Multiple sequence alignment - TraesCS5D01G384100

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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 TraesCS5D01G384100 chr5D 100.000 4797 0 0 1 4797 453812794 453817590 0.000000e+00 8859.0
1 TraesCS5D01G384100 chr5D 83.980 980 153 4 2818 3795 40092724 40091747 0.000000e+00 937.0
2 TraesCS5D01G384100 chr5A 89.803 2442 145 41 1897 4285 572838868 572841258 0.000000e+00 3035.0
3 TraesCS5D01G384100 chr5A 90.687 1267 70 22 637 1898 572837561 572838784 0.000000e+00 1642.0
4 TraesCS5D01G384100 chr5A 84.663 978 146 4 2822 3797 28105092 28104117 0.000000e+00 972.0
5 TraesCS5D01G384100 chr5A 94.270 541 26 1 4256 4791 572841261 572841801 0.000000e+00 822.0
6 TraesCS5D01G384100 chr5A 81.280 625 68 18 11 633 572834175 572834752 1.220000e-125 460.0
7 TraesCS5D01G384100 chr5B 94.827 1933 70 7 1897 3809 554512911 554514833 0.000000e+00 2988.0
8 TraesCS5D01G384100 chr5B 92.140 916 62 6 934 1845 554511671 554512580 0.000000e+00 1284.0
9 TraesCS5D01G384100 chr5B 84.694 980 146 4 2818 3795 33627695 33628672 0.000000e+00 976.0
10 TraesCS5D01G384100 chr5B 92.718 618 30 10 4190 4797 554515221 554515833 0.000000e+00 878.0
11 TraesCS5D01G384100 chr5B 94.960 377 12 3 3725 4094 554514834 554515210 6.920000e-163 584.0
12 TraesCS5D01G384100 chr5B 86.640 509 56 8 132 633 554509603 554510106 1.950000e-153 553.0
13 TraesCS5D01G384100 chr5B 93.950 281 4 4 638 913 554511213 554511485 3.450000e-111 412.0
14 TraesCS5D01G384100 chr5B 98.462 65 0 1 1835 1898 554512763 554512827 3.920000e-21 113.0
15 TraesCS5D01G384100 chr4B 88.806 402 37 5 811 1208 609768007 609767610 2.010000e-133 486.0
16 TraesCS5D01G384100 chr7A 86.911 191 17 5 1021 1209 735050119 735049935 1.750000e-49 207.0
17 TraesCS5D01G384100 chr7D 93.443 61 4 0 811 871 70219708 70219768 1.840000e-14 91.6


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 TraesCS5D01G384100 chr5D 453812794 453817590 4796 False 8859.000000 8859 100.000000 1 4797 1 chr5D.!!$F1 4796
1 TraesCS5D01G384100 chr5D 40091747 40092724 977 True 937.000000 937 83.980000 2818 3795 1 chr5D.!!$R1 977
2 TraesCS5D01G384100 chr5A 572834175 572841801 7626 False 1489.750000 3035 89.010000 11 4791 4 chr5A.!!$F1 4780
3 TraesCS5D01G384100 chr5A 28104117 28105092 975 True 972.000000 972 84.663000 2822 3797 1 chr5A.!!$R1 975
4 TraesCS5D01G384100 chr5B 33627695 33628672 977 False 976.000000 976 84.694000 2818 3795 1 chr5B.!!$F1 977
5 TraesCS5D01G384100 chr5B 554509603 554515833 6230 False 973.142857 2988 93.385286 132 4797 7 chr5B.!!$F2 4665

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
519 525 0.034896 GTCGTGAGGCTCCCAAAGAA 59.965 55.0 12.86 0.00 0.00 2.52 F
558 564 0.107017 TATTCTGCTTGGGCTGCCTC 60.107 55.0 19.68 9.39 39.59 4.70 F
1937 5339 0.326264 AGGGCTTGAGTGGATGTGAC 59.674 55.0 0.00 0.00 0.00 3.67 F
1938 5340 0.326264 GGGCTTGAGTGGATGTGACT 59.674 55.0 0.00 0.00 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 4461 0.307760 CCTTGGTCTGCACACGAAAC 59.692 55.000 0.00 0.0 0.00 2.78 R
