Multiple sequence alignment - TraesCS2D01G268600

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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 TraesCS2D01G268600 chr2D 100.000 2330 0 0 1 2330 329862267 329859938 0.000000e+00 4303.0
1 TraesCS2D01G268600 chr2D 92.248 129 8 1 1 127 269137309 269137437 5.110000e-42 182.0
2 TraesCS2D01G268600 chr2D 83.333 84 12 2 2040 2121 618985937 618986020 2.480000e-10 76.8
3 TraesCS2D01G268600 chr2B 94.207 1588 71 10 1 1578 398396084 398394508 0.000000e+00 2403.0
4 TraesCS2D01G268600 chr2B 95.824 455 16 2 1578 2029 398394420 398393966 0.000000e+00 732.0
5 TraesCS2D01G268600 chr2B 84.977 213 9 10 2123 2330 398393675 398393481 6.570000e-46 195.0
6 TraesCS2D01G268600 chr2A 95.270 1501 47 13 546 2032 436721792 436720302 0.000000e+00 2357.0
7 TraesCS2D01G268600 chr2A 84.818 303 35 8 246 547 436722245 436721953 6.300000e-76 294.0
8 TraesCS2D01G268600 chr2A 94.118 136 6 2 112 247 436722433 436722300 3.030000e-49 206.0
9 TraesCS2D01G268600 chr2A 93.939 132 7 1 2128 2258 436720259 436720128 5.080000e-47 198.0
10 TraesCS2D01G268600 chr2A 86.207 87 11 1 2040 2125 487346564 487346478 2.470000e-15 93.5
11 TraesCS2D01G268600 chr6B 84.830 501 53 19 842 1333 21872877 21873363 1.250000e-132 483.0
12 TraesCS2D01G268600 chr6B 91.011 89 8 0 723 811 21870014 21870102 1.130000e-23 121.0
13 TraesCS2D01G268600 chr6D 91.445 339 23 5 993 1331 11921616 11921948 5.870000e-126 460.0
14 TraesCS2D01G268600 chr6D 91.011 89 8 0 723 811 11919099 11919187 1.130000e-23 121.0
15 TraesCS2D01G268600 chr6A 91.150 339 24 5 993 1331 13434443 13434775 2.730000e-124 455.0
16 TraesCS2D01G268600 chr3D 95.798 119 5 0 1 119 243608180 243608062 2.360000e-45 193.0
17 TraesCS2D01G268600 chr7B 96.522 115 4 0 1 115 298318643 298318529 8.500000e-45 191.0
18 TraesCS2D01G268600 chr7B 96.154 52 2 0 2074 2125 41189366 41189315 4.130000e-13 86.1
19 TraesCS2D01G268600 chr5D 94.309 123 5 2 1 123 143308147 143308267 1.100000e-43 187.0
20 TraesCS2D01G268600 chr5D 94.958 119 4 2 1 119 186403211 186403095 3.950000e-43 185.0
21 TraesCS2D01G268600 chr4B 95.726 117 4 1 1 117 345590780 345590895 1.100000e-43 187.0
22 TraesCS2D01G268600 chr4B 77.358 159 29 7 1145 1298 599356854 599356698 1.150000e-13 87.9
23 TraesCS2D01G268600 chr1B 92.857 126 7 2 1 126 246018884 246019007 5.110000e-42 182.0
24 TraesCS2D01G268600 chr1D 90.977 133 10 2 1 132 493464099 493463968 6.620000e-41 178.0
25 TraesCS2D01G268600 chr4D 78.616 159 27 7 1145 1298 474918798 474918954 5.300000e-17 99.0
26 TraesCS2D01G268600 chr4A 78.616 159 27 7 1145 1298 681178874 681178718 5.300000e-17 99.0
