Multiple sequence alignment - TraesCS1D01G325100

Loading Multiple Alignment...

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 TraesCS1D01G325100 chr1D 100.000 2881 0 0 1 2881 417571776 417574656 0.000000e+00 5321.0
1 TraesCS1D01G325100 chr1D 87.013 77 7 3 371 445 492364855 492364780 1.840000e-12 84.2
2 TraesCS1D01G325100 chr1B 89.356 1879 82 45 72 1892 564160422 564162240 0.000000e+00 2254.0
3 TraesCS1D01G325100 chr1B 94.283 997 28 8 1899 2881 564162283 564163264 0.000000e+00 1498.0
4 TraesCS1D01G325100 chr1A 91.304 1541 45 30 417 1892 514549068 514550584 0.000000e+00 2021.0
5 TraesCS1D01G325100 chr1A 91.634 1016 48 20 1899 2881 514550628 514551639 0.000000e+00 1371.0
6 TraesCS1D01G325100 chr1A 95.588 272 11 1 32 303 514546019 514546289 4.410000e-118 435.0
7 TraesCS1D01G325100 chr1A 78.803 618 86 27 1288 1895 566590688 566590106 9.750000e-100 374.0
8 TraesCS1D01G325100 chr1A 94.118 119 6 1 299 416 514548917 514549035 2.280000e-41 180.0
9 TraesCS1D01G325100 chrUn 90.964 332 13 6 1899 2226 240128410 240128728 5.700000e-117 431.0
10 TraesCS1D01G325100 chrUn 91.159 328 13 5 1899 2223 435744612 435744926 5.700000e-117 431.0
11 TraesCS1D01G325100 chr2B 90.881 329 19 8 1899 2226 77876786 77877104 5.700000e-117 431.0
12 TraesCS1D01G325100 chr2B 90.588 85 6 2 1661 1743 331027359 331027275 8.440000e-21 111.0
13 TraesCS1D01G325100 chr2B 89.189 74 6 2 374 447 619681411 619681482 1.100000e-14 91.6
14 TraesCS1D01G325100 chr6B 90.361 332 15 9 1899 2226 91905142 91904824 1.230000e-113 420.0
15 TraesCS1D01G325100 chr6B 90.274 329 21 8 1899 2226 418246366 418246684 1.230000e-113 420.0
16 TraesCS1D01G325100 chr4B 90.361 332 15 6 1899 2226 517726631 517726313 1.230000e-113 420.0
17 TraesCS1D01G325100 chr3B 90.361 332 15 10 1899 2226 170507589 170507271 1.230000e-113 420.0
18 TraesCS1D01G325100 chr5B 89.970 329 22 8 1899 2226 140516982 140517300 5.740000e-112 414.0
19 TraesCS1D01G325100 chr5A 89.970 329 22 8 1899 2226 88286023 88286341 5.740000e-112 414.0
20 TraesCS1D01G325100 chr5A 87.255 102 13 0 1637 1738 66049193 66049294 1.810000e-22 117.0
21 TraesCS1D01G325100 chr2A 78.646 576 66 31 2349 2881 733432049 733431488 2.140000e-86 329.0
22 TraesCS1D01G325100 chr2D 78.070 570 78 32 2349 2881 493194629 493195188 1.670000e-82 316.0
23 TraesCS1D01G325100 chr7D 91.139 79 7 0 1660 1738 326034627 326034705 1.090000e-19 108.0
