Multiple sequence alignment - TraesCS1D01G042800

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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 TraesCS1D01G042800 chr1D 100.000 2621 0 0 1 2621 21823806 21826426 0.000000e+00 4841.0
1 TraesCS1D01G042800 chr1A 95.643 987 36 4 672 1657 23126044 23127024 0.000000e+00 1578.0
2 TraesCS1D01G042800 chr1A 93.816 663 35 3 1662 2319 23127109 23127770 0.000000e+00 992.0
3 TraesCS1D01G042800 chr1A 82.892 982 124 25 672 1649 23117308 23118249 0.000000e+00 843.0
4 TraesCS1D01G042800 chr1A 90.796 402 16 8 1 386 23125529 23125925 3.870000e-143 518.0
5 TraesCS1D01G042800 chr1A 93.455 275 16 2 2348 2621 23127880 23128153 8.730000e-110 407.0
6 TraesCS1D01G042800 chr1A 97.619 42 1 0 2314 2355 23127745 23127786 3.620000e-09 73.1
7 TraesCS1D01G042800 chr1B 85.394 1205 112 30 466 1657 36274213 36273060 0.000000e+00 1192.0
8 TraesCS1D01G042800 chr1B 92.952 681 33 7 1651 2319 36272983 36272306 0.000000e+00 977.0
9 TraesCS1D01G042800 chr1B 93.366 618 35 3 1651 2263 287381145 287380529 0.000000e+00 909.0
10 TraesCS1D01G042800 chr1B 93.382 272 15 3 2351 2621 36272193 36271924 1.460000e-107 399.0
11 TraesCS1D01G042800 chr1B 87.402 127 9 6 144 267 36275582 36275460 3.520000e-29 139.0
12 TraesCS1D01G042800 chr1B 94.737 76 2 1 1 74 36277098 36277023 1.650000e-22 117.0
13 TraesCS1D01G042800 chr1B 94.231 52 3 0 2310 2361 36272335 36272284 2.160000e-11 80.5
14 TraesCS1D01G042800 chr4B 93.528 618 34 3 1651 2263 72276630 72276014 0.000000e+00 915.0
15 TraesCS1D01G042800 chr4B 93.366 618 35 3 1651 2263 528246229 528245613 0.000000e+00 909.0
16 TraesCS1D01G042800 chr3B 93.528 618 34 3 1651 2263 667534625 667534009 0.000000e+00 915.0
17 TraesCS1D01G042800 chr3B 93.376 619 35 3 1650 2263 755836279 755836896 0.000000e+00 911.0
18 TraesCS1D01G042800 chr5B 93.366 618 35 3 1651 2263 567383381 567382765 0.000000e+00 909.0
19 TraesCS1D01G042800 chr5B 85.849 424 28 12 1891 2288 473795155 473795572 3.120000e-114 422.0
20 TraesCS1D01G042800 chr5B 92.350 183 11 3 2348 2527 473797013 473797195 9.310000e-65 257.0
21 TraesCS1D01G042800 chr2B 93.366 618 35 3 1651 2263 463994939 463995555 0.000000e+00 909.0
22 TraesCS1D01G042800 chr6B 92.754 276 17 3 2348 2621 218964945 218965219 1.890000e-106 396.0
23 TraesCS1D01G042800 chr6B 84.762 420 24 15 1896 2285 218964390 218964799 4.090000e-103 385.0


