Multiple sequence alignment - TraesCS4D01G123000

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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 TraesCS4D01G123000 chr4D 100.000 2645 0 0 1 2645 107436304 107433660 0.000000e+00 4885.0
1 TraesCS4D01G123000 chr4D 91.980 611 42 3 1032 1636 106739292 106738683 0.000000e+00 850.0
2 TraesCS4D01G123000 chr4B 91.641 2249 118 24 1 2211 169596556 169598772 0.000000e+00 3048.0
3 TraesCS4D01G123000 chr4B 93.148 613 34 4 1030 1636 169792521 169793131 0.000000e+00 893.0
4 TraesCS4D01G123000 chr4B 96.522 115 3 1 2389 2503 169598871 169598984 3.480000e-44 189.0
5 TraesCS4D01G123000 chr4B 94.030 67 3 1 2279 2345 169598804 169598869 1.680000e-17 100.0
6 TraesCS4D01G123000 chr4A 94.238 1805 84 10 422 2211 468756904 468758703 0.000000e+00 2739.0
7 TraesCS4D01G123000 chr4A 91.503 612 42 6 1032 1636 469101928 469102536 0.000000e+00 833.0
8 TraesCS4D01G123000 chr4A 89.008 373 20 13 2216 2585 468758757 468759111 2.420000e-120 442.0
9 TraesCS4D01G123000 chr4A 87.738 367 37 6 2 365 468756539 468756900 3.150000e-114 422.0
10 TraesCS4D01G123000 chr5B 89.298 299 32 0 1238 1536 704276900 704276602 2.490000e-100 375.0
11 TraesCS4D01G123000 chr5B 79.938 324 42 13 1117 1439 704272904 704272603 1.590000e-52 217.0
12 TraesCS4D01G123000 chr2D 81.761 159 24 4 1686 1842 381201042 381200887 7.680000e-26 128.0
13 TraesCS4D01G123000 chr2D 95.082 61 3 0 1686 1746 381301387 381301447 2.170000e-16 97.1
14 TraesCS4D01G123000 chr2B 95.238 63 3 0 1686 1748 795271347 795271285 1.680000e-17 100.0
15 TraesCS4D01G123000 chr2A 93.651 63 4 0 1686 1748 762156486 762156548 7.790000e-16 95.3


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 TraesCS4D01G123000 chr4D 107433660 107436304 2644 True 4885.000000 4885 100.000000 1 2645 1 chr4D.!!$R2 2644
1 TraesCS4D01G123000 chr4D 106738683 106739292 609 True 850.000000 850 91.980000 1032 1636 1 chr4D.!!$R1 604
2 TraesCS4D01G123000 chr4B 169596556 169598984 2428 False 1112.333333 3048 94.064333 1 2503 3 chr4B.!!$F2 2502
3 TraesCS4D01G123000 chr4B 169792521 169793131 610 False 893.000000 893 93.148000 1030 1636 1 chr4B.!!$F1 606
4 TraesCS4D01G123000 chr4A 468756539 468759111 2572 False 1201.000000 2739 90.328000 2 2585 3 chr4A.!!$F2 2583
5 TraesCS4D01G123000 chr4A 469101928 469102536 608 False 833.000000 833 91.503000 1032 1636 1 chr4A.!!$F1 604
6 TraesCS4D01G123000 chr5B 704272603 704276900 4297 True 296.000000 375 84.618000 1117 1536 2 chr5B.!!$R1 419

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