2139 5546 0.599558 TGCAATTCACTGAAGCAGCC 59.400 50.000 2.37 0.0 34.37 4.85 R
3007 6437 1.303317 AACTCCCATGCCGGTGAAC 60.303 57.895 1.90 0.0 0.00 3.18 R
3800 7315 1.419374 ACGATGCTGAAACAGACGAC 58.581 50.000 15.09 0.0 32.44 4.34 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
28 29 1.596477 GATGTGGAGGCGGAGATGC 60.596 63.158 0.00 0.00 0.00 3.91
30 31 0.760567 ATGTGGAGGCGGAGATGCTA 60.761 55.000 0.00 0.00 34.52 3.49
32 33 0.037790 GTGGAGGCGGAGATGCTATC 60.038 60.000 0.00 0.00 34.52 2.08
33 34 1.214062 GGAGGCGGAGATGCTATCG 59.786 63.158 0.00 0.00 34.52 2.92
45 46 3.196685 AGATGCTATCGGGGAGAATAAGC 59.803 47.826 0.00 0.00 35.22 3.09
67 68 4.883354 CGCCTTGCCATCCCCTCC 62.883 72.222 0.00 0.00 0.00 4.30
74 75 3.781307 CCATCCCCTCCGCGACAA 61.781 66.667 8.23 0.00 0.00 3.18
87 88 1.077089 GCGACAACGTCTTCTAGGGC 61.077 60.000 0.00 0.00 41.98 5.19
94 95 0.248134 CGTCTTCTAGGGCTTCGTCG 60.248 60.000 0.00 0.00 0.00 5.12
95 96 0.810016 GTCTTCTAGGGCTTCGTCGT 59.190 55.000 0.00 0.00 0.00 4.34
96 97 1.093159 TCTTCTAGGGCTTCGTCGTC 58.907 55.000 0.00 0.00 0.00 4.20
97 98 0.248134 CTTCTAGGGCTTCGTCGTCG 60.248 60.000 0.00 0.00 38.55 5.12
98 99 0.674581 TTCTAGGGCTTCGTCGTCGA 60.675 55.000 0.00 0.00 44.66 4.20
99 100 0.463295 TCTAGGGCTTCGTCGTCGAT 60.463 55.000 5.44 0.00 45.65 3.59
100 101 0.381089 CTAGGGCTTCGTCGTCGATT 59.619 55.000 5.44 0.00 45.65 3.34
101 102 0.813184 TAGGGCTTCGTCGTCGATTT 59.187 50.000 5.44 0.00 45.65 2.17
102 103 0.736325 AGGGCTTCGTCGTCGATTTG 60.736 55.000 5.44 1.21 45.65 2.32
103 104 1.693083 GGGCTTCGTCGTCGATTTGG 61.693 60.000 5.44 0.00 45.65 3.28
104 105 1.058903 GCTTCGTCGTCGATTTGGC 59.941 57.895 5.44 5.07 45.65 4.52
105 106 1.340465 CTTCGTCGTCGATTTGGCG 59.660 57.895 5.44 3.32 45.65 5.69
106 107 2.009625 CTTCGTCGTCGATTTGGCGG 62.010 60.000 5.44 0.00 45.65 6.13
107 108 4.204891 CGTCGTCGATTTGGCGGC 62.205 66.667 0.00 0.00 39.71 6.53
108 109 2.813908 GTCGTCGATTTGGCGGCT 60.814 61.111 11.43 0.00 32.90 5.52
109 110 2.047655 TCGTCGATTTGGCGGCTT 60.048 55.556 11.43 0.00 32.90 4.35
110 111 1.669760 TCGTCGATTTGGCGGCTTT 60.670 52.632 11.43 0.00 32.90 3.51
111 112 1.209127 CGTCGATTTGGCGGCTTTT 59.791 52.632 11.43 0.00 32.90 2.27
112 113 1.065031 CGTCGATTTGGCGGCTTTTG 61.065 55.000 11.43 0.00 32.90 2.44
113 114 0.732538 GTCGATTTGGCGGCTTTTGG 60.733 55.000 11.43 0.00 32.23 3.28
120 121 3.660111 GCGGCTTTTGGTGCTCGT 61.660 61.111 0.00 0.00 0.00 4.18
211 212 0.610785 TGGGGATTTTGTCCTTCGGC 60.611 55.000 0.00 0.00 46.91 5.54
215 216 1.613255 GGATTTTGTCCTTCGGCCAGA 60.613 52.381 2.24 0.00 44.16 3.86
245 246 0.318275 CTGACGATTCCTCTAGCCGC 60.318 60.000 0.00 0.00 0.00 6.53
248 249 2.340443 GATTCCTCTAGCCGCGGG 59.660 66.667 29.38 10.87 0.00 6.13
270 271 4.442454 GGCCTGGTAAGGTGGGGC 62.442 72.222 0.00 0.00 46.43 5.80
332 333 3.159213 AGTGTTTCTGATGGCATTGGA 57.841 42.857 0.00 0.00 0.00 3.53
356 357 1.599606 GGTCGCTCTTCTCAGGCTCA 61.600 60.000 0.00 0.00 0.00 4.26
388 389 1.653094 GGCGATGCCGTTCAATCCAA 61.653 55.000 0.00 0.00 39.62 3.53
390 391 0.378257 CGATGCCGTTCAATCCAAGG 59.622 55.000 0.00 0.00 0.00 3.61