24 TraesCS1D01G325100 chr7B 90.411 73 5 2 372 442 457244583 457244655 8.500000e-16 95.3
25 TraesCS1D01G325100 chr7B 90.278 72 4 3 371 442 660336791 660336859 1.100000e-14 91.6
26 TraesCS1D01G325100 chr6A 91.304 69 2 2 375 442 153375144 153375209 1.100000e-14 91.6
27 TraesCS1D01G325100 chr5D 90.000 70 5 2 375 442 377299912 377299843 3.950000e-14 89.8
28 TraesCS1D01G325100 chr7A 88.000 75 5 2 372 442 28155546 28155620 5.110000e-13 86.1
29 TraesCS1D01G325100 chr7A 88.158 76 4 2 372 442 608219998 608220073 5.110000e-13 86.1


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 TraesCS1D01G325100 chr1D 417571776 417574656 2880 False 5321.00 5321 100.0000 1 2881 1 chr1D.!!$F1 2880
1 TraesCS1D01G325100 chr1B 564160422 564163264 2842 False 1876.00 2254 91.8195 72 2881 2 chr1B.!!$F1 2809
2 TraesCS1D01G325100 chr1A 514546019 514551639 5620 False 1001.75 2021 93.1610 32 2881 4 chr1A.!!$F1 2849
3 TraesCS1D01G325100 chr1A 566590106 566590688 582 True 374.00 374 78.8030 1288 1895 1 chr1A.!!$R1 607
4 TraesCS1D01G325100 chr2A 733431488 733432049 561 True 329.00 329 78.6460 2349 2881 1 chr2A.!!$R1 532
5 TraesCS1D01G325100 chr2D 493194629 493195188 559 False 316.00 316 78.0700 2349 2881 1 chr2D.!!$F1 532

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
124 125 0.037590 TGGGAAAACCGGTCATCCTG 59.962 55.0 28.18 0.0 44.64 3.86 F
758 3443 1.151668 CTTTCCGTGGAACAGAGCAG 58.848 55.0 0.00 0.0 41.80 4.24 F
1053 3770 0.035458 AAGGACAAGGACAAGGAGCG 59.965 55.0 0.00 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1019 3736 1.072331 GTCCTTGTCCTTGCTTGGAGA 59.928 52.381 0.00 0.0 36.69 3.71 R
1838 4594 1.466851 AAGCAGCCAAGGCAAAGGAC 61.467 55.000 14.40 0.0 44.88 3.85 R
1897 4659 3.039252 AGGGTGTCTCTGCTAGCTTAT 57.961 47.619 17.23 0.0 0.00 1.73 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
17 18 4.457496 ATGCAGAGACGCCGTGGG 62.457 66.667 0.00 0.00 0.00 4.61
19 20 4.803426 GCAGAGACGCCGTGGGAG 62.803 72.222 0.00 0.00 0.00 4.30
20 21 4.135153 CAGAGACGCCGTGGGAGG 62.135 72.222 0.00 0.00 0.00 4.30
21 22 4.680537 AGAGACGCCGTGGGAGGT 62.681 66.667 0.00 0.00 0.00 3.85
22 23 4.436998 GAGACGCCGTGGGAGGTG 62.437 72.222 0.00 0.00 46.65 4.00
23 24 4.988716 AGACGCCGTGGGAGGTGA 62.989 66.667 0.00 0.00 44.18 4.02
24 25 3.771160 GACGCCGTGGGAGGTGAT 61.771 66.667 0.00 0.00 44.18 3.06
