Multiple sequence alignment - TraesCS2A01G307300

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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 TraesCS2A01G307300 chr2A 100.000 4607 0 0 1 4607 528120310 528115704 0.000000e+00 8508.0
1 TraesCS2A01G307300 chr2B 92.348 3071 169 32 794 3834 462949812 462946778 0.000000e+00 4309.0
2 TraesCS2A01G307300 chr2B 86.047 172 16 4 4384 4549 462946436 462946267 1.320000e-40 178.0
3 TraesCS2A01G307300 chr2B 80.342 234 17 18 3877 4083 462946782 462946551 2.870000e-32 150.0
4 TraesCS2A01G307300 chr2B 94.231 52 3 0 4556 4607 462946179 462946128 3.820000e-11 80.5
5 TraesCS2A01G307300 chr2D 95.585 2446 82 15 2173 4607 391390110 391387680 0.000000e+00 3895.0
6 TraesCS2A01G307300 chr2D 89.907 1397 87 28 792 2175 391392251 391390896 0.000000e+00 1749.0
7 TraesCS2A01G307300 chr6B 94.743 799 37 4 1 797 714389782 714388987 0.000000e+00 1238.0
8 TraesCS2A01G307300 chr6B 100.000 28 0 0 769 796 512465327 512465300 8.000000e-03 52.8
9 TraesCS2A01G307300 chr5A 92.956 795 44 7 2 794 181023679 181024463 0.000000e+00 1147.0
10 TraesCS2A01G307300 chr7B 91.855 798 49 9 1 795 106926675 106927459 0.000000e+00 1099.0
11 TraesCS2A01G307300 chr1D 93.379 725 39 5 1 721 433195895 433195176 0.000000e+00 1064.0
12 TraesCS2A01G307300 chr4D 93.094 724 39 6 1 721 365083159 365082444 0.000000e+00 1050.0
13 TraesCS2A01G307300 chrUn 92.127 724 49 6 1 721 307997986 307997268 0.000000e+00 1014.0
14 TraesCS2A01G307300 chr4A 92.127 724 49 6 1 721 405591976 405592694 0.000000e+00 1014.0
15 TraesCS2A01G307300 chr3B 92.127 724 49 6 1 721 696720588 696719870 0.000000e+00 1014.0
16 TraesCS2A01G307300 chr3B 95.349 43 2 0 752 794 696701892 696701850 8.270000e-08 69.4
17 TraesCS2A01G307300 chr3A 92.127 724 49 6 1 721 623807903 623808621 0.000000e+00 1014.0
18 TraesCS2A01G307300 chr3D 93.333 45 2 1 764 807 505800334 505800378 1.070000e-06 65.8
19 TraesCS2A01G307300 chr1A 97.222 36 1 0 764 799 568735376 568735341 1.380000e-05 62.1
20 TraesCS2A01G307300 chr4B 96.774 31 1 0 766 796 402842577 402842607 8.000000e-03 52.8


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 TraesCS2A01G307300 chr2A 528115704 528120310 4606 True 8508.000 8508 100.000 1 4607 1 chr2A.!!$R1 4606
1 TraesCS2A01G307300 chr2B 462946128 462949812 3684 True 1179.375 4309 88.242 794 4607 4 chr2B.!!$R1 3813
