Multiple sequence alignment - TraesCS6A01G289400

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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 TraesCS6A01G289400 chr6A 100.000 2202 0 0 1 2202 521454784 521452583 0.000000e+00 4067.0
1 TraesCS6A01G289400 chr6A 100.000 1593 0 0 2484 4076 521452301 521450709 0.000000e+00 2942.0
2 TraesCS6A01G289400 chr6A 94.643 56 3 0 2484 2539 435059179 435059234 2.020000e-13 87.9
3 TraesCS6A01G289400 chr6D 97.713 2186 47 3 1 2185 379571212 379573395 0.000000e+00 3757.0
4 TraesCS6A01G289400 chr6D 96.940 1536 40 4 2542 4076 379573379 379574908 0.000000e+00 2569.0
5 TraesCS6A01G289400 chr6B 95.319 1538 60 10 2542 4076 567398249 567396721 0.000000e+00 2431.0
6 TraesCS6A01G289400 chr6B 96.822 1227 34 4 962 2185 567399457 567398233 0.000000e+00 2045.0
7 TraesCS6A01G289400 chr6B 93.073 895 55 6 1 892 567400354 567399464 0.000000e+00 1303.0
8 TraesCS6A01G289400 chr7A 78.392 398 61 14 2686 3078 174205059 174205436 6.810000e-58 235.0
9 TraesCS6A01G289400 chr7D 78.141 398 62 14 2686 3078 171313850 171314227 3.170000e-56 230.0
10 TraesCS6A01G289400 chr7B 81.273 267 43 6 2814 3078 137795736 137795997 4.130000e-50 209.0
11 TraesCS6A01G289400 chr7B 78.571 182 32 6 78 255 137793006 137793184 3.330000e-21 113.0
12 TraesCS6A01G289400 chr2B 96.721 61 1 1 2484 2544 353569150 353569209 2.590000e-17 100.0


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 TraesCS6A01G289400 chr6A 521450709 521454784 4075 True 3504.500000 4067 100.000000 1 4076 2 chr6A.!!$R1 4075
1 TraesCS6A01G289400 chr6D 379571212 379574908 3696 False 3163.000000 3757 97.326500 1 4076 2 chr6D.!!$F1 4075
2 TraesCS6A01G289400 chr6B 567396721 567400354 3633 True 1926.333333 2431 95.071333 1 4076 3 chr6B.!!$R1 4075

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
956 960 2.685897 GGACACACTAGAGACTAGCCAG 59.314 54.545 0.00 0.46 0.00 4.85 F
1716 1723 0.318784 CTGCCTCCGTTACCGCTATC 60.319 60.000 0.00 0.00 0.00 2.08 F
2516 2523 1.063114 ACAATCCTCCTAGTAGGCGGT 60.063 52.381 22.11 9.24 41.08 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2510 2517 1.066143 CATCCAGAGTTGTAACCGCCT 60.066 52.381 0.0 0.0 0.0 5.52 R
2746 2754 2.303022 CTGGTCTGGTGTTGTCTGGTAT 59.697 50.000 0.0 0.0 0.0 2.73 R