152 153 0.179124 CTTCCCGCTTCGAAGAGAGG 60.179 60.0 28.95 24.66 39.29 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2255 1.115467 AGATAGACCCGAGCAAGTGG 58.885 55.0 0.0 0.0 0.0 4.0 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
96 97 7.444792 AGGTAAACTATACTATCACAGTCTCCG 59.555 40.741 0.00 0.00 38.80 4.63
152 153 0.179124 CTTCCCGCTTCGAAGAGAGG 60.179 60.000 28.95 24.66 39.29 3.69
153 154 1.605058 TTCCCGCTTCGAAGAGAGGG 61.605 60.000 31.32 31.32 42.56 4.30
169 170 1.003580 GAGGGATCAAAGACACCTGCA 59.996 52.381 0.00 0.00 0.00 4.41
171 172 1.003580 GGGATCAAAGACACCTGCAGA 59.996 52.381 17.39 0.00 0.00 4.26
173 174 3.350833 GGATCAAAGACACCTGCAGAAT 58.649 45.455 17.39 0.00 0.00 2.40
179 180 8.757982 ATCAAAGACACCTGCAGAATAATAAT 57.242 30.769 17.39 0.00 0.00 1.28
349 350 6.483640 ACTTCCGCATGAAAAATATCCTACTC 59.516 38.462 0.00 0.00 31.06 2.59
350 351 4.988540 TCCGCATGAAAAATATCCTACTCG 59.011 41.667 0.00 0.00 0.00 4.18
432 433 5.134661 ACCCAAGAAACGGAGAACAATTTA 58.865 37.500 0.00 0.00 0.00 1.40
454 455 9.686683 ATTTACTCAGGAATACAAATAGCAAGT 57.313 29.630 0.00 0.00 0.00 3.16
469 472 9.180678 CAAATAGCAAGTACAAGAAAAACGAAT 57.819 29.630 0.00 0.00 0.00 3.34
511 514 6.560003 AAAAAGATGAAAACCCTTCCAAGT 57.440 33.333 0.00 0.00 0.00 3.16
713 716 2.900273 CGGCCGATGGGAGAGAAA 59.100 61.111 24.07 0.00 34.06 2.52
801 804 1.143889 CCTAATTTCCTGCTCCTCCCC 59.856 57.143 0.00 0.00 0.00 4.81
802 805 1.143889 CTAATTTCCTGCTCCTCCCCC 59.856 57.143 0.00 0.00 0.00 5.40
803 806 1.926426 AATTTCCTGCTCCTCCCCCG 61.926 60.000 0.00 0.00 0.00 5.73
835 838 1.153127 GACGACAACAACCCACCCA 60.153 57.895 0.00 0.00 0.00 4.51
843 851 1.379843 CAACCCACCCATAGGCCAC 60.380 63.158 5.01 0.00 36.11 5.01
848 856 0.394352 CCACCCATAGGCCACAGAAC 60.394 60.000 5.01 0.00 36.11 3.01
881 889 2.092323 GAGGCCCACATAAAGTCCAAC 58.908 52.381 0.00 0.00 0.00 3.77
890 898 4.095483 CACATAAAGTCCAACTGATCAGCC 59.905 45.833 22.83 5.81 0.00 4.85
899 907 3.839353 CTGATCAGCCCGGCCCATC 62.839 68.421 10.38 8.46 0.00 3.51
906 914 4.506255 CCCGGCCCATCACCTTCC 62.506 72.222 0.00 0.00 0.00 3.46
909 917 2.440980 GGCCCATCACCTTCCAGC 60.441 66.667 0.00 0.00 0.00 4.85
911 919 1.000396 GCCCATCACCTTCCAGCTT 60.000 57.895 0.00 0.00 0.00 3.74
918 926 2.045926 CCTTCCAGCTTGGTCCCG 60.046 66.667 0.00 0.00 39.03 5.14
928 936 1.299541 CTTGGTCCCGCATGTCATAC 58.700 55.000 0.00 0.00 0.00 2.39
929 937 0.615850 TTGGTCCCGCATGTCATACA 59.384 50.000 0.00 0.00 0.00 2.29
981 989 2.823747 ACGCCTCCACGCTATATAATCA 59.176 45.455 0.00 0.00 36.19 2.57
1008 1016 1.908793 CCGCCGTGATCCCCTCTAT 60.909 63.158 0.00 0.00 0.00 1.98
