Multiple sequence alignment - TraesCS3D01G541800

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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 TraesCS3D01G541800 chr3D 100.000 4014 0 0 228 4241 612904770 612900757 0.000000e+00 7413.0
1 TraesCS3D01G541800 chr3D 90.382 655 39 6 305 956 612085488 612086121 0.000000e+00 839.0
2 TraesCS3D01G541800 chr3D 96.774 496 16 0 1957 2452 612086358 612086853 0.000000e+00 828.0
3 TraesCS3D01G541800 chr3D 88.930 271 16 5 3270 3529 612087254 612087521 5.290000e-84 322.0
4 TraesCS3D01G541800 chr3D 96.257 187 7 0 2667 2853 612087062 612087248 1.480000e-79 307.0
5 TraesCS3D01G541800 chr3D 81.963 377 44 14 3530 3903 612087488 612087843 8.910000e-77 298.0
6 TraesCS3D01G541800 chr3D 97.633 169 4 0 1022 1190 612086128 612086296 1.490000e-74 291.0
7 TraesCS3D01G541800 chr3D 84.848 231 13 6 3938 4167 612087840 612088049 3.320000e-51 213.0
8 TraesCS3D01G541800 chr3D 100.000 70 0 0 1 70 612904997 612904928 3.440000e-26 130.0
9 TraesCS3D01G541800 chr3D 95.918 49 2 0 7 55 612904299 612904251 3.520000e-11 80.5
10 TraesCS3D01G541800 chr3D 94.231 52 3 0 7 58 612948962 612948911 3.520000e-11 80.5
11 TraesCS3D01G541800 chr3D 97.059 34 1 0 3494 3527 612901470 612901437 1.650000e-04 58.4
12 TraesCS3D01G541800 chr3D 97.059 34 1 0 3528 3561 612901504 612901471 1.650000e-04 58.4
13 TraesCS3D01G541800 chr3B 96.777 3382 82 11 228 3598 826081547 826084912 0.000000e+00 5616.0
14 TraesCS3D01G541800 chr3B 87.518 705 67 11 3530 4227 830659318 830660008 0.000000e+00 795.0
15 TraesCS3D01G541800 chr3B 93.542 542 17 4 2283 2824 830369242 830369765 0.000000e+00 791.0
16 TraesCS3D01G541800 chr3B 87.376 705 67 12 3530 4227 830370628 830371317 0.000000e+00 789.0
17 TraesCS3D01G541800 chr3B 89.527 592 43 7 293 881 830368397 830368972 0.000000e+00 732.0
18 TraesCS3D01G541800 chr3B 89.527 592 43 7 293 881 830657214 830657789 0.000000e+00 732.0
19 TraesCS3D01G541800 chr3B 98.077 260 5 0 2565 2824 830658196 830658455 1.800000e-123 453.0
20 TraesCS3D01G541800 chr3B 90.431 209 17 3 3319 3527 830370454 830370659 5.400000e-69 272.0
21 TraesCS3D01G541800 chr3B 90.431 209 17 3 3319 3527 830659144 830659349 5.400000e-69 272.0
22 TraesCS3D01G541800 chr3B 97.059 136 4 0 2856 2991 830369761 830369896 3.300000e-56 230.0
23 TraesCS3D01G541800 chr3B 95.588 136 6 0 2856 2991 830658451 830658586 7.140000e-53 219.0
24 TraesCS3D01G541800 chr3B 95.918 49 2 0 7 55 826082019 826082067 3.520000e-11 80.5
25 TraesCS3D01G541800 chr3B 97.500 40 1 0 1992 2031 830369206 830369245 7.610000e-08 69.4
