.000 0.00 0.00 36.48 3.32
2533 9289 9.525826 AATTGAGTGGATATGAGAAAGAAAGTT 57.474 29.630 0.00 0.00 0.00 2.66
2538 9294 6.803807 GTGGATATGAGAAAGAAAGTTGTTGC 59.196 38.462 0.00 0.00 0.00 4.17
2558 9314 5.503662 TGCATGTGTCATTATCATCCAAC 57.496 39.130 0.00 0.00 0.00 3.77
2562 9318 4.198530 TGTGTCATTATCATCCAACGCAT 58.801 39.130 0.00 0.00 0.00 4.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.291584 TGTGTTCCTGGTTGTTTATGCA 58.708 40.909 0.00 0.00 0.00 3.96
1 2 4.202111 ACTTGTGTTCCTGGTTGTTTATGC 60.202 41.667 0.00 0.00 0.00 3.14
2 3 5.163561 ACACTTGTGTTCCTGGTTGTTTATG 60.164 40.000 0.00 0.00 0.00 1.90
3 4 4.953579 ACACTTGTGTTCCTGGTTGTTTAT 59.046 37.500 0.00 0.00 0.00 1.40
4 5 4.337145 ACACTTGTGTTCCTGGTTGTTTA 58.663 39.130 0.00 0.00 0.00 2.01
5 6 3.161866 ACACTTGTGTTCCTGGTTGTTT 58.838 40.909 0.00 0.00 0.00 2.83
6 7 2.802719 ACACTTGTGTTCCTGGTTGTT 58.197 42.857 0.00 0.00 0.00 2.83
7 8 2.507407 ACACTTGTGTTCCTGGTTGT 57.493 45.000 0.00 0.00 0.00 3.32
8 9 5.514274 AAATACACTTGTGTTCCTGGTTG 57.486 39.130 11.80 0.00 0.00 3.77
9 10 6.538945 AAAAATACACTTGTGTTCCTGGTT 57.461 33.333 11.80 0.00 0.00 3.67
51 52 2.102420 CTGTATCCCACGAGGCACATAA 59.898 50.000 0.00 0.00 31.97 1.90
56 57 0.535335 GTTCTGTATCCCACGAGGCA 59.465 55.000 0.00 0.00 34.51 4.75
60 61 1.471287 CACTCGTTCTGTATCCCACGA 59.529 52.381 0.00 0.00 39.27 4.35
61 62 1.469251 CCACTCGTTCTGTATCCCACG 60.469 57.143 0.00 0.00 0.00 4.94
62 63 1.822990 TCCACTCGTTCTGTATCCCAC 59.177 52.381 0.00 0.00 0.00 4.61
63 64 2.225382 TCCACTCGTTCTGTATCCCA 57.775 50.000 0.00 0.00 0.00 4.37
70 71 0.679505 TGACCCTTCCACTCGTTCTG 59.320 55.000 0.00 0.00 0.00 3.02
72 73 0.966920 TCTGACCCTTCCACTCGTTC 59.033 55.000 0.00 0.00 0.00 3.95
75 76 1.550524 TCAATCTGACCCTTCCACTCG 59.449 52.381 0.00 0.00 0.00 4.18
77 78 2.907892 TCTCAATCTGACCCTTCCACT 58.092 47.619 0.00 0.00 0.00 4.00
78 79 3.703001 TTCTCAATCTGACCCTTCCAC 57.297 47.619 0.00 0.00 0.00 4.02
79 80 4.934797 ATTTCTCAATCTGACCCTTCCA 57.065 40.909 0.00 0.00 0.00 3.53
80 81 4.811557 CGTATTTCTCAATCTGACCCTTCC 59.188 45.833 0.00 0.00 0.00 3.46
81 82 4.271291 GCGTATTTCTCAATCTGACCCTTC 59.729 45.833 0.00 0.00 0.00 3.46
87 91 3.130516 AGTCCGCGTATTTCTCAATCTGA 59.869 43.478 4.92 0.00 0.00 3.27
92 96 2.477357 CGAGAGTCCGCGTATTTCTCAA 60.477 50.000 19.87 0.00 35.22 3.02
