Multiple sequence alignment - TraesCS2A01G571100

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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 TraesCS2A01G571100 chr2A 100.000 3179 0 0 1 3179 768213165 768216343 0.000000e+00 5871.0
1 TraesCS2A01G571100 chr2A 77.786 1355 255 32 1075 2396 768195015 768193674 0.000000e+00 793.0
2 TraesCS2A01G571100 chr2A 96.000 50 1 1 629 677 151253476 151253427 2.630000e-11 80.5
3 TraesCS2A01G571100 chr2D 96.551 3044 89 10 141 3179 643314606 643317638 0.000000e+00 5025.0
4 TraesCS2A01G571100 chr2D 85.867 2151 273 17 1047 3179 643320674 643322811 0.000000e+00 2259.0
5 TraesCS2A01G571100 chr2D 82.600 1977 308 22 999 2958 643268918 643266961 0.000000e+00 1712.0
6 TraesCS2A01G571100 chr2D 77.755 1434 246 33 999 2396 643259493 643258097 0.000000e+00 813.0
7 TraesCS2A01G571100 chr2D 81.758 603 96 10 2394 2986 643258001 643257403 2.850000e-135 492.0
8 TraesCS2A01G571100 chr2D 96.429 140 5 0 1 140 643314510 643314649 6.860000e-57 231.0
9 TraesCS2A01G571100 chr2B 96.794 2277 57 3 919 3179 793532131 793529855 0.000000e+00 3786.0
10 TraesCS2A01G571100 chr2B 85.057 2282 294 24 919 3179 793527145 793524890 0.000000e+00 2281.0
11 TraesCS2A01G571100 chr2B 83.696 736 85 27 185 912 793532879 793532171 0.000000e+00 662.0
12 TraesCS2A01G571100 chr2B 96.875 128 4 0 1 128 793533009 793532882 6.910000e-52 215.0
13 TraesCS2A01G571100 chr2B 79.121 91 11 5 1447 1536 4770953 4770870 4.430000e-04 56.5
14 TraesCS2A01G571100 chrUn 79.695 1443 217 40 999 2396 266539122 266537711 0.000000e+00 972.0
15 TraesCS2A01G571100 chrUn 79.515 825 153 15 999 1818 31726293 31725480 9.890000e-160 573.0
16 TraesCS2A01G571100 chrUn 85.135 444 51 4 1967 2396 31725301 31724859 1.050000e-119 440.0
17 TraesCS2A01G571100 chr3A 80.862 998 152 25 2017 2986 43119573 43118587 0.000000e+00 749.0
18 TraesCS2A01G571100 chr3A 80.762 998 153 25 2017 2986 43729395 43728409 0.000000e+00 743.0
19 TraesCS2A01G571100 chr3A 94.118 51 2 1 629 678 8602123 8602173 3.400000e-10 76.8
20 TraesCS2A01G571100 chr7B 81.436 404 58 9 1995 2396 392814765 392814377 6.620000e-82 315.0
21 TraesCS2A01G571100 chr7B 92.157 51 2 1 629 679 32469316 32469364 1.580000e-08 71.3
22 TraesCS2A01G571100 chr7A 80.988 405 60 9 1994 2396 445624618 445624229 3.980000e-79 305.0
23 TraesCS2A01G571100 chr3D 77.007 274 49 7 2910 3179 601225319 601225582 9.190000e-31 145.0
24 TraesCS2A01G571100 chr3D 89.286 56 4 2 613 667 505557293 505557347 5.690000e-08 69.4
25 TraesCS2A01G571100 chr3B 92.157 51 2 2 610 660 111565264 111565312 1.580000e-08 71.3
26 TraesCS2A01G571100 chr6B 89.474 57 2 3 628 680 7144800 7144744 5.690000e-08 69.4
