Multiple sequence alignment - TraesCS5B01G221100

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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 TraesCS5B01G221100 chr5B 100.000 5125 0 0 1 5125 395684867 395679743 0.000000e+00 9465.0
1 TraesCS5B01G221100 chr5B 94.377 1067 51 5 872 1935 395709768 395708708 0.000000e+00 1629.0
2 TraesCS5B01G221100 chr5B 93.093 999 31 8 1931 2924 395708225 395707260 0.000000e+00 1428.0
3 TraesCS5B01G221100 chr5B 91.749 303 21 1 3147 3445 395707262 395706960 7.940000e-113 418.0
4 TraesCS5B01G221100 chr5B 85.849 318 33 6 72 381 395710599 395710286 1.380000e-85 327.0
5 TraesCS5B01G221100 chr5B 94.444 180 10 0 691 870 395710110 395709931 1.410000e-70 278.0
6 TraesCS5B01G221100 chr5B 82.353 272 20 13 4106 4354 395706851 395706585 1.450000e-50 211.0
7 TraesCS5B01G221100 chr5B 94.400 125 7 0 532 656 395710226 395710102 5.240000e-45 193.0
8 TraesCS5B01G221100 chr5B 93.103 116 5 1 3961 4076 395706960 395706848 3.170000e-37 167.0
9 TraesCS5B01G221100 chr5A 95.265 4287 143 20 1 4242 438358537 438354266 0.000000e+00 6737.0
10 TraesCS5B01G221100 chr5A 90.028 3600 266 38 785 4354 438410848 438407312 0.000000e+00 4573.0
11 TraesCS5B01G221100 chr5A 88.528 462 31 12 4441 4893 438353906 438353458 1.620000e-149 540.0
12 TraesCS5B01G221100 chr5A 86.905 336 30 5 72 400 438412342 438412014 1.050000e-96 364.0
13 TraesCS5B01G221100 chr5A 89.952 209 16 3 4227 4435 438354249 438354046 1.090000e-66 265.0
14 TraesCS5B01G221100 chr5A 90.625 128 11 1 632 759 438411887 438411761 8.830000e-38 169.0
15 TraesCS5B01G221100 chr5A 86.607 112 6 7 495 603 438411965 438411860 1.170000e-21 115.0
16 TraesCS5B01G221100 chr5D 93.625 4141 242 12 144 4277 337186614 337182489 0.000000e+00 6165.0
17 TraesCS5B01G221100 chr5D 93.551 1349 63 12 2613 3958 337216431 337215104 0.000000e+00 1988.0
18 TraesCS5B01G221100 chr5D 92.178 1304 86 8 632 1935 337218829 337217542 0.000000e+00 1829.0
19 TraesCS5B01G221100 chr5D 95.593 658 20 3 1931 2580 337217085 337216429 0.000000e+00 1046.0
20 TraesCS5B01G221100 chr5D 90.743 713 37 17 4425 5125 337182183 337181488 0.000000e+00 924.0
21 TraesCS5B01G221100 chr5D 92.913 254 17 1 4475 4728 337154400 337154652 8.110000e-98 368.0
22 TraesCS5B01G221100 chr5D 84.211 342 22 11 60 400 337219262 337218952 2.320000e-78 303.0
23 TraesCS5B01G221100 chr5D 97.973 148 3 0 1 148 337186881 337186734 1.830000e-64 257.0
24 TraesCS5B01G221100 chr5D 93.168 161 11 0 4275 4435 337182371 337182211 2.390000e-58 237.0
25 TraesCS5B01G221100 chr5D 95.122 123 6 0 3954 4076 337209677 337209555 1.460000e-45 195.0