3800 3810 1.968704 TTGGTCAACATACAACGCCA 58.031 45.000 0.0 0.0 0.0 5.69 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
72 73 2.945668 GCCAGTAAATGCACTTCCTAGG 59.054 50.000 0.82 0.82 0.00 3.02
335 337 3.891977 TGCCTGCTTTTGTTATACCACAA 59.108 39.130 0.00 0.00 34.76 3.33
443 445 9.612620 ACGATTTGCTTTAGAAAATTCTTAGTG 57.387 29.630 0.29 0.00 38.70 2.74
564 566 5.479124 TTAGTAAGTCTCCAAACTGGGTC 57.521 43.478 0.00 0.00 38.32 4.46
586 589 4.516698 TCTCTCAAATGTTTTGACTCCTGC 59.483 41.667 0.00 0.00 0.00 4.85
639 642 8.859236 AAGTTGTTACCCTTTTATTCTCTACC 57.141 34.615 0.00 0.00 0.00 3.18
852 856 3.498774 ATTCCAACACTGACTGCTTCT 57.501 42.857 0.00 0.00 0.00 2.85
888 892 9.455847 CAAGTAAGTTCAAGAAAAGGATCAAAG 57.544 33.333 0.00 0.00 0.00 2.77
892 896 2.819608 TCAAGAAAAGGATCAAAGGCCG 59.180 45.455 0.00 0.00 0.00 6.13
930 934 9.421806 GAACATGAGAAGATATGTATTCTCCTG 57.578 37.037 21.77 21.77 46.96 3.86
956 960 2.685897 GGACACACTAGAGACTAGCCAG 59.314 54.545 0.00 0.46 0.00 4.85
960 964 4.013728 CACACTAGAGACTAGCCAGAGTT 58.986 47.826 0.00 0.00 0.00 3.01
1445 1449 0.390472 GAGGAAGTGGACTCTTGGCG 60.390 60.000 0.00 0.00 0.00 5.69
1528 1532 8.644216 ACCTTGTCGGATACAATATGTATTACA 58.356 33.333 4.64 0.00 46.81 2.41
1583 1590 4.093514 CAATACAGAATGCAAGAACAGCG 58.906 43.478 0.00 0.00 42.53 5.18
1609 1616 3.182967 CAGAACAGGTACATCGAGAAGC 58.817 50.000 0.00 0.00 0.00 3.86
1682 1689 4.683781 GCAAGAGAGCGATTATGGAACTAG 59.316 45.833 0.00 0.00 0.00 2.57
1716 1723 0.318784 CTGCCTCCGTTACCGCTATC 60.319 60.000 0.00 0.00 0.00 2.08
1848 1855 3.584848 AGCTCAGGTTAGTCCATTTCTGT 59.415 43.478 0.00 0.00 39.02 3.41
1950 1957 7.027874 TGCCTATTTTCTCCTTCCTCTTTTA 57.972 36.000 0.00 0.00 0.00 1.52
1963 1970 6.127083 CCTTCCTCTTTTATCTCTTCTCTGCT 60.127 42.308 0.00 0.00 0.00 4.24
1996 2003 4.532521 TCTTCTAGGTCAGGCTTTTTAGCT 59.467 41.667 0.00 0.00 34.73 3.32
2007 2014 7.547227 TCAGGCTTTTTAGCTTGATATTTTCC 58.453 34.615 7.73 0.00 44.19 3.13
2097 2104 8.691661 TTATTCCCTCAGACCTAAAATAATGC 57.308 34.615 0.00 0.00 0.00 3.56
2168 2175 2.740981 CAGCTTGTTCCTCTGCAACTAG 59.259 50.000 0.00 0.00 31.94 2.57
2169 2176 2.634940 AGCTTGTTCCTCTGCAACTAGA 59.365 45.455 0.00 0.00 30.77 2.43
2170 2177 2.739379 GCTTGTTCCTCTGCAACTAGAC 59.261 50.000 0.00 0.00 30.77 2.59
2171 2178 3.556004 GCTTGTTCCTCTGCAACTAGACT 60.556 47.826 0.00 0.00 30.77 3.24