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 TraesCS1D01G042800 chr1D 21823806 21826426 2620 False 4841.000000 4841 100.000000 1 2621 1 chr1D.!!$F1 2620
1 TraesCS1D01G042800 chr1A 23117308 23118249 941 False 843.000000 843 82.892000 672 1649 1 chr1A.!!$F1 977
2 TraesCS1D01G042800 chr1A 23125529 23128153 2624 False 713.620000 1578 94.265800 1 2621 5 chr1A.!!$F2 2620
3 TraesCS1D01G042800 chr1B 287380529 287381145 616 True 909.000000 909 93.366000 1651 2263 1 chr1B.!!$R1 612
4 TraesCS1D01G042800 chr1B 36271924 36277098 5174 True 484.083333 1192 91.349667 1 2621 6 chr1B.!!$R2 2620
5 TraesCS1D01G042800 chr4B 72276014 72276630 616 True 915.000000 915 93.528000 1651 2263 1 chr4B.!!$R1 612
6 TraesCS1D01G042800 chr4B 528245613 528246229 616 True 909.000000 909 93.366000 1651 2263 1 chr4B.!!$R2 612
7 TraesCS1D01G042800 chr3B 667534009 667534625 616 True 915.000000 915 93.528000 1651 2263 1 chr3B.!!$R1 612
8 TraesCS1D01G042800 chr3B 755836279 755836896 617 False 911.000000 911 93.376000 1650 2263 1 chr3B.!!$F1 613
9 TraesCS1D01G042800 chr5B 567382765 567383381 616 True 909.000000 909 93.366000 1651 2263 1 chr5B.!!$R1 612
10 TraesCS1D01G042800 chr5B 473795155 473797195 2040 False 339.500000 422 89.099500 1891 2527 2 chr5B.!!$F1 636
11 TraesCS1D01G042800 chr2B 463994939 463995555 616 False 909.000000 909 93.366000 1651 2263 1 chr2B.!!$F1 612
12 TraesCS1D01G042800 chr6B 218964390 218965219 829 False 390.500000 396 88.758000 1896 2621 2 chr6B.!!$F1 725

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
310 1803 0.03601 CGGAGTGGATTGGCTTCACT 60.036 55.0 0.0 0.0 43.5 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2205 4846 1.135199 GCCCAGAACTTGCATGACATG 60.135 52.381 11.27 11.27 0.0 3.21 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
71 1499 3.490439 TCAAAGACTGCAATCCAGACA 57.510 42.857 0.00 0.00 44.64 3.41
80 1508 6.820656 AGACTGCAATCCAGACAAATAGTTAG 59.179 38.462 0.00 0.00 44.64 2.34
108 1536 3.569491 AGATGTGGATTGCCCCTTATTG 58.431 45.455 0.00 0.00 0.00 1.90
127 1555 7.255942 CCTTATTGGTTTCAAGGTGTTTGATCT 60.256 37.037 0.00 0.00 44.90 2.75
131 1559 6.337356 TGGTTTCAAGGTGTTTGATCTTTTC 58.663 36.000 0.00 0.00 44.90 2.29
135 1563 3.897505 CAAGGTGTTTGATCTTTTCCCCT 59.102 43.478 0.00 0.00 39.21 4.79
240 1670 2.002586 CGGAGCACATCAAACTCGAAT 58.997 47.619 0.00 0.00 0.00 3.34