415 416 2.513026 CTTCTGGACGAGCAGGGTGG 62.513 65.000 0.00 0.00 0.00 4.61
429 430 1.302832 GGTGGCTTCCTGACTGTGG 60.303 63.158 0.00 0.00 0.00 4.17
463 469 3.121030 CAAGGTTGAGGAGCGGCG 61.121 66.667 0.51 0.51 0.00 6.46
518 524 1.671742 GTCGTGAGGCTCCCAAAGA 59.328 57.895 12.86 0.00 0.00 2.52
519 525 0.034896 GTCGTGAGGCTCCCAAAGAA 59.965 55.000 12.86 0.00 0.00 2.52
520 526 0.321671 TCGTGAGGCTCCCAAAGAAG 59.678 55.000 12.86 0.00 0.00 2.85
538 544 2.626780 GGACGGGCTTGCAGTTTCC 61.627 63.158 0.00 0.00 0.00 3.13
558 564 0.107017 TATTCTGCTTGGGCTGCCTC 60.107 55.000 19.68 9.39 39.59 4.70
559 565 2.146146 ATTCTGCTTGGGCTGCCTCA 62.146 55.000 19.68 12.08 39.59 3.86
633 641 6.995091 ACTGCAGTTTCAAGTTAAGAATCTCT 59.005 34.615 15.25 0.00 0.00 3.10
635 643 8.539770 TGCAGTTTCAAGTTAAGAATCTCTAG 57.460 34.615 0.00 0.00 0.00 2.43
636 644 8.367911 TGCAGTTTCAAGTTAAGAATCTCTAGA 58.632 33.333 0.00 0.00 0.00 2.43
730 3666 2.771372 TGAGATCAAATCCGTCCATCCA 59.229 45.455 0.00 0.00 0.00 3.41
731 3667 3.392285 TGAGATCAAATCCGTCCATCCAT 59.608 43.478 0.00 0.00 0.00 3.41
732 3668 4.141413 TGAGATCAAATCCGTCCATCCATT 60.141 41.667 0.00 0.00 0.00 3.16
733 3669 4.392940 AGATCAAATCCGTCCATCCATTC 58.607 43.478 0.00 0.00 0.00 2.67
888 3830 1.580942 CACCTGCATTCCACCAACG 59.419 57.895 0.00 0.00 0.00 4.10
983 4090 3.174265 CCCAGCCCCCAGATCTCC 61.174 72.222 0.00 0.00 0.00 3.71
1087 4198 0.999406 CAAATCCGCGTCAGGTAGTG 59.001 55.000 4.92 0.00 0.00 2.74
1115 4226 3.467119 CGTCCGTGGTTCTTCGCG 61.467 66.667 0.00 0.00 39.97 5.87
1123 4234 2.807895 GTTCTTCGCGCGTGGCTA 60.808 61.111 30.98 6.92 40.44 3.93
1130 4241 4.899239 GCGCGTGGCTAGCTGGAT 62.899 66.667 15.72 0.00 39.11 3.41
1131 4242 2.659897 CGCGTGGCTAGCTGGATC 60.660 66.667 15.72 0.00 0.00 3.36
1132 4243 2.818132 GCGTGGCTAGCTGGATCT 59.182 61.111 15.72 0.00 0.00 2.75
1167 4278 0.993746 CGTGCGTTTTTCTCTGCTGC 60.994 55.000 0.00 0.00 0.00 5.25
1288 4399 4.248859 TGCTCTGAGAATCTTTTCCTTCG 58.751 43.478 9.28 0.00 34.92 3.79
1301 4412 1.787012 TCCTTCGTAACTTCGTTGCC 58.213 50.000 0.00 0.00 0.00 4.52
1304 4415 2.132762 CTTCGTAACTTCGTTGCCTGT 58.867 47.619 0.00 0.00 0.00 4.00
1350 4461 4.245660 TGTTCGCTTAATCTTCTCTGTGG 58.754 43.478 0.00 0.00 0.00 4.17
1424 4535 5.850614 GTCTGAAGGGTAAGACTGTAACAA 58.149 41.667 0.00 0.00 39.79 2.83
1453 4564 1.206610 CTCGCCTGCCTGATATATGCT 59.793 52.381 0.00 0.00 0.00 3.79
1484 4595 4.498894 TCCTGAGTGCTCATGATGAATT 57.501 40.909 0.00 0.00 39.13 2.17
1485 4596 4.196971 TCCTGAGTGCTCATGATGAATTG 58.803 43.478 0.00 0.00 39.13 2.32
1548 4659 6.751425 TGCAATACCAACGATTCAATTGATTC 59.249 34.615 16.84 16.84 0.00 2.52
1560 4671 8.775527 CGATTCAATTGATTCTTCATCTCTCAT 58.224 33.333 21.76 4.48 32.34 2.90
1573 4684 8.045507 TCTTCATCTCTCATGAGCTAACAATTT 58.954 33.333 18.36 0.00 40.03 1.82
1582 4693 7.988737 TCATGAGCTAACAATTTGAGTATTGG 58.011 34.615 2.79 0.00 39.33 3.16
1615 4726 4.024556 AGCTTAGATTTGATTGGATTCGCG 60.025 41.667 0.00 0.00 0.00 5.87
1616 4727 4.024893 GCTTAGATTTGATTGGATTCGCGA 60.025 41.667 3.71 3.71 0.00 5.87
1623 4734 3.059884 TGATTGGATTCGCGATCTTAGC 58.940 45.455 10.88 0.00 35.02 3.09