2172 2179 4.636249 CTTGTTCCTCTGCAACTAGACTT 58.364 43.478 0.00 0.00 30.77 3.01
2173 2180 4.689612 TGTTCCTCTGCAACTAGACTTT 57.310 40.909 0.00 0.00 0.00 2.66
2174 2181 4.380531 TGTTCCTCTGCAACTAGACTTTG 58.619 43.478 0.00 0.00 0.00 2.77
2175 2182 4.100963 TGTTCCTCTGCAACTAGACTTTGA 59.899 41.667 0.00 0.00 0.00 2.69
2176 2183 4.955811 TCCTCTGCAACTAGACTTTGAA 57.044 40.909 0.00 0.00 0.00 2.69
2177 2184 4.632153 TCCTCTGCAACTAGACTTTGAAC 58.368 43.478 0.00 0.00 0.00 3.18
2178 2185 4.345257 TCCTCTGCAACTAGACTTTGAACT 59.655 41.667 0.00 0.00 0.00 3.01
2179 2186 4.450419 CCTCTGCAACTAGACTTTGAACTG 59.550 45.833 0.00 0.00 0.00 3.16
2180 2187 3.809832 TCTGCAACTAGACTTTGAACTGC 59.190 43.478 0.00 0.00 0.00 4.40
2181 2188 3.808728 TGCAACTAGACTTTGAACTGCT 58.191 40.909 0.00 0.00 0.00 4.24
2182 2189 3.561310 TGCAACTAGACTTTGAACTGCTG 59.439 43.478 0.00 0.00 0.00 4.41
2183 2190 3.561725 GCAACTAGACTTTGAACTGCTGT 59.438 43.478 0.00 0.00 0.00 4.40
2184 2191 4.035675 GCAACTAGACTTTGAACTGCTGTT 59.964 41.667 8.91 8.91 39.42 3.16
2185 2192 5.449177 GCAACTAGACTTTGAACTGCTGTTT 60.449 40.000 10.54 0.00 36.39 2.83
2186 2193 6.555315 CAACTAGACTTTGAACTGCTGTTTT 58.445 36.000 10.54 0.00 36.39 2.43
2187 2194 6.759497 ACTAGACTTTGAACTGCTGTTTTT 57.241 33.333 10.54 0.00 36.39 1.94
2188 2195 6.786207 ACTAGACTTTGAACTGCTGTTTTTC 58.214 36.000 10.54 0.00 36.39 2.29
2189 2196 4.662145 AGACTTTGAACTGCTGTTTTTCG 58.338 39.130 10.54 3.42 36.39 3.46
2190 2197 4.394920 AGACTTTGAACTGCTGTTTTTCGA 59.605 37.500 10.54 0.00 36.39 3.71
2191 2198 4.662145 ACTTTGAACTGCTGTTTTTCGAG 58.338 39.130 10.54 7.36 36.39 4.04
2192 2199 4.394920 ACTTTGAACTGCTGTTTTTCGAGA 59.605 37.500 10.54 0.00 36.39 4.04
2193 2200 4.955925 TTGAACTGCTGTTTTTCGAGAA 57.044 36.364 10.54 0.00 36.39 2.87
2194 2201 4.955925 TGAACTGCTGTTTTTCGAGAAA 57.044 36.364 10.54 0.00 36.39 2.52
2195 2202 5.303747 TGAACTGCTGTTTTTCGAGAAAA 57.696 34.783 10.54 6.89 38.40 2.29
2196 2203 5.092781 TGAACTGCTGTTTTTCGAGAAAAC 58.907 37.500 19.89 19.89 39.70 2.43
2197 2204 3.680789 ACTGCTGTTTTTCGAGAAAACG 58.319 40.909 20.62 17.56 41.62 3.60
2198 2205 2.446282 TGCTGTTTTTCGAGAAAACGC 58.554 42.857 24.09 24.09 41.62 4.84
2199 2206 2.159503 TGCTGTTTTTCGAGAAAACGCA 60.160 40.909 26.36 26.36 41.85 5.24