253 1683 7.461182 TCAAACTCGAATGGGAAAATAACAT 57.539 32.000 0.00 0.00 0.00 2.71
310 1803 0.036010 CGGAGTGGATTGGCTTCACT 60.036 55.000 0.00 0.00 43.50 3.41
311 1804 1.207089 CGGAGTGGATTGGCTTCACTA 59.793 52.381 0.00 0.00 41.24 2.74
348 2762 1.600957 CTCAACCTGTTGACAGTGCAG 59.399 52.381 8.58 0.00 43.90 4.41
408 2847 2.076100 CGACAACTTTGCTGATGGCTA 58.924 47.619 0.00 0.00 42.39 3.93
413 2852 2.076863 ACTTTGCTGATGGCTAACGTC 58.923 47.619 0.00 0.00 42.39 4.34
417 2856 1.281899 GCTGATGGCTAACGTCTGAC 58.718 55.000 0.00 0.00 36.47 3.51
418 2857 1.404181 GCTGATGGCTAACGTCTGACA 60.404 52.381 8.73 0.00 36.47 3.58
437 2876 7.283127 GTCTGACAAATGAAATGGATAGCCTAA 59.717 37.037 2.24 0.00 34.31 2.69
444 2883 6.266131 TGAAATGGATAGCCTAAACAGGAT 57.734 37.500 0.00 0.00 34.31 3.24
448 2887 5.552870 TGGATAGCCTAAACAGGATTCTC 57.447 43.478 0.00 0.00 34.31 2.87
455 2894 9.975218 ATAGCCTAAACAGGATTCTCTTTTTAA 57.025 29.630 0.00 0.00 0.00 1.52
456 2895 8.885693 AGCCTAAACAGGATTCTCTTTTTAAT 57.114 30.769 0.00 0.00 0.00 1.40
498 3003 5.962433 TGTTTCTTACAGGAGTAGAATCGG 58.038 41.667 0.00 0.00 31.68 4.18
514 3019 2.851263 TCGGCTAGCTTCAGGAAAAA 57.149 45.000 15.72 0.00 0.00 1.94
539 3046 2.097791 TGTGCAAGTCGTTGTTAAACCC 59.902 45.455 0.00 0.00 35.92 4.11
546 3053 3.143728 GTCGTTGTTAAACCCAGTCCAT 58.856 45.455 0.00 0.00 32.23 3.41
548 3055 4.037089 GTCGTTGTTAAACCCAGTCCATTT 59.963 41.667 0.00 0.00 32.23 2.32
557 3064 4.879295 ACCCAGTCCATTTATCCATCAA 57.121 40.909 0.00 0.00 0.00 2.57
579 3086 3.442076 ACTGAACGGGTAGATCTTCCTT 58.558 45.455 17.02 5.57 0.00 3.36
586 3093 6.616237 ACGGGTAGATCTTCCTTTTTCTAA 57.384 37.500 17.02 0.00 0.00 2.10
590 3097 7.278203 CGGGTAGATCTTCCTTTTTCTAAGTTC 59.722 40.741 17.02 0.00 0.00 3.01
615 3122 9.958180 TCTTCCATGATTTAAATGTGAGAACTA 57.042 29.630 5.17 0.00 0.00 2.24
624 3131 7.843490 TTAAATGTGAGAACTACTATGGTGC 57.157 36.000 0.00 0.00 0.00 5.01
638 3145 0.976641 TGGTGCCTCCAACTAGACAG 59.023 55.000 0.00 0.00 44.12 3.51
642 3149 2.038557 GTGCCTCCAACTAGACAGGAAA 59.961 50.000 0.00 0.00 0.00 3.13
643 3150 2.708861 TGCCTCCAACTAGACAGGAAAA 59.291 45.455 0.00 0.00 0.00 2.29
644 3151 3.244561 TGCCTCCAACTAGACAGGAAAAG 60.245 47.826 0.00 0.00 0.00 2.27
647 3154 4.998033 CCTCCAACTAGACAGGAAAAGTTC 59.002 45.833 0.00 0.00 29.93 3.01
648 3155 5.454755 CCTCCAACTAGACAGGAAAAGTTCA 60.455 44.000 0.00 0.00 29.93 3.18