27 TraesCS2A01G571100 chr5A 86.567 67 3 5 605 667 70174879 70174943 5.690000e-08 69.4
28 TraesCS2A01G571100 chr1D 90.741 54 2 1 627 677 465402170 465402117 5.690000e-08 69.4


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 TraesCS2A01G571100 chr2A 768213165 768216343 3178 False 5871.0 5871 100.0000 1 3179 1 chr2A.!!$F1 3178
1 TraesCS2A01G571100 chr2A 768193674 768195015 1341 True 793.0 793 77.7860 1075 2396 1 chr2A.!!$R2 1321
2 TraesCS2A01G571100 chr2D 643314510 643322811 8301 False 2505.0 5025 92.9490 1 3179 3 chr2D.!!$F1 3178
3 TraesCS2A01G571100 chr2D 643266961 643268918 1957 True 1712.0 1712 82.6000 999 2958 1 chr2D.!!$R1 1959
4 TraesCS2A01G571100 chr2D 643257403 643259493 2090 True 652.5 813 79.7565 999 2986 2 chr2D.!!$R2 1987
5 TraesCS2A01G571100 chr2B 793524890 793533009 8119 True 1736.0 3786 90.6055 1 3179 4 chr2B.!!$R2 3178
6 TraesCS2A01G571100 chrUn 266537711 266539122 1411 True 972.0 972 79.6950 999 2396 1 chrUn.!!$R1 1397
7 TraesCS2A01G571100 chrUn 31724859 31726293 1434 True 506.5 573 82.3250 999 2396 2 chrUn.!!$R2 1397
8 TraesCS2A01G571100 chr3A 43118587 43119573 986 True 749.0 749 80.8620 2017 2986 1 chr3A.!!$R1 969
9 TraesCS2A01G571100 chr3A 43728409 43729395 986 True 743.0 743 80.7620 2017 2986 1 chr3A.!!$R2 969

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
866 880 0.099436 GGGCGACTGCATTTTAGCTG 59.901 55.0 0.0 0.0 45.35 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2572 12902 0.033503 TCCCTGAGACTGCGGTCATA 60.034 55.0 27.02 14.14 44.36 2.15 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
81 82 8.950007 TTGGATAGGGGAATGGAAAAATATAC 57.050 34.615 0.00 0.00 0.00 1.47
120 121 6.024552 AGCAAGTTCACTGTTCTTTTCAAA 57.975 33.333 0.00 0.00 0.00 2.69
164 165 9.915629 TTTAGCAAGTTAACTGTTCTTTTCAAA 57.084 25.926 9.34 2.23 0.00 2.69
165 166 9.567848 TTAGCAAGTTAACTGTTCTTTTCAAAG 57.432 29.630 9.34 0.00 37.36 2.77
166 167 7.826690 AGCAAGTTAACTGTTCTTTTCAAAGA 58.173 30.769 9.34 0.00 42.91 2.52
191 192 5.999205 ATGAATTAAGTGTTGGGCAATGA 57.001 34.783 0.00 0.00 0.00 2.57
197 198 2.446435 AGTGTTGGGCAATGATGTACC 58.554 47.619 0.00 0.00 0.00 3.34
223 224 4.461081 TGTGGGTGTTTACTTATGGAATGC 59.539 41.667 0.00 0.00 0.00 3.56
234 235 2.627791 TGGAATGCCACAGACAACG 58.372 52.632 0.00 0.00 39.92 4.10
237 238 2.513065 GAATGCCACAGACAACGCCG 62.513 60.000 0.00 0.00 0.00 6.46
256 257 3.635331 CCGATCAGCAATTTAGCAATGG 58.365 45.455 0.00 0.00 36.85 3.16
470 472 8.705594 ACCATATTGTAGCTGTCTTAACATAGT 58.294 33.333 0.00 0.00 34.13 2.12
471 473 8.982685 CCATATTGTAGCTGTCTTAACATAGTG 58.017 37.037 0.00 0.00 34.13 2.74