2200 2207 2.849473 GCTGTTTTTCGAGAAAACGCAA 59.151 40.909 24.83 14.00 41.62 4.85
2201 2208 3.302170 GCTGTTTTTCGAGAAAACGCAAA 59.698 39.130 24.83 13.80 41.62 3.68
2509 2516 8.712103 GGGTTAAATAGTTACAATCCTCCTAGT 58.288 37.037 0.00 0.00 0.00 2.57
2513 2520 7.541916 AATAGTTACAATCCTCCTAGTAGGC 57.458 40.000 11.75 0.00 36.51 3.93
2514 2521 3.890147 AGTTACAATCCTCCTAGTAGGCG 59.110 47.826 11.75 5.15 36.51 5.52
2515 2522 1.705873 ACAATCCTCCTAGTAGGCGG 58.294 55.000 17.95 17.95 41.66 6.13
2516 2523 1.063114 ACAATCCTCCTAGTAGGCGGT 60.063 52.381 22.11 9.24 41.08 5.68
2517 2524 2.040178 CAATCCTCCTAGTAGGCGGTT 58.960 52.381 22.11 13.09 41.08 4.44
2518 2525 3.228453 CAATCCTCCTAGTAGGCGGTTA 58.772 50.000 22.11 7.05 41.08 2.85
2519 2526 2.355010 TCCTCCTAGTAGGCGGTTAC 57.645 55.000 22.11 0.00 41.08 2.50
2520 2527 1.565759 TCCTCCTAGTAGGCGGTTACA 59.434 52.381 22.11 2.97 41.08 2.41
2521 2528 2.025037 TCCTCCTAGTAGGCGGTTACAA 60.025 50.000 22.11 2.61 41.08 2.41
2522 2529 2.100418 CCTCCTAGTAGGCGGTTACAAC 59.900 54.545 16.10 0.00 35.51 3.32
2523 2530 3.022406 CTCCTAGTAGGCGGTTACAACT 58.978 50.000 11.75 0.00 34.61 3.16
2524 2531 3.019564 TCCTAGTAGGCGGTTACAACTC 58.980 50.000 11.75 0.00 34.61 3.01
2525 2532 3.022406 CCTAGTAGGCGGTTACAACTCT 58.978 50.000 2.46 0.00 0.00 3.24
2526 2533 3.181489 CCTAGTAGGCGGTTACAACTCTG 60.181 52.174 2.46 0.00 0.00 3.35
2527 2534 1.549170 AGTAGGCGGTTACAACTCTGG 59.451 52.381 0.00 0.00 0.00 3.86
2528 2535 1.547372 GTAGGCGGTTACAACTCTGGA 59.453 52.381 0.00 0.00 0.00 3.86
2529 2536 1.276622 AGGCGGTTACAACTCTGGAT 58.723 50.000 0.00 0.00 0.00 3.41
2530 2537 1.066143 AGGCGGTTACAACTCTGGATG 60.066 52.381 0.00 0.00 0.00 3.51
2531 2538 1.369625 GCGGTTACAACTCTGGATGG 58.630 55.000 0.00 0.00 0.00 3.51
2532 2539 1.338769 GCGGTTACAACTCTGGATGGT 60.339 52.381 0.00 0.00 0.00 3.55
2533 2540 2.093869 GCGGTTACAACTCTGGATGGTA 60.094 50.000 0.00 0.00 0.00 3.25
2534 2541 3.782046 CGGTTACAACTCTGGATGGTAG 58.218 50.000 0.00 0.00 0.00 3.18
2535 2542 3.194968 CGGTTACAACTCTGGATGGTAGT 59.805 47.826 0.00 0.00 0.00 2.73
2536 2543 4.677250 CGGTTACAACTCTGGATGGTAGTC 60.677 50.000 0.00 0.00 0.00 2.59
2537 2544 4.222145 GGTTACAACTCTGGATGGTAGTCA 59.778 45.833 0.00 0.00 0.00 3.41
2538 2545 5.279809 GGTTACAACTCTGGATGGTAGTCAA 60.280 44.000 0.00 0.00 0.00 3.18