649 3156 6.187727 TCCAACTAGACAGGAAAAGTTCAT 57.812 37.500 0.00 0.00 29.93 2.57
650 3157 5.997746 TCCAACTAGACAGGAAAAGTTCATG 59.002 40.000 0.00 1.37 46.17 3.07
660 3167 7.678947 CAGGAAAAGTTCATGTCTCACTATT 57.321 36.000 0.00 0.00 36.75 1.73
662 3169 8.233190 CAGGAAAAGTTCATGTCTCACTATTTC 58.767 37.037 0.00 0.68 36.75 2.17
664 3171 8.787852 GGAAAAGTTCATGTCTCACTATTTCTT 58.212 33.333 0.00 0.00 0.00 2.52
665 3172 9.818796 GAAAAGTTCATGTCTCACTATTTCTTC 57.181 33.333 0.00 0.00 0.00 2.87
666 3173 8.908786 AAAGTTCATGTCTCACTATTTCTTCA 57.091 30.769 0.00 0.00 0.00 3.02
667 3174 8.908786 AAGTTCATGTCTCACTATTTCTTCAA 57.091 30.769 0.00 0.00 0.00 2.69
668 3175 9.512588 AAGTTCATGTCTCACTATTTCTTCAAT 57.487 29.630 0.00 0.00 0.00 2.57
743 3253 1.603678 GCCCATATGCATCCAAAAGCG 60.604 52.381 0.19 0.00 0.00 4.68
750 3260 0.530288 GCATCCAAAAGCGGGCTTAA 59.470 50.000 6.31 0.00 34.84 1.85
751 3261 1.136891 GCATCCAAAAGCGGGCTTAAT 59.863 47.619 6.31 0.00 34.84 1.40
752 3262 2.360801 GCATCCAAAAGCGGGCTTAATA 59.639 45.455 6.31 0.00 34.84 0.98
753 3263 3.005791 GCATCCAAAAGCGGGCTTAATAT 59.994 43.478 6.31 0.00 34.84 1.28
874 3389 8.261522 TCCCAACAAAGTAAGCTGTTTAATTTT 58.738 29.630 6.91 0.00 37.42 1.82
984 3499 4.832266 ACCCAAACATCATCAACAAGCTTA 59.168 37.500 0.00 0.00 0.00 3.09
991 3506 5.412594 ACATCATCAACAAGCTTAACGACAT 59.587 36.000 0.00 0.00 0.00 3.06
1007 3522 3.066380 CGACATCCGATTCAATGGCATA 58.934 45.455 0.00 0.00 41.76 3.14
1098 3613 0.968901 ACATCCTGGCCGACTTCGTA 60.969 55.000 0.00 0.00 37.74 3.43
1099 3614 0.174845 CATCCTGGCCGACTTCGTAA 59.825 55.000 0.00 0.00 37.74 3.18
1139 3654 1.200716 GACGAACATCACCGGTGACTA 59.799 52.381 38.46 18.59 43.11 2.59
1260 3775 1.878522 GTCCTACGCCATGCTCACG 60.879 63.158 0.00 0.00 0.00 4.35
1548 4063 0.949105 GCATCGACAACACCGTCCTT 60.949 55.000 0.00 0.00 31.91 3.36
1653 4251 1.375908 CCTGCGTACCATGCTGTGT 60.376 57.895 0.00 0.00 0.00 3.72
1695 4293 7.277174 AGGTTTATTATATCAGGCAAGCAAC 57.723 36.000 0.00 0.00 0.00 4.17
1776 4374 9.815936 GGTTCATGTGAAATGAAAATTGATTTC 57.184 29.630 0.00 10.06 39.96 2.17
1855 4453 6.148315 ACCTCTTTTAACCGAAGAAAATACCG 59.852 38.462 0.00 0.00 33.10 4.02
1904 4502 3.051081 AGGCTTTGCTCTGACAGTAAG 57.949 47.619 1.59 4.15 0.00 2.34
1907 4505 3.134458 GCTTTGCTCTGACAGTAAGTGT 58.866 45.455 1.59 0.00 44.49 3.55