96 100 1.207377 GCCGAGAGTCCGCGTATTTC 61.207 60.000 4.92 0.00 33.68 2.17
110 114 2.045340 ACCCAAAATCCCGCCGAG 60.045 61.111 0.00 0.00 0.00 4.63
112 116 4.128388 GCACCCAAAATCCCGCCG 62.128 66.667 0.00 0.00 0.00 6.46
113 117 1.379309 TAGCACCCAAAATCCCGCC 60.379 57.895 0.00 0.00 0.00 6.13
127 131 4.323477 GGCCACCACCGTGTAGCA 62.323 66.667 0.00 0.00 38.41 3.49
145 149 3.535280 AACCGGATGCAAAACAGTTTT 57.465 38.095 9.46 5.37 0.00 2.43
157 178 2.166254 CCAAATTCCCTCAAACCGGATG 59.834 50.000 9.46 7.12 0.00 3.51
176 197 3.680156 GGTGTACCCGTACGTCCA 58.320 61.111 15.21 2.00 38.85 4.02
186 207 1.574702 GCCTCAAACAGCGGTGTACC 61.575 60.000 22.18 2.34 35.08 3.34
187 208 1.574702 GGCCTCAAACAGCGGTGTAC 61.575 60.000 22.18 6.48 35.08 2.90
188 209 1.302192 GGCCTCAAACAGCGGTGTA 60.302 57.895 22.18 4.43 35.08 2.90
192 213 4.659172 TGGGGCCTCAAACAGCGG 62.659 66.667 0.25 0.00 0.00 5.52
247 268 2.486191 CCACATAAGCCTGATGAGGACC 60.486 54.545 0.77 0.00 42.93 4.46
277 2546 4.602995 TCACTTGTTTTATGGTTGTTCGC 58.397 39.130 0.00 0.00 0.00 4.70
278 2547 7.513190 TTTTCACTTGTTTTATGGTTGTTCG 57.487 32.000 0.00 0.00 0.00 3.95
306 2575 7.254319 CCAGTAATTTTCACGTATCGCATTAGT 60.254 37.037 0.00 0.00 0.00 2.24
313 2582 7.925703 ATACTCCAGTAATTTTCACGTATCG 57.074 36.000 0.00 0.00 33.76 2.92
367 2643 1.084018 TTTCTCCCTCCCTGGCAAAT 58.916 50.000 0.00 0.00 0.00 2.32
429 2706 7.335673 TCTGTGTGAGTCTGTTTGATGTTTTAA 59.664 33.333 0.00 0.00 0.00 1.52
470 2752 2.674380 CCAAGAGCCGCAAAGCCT 60.674 61.111 0.00 0.00 0.00 4.58
536 2818 0.539986 GTTTCCTGCCCCTCGTCATA 59.460 55.000 0.00 0.00 0.00 2.15
537 2819 1.201429 AGTTTCCTGCCCCTCGTCAT 61.201 55.000 0.00 0.00 0.00 3.06
550 2832 8.304596 AGGTTAATGCTAGCTTTTAAAGTTTCC 58.695 33.333 19.68 15.82 0.00 3.13
636 3246 3.130734 TGCCCTACTTCCTAGACCAAT 57.869 47.619 0.00 0.00 0.00 3.16
675 3285 7.170277 TGTTCCATCAGAATTCAGATTCAGAA 58.830 34.615 10.40 10.74 43.35 3.02
854 4187 7.066781 TGGTATGGTTTCTTCCTTTTCTTTCT 58.933 34.615 0.00 0.00 0.00 2.52
865 4198 4.864704 TGGCTTTTGGTATGGTTTCTTC 57.135 40.909 0.00 0.00 0.00 2.87
878 4211 1.070445 TGGCAATGGTCTTGGCTTTTG 59.930 47.619 11.95 0.00 44.21 2.44
889 4222 0.105760 TGTCTGGGTTTGGCAATGGT 60.106 50.000 0.00 0.00 0.00 3.55
1017 4350 2.203294 GAGGCGGTGTGGTTGGTT 60.203 61.111 0.00 0.00 0.00 3.67
1118 4451 3.289211 TGGAGTAGGGGCCCCAGA 61.289 66.667 42.48 27.36 38.92 3.86