27 TraesCS2D01G268600 chr4A 94.595 37 2 0 2084 2120 644450324 644450360 8.990000e-05 58.4
28 TraesCS2D01G268600 chr3B 93.333 45 3 0 2088 2132 762638695 762638651 1.490000e-07 67.6


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 TraesCS2D01G268600 chr2D 329859938 329862267 2329 True 4303.00 4303 100.000000 1 2330 1 chr2D.!!$R1 2329
1 TraesCS2D01G268600 chr2B 398393481 398396084 2603 True 1110.00 2403 91.669333 1 2330 3 chr2B.!!$R1 2329
2 TraesCS2D01G268600 chr2A 436720128 436722433 2305 True 763.75 2357 92.036250 112 2258 4 chr2A.!!$R2 2146
3 TraesCS2D01G268600 chr6B 21870014 21873363 3349 False 302.00 483 87.920500 723 1333 2 chr6B.!!$F1 610
4 TraesCS2D01G268600 chr6D 11919099 11921948 2849 False 290.50 460 91.228000 723 1331 2 chr6D.!!$F1 608

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
664 883 1.133699 TGGCCATCCATTCTGTGATCC 60.134 52.381 0.0 0.0 37.47 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 5376 0.250124 CACCACAGCCAAACGGTAGA 60.25 55.0 0.0 0.0 0.0 2.59 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
31 32 8.024285 TGAAAGTACCTGGTAATTTAATTTGCG 58.976 33.333 26.60 0.00 36.63 4.85
35 36 3.545873 CCTGGTAATTTAATTTGCGTGCG 59.454 43.478 0.00 0.00 0.00 5.34
55 56 2.033550 CGCGAGCTCTAGTAATTGGTCT 59.966 50.000 12.85 0.00 0.00 3.85
77 78 3.318313 AGTATGTATAGCAGCAGGGGTT 58.682 45.455 0.00 0.00 0.00 4.11
276 332 1.462731 GGTGTTGCATGGACTTGGCA 61.463 55.000 0.00 0.00 35.41 4.92
287 343 4.150897 TGGACTTGGCATACTTGGTATC 57.849 45.455 0.00 0.00 0.00 2.24
366 423 4.532834 GACCTTTGGTTGGATGGCTATAA 58.467 43.478 0.00 0.00 35.25 0.98
383 440 2.005370 TAAGTGGAGGTGACGTTCCT 57.995 50.000 12.04 12.04 38.09 3.36
440 497 3.995199 ACTTGTCAGCTCAATCTTTCGA 58.005 40.909 0.00 0.00 0.00 3.71
458 516 7.272244 TCTTTCGAAATTGCTCATAGGTATGA 58.728 34.615 11.70 0.00 40.19 2.15
463 521 6.203530 CGAAATTGCTCATAGGTATGATGTGT 59.796 38.462 0.13 0.00 41.46 3.72
467 525 4.651045 TGCTCATAGGTATGATGTGTGTCT 59.349 41.667 0.13 0.00 41.46 3.41
472 530 7.661040 TCATAGGTATGATGTGTGTCTATGTG 58.339 38.462 0.00 0.00 37.76 3.21
476 534 7.265673 AGGTATGATGTGTGTCTATGTGTTAC 58.734 38.462 0.00 0.00 0.00 2.50
496 554 3.405831 ACTAGCGGCGAGTGTATGTATA 58.594 45.455 15.08 0.00 0.00 1.47
599 818 5.242171 TCCATCGTTATTATAGACGGCTTCA 59.758 40.000 0.00 0.00 39.59 3.02
617 836 4.992951 GCTTCAATGACCATCTTGCTTTTT 59.007 37.500 0.00 0.00 0.00 1.94
639 858 1.150536 GGCCCAGAGGAACACAACA 59.849 57.895 0.00 0.00 33.47 3.33
664 883 1.133699 TGGCCATCCATTCTGTGATCC 60.134 52.381 0.00 0.00 37.47 3.36
817 2819 4.783621 GCCGATGCAGGAGCCACA 62.784 66.667 0.00 0.00 41.13 4.17
857 4056 1.262640 ACGTCATCCCGGTAGCCTTT 61.263 55.000 0.00 0.00 0.00 3.11