1967 4565 1.002544 CCAGTGTGTTCTCCCTTCTCC 59.997 57.143 0.00 0.00 0.00 3.71
2021 4619 3.511146 GCAAAACCATCAAGGATCTGGAA 59.489 43.478 5.02 0.00 41.22 3.53
2142 4751 9.241317 GTGATATATCCAAAAGCTCAATTTGTG 57.759 33.333 10.25 0.00 36.31 3.33
2143 4752 7.922278 TGATATATCCAAAAGCTCAATTTGTGC 59.078 33.333 14.06 14.06 36.31 4.57
2185 4804 6.237901 TCTATGTGGATGCTAACAAACAACT 58.762 36.000 0.00 0.00 0.00 3.16
2186 4805 5.789643 ATGTGGATGCTAACAAACAACTT 57.210 34.783 0.00 0.00 0.00 2.66
2192 4833 5.691754 GGATGCTAACAAACAACTTCCAAAG 59.308 40.000 0.00 0.00 0.00 2.77
2204 4845 4.307443 ACTTCCAAAGTAGCAAAACTGC 57.693 40.909 0.00 0.00 40.69 4.40
2205 4846 3.068165 ACTTCCAAAGTAGCAAAACTGCC 59.932 43.478 0.00 0.00 40.69 4.85
2269 4910 6.409524 AAAATGCAAGTGGATTTCTCTGAA 57.590 33.333 10.67 0.00 43.69 3.02
2288 4929 4.655963 TGAAAAGTAAAGCATCTGAGCCT 58.344 39.130 0.00 0.00 34.23 4.58
2289 4930 5.072741 TGAAAAGTAAAGCATCTGAGCCTT 58.927 37.500 0.00 0.00 34.23 4.35
2290 4931 6.237901 TGAAAAGTAAAGCATCTGAGCCTTA 58.762 36.000 0.00 0.00 34.23 2.69
2291 4932 6.886459 TGAAAAGTAAAGCATCTGAGCCTTAT 59.114 34.615 0.00 0.00 34.23 1.73
2292 4933 8.046708 TGAAAAGTAAAGCATCTGAGCCTTATA 58.953 33.333 0.00 0.00 34.23 0.98
2293 4934 8.443953 AAAAGTAAAGCATCTGAGCCTTATAG 57.556 34.615 0.00 0.00 34.23 1.31
2294 4935 6.985653 AGTAAAGCATCTGAGCCTTATAGA 57.014 37.500 0.00 0.00 34.23 1.98
2295 4936 7.366847 AGTAAAGCATCTGAGCCTTATAGAA 57.633 36.000 0.00 0.00 34.23 2.10
2296 4937 7.441017 AGTAAAGCATCTGAGCCTTATAGAAG 58.559 38.462 0.00 0.00 34.23 2.85
2297 4938 5.885449 AAGCATCTGAGCCTTATAGAAGT 57.115 39.130 0.00 0.00 34.23 3.01
2298 4939 5.885449 AGCATCTGAGCCTTATAGAAGTT 57.115 39.130 0.00 0.00 34.23 2.66
2299 4940 5.609423 AGCATCTGAGCCTTATAGAAGTTG 58.391 41.667 0.00 0.00 34.23 3.16
2300 4941 4.213059 GCATCTGAGCCTTATAGAAGTTGC 59.787 45.833 0.00 0.00 0.00 4.17
2301 4942 5.363101 CATCTGAGCCTTATAGAAGTTGCA 58.637 41.667 0.00 0.00 0.00 4.08
2302 4943 5.620738 TCTGAGCCTTATAGAAGTTGCAT 57.379 39.130 0.00 0.00 0.00 3.96
2303 4944 5.605534 TCTGAGCCTTATAGAAGTTGCATC 58.394 41.667 0.00 0.00 0.00 3.91
2304 4945 5.129320 TCTGAGCCTTATAGAAGTTGCATCA 59.871 40.000 0.00 0.21 0.00 3.07
2305 4946 5.933617 TGAGCCTTATAGAAGTTGCATCAT 58.066 37.500 0.00 0.00 0.00 2.45
2306 4947 5.761726 TGAGCCTTATAGAAGTTGCATCATG 59.238 40.000 0.00 0.00 0.00 3.07
2307 4948 5.688807 AGCCTTATAGAAGTTGCATCATGT 58.311 37.500 0.00 0.00 0.00 3.21