1170 4503 1.445095 GCAGGCGAGGATGATGAGT 59.555 57.895 0.00 0.00 0.00 3.41
1333 4678 0.250513 GCCTCCACAGAGAATTCGGT 59.749 55.000 0.00 0.00 43.39 4.69
1636 4981 2.802247 CACTTGATGTCGCTTCTTGTCA 59.198 45.455 0.00 0.00 0.00 3.58
1792 5137 4.082665 TGAGAATGCAAGAGGGATGATC 57.917 45.455 0.00 0.00 0.00 2.92
1807 5152 7.692460 TGCAAGTTTTACATGAGATGAGAAT 57.308 32.000 0.00 0.00 0.00 2.40
1822 5167 2.725723 CGAACGATGCAATGCAAGTTTT 59.274 40.909 24.97 12.36 43.62 2.43
1839 5184 2.295253 ATCCAACGGATGAGTCGAAC 57.705 50.000 0.00 0.00 41.43 3.95
1845 5190 1.328680 CGCAAGAATCCAACGGATGAG 59.671 52.381 0.00 0.00 42.27 2.90
1854 5199 3.126879 CGGCTGCGCAAGAATCCA 61.127 61.111 13.05 0.00 43.02 3.41
1868 5213 3.056313 GCAGGCCTTCATCAACGGC 62.056 63.158 0.00 0.00 43.03 5.68
1890 5255 1.160329 GCTATGCTCGGACGCCAAAT 61.160 55.000 0.00 0.00 0.00 2.32
1906 5271 1.674651 ACTGACGACGAGCCTGCTA 60.675 57.895 0.00 0.00 0.00 3.49
1977 5342 1.783031 CGTATCCACTCTAGCGCGGT 61.783 60.000 17.70 17.70 0.00 5.68
1978 5343 1.082038 CGTATCCACTCTAGCGCGG 60.082 63.158 8.83 0.00 0.00 6.46
1979 5344 0.110599 CTCGTATCCACTCTAGCGCG 60.111 60.000 0.00 0.00 0.00 6.86
1980 5345 1.069771 GTCTCGTATCCACTCTAGCGC 60.070 57.143 0.00 0.00 0.00 5.92
1981 5346 2.210961 TGTCTCGTATCCACTCTAGCG 58.789 52.381 0.00 0.00 0.00 4.26
1982 5347 3.878103 TCTTGTCTCGTATCCACTCTAGC 59.122 47.826 0.00 0.00 0.00 3.42
1983 5348 5.818336 TCTTCTTGTCTCGTATCCACTCTAG 59.182 44.000 0.00 0.00 0.00 2.43
1984 5349 5.742063 TCTTCTTGTCTCGTATCCACTCTA 58.258 41.667 0.00 0.00 0.00 2.43
2076 5441 1.623811 AGCCCCACCGCTAGTAATATG 59.376 52.381 0.00 0.00 37.32 1.78
2340 5710 2.409948 ATTTGAGTAGCCTGAGCCAC 57.590 50.000 0.00 0.00 41.25 5.01
2341 5711 3.682718 GCTTATTTGAGTAGCCTGAGCCA 60.683 47.826 0.00 0.00 41.25 4.75
2342 5712 2.875317 GCTTATTTGAGTAGCCTGAGCC 59.125 50.000 0.00 0.00 41.25 4.70
2343 5713 3.535561 TGCTTATTTGAGTAGCCTGAGC 58.464 45.455 0.00 0.00 40.32 4.26
2344 5714 7.157347 TGATATGCTTATTTGAGTAGCCTGAG 58.843 38.462 0.00 0.00 34.03 3.35
2345 5715 7.066307 TGATATGCTTATTTGAGTAGCCTGA 57.934 36.000 0.00 0.00 34.03 3.86
2346 5716 7.918536 ATGATATGCTTATTTGAGTAGCCTG 57.081 36.000 0.00 0.00 34.03 4.85
2365 5735 9.780413 CGACTGTCGTATACTAGTAGTATGATA 57.220 37.037 26.48 15.90 41.23 2.15
2366 5736 7.275341 GCGACTGTCGTATACTAGTAGTATGAT 59.725 40.741 28.38 10.39 39.82 2.45