2 TraesCS2A01G307300 chr2D 391387680 391392251 4571 True 2822.000 3895 92.746 792 4607 2 chr2D.!!$R1 3815
3 TraesCS2A01G307300 chr6B 714388987 714389782 795 True 1238.000 1238 94.743 1 797 1 chr6B.!!$R2 796
4 TraesCS2A01G307300 chr5A 181023679 181024463 784 False 1147.000 1147 92.956 2 794 1 chr5A.!!$F1 792
5 TraesCS2A01G307300 chr7B 106926675 106927459 784 False 1099.000 1099 91.855 1 795 1 chr7B.!!$F1 794
6 TraesCS2A01G307300 chr1D 433195176 433195895 719 True 1064.000 1064 93.379 1 721 1 chr1D.!!$R1 720
7 TraesCS2A01G307300 chr4D 365082444 365083159 715 True 1050.000 1050 93.094 1 721 1 chr4D.!!$R1 720
8 TraesCS2A01G307300 chrUn 307997268 307997986 718 True 1014.000 1014 92.127 1 721 1 chrUn.!!$R1 720
9 TraesCS2A01G307300 chr4A 405591976 405592694 718 False 1014.000 1014 92.127 1 721 1 chr4A.!!$F1 720
10 TraesCS2A01G307300 chr3B 696719870 696720588 718 True 1014.000 1014 92.127 1 721 1 chr3B.!!$R2 720
11 TraesCS2A01G307300 chr3A 623807903 623808621 718 False 1014.000 1014 92.127 1 721 1 chr3A.!!$F1 720

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
872 881 0.101759 TCGAAGGCGTATTTCTCGGG 59.898 55.0 0.0 0.0 38.98 5.14 F
1292 1309 0.106419 GATGTCGAGGAGGAGGAGGT 60.106 60.0 0.0 0.0 0.00 3.85 F
1550 1574 0.179032 AACATGCACCGTCAGGAACA 60.179 50.0 0.0 0.0 41.02 3.18 F
1551 1575 0.603707 ACATGCACCGTCAGGAACAG 60.604 55.0 0.0 0.0 41.02 3.16 F
2515 3334 0.610687 CCGAGGAGGTTTCAGCTTCT 59.389 55.0 0.0 0.0 33.44 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2491 3310 0.250727 CTGAAACCTCCTCGGCCAAA 60.251 55.000 2.24 0.0 35.61 3.28 R
2768 3587 2.291475 TGTGCTTGCCTTCATATTCCCA 60.291 45.455 0.00 0.0 0.00 4.37 R
3426 4246 1.813513 AGGAAATGAGCCTGAACACG 58.186 50.000 0.00 0.0 33.59 4.49 R
3513 4333 3.085223 CTCAGAGGCCTGCCCTTT 58.915 61.111 12.00 0.0 46.60 3.11 R
3653 4473 1.531578 GCAAAACTGGACGAGGTTCTC 59.468 52.381 0.00 0.0 26.21 2.87 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
71 72 5.181811 CACTGCTGAGGTAACATCAAATTCA 59.818 40.000 0.00 0.00 41.41 2.57
90 91 6.755461 ATTCATCTAATACTTGTTCTCGCG 57.245 37.500 0.00 0.00 0.00 5.87
112 113 6.371389 GCGTGTAGAAGTAAAATGCTCTTTT 58.629 36.000 3.62 3.62 0.00 2.27
188 190 6.309712 TGATTGCTCTTTATGCTAATCTGC 57.690 37.500 0.00 0.00 33.48 4.26
270 275 7.993101 TCTATTTTTCCATTGCAATGAGAGAG 58.007 34.615 35.47 20.62 38.70 3.20