1628 4739 1.789464 GATTCGCGATCTTAGCCTGTG 59.211 52.381 10.88 0.00 0.00 3.66
1631 4742 0.647410 CGCGATCTTAGCCTGTGTTG 59.353 55.000 0.00 0.00 0.00 3.33
1672 4783 4.616953 ACTTCCAATTTTGTTACGGCTTG 58.383 39.130 0.00 0.00 0.00 4.01
1673 4784 4.098807 ACTTCCAATTTTGTTACGGCTTGT 59.901 37.500 0.00 0.00 0.00 3.16
1773 4886 7.309805 GCTGTTTAAACTTTGATATGACCCCTT 60.310 37.037 18.72 0.00 0.00 3.95
1777 4890 3.886123 ACTTTGATATGACCCCTTTCGG 58.114 45.455 0.00 0.00 0.00 4.30
1801 4914 1.415659 CACATGGGGTTTTGGAAAGCA 59.584 47.619 0.00 0.00 0.00 3.91
1937 5339 0.326264 AGGGCTTGAGTGGATGTGAC 59.674 55.000 0.00 0.00 0.00 3.67
1938 5340 0.326264 GGGCTTGAGTGGATGTGACT 59.674 55.000 0.00 0.00 0.00 3.41
1939 5341 1.271597 GGGCTTGAGTGGATGTGACTT 60.272 52.381 0.00 0.00 0.00 3.01
1940 5342 1.808945 GGCTTGAGTGGATGTGACTTG 59.191 52.381 0.00 0.00 0.00 3.16
1941 5343 2.550855 GGCTTGAGTGGATGTGACTTGA 60.551 50.000 0.00 0.00 0.00 3.02
1942 5344 3.141398 GCTTGAGTGGATGTGACTTGAA 58.859 45.455 0.00 0.00 0.00 2.69
1943 5345 3.565482 GCTTGAGTGGATGTGACTTGAAA 59.435 43.478 0.00 0.00 0.00 2.69
1944 5346 4.217118 GCTTGAGTGGATGTGACTTGAAAT 59.783 41.667 0.00 0.00 0.00 2.17
1945 5347 5.618640 GCTTGAGTGGATGTGACTTGAAATC 60.619 44.000 0.00 0.00 0.00 2.17
1946 5348 4.971939 TGAGTGGATGTGACTTGAAATCA 58.028 39.130 0.00 0.00 0.00 2.57
2027 5434 8.680903 CAATTTCCTAATAGATGATATGCACCC 58.319 37.037 0.00 0.00 0.00 4.61
2044 5451 2.100989 ACCCGATCTTCTGGTAGACAC 58.899 52.381 0.00 0.00 31.94 3.67
2139 5546 5.712446 TGCAGTATATCTAGGGAGTAAGCAG 59.288 44.000 0.00 0.00 0.00 4.24
2356 5763 8.950208 AGCACTTAACCTTTGATTAGTAGATC 57.050 34.615 0.00 0.00 0.00 2.75
2486 5894 0.608130 TCAGTTGGTGGGATCTGTCG 59.392 55.000 0.00 0.00 0.00 4.35
2533 5941 9.506018 AACTGGATTTATTTTCCAAAATTCAGG 57.494 29.630 16.49 3.81 46.38 3.86
2536 5944 9.669887 TGGATTTATTTTCCAAAATTCAGGATG 57.330 29.630 2.68 0.00 40.29 3.51
2646 6063 2.730604 CGTTTGCTGGCTTTGGCG 60.731 61.111 0.00 0.00 39.81 5.69
2658 6075 1.604278 GCTTTGGCGTTTCAACTCTCT 59.396 47.619 0.00 0.00 0.00 3.10
2701 6130 7.014711 TGGTCTTTAAAATTCAACTATGCCACA 59.985 33.333 0.00 0.00 0.00 4.17
2811 6241 4.218417 GTGCAAGTCCCTGATTGTGTAATT 59.782 41.667 0.00 0.00 0.00 1.40
2833 6263 6.921486 TTACCTTTGTGTAGTCATGAGGTA 57.079 37.500 0.00 0.00 35.84 3.08
2926 6356 2.430694 TGAAGATGTCGGTCACTATGGG 59.569 50.000 0.00 0.00 0.00 4.00
2986 6416 2.223971 TGGAGACCTTCGTGTTCTTGAC 60.224 50.000 0.00 0.00 0.00 3.18
3007 6437 2.096069 CACACCAATTGCTGAGAACTCG 60.096 50.000 7.75 0.00 0.00 4.18
3697 7127 1.303948 CCCCATCATGTGCCTGTCA 59.696 57.895 0.00 0.00 0.00 3.58
3772 7287 2.879907 CCTGCCCAGATTGTTGCG 59.120 61.111 0.00 0.00 0.00 4.85
3938 7453 5.695851 ATTCCTGCTTGAGTTAACACTTG 57.304 39.130 8.61 0.47 31.22 3.16
4044 7559 6.151985 TGGGCAAGGTATAACTATGTGTTTTG 59.848 38.462 0.00 0.00 39.89 2.44
4060 7575 6.166279 TGTGTTTTGGTTATCTTTGTTTGCA 58.834 32.000 0.00 0.00 0.00 4.08
4065 7580 9.008289 GTTTTGGTTATCTTTGTTTGCATTTTG 57.992 29.630 0.00 0.00 0.00 2.44
4066 7581 6.857777 TGGTTATCTTTGTTTGCATTTTGG 57.142 33.333 0.00 0.00 0.00 3.28