2367 5737 6.584184 GCGACTGTCGTATACTAGTAGTATGA 59.416 42.308 28.38 16.34 39.82 2.15
2369 5739 6.686630 AGCGACTGTCGTATACTAGTAGTAT 58.313 40.000 28.38 23.09 42.81 2.12
2371 5741 4.942852 AGCGACTGTCGTATACTAGTAGT 58.057 43.478 28.38 8.14 42.81 2.73
2372 5742 4.385447 GGAGCGACTGTCGTATACTAGTAG 59.615 50.000 28.38 0.00 42.81 2.57
2373 5743 4.202151 TGGAGCGACTGTCGTATACTAGTA 60.202 45.833 28.38 4.77 42.81 1.82
2374 5744 3.129871 GGAGCGACTGTCGTATACTAGT 58.870 50.000 28.38 0.00 42.81 2.57
2377 5747 2.034104 TGGAGCGACTGTCGTATACT 57.966 50.000 28.38 17.98 42.81 2.12
2379 5749 3.630769 AGAAATGGAGCGACTGTCGTATA 59.369 43.478 28.38 14.63 42.81 1.47
2380 5750 2.427453 AGAAATGGAGCGACTGTCGTAT 59.573 45.455 28.38 18.78 42.81 3.06
2381 5751 1.816835 AGAAATGGAGCGACTGTCGTA 59.183 47.619 28.38 14.64 42.81 3.43
2382 5752 0.603569 AGAAATGGAGCGACTGTCGT 59.396 50.000 28.38 16.68 42.81 4.34
2383 5753 2.561733 TAGAAATGGAGCGACTGTCG 57.438 50.000 24.78 24.78 43.89 4.35
2384 5754 6.678878 TGTATATAGAAATGGAGCGACTGTC 58.321 40.000 0.00 0.00 0.00 3.51
2385 5755 6.650427 TGTATATAGAAATGGAGCGACTGT 57.350 37.500 0.00 0.00 0.00 3.55
2387 5757 7.526142 TCTTGTATATAGAAATGGAGCGACT 57.474 36.000 0.00 0.00 0.00 4.18
2388 5758 8.029522 TGATCTTGTATATAGAAATGGAGCGAC 58.970 37.037 0.00 0.00 0.00 5.19
2389 5759 8.122472 TGATCTTGTATATAGAAATGGAGCGA 57.878 34.615 0.00 0.00 0.00 4.93
2390 5760 8.246871 TCTGATCTTGTATATAGAAATGGAGCG 58.753 37.037 0.00 0.00 0.00 5.03
2391 5761 9.364989 GTCTGATCTTGTATATAGAAATGGAGC 57.635 37.037 0.00 0.00 0.00 4.70
2431 9173 7.855904 CGCAGAGCCGTTATTAAATTTTATCTT 59.144 33.333 0.00 0.00 0.00 2.40
2432 9174 7.225931 TCGCAGAGCCGTTATTAAATTTTATCT 59.774 33.333 0.00 0.00 0.00 1.98
2433 9175 7.349711 TCGCAGAGCCGTTATTAAATTTTATC 58.650 34.615 0.00 0.00 0.00 1.75
2449 9196 1.443802 AAAAGCTAGTTCGCAGAGCC 58.556 50.000 0.00 0.00 39.04 4.70
2470 9217 9.791801 TGCATGCATCCTATTAATTAACTAGAA 57.208 29.630 18.46 0.00 0.00 2.10
2487 9243 7.843482 TCAATTTTATCGAATTTGCATGCATC 58.157 30.769 23.37 15.40 31.71 3.91
2528 9284 6.747125 TGATAATGACACATGCAACAACTTT 58.253 32.000 0.00 0.00 0.00 2.66
2533 9289 4.948621 TGGATGATAATGACACATGCAACA 59.051 37.500 0.00 0.00 38.84 3.33
2538 9294 4.035441 TGCGTTGGATGATAATGACACATG 59.965 41.667 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.