278 283 7.937649 TCCATTGCAATGAGAGAGAAAATATG 58.062 34.615 35.47 16.33 38.70 1.78
385 390 5.860182 TGCTACTGACGTTGTGATAGTTAAC 59.140 40.000 0.00 0.00 0.00 2.01
396 401 8.430063 CGTTGTGATAGTTAACGTTTCATACTT 58.570 33.333 5.91 0.00 41.43 2.24
399 404 9.647797 TGTGATAGTTAACGTTTCATACTTCAT 57.352 29.630 5.91 0.00 0.00 2.57
430 436 4.447724 TCTTCTTCAGACAAATCGAAACCG 59.552 41.667 0.00 0.00 0.00 4.44
674 682 6.970484 AGTCAAAGCTAAAAGTGTGTATTGG 58.030 36.000 0.00 0.00 0.00 3.16
729 737 4.872691 GCCGTAAGCTCATAATCTATGCAT 59.127 41.667 3.79 3.79 38.99 3.96
817 826 8.488668 AGTAACTCCTAGGTTGTGTTTTCTAAA 58.511 33.333 9.08 0.00 0.00 1.85
829 838 2.194201 TTTCTAAAGGAAGCGGGGTG 57.806 50.000 0.00 0.00 35.16 4.61
866 875 0.741927 CCCCGTTCGAAGGCGTATTT 60.742 55.000 12.30 0.00 38.98 1.40
872 881 0.101759 TCGAAGGCGTATTTCTCGGG 59.898 55.000 0.00 0.00 38.98 5.14
878 887 1.436336 CGTATTTCTCGGGAGGCGT 59.564 57.895 0.00 0.00 0.00 5.68
970 984 1.784062 CCGCTCTCGCTCTGTTTTG 59.216 57.895 0.00 0.00 0.00 2.44
1024 1041 2.398754 TTTGGTCTCTGGGAGAGTGA 57.601 50.000 0.00 0.00 42.83 3.41
1029 1046 2.430332 GGTCTCTGGGAGAGTGATTCAG 59.570 54.545 0.00 0.00 42.83 3.02
1095 1112 1.228675 CCTGCTTGGTTCTTGGGCT 60.229 57.895 0.00 0.00 0.00 5.19
1096 1113 1.530013 CCTGCTTGGTTCTTGGGCTG 61.530 60.000 0.00 0.00 0.00 4.85
1097 1114 2.151049 CTGCTTGGTTCTTGGGCTGC 62.151 60.000 0.00 0.00 0.00 5.25
1128 1145 2.802667 CGCGTTTCCTGGATGCTCG 61.803 63.158 0.00 1.82 0.00 5.03
1154 1171 3.674423 CGCTAGCTGTTTGTAGAAATGC 58.326 45.455 13.93 5.55 0.00 3.56
1155 1172 3.485877 CGCTAGCTGTTTGTAGAAATGCC 60.486 47.826 13.93 0.00 0.00 4.40
1247 1264 6.310764 AGAGAAAGATGATGTTCCTGATGT 57.689 37.500 0.00 0.00 0.00 3.06
1253 1270 6.111669 AGATGATGTTCCTGATGTGATAGG 57.888 41.667 0.00 0.00 35.34 2.57
1277 1294 2.093973 GTGAGGTCGAGGATGTTGATGT 60.094 50.000 0.00 0.00 0.00 3.06
1292 1309 0.106419 GATGTCGAGGAGGAGGAGGT 60.106 60.000 0.00 0.00 0.00 3.85
1305 1322 3.519930 GAGGTCGGCGAGGAGGAC 61.520 72.222 11.20 0.00 0.00 3.85
1344 1361 4.710324 ACGGTTTTCTGTATTCTGGTGAA 58.290 39.130 0.00 0.00 37.69 3.18
1383 1400 2.031120 CCTTGTGAGCTTTGGGTTCAA 58.969 47.619 0.00 0.00 36.94 2.69
1384 1401 2.223805 CCTTGTGAGCTTTGGGTTCAAC 60.224 50.000 0.00 0.00 36.94 3.18
1385 1402 2.435372 TGTGAGCTTTGGGTTCAACT 57.565 45.000 0.00 0.00 36.94 3.16