4074 7596 6.822676 TCTTTGTTTGCATTTTGGTCATCTTT 59.177 30.769 0.00 0.00 0.00 2.52
4086 7609 3.820467 TGGTCATCTTTGTCACATGGTTC 59.180 43.478 0.00 0.00 0.00 3.62
4116 7653 6.939622 TCAAGAAAGCTTAGATCATGTCAGA 58.060 36.000 0.00 0.00 31.81 3.27
4143 7680 0.609662 GCCTCACCACCAATTGCAAT 59.390 50.000 5.99 5.99 0.00 3.56
4144 7681 1.673626 GCCTCACCACCAATTGCAATG 60.674 52.381 13.82 3.77 0.00 2.82
4145 7682 1.066716 CCTCACCACCAATTGCAATGG 60.067 52.381 13.82 17.73 43.84 3.16
4165 7702 4.728772 TGGTGAAAGGAAGATCACAACAT 58.271 39.130 8.04 0.00 46.07 2.71
4167 7704 4.142816 GGTGAAAGGAAGATCACAACATCG 60.143 45.833 8.04 0.00 46.07 3.84
4185 7722 2.896443 CTTCTCCAGGGGACGAGC 59.104 66.667 0.00 0.00 0.00 5.03
4211 7748 3.754965 TGTTTGATCAGCCAAGCTACTT 58.245 40.909 0.00 0.00 36.40 2.24
4212 7749 4.905429 TGTTTGATCAGCCAAGCTACTTA 58.095 39.130 0.00 0.00 36.40 2.24
4389 7963 4.893601 TCAAACACGTGGCGCCGA 62.894 61.111 23.90 8.37 0.00 5.54
4524 8098 2.770048 AGGCGGATGGAGAAGGGG 60.770 66.667 0.00 0.00 0.00 4.79
4560 8137 1.148273 AGAAAGCTTCCACACCGCA 59.852 52.632 0.00 0.00 0.00 5.69
4744 8321 1.068083 CAGTCACAGGTCACGCTGT 59.932 57.895 0.00 0.00 0.00 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.397941 CCTCCACATCACCGCCATAT 59.602 55.000 0.00 0.00 0.00 1.78
1 2 1.829456 CCTCCACATCACCGCCATA 59.171 57.895 0.00 0.00 0.00 2.74
2 3 2.591753 CCTCCACATCACCGCCAT 59.408 61.111 0.00 0.00 0.00 4.40
3 4 4.408821 GCCTCCACATCACCGCCA 62.409 66.667 0.00 0.00 0.00 5.69
6 7 3.723235 CTCCGCCTCCACATCACCG 62.723 68.421 0.00 0.00 0.00 4.94
7 8 1.690219 ATCTCCGCCTCCACATCACC 61.690 60.000 0.00 0.00 0.00 4.02
8 9 0.531532 CATCTCCGCCTCCACATCAC 60.532 60.000 0.00 0.00 0.00 3.06
9 10 1.825341 CATCTCCGCCTCCACATCA 59.175 57.895 0.00 0.00 0.00 3.07
28 29 2.927014 GCACGCTTATTCTCCCCGATAG 60.927 54.545 0.00 0.00 0.00 2.08
30 31 0.249911 GCACGCTTATTCTCCCCGAT 60.250 55.000 0.00 0.00 0.00 4.18
32 33 1.887707 GGCACGCTTATTCTCCCCG 60.888 63.158 0.00 0.00 0.00 5.73
33 34 4.142780 GGCACGCTTATTCTCCCC 57.857 61.111 0.00 0.00 0.00 4.81
67 68 0.797249 CCCTAGAAGACGTTGTCGCG 60.797 60.000 0.00 0.00 41.18 5.87
71 72 1.067776 CGAAGCCCTAGAAGACGTTGT 60.068 52.381 0.00 0.00 0.00 3.32
74 75 0.810016 GACGAAGCCCTAGAAGACGT 59.190 55.000 0.00 0.00 35.31 4.34
94 95 0.732538 CCAAAAGCCGCCAAATCGAC 60.733 55.000 0.00 0.00 0.00 4.20
95 96 1.175983 ACCAAAAGCCGCCAAATCGA 61.176 50.000 0.00 0.00 0.00 3.59
96 97 1.008361 CACCAAAAGCCGCCAAATCG 61.008 55.000 0.00 0.00 0.00 3.34
97 98 1.291184 GCACCAAAAGCCGCCAAATC 61.291 55.000 0.00 0.00 0.00 2.17
98 99 1.301637 GCACCAAAAGCCGCCAAAT 60.302 52.632 0.00 0.00 0.00 2.32
99 100 2.107953 GCACCAAAAGCCGCCAAA 59.892 55.556 0.00 0.00 0.00 3.28
100 101 2.837291 AGCACCAAAAGCCGCCAA 60.837 55.556 0.00 0.00 0.00 4.52
101 102 3.294493 GAGCACCAAAAGCCGCCA 61.294 61.111 0.00 0.00 0.00 5.69
102 103 4.404654 CGAGCACCAAAAGCCGCC 62.405 66.667 0.00 0.00 0.00 6.13
103 104 3.660111 ACGAGCACCAAAAGCCGC 61.660 61.111 0.00 0.00 31.79 6.53
104 105 2.252260 CACGAGCACCAAAAGCCG 59.748 61.111 0.00 0.00 33.79 5.52