26 TraesCS3D01G541800 chr3B 97.500 40 1 0 1992 2031 830658023 830658062 7.610000e-08 69.4
27 TraesCS3D01G541800 chr3B 97.059 34 1 0 3528 3561 826084808 826084841 1.650000e-04 58.4
28 TraesCS3D01G541800 chr3A 96.948 3342 79 7 228 3561 747629210 747625884 0.000000e+00 5585.0
29 TraesCS3D01G541800 chr3A 92.339 744 34 8 3494 4227 747625883 747625153 0.000000e+00 1037.0
30 TraesCS3D01G541800 chr3A 94.701 585 30 1 2049 2632 747869189 747868605 0.000000e+00 907.0
31 TraesCS3D01G541800 chr3A 94.186 430 24 1 2049 2477 747835389 747834960 0.000000e+00 654.0
32 TraesCS3D01G541800 chr3A 93.182 352 21 3 379 728 747870625 747870275 8.130000e-142 514.0
33 TraesCS3D01G541800 chr3A 93.617 329 19 2 402 728 747836803 747836475 1.370000e-134 490.0
34 TraesCS3D01G541800 chr3A 97.537 203 4 1 1293 1494 747869384 747869182 3.140000e-91 346.0
35 TraesCS3D01G541800 chr3A 97.044 203 5 1 1293 1494 747835584 747835382 1.460000e-89 340.0
36 TraesCS3D01G541800 chr3A 91.617 167 13 1 1142 1308 747836481 747836316 3.300000e-56 230.0
37 TraesCS3D01G541800 chr3A 97.059 68 2 0 3494 3561 747625917 747625850 9.640000e-22 115.0
38 TraesCS3D01G541800 chr3A 89.831 59 6 0 7 65 747645413 747645355 4.550000e-10 76.8
39 TraesCS3D01G541800 chr3A 96.875 32 1 0 3494 3525 747625849 747625818 2.000000e-03 54.7
40 TraesCS3D01G541800 chr4D 81.424 2724 373 67 765 3400 481167894 481170572 0.000000e+00 2104.0
41 TraesCS3D01G541800 chr5A 82.851 1901 241 35 1553 3400 662341591 662339723 0.000000e+00 1626.0
42 TraesCS3D01G541800 chr5A 83.993 606 85 2 963 1568 662342202 662341609 4.760000e-159 571.0
43 TraesCS3D01G541800 chr4B 82.762 1839 224 38 1553 3341 609497204 609498999 0.000000e+00 1554.0
44 TraesCS3D01G541800 chr4B 80.454 793 116 20 765 1538 609496120 609496892 1.710000e-158 569.0
45 TraesCS3D01G541800 chrUn 94.186 430 24 1 2049 2477 184782186 184781757 0.000000e+00 654.0
46 TraesCS3D01G541800 chrUn 95.294 340 16 0 2049 2388 33651701 33651362 1.340000e-149 540.0
47 TraesCS3D01G541800 chrUn 93.429 350 20 3 381 728 389846157 389845809 2.260000e-142 516.0
48 TraesCS3D01G541800 chrUn 92.614 352 20 4 379 728 184783619 184783272 6.330000e-138 501.0
49 TraesCS3D01G541800 chrUn 93.617 329 19 2 402 728 33653115 33652787 1.370000e-134 490.0
50 TraesCS3D01G541800 chrUn 93.625 251 15 1 2383 2632 184781682 184781432 1.440000e-99 374.0
51 TraesCS3D01G541800 chrUn 93.625 251 15 1 2383 2632 398649928 398650178 1.440000e-99 374.0
52 TraesCS3D01G541800 chrUn 97.537 203 4 1 1293 1494 33651896 33651694 3.140000e-91 346.0