475 477 6.999950 TGTAGCTGTCTTAACATAGTGGAAA 58.000 36.000 0.00 0.00 34.13 3.13
490 492 9.314321 ACATAGTGGAAATTAGAAGATGTTACG 57.686 33.333 0.00 0.00 0.00 3.18
491 493 9.314321 CATAGTGGAAATTAGAAGATGTTACGT 57.686 33.333 0.00 0.00 0.00 3.57
492 494 9.886132 ATAGTGGAAATTAGAAGATGTTACGTT 57.114 29.630 0.00 0.00 0.00 3.99
538 540 5.481200 TTCATGACGTGGTTTAACGAAAA 57.519 34.783 0.00 0.00 46.49 2.29
633 646 7.362229 GCCTGTACATGAGGATATGTAGTACTC 60.362 44.444 0.00 0.00 42.44 2.59
658 671 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
768 781 1.578206 CTCGTCTCCGCTCTGTGTCA 61.578 60.000 0.00 0.00 0.00 3.58
781 794 4.707768 TGTCATCCCCGTCCCCGT 62.708 66.667 0.00 0.00 0.00 5.28
866 880 0.099436 GGGCGACTGCATTTTAGCTG 59.901 55.000 0.00 0.00 45.35 4.24
957 1004 3.242870 CCTGGCGTTTCTCTTTATGCATC 60.243 47.826 0.19 0.00 0.00 3.91
983 1041 7.486232 CGTATAATAGAGTTGATGCATCGTGAT 59.514 37.037 21.34 7.65 0.00 3.06
1194 1273 3.307906 AGCGCCAACAGGTACGGA 61.308 61.111 2.29 0.00 0.00 4.69
1288 1367 2.186826 GTTGCCAGCTTCACCACGT 61.187 57.895 0.00 0.00 0.00 4.49
1409 1488 1.541310 TACAACCTCGCCCTCACCAG 61.541 60.000 0.00 0.00 0.00 4.00
1809 1921 5.485353 ACACTCTTGGTCCTTCATATCTTCA 59.515 40.000 0.00 0.00 0.00 3.02
1872 2020 3.248248 AAGGCTGGGTCCGGGAGTA 62.248 63.158 0.00 0.00 0.00 2.59
2400 12730 0.395686 ACATGGCCGATGAGGATGAG 59.604 55.000 18.41 0.00 45.00 2.90
2408 12738 3.425659 CCGATGAGGATGAGGATAGTGA 58.574 50.000 0.00 0.00 45.00 3.41
2416 12746 3.195396 GGATGAGGATAGTGATGGAGCTC 59.805 52.174 4.71 4.71 0.00 4.09
2489 12819 0.961019 GAACATCAAGCCCAGCAACA 59.039 50.000 0.00 0.00 0.00 3.33
2506 12836 3.774066 CAACATGATGCTAGACGAGTCA 58.226 45.455 0.00 0.00 0.00 3.41
2515 12845 2.159170 GCTAGACGAGTCATTTGGAGCT 60.159 50.000 5.99 0.00 0.00 4.09
2521 12851 2.606725 CGAGTCATTTGGAGCTAAGCTG 59.393 50.000 0.00 0.00 39.88 4.24
2617 12947 1.489560 GCTACTTGGACCCCCAGTGT 61.490 60.000 0.00 0.00 44.60 3.55
2685 13022 1.770110 TGGTTCTGCTGGAGGTGGT 60.770 57.895 0.00 0.00 0.00 4.16
2717 13054 1.153765 CCGATGAGCTTCACTGCGA 60.154 57.895 0.00 0.00 38.13 5.10
2722 13059 1.153745 GAGCTTCACTGCGACCGAT 60.154 57.895 0.00 0.00 38.13 4.18
2734 13074 1.596934 GACCGATCAGGACCAGCAA 59.403 57.895 10.05 0.00 45.00 3.91
2735 13075 0.741221 GACCGATCAGGACCAGCAAC 60.741 60.000 10.05 0.00 45.00 4.17
2736 13076 1.296392 CCGATCAGGACCAGCAACA 59.704 57.895 0.00 0.00 45.00 3.33
2737 13077 0.321564 CCGATCAGGACCAGCAACAA 60.322 55.000 0.00 0.00 45.00 2.83
2746 13086 1.404035 GACCAGCAACAAAAGAACGGT 59.596 47.619 0.00 0.00 0.00 4.83
2752 13092 0.099791 AACAAAAGAACGGTGGCGTG 59.900 50.000 0.00 0.00 0.00 5.34