2308 4949 5.530171 AGCCTTATAGAAGTTGCATCATGTG 59.470 40.000 0.00 0.00 0.00 3.21
2355 6398 8.856247 GGTAAAAAGTACAAACAAAACACTGAG 58.144 33.333 0.00 0.00 0.00 3.35
2393 6436 4.405116 TCAGGCAAAGCAAACAGATTTT 57.595 36.364 0.00 0.00 32.59 1.82
2395 6438 4.121317 CAGGCAAAGCAAACAGATTTTGA 58.879 39.130 0.91 0.00 32.59 2.69
2474 6517 2.360801 TGTACTGGCCAAAGAAAAGCAC 59.639 45.455 7.01 0.00 0.00 4.40
2476 6519 0.940991 CTGGCCAAAGAAAAGCACGC 60.941 55.000 7.01 0.00 0.00 5.34
2528 6574 5.896678 AGGTTCAGTATAAGCTGATGAGACT 59.103 40.000 0.00 0.00 43.99 3.24
2562 6608 0.593128 CAGACCAAAGGCTTTGACCG 59.407 55.000 35.18 22.94 43.26 4.79
2563 6609 0.472471 AGACCAAAGGCTTTGACCGA 59.528 50.000 35.18 0.00 43.26 4.69
2565 6611 1.172812 ACCAAAGGCTTTGACCGAGC 61.173 55.000 35.18 0.00 43.26 5.03
2581 6627 3.119495 ACCGAGCCAATAAGTGCAATTTC 60.119 43.478 4.05 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 1499 9.965902 AATCCACATCTTTCTCACTAACTATTT 57.034 29.630 0.00 0.00 0.00 1.40
80 1508 2.424956 GGGCAATCCACATCTTTCTCAC 59.575 50.000 0.00 0.00 35.00 3.51
127 1555 2.492567 CCACATTGGAGGAAGGGGAAAA 60.493 50.000 0.00 0.00 40.96 2.29
131 1559 2.397815 TCCACATTGGAGGAAGGGG 58.602 57.895 0.00 0.00 42.67 4.79
150 1578 6.068010 TGAATGAGACCCTAAAGCTTGAAAA 58.932 36.000 0.00 0.00 0.00 2.29
227 1657 7.312154 TGTTATTTTCCCATTCGAGTTTGATG 58.688 34.615 0.00 0.00 0.00 3.07
240 1670 9.575868 TTCAGTTAACTGTATGTTATTTTCCCA 57.424 29.630 29.83 6.91 44.12 4.37
310 1803 2.040606 AAGGAGCGGAGGGCCTTA 59.959 61.111 7.89 0.00 45.17 2.69
311 1804 3.403558 GAAGGAGCGGAGGGCCTT 61.404 66.667 7.89 0.00 44.32 4.35
348 2762 0.890542 TGCATGTCCTGTGGAACTGC 60.891 55.000 12.10 12.10 39.97 4.40
376 2790 3.268603 TTGTCGCCGTGTGCACTG 61.269 61.111 19.41 10.49 41.33 3.66
408 2847 5.964958 ATCCATTTCATTTGTCAGACGTT 57.035 34.783 0.00 0.00 0.00 3.99
413 2852 7.572523 TTAGGCTATCCATTTCATTTGTCAG 57.427 36.000 0.00 0.00 33.74 3.51
417 2856 7.068593 TCCTGTTTAGGCTATCCATTTCATTTG 59.931 37.037 0.00 0.00 44.22 2.32
418 2857 7.125391 TCCTGTTTAGGCTATCCATTTCATTT 58.875 34.615 0.00 0.00 44.22 2.32
483 2985 1.957877 GCTAGCCGATTCTACTCCTGT 59.042 52.381 2.29 0.00 0.00 4.00
484 2986 2.235016 AGCTAGCCGATTCTACTCCTG 58.765 52.381 12.13 0.00 0.00 3.86
514 3019 4.688511 TTAACAACGACTTGCACAGTTT 57.311 36.364 0.00 0.00 35.01 2.66