1043 1051 2.662596 CCTAGCCAAGCACACCGA 59.337 61.111 0.00 0.00 0.00 4.69
1341 1350 3.073209 AGACGAGCCAGATCTACTCCATA 59.927 47.826 15.74 0.00 0.00 2.74
1461 1470 3.209812 CTCCTCGTCGCCGATCCA 61.210 66.667 0.00 0.00 43.27 3.41
1706 1721 8.713708 TGAAGAAGGGGTTTTGTTATCATAAA 57.286 30.769 0.00 0.00 0.00 1.40
1896 2017 1.539065 CCTGATGCTGTGATCGTACCC 60.539 57.143 0.00 0.00 0.00 3.69
1964 2090 6.286758 CAAGATTAAGCATCTCCTTCAGCTA 58.713 40.000 0.00 0.00 41.93 3.32
2052 2178 1.959042 ATCCTGTGATGCCGATTCAC 58.041 50.000 5.68 5.68 43.04 3.18
2123 2251 7.512992 CATTTCTATCTGGGTTAGATTGAGGT 58.487 38.462 0.00 0.00 43.68 3.85
2127 2255 2.838202 TCTGGGTTAGATTGAGGTCCAC 59.162 50.000 0.00 0.00 0.00 4.02
2143 2271 1.541310 CCACCACTTGCTCGGGTCTA 61.541 60.000 0.00 0.00 31.03 2.59
2211 2339 2.107204 GCCCAATCTGATATCCCAGTGT 59.893 50.000 0.00 0.00 35.71 3.55
2213 2341 3.649981 CCCAATCTGATATCCCAGTGTCT 59.350 47.826 0.00 0.00 35.71 3.41
2214 2342 4.840680 CCCAATCTGATATCCCAGTGTCTA 59.159 45.833 0.00 0.00 35.71 2.59
2216 2344 5.777223 CCAATCTGATATCCCAGTGTCTAGA 59.223 44.000 0.00 0.00 35.71 2.43
2217 2345 6.268617 CCAATCTGATATCCCAGTGTCTAGAA 59.731 42.308 0.00 0.00 35.71 2.10
2218 2346 7.202038 CCAATCTGATATCCCAGTGTCTAGAAA 60.202 40.741 0.00 0.00 35.71 2.52
2220 2348 7.295322 TCTGATATCCCAGTGTCTAGAAATG 57.705 40.000 0.00 0.00 35.71 2.32
2222 2350 6.143206 TGATATCCCAGTGTCTAGAAATGGA 58.857 40.000 16.89 9.94 32.55 3.41
2224 2352 3.791320 TCCCAGTGTCTAGAAATGGACT 58.209 45.455 16.89 3.20 32.55 3.85
2225 2353 3.769844 TCCCAGTGTCTAGAAATGGACTC 59.230 47.826 16.89 0.00 32.55 3.36
2226 2354 3.515502 CCCAGTGTCTAGAAATGGACTCA 59.484 47.826 16.89 0.00 32.55 3.41
2227 2355 4.163078 CCCAGTGTCTAGAAATGGACTCAT 59.837 45.833 16.89 0.00 32.55 2.90
2228 2356 5.355596 CCAGTGTCTAGAAATGGACTCATC 58.644 45.833 11.89 0.00 32.55 2.92
2236 2411 9.308318 GTCTAGAAATGGACTCATCTCTAAAAC 57.692 37.037 0.00 0.00 33.85 2.43
2244 2613 8.842358 TGGACTCATCTCTAAAACGTATTTTT 57.158 30.769 0.00 0.00 38.91 1.94
2295 4664 2.368875 ACTCTCTGGCCGTTTATATGGG 59.631 50.000 0.00 0.00 0.00 4.00
2297 4666 3.042682 TCTCTGGCCGTTTATATGGGAA 58.957 45.455 0.00 0.00 0.00 3.97
2300 4669 4.798882 TCTGGCCGTTTATATGGGAATTT 58.201 39.130 0.00 0.00 0.00 1.82
2367 4736 9.612620 GGTAGTCTTTGTATTTTCATTGACTTG 57.387 33.333 0.00 0.00 34.64 3.16
2371 4740 9.515020 GTCTTTGTATTTTCATTGACTTGTTGA 57.485 29.630 0.00 0.00 0.00 3.18
2399 4768 1.268352 GTGGGCTCGTAATTTTGTGCA 59.732 47.619 6.16 0.00 0.00 4.57
2505 4874 1.492133 CCTGGAACCTTGCCCTCTGA 61.492 60.000 0.00 0.00 0.00 3.27