2772 13112 3.953775 CCGGCTGGTTGAGTGGGT 61.954 66.667 2.29 0.00 0.00 4.51
2779 13120 1.533033 GGTTGAGTGGGTTTGGGGG 60.533 63.158 0.00 0.00 0.00 5.40
2797 13138 2.838225 CTGTACGGCCGGGGATCT 60.838 66.667 31.76 9.87 0.00 2.75
2800 13141 0.470456 TGTACGGCCGGGGATCTATT 60.470 55.000 31.76 7.29 0.00 1.73
2807 13148 1.694696 GCCGGGGATCTATTCTTGAGT 59.305 52.381 2.18 0.00 0.00 3.41
2820 13161 2.771763 CTTGAGTCCGCCGACAAGCT 62.772 60.000 7.93 0.00 41.87 3.74
2827 13168 2.393768 CGCCGACAAGCTGCTGAAT 61.394 57.895 1.35 0.00 0.00 2.57
2830 13171 0.957395 CCGACAAGCTGCTGAATGGT 60.957 55.000 1.35 0.00 0.00 3.55
2835 13176 1.884579 CAAGCTGCTGAATGGTGACTT 59.115 47.619 1.35 0.00 0.00 3.01
2836 13177 3.076621 CAAGCTGCTGAATGGTGACTTA 58.923 45.455 1.35 0.00 0.00 2.24
2845 13186 0.608130 ATGGTGACTTAGACGCAGCA 59.392 50.000 0.00 0.00 43.13 4.41
2846 13187 0.319555 TGGTGACTTAGACGCAGCAC 60.320 55.000 0.00 0.00 35.39 4.40
2861 13202 2.348998 CACAGGTGGAGAGGGTGC 59.651 66.667 0.00 0.00 0.00 5.01
2881 13222 4.295119 GTCGTCGGGCTGTGGTGT 62.295 66.667 0.00 0.00 0.00 4.16
2884 13225 4.927782 GTCGGGCTGTGGTGTGCA 62.928 66.667 0.00 0.00 0.00 4.57
2931 13272 0.627451 ATCAGAGAAGCCATGGCCAA 59.373 50.000 33.14 11.08 43.17 4.52
2951 13292 1.816863 GCTCCACTCCAAGGTCGACA 61.817 60.000 18.91 0.00 0.00 4.35
2992 13345 1.301716 GATGCCGGTGCCGACATAT 60.302 57.895 12.12 1.31 42.19 1.78
2995 13348 2.108976 CCGGTGCCGACATATGCT 59.891 61.111 12.71 0.00 42.83 3.79
2996 13349 1.956170 CCGGTGCCGACATATGCTC 60.956 63.158 12.71 0.00 42.83 4.26
2997 13350 1.227234 CGGTGCCGACATATGCTCA 60.227 57.895 4.35 0.00 42.83 4.26
3001 13354 1.227645 GCCGACATATGCTCAGCCA 60.228 57.895 1.58 0.00 0.00 4.75
3005 13358 0.179073 GACATATGCTCAGCCACCGT 60.179 55.000 1.58 0.00 0.00 4.83
3006 13359 0.179073 ACATATGCTCAGCCACCGTC 60.179 55.000 1.58 0.00 0.00 4.79
3022 13375 3.000819 TCCGCCTTGGACGTGGAT 61.001 61.111 0.00 0.00 43.74 3.41
3024 13377 2.264480 CGCCTTGGACGTGGATGA 59.736 61.111 0.00 0.00 0.00 2.92
3039 13392 1.453155 GATGATGGGCTGTCAACGTT 58.547 50.000 0.00 0.00 0.00 3.99
3044 13397 2.050985 GGCTGTCAACGTTGCTGC 60.051 61.111 28.73 28.73 0.00 5.25
3046 13399 2.833533 GCTGTCAACGTTGCTGCCA 61.834 57.895 27.55 19.00 0.00 4.92
3052 13405 2.325082 AACGTTGCTGCCATCGTCC 61.325 57.895 0.00 0.00 44.14 4.79
3053 13406 2.741985 CGTTGCTGCCATCGTCCA 60.742 61.111 0.00 0.00 31.35 4.02
3054 13407 2.870372 GTTGCTGCCATCGTCCAC 59.130 61.111 0.00 0.00 0.00 4.02
3059 13412 3.610619 CTGCCATCGTCCACCAGCA 62.611 63.158 0.00 0.00 0.00 4.41
3083 13436 3.484806 TCCCACCGCACACCACTT 61.485 61.111 0.00 0.00 0.00 3.16
3094 13447 2.478879 GCACACCACTTGTACAACAACC 60.479 50.000 3.59 0.00 35.67 3.77