26 TraesCS5B01G221100 chr5D 81.421 183 12 11 4106 4266 337209558 337209376 4.160000e-26 130.0
27 TraesCS5B01G221100 chr5D 84.821 112 8 7 495 603 337218907 337218802 2.520000e-18 104.0
28 TraesCS5B01G221100 chr5D 86.667 90 7 5 4267 4354 337207539 337207453 1.520000e-15 95.3
29 TraesCS5B01G221100 chr5D 96.429 56 2 0 72 127 337219396 337219341 5.460000e-15 93.5


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 TraesCS5B01G221100 chr5B 395679743 395684867 5124 True 9465.000000 9465 100.000000 1 5125 1 chr5B.!!$R1 5124
1 TraesCS5B01G221100 chr5B 395706585 395710599 4014 True 581.375000 1629 91.171000 72 4354 8 chr5B.!!$R2 4282
2 TraesCS5B01G221100 chr5A 438353458 438358537 5079 True 2514.000000 6737 91.248333 1 4893 3 chr5A.!!$R1 4892
3 TraesCS5B01G221100 chr5A 438407312 438412342 5030 True 1305.250000 4573 88.541250 72 4354 4 chr5A.!!$R2 4282
4 TraesCS5B01G221100 chr5D 337181488 337186881 5393 True 1895.750000 6165 93.877250 1 5125 4 chr5D.!!$R1 5124
5 TraesCS5B01G221100 chr5D 337215104 337219396 4292 True 893.916667 1988 91.130500 60 3958 6 chr5D.!!$R3 3898

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
62 63 0.390603 CATGACAGACGCCCCGTAAA 60.391 55.000 0.00 0.00 41.37 2.01 F
63 64 0.390735 ATGACAGACGCCCCGTAAAC 60.391 55.000 0.00 0.00 41.37 2.01 F
1376 2705 1.203287 CAAGAGCCTCGACATGTCTCA 59.797 52.381 22.95 9.01 0.00 3.27 F
1860 3189 0.113190 CCAACCTGGAGCCCTTCTTT 59.887 55.000 0.00 0.00 40.96 2.52 F
2673 4501 1.001378 GCAAACCTGACGAAATGCACT 60.001 47.619 0.00 0.00 34.10 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 2913 0.442699 GATCGTTGTTGCCGAAGTCC 59.557 55.0 0.0 0.0 37.93 3.85 R
1833 3162 0.467290 GCTCCAGGTTGGTGTTTCCA 60.467 55.0 0.0 0.0 45.60 3.53 R
2398 4226 0.393132 TGGTTGTGCGACAGGTTCAA 60.393 50.0 0.0 0.0 0.00 2.69 R
3498 5331 0.321210 CCACACCGCCAACACTCATA 60.321 55.0 0.0 0.0 0.00 2.15 R
4476 6634 0.106708 ACACATTCAGGAGTGCGTGT 59.893 50.0 0.0 0.0 39.30 4.49 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
59 60 4.760047 GCATGACAGACGCCCCGT 62.760 66.667 0.00 0.00 45.10 5.28
61 62 1.216977 CATGACAGACGCCCCGTAA 59.783 57.895 0.00 0.00 41.37 3.18
62 63 0.390603 CATGACAGACGCCCCGTAAA 60.391 55.000 0.00 0.00 41.37 2.01
63 64 0.390735 ATGACAGACGCCCCGTAAAC 60.391 55.000 0.00 0.00 41.37 2.01
121 197 6.060788 AGCCTGAAACCAGATAATTGAGATC 58.939 40.000 0.00 0.00 33.56 2.75
182 384 4.569162 TGTGCTTCTAGTTGTTACACACAC 59.431 41.667 0.00 0.00 33.98 3.82
234 436 2.019249 TGCAGCTGCTTGGTATGAATC 58.981 47.619 36.61 6.22 42.66 2.52
846 1980 2.238646 TCCCAGTCCATATTTTCTGCGT 59.761 45.455 0.00 0.00 0.00 5.24