2512 4881 1.203313 ACCTTGCCCTCTGAGGTCTTA 60.203 52.381 21.70 1.86 39.55 2.10
2513 4882 1.909302 CCTTGCCCTCTGAGGTCTTAA 59.091 52.381 21.70 10.12 31.93 1.85
2514 4883 2.305927 CCTTGCCCTCTGAGGTCTTAAA 59.694 50.000 21.70 7.96 31.93 1.52
2515 4884 3.244911 CCTTGCCCTCTGAGGTCTTAAAA 60.245 47.826 21.70 6.42 31.93 1.52
2516 4885 4.568592 CCTTGCCCTCTGAGGTCTTAAAAT 60.569 45.833 21.70 0.00 31.93 1.82
2517 4886 4.657814 TGCCCTCTGAGGTCTTAAAATT 57.342 40.909 21.70 0.00 31.93 1.82
2518 4887 4.998051 TGCCCTCTGAGGTCTTAAAATTT 58.002 39.130 21.70 0.00 31.93 1.82
2519 4888 4.766891 TGCCCTCTGAGGTCTTAAAATTTG 59.233 41.667 21.70 3.68 31.93 2.32
2520 4889 4.380973 GCCCTCTGAGGTCTTAAAATTTGC 60.381 45.833 21.70 9.74 31.93 3.68
2521 4890 4.766891 CCCTCTGAGGTCTTAAAATTTGCA 59.233 41.667 21.70 0.00 31.93 4.08
2522 4891 5.335976 CCCTCTGAGGTCTTAAAATTTGCAC 60.336 44.000 21.70 0.00 31.93 4.57
2523 4892 5.241506 CCTCTGAGGTCTTAAAATTTGCACA 59.758 40.000 15.76 0.00 0.00 4.57
2524 4893 6.239008 CCTCTGAGGTCTTAAAATTTGCACAA 60.239 38.462 15.76 0.00 0.00 3.33
2525 4894 6.503524 TCTGAGGTCTTAAAATTTGCACAAC 58.496 36.000 0.00 0.00 0.00 3.32
2526 4895 6.321181 TCTGAGGTCTTAAAATTTGCACAACT 59.679 34.615 0.00 0.00 0.00 3.16
2527 4896 6.272318 TGAGGTCTTAAAATTTGCACAACTG 58.728 36.000 0.00 0.00 0.00 3.16
2528 4897 6.127479 TGAGGTCTTAAAATTTGCACAACTGT 60.127 34.615 0.00 0.00 0.00 3.55
2529 4898 6.639563 AGGTCTTAAAATTTGCACAACTGTT 58.360 32.000 0.00 0.00 0.00 3.16
2530 4899 7.777095 AGGTCTTAAAATTTGCACAACTGTTA 58.223 30.769 0.00 0.00 0.00 2.41
2531 4900 8.421002 AGGTCTTAAAATTTGCACAACTGTTAT 58.579 29.630 0.00 0.00 0.00 1.89
2532 4901 9.040939 GGTCTTAAAATTTGCACAACTGTTATT 57.959 29.630 0.00 0.00 0.00 1.40
2535 4904 9.862585 CTTAAAATTTGCACAACTGTTATTTCC 57.137 29.630 0.00 0.00 0.00 3.13
2536 4905 9.606631 TTAAAATTTGCACAACTGTTATTTCCT 57.393 25.926 0.00 0.00 0.00 3.36
2538 4907 8.816640 AAATTTGCACAACTGTTATTTCCTAG 57.183 30.769 0.00 0.00 0.00 3.02
2539 4908 7.759489 ATTTGCACAACTGTTATTTCCTAGA 57.241 32.000 0.00 0.00 0.00 2.43
2540 4909 7.575414 TTTGCACAACTGTTATTTCCTAGAA 57.425 32.000 0.00 0.00 0.00 2.10
2541 4910 7.575414 TTGCACAACTGTTATTTCCTAGAAA 57.425 32.000 0.00 0.00 0.00 2.52
2542 4911 7.575414 TGCACAACTGTTATTTCCTAGAAAA 57.425 32.000 0.00 0.00 0.00 2.29
2543 4912 8.177119 TGCACAACTGTTATTTCCTAGAAAAT 57.823 30.769 0.00 0.00 33.54 1.82
2544 4913 8.296713 TGCACAACTGTTATTTCCTAGAAAATC 58.703 33.333 0.00 0.00 31.50 2.17
2545 4914 8.296713 GCACAACTGTTATTTCCTAGAAAATCA 58.703 33.333 0.00 0.00 31.50 2.57