25 26 4.082523 ACGCCGTGGGAGGTGATG 62.083 66.667 3.39 0.00 44.18 3.07
26 27 3.770040 CGCCGTGGGAGGTGATGA 61.770 66.667 0.00 0.00 44.18 2.92
27 28 2.125106 GCCGTGGGAGGTGATGAC 60.125 66.667 0.00 0.00 0.00 3.06
28 29 2.954684 GCCGTGGGAGGTGATGACA 61.955 63.158 0.00 0.00 0.00 3.58
29 30 1.676968 CCGTGGGAGGTGATGACAA 59.323 57.895 0.00 0.00 0.00 3.18
30 31 0.673644 CCGTGGGAGGTGATGACAAC 60.674 60.000 0.00 0.00 0.00 3.32
32 33 1.270839 CGTGGGAGGTGATGACAACTT 60.271 52.381 0.00 0.00 44.82 2.66
33 34 2.154462 GTGGGAGGTGATGACAACTTG 58.846 52.381 0.00 0.00 44.82 3.16
34 35 1.774254 TGGGAGGTGATGACAACTTGT 59.226 47.619 0.00 0.00 44.82 3.16
35 36 2.154462 GGGAGGTGATGACAACTTGTG 58.846 52.381 0.00 0.00 44.82 3.33
36 37 2.487265 GGGAGGTGATGACAACTTGTGT 60.487 50.000 0.00 0.00 44.82 3.72
48 49 4.389374 ACAACTTGTGTGAGGATAAGGTG 58.611 43.478 0.00 0.00 42.13 4.00
51 52 3.646162 ACTTGTGTGAGGATAAGGTGACA 59.354 43.478 0.00 0.00 0.00 3.58
124 125 0.037590 TGGGAAAACCGGTCATCCTG 59.962 55.000 28.18 0.00 44.64 3.86
195 196 4.242475 CAAATGCATGCATCAACAGACTT 58.758 39.130 32.25 17.59 35.31 3.01
200 201 3.818387 CATGCATCAACAGACTTGTCAC 58.182 45.455 0.00 0.00 36.23 3.67
203 204 1.195448 CATCAACAGACTTGTCACGGC 59.805 52.381 3.49 0.00 36.23 5.68
223 224 2.029560 GCGCTACTCATGAGGATGATGA 60.030 50.000 26.08 2.33 36.00 2.92
311 2949 6.461509 GGAATGGAAGAGAAAGAAAACAAGCA 60.462 38.462 0.00 0.00 0.00 3.91
313 2951 5.650543 TGGAAGAGAAAGAAAACAAGCAAC 58.349 37.500 0.00 0.00 0.00 4.17
562 3246 4.441792 CAGCATGCATGGTACTACAGTAA 58.558 43.478 29.48 0.00 36.64 2.24
657 3341 1.336403 ATCAATTGCGTTGCGTTGCG 61.336 50.000 0.00 0.00 37.74 4.85
758 3443 1.151668 CTTTCCGTGGAACAGAGCAG 58.848 55.000 0.00 0.00 41.80 4.24
847 3537 2.998949 GGACGGGCCCATCTCTTT 59.001 61.111 24.92 0.00 0.00 2.52
863 3553 2.415512 CTCTTTCCCAATTTCGTCGTCC 59.584 50.000 0.00 0.00 0.00 4.79
880 3570 1.728971 GTCCTCGTCGTCGTCTTCTTA 59.271 52.381 1.33 0.00 38.33 2.10
963 3668 9.189156 GATCAATCTACCTATCTATCTGCTTCT 57.811 37.037 0.00 0.00 0.00 2.85
964 3669 8.347004 TCAATCTACCTATCTATCTGCTTCTG 57.653 38.462 0.00 0.00 0.00 3.02
995 3712 8.649973 TCTTCTTCTTCTTCTTAACACTGAAC 57.350 34.615 0.00 0.00 0.00 3.18
1019 3736 1.229131 ATGTGGCTTGGGATCTCCAT 58.771 50.000 4.04 0.00 46.52 3.41
1045 3762 1.202818 AGCAAGGACAAGGACAAGGAC 60.203 52.381 0.00 0.00 0.00 3.85