105 106 2.644992 CCACGAGCACCAAAAGCC 59.355 61.111 0.00 0.00 0.00 4.35
106 107 2.130073 GACCCACGAGCACCAAAAGC 62.130 60.000 0.00 0.00 0.00 3.51
107 108 1.515521 GGACCCACGAGCACCAAAAG 61.516 60.000 0.00 0.00 0.00 2.27
108 109 1.527380 GGACCCACGAGCACCAAAA 60.527 57.895 0.00 0.00 0.00 2.44
109 110 2.112297 GGACCCACGAGCACCAAA 59.888 61.111 0.00 0.00 0.00 3.28
110 111 3.164977 TGGACCCACGAGCACCAA 61.165 61.111 0.00 0.00 0.00 3.67
111 112 3.936203 GTGGACCCACGAGCACCA 61.936 66.667 3.13 0.00 37.19 4.17
211 212 3.250323 CAGCGCATCGACGTCTGG 61.250 66.667 14.70 3.82 35.21 3.86
225 226 0.318275 CGGCTAGAGGAATCGTCAGC 60.318 60.000 14.42 14.42 0.00 4.26
232 233 2.444140 ACCCGCGGCTAGAGGAAT 60.444 61.111 22.85 0.00 43.02 3.01
245 246 3.622060 CTTACCAGGCCCACACCCG 62.622 68.421 0.00 0.00 0.00 5.28
248 249 1.303317 CACCTTACCAGGCCCACAC 60.303 63.158 0.00 0.00 45.56 3.82
388 389 1.878656 CTCGTCCAGAAGAACCGCCT 61.879 60.000 0.00 0.00 0.00 5.52
390 391 2.095252 GCTCGTCCAGAAGAACCGC 61.095 63.158 0.00 0.00 0.00 5.68
415 416 1.298014 CCTCCCACAGTCAGGAAGC 59.702 63.158 0.00 0.00 0.00 3.86
429 430 0.393808 TTGTTTATGAGCCGGCCTCC 60.394 55.000 26.15 13.78 39.98 4.30
441 442 2.711542 CCGCTCCTCAACCTTGTTTAT 58.288 47.619 0.00 0.00 0.00 1.40
442 443 1.880646 GCCGCTCCTCAACCTTGTTTA 60.881 52.381 0.00 0.00 0.00 2.01
485 491 2.971452 GACCTCCACGTCCAGGAC 59.029 66.667 15.03 9.92 33.52 3.85
518 524 1.152756 AAACTGCAAGCCCGTCCTT 60.153 52.632 0.00 0.00 37.60 3.36
519 525 1.600916 GAAACTGCAAGCCCGTCCT 60.601 57.895 0.00 0.00 37.60 3.85
520 526 2.626780 GGAAACTGCAAGCCCGTCC 61.627 63.158 0.00 0.00 37.60 4.79
538 544 0.106819 AGGCAGCCCAAGCAGAATAG 60.107 55.000 8.22 0.00 43.56 1.73
546 552 0.672342 GCATTATGAGGCAGCCCAAG 59.328 55.000 8.22 0.05 31.66 3.61
589 596 7.223387 ACTGCAGTTTTTCTTTTGCAAAGATAG 59.777 33.333 15.25 7.48 44.94 2.08
592 599 5.237048 ACTGCAGTTTTTCTTTTGCAAAGA 58.763 33.333 15.25 9.30 44.94 2.52
608 616 6.995091 AGAGATTCTTAACTTGAAACTGCAGT 59.005 34.615 15.25 15.25 28.92 4.40
636 644 9.030301 GGAATTATTTAGCGTGTTTTGCATAAT 57.970 29.630 0.00 0.00 33.85 1.28
730 3666 1.004044 GGCCGATGGAGATGGATGAAT 59.996 52.381 0.00 0.00 0.00 2.57
731 3667 0.397941 GGCCGATGGAGATGGATGAA 59.602 55.000 0.00 0.00 0.00 2.57
732 3668 1.483595 GGGCCGATGGAGATGGATGA 61.484 60.000 0.00 0.00 0.00 2.92
733 3669 1.002868 GGGCCGATGGAGATGGATG 60.003 63.158 0.00 0.00 0.00 3.51
843 3784 3.089874 TGGCGGAGGAATGGAGGG 61.090 66.667 0.00 0.00 0.00 4.30
983 4090 0.754217 CATTGCAGATGGGAGGGGTG 60.754 60.000 0.00 0.00 0.00 4.61
1107 4218 2.506217 CTAGCCACGCGCGAAGAA 60.506 61.111 39.36 16.11 44.76 2.52
1115 4226 0.878086 GAAGATCCAGCTAGCCACGC 60.878 60.000 12.13 0.00 0.00 5.34
1123 4234 1.189752 TCAGCGAAGAAGATCCAGCT 58.810 50.000 0.00 0.00 35.06 4.24
1126 4237 3.127548 GCAAAATCAGCGAAGAAGATCCA 59.872 43.478 0.00 0.00 0.00 3.41
1152 4263 0.723790 CGCTGCAGCAGAGAAAAACG 60.724 55.000 36.03 13.85 42.21 3.60
1215 4326 4.421515 CCACCAGCCTGCCTCCAG 62.422 72.222 0.00 0.00 38.85 3.86
1301 4412 1.880894 CACCAGCAGATGCCAACAG 59.119 57.895 0.14 0.00 43.38 3.16