517 3022 3.359654 GGTTTAACAACGACTTGCACAG 58.640 45.455 0.00 0.00 33.13 3.66
530 3035 5.893500 TGGATAAATGGACTGGGTTTAACA 58.106 37.500 0.00 0.00 0.00 2.41
539 3046 7.253422 GTTCAGTTTGATGGATAAATGGACTG 58.747 38.462 0.00 0.00 34.76 3.51
546 3053 4.658063 ACCCGTTCAGTTTGATGGATAAA 58.342 39.130 0.00 0.00 0.00 1.40
548 3055 3.992943 ACCCGTTCAGTTTGATGGATA 57.007 42.857 0.00 0.00 0.00 2.59
557 3064 3.442076 AGGAAGATCTACCCGTTCAGTT 58.558 45.455 0.00 0.00 0.00 3.16
586 3093 8.868522 TCTCACATTTAAATCATGGAAGAACT 57.131 30.769 0.00 0.00 0.00 3.01
590 3097 9.994432 GTAGTTCTCACATTTAAATCATGGAAG 57.006 33.333 0.00 0.00 0.00 3.46
605 3112 3.441101 AGGCACCATAGTAGTTCTCACA 58.559 45.455 0.00 0.00 0.00 3.58
606 3113 3.181474 GGAGGCACCATAGTAGTTCTCAC 60.181 52.174 0.00 0.00 38.79 3.51
609 3116 3.116096 TGGAGGCACCATAGTAGTTCT 57.884 47.619 0.00 0.00 44.64 3.01
623 3130 3.244596 ACTTTTCCTGTCTAGTTGGAGGC 60.245 47.826 0.00 0.00 0.00 4.70
624 3131 4.625607 ACTTTTCCTGTCTAGTTGGAGG 57.374 45.455 0.00 0.00 0.00 4.30
636 3143 7.678947 AATAGTGAGACATGAACTTTTCCTG 57.321 36.000 0.00 0.00 0.00 3.86
638 3145 8.329203 AGAAATAGTGAGACATGAACTTTTCC 57.671 34.615 0.00 0.00 30.18 3.13
642 3149 8.908786 TTGAAGAAATAGTGAGACATGAACTT 57.091 30.769 0.00 0.00 0.00 2.66
658 3165 9.739276 TGGTAAAGATGACACTATTGAAGAAAT 57.261 29.630 0.00 0.00 0.00 2.17
660 3167 9.219603 CTTGGTAAAGATGACACTATTGAAGAA 57.780 33.333 0.00 0.00 35.19 2.52
662 3169 8.777865 TCTTGGTAAAGATGACACTATTGAAG 57.222 34.615 0.00 0.00 37.51 3.02
664 3171 8.999431 GTTTCTTGGTAAAGATGACACTATTGA 58.001 33.333 0.00 0.00 42.04 2.57
665 3172 8.237267 GGTTTCTTGGTAAAGATGACACTATTG 58.763 37.037 0.00 0.00 42.04 1.90
666 3173 7.393515 GGGTTTCTTGGTAAAGATGACACTATT 59.606 37.037 0.00 0.00 42.04 1.73
667 3174 6.884836 GGGTTTCTTGGTAAAGATGACACTAT 59.115 38.462 0.00 0.00 42.04 2.12
668 3175 6.235664 GGGTTTCTTGGTAAAGATGACACTA 58.764 40.000 0.00 0.00 42.04 2.74
669 3176 5.070685 GGGTTTCTTGGTAAAGATGACACT 58.929 41.667 0.00 0.00 42.04 3.55
670 3177 4.083484 CGGGTTTCTTGGTAAAGATGACAC 60.083 45.833 0.00 0.00 42.04 3.67
743 3253 6.773976 TGCTGGCAAATATATATTAAGCCC 57.226 37.500 30.13 22.28 42.01 5.19
752 3262 9.442047 GAGACTAACTATTGCTGGCAAATATAT 57.558 33.333 12.06 0.00 39.55 0.86
753 3263 8.651389 AGAGACTAACTATTGCTGGCAAATATA 58.349 33.333 12.06 0.19 39.55 0.86
884 3399 1.407656 GGTGGTGACTGGTGAGGACA 61.408 60.000 0.00 0.00 0.00 4.02