1046 3763 1.476833 GCAAGGACAAGGACAAGGACA 60.477 52.381 0.00 0.00 0.00 4.02
1047 3764 2.930950 CAAGGACAAGGACAAGGACAA 58.069 47.619 0.00 0.00 0.00 3.18
1048 3765 2.880890 CAAGGACAAGGACAAGGACAAG 59.119 50.000 0.00 0.00 0.00 3.16
1049 3766 1.421646 AGGACAAGGACAAGGACAAGG 59.578 52.381 0.00 0.00 0.00 3.61
1050 3767 1.420138 GGACAAGGACAAGGACAAGGA 59.580 52.381 0.00 0.00 0.00 3.36
1051 3768 2.551071 GGACAAGGACAAGGACAAGGAG 60.551 54.545 0.00 0.00 0.00 3.69
1052 3769 1.202818 ACAAGGACAAGGACAAGGAGC 60.203 52.381 0.00 0.00 0.00 4.70
1053 3770 0.035458 AAGGACAAGGACAAGGAGCG 59.965 55.000 0.00 0.00 0.00 5.03
1054 3771 1.376037 GGACAAGGACAAGGAGCGG 60.376 63.158 0.00 0.00 0.00 5.52
1055 3772 2.032681 ACAAGGACAAGGAGCGGC 59.967 61.111 0.00 0.00 0.00 6.53
1056 3773 3.121030 CAAGGACAAGGAGCGGCG 61.121 66.667 0.51 0.51 0.00 6.46
1057 3774 4.394712 AAGGACAAGGAGCGGCGG 62.395 66.667 9.78 0.00 0.00 6.13
1080 3797 2.578163 TAGCAGTGGTCGCCATGCTC 62.578 60.000 24.11 7.27 42.61 4.26
1102 3819 2.616510 GGCCTCTGCACCATATCCATAC 60.617 54.545 0.00 0.00 40.13 2.39
1176 3898 6.565234 ACATACATATTCTTCCCGATCGATC 58.435 40.000 18.66 15.68 0.00 3.69
1190 3912 2.755952 TCGATCCATCTTCTCCTCCA 57.244 50.000 0.00 0.00 0.00 3.86
1191 3913 3.251016 TCGATCCATCTTCTCCTCCAT 57.749 47.619 0.00 0.00 0.00 3.41
1192 3914 2.896044 TCGATCCATCTTCTCCTCCATG 59.104 50.000 0.00 0.00 0.00 3.66
1195 3917 2.034878 TCCATCTTCTCCTCCATGTCG 58.965 52.381 0.00 0.00 0.00 4.35
1196 3918 2.034878 CCATCTTCTCCTCCATGTCGA 58.965 52.381 0.00 0.00 0.00 4.20
1199 3921 1.950216 TCTTCTCCTCCATGTCGATCG 59.050 52.381 9.36 9.36 0.00 3.69
1200 3922 1.950216 CTTCTCCTCCATGTCGATCGA 59.050 52.381 15.15 15.15 0.00 3.59
1201 3923 2.278332 TCTCCTCCATGTCGATCGAT 57.722 50.000 22.50 2.68 0.00 3.59
1202 3924 2.155279 TCTCCTCCATGTCGATCGATC 58.845 52.381 22.50 15.68 0.00 3.69
1203 3925 1.201181 CTCCTCCATGTCGATCGATCC 59.799 57.143 22.50 10.03 0.00 3.36
1204 3926 0.961753 CCTCCATGTCGATCGATCCA 59.038 55.000 22.50 15.84 0.00 3.41
1243 3971 1.345089 TGCATGTGCTTGGCTCATTTT 59.655 42.857 6.55 0.00 40.13 1.82
1838 4594 4.778415 CTCACCGCCGGAGTCACG 62.778 72.222 11.71 0.00 0.00 4.35
1896 4658 8.011883 TCCTCCTCTAGTCTAGTCTAGTAATGA 58.988 40.741 19.35 12.35 38.66 2.57
1897 4659 8.653191 CCTCCTCTAGTCTAGTCTAGTAATGAA 58.347 40.741 19.35 3.30 38.66 2.57
1917 4716 2.534042 TAAGCTAGCAGAGACACCCT 57.466 50.000 18.83 0.00 0.00 4.34