2539 2546 6.407202 GTTACAACTCTGGATGGTAGTCAAT 58.593 40.000 0.00 0.00 0.00 2.57
2540 2547 4.836825 ACAACTCTGGATGGTAGTCAATG 58.163 43.478 0.00 0.00 0.00 2.82
2567 2574 8.726870 ACTTTGAACTGCTGTTAGTTACTTAA 57.273 30.769 9.14 0.00 40.78 1.85
2746 2754 5.223655 TCTCATCAATGGAGGTGGGTATAA 58.776 41.667 0.00 0.00 33.18 0.98
2794 2802 2.880268 TCAAACAGCAACATCCTGACTG 59.120 45.455 0.00 0.00 34.47 3.51
2901 2909 3.006967 GGTACAAGGAGAAGAAGCAGACA 59.993 47.826 0.00 0.00 0.00 3.41
2943 2951 3.160679 AGGTATGCAACAAGGAAAGCT 57.839 42.857 0.00 0.00 0.00 3.74
3051 3059 3.759618 CAGCCCTACCAGATACTAGTAGC 59.240 52.174 10.21 10.21 33.61 3.58
3383 3391 2.102252 CTGCTTTGCCTTGGGTAAACAA 59.898 45.455 0.00 0.00 32.68 2.83
3384 3392 2.159028 TGCTTTGCCTTGGGTAAACAAC 60.159 45.455 0.00 0.00 32.68 3.32
3385 3393 2.159028 GCTTTGCCTTGGGTAAACAACA 60.159 45.455 0.00 0.00 32.68 3.33
3497 3507 6.494893 TCATGGCTTAACATTAACAGACAC 57.505 37.500 0.00 0.00 0.00 3.67
3584 3594 2.757314 TGCAGGTTCACACACAATTTCA 59.243 40.909 0.00 0.00 0.00 2.69
3776 3786 6.979817 GGCACATAAATTTCAATATGCTGTCA 59.020 34.615 4.64 0.00 33.71 3.58
3795 3805 3.664025 GTCACGCTATGTTGAGCAAAAAC 59.336 43.478 0.00 0.00 42.99 2.43
3796 3806 3.313803 TCACGCTATGTTGAGCAAAAACA 59.686 39.130 1.98 1.98 42.99 2.83
3798 3808 4.502282 CACGCTATGTTGAGCAAAAACAAA 59.498 37.500 3.43 0.00 42.99 2.83
3800 3810 5.752955 ACGCTATGTTGAGCAAAAACAAATT 59.247 32.000 3.43 0.00 42.99 1.82
3801 3811 6.066410 CGCTATGTTGAGCAAAAACAAATTG 58.934 36.000 3.43 0.00 42.99 2.32
3802 3812 6.365050 GCTATGTTGAGCAAAAACAAATTGG 58.635 36.000 0.00 0.00 40.69 3.16
3950 3960 8.677300 CAGTTTGACCTAAGTATGCATAAATGT 58.323 33.333 8.28 1.85 0.00 2.71
4072 4082 6.039717 AGCTTTATATGCAATGATGAAACGGT 59.960 34.615 0.00 0.00 0.00 4.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 6.925610 TTTCTTCGCTGCAGTTATTCATAT 57.074 33.333 16.64 0.00 0.00 1.78
72 73 6.038603 TGCAAATATCTAAGGTGATGTTCAGC 59.961 38.462 0.00 0.00 44.62 4.26
335 337 7.230027 CCAAAGATAGGAGAATTAGAAGGCAT 58.770 38.462 0.00 0.00 0.00 4.40
443 445 9.431887 TCCTAATGAATTCGTAATTATAGGCAC 57.568 33.333 14.03 0.00 34.73 5.01
564 566 4.518211 AGCAGGAGTCAAAACATTTGAGAG 59.482 41.667 5.81 0.00 0.00 3.20
586 589 9.655769 CACGTAATTTGGAATCATCTAATTGAG 57.344 33.333 0.00 0.00 0.00 3.02