861 4060 3.056754 ATCCCGGTAGCCTTTGCCC 62.057 63.158 0.00 0.00 38.69 5.36
1192 4413 1.507174 GAGCGCTACCTCAACGACT 59.493 57.895 11.50 0.00 0.00 4.18
1367 4588 3.901844 TGTCTGCCCTGGGTAAGATATAC 59.098 47.826 19.18 10.33 0.00 1.47
1368 4589 4.161102 GTCTGCCCTGGGTAAGATATACT 58.839 47.826 19.18 0.00 0.00 2.12
1369 4590 4.021016 GTCTGCCCTGGGTAAGATATACTG 60.021 50.000 19.18 3.43 0.00 2.74
1370 4591 3.904339 CTGCCCTGGGTAAGATATACTGT 59.096 47.826 15.56 0.00 0.00 3.55
1371 4592 5.082633 TGCCCTGGGTAAGATATACTGTA 57.917 43.478 15.56 0.00 0.00 2.74
1411 4632 3.077556 CTACCTGGCAGGACGGCT 61.078 66.667 38.99 19.27 37.67 5.52
1446 4667 8.792830 ATATATTACCACCGTACGTATGTAGT 57.207 34.615 15.21 10.65 0.00 2.73
1447 4668 9.884636 ATATATTACCACCGTACGTATGTAGTA 57.115 33.333 15.21 12.28 0.00 1.82
1466 4687 6.799925 TGTAGTATTGTATATGTGTGCGATCG 59.200 38.462 11.69 11.69 0.00 3.69
1534 4755 2.285834 GCATGTGTGTAGCTCAATACGC 60.286 50.000 0.00 0.00 36.82 4.42
1803 5116 2.288640 GGCTTGCCATGATATTTCAGCC 60.289 50.000 6.79 0.00 34.73 4.85
1947 5262 2.038557 GGTCCAGAGCACCTTAGAAACA 59.961 50.000 0.00 0.00 0.00 2.83
2024 5339 2.622436 GAGATTAAGCTCGCACCTGTT 58.378 47.619 4.74 0.00 0.00 3.16
2032 5347 0.583438 CTCGCACCTGTTGTCTGTTG 59.417 55.000 0.00 0.00 0.00 3.33
2033 5348 0.107897 TCGCACCTGTTGTCTGTTGT 60.108 50.000 0.00 0.00 0.00 3.32
2035 5350 0.248621 GCACCTGTTGTCTGTTGTGC 60.249 55.000 0.00 0.00 41.75 4.57
2036 5351 1.093972 CACCTGTTGTCTGTTGTGCA 58.906 50.000 0.00 0.00 0.00 4.57
2037 5352 1.472082 CACCTGTTGTCTGTTGTGCAA 59.528 47.619 0.00 0.00 0.00 4.08
2038 5353 1.472480 ACCTGTTGTCTGTTGTGCAAC 59.528 47.619 8.01 8.01 41.81 4.17
2040 5355 2.478370 CCTGTTGTCTGTTGTGCAACTG 60.478 50.000 14.97 14.16 41.93 3.16
2041 5356 2.158559 TGTTGTCTGTTGTGCAACTGT 58.841 42.857 14.97 0.00 41.93 3.55
2042 5357 2.095314 TGTTGTCTGTTGTGCAACTGTG 60.095 45.455 14.97 6.74 41.93 3.66
2043 5358 1.819928 TGTCTGTTGTGCAACTGTGT 58.180 45.000 14.97 0.00 41.67 3.72
2044 5359 1.468127 TGTCTGTTGTGCAACTGTGTG 59.532 47.619 14.97 2.76 41.67 3.82
2045 5360 0.451383 TCTGTTGTGCAACTGTGTGC 59.549 50.000 14.97 7.66 45.15 4.57
2051 5366 3.209097 GCAACTGTGTGCGTGGGT 61.209 61.111 0.55 0.00 34.21 4.51
2052 5367 2.715005 CAACTGTGTGCGTGGGTG 59.285 61.111 0.00 0.00 0.00 4.61
2053 5368 1.817520 CAACTGTGTGCGTGGGTGA 60.818 57.895 0.00 0.00 0.00 4.02
2054 5369 1.078072 AACTGTGTGCGTGGGTGAA 60.078 52.632 0.00 0.00 0.00 3.18
2055 5370 1.373590 AACTGTGTGCGTGGGTGAAC 61.374 55.000 0.00 0.00 0.00 3.18
2056 5371 2.515057 TGTGTGCGTGGGTGAACC 60.515 61.111 0.00 0.00 40.81 3.62
2057 5372 2.203153 GTGTGCGTGGGTGAACCT 60.203 61.111 0.00 0.00 41.11 3.50
2058 5373 1.822186 GTGTGCGTGGGTGAACCTT 60.822 57.895 0.00 0.00 41.11 3.50