852 1986 1.334869 CCATATTTTCTGCGTCCTGCC 59.665 52.381 0.00 0.00 45.60 4.85
905 2215 5.163034 ACATCCAGCCTATAGAGTAGTGACT 60.163 44.000 0.00 0.00 39.20 3.41
1017 2331 2.697263 ATGAGGGCTCCCATGGCA 60.697 61.111 6.09 0.00 38.92 4.92
1178 2507 3.744559 GCTCCTGGCGTTGAAACA 58.255 55.556 0.00 0.00 0.00 2.83
1299 2628 2.818132 GTCATCGGCCTCTCCCTG 59.182 66.667 0.00 0.00 0.00 4.45
1376 2705 1.203287 CAAGAGCCTCGACATGTCTCA 59.797 52.381 22.95 9.01 0.00 3.27
1455 2784 2.351276 GACCTCGGCCACAACCAT 59.649 61.111 2.24 0.00 0.00 3.55
1465 2794 1.672030 CACAACCATCTCAGCGGCA 60.672 57.895 1.45 0.00 0.00 5.69
1492 2821 1.882989 GCCGTCCTTCTCTGAGCTGT 61.883 60.000 0.00 0.00 0.00 4.40
1497 2826 1.898472 TCCTTCTCTGAGCTGTCAAGG 59.102 52.381 13.27 13.27 30.73 3.61
1555 2884 2.735237 CTATCCCGGCCGTTCTCC 59.265 66.667 26.12 0.00 0.00 3.71
1707 3036 1.374758 GTGGCTCGCTAACTGCACT 60.375 57.895 0.00 0.00 43.06 4.40
1860 3189 0.113190 CCAACCTGGAGCCCTTCTTT 59.887 55.000 0.00 0.00 40.96 2.52
2103 3919 3.565961 TTCCATCTGCGGCTTGCCA 62.566 57.895 12.45 0.00 45.60 4.92
2163 3979 1.731433 GCATGATCCCAGCGTGCATT 61.731 55.000 0.00 0.00 45.25 3.56
2242 4062 4.812476 CGAGCGGCATCGGAACCA 62.812 66.667 1.45 0.00 39.04 3.67
2398 4226 4.588951 TCTCTGGCACCGACATTATATCTT 59.411 41.667 0.00 0.00 0.00 2.40
2673 4501 1.001378 GCAAACCTGACGAAATGCACT 60.001 47.619 0.00 0.00 34.10 4.40
3234 5063 1.126488 ACCTCATGCGGATCATCACT 58.874 50.000 9.17 0.00 31.79 3.41
3360 5193 2.671177 GCGCGTCAACATCTGCAGT 61.671 57.895 14.67 0.00 0.00 4.40
3405 5238 4.619227 CACCACCACTCGCCGGTT 62.619 66.667 1.90 0.00 33.25 4.44
3462 5295 3.883489 TCCTCATCAACGACGATATGACT 59.117 43.478 0.00 0.00 0.00 3.41
3465 5298 2.931512 TCAACGACGATATGACTGCA 57.068 45.000 0.00 0.00 0.00 4.41
3471 5304 2.464865 GACGATATGACTGCACTGGTC 58.535 52.381 0.00 0.00 0.00 4.02
3498 5331 2.679996 GGCATTTCCCGGCTGGTT 60.680 61.111 11.58 0.00 34.77 3.67
3504 5337 0.988832 TTTCCCGGCTGGTTATGAGT 59.011 50.000 11.58 0.00 34.77 3.41
3609 5442 2.920524 ACGTACCATGAAACCACACAA 58.079 42.857 0.00 0.00 0.00 3.33
3656 5490 2.283298 CCGTGATGAGTTCCCAGATTG 58.717 52.381 0.00 0.00 0.00 2.67
3794 5628 1.640917 TGGTAACGAGGAAGAAGCCT 58.359 50.000 0.00 0.00 42.17 4.58
4052 5886 2.494918 CTCAAGCGGTACCTCGGG 59.505 66.667 10.90 0.00 0.00 5.14
4374 6397 5.641636 TCTTCTGTTTTTCCCTTTGTTTTGC 59.358 36.000 0.00 0.00 0.00 3.68
4377 6400 3.009584 TGTTTTTCCCTTTGTTTTGCCCT 59.990 39.130 0.00 0.00 0.00 5.19
4378 6401 2.998316 TTTCCCTTTGTTTTGCCCTG 57.002 45.000 0.00 0.00 0.00 4.45
4384 6407 1.000717 CTTTGTTTTGCCCTGGTACCG 60.001 52.381 7.57 1.95 0.00 4.02