1386 1403 2.733956 TGTGAGCTTTGGGTTCAACTT 58.266 42.857 0.00 0.00 36.94 2.66
1387 1404 2.687935 TGTGAGCTTTGGGTTCAACTTC 59.312 45.455 0.00 0.00 36.94 3.01
1388 1405 2.687935 GTGAGCTTTGGGTTCAACTTCA 59.312 45.455 0.00 0.00 36.94 3.02
1398 1415 4.163458 TGGGTTCAACTTCAGTCTACTGTT 59.837 41.667 9.81 0.00 44.12 3.16
1546 1570 3.179443 ACTATAACATGCACCGTCAGG 57.821 47.619 0.00 0.00 45.13 3.86
1549 1573 1.803334 TAACATGCACCGTCAGGAAC 58.197 50.000 0.00 0.00 41.02 3.62
1550 1574 0.179032 AACATGCACCGTCAGGAACA 60.179 50.000 0.00 0.00 41.02 3.18
1551 1575 0.603707 ACATGCACCGTCAGGAACAG 60.604 55.000 0.00 0.00 41.02 3.16
1552 1576 1.003355 ATGCACCGTCAGGAACAGG 60.003 57.895 0.00 0.00 41.02 4.00
1553 1577 3.050275 GCACCGTCAGGAACAGGC 61.050 66.667 0.00 0.00 41.02 4.85
1554 1578 2.358737 CACCGTCAGGAACAGGCC 60.359 66.667 0.00 0.00 41.02 5.19
1555 1579 2.526873 ACCGTCAGGAACAGGCCT 60.527 61.111 0.00 0.00 41.02 5.19
1585 1609 3.388024 AGATTGTATGTGCGTGGGAGTAT 59.612 43.478 0.00 0.00 0.00 2.12
1602 1626 5.453648 GGAGTATAGCAGTGTGTATCTTCG 58.546 45.833 0.00 0.00 0.00 3.79
1647 1671 3.071874 TCAGGCCAAGTGGAACAATAG 57.928 47.619 5.01 0.00 44.16 1.73
1720 1747 6.924111 ACTTCATAGTTTAATTGGGTGCTTG 58.076 36.000 0.00 0.00 0.00 4.01
1810 1837 1.072331 CCCAATCCCTCGGTTGGATAG 59.928 57.143 3.67 0.00 46.15 2.08
1821 1849 6.204882 CCCTCGGTTGGATAGTTTATCATTTC 59.795 42.308 0.00 0.00 36.91 2.17
1928 1957 7.416964 CTCTATATAAAGAGGACCCTCCATG 57.583 44.000 12.19 0.00 43.70 3.66
2002 2031 1.203250 GCTAGAGCCCTCCCCTTATCT 60.203 57.143 0.00 0.00 34.31 1.98
2003 2032 2.815158 CTAGAGCCCTCCCCTTATCTC 58.185 57.143 0.00 0.00 0.00 2.75
2033 2062 1.628846 ACCCACAGTTGATGTCCTACC 59.371 52.381 0.00 0.00 41.41 3.18
2044 2073 5.080969 TGATGTCCTACCCGTCTAAAAAG 57.919 43.478 0.00 0.00 0.00 2.27
2074 2103 1.302383 TGATAAACCTGGGTTGCGCG 61.302 55.000 7.38 0.00 38.47 6.86
2075 2104 1.988834 GATAAACCTGGGTTGCGCGG 61.989 60.000 8.83 0.00 38.47 6.46
2115 2145 9.250624 GTAAGTTGAATCTATGTAGGACATGTC 57.749 37.037 17.91 17.91 39.53 3.06
2165 2196 9.137459 TCCAGTGTATTTTTGTATTTTCCTCAA 57.863 29.630 0.00 0.00 0.00 3.02
2348 3167 9.113838 GTGATGATGAACAAGACCTTTATGTAT 57.886 33.333 0.00 0.00 0.00 2.29
2452 3271 2.281761 GGTGCTGGTGGTGGAGTG 60.282 66.667 0.00 0.00 0.00 3.51
2512 3331 2.665603 GCCGAGGAGGTTTCAGCT 59.334 61.111 0.00 0.00 43.70 4.24