2059 5374 1.821759 TGTGCGTGGGTGAACCTTG 60.822 57.895 0.00 0.00 41.11 3.61
2060 5375 1.822186 GTGCGTGGGTGAACCTTGT 60.822 57.895 0.00 0.00 41.11 3.16
2061 5376 1.077357 TGCGTGGGTGAACCTTGTT 60.077 52.632 0.00 0.00 41.11 2.83
2062 5377 1.098712 TGCGTGGGTGAACCTTGTTC 61.099 55.000 0.00 0.07 41.11 3.18
2063 5378 0.818040 GCGTGGGTGAACCTTGTTCT 60.818 55.000 8.30 0.00 41.11 3.01
2064 5379 1.541670 GCGTGGGTGAACCTTGTTCTA 60.542 52.381 8.30 0.00 41.11 2.10
2065 5380 2.140717 CGTGGGTGAACCTTGTTCTAC 58.859 52.381 8.30 5.20 41.11 2.59
2066 5381 2.501261 GTGGGTGAACCTTGTTCTACC 58.499 52.381 14.70 14.70 41.11 3.18
2067 5382 1.071071 TGGGTGAACCTTGTTCTACCG 59.929 52.381 15.70 0.00 41.11 4.02
2068 5383 1.071228 GGGTGAACCTTGTTCTACCGT 59.929 52.381 15.70 0.00 35.85 4.83
2069 5384 2.486013 GGGTGAACCTTGTTCTACCGTT 60.486 50.000 15.70 0.00 35.85 4.44
2070 5385 3.208594 GGTGAACCTTGTTCTACCGTTT 58.791 45.455 8.30 0.00 0.00 3.60
2071 5386 3.002965 GGTGAACCTTGTTCTACCGTTTG 59.997 47.826 8.30 0.00 0.00 2.93
2072 5387 3.002965 GTGAACCTTGTTCTACCGTTTGG 59.997 47.826 8.30 0.00 42.84 3.28
2073 5388 1.601166 ACCTTGTTCTACCGTTTGGC 58.399 50.000 0.00 0.00 39.70 4.52
2074 5389 1.142262 ACCTTGTTCTACCGTTTGGCT 59.858 47.619 0.00 0.00 39.70 4.75
2075 5390 1.535462 CCTTGTTCTACCGTTTGGCTG 59.465 52.381 0.00 0.00 39.70 4.85
2076 5391 2.218603 CTTGTTCTACCGTTTGGCTGT 58.781 47.619 0.00 0.00 39.70 4.40
2077 5392 1.588674 TGTTCTACCGTTTGGCTGTG 58.411 50.000 0.00 0.00 39.70 3.66
2078 5393 0.872388 GTTCTACCGTTTGGCTGTGG 59.128 55.000 0.00 0.00 39.70 4.17
2079 5394 0.470766 TTCTACCGTTTGGCTGTGGT 59.529 50.000 0.00 0.00 39.70 4.16
2080 5395 0.250124 TCTACCGTTTGGCTGTGGTG 60.250 55.000 0.00 0.00 39.70 4.17
2081 5396 1.228003 TACCGTTTGGCTGTGGTGG 60.228 57.895 0.00 0.00 39.70 4.61
2082 5397 1.985460 TACCGTTTGGCTGTGGTGGT 61.985 55.000 0.00 0.00 39.70 4.16
2083 5398 2.124693 CCGTTTGGCTGTGGTGGTT 61.125 57.895 0.00 0.00 0.00 3.67
2084 5399 1.671901 CCGTTTGGCTGTGGTGGTTT 61.672 55.000 0.00 0.00 0.00 3.27
2085 5400 0.527385 CGTTTGGCTGTGGTGGTTTG 60.527 55.000 0.00 0.00 0.00 2.93
2086 5401 0.820871 GTTTGGCTGTGGTGGTTTGA 59.179 50.000 0.00 0.00 0.00 2.69
2087 5402 1.412343 GTTTGGCTGTGGTGGTTTGAT 59.588 47.619 0.00 0.00 0.00 2.57
2088 5403 1.786937 TTGGCTGTGGTGGTTTGATT 58.213 45.000 0.00 0.00 0.00 2.57
2089 5404 1.786937 TGGCTGTGGTGGTTTGATTT 58.213 45.000 0.00 0.00 0.00 2.17
2090 5405 2.950781 TGGCTGTGGTGGTTTGATTTA 58.049 42.857 0.00 0.00 0.00 1.40
2091 5406 3.505386 TGGCTGTGGTGGTTTGATTTAT 58.495 40.909 0.00 0.00 0.00 1.40
2092 5407 3.900601 TGGCTGTGGTGGTTTGATTTATT 59.099 39.130 0.00 0.00 0.00 1.40
2093 5408 4.346418 TGGCTGTGGTGGTTTGATTTATTT 59.654 37.500 0.00 0.00 0.00 1.40