1304 4415 3.057548 CGCACCAGCAGATGCCAA 61.058 61.111 0.14 0.00 43.38 4.52
1350 4461 0.307760 CCTTGGTCTGCACACGAAAC 59.692 55.000 0.00 0.00 0.00 2.78
1424 4535 2.031163 GCAGGCGAGGAAGTGTGT 59.969 61.111 0.00 0.00 0.00 3.72
1453 4564 1.486310 AGCACTCAGGAACACAGTTGA 59.514 47.619 0.00 0.00 0.00 3.18
1484 4595 2.238646 AGATAGTTTTGCGTGGATCCCA 59.761 45.455 9.90 0.00 0.00 4.37
1485 4596 2.919228 AGATAGTTTTGCGTGGATCCC 58.081 47.619 9.90 0.00 0.00 3.85
1528 4639 7.680442 TGAAGAATCAATTGAATCGTTGGTA 57.320 32.000 13.09 0.00 30.99 3.25
1548 4659 7.789273 AATTGTTAGCTCATGAGAGATGAAG 57.211 36.000 27.04 0.00 44.98 3.02
1560 4671 7.168219 AGTCCAATACTCAAATTGTTAGCTCA 58.832 34.615 0.00 0.00 35.48 4.26
1582 4693 8.394121 CCAATCAAATCTAAGCTAAGTTGAGTC 58.606 37.037 10.82 0.00 0.00 3.36
1589 4700 7.074502 GCGAATCCAATCAAATCTAAGCTAAG 58.925 38.462 0.00 0.00 0.00 2.18
1628 4739 1.071699 TGAACTGGAGTGTAGCCCAAC 59.928 52.381 0.00 0.00 31.11 3.77
1631 4742 1.066787 GTCTGAACTGGAGTGTAGCCC 60.067 57.143 0.00 0.00 0.00 5.19
1672 4783 7.493645 AGTGACACCTAACACTAAAAACTACAC 59.506 37.037 0.84 0.00 44.06 2.90
1673 4784 7.558604 AGTGACACCTAACACTAAAAACTACA 58.441 34.615 0.84 0.00 44.06 2.74
1741 4853 0.677288 AAAGTTTAAACAGCCCGCCC 59.323 50.000 20.06 0.00 0.00 6.13
1744 4856 6.027749 GTCATATCAAAGTTTAAACAGCCCG 58.972 40.000 20.06 4.37 0.00 6.13
1773 4886 2.074729 AAACCCCATGTGTTTCCGAA 57.925 45.000 5.11 0.00 30.34 4.30
1777 4890 3.828875 TTCCAAAACCCCATGTGTTTC 57.171 42.857 10.08 0.00 34.97 2.78
1801 4914 1.134670 GGTAGAGAAGCTTCACCGCAT 60.135 52.381 27.57 6.28 0.00 4.73
1942 5344 5.717078 ACTGACTGCAAAATCATGTGATT 57.283 34.783 2.48 2.48 45.91 2.57
1943 5345 5.717078 AACTGACTGCAAAATCATGTGAT 57.283 34.783 0.00 0.00 36.07 3.06
1944 5346 6.262944 ACTTAACTGACTGCAAAATCATGTGA 59.737 34.615 0.00 0.00 0.00 3.58
1945 5347 6.441274 ACTTAACTGACTGCAAAATCATGTG 58.559 36.000 0.00 0.00 0.00 3.21
1946 5348 6.639632 ACTTAACTGACTGCAAAATCATGT 57.360 33.333 0.00 0.00 0.00 3.21
2056 5463 6.653320 TGGCTTGCTATTAGGATTATTAACGG 59.347 38.462 0.00 0.00 0.00 4.44
2139 5546 0.599558 TGCAATTCACTGAAGCAGCC 59.400 50.000 2.37 0.00 34.37 4.85
2356 5763 1.001974 GCCAAACCCAGGCCTTAAAAG 59.998 52.381 0.00 0.00 46.50 2.27
2486 5894 4.552166 TTACTTAGCCGGACGTACATAC 57.448 45.455 5.05 0.00 0.00 2.39
2533 5941 5.792741 CATCCTATCTCCTCTTGGTTCATC 58.207 45.833 0.00 0.00 34.23 2.92
2536 5944 3.244387 GGCATCCTATCTCCTCTTGGTTC 60.244 52.174 0.00 0.00 34.23 3.62
2543 5959 2.566724 CCAAGAGGCATCCTATCTCCTC 59.433 54.545 0.00 0.00 44.09 3.71
2547 5963 3.342926 AGTCCAAGAGGCATCCTATCT 57.657 47.619 0.00 0.00 31.76 1.98
2646 6063 5.929415 CCAGTTTAGAGGAGAGAGTTGAAAC 59.071 44.000 0.00 0.00 0.00 2.78
2658 6075 2.374170 GACCAAACCCCAGTTTAGAGGA 59.626 50.000 0.00 0.00 44.47 3.71
2811 6241 7.327975 CAATACCTCATGACTACACAAAGGTA 58.672 38.462 7.04 7.04 41.67 3.08
2833 6263 1.808945 CGAAGAGCCTCAAACAGCAAT 59.191 47.619 0.00 0.00 0.00 3.56
2926 6356 2.943036 TGGTCACCTTGTAAGAACCC 57.057 50.000 0.00 0.00 0.00 4.11
2986 6416 2.096069 CGAGTTCTCAGCAATTGGTGTG 60.096 50.000 30.77 28.30 43.46 3.82