2515 3334 0.610687 CCGAGGAGGTTTCAGCTTCT 59.389 55.000 0.00 0.00 33.44 2.85
2637 3456 3.641434 ACAGGCATATGCTGAACTTCT 57.359 42.857 26.12 10.75 41.70 2.85
2680 3499 1.264288 GTTTGTTGAAGCCTCGAGTGG 59.736 52.381 12.31 0.00 0.00 4.00
2750 3569 5.236695 GTCTGTTTCAAGGGTGAGTAACTTC 59.763 44.000 0.00 0.00 34.49 3.01
2751 3570 5.104693 TCTGTTTCAAGGGTGAGTAACTTCA 60.105 40.000 0.00 0.00 34.49 3.02
2784 3603 6.494491 CCAATATTCTGGGAATATGAAGGCAA 59.506 38.462 11.86 0.00 32.32 4.52
2792 3611 3.181493 GGAATATGAAGGCAAGCACACAG 60.181 47.826 0.00 0.00 0.00 3.66
3000 3819 8.027189 GTCAAAGTTGTCTTTTTGTAACCTTCT 58.973 33.333 0.00 0.00 41.31 2.85
3024 3843 9.496873 TCTTTCTATTTTCGGTCATTTGTCTTA 57.503 29.630 0.00 0.00 0.00 2.10
3064 3883 4.885907 TCTGTTACTAGGTATGGTTCTCCG 59.114 45.833 0.00 0.00 36.30 4.63
3091 3910 4.863152 TGATGACATTGAAGCATACACG 57.137 40.909 0.00 0.00 0.00 4.49
3239 4058 4.463539 TGGCACAAACTGATAGCATCAATT 59.536 37.500 0.00 0.00 34.84 2.32
3282 4102 2.604046 AGCACTAAGGCATACTTCCG 57.396 50.000 0.00 0.00 40.64 4.30
3409 4229 4.819761 GCGAGGATGCAGCCACGA 62.820 66.667 38.57 0.00 43.38 4.35
3597 4417 2.097110 AGTTGGTCAGGGTGTACTCA 57.903 50.000 0.00 0.00 0.00 3.41
3632 4452 6.307318 GCAGCTTCTTTGACTAAATCATTGTG 59.693 38.462 0.00 0.00 37.11 3.33
3639 4459 7.884877 TCTTTGACTAAATCATTGTGTCCATCT 59.115 33.333 0.00 0.00 37.11 2.90
3647 4467 5.698741 TCATTGTGTCCATCTGAGGTAAT 57.301 39.130 0.00 0.00 0.00 1.89
3650 4470 6.375174 TCATTGTGTCCATCTGAGGTAATTTG 59.625 38.462 0.00 0.00 0.00 2.32
3653 4473 6.406370 TGTGTCCATCTGAGGTAATTTGTAG 58.594 40.000 0.00 0.00 0.00 2.74
3667 4487 3.936372 TTTGTAGAGAACCTCGTCCAG 57.064 47.619 0.00 0.00 35.36 3.86
3693 4513 4.086457 TGCTGAACTACCACTGATAGTCA 58.914 43.478 0.00 0.00 31.51 3.41
3706 4526 2.029020 TGATAGTCAGTCCAGTGTGTGC 60.029 50.000 0.00 0.00 0.00 4.57
3707 4527 1.408969 TAGTCAGTCCAGTGTGTGCA 58.591 50.000 0.00 0.00 0.00 4.57
3743 4563 4.104776 GTTGCACCATTTGTTCATATCCG 58.895 43.478 0.00 0.00 0.00 4.18
3794 4618 3.904339 ACAGATAACACCTGAACTGTCCT 59.096 43.478 0.00 0.00 34.21 3.85
3795 4619 4.021016 ACAGATAACACCTGAACTGTCCTC 60.021 45.833 0.00 0.00 34.21 3.71
3805 4635 3.620488 TGAACTGTCCTCAAGTTTTGCT 58.380 40.909 0.00 0.00 0.00 3.91
3816 4646 5.163622 CCTCAAGTTTTGCTCTCTTGTTTGA 60.164 40.000 0.00 0.00 39.36 2.69
3817 4647 5.640732 TCAAGTTTTGCTCTCTTGTTTGAC 58.359 37.500 0.00 0.00 39.36 3.18