2546 4915 9.612620 CACAACTGTTATTTCCTAGAAAATCAC 57.387 33.333 0.00 0.00 31.50 3.06
2547 4916 9.349713 ACAACTGTTATTTCCTAGAAAATCACA 57.650 29.630 2.06 2.06 33.78 3.58
2562 4931 1.593196 TCACAAGGAAGAAACCTGCG 58.407 50.000 0.00 0.00 40.49 5.18
2575 4944 2.989422 ACCTGCGCAACTGTTATTTC 57.011 45.000 13.05 0.00 0.00 2.17
2578 4947 1.539388 CTGCGCAACTGTTATTTCCCA 59.461 47.619 13.05 0.00 0.00 4.37
2582 4951 3.305064 GCGCAACTGTTATTTCCCAGAAA 60.305 43.478 0.30 0.00 32.93 2.52
2583 4952 4.794655 GCGCAACTGTTATTTCCCAGAAAA 60.795 41.667 0.30 0.00 32.93 2.29
2584 4953 5.469479 CGCAACTGTTATTTCCCAGAAAAT 58.531 37.500 0.00 0.00 33.54 1.82
2586 4955 5.869344 GCAACTGTTATTTCCCAGAAAATCC 59.131 40.000 0.00 0.00 31.50 3.01
2588 4957 6.590234 ACTGTTATTTCCCAGAAAATCCAC 57.410 37.500 0.00 0.00 31.50 4.02
2589 4958 6.314917 ACTGTTATTTCCCAGAAAATCCACT 58.685 36.000 0.00 0.00 31.50 4.00
2591 4960 7.947890 ACTGTTATTTCCCAGAAAATCCACTAA 59.052 33.333 0.00 0.00 31.50 2.24
2592 4961 8.893563 TGTTATTTCCCAGAAAATCCACTAAT 57.106 30.769 0.00 0.00 31.50 1.73
2593 4962 8.748412 TGTTATTTCCCAGAAAATCCACTAATG 58.252 33.333 0.00 0.00 31.50 1.90
2594 4963 5.659440 TTTCCCAGAAAATCCACTAATGC 57.341 39.130 0.00 0.00 0.00 3.56
2595 4964 4.314522 TCCCAGAAAATCCACTAATGCA 57.685 40.909 0.00 0.00 0.00 3.96
2596 4965 4.272489 TCCCAGAAAATCCACTAATGCAG 58.728 43.478 0.00 0.00 0.00 4.41
2597 4966 4.018506 TCCCAGAAAATCCACTAATGCAGA 60.019 41.667 0.00 0.00 0.00 4.26
2600 4969 5.338365 CAGAAAATCCACTAATGCAGAAGC 58.662 41.667 0.00 0.00 42.57 3.86
2601 4970 5.125097 CAGAAAATCCACTAATGCAGAAGCT 59.875 40.000 0.00 0.00 42.74 3.74
2602 4971 4.978083 AAATCCACTAATGCAGAAGCTG 57.022 40.909 0.00 0.00 42.74 4.24
2616 5890 2.225019 AGAAGCTGCGATCTTGTTTGTG 59.775 45.455 5.36 0.00 0.00 3.33
2634 5908 4.680237 CGGAGCTGCAACCACCGA 62.680 66.667 15.20 0.00 45.31 4.69
2639 5913 3.052082 CTGCAACCACCGAGGCTG 61.052 66.667 0.00 0.00 43.14 4.85
2643 5917 1.079543 CAACCACCGAGGCTGAGAG 60.080 63.158 0.00 0.00 43.14 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 7.308469 CCCGGAGACTGTGATAGTATAGTTTAC 60.308 44.444 0.73 0.00 40.53 2.01
96 97 4.250464 TGTTTGAGACGAATACATGACCC 58.750 43.478 0.00 0.00 0.00 4.46
132 133 0.179124 CTCTCTTCGAAGCGGGAAGG 60.179 60.000 20.56 3.20 40.95 3.46
152 153 2.479566 TCTGCAGGTGTCTTTGATCC 57.520 50.000 15.13 0.00 0.00 3.36
153 154 6.690194 ATTATTCTGCAGGTGTCTTTGATC 57.310 37.500 15.13 0.00 0.00 2.92
179 180 8.795513 TGCTGAAATTTCACAGAATTCTGATTA 58.204 29.630 36.15 20.02 46.36 1.75
258 259 9.431887 GTGTTTAATCTCTTGTCCAATACTACA 57.568 33.333 0.00 0.00 0.00 2.74