3096 13449 3.013921 ACACCACTTGTACAACAACCAG 58.986 45.455 3.59 0.00 36.32 4.00
3097 13450 3.013921 CACCACTTGTACAACAACCAGT 58.986 45.455 3.59 0.00 33.96 4.00
3098 13451 3.442273 CACCACTTGTACAACAACCAGTT 59.558 43.478 3.59 0.00 42.42 3.16
3099 13452 3.692593 ACCACTTGTACAACAACCAGTTC 59.307 43.478 3.59 0.00 38.74 3.01
3103 13456 5.123186 CACTTGTACAACAACCAGTTCTTCA 59.877 40.000 3.59 0.00 38.74 3.02
3104 13457 5.354234 ACTTGTACAACAACCAGTTCTTCAG 59.646 40.000 3.59 0.00 38.74 3.02
3105 13458 5.092554 TGTACAACAACCAGTTCTTCAGA 57.907 39.130 0.00 0.00 38.74 3.27
3108 13461 2.240493 ACAACCAGTTCTTCAGACGG 57.760 50.000 0.00 0.00 0.00 4.79
3109 13462 1.760613 ACAACCAGTTCTTCAGACGGA 59.239 47.619 0.00 0.00 0.00 4.69
3110 13463 2.135933 CAACCAGTTCTTCAGACGGAC 58.864 52.381 0.00 0.00 0.00 4.79
3111 13464 1.410004 ACCAGTTCTTCAGACGGACA 58.590 50.000 0.00 0.00 0.00 4.02
3112 13465 1.971357 ACCAGTTCTTCAGACGGACAT 59.029 47.619 0.00 0.00 0.00 3.06
3113 13466 2.289072 ACCAGTTCTTCAGACGGACATG 60.289 50.000 0.00 0.00 0.00 3.21
3114 13467 2.341257 CAGTTCTTCAGACGGACATGG 58.659 52.381 0.00 0.00 0.00 3.66
3135 13488 0.892358 AGCACCTCGACGACCAGTTA 60.892 55.000 0.00 0.00 0.00 2.24
3141 13494 2.473984 CCTCGACGACCAGTTAAAACAC 59.526 50.000 0.00 0.00 0.00 3.32
3147 13500 2.737783 CGACCAGTTAAAACACGGCATA 59.262 45.455 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 3.620374 ACTTGCTATGCTGAGATTTCACG 59.380 43.478 0.00 0.00 0.00 4.35
140 141 8.952278 TCTTTGAAAAGAACAGTTAACTTGCTA 58.048 29.630 5.07 0.00 41.75 3.49
141 142 7.826690 TCTTTGAAAAGAACAGTTAACTTGCT 58.173 30.769 5.07 0.57 41.75 3.91
142 143 8.460831 TTCTTTGAAAAGAACAGTTAACTTGC 57.539 30.769 12.99 0.00 46.80 4.01
159 160 9.323985 CCCAACACTTAATTCATTTTCTTTGAA 57.676 29.630 0.00 0.00 37.49 2.69
160 161 7.440856 GCCCAACACTTAATTCATTTTCTTTGA 59.559 33.333 0.00 0.00 0.00 2.69
161 162 7.226325 TGCCCAACACTTAATTCATTTTCTTTG 59.774 33.333 0.00 0.00 0.00 2.77
162 163 7.278875 TGCCCAACACTTAATTCATTTTCTTT 58.721 30.769 0.00 0.00 0.00 2.52
163 164 6.825610 TGCCCAACACTTAATTCATTTTCTT 58.174 32.000 0.00 0.00 0.00 2.52
164 165 6.418057 TGCCCAACACTTAATTCATTTTCT 57.582 33.333 0.00 0.00 0.00 2.52
165 166 7.387397 TCATTGCCCAACACTTAATTCATTTTC 59.613 33.333 0.00 0.00 0.00 2.29
166 167 7.222872 TCATTGCCCAACACTTAATTCATTTT 58.777 30.769 0.00 0.00 0.00 1.82
167 168 6.767456 TCATTGCCCAACACTTAATTCATTT 58.233 32.000 0.00 0.00 0.00 2.32
168 169 6.357579 TCATTGCCCAACACTTAATTCATT 57.642 33.333 0.00 0.00 0.00 2.57
169 170 5.999205 TCATTGCCCAACACTTAATTCAT 57.001 34.783 0.00 0.00 0.00 2.57
170 171 5.245751 ACATCATTGCCCAACACTTAATTCA 59.754 36.000 0.00 0.00 0.00 2.57