3818 4648 5.182950 TCAAGTTTTGCTCTCTTGTTTGACA 59.817 36.000 0.00 0.00 39.36 3.58
3819 4649 5.841957 AGTTTTGCTCTCTTGTTTGACAT 57.158 34.783 0.00 0.00 0.00 3.06
3820 4650 5.585390 AGTTTTGCTCTCTTGTTTGACATG 58.415 37.500 0.00 0.00 0.00 3.21
3829 4659 5.466728 TCTCTTGTTTGACATGCTCTTACAC 59.533 40.000 0.00 0.00 0.00 2.90
3901 4731 5.361857 AGTTCTTTCATTTGGCCCTGATATG 59.638 40.000 0.00 0.00 0.00 1.78
3996 4852 6.405953 CGAGTAGGAAAGTTGATCCAGTACAT 60.406 42.308 0.00 0.00 39.55 2.29
4026 4882 6.459923 AGACCAGCTAGTATAAATAAGCAGC 58.540 40.000 0.00 0.00 37.44 5.25
4151 5007 1.804151 GCGTGCTAGTTGGACATTTGA 59.196 47.619 0.00 0.00 36.78 2.69
4262 5120 5.401550 CATTACAGATTTGGTGTTTCGCAT 58.598 37.500 0.00 0.00 0.00 4.73
4274 5132 5.106475 TGGTGTTTCGCATTATTGAACCTAC 60.106 40.000 0.00 0.00 0.00 3.18
4276 5134 4.093703 TGTTTCGCATTATTGAACCTACGG 59.906 41.667 0.00 0.00 0.00 4.02
4326 5185 3.641437 TTGAGGGAAAAAGATTGTGCG 57.359 42.857 0.00 0.00 0.00 5.34
4442 5327 4.241590 TCACATTTCAGATTGTGCAACC 57.758 40.909 8.51 0.00 42.31 3.77
4448 5333 5.843673 TTTCAGATTGTGCAACCTGTTTA 57.156 34.783 6.22 0.00 34.36 2.01
4453 5338 6.922957 TCAGATTGTGCAACCTGTTTATTTTC 59.077 34.615 6.22 0.00 34.36 2.29
4513 5403 8.574251 ACAAATTTGACACTATATGCCAAGTA 57.426 30.769 24.64 0.00 0.00 2.24
4543 5433 8.281893 CACCTTAAAAACCTAAAATTGCACATG 58.718 33.333 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 4.995124 ACACGCGAGAACAAGTATTAGAT 58.005 39.130 15.93 0.00 0.00 1.98
147 149 7.081976 AGCAATCAATCGTAGTTTGTTAAACC 58.918 34.615 1.14 0.00 42.34 3.27
161 163 7.745155 CAGATTAGCATAAAGAGCAATCAATCG 59.255 37.037 0.00 0.00 34.72 3.34
263 266 7.493645 CACTGCATGTACATATTTTCTCTCTCA 59.506 37.037 8.32 0.00 0.00 3.27
270 275 5.247507 TGGCACTGCATGTACATATTTTC 57.752 39.130 8.32 0.00 0.00 2.29
278 283 1.402968 CTCCATTGGCACTGCATGTAC 59.597 52.381 2.82 0.00 0.00 2.90
322 327 4.234550 AGATGTATAGTGCCCAAGATGGA 58.765 43.478 0.00 0.00 40.96 3.41
430 436 9.494271 TGCAAGAAGGTGAATAATATGATAGAC 57.506 33.333 0.00 0.00 0.00 2.59
573 581 6.170506 GCCAAGAAATGTCATATACCGGATA 58.829 40.000 9.46 1.75 0.00 2.59
579 587 5.295787 TGAACGGCCAAGAAATGTCATATAC 59.704 40.000 2.24 0.00 0.00 1.47
783 792 8.386264 ACACAACCTAGGAGTTACTAGTAAGTA 58.614 37.037 20.50 7.02 39.01 2.24
817 826 3.953775 CACACCACCCCGCTTCCT 61.954 66.667 0.00 0.00 0.00 3.36