53 TraesCS3D01G541800 chrUn 97.537 203 4 1 1293 1494 184782381 184782179 3.140000e-91 346.0
54 TraesCS3D01G541800 chrUn 91.617 167 13 1 1142 1308 33652793 33652628 3.300000e-56 230.0
55 TraesCS3D01G541800 chrUn 91.617 167 13 1 1142 1308 184783278 184783113 3.300000e-56 230.0
56 TraesCS3D01G541800 chrUn 91.617 167 13 1 1142 1308 389845815 389845650 3.300000e-56 230.0


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 TraesCS3D01G541800 chr3D 612900757 612904997 4240 True 1548.060000 7413 98.007200 1 4241 5 chr3D.!!$R2 4240
1 TraesCS3D01G541800 chr3D 612085488 612088049 2561 False 442.571429 839 90.969571 305 4167 7 chr3D.!!$F1 3862
2 TraesCS3D01G541800 chr3B 826081547 826084912 3365 False 1918.300000 5616 96.584667 7 3598 3 chr3B.!!$F1 3591
3 TraesCS3D01G541800 chr3B 830368397 830371317 2920 False 480.566667 791 92.572500 293 4227 6 chr3B.!!$F2 3934
4 TraesCS3D01G541800 chr3B 830657214 830660008 2794 False 423.400000 795 93.106833 293 4227 6 chr3B.!!$F3 3934
5 TraesCS3D01G541800 chr3A 747625153 747629210 4057 True 1697.925000 5585 95.805250 228 4227 4 chr3A.!!$R2 3999
6 TraesCS3D01G541800 chr3A 747868605 747870625 2020 True 589.000000 907 95.140000 379 2632 3 chr3A.!!$R4 2253
7 TraesCS3D01G541800 chr3A 747834960 747836803 1843 True 428.500000 654 94.116000 402 2477 4 chr3A.!!$R3 2075
8 TraesCS3D01G541800 chr4D 481167894 481170572 2678 False 2104.000000 2104 81.424000 765 3400 1 chr4D.!!$F1 2635
9 TraesCS3D01G541800 chr5A 662339723 662342202 2479 True 1098.500000 1626 83.422000 963 3400 2 chr5A.!!$R1 2437
10 TraesCS3D01G541800 chr4B 609496120 609498999 2879 False 1061.500000 1554 81.608000 765 3341 2 chr4B.!!$F1 2576
11 TraesCS3D01G541800 chrUn 184781432 184783619 2187 True 421.000000 654 93.915800 379 2632 5 chrUn.!!$R2 2253
12 TraesCS3D01G541800 chrUn 33651362 33653115 1753 True 401.500000 540 94.516250 402 2388 4 chrUn.!!$R1 1986
13 TraesCS3D01G541800 chrUn 389845650 389846157 507 True 373.000000 516 92.523000 381 1308 2 chrUn.!!$R3 927

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
693 699 0.034186 GTCATCCATTGTGCCCCAGA 60.034 55.000 0.00 0.00 0.0 3.86 F
1469 2238 0.449388 GCAACCAATGGCTTCGAGAG 59.551 55.000 0.00 0.00 0.0 3.20 F
1774 2867 2.306805 ACTGAGGATGTTCATGCAGGAA 59.693 45.455 10.22 10.22 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1774 2867 0.038744 CCACTGATGTTTGAGCCCCT 59.961 55.0 0.0 0.0 0.00 4.79 R
3114 4521 0.250727 CGTTTGGAGCTTCTTCCCCA 60.251 55.0 0.0 0.0 36.35 4.96 R