2014 4813 8.743085 TCATTTTTCAAAACATTTGGGATTCA 57.257 26.923 3.25 0.00 0.00 2.57
2128 4927 1.662629 GAGCAGTCCATGTTCATCGTG 59.337 52.381 0.00 0.00 38.88 4.35
2129 4928 1.002430 AGCAGTCCATGTTCATCGTGT 59.998 47.619 0.00 0.00 0.00 4.49
2328 5158 4.287067 TCCTCAGCTCACTCTACCATTTTT 59.713 41.667 0.00 0.00 0.00 1.94
2329 5159 4.394300 CCTCAGCTCACTCTACCATTTTTG 59.606 45.833 0.00 0.00 0.00 2.44
2330 5160 5.227569 TCAGCTCACTCTACCATTTTTGA 57.772 39.130 0.00 0.00 0.00 2.69
2331 5161 5.240891 TCAGCTCACTCTACCATTTTTGAG 58.759 41.667 0.00 0.00 34.77 3.02
2332 5162 4.348198 GCTCACTCTACCATTTTTGAGC 57.652 45.455 5.69 5.69 46.51 4.26
2335 5165 6.900568 CTCACTCTACCATTTTTGAGCTAG 57.099 41.667 0.00 0.00 0.00 3.42
2469 5309 3.900601 TGCAACCAAATCACTAACCCAAT 59.099 39.130 0.00 0.00 0.00 3.16
2476 5316 7.110155 ACCAAATCACTAACCCAATACTACAG 58.890 38.462 0.00 0.00 0.00 2.74
2477 5317 7.037873 ACCAAATCACTAACCCAATACTACAGA 60.038 37.037 0.00 0.00 0.00 3.41
2748 5612 2.350772 GGTGATCCACGAAAAACTGCTG 60.351 50.000 0.00 0.00 34.83 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.457496 CCCACGGCGTCTCTGCAT 62.457 66.667 10.85 0.00 36.28 3.96
3 4 4.135153 CCTCCCACGGCGTCTCTG 62.135 72.222 10.85 0.00 0.00 3.35
4 5 4.680537 ACCTCCCACGGCGTCTCT 62.681 66.667 10.85 0.00 0.00 3.10
5 6 4.436998 CACCTCCCACGGCGTCTC 62.437 72.222 10.85 0.00 0.00 3.36
6 7 4.988716 TCACCTCCCACGGCGTCT 62.989 66.667 10.85 0.00 0.00 4.18
7 8 3.771160 ATCACCTCCCACGGCGTC 61.771 66.667 10.85 0.00 0.00 5.19
8 9 4.082523 CATCACCTCCCACGGCGT 62.083 66.667 6.77 6.77 0.00 5.68
9 10 3.770040 TCATCACCTCCCACGGCG 61.770 66.667 4.80 4.80 0.00 6.46
10 11 2.125106 GTCATCACCTCCCACGGC 60.125 66.667 0.00 0.00 0.00 5.68
11 12 0.673644 GTTGTCATCACCTCCCACGG 60.674 60.000 0.00 0.00 0.00 4.94
12 13 0.321671 AGTTGTCATCACCTCCCACG 59.678 55.000 0.00 0.00 0.00 4.94
13 14 2.154462 CAAGTTGTCATCACCTCCCAC 58.846 52.381 0.00 0.00 0.00 4.61
14 15 1.774254 ACAAGTTGTCATCACCTCCCA 59.226 47.619 1.64 0.00 0.00 4.37
15 16 2.154462 CACAAGTTGTCATCACCTCCC 58.846 52.381 5.27 0.00 0.00 4.30
16 17 2.549754 CACACAAGTTGTCATCACCTCC 59.450 50.000 5.27 0.00 35.67 4.30
17 18 3.466836 TCACACAAGTTGTCATCACCTC 58.533 45.455 5.27 0.00 35.67 3.85
18 19 3.470709 CTCACACAAGTTGTCATCACCT 58.529 45.455 5.27 0.00 35.67 4.00
19 20 2.549754 CCTCACACAAGTTGTCATCACC 59.450 50.000 5.27 0.00 35.67 4.02