2094 5409 5.540337 TGGCTGTGGTGGTTTGATTTATTTA 59.460 36.000 0.00 0.00 0.00 1.40
2095 5410 6.212388 TGGCTGTGGTGGTTTGATTTATTTAT 59.788 34.615 0.00 0.00 0.00 1.40
2096 5411 7.397476 TGGCTGTGGTGGTTTGATTTATTTATA 59.603 33.333 0.00 0.00 0.00 0.98
2097 5412 8.254508 GGCTGTGGTGGTTTGATTTATTTATAA 58.745 33.333 0.00 0.00 0.00 0.98
2098 5413 9.646427 GCTGTGGTGGTTTGATTTATTTATAAA 57.354 29.630 0.00 0.00 36.75 1.40
2100 5415 9.646427 TGTGGTGGTTTGATTTATTTATAAAGC 57.354 29.630 3.94 4.06 38.67 3.51
2101 5416 9.646427 GTGGTGGTTTGATTTATTTATAAAGCA 57.354 29.630 8.61 8.61 44.11 3.91
2109 5424 9.862371 TTGATTTATTTATAAAGCAAGGCGAAA 57.138 25.926 17.29 0.28 47.00 3.46
2110 5425 9.515020 TGATTTATTTATAAAGCAAGGCGAAAG 57.485 29.630 9.91 0.00 43.22 2.62
2111 5426 8.352752 ATTTATTTATAAAGCAAGGCGAAAGC 57.647 30.769 3.94 0.00 45.01 3.51
2258 5775 3.388024 ACCACTATTACGGACATGCTCAT 59.612 43.478 0.00 0.00 0.00 2.90
2259 5776 3.990469 CCACTATTACGGACATGCTCATC 59.010 47.826 0.00 0.00 0.00 2.92
2261 5778 5.048013 CCACTATTACGGACATGCTCATCTA 60.048 44.000 0.00 0.00 0.00 1.98
2262 5779 6.447162 CACTATTACGGACATGCTCATCTAA 58.553 40.000 0.00 0.00 0.00 2.10
2263 5780 6.584184 CACTATTACGGACATGCTCATCTAAG 59.416 42.308 0.00 0.00 0.00 2.18
2264 5781 5.791336 ATTACGGACATGCTCATCTAAGA 57.209 39.130 0.00 0.00 0.00 2.10
2265 5782 5.791336 TTACGGACATGCTCATCTAAGAT 57.209 39.130 0.00 0.00 0.00 2.40
2266 5783 3.987547 ACGGACATGCTCATCTAAGATG 58.012 45.455 0.00 0.00 0.00 2.90
2267 5784 3.244009 ACGGACATGCTCATCTAAGATGG 60.244 47.826 0.00 0.00 0.00 3.51
2268 5785 3.672808 GGACATGCTCATCTAAGATGGG 58.327 50.000 0.00 0.00 0.00 4.00
2269 5786 3.072184 GGACATGCTCATCTAAGATGGGT 59.928 47.826 0.00 0.00 0.00 4.51
2270 5787 4.284490 GGACATGCTCATCTAAGATGGGTA 59.716 45.833 0.00 0.00 0.00 3.69
2271 5788 5.221722 GGACATGCTCATCTAAGATGGGTAA 60.222 44.000 0.00 0.00 0.00 2.85
2272 5789 6.445451 ACATGCTCATCTAAGATGGGTAAT 57.555 37.500 0.00 0.00 0.00 1.89
2273 5790 6.471146 ACATGCTCATCTAAGATGGGTAATC 58.529 40.000 0.00 0.00 35.29 1.75
2274 5791 6.043590 ACATGCTCATCTAAGATGGGTAATCA 59.956 38.462 0.00 0.00 37.81 2.57
2275 5792 5.858381 TGCTCATCTAAGATGGGTAATCAC 58.142 41.667 0.00 0.00 37.81 3.06
2276 5793 5.366477 TGCTCATCTAAGATGGGTAATCACA 59.634 40.000 0.00 0.00 37.81 3.58
2307 5824 6.837992 TCCGAAAAGAAGATTAAACATTCCG 58.162 36.000 0.00 0.00 0.00 4.30
2311 5828 4.236527 AGAAGATTAAACATTCCGGCCT 57.763 40.909 0.00 0.00 0.00 5.19
2312 5829 4.200092 AGAAGATTAAACATTCCGGCCTC 58.800 43.478 0.00 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.024285 CGCAAATTAAATTACCAGGTACTTTCA 58.976 33.333 16.28 8.17 34.60 2.69