2992 6422 2.808543 GGTGAACGAGTTCTCAGCAATT 59.191 45.455 15.80 0.00 39.36 2.32
3007 6437 1.303317 AACTCCCATGCCGGTGAAC 60.303 57.895 1.90 0.00 0.00 3.18
3625 7055 2.895680 GATCTCAGACTGGCGCCA 59.104 61.111 30.59 30.59 0.00 5.69
3772 7287 3.256620 GCATATTTGCTCAACGGCC 57.743 52.632 0.35 0.00 45.77 6.13
3800 7315 1.419374 ACGATGCTGAAACAGACGAC 58.581 50.000 15.09 0.00 32.44 4.34
3803 7318 6.142817 ACAAATTAACGATGCTGAAACAGAC 58.857 36.000 2.81 0.00 32.44 3.51
3938 7453 9.130312 GCATAATACAGTACAGTTATGTAGCTC 57.870 37.037 11.53 0.00 42.53 4.09
4032 7547 9.528018 CAAACAAAGATAACCAAAACACATAGT 57.472 29.630 0.00 0.00 0.00 2.12
4044 7559 6.481644 TGACCAAAATGCAAACAAAGATAACC 59.518 34.615 0.00 0.00 0.00 2.85
4060 7575 5.305128 ACCATGTGACAAAGATGACCAAAAT 59.695 36.000 0.00 0.00 31.04 1.82
4065 7580 3.820467 TGAACCATGTGACAAAGATGACC 59.180 43.478 0.00 0.00 31.04 4.02
4066 7581 5.009010 ACTTGAACCATGTGACAAAGATGAC 59.991 40.000 0.00 0.00 31.04 3.06
4074 7596 3.836365 TGAGACTTGAACCATGTGACA 57.164 42.857 0.00 0.00 0.00 3.58
4086 7609 7.333921 ACATGATCTAAGCTTTCTTGAGACTTG 59.666 37.037 3.20 7.06 33.85 3.16
4143 7680 4.163441 TGTTGTGATCTTCCTTTCACCA 57.837 40.909 0.00 0.00 41.22 4.17
4144 7681 4.142816 CGATGTTGTGATCTTCCTTTCACC 60.143 45.833 0.00 0.00 41.22 4.02
4145 7682 4.670221 GCGATGTTGTGATCTTCCTTTCAC 60.670 45.833 0.00 0.00 42.05 3.18
4151 7688 3.265791 AGAAGCGATGTTGTGATCTTCC 58.734 45.455 0.00 0.00 32.62 3.46
4165 7702 3.068691 CGTCCCCTGGAGAAGCGA 61.069 66.667 0.00 0.00 29.39 4.93
4167 7704 2.896443 CTCGTCCCCTGGAGAAGC 59.104 66.667 0.00 0.00 29.39 3.86
4185 7722 0.597568 TTGGCTGATCAAACAAGCGG 59.402 50.000 7.45 0.00 0.00 5.52
4234 7771 5.186797 CCTGGAGTCTTACAATCTCTGAAGT 59.813 44.000 0.00 0.00 0.00 3.01
4235 7772 5.659463 CCTGGAGTCTTACAATCTCTGAAG 58.341 45.833 0.00 0.00 0.00 3.02
4236 7773 4.081420 GCCTGGAGTCTTACAATCTCTGAA 60.081 45.833 0.00 0.00 0.00 3.02
4237 7774 3.449018 GCCTGGAGTCTTACAATCTCTGA 59.551 47.826 0.00 0.00 0.00 3.27
4238 7775 3.450457 AGCCTGGAGTCTTACAATCTCTG 59.550 47.826 0.00 0.00 0.00 3.35
4242 7779 4.123506 GCTTAGCCTGGAGTCTTACAATC 58.876 47.826 0.00 0.00 0.00 2.67
4243 7780 3.777522 AGCTTAGCCTGGAGTCTTACAAT 59.222 43.478 0.00 0.00 0.00 2.71
4244 7781 3.173965 AGCTTAGCCTGGAGTCTTACAA 58.826 45.455 0.00 0.00 0.00 2.41
4246 7783 3.700038 TGTAGCTTAGCCTGGAGTCTTAC 59.300 47.826 0.00 0.00 0.00 2.34
4247 7784 3.700038 GTGTAGCTTAGCCTGGAGTCTTA 59.300 47.826 0.00 0.00 0.00 2.10
4280 7849 0.645868 GTGAGAATGTAAGCCGCGAC 59.354 55.000 8.23 0.00 0.00 5.19
4367 7941 2.903547 CGCCACGTGTTTGAAGGGG 61.904 63.158 15.65 1.36 0.00 4.79
4404 7978 2.747686 GTGGCGGTGAGGGAAAGA 59.252 61.111 0.00 0.00 0.00 2.52
4509 8083 4.570874 GGCCCCTTCTCCATCCGC 62.571 72.222 0.00 0.00 0.00 5.54
4539 8113 1.237285 CGGTGTGGAAGCTTTCTGGG 61.237 60.000 6.25 0.00 0.00 4.45
4542 8116 1.148273 TGCGGTGTGGAAGCTTTCT 59.852 52.632 6.25 0.00 0.00 2.52
4560 8137 2.937689 ATGCAGCAGTCCTGGGGT 60.938 61.111 0.00 0.00 42.03 4.95
4744 8321 4.446385 GTCGTGTTAGCATTTGTGTCTGTA 59.554 41.667 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.