171 172 5.723295 ACATCATTGCCCAACACTTAATTC 58.277 37.500 0.00 0.00 0.00 2.17
172 173 5.743636 ACATCATTGCCCAACACTTAATT 57.256 34.783 0.00 0.00 0.00 1.40
173 174 5.127031 GGTACATCATTGCCCAACACTTAAT 59.873 40.000 0.00 0.00 0.00 1.40
174 175 4.461081 GGTACATCATTGCCCAACACTTAA 59.539 41.667 0.00 0.00 0.00 1.85
175 176 4.013728 GGTACATCATTGCCCAACACTTA 58.986 43.478 0.00 0.00 0.00 2.24
176 177 2.825532 GGTACATCATTGCCCAACACTT 59.174 45.455 0.00 0.00 0.00 3.16
177 178 2.446435 GGTACATCATTGCCCAACACT 58.554 47.619 0.00 0.00 0.00 3.55
178 179 1.476488 GGGTACATCATTGCCCAACAC 59.524 52.381 0.00 0.00 40.76 3.32
179 180 1.846007 GGGTACATCATTGCCCAACA 58.154 50.000 0.00 0.00 40.76 3.33
183 184 1.682854 CACATGGGTACATCATTGCCC 59.317 52.381 0.00 0.00 41.42 5.36
197 198 4.594970 TCCATAAGTAAACACCCACATGG 58.405 43.478 0.00 0.00 41.37 3.66
199 200 5.127031 GCATTCCATAAGTAAACACCCACAT 59.873 40.000 0.00 0.00 0.00 3.21
205 206 5.414454 TCTGTGGCATTCCATAAGTAAACAC 59.586 40.000 0.00 0.00 45.62 3.32
223 224 1.354337 CTGATCGGCGTTGTCTGTGG 61.354 60.000 6.85 0.00 0.00 4.17
232 233 0.657840 GCTAAATTGCTGATCGGCGT 59.342 50.000 21.30 10.06 34.52 5.68
234 235 2.849880 TTGCTAAATTGCTGATCGGC 57.150 45.000 20.08 20.08 0.00 5.54
237 238 5.252969 TGACCATTGCTAAATTGCTGATC 57.747 39.130 0.00 0.00 0.00 2.92
256 257 2.864343 GTTAGTCCGCACATACCATGAC 59.136 50.000 0.00 0.00 0.00 3.06
470 472 8.610248 TTGAACGTAACATCTTCTAATTTCCA 57.390 30.769 0.00 0.00 0.00 3.53
505 507 8.644318 AAACCACGTCATGAATAATAGTACTC 57.356 34.615 0.00 0.00 0.00 2.59
508 510 9.022915 CGTTAAACCACGTCATGAATAATAGTA 57.977 33.333 0.00 0.00 35.34 1.82
509 511 7.760794 TCGTTAAACCACGTCATGAATAATAGT 59.239 33.333 0.00 0.00 41.16 2.12
510 512 8.122306 TCGTTAAACCACGTCATGAATAATAG 57.878 34.615 0.00 0.00 41.16 1.73
511 513 8.476657 TTCGTTAAACCACGTCATGAATAATA 57.523 30.769 0.00 0.00 41.16 0.98
576 578 6.153067 TCGTCAAAAGAAAAAGCTGAACAAA 58.847 32.000 0.00 0.00 0.00 2.83
578 580 5.303747 TCGTCAAAAGAAAAAGCTGAACA 57.696 34.783 0.00 0.00 0.00 3.18
657 670 5.359292 AGATGTACTCCCTCCGTAAACTAAC 59.641 44.000 0.00 0.00 0.00 2.34
658 671 5.359009 CAGATGTACTCCCTCCGTAAACTAA 59.641 44.000 0.00 0.00 0.00 2.24
660 673 3.700038 CAGATGTACTCCCTCCGTAAACT 59.300 47.826 0.00 0.00 0.00 2.66
661 674 3.446516 ACAGATGTACTCCCTCCGTAAAC 59.553 47.826 0.00 0.00 0.00 2.01
662 675 3.705051 ACAGATGTACTCCCTCCGTAAA 58.295 45.455 0.00 0.00 0.00 2.01
781 794 5.280654 TCCGTGATTCATGATGATCAAGA 57.719 39.130 19.02 12.94 0.00 3.02
866 880 6.740411 AGAAACTCAGATTTTCTGCAGATC 57.260 37.500 19.04 12.57 43.95 2.75
957 1004 6.801862 TCACGATGCATCAACTCTATTATACG 59.198 38.462 25.70 9.96 0.00 3.06