4402 6425 2.803956 ACCGTGTACTCCAAAACAATCG 59.196 45.455 0.00 0.00 0.00 3.34
4411 6434 4.256920 CTCCAAAACAATCGGATGTCTCT 58.743 43.478 0.00 0.00 31.81 3.10
4435 6458 5.924475 TTTTGTTCGGCAAACTTGAAAAA 57.076 30.435 5.75 0.00 45.70 1.94
4472 6630 6.681729 AGTATTGGAGTACACTGAAAAGGA 57.318 37.500 0.00 0.00 0.00 3.36
4473 6631 6.702329 AGTATTGGAGTACACTGAAAAGGAG 58.298 40.000 0.00 0.00 0.00 3.69
4474 6632 5.568620 ATTGGAGTACACTGAAAAGGAGT 57.431 39.130 0.00 0.00 0.00 3.85
4475 6633 4.602340 TGGAGTACACTGAAAAGGAGTC 57.398 45.455 0.00 0.00 0.00 3.36
4476 6634 3.964688 TGGAGTACACTGAAAAGGAGTCA 59.035 43.478 0.00 0.00 0.00 3.41
4477 6635 4.202223 TGGAGTACACTGAAAAGGAGTCAC 60.202 45.833 0.00 0.00 0.00 3.67
4478 6636 4.202223 GGAGTACACTGAAAAGGAGTCACA 60.202 45.833 0.00 0.00 0.00 3.58
4485 6644 1.527311 GAAAAGGAGTCACACGCACTC 59.473 52.381 0.00 0.00 39.78 3.51
4493 6652 0.392706 TCACACGCACTCCTGAATGT 59.607 50.000 0.00 0.00 0.00 2.71
4507 6666 3.548587 CTGAATGTGTCGAAAGCACAAG 58.451 45.455 10.88 1.87 45.83 3.16
4592 6751 1.065551 GCAAGAACGACAGCCTTTTGT 59.934 47.619 0.00 0.00 0.00 2.83
4596 6755 1.001378 GAACGACAGCCTTTTGTGCAT 60.001 47.619 0.00 0.00 0.00 3.96
4597 6756 1.890876 ACGACAGCCTTTTGTGCATA 58.109 45.000 0.00 0.00 0.00 3.14
4598 6757 1.806542 ACGACAGCCTTTTGTGCATAG 59.193 47.619 0.00 0.00 0.00 2.23
4599 6758 1.131126 CGACAGCCTTTTGTGCATAGG 59.869 52.381 0.00 0.00 0.00 2.57
4600 6759 2.436417 GACAGCCTTTTGTGCATAGGA 58.564 47.619 10.27 0.00 0.00 2.94
4601 6760 2.819608 GACAGCCTTTTGTGCATAGGAA 59.180 45.455 10.27 0.00 0.00 3.36
4602 6761 2.558359 ACAGCCTTTTGTGCATAGGAAC 59.442 45.455 10.27 0.00 0.00 3.62
4603 6762 2.557924 CAGCCTTTTGTGCATAGGAACA 59.442 45.455 10.27 0.00 0.00 3.18
4604 6763 2.558359 AGCCTTTTGTGCATAGGAACAC 59.442 45.455 10.27 0.00 30.17 3.32
4605 6764 2.668279 GCCTTTTGTGCATAGGAACACG 60.668 50.000 10.27 0.00 39.71 4.49
4607 6766 3.252215 CCTTTTGTGCATAGGAACACGAA 59.748 43.478 0.00 0.00 39.71 3.85
4608 6767 4.466828 CTTTTGTGCATAGGAACACGAAG 58.533 43.478 0.00 0.00 40.37 3.79
4610 6769 3.120321 TGTGCATAGGAACACGAAGTT 57.880 42.857 0.00 0.00 41.61 2.66
4611 6770 2.805671 TGTGCATAGGAACACGAAGTTG 59.194 45.455 0.00 0.00 41.61 3.16
4612 6771 3.064207 GTGCATAGGAACACGAAGTTGA 58.936 45.455 0.00 0.00 41.61 3.18
4613 6772 3.064207 TGCATAGGAACACGAAGTTGAC 58.936 45.455 2.93 0.00 41.61 3.18
4614 6773 3.064207 GCATAGGAACACGAAGTTGACA 58.936 45.455 2.93 0.00 41.61 3.58
4615 6774 3.120649 GCATAGGAACACGAAGTTGACAC 60.121 47.826 2.93 0.00 41.61 3.67
4616 6775 2.981859 AGGAACACGAAGTTGACACT 57.018 45.000 2.93 0.00 41.61 3.55