3268 4676 0.960364 GGCGGGCAGATCAACAAAGA 60.960 55.0 0.0 0.0 0.00 2.52 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
42 43 8.706492 TGGCAATTTTGTATCTTCAATTGATC 57.294 30.769 9.40 0.00 38.41 2.92
43 44 7.765360 TGGCAATTTTGTATCTTCAATTGATCC 59.235 33.333 9.40 0.00 38.41 3.36
44 45 7.983484 GGCAATTTTGTATCTTCAATTGATCCT 59.017 33.333 9.40 0.00 38.41 3.24
45 46 8.814235 GCAATTTTGTATCTTCAATTGATCCTG 58.186 33.333 9.40 0.83 38.41 3.86
48 49 6.932356 TTGTATCTTCAATTGATCCTGAGC 57.068 37.500 9.40 4.50 0.00 4.26
49 50 5.993055 TGTATCTTCAATTGATCCTGAGCA 58.007 37.500 9.40 6.60 0.00 4.26
50 51 6.598503 TGTATCTTCAATTGATCCTGAGCAT 58.401 36.000 9.40 2.54 0.00 3.79
51 52 7.058525 TGTATCTTCAATTGATCCTGAGCATT 58.941 34.615 9.40 0.00 0.00 3.56
52 53 7.558807 TGTATCTTCAATTGATCCTGAGCATTT 59.441 33.333 9.40 0.00 0.00 2.32
53 54 9.060347 GTATCTTCAATTGATCCTGAGCATTTA 57.940 33.333 9.40 0.00 0.00 1.40
54 55 8.707796 ATCTTCAATTGATCCTGAGCATTTAT 57.292 30.769 9.40 0.00 0.00 1.40
55 56 7.937649 TCTTCAATTGATCCTGAGCATTTATG 58.062 34.615 9.40 0.00 0.00 1.90
56 57 7.558807 TCTTCAATTGATCCTGAGCATTTATGT 59.441 33.333 9.40 0.00 0.00 2.29
57 58 7.034685 TCAATTGATCCTGAGCATTTATGTG 57.965 36.000 3.38 0.00 0.00 3.21
58 59 4.906065 TTGATCCTGAGCATTTATGTGC 57.094 40.909 0.00 0.00 45.38 4.57
64 65 4.783903 GCATTTATGTGCGCCGTT 57.216 50.000 4.18 0.00 35.10 4.44
65 66 3.028760 GCATTTATGTGCGCCGTTT 57.971 47.368 4.18 0.00 35.10 3.60
66 67 1.345410 GCATTTATGTGCGCCGTTTT 58.655 45.000 4.18 0.00 35.10 2.43
67 68 1.724082 GCATTTATGTGCGCCGTTTTT 59.276 42.857 4.18 0.00 35.10 1.94
361 363 0.108585 GGAAGATATTGCGGGGCTCA 59.891 55.000 0.00 0.00 0.00 4.26
388 390 8.970859 AGGTCTGATATTTCTCCAAGTAAATG 57.029 34.615 0.00 0.00 0.00 2.32
536 538 9.527157 TGTATCTTTCAATTCAATTGGTCCTTA 57.473 29.630 10.30 0.00 40.61 2.69
546 548 4.941263 TCAATTGGTCCTTAATTCCGTGAG 59.059 41.667 5.42 0.00 0.00 3.51
578 580 3.596310 TGCATGCTACGGTAGTGTTTA 57.404 42.857 20.33 0.00 0.00 2.01
579 581 4.131649 TGCATGCTACGGTAGTGTTTAT 57.868 40.909 20.33 2.18 0.00 1.40
632 635 8.306038 TGCTAAGACGGTTACTGTAAATTTCTA 58.694 33.333 1.10 0.00 0.00 2.10
693 699 0.034186 GTCATCCATTGTGCCCCAGA 60.034 55.000 0.00 0.00 0.00 3.86
961 984 2.433868 TCTCCAAGTACACTGCGAAC 57.566 50.000 0.00 0.00 0.00 3.95
981 1004 1.781025 GCGTGCCTGCTGTTTGTACA 61.781 55.000 0.00 0.00 0.00 2.90
1218 1241 9.515226 AATGACTATTACTCTATCCTCTCTGTC 57.485 37.037 0.00 0.00 0.00 3.51
1242 1265 2.738314 CACGTCAGCAGATGATGAAACA 59.262 45.455 14.93 0.00 46.30 2.83
1469 2238 0.449388 GCAACCAATGGCTTCGAGAG 59.551 55.000 0.00 0.00 0.00 3.20