1194 1273 2.283298 CCATTGCTGTAGTCGATGCTT 58.717 47.619 0.00 0.00 0.00 3.91
1288 1367 1.135373 GGAGATGACGAACGAGAAGCA 60.135 52.381 0.14 0.00 0.00 3.91
1872 2020 4.883354 GCAGCTGCCCCGGCTATT 62.883 66.667 28.76 0.00 45.14 1.73
2400 12730 0.605589 CCCGAGCTCCATCACTATCC 59.394 60.000 8.47 0.00 0.00 2.59
2408 12738 3.461773 CACGGACCCGAGCTCCAT 61.462 66.667 16.07 0.00 42.83 3.41
2416 12746 3.449227 TAGAGCAGCACGGACCCG 61.449 66.667 6.94 6.94 46.03 5.28
2424 12754 1.304134 TCGTGGAGGTAGAGCAGCA 60.304 57.895 0.00 0.00 0.00 4.41
2471 12801 1.274167 CATGTTGCTGGGCTTGATGTT 59.726 47.619 0.00 0.00 0.00 2.71
2489 12819 4.100035 TCCAAATGACTCGTCTAGCATCAT 59.900 41.667 0.00 0.00 0.00 2.45
2497 12827 3.677424 GCTTAGCTCCAAATGACTCGTCT 60.677 47.826 0.00 0.00 0.00 4.18
2506 12836 0.749454 CGCCCAGCTTAGCTCCAAAT 60.749 55.000 2.68 0.00 36.40 2.32
2515 12845 2.577059 CCGAAGTCGCCCAGCTTA 59.423 61.111 0.00 0.00 38.18 3.09
2572 12902 0.033503 TCCCTGAGACTGCGGTCATA 60.034 55.000 27.02 14.14 44.36 2.15
2647 12984 1.080705 GCCGAAGCTGTACACGTCT 60.081 57.895 0.00 0.00 35.50 4.18
2708 13045 1.215382 CCTGATCGGTCGCAGTGAA 59.785 57.895 0.00 0.00 0.00 3.18
2710 13047 1.517257 GTCCTGATCGGTCGCAGTG 60.517 63.158 0.00 0.00 0.00 3.66
2717 13054 1.296715 GTTGCTGGTCCTGATCGGT 59.703 57.895 0.00 0.00 0.00 4.69
2722 13059 2.687935 GTTCTTTTGTTGCTGGTCCTGA 59.312 45.455 0.00 0.00 0.00 3.86
2752 13092 1.966451 CCACTCAACCAGCCGGAAC 60.966 63.158 5.05 0.00 35.59 3.62
2779 13120 4.603946 GATCCCCGGCCGTACAGC 62.604 72.222 26.12 5.60 0.00 4.40
2795 13136 1.404391 GTCGGCGGACTCAAGAATAGA 59.596 52.381 16.52 0.00 40.15 1.98
2797 13138 1.179152 TGTCGGCGGACTCAAGAATA 58.821 50.000 22.99 0.00 43.79 1.75
2800 13141 1.289066 CTTGTCGGCGGACTCAAGA 59.711 57.895 22.99 1.86 43.79 3.02
2820 13161 2.930887 GCGTCTAAGTCACCATTCAGCA 60.931 50.000 0.00 0.00 0.00 4.41
2827 13168 0.319555 GTGCTGCGTCTAAGTCACCA 60.320 55.000 0.00 0.00 0.00 4.17
2830 13171 0.038251 CCTGTGCTGCGTCTAAGTCA 60.038 55.000 0.00 0.00 0.00 3.41
2835 13176 1.877576 CTCCACCTGTGCTGCGTCTA 61.878 60.000 0.00 0.00 0.00 2.59
2836 13177 3.231889 CTCCACCTGTGCTGCGTCT 62.232 63.158 0.00 0.00 0.00 4.18
2845 13186 2.205462 AGCACCCTCTCCACCTGT 59.795 61.111 0.00 0.00 0.00 4.00
2846 13187 2.667418 CAGCACCCTCTCCACCTG 59.333 66.667 0.00 0.00 0.00 4.00
2861 13202 4.742201 CCACAGCCCGACGACCAG 62.742 72.222 0.00 0.00 0.00 4.00
2931 13272 1.228894 TCGACCTTGGAGTGGAGCT 60.229 57.895 0.00 0.00 0.00 4.09
2951 13292 4.357279 GGGGAGCACTGGCAGCTT 62.357 66.667 15.89 0.00 43.58 3.74
3005 13358 3.000819 ATCCACGTCCAAGGCGGA 61.001 61.111 7.60 0.00 43.61 5.54