4617 6776 3.261981 AGGAACACGAAGTTGACACTT 57.738 42.857 2.93 0.00 46.64 3.16
4618 6777 3.606687 AGGAACACGAAGTTGACACTTT 58.393 40.909 2.93 0.00 43.79 2.66
4619 6778 4.761975 AGGAACACGAAGTTGACACTTTA 58.238 39.130 2.93 0.00 43.79 1.85
4620 6779 5.180271 AGGAACACGAAGTTGACACTTTAA 58.820 37.500 2.93 0.00 43.79 1.52
4718 6877 3.418684 AGTTTGGTCCATGTACACCTC 57.581 47.619 0.00 0.00 33.36 3.85
4719 6878 2.979678 AGTTTGGTCCATGTACACCTCT 59.020 45.455 0.00 0.00 33.36 3.69
4720 6879 4.164981 AGTTTGGTCCATGTACACCTCTA 58.835 43.478 0.00 0.00 33.36 2.43
4723 6882 4.753516 TGGTCCATGTACACCTCTAATG 57.246 45.455 0.00 0.00 33.36 1.90
4728 6887 7.014905 TGGTCCATGTACACCTCTAATGTATAC 59.985 40.741 0.00 0.00 35.11 1.47
4729 6888 7.232941 GGTCCATGTACACCTCTAATGTATACT 59.767 40.741 0.00 0.00 35.11 2.12
4730 6889 8.298140 GTCCATGTACACCTCTAATGTATACTC 58.702 40.741 0.00 0.00 35.11 2.59
4731 6890 8.225416 TCCATGTACACCTCTAATGTATACTCT 58.775 37.037 0.00 0.00 35.11 3.24
4732 6891 9.516546 CCATGTACACCTCTAATGTATACTCTA 57.483 37.037 0.00 0.00 35.11 2.43
4734 6893 8.599055 TGTACACCTCTAATGTATACTCTACG 57.401 38.462 4.17 0.00 35.11 3.51
4735 6894 8.424133 TGTACACCTCTAATGTATACTCTACGA 58.576 37.037 4.17 0.00 35.11 3.43
4736 6895 7.966246 ACACCTCTAATGTATACTCTACGAG 57.034 40.000 4.17 4.11 35.52 4.18
4737 6896 6.935771 ACACCTCTAATGTATACTCTACGAGG 59.064 42.308 18.58 18.58 40.90 4.63
4846 7011 0.366871 GCGTATCACTGTTGTGCTCG 59.633 55.000 0.00 0.00 43.49 5.03
4852 7017 2.412870 TCACTGTTGTGCTCGTAATGG 58.587 47.619 0.00 0.00 43.49 3.16
4931 7096 4.435518 GCACATATGTGGCCGTAATTATCG 60.436 45.833 31.63 6.81 45.72 2.92
4957 7122 6.156949 TGGACAGTTCTAGCTAAGGATGAAAT 59.843 38.462 0.00 0.00 0.00 2.17
4970 7135 6.998968 AAGGATGAAATTAGAGCAACTCTG 57.001 37.500 7.37 0.00 41.37 3.35
4974 7139 4.005650 TGAAATTAGAGCAACTCTGGCAG 58.994 43.478 8.58 8.58 41.37 4.85
5045 7210 5.306394 ACTCCTTAAACCAAGTTCTGCTAC 58.694 41.667 0.00 0.00 31.77 3.58
5067 7232 9.442047 GCTACAAATAGTTCAATATATCTGCCT 57.558 33.333 0.00 0.00 0.00 4.75
5095 7260 8.498054 ACATGGTACTTCATTGTCATTCTAAG 57.502 34.615 0.00 0.00 0.00 2.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 2.030958 GGTGTTTACGGGGCGTCTG 61.031 63.158 0.00 0.00 41.54 3.51
59 60 5.269991 ACTAGCAGAGTATCAGGGTGTTTA 58.730 41.667 0.00 0.00 36.27 2.01
61 62 3.702045 GACTAGCAGAGTATCAGGGTGTT 59.298 47.826 0.00 0.00 39.06 3.32
62 63 3.053245 AGACTAGCAGAGTATCAGGGTGT 60.053 47.826 0.00 0.00 39.06 4.16
63 64 3.561143 AGACTAGCAGAGTATCAGGGTG 58.439 50.000 0.00 0.00 39.06 4.61
182 384 5.678483 GCAGTTATACATGTCAAATCTTGCG 59.322 40.000 0.00 0.00 0.00 4.85