1772 2865 2.414994 ACTGAGGATGTTCATGCAGG 57.585 50.000 7.02 0.00 0.00 4.85
1774 2867 2.306805 ACTGAGGATGTTCATGCAGGAA 59.693 45.455 10.22 10.22 0.00 3.36
1816 2909 2.703416 CACCTCAAGATGCAAGCACTA 58.297 47.619 0.00 0.00 0.00 2.74
2281 3398 7.940850 TCTTAAGAGAATTTTGGTTGACAAGG 58.059 34.615 0.00 0.00 40.82 3.61
2841 4248 3.981308 CCACGTGGGATGGTCAAC 58.019 61.111 27.57 0.00 40.01 3.18
3063 4470 2.586258 ACGTCATCAAGAGGATTCCG 57.414 50.000 0.00 0.00 36.06 4.30
3114 4521 3.275228 AGGTCCCCTTCTATAGGTTGTCT 59.725 47.826 0.00 0.00 43.07 3.41
3268 4676 2.296190 TGATGCTGCGACTCCGTTATAT 59.704 45.455 0.00 0.00 38.24 0.86
3278 4686 5.462398 GCGACTCCGTTATATCTTTGTTGAT 59.538 40.000 0.00 0.00 38.24 2.57
3301 4709 1.135315 CCGCCGTTTTGCATCAGAG 59.865 57.895 0.00 0.00 0.00 3.35
3521 5488 4.116961 GCTGTTTTACCTTGTCCAAAACC 58.883 43.478 6.68 0.00 40.02 3.27
3785 5756 8.504815 CAAATCATCATGCAAGATACTAGAAGG 58.495 37.037 3.75 0.00 0.00 3.46
3813 5785 2.363975 GGATGCCCTGTGGACCGTA 61.364 63.158 0.00 0.00 0.00 4.02
4040 6020 1.486310 ACACTCTTTCAGGCTGTCACA 59.514 47.619 15.27 0.00 0.00 3.58
4139 6119 7.552687 TGAAGTGTATCTTTTGTTCTTGTCTGT 59.447 33.333 0.00 0.00 36.40 3.41
4227 6209 1.141019 GCAGCATTGTCTGGGCATG 59.859 57.895 9.22 0.00 34.74 4.06
4228 6210 1.601419 GCAGCATTGTCTGGGCATGT 61.601 55.000 0.00 0.00 34.74 3.21
4229 6211 0.172578 CAGCATTGTCTGGGCATGTG 59.827 55.000 0.00 0.00 0.00 3.21
4230 6212 0.038599 AGCATTGTCTGGGCATGTGA 59.961 50.000 0.00 0.00 0.00 3.58
4231 6213 0.889994 GCATTGTCTGGGCATGTGAA 59.110 50.000 0.00 0.00 0.00 3.18
4232 6214 1.135199 GCATTGTCTGGGCATGTGAAG 60.135 52.381 0.00 0.00 0.00 3.02
4233 6215 2.439409 CATTGTCTGGGCATGTGAAGA 58.561 47.619 0.00 0.00 0.00 2.87
4234 6216 2.655090 TTGTCTGGGCATGTGAAGAA 57.345 45.000 0.00 0.00 0.00 2.52
4235 6217 2.655090 TGTCTGGGCATGTGAAGAAA 57.345 45.000 0.00 0.00 0.00 2.52
4236 6218 2.507484 TGTCTGGGCATGTGAAGAAAG 58.493 47.619 0.00 0.00 0.00 2.62
4237 6219 1.200948 GTCTGGGCATGTGAAGAAAGC 59.799 52.381 0.00 0.00 0.00 3.51
4238 6220 1.074405 TCTGGGCATGTGAAGAAAGCT 59.926 47.619 0.00 0.00 0.00 3.74
4239 6221 1.471684 CTGGGCATGTGAAGAAAGCTC 59.528 52.381 0.00 0.00 0.00 4.09
4240 6222 1.074405 TGGGCATGTGAAGAAAGCTCT 59.926 47.619 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 9.321562 GATCAATTGAAGATACAAAATTGCCAT 57.678 29.630 13.09 0.00 39.02 4.40
17 18 7.765360 GGATCAATTGAAGATACAAAATTGCCA 59.235 33.333 13.09 0.00 39.02 4.92
18 19 7.983484 AGGATCAATTGAAGATACAAAATTGCC 59.017 33.333 13.09 0.00 39.02 4.52