984 3499 1.670811 GCCATTGAATCGGATGTCGTT 59.329 47.619 0.00 0.00 40.32 3.85
991 3506 3.876914 GAGTTGTATGCCATTGAATCGGA 59.123 43.478 0.00 0.00 0.00 4.55
1007 3522 2.132686 ACAACAAGGGGTAGGAGTTGT 58.867 47.619 0.00 0.00 45.48 3.32
1098 3613 1.187567 GGTTGGTGCTTGCTGGGATT 61.188 55.000 0.00 0.00 0.00 3.01
1099 3614 1.607467 GGTTGGTGCTTGCTGGGAT 60.607 57.895 0.00 0.00 0.00 3.85
1139 3654 1.270678 GGAAGCCGGTGTAAGTGAAGT 60.271 52.381 1.90 0.00 0.00 3.01
1548 4063 1.138069 TCAGTCTTGAACGACTTGGCA 59.862 47.619 0.00 0.00 42.10 4.92
1855 4453 6.663944 AGTTTCGTCAGCTTATAATGAACC 57.336 37.500 0.00 0.00 0.00 3.62
1967 4565 7.038729 TCCTCTGCTATATGGATTACCTTCTTG 60.039 40.741 0.00 0.00 37.04 3.02
2142 4751 9.579768 CACATAGAGGTCTTCATACATAATAGC 57.420 37.037 0.00 0.00 0.00 2.97
2204 4845 1.475280 CCCAGAACTTGCATGACATGG 59.525 52.381 17.03 9.93 0.00 3.66
2205 4846 1.135199 GCCCAGAACTTGCATGACATG 60.135 52.381 11.27 11.27 0.00 3.21
2269 4910 7.796054 TCTATAAGGCTCAGATGCTTTACTTT 58.204 34.615 0.00 0.00 37.34 2.66
2300 4941 5.996669 TGCAACTTCTATAGCACATGATG 57.003 39.130 0.00 0.00 31.05 3.07
2301 4942 6.293698 TGATGCAACTTCTATAGCACATGAT 58.706 36.000 0.00 0.00 40.14 2.45
2302 4943 5.673514 TGATGCAACTTCTATAGCACATGA 58.326 37.500 0.00 0.00 40.14 3.07
2303 4944 5.996669 TGATGCAACTTCTATAGCACATG 57.003 39.130 0.00 0.00 40.14 3.21
2304 4945 6.017357 CACATGATGCAACTTCTATAGCACAT 60.017 38.462 0.00 0.00 40.14 3.21
2305 4946 5.295045 CACATGATGCAACTTCTATAGCACA 59.705 40.000 0.00 0.00 40.14 4.57
2306 4947 5.277683 CCACATGATGCAACTTCTATAGCAC 60.278 44.000 0.00 0.00 40.14 4.40
2307 4948 4.818005 CCACATGATGCAACTTCTATAGCA 59.182 41.667 0.00 0.00 41.73 3.49
2308 4949 4.818546 ACCACATGATGCAACTTCTATAGC 59.181 41.667 0.00 0.00 0.00 2.97
2393 6436 2.829720 AGAGGGTGCGTAATACAGTTCA 59.170 45.455 0.00 0.00 0.00 3.18
2395 6438 2.565834 ACAGAGGGTGCGTAATACAGTT 59.434 45.455 0.00 0.00 0.00 3.16
2522 6568 6.650807 GTCTGTGTGATCCAAAATAAGTCTCA 59.349 38.462 0.00 0.00 0.00 3.27
2528 6574 6.015519 CCTTTGGTCTGTGTGATCCAAAATAA 60.016 38.462 9.04 0.00 41.08 1.40
2562 6608 4.454728 TGGAAATTGCACTTATTGGCTC 57.545 40.909 0.00 0.00 0.00 4.70
2563 6609 4.888326 TTGGAAATTGCACTTATTGGCT 57.112 36.364 0.00 0.00 0.00 4.75
2565 6611 7.670009 TTGATTTGGAAATTGCACTTATTGG 57.330 32.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.