20 21 3.466836 TCCTCACACAAGTTGTCATCAC 58.533 45.455 5.27 0.00 35.67 3.06
21 22 3.836365 TCCTCACACAAGTTGTCATCA 57.164 42.857 5.27 0.00 35.67 3.07
22 23 5.352569 CCTTATCCTCACACAAGTTGTCATC 59.647 44.000 5.27 0.00 35.67 2.92
23 24 5.221925 ACCTTATCCTCACACAAGTTGTCAT 60.222 40.000 5.27 0.00 35.67 3.06
24 25 4.102524 ACCTTATCCTCACACAAGTTGTCA 59.897 41.667 5.27 0.00 35.67 3.58
25 26 4.452455 CACCTTATCCTCACACAAGTTGTC 59.548 45.833 5.27 0.00 35.67 3.18
26 27 4.102524 TCACCTTATCCTCACACAAGTTGT 59.897 41.667 1.64 1.64 39.97 3.32
27 28 4.452455 GTCACCTTATCCTCACACAAGTTG 59.548 45.833 0.00 0.00 0.00 3.16
28 29 4.102524 TGTCACCTTATCCTCACACAAGTT 59.897 41.667 0.00 0.00 0.00 2.66
29 30 3.646162 TGTCACCTTATCCTCACACAAGT 59.354 43.478 0.00 0.00 0.00 3.16
30 31 4.021104 TCTGTCACCTTATCCTCACACAAG 60.021 45.833 0.00 0.00 0.00 3.16
31 32 3.901222 TCTGTCACCTTATCCTCACACAA 59.099 43.478 0.00 0.00 0.00 3.33
32 33 3.506398 TCTGTCACCTTATCCTCACACA 58.494 45.455 0.00 0.00 0.00 3.72
33 34 3.511934 ACTCTGTCACCTTATCCTCACAC 59.488 47.826 0.00 0.00 0.00 3.82
34 35 3.511540 CACTCTGTCACCTTATCCTCACA 59.488 47.826 0.00 0.00 0.00 3.58
35 36 3.677424 GCACTCTGTCACCTTATCCTCAC 60.677 52.174 0.00 0.00 0.00 3.51
36 37 2.497675 GCACTCTGTCACCTTATCCTCA 59.502 50.000 0.00 0.00 0.00 3.86
48 49 1.733399 GACCGTTCCGCACTCTGTC 60.733 63.158 0.00 0.00 0.00 3.51
51 52 0.892358 TACAGACCGTTCCGCACTCT 60.892 55.000 0.00 0.00 0.00 3.24
85 86 7.610580 TCCCAAATAACAGACCAAAAATTCT 57.389 32.000 0.00 0.00 0.00 2.40
124 125 0.730494 GCTCAACAATGTCCTTGCGC 60.730 55.000 0.00 0.00 38.50 6.09
195 196 1.153842 CATGAGTAGCGCCGTGACA 60.154 57.895 2.29 0.00 0.00 3.58
200 201 0.665670 CATCCTCATGAGTAGCGCCG 60.666 60.000 21.11 4.37 30.57 6.46
203 204 3.367190 CCTCATCATCCTCATGAGTAGCG 60.367 52.174 21.11 6.19 44.05 4.26
223 224 0.673437 CGCCCACAAATGTTGAACCT 59.327 50.000 0.00 0.00 0.00 3.50
298 299 1.917303 CACGCGTTGCTTGTTTTCTTT 59.083 42.857 10.22 0.00 0.00 2.52
311 2949 4.244802 CCGCCAAACACACGCGTT 62.245 61.111 10.22 0.00 44.29 4.84
313 2951 2.376231 TTTACCGCCAAACACACGCG 62.376 55.000 3.53 3.53 45.32 6.01
396 3034 6.952773 AGAGATAGTGATCTAAACGCTCTT 57.047 37.500 0.00 0.00 42.80 2.85
442 3113 7.678947 TTTCCTACTACTGTCTACACTGTAC 57.321 40.000 0.00 0.00 36.24 2.90
562 3246 2.530701 CTCCTCCACTACCACTGTCTT 58.469 52.381 0.00 0.00 0.00 3.01