19 20 8.814235 CAGGATCAATTGAAGATACAAAATTGC 58.186 33.333 13.09 0.00 39.02 3.56
22 23 8.411683 GCTCAGGATCAATTGAAGATACAAAAT 58.588 33.333 13.09 0.00 33.44 1.82
23 24 7.394077 TGCTCAGGATCAATTGAAGATACAAAA 59.606 33.333 13.09 0.00 33.44 2.44
24 25 6.885918 TGCTCAGGATCAATTGAAGATACAAA 59.114 34.615 13.09 0.00 33.44 2.83
25 26 6.417258 TGCTCAGGATCAATTGAAGATACAA 58.583 36.000 13.09 0.00 0.00 2.41
26 27 5.993055 TGCTCAGGATCAATTGAAGATACA 58.007 37.500 13.09 7.13 0.00 2.29
27 28 7.507733 AATGCTCAGGATCAATTGAAGATAC 57.492 36.000 13.09 0.00 0.00 2.24
28 29 9.803507 ATAAATGCTCAGGATCAATTGAAGATA 57.196 29.630 13.09 0.00 0.00 1.98
29 30 8.577296 CATAAATGCTCAGGATCAATTGAAGAT 58.423 33.333 13.09 0.00 0.00 2.40
30 31 7.558807 ACATAAATGCTCAGGATCAATTGAAGA 59.441 33.333 13.09 7.54 0.00 2.87
31 32 7.648112 CACATAAATGCTCAGGATCAATTGAAG 59.352 37.037 13.09 5.98 0.00 3.02
32 33 7.485810 CACATAAATGCTCAGGATCAATTGAA 58.514 34.615 13.09 0.00 0.00 2.69
33 34 6.460537 GCACATAAATGCTCAGGATCAATTGA 60.461 38.462 11.26 11.26 42.62 2.57
34 35 5.690409 GCACATAAATGCTCAGGATCAATTG 59.310 40.000 0.00 0.00 42.62 2.32
35 36 5.506815 CGCACATAAATGCTCAGGATCAATT 60.507 40.000 0.00 0.00 43.80 2.32
36 37 4.023450 CGCACATAAATGCTCAGGATCAAT 60.023 41.667 0.00 0.00 43.80 2.57
37 38 3.313249 CGCACATAAATGCTCAGGATCAA 59.687 43.478 0.00 0.00 43.80 2.57
38 39 2.874086 CGCACATAAATGCTCAGGATCA 59.126 45.455 0.00 0.00 43.80 2.92
39 40 2.350197 GCGCACATAAATGCTCAGGATC 60.350 50.000 0.30 0.00 43.80 3.36
40 41 1.605710 GCGCACATAAATGCTCAGGAT 59.394 47.619 0.30 0.00 43.80 3.24
41 42 1.016627 GCGCACATAAATGCTCAGGA 58.983 50.000 0.30 0.00 43.80 3.86
42 43 0.029834 GGCGCACATAAATGCTCAGG 59.970 55.000 10.83 0.00 43.80 3.86
43 44 0.316442 CGGCGCACATAAATGCTCAG 60.316 55.000 10.83 0.00 43.80 3.35
44 45 1.024046 ACGGCGCACATAAATGCTCA 61.024 50.000 10.83 0.00 43.80 4.26
45 46 0.098728 AACGGCGCACATAAATGCTC 59.901 50.000 10.83 0.00 43.80 4.26
46 47 0.525761 AAACGGCGCACATAAATGCT 59.474 45.000 10.83 0.00 43.80 3.79
47 48 1.345410 AAAACGGCGCACATAAATGC 58.655 45.000 10.83 0.00 42.48 3.56
298 300 4.202461 TGACCATACAAGAAGCTTCCAAGT 60.202 41.667 22.81 19.34 0.00 3.16
361 363 7.979786 TTACTTGGAGAAATATCAGACCTCT 57.020 36.000 0.00 0.00 0.00 3.69
388 390 5.764487 AGCCCTAGTACGAAACATAGTAC 57.236 43.478 0.00 0.00 42.42 2.73
536 538 1.876416 CGGACAACACCTCACGGAATT 60.876 52.381 0.00 0.00 0.00 2.17
546 548 1.371635 GCATGCAACGGACAACACC 60.372 57.895 14.21 0.00 0.00 4.16
578 580 7.012327 AGACATAACTGTAAATGCGCATAACAT 59.988 33.333 28.45 20.68 35.14 2.71