234 436 5.175859 TCTGATTAGTTTAAGCCTGAACCG 58.824 41.667 0.00 0.00 0.00 4.44
361 593 7.353414 AGTTGAGCATGATAAAGCTAGAGTA 57.647 36.000 0.00 0.00 42.04 2.59
846 1980 1.004745 GGAAAGGATGTTGAGGCAGGA 59.995 52.381 0.00 0.00 0.00 3.86
852 1986 3.266510 TGGATCGGAAAGGATGTTGAG 57.733 47.619 0.00 0.00 0.00 3.02
1029 2343 1.745264 GAGGAGGAGGAGAATGGCG 59.255 63.158 0.00 0.00 0.00 5.69
1096 2425 3.877450 GGCGATCATCCCAGCCCA 61.877 66.667 0.00 0.00 43.54 5.36
1178 2507 1.005630 GACAGCAAGGTGAGCGAGT 60.006 57.895 6.23 0.00 37.01 4.18
1299 2628 1.293924 CAGAGATGTTCATGTCGCCC 58.706 55.000 4.69 0.00 0.00 6.13
1376 2705 0.962356 CTGCCCTGCGAGGAAATTGT 60.962 55.000 4.00 0.00 37.67 2.71
1455 2784 2.501128 GGTATGCTGCCGCTGAGA 59.499 61.111 0.70 0.00 36.97 3.27
1465 2794 2.017559 GAGAAGGACGGCGGTATGCT 62.018 60.000 13.24 2.29 45.43 3.79
1497 2826 1.267121 TGAGACTGAGGTAGGCCAAC 58.733 55.000 5.01 0.00 33.59 3.77
1512 2841 4.588106 CCTGAGAGCTGATTATCCTTGAGA 59.412 45.833 0.00 0.00 0.00 3.27
1555 2884 2.540265 AGACTGGTGCAGTTCTTGAG 57.460 50.000 0.00 0.00 45.44 3.02
1584 2913 0.442699 GATCGTTGTTGCCGAAGTCC 59.557 55.000 0.00 0.00 37.93 3.85
1707 3036 4.408596 TCCACATCCAGCATGTACAGATAA 59.591 41.667 0.33 0.00 44.60 1.75
1833 3162 0.467290 GCTCCAGGTTGGTGTTTCCA 60.467 55.000 0.00 0.00 45.60 3.53
1836 3165 1.152546 GGGCTCCAGGTTGGTGTTT 60.153 57.895 0.00 0.00 39.03 2.83
2103 3919 2.183046 GAGAGCCGCTCGAGCTTT 59.817 61.111 32.88 18.89 41.75 3.51
2238 4058 0.846693 AGAGGTTGACAAGCCTGGTT 59.153 50.000 13.60 0.00 34.81 3.67
2242 4062 1.625818 CAGGTAGAGGTTGACAAGCCT 59.374 52.381 13.60 10.78 37.91 4.58
2398 4226 0.393132 TGGTTGTGCGACAGGTTCAA 60.393 50.000 0.00 0.00 0.00 2.69
2673 4501 4.469657 ACAGGTTGAAATGTTTCAGGCTA 58.530 39.130 8.07 0.00 46.68 3.93
2727 4556 2.110213 TCCGCAAAGACGCCAGTT 59.890 55.556 0.00 0.00 0.00 3.16
3303 5136 3.550431 GGCGGCCCAGCATAGAGA 61.550 66.667 8.12 0.00 39.27 3.10
3324 5157 3.243816 TGCACCAGGCTGAGCTCA 61.244 61.111 24.99 17.19 45.15 4.26
3405 5238 4.422057 TGAGGTCACAGTGGATAACCTTA 58.578 43.478 11.93 6.37 40.39 2.69
3456 5289 2.493675 GTCAGAGACCAGTGCAGTCATA 59.506 50.000 7.27 0.00 36.68 2.15
3462 5295 1.202687 CCAAAGTCAGAGACCAGTGCA 60.203 52.381 0.00 0.00 32.18 4.57
3465 5298 1.131638 TGCCAAAGTCAGAGACCAGT 58.868 50.000 0.00 0.00 32.18 4.00
3471 5304 1.470098 CGGGAAATGCCAAAGTCAGAG 59.530 52.381 0.00 0.00 38.95 3.35
3498 5331 0.321210 CCACACCGCCAACACTCATA 60.321 55.000 0.00 0.00 0.00 2.15
3609 5442 7.814264 ATAGCTTGTGAATTAGCTTTAGCAT 57.186 32.000 5.80 0.00 45.16 3.79
3656 5490 5.203060 ACCACTCAGAAGTCAGAACTAAC 57.797 43.478 0.00 0.00 33.48 2.34