260 261 8.525316 TCGTGTTTAATCTCTTGTCCAATACTA 58.475 33.333 0.00 0.00 0.00 1.82
432 433 7.620880 TGTACTTGCTATTTGTATTCCTGAGT 58.379 34.615 0.00 0.00 0.00 3.41
511 514 8.635765 AACAATCTCCATTACTTTCTTGCTTA 57.364 30.769 0.00 0.00 0.00 3.09
785 788 2.378634 CGGGGGAGGAGCAGGAAAT 61.379 63.158 0.00 0.00 0.00 2.17
786 789 3.009115 CGGGGGAGGAGCAGGAAA 61.009 66.667 0.00 0.00 0.00 3.13
801 804 1.067582 GTCGATAAGAGGGTGCCGG 59.932 63.158 0.00 0.00 0.00 6.13
802 805 1.299165 CGTCGATAAGAGGGTGCCG 60.299 63.158 0.00 0.00 0.00 5.69
803 806 0.248949 GTCGTCGATAAGAGGGTGCC 60.249 60.000 0.00 0.00 35.58 5.01
806 809 2.165167 TGTTGTCGTCGATAAGAGGGT 58.835 47.619 4.51 0.00 35.58 4.34
843 851 2.620112 CCAAGTGCTGGGCGTTCTG 61.620 63.158 0.00 0.00 42.17 3.02
855 863 2.094675 CTTTATGTGGGCCTCCAAGTG 58.905 52.381 4.53 0.00 46.04 3.16
881 889 3.839353 GATGGGCCGGGCTGATCAG 62.839 68.421 28.80 18.84 0.00 2.90
890 898 3.704231 CTGGAAGGTGATGGGCCGG 62.704 68.421 0.00 0.00 0.00 6.13
906 914 2.360350 ACATGCGGGACCAAGCTG 60.360 61.111 11.69 9.68 0.00 4.24
909 917 1.299541 GTATGACATGCGGGACCAAG 58.700 55.000 0.00 0.00 0.00 3.61
911 919 0.615850 TTGTATGACATGCGGGACCA 59.384 50.000 0.00 0.00 0.00 4.02
918 926 2.523015 GCAGCACTTTGTATGACATGC 58.477 47.619 0.00 0.00 33.21 4.06
944 952 3.493440 GTTAGGGTTTCGGCCGCG 61.493 66.667 23.51 0.00 0.00 6.46
946 954 3.493440 GCGTTAGGGTTTCGGCCG 61.493 66.667 22.12 22.12 0.00 6.13
981 989 2.685387 GATCACGGCGGCGAGAGAAT 62.685 60.000 38.93 20.51 0.00 2.40
1128 1137 4.388499 GCGGTCTTCTTCCGGCCA 62.388 66.667 2.24 0.00 46.90 5.36
1636 1651 7.095910 ACAACTCACAGTTCTTAGAGATCATG 58.904 38.462 0.00 0.00 36.03 3.07
1684 1699 8.721133 AAGTTTATGATAACAAAACCCCTTCT 57.279 30.769 0.00 0.00 34.39 2.85
1783 1810 9.846248 ATTCACAGATTCTAAATAAAACTGCAC 57.154 29.630 0.00 0.00 0.00 4.57
1964 2090 4.220602 GCAGGGTCTTCAACAATTACCAAT 59.779 41.667 0.00 0.00 31.58 3.16
2052 2178 2.110990 CAATGGCGCATAAACATGTCG 58.889 47.619 10.83 0.00 0.00 4.35
2123 2251 2.847234 ACCCGAGCAAGTGGTGGA 60.847 61.111 0.00 0.00 0.00 4.02
2127 2255 1.115467 AGATAGACCCGAGCAAGTGG 58.885 55.000 0.00 0.00 0.00 4.00
2143 2271 3.552273 CGGCGTAATACCAAGCTACAGAT 60.552 47.826 0.00 0.00 0.00 2.90
2186 2314 3.762288 CTGGGATATCAGATTGGGCATTG 59.238 47.826 4.83 0.00 36.93 2.82
2203 2331 3.769844 GAGTCCATTTCTAGACACTGGGA 59.230 47.826 12.31 3.92 35.38 4.37
2211 2339 8.191446 CGTTTTAGAGATGAGTCCATTTCTAGA 58.809 37.037 0.00 0.00 43.21 2.43
2213 2341 7.837863 ACGTTTTAGAGATGAGTCCATTTCTA 58.162 34.615 0.00 0.00 40.99 2.10
2214 2342 6.702329 ACGTTTTAGAGATGAGTCCATTTCT 58.298 36.000 0.00 0.00 43.86 2.52