579 581 6.315144 AGACATAACTGTAAATGCGCATAACA 59.685 34.615 27.23 27.23 35.14 2.41
632 635 2.309613 TGCAAGACCAAGTGCAGATTT 58.690 42.857 0.00 0.00 45.52 2.17
678 683 0.324552 CCATTCTGGGGCACAATGGA 60.325 55.000 14.14 0.00 46.66 3.41
859 873 2.390225 TAAAGCCCTGCCCAAAAGAA 57.610 45.000 0.00 0.00 0.00 2.52
926 948 4.655762 TGGAGAAATATCAGACCTCACG 57.344 45.455 0.00 0.00 0.00 4.35
927 949 5.983540 ACTTGGAGAAATATCAGACCTCAC 58.016 41.667 0.00 0.00 0.00 3.51
961 984 2.603247 TACAAACAGCAGGCACGCG 61.603 57.895 3.53 3.53 36.85 6.01
981 1004 0.320374 TTCCGTCGCAGGTCAAGAAT 59.680 50.000 0.00 0.00 0.00 2.40
1218 1241 0.919300 CATCATCTGCTGACGTGTCG 59.081 55.000 0.00 0.00 36.48 4.35
1242 1265 3.643792 ACTTCCTGTACTGCTTCTTCACT 59.356 43.478 0.00 0.00 0.00 3.41
1469 2238 0.598065 AGGTGATTTGGCTGCGAAAC 59.402 50.000 12.01 7.23 0.00 2.78
1772 2865 1.815003 CACTGATGTTTGAGCCCCTTC 59.185 52.381 0.00 0.00 0.00 3.46
1774 2867 0.038744 CCACTGATGTTTGAGCCCCT 59.961 55.000 0.00 0.00 0.00 4.79
1816 2909 3.500471 GGACCCCACTGAAAATTTCTCCT 60.500 47.826 7.29 0.00 0.00 3.69
1906 2999 6.820656 ACTTTCTCATATGTCTGATGAACCAC 59.179 38.462 1.90 0.00 33.01 4.16
2272 3389 1.865865 TCGCTCTTCACCTTGTCAAC 58.134 50.000 0.00 0.00 0.00 3.18
2281 3398 3.589988 TCTCCTTCAAATCGCTCTTCAC 58.410 45.455 0.00 0.00 0.00 3.18
2326 3443 5.630121 ACCATCAACAGTAACTTGGATTGA 58.370 37.500 0.00 0.00 0.00 2.57
2833 4240 1.515081 CGTGGGTAAACGTTGACCAT 58.485 50.000 31.58 5.91 38.74 3.55
2841 4248 2.036571 GCCTTCCCGTGGGTAAACG 61.037 63.158 4.53 0.00 43.20 3.60
3063 4470 5.238650 TGAAAACCGAAACATCTCCTCTTTC 59.761 40.000 0.00 0.00 0.00 2.62
3114 4521 0.250727 CGTTTGGAGCTTCTTCCCCA 60.251 55.000 0.00 0.00 36.35 4.96
3268 4676 0.960364 GGCGGGCAGATCAACAAAGA 60.960 55.000 0.00 0.00 0.00 2.52
3301 4709 5.412904 AGAAACTAGCTAGTGCCAACAAATC 59.587 40.000 26.70 12.92 40.80 2.17
3484 5380 8.322091 AGGTAAAACAGCACATATAAGAGACTT 58.678 33.333 0.00 0.00 0.00 3.01
3486 5382 8.391106 CAAGGTAAAACAGCACATATAAGAGAC 58.609 37.037 0.00 0.00 0.00 3.36
3490 5386 7.120579 TGGACAAGGTAAAACAGCACATATAAG 59.879 37.037 0.00 0.00 0.00 1.73
3521 5488 6.515272 AGGTAAAACAGCACATATTTCCAG 57.485 37.500 0.00 0.00 0.00 3.86
3785 5756 1.215423 ACAGGGCATCCTATGAAACCC 59.785 52.381 0.00 0.00 42.67 4.11
3813 5785 3.157881 TCTGGAGTCGAAATGTCACTCT 58.842 45.455 12.41 0.00 34.74 3.24
4066 6046 8.141909 CAGCCACAAATACTAATACTAGCACTA 58.858 37.037 0.00 0.00 0.00 2.74
4139 6119 0.459489 AAAAAGGCAAGCTTCGCACA 59.541 45.000 18.36 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.