4374 6397 0.612732 TGGAGTACACGGTACCAGGG 60.613 60.000 13.54 8.57 0.00 4.45
4377 6400 2.433604 TGTTTTGGAGTACACGGTACCA 59.566 45.455 13.54 0.00 0.00 3.25
4378 6401 3.110447 TGTTTTGGAGTACACGGTACC 57.890 47.619 0.16 0.16 0.00 3.34
4384 6407 4.454504 ACATCCGATTGTTTTGGAGTACAC 59.545 41.667 0.00 0.00 41.47 2.90
4435 6458 7.823745 ACTCCAATACTTCAAAACATCAGTT 57.176 32.000 0.00 0.00 40.40 3.16
4436 6459 7.936847 TGTACTCCAATACTTCAAAACATCAGT 59.063 33.333 0.00 0.00 0.00 3.41
4437 6460 8.230486 GTGTACTCCAATACTTCAAAACATCAG 58.770 37.037 0.00 0.00 0.00 2.90
4438 6461 7.936847 AGTGTACTCCAATACTTCAAAACATCA 59.063 33.333 0.00 0.00 0.00 3.07
4439 6462 8.230486 CAGTGTACTCCAATACTTCAAAACATC 58.770 37.037 0.00 0.00 0.00 3.06
4442 6465 7.724305 TCAGTGTACTCCAATACTTCAAAAC 57.276 36.000 0.00 0.00 0.00 2.43
4444 6467 8.740123 TTTTCAGTGTACTCCAATACTTCAAA 57.260 30.769 0.00 0.00 0.00 2.69
4445 6468 7.444183 CCTTTTCAGTGTACTCCAATACTTCAA 59.556 37.037 0.00 0.00 0.00 2.69
4454 6612 3.964688 TGACTCCTTTTCAGTGTACTCCA 59.035 43.478 0.00 0.00 0.00 3.86
4472 6630 0.681733 ATTCAGGAGTGCGTGTGACT 59.318 50.000 0.00 0.00 0.00 3.41
4473 6631 0.792640 CATTCAGGAGTGCGTGTGAC 59.207 55.000 0.00 0.00 0.00 3.67
4474 6632 0.392706 ACATTCAGGAGTGCGTGTGA 59.607 50.000 0.00 0.00 0.00 3.58
4475 6633 0.514255 CACATTCAGGAGTGCGTGTG 59.486 55.000 0.00 0.00 34.56 3.82
4476 6634 0.106708 ACACATTCAGGAGTGCGTGT 59.893 50.000 0.00 0.00 39.30 4.49
4477 6635 0.792640 GACACATTCAGGAGTGCGTG 59.207 55.000 0.00 0.00 39.30 5.34
4478 6636 0.667487 CGACACATTCAGGAGTGCGT 60.667 55.000 0.00 0.00 39.30 5.24
4485 6644 1.872952 TGTGCTTTCGACACATTCAGG 59.127 47.619 3.42 0.00 42.88 3.86
4493 6652 3.189495 TGAAACAACTTGTGCTTTCGACA 59.811 39.130 0.00 0.00 33.51 4.35
4507 6666 7.199766 TGGTGTATCACAGAAAATGAAACAAC 58.800 34.615 2.41 0.00 35.86 3.32
4580 6739 2.436417 TCCTATGCACAAAAGGCTGTC 58.564 47.619 0.00 0.00 0.00 3.51
4592 6751 3.064207 GTCAACTTCGTGTTCCTATGCA 58.936 45.455 0.00 0.00 36.63 3.96
4596 6755 4.395959 AAGTGTCAACTTCGTGTTCCTA 57.604 40.909 0.00 0.00 43.34 2.94
4597 6756 2.981859 AGTGTCAACTTCGTGTTCCT 57.018 45.000 0.00 0.00 36.63 3.36
4598 6757 5.473796 TTAAAGTGTCAACTTCGTGTTCC 57.526 39.130 0.00 0.00 46.15 3.62
4599 6758 7.964545 AAATTAAAGTGTCAACTTCGTGTTC 57.035 32.000 0.00 0.00 46.15 3.18
4600 6759 8.241367 AGAAAATTAAAGTGTCAACTTCGTGTT 58.759 29.630 0.00 0.00 46.15 3.32
4601 6760 7.758495 AGAAAATTAAAGTGTCAACTTCGTGT 58.242 30.769 0.00 0.00 46.15 4.49
4602 6761 9.155053 GTAGAAAATTAAAGTGTCAACTTCGTG 57.845 33.333 0.00 0.00 46.15 4.35
4603 6762 8.060090 CGTAGAAAATTAAAGTGTCAACTTCGT 58.940 33.333 0.00 0.00 46.15 3.85