638 641 0.958091 TCGTTGGAATTTGGCACAGG 59.042 50.000 0.00 0.00 42.39 4.00
639 642 2.791383 TTCGTTGGAATTTGGCACAG 57.209 45.000 0.00 0.00 42.39 3.66
726 729 1.730547 GCATCTTGTGGTTGCACGC 60.731 57.895 0.00 0.00 39.63 5.34
852 856 2.703536 TGAACTTACTTGGGAGTGAGCA 59.296 45.455 0.00 0.00 41.79 4.26
892 896 0.537188 TCATGTTCCTCTTCTCCCGC 59.463 55.000 0.00 0.00 0.00 6.13
930 934 5.239963 GGCTAGTCTCTAGTGTGTCCTATTC 59.760 48.000 5.82 0.00 0.00 1.75
956 960 2.354503 GGAGGGGTCTTACCGAAAACTC 60.355 54.545 0.00 0.00 39.83 3.01
960 964 0.978907 GTGGAGGGGTCTTACCGAAA 59.021 55.000 0.00 0.00 39.83 3.46
1528 1532 3.011566 TGGGTCACAAGTGATGTTGTT 57.988 42.857 6.15 0.00 41.46 2.83
1583 1590 1.726791 CGATGTACCTGTTCTGCACAC 59.273 52.381 0.00 0.00 0.00 3.82
1609 1616 2.910688 ACTACACACTCACACCCTTG 57.089 50.000 0.00 0.00 0.00 3.61
1682 1689 4.486503 CAGCCTGCCCTGCTCCTC 62.487 72.222 0.00 0.00 36.81 3.71
1716 1723 2.353803 GGAAGCTGTGTAGGTACTGGTG 60.354 54.545 0.00 0.00 41.52 4.17
1896 1903 5.893824 TCTGCATCTTGTATCCTAAGTGAGA 59.106 40.000 0.00 0.00 0.00 3.27
1996 2003 6.866248 GGAAAAGAACTTGCGGAAAATATCAA 59.134 34.615 0.00 0.00 0.00 2.57
2007 2014 3.502211 AGTATGTGGGAAAAGAACTTGCG 59.498 43.478 0.00 0.00 0.00 4.85
2065 2072 3.846588 AGGTCTGAGGGAATAAAGAGCAA 59.153 43.478 0.00 0.00 39.14 3.91
2134 2141 3.326836 ACAAGCTGCCTAAGTTCTCTC 57.673 47.619 0.00 0.00 0.00 3.20
2164 2171 6.456988 CGAAAAACAGCAGTTCAAAGTCTAGT 60.457 38.462 0.00 0.00 36.84 2.57
2168 2175 4.658071 TCGAAAAACAGCAGTTCAAAGTC 58.342 39.130 0.00 0.00 36.84 3.01
2169 2176 4.394920 TCTCGAAAAACAGCAGTTCAAAGT 59.605 37.500 0.00 0.00 36.84 2.66
2170 2177 4.908736 TCTCGAAAAACAGCAGTTCAAAG 58.091 39.130 0.00 0.00 36.84 2.77
2171 2178 4.955925 TCTCGAAAAACAGCAGTTCAAA 57.044 36.364 0.00 0.00 36.84 2.69
2172 2179 4.955925 TTCTCGAAAAACAGCAGTTCAA 57.044 36.364 0.00 0.00 36.84 2.69
2173 2180 4.955925 TTTCTCGAAAAACAGCAGTTCA 57.044 36.364 0.00 0.00 36.84 3.18
2174 2181 4.202358 CGTTTTCTCGAAAAACAGCAGTTC 59.798 41.667 23.27 6.39 41.37 3.01
2175 2182 4.095610 CGTTTTCTCGAAAAACAGCAGTT 58.904 39.130 23.27 0.00 41.37 3.16
2176 2183 3.680789 CGTTTTCTCGAAAAACAGCAGT 58.319 40.909 23.27 0.00 41.37 4.40
2177 2184 2.464016 GCGTTTTCTCGAAAAACAGCAG 59.536 45.455 24.83 16.22 41.37 4.24