6 7 8.024865 ACGCAAATTAAATTACCAGGTACTTTC 58.975 33.333 16.28 3.28 34.60 2.62
10 11 5.513849 GCACGCAAATTAAATTACCAGGTAC 59.486 40.000 0.00 0.00 0.00 3.34
16 17 2.036086 CGCGCACGCAAATTAAATTACC 60.036 45.455 16.04 0.00 42.06 2.85
28 29 4.836688 CTAGAGCTCGCGCACGCA 62.837 66.667 18.45 1.60 42.06 5.24
29 30 2.914797 TTACTAGAGCTCGCGCACGC 62.915 60.000 8.75 9.28 39.84 5.34
31 32 1.518929 CAATTACTAGAGCTCGCGCAC 59.481 52.381 8.75 0.00 39.10 5.34
35 36 3.719173 AGACCAATTACTAGAGCTCGC 57.281 47.619 8.37 0.00 0.00 5.03
55 56 4.127918 ACCCCTGCTGCTATACATACTA 57.872 45.455 0.00 0.00 0.00 1.82
77 78 6.889177 ACATCAATATCATTGTTACACCCACA 59.111 34.615 0.00 0.00 0.00 4.17
146 147 3.181482 CGCCCTCGAGCATATAGATGATT 60.181 47.826 6.99 0.00 38.10 2.57
331 387 5.687166 ACCAAAGGTCGGTTCTCATATTA 57.313 39.130 0.00 0.00 30.53 0.98
333 389 4.261801 CAACCAAAGGTCGGTTCTCATAT 58.738 43.478 0.00 0.00 45.06 1.78
349 405 3.525609 TCCACTTATAGCCATCCAACCAA 59.474 43.478 0.00 0.00 0.00 3.67
359 415 1.755380 ACGTCACCTCCACTTATAGCC 59.245 52.381 0.00 0.00 0.00 3.93
366 423 0.759436 ACAGGAACGTCACCTCCACT 60.759 55.000 10.67 0.00 35.35 4.00
383 440 1.753078 AGGCACCTCGCTATCGACA 60.753 57.895 0.00 0.00 40.21 4.35
440 497 6.830324 ACACACATCATACCTATGAGCAATTT 59.170 34.615 1.68 0.00 45.01 1.82
458 516 5.340803 CGCTAGTAACACATAGACACACAT 58.659 41.667 0.00 0.00 0.00 3.21
463 521 2.223409 CGCCGCTAGTAACACATAGACA 60.223 50.000 0.00 0.00 0.00 3.41
467 525 2.019249 ACTCGCCGCTAGTAACACATA 58.981 47.619 0.00 0.00 0.00 2.29
472 530 2.223433 ACATACACTCGCCGCTAGTAAC 60.223 50.000 0.00 0.00 0.00 2.50
476 534 2.991434 ATACATACACTCGCCGCTAG 57.009 50.000 0.00 0.00 0.00 3.42
496 554 6.814954 ATAGACACAGACCCTCATAAACAT 57.185 37.500 0.00 0.00 0.00 2.71
599 818 4.549458 CACGAAAAAGCAAGATGGTCATT 58.451 39.130 0.00 0.00 0.00 2.57
617 836 2.525629 TGTTCCTCTGGGCCACGA 60.526 61.111 0.00 3.60 0.00 4.35
664 883 4.387559 TCGAATACTGACAATCAACCGTTG 59.612 41.667 4.78 4.78 0.00 4.10
817 2819 1.677820 GGGTGCACTGCTTATTACGGT 60.678 52.381 17.98 0.00 0.00 4.83
857 4056 2.303022 GTGCAGAGCTTATATAGGGGCA 59.697 50.000 0.00 0.00 0.00 5.36
861 4060 5.736951 AGAAGGTGCAGAGCTTATATAGG 57.263 43.478 0.00 0.00 40.07 2.57
1167 4388 4.400251 AGGTAGCGCTCCCACCCT 62.400 66.667 22.18 13.41 32.43 4.34
1192 4413 2.343758 GAACTGGAGCAGGCACGA 59.656 61.111 0.00 0.00 35.51 4.35
1367 4588 4.706035 AGACTACCTCGTGGTATCTACAG 58.294 47.826 16.28 8.36 46.67 2.74
1368 4589 4.767578 AGACTACCTCGTGGTATCTACA 57.232 45.455 16.28 0.00 46.67 2.74
1369 4590 4.210955 CGAAGACTACCTCGTGGTATCTAC 59.789 50.000 16.28 8.56 46.67 2.59
1370 4591 4.141846 ACGAAGACTACCTCGTGGTATCTA 60.142 45.833 16.28 0.00 46.67 1.98
1371 4592 3.204526 CGAAGACTACCTCGTGGTATCT 58.795 50.000 16.28 16.30 46.67 1.98