3006 13359 2.593468 ATCATCCACGTCCAAGGCGG 62.593 60.000 7.60 0.00 0.00 6.13
3015 13368 1.221840 GACAGCCCATCATCCACGT 59.778 57.895 0.00 0.00 0.00 4.49
3018 13371 0.392863 CGTTGACAGCCCATCATCCA 60.393 55.000 0.00 0.00 0.00 3.41
3019 13372 0.392998 ACGTTGACAGCCCATCATCC 60.393 55.000 0.00 0.00 0.00 3.51
3022 13375 1.514678 GCAACGTTGACAGCCCATCA 61.515 55.000 31.62 0.00 0.00 3.07
3024 13377 1.228245 AGCAACGTTGACAGCCCAT 60.228 52.632 31.62 3.61 0.00 4.00
3039 13392 3.610619 CTGGTGGACGATGGCAGCA 62.611 63.158 2.73 0.00 0.00 4.41
3044 13397 2.436646 GGTGCTGGTGGACGATGG 60.437 66.667 0.00 0.00 35.23 3.51
3046 13399 2.665000 CTGGTGCTGGTGGACGAT 59.335 61.111 0.00 0.00 35.23 3.73
3067 13420 2.668185 TACAAGTGGTGTGCGGTGGG 62.668 60.000 0.00 0.00 41.89 4.61
3070 13423 0.107606 TTGTACAAGTGGTGTGCGGT 60.108 50.000 3.59 0.00 45.16 5.68
3073 13426 2.478879 GGTTGTTGTACAAGTGGTGTGC 60.479 50.000 8.98 0.00 41.89 4.57
3075 13428 3.013921 CTGGTTGTTGTACAAGTGGTGT 58.986 45.455 8.98 0.00 39.00 4.16
3076 13429 3.013921 ACTGGTTGTTGTACAAGTGGTG 58.986 45.455 8.98 1.08 39.00 4.17
3080 13433 5.250200 TGAAGAACTGGTTGTTGTACAAGT 58.750 37.500 8.98 0.00 39.00 3.16
3083 13436 4.873827 GTCTGAAGAACTGGTTGTTGTACA 59.126 41.667 0.66 0.00 39.30 2.90
3094 13447 2.289072 ACCATGTCCGTCTGAAGAACTG 60.289 50.000 0.00 0.00 0.00 3.16
3096 13449 2.457366 ACCATGTCCGTCTGAAGAAC 57.543 50.000 0.00 0.00 0.00 3.01
3097 13450 2.094182 GCTACCATGTCCGTCTGAAGAA 60.094 50.000 0.00 0.00 0.00 2.52
3098 13451 1.476891 GCTACCATGTCCGTCTGAAGA 59.523 52.381 0.00 0.00 0.00 2.87
3099 13452 1.204704 TGCTACCATGTCCGTCTGAAG 59.795 52.381 0.00 0.00 0.00 3.02
3103 13456 0.614979 AGGTGCTACCATGTCCGTCT 60.615 55.000 7.86 0.00 41.95 4.18
3104 13457 0.179108 GAGGTGCTACCATGTCCGTC 60.179 60.000 7.86 0.00 41.95 4.79
3105 13458 1.898154 GAGGTGCTACCATGTCCGT 59.102 57.895 7.86 0.00 41.95 4.69
3108 13461 0.525668 CGTCGAGGTGCTACCATGTC 60.526 60.000 7.86 0.00 41.95 3.06
3109 13462 0.963856 TCGTCGAGGTGCTACCATGT 60.964 55.000 4.85 0.00 41.95 3.21
3110 13463 0.525668 GTCGTCGAGGTGCTACCATG 60.526 60.000 4.85 0.00 41.95 3.66
3111 13464 1.664321 GGTCGTCGAGGTGCTACCAT 61.664 60.000 4.85 0.00 41.95 3.55
3112 13465 2.338015 GGTCGTCGAGGTGCTACCA 61.338 63.158 4.85 0.00 41.95 3.25
3113 13466 2.267681 CTGGTCGTCGAGGTGCTACC 62.268 65.000 4.85 5.93 38.99 3.18
3114 13467 1.136984 CTGGTCGTCGAGGTGCTAC 59.863 63.158 4.85 0.00 0.00 3.58
3135 13488 6.313905 CAGTAGAGAAGAATATGCCGTGTTTT 59.686 38.462 0.00 0.00 0.00 2.43
3141 13494 6.042777 TGTTTCAGTAGAGAAGAATATGCCG 58.957 40.000 0.00 0.00 0.00 5.69


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

AutoCloner maintained by Alex Coulton.