2178 2185 2.159503 TGCGTTTTCTCGAAAAACAGCA 60.160 40.909 26.36 26.36 41.37 4.41
2179 2186 2.446282 TGCGTTTTCTCGAAAAACAGC 58.554 42.857 23.27 23.72 41.37 4.40
2483 2490 8.712103 ACTAGGAGGATTGTAACTATTTAACCC 58.288 37.037 0.00 0.00 0.00 4.11
2487 2494 9.086758 GCCTACTAGGAGGATTGTAACTATTTA 57.913 37.037 26.46 0.00 37.67 1.40
2488 2495 7.255871 CGCCTACTAGGAGGATTGTAACTATTT 60.256 40.741 26.46 0.00 37.67 1.40
2489 2496 6.208994 CGCCTACTAGGAGGATTGTAACTATT 59.791 42.308 26.46 0.00 37.67 1.73
2490 2497 5.711036 CGCCTACTAGGAGGATTGTAACTAT 59.289 44.000 26.46 0.00 37.67 2.12
2491 2498 5.068636 CGCCTACTAGGAGGATTGTAACTA 58.931 45.833 26.46 0.00 37.67 2.24
2492 2499 3.890147 CGCCTACTAGGAGGATTGTAACT 59.110 47.826 26.46 0.00 37.67 2.24
2493 2500 4.240175 CGCCTACTAGGAGGATTGTAAC 57.760 50.000 26.46 3.73 37.67 2.50
2502 2509 3.022406 AGTTGTAACCGCCTACTAGGAG 58.978 50.000 6.26 2.39 37.67 3.69
2503 2510 3.019564 GAGTTGTAACCGCCTACTAGGA 58.980 50.000 6.26 0.00 37.67 2.94
2504 2511 3.022406 AGAGTTGTAACCGCCTACTAGG 58.978 50.000 0.00 0.00 38.80 3.02
2505 2512 3.181489 CCAGAGTTGTAACCGCCTACTAG 60.181 52.174 0.00 0.00 0.00 2.57
2506 2513 2.756760 CCAGAGTTGTAACCGCCTACTA 59.243 50.000 0.00 0.00 0.00 1.82
2507 2514 1.549170 CCAGAGTTGTAACCGCCTACT 59.451 52.381 0.00 0.00 0.00 2.57
2508 2515 1.547372 TCCAGAGTTGTAACCGCCTAC 59.453 52.381 0.00 0.00 0.00 3.18
2509 2516 1.927487 TCCAGAGTTGTAACCGCCTA 58.073 50.000 0.00 0.00 0.00 3.93
2510 2517 1.066143 CATCCAGAGTTGTAACCGCCT 60.066 52.381 0.00 0.00 0.00 5.52
2511 2518 1.369625 CATCCAGAGTTGTAACCGCC 58.630 55.000 0.00 0.00 0.00 6.13
2512 2519 1.338769 ACCATCCAGAGTTGTAACCGC 60.339 52.381 0.00 0.00 0.00 5.68
2513 2520 2.762535 ACCATCCAGAGTTGTAACCG 57.237 50.000 0.00 0.00 0.00 4.44
2514 2521 4.222145 TGACTACCATCCAGAGTTGTAACC 59.778 45.833 0.00 0.00 0.00 2.85
2515 2522 5.401531 TGACTACCATCCAGAGTTGTAAC 57.598 43.478 0.00 0.00 0.00 2.50
2516 2523 6.406370 CATTGACTACCATCCAGAGTTGTAA 58.594 40.000 0.00 0.00 0.00 2.41
2517 2524 5.104941 CCATTGACTACCATCCAGAGTTGTA 60.105 44.000 0.00 0.00 0.00 2.41
2518 2525 4.323792 CCATTGACTACCATCCAGAGTTGT 60.324 45.833 0.00 0.00 0.00 3.32
2519 2526 4.080919 TCCATTGACTACCATCCAGAGTTG 60.081 45.833 0.00 0.00 0.00 3.16
2520 2527 4.080863 GTCCATTGACTACCATCCAGAGTT 60.081 45.833 0.00 0.00 38.53 3.01