2216 2344 9.449719 AAATACGTTTTAGAGATGAGTCCATTT 57.550 29.630 0.00 0.00 32.09 2.32
2217 2345 9.449719 AAAATACGTTTTAGAGATGAGTCCATT 57.550 29.630 0.00 0.00 35.83 3.16
2218 2346 9.449719 AAAAATACGTTTTAGAGATGAGTCCAT 57.550 29.630 0.00 0.00 37.67 3.41
2295 4664 6.165577 ACATCAAACACAAGGGCATAAATTC 58.834 36.000 0.00 0.00 0.00 2.17
2297 4666 5.743636 ACATCAAACACAAGGGCATAAAT 57.256 34.783 0.00 0.00 0.00 1.40
2300 4669 5.073428 TGTAACATCAAACACAAGGGCATA 58.927 37.500 0.00 0.00 0.00 3.14
2367 4736 2.132762 CGAGCCCACCGTATAATCAAC 58.867 52.381 0.00 0.00 0.00 3.18
2368 4737 1.758280 ACGAGCCCACCGTATAATCAA 59.242 47.619 0.00 0.00 38.61 2.57
2369 4738 1.405872 ACGAGCCCACCGTATAATCA 58.594 50.000 0.00 0.00 38.61 2.57
2371 4740 4.612264 AATTACGAGCCCACCGTATAAT 57.388 40.909 0.00 0.00 41.36 1.28
2372 4741 4.405116 AAATTACGAGCCCACCGTATAA 57.595 40.909 0.00 0.00 41.36 0.98
2399 4768 6.091555 TGTAGGGGATATAGAAATTGCCTCT 58.908 40.000 0.00 0.00 0.00 3.69
2505 4874 6.220726 ACAGTTGTGCAAATTTTAAGACCT 57.779 33.333 0.00 0.00 0.00 3.85
2512 4881 9.260002 CTAGGAAATAACAGTTGTGCAAATTTT 57.740 29.630 0.00 0.00 0.00 1.82
2513 4882 8.637986 TCTAGGAAATAACAGTTGTGCAAATTT 58.362 29.630 0.00 0.00 0.00 1.82
2514 4883 8.177119 TCTAGGAAATAACAGTTGTGCAAATT 57.823 30.769 0.00 0.00 0.00 1.82
2515 4884 7.759489 TCTAGGAAATAACAGTTGTGCAAAT 57.241 32.000 0.00 0.00 0.00 2.32
2516 4885 7.575414 TTCTAGGAAATAACAGTTGTGCAAA 57.425 32.000 0.00 0.00 0.00 3.68
2517 4886 7.575414 TTTCTAGGAAATAACAGTTGTGCAA 57.425 32.000 0.00 0.00 0.00 4.08
2518 4887 7.575414 TTTTCTAGGAAATAACAGTTGTGCA 57.425 32.000 0.00 0.00 0.00 4.57
2519 4888 8.296713 TGATTTTCTAGGAAATAACAGTTGTGC 58.703 33.333 9.07 0.00 29.75 4.57
2520 4889 9.612620 GTGATTTTCTAGGAAATAACAGTTGTG 57.387 33.333 16.57 0.00 32.73 3.33
2521 4890 9.349713 TGTGATTTTCTAGGAAATAACAGTTGT 57.650 29.630 19.34 0.00 36.10 3.32
2524 4893 9.014297 CCTTGTGATTTTCTAGGAAATAACAGT 57.986 33.333 21.33 0.00 40.01 3.55
2525 4894 9.231297 TCCTTGTGATTTTCTAGGAAATAACAG 57.769 33.333 21.33 16.35 40.01 3.16
2526 4895 9.581289 TTCCTTGTGATTTTCTAGGAAATAACA 57.419 29.630 19.34 19.34 41.23 2.41
2530 4899 8.940397 TTCTTCCTTGTGATTTTCTAGGAAAT 57.060 30.769 8.84 8.84 42.60 2.17
2531 4900 8.630037 GTTTCTTCCTTGTGATTTTCTAGGAAA 58.370 33.333 0.00 0.00 42.60 3.13
2532 4901 7.230712 GGTTTCTTCCTTGTGATTTTCTAGGAA 59.769 37.037 0.00 0.00 41.64 3.36
2533 4902 6.715264 GGTTTCTTCCTTGTGATTTTCTAGGA 59.285 38.462 0.00 0.00 35.69 2.94
2534 4903 6.717084 AGGTTTCTTCCTTGTGATTTTCTAGG 59.283 38.462 0.00 0.00 33.52 3.02