1411 4632 4.142116 CGGTGGTAATATATATGACGGCCA 60.142 45.833 2.24 9.52 0.00 5.36
1445 4666 6.684609 TTCGATCGCACACATATACAATAC 57.315 37.500 11.09 0.00 0.00 1.89
1446 4667 7.883229 ATTTCGATCGCACACATATACAATA 57.117 32.000 11.09 0.00 0.00 1.90
1447 4668 6.785488 ATTTCGATCGCACACATATACAAT 57.215 33.333 11.09 0.00 0.00 2.71
1593 4905 6.237901 TCAAGCTTCACAAACCATACACTAT 58.762 36.000 0.00 0.00 0.00 2.12
2024 5339 1.468127 CACACAGTTGCACAACAGACA 59.532 47.619 15.40 0.00 43.47 3.41
2032 5347 2.024588 CCACGCACACAGTTGCAC 59.975 61.111 0.00 0.00 43.15 4.57
2033 5348 3.208383 CCCACGCACACAGTTGCA 61.208 61.111 8.01 0.00 43.15 4.08
2035 5350 1.372838 TTCACCCACGCACACAGTTG 61.373 55.000 0.00 0.00 0.00 3.16
2036 5351 1.078072 TTCACCCACGCACACAGTT 60.078 52.632 0.00 0.00 0.00 3.16
2037 5352 1.817941 GTTCACCCACGCACACAGT 60.818 57.895 0.00 0.00 0.00 3.55
2038 5353 2.542907 GGTTCACCCACGCACACAG 61.543 63.158 0.00 0.00 0.00 3.66
2040 5355 1.822186 AAGGTTCACCCACGCACAC 60.822 57.895 0.00 0.00 36.42 3.82
2041 5356 1.821759 CAAGGTTCACCCACGCACA 60.822 57.895 0.00 0.00 36.42 4.57
2042 5357 1.381165 AACAAGGTTCACCCACGCAC 61.381 55.000 0.00 0.00 36.42 5.34
2043 5358 1.077357 AACAAGGTTCACCCACGCA 60.077 52.632 0.00 0.00 36.42 5.24
2044 5359 0.818040 AGAACAAGGTTCACCCACGC 60.818 55.000 11.28 0.00 36.42 5.34
2045 5360 2.140717 GTAGAACAAGGTTCACCCACG 58.859 52.381 11.28 0.00 36.42 4.94
2046 5361 2.501261 GGTAGAACAAGGTTCACCCAC 58.499 52.381 11.28 4.03 36.42 4.61
2047 5362 1.071071 CGGTAGAACAAGGTTCACCCA 59.929 52.381 11.28 0.00 36.42 4.51
2048 5363 1.071228 ACGGTAGAACAAGGTTCACCC 59.929 52.381 11.28 8.81 36.42 4.61
2049 5364 2.538512 ACGGTAGAACAAGGTTCACC 57.461 50.000 11.28 13.48 0.00 4.02
2050 5365 3.002965 CCAAACGGTAGAACAAGGTTCAC 59.997 47.826 11.28 7.29 0.00 3.18
2051 5366 3.207778 CCAAACGGTAGAACAAGGTTCA 58.792 45.455 11.28 0.00 0.00 3.18
2052 5367 2.031420 GCCAAACGGTAGAACAAGGTTC 60.031 50.000 0.94 0.94 0.00 3.62
2053 5368 1.951602 GCCAAACGGTAGAACAAGGTT 59.048 47.619 0.00 0.00 0.00 3.50
2054 5369 1.142262 AGCCAAACGGTAGAACAAGGT 59.858 47.619 0.00 0.00 0.00 3.50
2055 5370 1.535462 CAGCCAAACGGTAGAACAAGG 59.465 52.381 0.00 0.00 0.00 3.61
2056 5371 2.032030 CACAGCCAAACGGTAGAACAAG 60.032 50.000 0.00 0.00 0.00 3.16
2057 5372 1.944024 CACAGCCAAACGGTAGAACAA 59.056 47.619 0.00 0.00 0.00 2.83
2058 5373 1.588674 CACAGCCAAACGGTAGAACA 58.411 50.000 0.00 0.00 0.00 3.18
2059 5374 0.872388 CCACAGCCAAACGGTAGAAC 59.128 55.000 0.00 0.00 0.00 3.01
2060 5375 0.470766 ACCACAGCCAAACGGTAGAA 59.529 50.000 0.00 0.00 0.00 2.10
2061 5376 0.250124 CACCACAGCCAAACGGTAGA 60.250 55.000 0.00 0.00 0.00 2.59