4604 6763 8.060090 ACGTAGAAAATTAAAGTGTCAACTTCG 58.940 33.333 0.00 0.00 46.15 3.79
4607 6766 8.985805 CCTACGTAGAAAATTAAAGTGTCAACT 58.014 33.333 24.15 0.00 38.71 3.16
4608 6767 7.743400 GCCTACGTAGAAAATTAAAGTGTCAAC 59.257 37.037 24.15 0.00 0.00 3.18
4609 6768 7.658575 AGCCTACGTAGAAAATTAAAGTGTCAA 59.341 33.333 24.15 0.00 0.00 3.18
4610 6769 7.156673 AGCCTACGTAGAAAATTAAAGTGTCA 58.843 34.615 24.15 0.00 0.00 3.58
4611 6770 7.592439 AGCCTACGTAGAAAATTAAAGTGTC 57.408 36.000 24.15 0.06 0.00 3.67
4612 6771 7.974482 AAGCCTACGTAGAAAATTAAAGTGT 57.026 32.000 24.15 0.00 0.00 3.55
4613 6772 9.750882 GTAAAGCCTACGTAGAAAATTAAAGTG 57.249 33.333 24.15 3.59 0.00 3.16
4614 6773 9.492973 TGTAAAGCCTACGTAGAAAATTAAAGT 57.507 29.630 24.15 1.36 0.00 2.66
4615 6774 9.968743 CTGTAAAGCCTACGTAGAAAATTAAAG 57.031 33.333 24.15 15.52 0.00 1.85
4616 6775 9.709495 TCTGTAAAGCCTACGTAGAAAATTAAA 57.291 29.630 24.15 10.89 0.00 1.52
4617 6776 9.709495 TTCTGTAAAGCCTACGTAGAAAATTAA 57.291 29.630 24.15 4.00 0.00 1.40
4618 6777 9.709495 TTTCTGTAAAGCCTACGTAGAAAATTA 57.291 29.630 24.15 13.37 31.88 1.40
4619 6778 8.611654 TTTCTGTAAAGCCTACGTAGAAAATT 57.388 30.769 24.15 14.27 31.88 1.82
4620 6779 7.333672 CCTTTCTGTAAAGCCTACGTAGAAAAT 59.666 37.037 24.15 9.70 40.73 1.82
4729 6888 1.952296 GCTCGGTTTATCCCTCGTAGA 59.048 52.381 0.00 0.00 0.00 2.59
4730 6889 1.334779 CGCTCGGTTTATCCCTCGTAG 60.335 57.143 0.00 0.00 0.00 3.51
4731 6890 0.664761 CGCTCGGTTTATCCCTCGTA 59.335 55.000 0.00 0.00 0.00 3.43
4732 6891 1.318158 ACGCTCGGTTTATCCCTCGT 61.318 55.000 0.00 0.00 0.00 4.18
4733 6892 0.870307 CACGCTCGGTTTATCCCTCG 60.870 60.000 0.00 0.00 0.00 4.63
4734 6893 1.152383 GCACGCTCGGTTTATCCCTC 61.152 60.000 0.00 0.00 0.00 4.30
4735 6894 1.153429 GCACGCTCGGTTTATCCCT 60.153 57.895 0.00 0.00 0.00 4.20
4736 6895 2.522638 CGCACGCTCGGTTTATCCC 61.523 63.158 0.00 0.00 0.00 3.85
4737 6896 1.749609 GACGCACGCTCGGTTTATCC 61.750 60.000 2.08 0.00 0.00 2.59
4834 6999 1.156736 GCCATTACGAGCACAACAGT 58.843 50.000 0.00 0.00 0.00 3.55
4846 7011 1.299541 CGTCATCAGTGGGCCATTAC 58.700 55.000 10.70 0.00 0.00 1.89
4852 7017 1.078848 AGAAGCGTCATCAGTGGGC 60.079 57.895 1.61 0.00 0.00 5.36
4931 7096 4.402793 TCATCCTTAGCTAGAACTGTCCAC 59.597 45.833 0.00 0.00 0.00 4.02
4957 7122 1.644509 TCCTGCCAGAGTTGCTCTAA 58.355 50.000 0.00 0.00 38.99 2.10
4970 7135 0.817013 TTCCGCATGATTTTCCTGCC 59.183 50.000 0.00 0.00 35.07 4.85
4974 7139 5.248870 ACTGTATTTCCGCATGATTTTCC 57.751 39.130 0.00 0.00 0.00 3.13


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

AutoCloner maintained by Alex Coulton.