2535 4904 7.588512 CAGGTTTCTTCCTTGTGATTTTCTAG 58.411 38.462 0.00 0.00 35.37 2.43
2536 4905 6.016276 GCAGGTTTCTTCCTTGTGATTTTCTA 60.016 38.462 0.00 0.00 35.37 2.10
2537 4906 5.221322 GCAGGTTTCTTCCTTGTGATTTTCT 60.221 40.000 0.00 0.00 35.37 2.52
2538 4907 4.984785 GCAGGTTTCTTCCTTGTGATTTTC 59.015 41.667 0.00 0.00 35.37 2.29
2539 4908 4.499696 CGCAGGTTTCTTCCTTGTGATTTT 60.500 41.667 0.00 0.00 35.37 1.82
2540 4909 3.004734 CGCAGGTTTCTTCCTTGTGATTT 59.995 43.478 0.00 0.00 35.37 2.17
2541 4910 2.554032 CGCAGGTTTCTTCCTTGTGATT 59.446 45.455 0.00 0.00 35.37 2.57
2542 4911 2.154462 CGCAGGTTTCTTCCTTGTGAT 58.846 47.619 0.00 0.00 35.37 3.06
2543 4912 1.593196 CGCAGGTTTCTTCCTTGTGA 58.407 50.000 0.00 0.00 35.37 3.58
2544 4913 0.040067 GCGCAGGTTTCTTCCTTGTG 60.040 55.000 0.30 0.00 35.37 3.33
2545 4914 0.465460 TGCGCAGGTTTCTTCCTTGT 60.465 50.000 5.66 0.00 35.37 3.16
2546 4915 0.667993 TTGCGCAGGTTTCTTCCTTG 59.332 50.000 11.31 0.00 35.37 3.61
2547 4916 0.668535 GTTGCGCAGGTTTCTTCCTT 59.331 50.000 11.31 0.00 35.37 3.36
2548 4917 0.179018 AGTTGCGCAGGTTTCTTCCT 60.179 50.000 11.31 0.00 38.51 3.36
2549 4918 0.040067 CAGTTGCGCAGGTTTCTTCC 60.040 55.000 11.31 0.00 0.00 3.46
2562 4931 5.869344 GGATTTTCTGGGAAATAACAGTTGC 59.131 40.000 0.00 0.00 36.17 4.17
2575 4944 4.272489 TCTGCATTAGTGGATTTTCTGGG 58.728 43.478 0.00 0.00 0.00 4.45
2578 4947 5.125097 CAGCTTCTGCATTAGTGGATTTTCT 59.875 40.000 0.00 0.00 42.74 2.52
2594 4963 2.225019 ACAAACAAGATCGCAGCTTCTG 59.775 45.455 0.00 0.00 34.12 3.02
2595 4964 2.225019 CACAAACAAGATCGCAGCTTCT 59.775 45.455 0.00 0.00 0.00 2.85
2596 4965 2.578495 CACAAACAAGATCGCAGCTTC 58.422 47.619 0.00 0.00 0.00 3.86
2597 4966 1.335324 GCACAAACAAGATCGCAGCTT 60.335 47.619 0.00 0.00 0.00 3.74
2600 4969 0.453282 CCGCACAAACAAGATCGCAG 60.453 55.000 0.00 0.00 0.00 5.18
2601 4970 0.882484 TCCGCACAAACAAGATCGCA 60.882 50.000 0.00 0.00 0.00 5.10
2602 4971 0.179215 CTCCGCACAAACAAGATCGC 60.179 55.000 0.00 0.00 0.00 4.58
2608 5882 1.661498 TTGCAGCTCCGCACAAACAA 61.661 50.000 0.00 0.00 42.87 2.83
2611 5885 2.721231 GTTGCAGCTCCGCACAAA 59.279 55.556 0.00 0.00 42.87 2.83
2613 5887 4.560743 TGGTTGCAGCTCCGCACA 62.561 61.111 0.00 0.00 42.87 4.57
2622 5896 3.052082 CAGCCTCGGTGGTTGCAG 61.052 66.667 0.00 0.00 40.11 4.41
2624 5898 2.743928 CTCAGCCTCGGTGGTTGC 60.744 66.667 7.92 0.00 45.29 4.17
2626 5900 1.228894 TCTCTCAGCCTCGGTGGTT 60.229 57.895 0.00 0.00 38.35 3.67
2627 5901 2.441051 TCTCTCAGCCTCGGTGGT 59.559 61.111 0.00 0.00 38.35 4.16


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

AutoCloner maintained by Alex Coulton.