2521 2528 3.452627 GTCCATTGACTACCATCCAGAGT 59.547 47.826 0.00 0.00 38.53 3.24
2522 2529 4.065321 GTCCATTGACTACCATCCAGAG 57.935 50.000 0.00 0.00 38.53 3.35
2531 2538 9.067541 AACAGCAGTTCAAAGTCCATTGACTAC 62.068 40.741 0.00 0.00 41.83 2.73
2532 2539 7.135261 AACAGCAGTTCAAAGTCCATTGACTA 61.135 38.462 0.00 0.00 41.83 2.59
2533 2540 6.384323 AACAGCAGTTCAAAGTCCATTGACT 61.384 40.000 0.00 0.00 43.52 3.41
2534 2541 3.316308 ACAGCAGTTCAAAGTCCATTGAC 59.684 43.478 0.00 0.00 38.95 3.18
2535 2542 3.554934 ACAGCAGTTCAAAGTCCATTGA 58.445 40.909 0.00 0.00 37.53 2.57
2536 2543 3.996150 ACAGCAGTTCAAAGTCCATTG 57.004 42.857 0.00 0.00 0.00 2.82
2537 2544 5.133221 ACTAACAGCAGTTCAAAGTCCATT 58.867 37.500 0.00 0.00 39.15 3.16
2538 2545 4.718961 ACTAACAGCAGTTCAAAGTCCAT 58.281 39.130 0.00 0.00 39.15 3.41
2539 2546 4.150897 ACTAACAGCAGTTCAAAGTCCA 57.849 40.909 0.00 0.00 39.15 4.02
2540 2547 5.758784 AGTAACTAACAGCAGTTCAAAGTCC 59.241 40.000 0.00 0.00 39.45 3.85
2567 2574 4.950475 TGTCGGTAGATGAGTTTGAGATCT 59.050 41.667 0.00 0.00 0.00 2.75
2746 2754 2.303022 CTGGTCTGGTGTTGTCTGGTAT 59.697 50.000 0.00 0.00 0.00 2.73
2751 2759 4.357325 AGATATCTGGTCTGGTGTTGTCT 58.643 43.478 3.89 0.00 0.00 3.41
2901 2909 6.839134 ACCTTATGGTTTTCTGAAACTTCCTT 59.161 34.615 1.58 6.97 46.05 3.36
3276 3284 6.757010 ACTCTTGATAATCGCGTGAAATACTT 59.243 34.615 5.77 0.00 0.00 2.24
3497 3507 6.470877 GCGTAACCATGGTTTATTGTTATGTG 59.529 38.462 34.04 10.27 36.76 3.21
3584 3594 6.400303 CGAAACTGATGTCGTAAACCGTTATT 60.400 38.462 0.00 0.00 37.94 1.40
3776 3786 3.980646 TGTTTTTGCTCAACATAGCGT 57.019 38.095 0.00 0.00 45.85 5.07
3795 3805 3.672867 GGTCAACATACAACGCCAATTTG 59.327 43.478 0.00 0.00 0.00 2.32
3796 3806 3.319405 TGGTCAACATACAACGCCAATTT 59.681 39.130 0.00 0.00 0.00 1.82
3798 3808 2.509569 TGGTCAACATACAACGCCAAT 58.490 42.857 0.00 0.00 0.00 3.16
3800 3810 1.968704 TTGGTCAACATACAACGCCA 58.031 45.000 0.00 0.00 0.00 5.69
3801 3811 3.569250 AATTGGTCAACATACAACGCC 57.431 42.857 0.00 0.00 0.00 5.68
3802 3812 4.541779 TCAAATTGGTCAACATACAACGC 58.458 39.130 0.00 0.00 0.00 4.84
3847 3857 2.225041 GCCTCTACCCCCTTCAAACTTT 60.225 50.000 0.00 0.00 0.00 2.66
3950 3960 2.616960 AGATGTCACGCGAGCATTTTA 58.383 42.857 15.93 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.