657 3341 2.618300 GCAAACGCAAACGCAACC 59.382 55.556 0.00 0.00 45.53 3.77
836 3526 2.099756 CGAAATTGGGAAAGAGATGGGC 59.900 50.000 0.00 0.00 0.00 5.36
847 3537 0.108992 CGAGGACGACGAAATTGGGA 60.109 55.000 0.00 0.00 42.66 4.37
863 3553 4.261736 AGAATAAGAAGACGACGACGAG 57.738 45.455 15.32 0.00 42.66 4.18
880 3570 0.682852 TGGACGGACACGGAAAGAAT 59.317 50.000 0.00 0.00 46.48 2.40
937 3637 9.189156 AGAAGCAGATAGATAGGTAGATTGATC 57.811 37.037 0.00 0.00 0.00 2.92
963 3668 7.987458 TGTTAAGAAGAAGAAGAAGAAGAAGCA 59.013 33.333 0.00 0.00 0.00 3.91
964 3669 8.279800 GTGTTAAGAAGAAGAAGAAGAAGAAGC 58.720 37.037 0.00 0.00 0.00 3.86
995 3712 0.734889 GATCCCAAGCCACATTGTCG 59.265 55.000 0.00 0.00 0.00 4.35
1019 3736 1.072331 GTCCTTGTCCTTGCTTGGAGA 59.928 52.381 0.00 0.00 36.69 3.71
1045 3762 4.451150 TACAGCCGCCGCTCCTTG 62.451 66.667 0.00 0.00 43.95 3.61
1046 3763 4.148825 CTACAGCCGCCGCTCCTT 62.149 66.667 0.00 0.00 43.95 3.36
1053 3770 4.394712 ACCACTGCTACAGCCGCC 62.395 66.667 0.00 0.00 41.18 6.13
1054 3771 2.815647 GACCACTGCTACAGCCGC 60.816 66.667 0.00 0.00 41.18 6.53
1055 3772 2.507102 CGACCACTGCTACAGCCG 60.507 66.667 0.00 0.00 41.18 5.52
1056 3773 2.815647 GCGACCACTGCTACAGCC 60.816 66.667 0.00 0.00 41.18 4.85
1057 3774 2.815647 GGCGACCACTGCTACAGC 60.816 66.667 0.00 0.00 42.50 4.40
1058 3775 1.086067 CATGGCGACCACTGCTACAG 61.086 60.000 0.50 0.00 35.80 2.74
1059 3776 1.079197 CATGGCGACCACTGCTACA 60.079 57.895 0.50 0.00 35.80 2.74
1060 3777 2.464459 GCATGGCGACCACTGCTAC 61.464 63.158 17.32 0.00 35.80 3.58
1061 3778 2.125147 GCATGGCGACCACTGCTA 60.125 61.111 17.32 0.00 35.80 3.49
1080 3797 1.302033 GGATATGGTGCAGAGGCCG 60.302 63.158 0.00 0.00 40.13 6.13
1102 3819 1.890979 GAGGCAGCATCGACATGGG 60.891 63.158 0.00 0.00 0.00 4.00
1176 3898 2.034878 TCGACATGGAGGAGAAGATGG 58.965 52.381 0.00 0.00 0.00 3.51
1190 3912 4.038522 ACAAGAAGATGGATCGATCGACAT 59.961 41.667 22.06 19.71 0.00 3.06
1191 3913 3.381590 ACAAGAAGATGGATCGATCGACA 59.618 43.478 22.06 15.49 0.00 4.35
1192 3914 3.971150 ACAAGAAGATGGATCGATCGAC 58.029 45.455 22.06 14.00 0.00 4.20
1195 3917 6.347240 GCACATAACAAGAAGATGGATCGATC 60.347 42.308 17.36 17.36 0.00 3.69
1196 3918 5.468072 GCACATAACAAGAAGATGGATCGAT 59.532 40.000 0.00 0.00 0.00 3.59
1199 3921 5.587844 ACAGCACATAACAAGAAGATGGATC 59.412 40.000 0.00 0.00 0.00 3.36
1200 3922 5.356190 CACAGCACATAACAAGAAGATGGAT 59.644 40.000 0.00 0.00 0.00 3.41