2062 5377 1.234615 CCACCACAGCCAAACGGTAG 61.235 60.000 0.00 0.00 0.00 3.18
2063 5378 1.228003 CCACCACAGCCAAACGGTA 60.228 57.895 0.00 0.00 0.00 4.02
2064 5379 2.518349 CCACCACAGCCAAACGGT 60.518 61.111 0.00 0.00 0.00 4.83
2065 5380 1.671901 AAACCACCACAGCCAAACGG 61.672 55.000 0.00 0.00 0.00 4.44
2066 5381 0.527385 CAAACCACCACAGCCAAACG 60.527 55.000 0.00 0.00 0.00 3.60
2067 5382 0.820871 TCAAACCACCACAGCCAAAC 59.179 50.000 0.00 0.00 0.00 2.93
2068 5383 1.786937 ATCAAACCACCACAGCCAAA 58.213 45.000 0.00 0.00 0.00 3.28
2069 5384 1.786937 AATCAAACCACCACAGCCAA 58.213 45.000 0.00 0.00 0.00 4.52
2070 5385 1.786937 AAATCAAACCACCACAGCCA 58.213 45.000 0.00 0.00 0.00 4.75
2071 5386 4.535526 AATAAATCAAACCACCACAGCC 57.464 40.909 0.00 0.00 0.00 4.85
2072 5387 9.646427 TTTATAAATAAATCAAACCACCACAGC 57.354 29.630 0.00 0.00 0.00 4.40
2074 5389 9.646427 GCTTTATAAATAAATCAAACCACCACA 57.354 29.630 0.00 0.00 32.36 4.17
2075 5390 9.646427 TGCTTTATAAATAAATCAAACCACCAC 57.354 29.630 0.00 0.00 32.36 4.16
2079 5394 9.377312 GCCTTGCTTTATAAATAAATCAAACCA 57.623 29.630 10.99 0.00 37.68 3.67
2080 5395 8.539674 CGCCTTGCTTTATAAATAAATCAAACC 58.460 33.333 10.99 6.15 37.68 3.27
2081 5396 9.296400 TCGCCTTGCTTTATAAATAAATCAAAC 57.704 29.630 10.99 7.11 37.68 2.93
2082 5397 9.862371 TTCGCCTTGCTTTATAAATAAATCAAA 57.138 25.926 10.99 0.00 37.68 2.69
2083 5398 9.862371 TTTCGCCTTGCTTTATAAATAAATCAA 57.138 25.926 9.93 9.93 36.55 2.57
2084 5399 9.515020 CTTTCGCCTTGCTTTATAAATAAATCA 57.485 29.630 0.00 0.00 32.36 2.57
2085 5400 8.480066 GCTTTCGCCTTGCTTTATAAATAAATC 58.520 33.333 0.00 0.00 32.36 2.17
2086 5401 8.352752 GCTTTCGCCTTGCTTTATAAATAAAT 57.647 30.769 0.00 0.00 32.36 1.40
2087 5402 7.749539 GCTTTCGCCTTGCTTTATAAATAAA 57.250 32.000 0.00 0.00 0.00 1.40
2104 5419 2.691984 TTACCGAAAAAGGCTTTCGC 57.308 45.000 13.76 7.41 46.89 4.70
2106 5421 9.499585 GAAATACTATTACCGAAAAAGGCTTTC 57.500 33.333 13.76 0.41 33.69 2.62
2107 5422 8.464404 GGAAATACTATTACCGAAAAAGGCTTT 58.536 33.333 6.68 6.68 33.69 3.51
2108 5423 7.067859 GGGAAATACTATTACCGAAAAAGGCTT 59.932 37.037 0.00 0.00 33.69 4.35
2109 5424 6.544931 GGGAAATACTATTACCGAAAAAGGCT 59.455 38.462 0.00 0.00 33.69 4.58
2110 5425 6.732154 GGGAAATACTATTACCGAAAAAGGC 58.268 40.000 0.00 0.00 33.69 4.35
2119 5434 5.994054 GGGTTCTTCGGGAAATACTATTACC 59.006 44.000 0.00 0.00 35.51 2.85
2120 5435 6.481313 GTGGGTTCTTCGGGAAATACTATTAC 59.519 42.308 0.00 0.00 35.51 1.89
2121 5436 6.156602 TGTGGGTTCTTCGGGAAATACTATTA 59.843 38.462 0.00 0.00 35.51 0.98
2228 5745 7.682741 GCATGTCCGTAATAGTGGTCTACTTTA 60.683 40.741 0.00 0.00 40.89 1.85
2295 5812 2.024414 GCAGAGGCCGGAATGTTTAAT 58.976 47.619 5.05 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.