1201 3923 4.696877 CACAGCACATAACAAGAAGATGGA 59.303 41.667 0.00 0.00 0.00 3.41
1202 3924 4.673580 GCACAGCACATAACAAGAAGATGG 60.674 45.833 0.00 0.00 0.00 3.51
1203 3925 4.083164 TGCACAGCACATAACAAGAAGATG 60.083 41.667 0.00 0.00 31.71 2.90
1204 3926 4.074259 TGCACAGCACATAACAAGAAGAT 58.926 39.130 0.00 0.00 31.71 2.40
1243 3971 1.993653 CCTCCTTCTGCACATCCCA 59.006 57.895 0.00 0.00 0.00 4.37
1475 4223 1.092348 CGTAGACCTCGGTGATGTCA 58.908 55.000 0.00 0.00 31.33 3.58
1774 4530 2.930019 TGGTGCAGGAGAGGGTGG 60.930 66.667 0.00 0.00 0.00 4.61
1834 4590 1.896660 GCCAAGGCAAAGGACGTGA 60.897 57.895 6.14 0.00 41.49 4.35
1838 4594 1.466851 AAGCAGCCAAGGCAAAGGAC 61.467 55.000 14.40 0.00 44.88 3.85
1896 4658 3.379452 AGGGTGTCTCTGCTAGCTTATT 58.621 45.455 17.23 0.00 0.00 1.40
1897 4659 3.039252 AGGGTGTCTCTGCTAGCTTAT 57.961 47.619 17.23 0.00 0.00 1.73
1948 4747 6.017605 ACTGACAGACTGTTTGAATAGCAAAG 60.018 38.462 10.01 0.00 46.48 2.77
2048 4847 5.220643 GCTGCTTATTTGTTTGTTTGTGCTT 60.221 36.000 0.00 0.00 0.00 3.91
2049 4848 4.270808 GCTGCTTATTTGTTTGTTTGTGCT 59.729 37.500 0.00 0.00 0.00 4.40
2128 4927 8.582437 TGAACTTGGGTAGTGTGCTATATATAC 58.418 37.037 0.00 0.00 37.12 1.47
2129 4928 8.715190 TGAACTTGGGTAGTGTGCTATATATA 57.285 34.615 0.00 0.00 37.12 0.86
2328 5158 3.935203 GCAGCATCTTGTAAACTAGCTCA 59.065 43.478 0.00 0.00 0.00 4.26
2329 5159 3.935203 TGCAGCATCTTGTAAACTAGCTC 59.065 43.478 0.00 0.00 0.00 4.09
2330 5160 3.942829 TGCAGCATCTTGTAAACTAGCT 58.057 40.909 0.00 0.00 0.00 3.32
2331 5161 4.260948 GGATGCAGCATCTTGTAAACTAGC 60.261 45.833 30.20 9.27 40.39 3.42
2332 5162 5.121811 AGGATGCAGCATCTTGTAAACTAG 58.878 41.667 30.20 0.00 40.39 2.57
2333 5163 5.102953 AGGATGCAGCATCTTGTAAACTA 57.897 39.130 30.20 0.00 40.39 2.24
2334 5164 3.960571 AGGATGCAGCATCTTGTAAACT 58.039 40.909 30.20 16.57 40.39 2.66
2335 5165 4.708726 AAGGATGCAGCATCTTGTAAAC 57.291 40.909 30.20 14.74 40.39 2.01
2469 5309 7.120051 AGTGAAGAAGAAGGCTATCTGTAGTA 58.880 38.462 0.00 0.00 0.00 1.82
2476 5316 6.773685 TCCTAGTAGTGAAGAAGAAGGCTATC 59.226 42.308 0.00 0.00 0.00 2.08
2477 5317 6.674573 TCCTAGTAGTGAAGAAGAAGGCTAT 58.325 40.000 0.00 0.00 0.00 2.97
2748 5612 4.246458 GTTAATAGATCTGCGGGATGACC 58.754 47.826 5.18 0.00 34.33 4.02


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

AutoCloner maintained by Alex Coulton.