829 838 2.233676 GGGGAAAACATGGAATCACACC 59.766 50.000 0.00 0.00 0.00 4.16
866 875 1.302192 CCAAAAACGCCTCCCGAGA 60.302 57.895 0.00 0.00 41.02 4.04
872 881 2.951458 CCGTCCCAAAAACGCCTC 59.049 61.111 0.00 0.00 38.77 4.70
878 887 2.296073 AAGGTATGCCGTCCCAAAAA 57.704 45.000 0.00 0.00 40.50 1.94
891 900 7.046033 CAGAGTTATCGGTTGGTTAAAGGTAT 58.954 38.462 0.00 0.00 0.00 2.73
970 984 2.476051 CACGCACGCACAAGGATC 59.524 61.111 0.00 0.00 0.00 3.36
1024 1041 2.543067 GAAGGCGAGCACCCCTGAAT 62.543 60.000 0.00 0.00 0.00 2.57
1029 1046 4.785453 CAGGAAGGCGAGCACCCC 62.785 72.222 0.00 0.00 0.00 4.95
1128 1145 1.623081 TACAAACAGCTAGCGCGCAC 61.623 55.000 35.10 21.93 42.32 5.34
1247 1264 0.106167 CTCGACCTCACCCCCTATCA 60.106 60.000 0.00 0.00 0.00 2.15
1253 1270 1.265454 AACATCCTCGACCTCACCCC 61.265 60.000 0.00 0.00 0.00 4.95
1277 1294 2.590645 CGACCTCCTCCTCCTCGA 59.409 66.667 0.00 0.00 0.00 4.04
1344 1361 6.536224 CACAAGGAAAAGAAAGCAATGAAACT 59.464 34.615 0.00 0.00 0.00 2.66
1383 1400 2.700897 ACAGGCAACAGTAGACTGAAGT 59.299 45.455 16.44 2.97 46.59 3.01
1384 1401 3.062763 CACAGGCAACAGTAGACTGAAG 58.937 50.000 16.44 8.80 46.59 3.02
1385 1402 2.224281 CCACAGGCAACAGTAGACTGAA 60.224 50.000 16.44 0.00 46.59 3.02
1386 1403 1.344438 CCACAGGCAACAGTAGACTGA 59.656 52.381 16.44 0.00 46.59 3.41
1388 1405 1.717032 TCCACAGGCAACAGTAGACT 58.283 50.000 0.00 0.00 41.41 3.24
1398 1415 1.565390 CCTCCATCCTTCCACAGGCA 61.565 60.000 0.00 0.00 43.55 4.75
1500 1524 2.741759 TAACTCGCATTCAGCAGACA 57.258 45.000 0.00 0.00 46.13 3.41
1546 1570 0.898320 TCTACTGCAGAGGCCTGTTC 59.102 55.000 23.35 0.00 42.35 3.18
1549 1573 1.209019 ACAATCTACTGCAGAGGCCTG 59.791 52.381 23.35 13.75 43.22 4.85
1550 1574 1.577736 ACAATCTACTGCAGAGGCCT 58.422 50.000 23.35 3.86 40.13 5.19
1551 1575 3.181461 ACATACAATCTACTGCAGAGGCC 60.181 47.826 23.35 0.00 40.13 5.19
1552 1576 3.806521 CACATACAATCTACTGCAGAGGC 59.193 47.826 23.35 0.00 36.48 4.70
1553 1577 3.806521 GCACATACAATCTACTGCAGAGG 59.193 47.826 23.35 12.38 36.48 3.69
1554 1578 3.488678 CGCACATACAATCTACTGCAGAG 59.511 47.826 23.35 13.48 36.48 3.35
1555 1579 3.119137 ACGCACATACAATCTACTGCAGA 60.119 43.478 23.35 0.00 37.79 4.26
1585 1609 1.822371 TGCCGAAGATACACACTGCTA 59.178 47.619 0.00 0.00 0.00 3.49
1647 1671 3.921119 TGAATGCCATCTGTTCACAAC 57.079 42.857 0.00 0.00 0.00 3.32
1821 1849 9.846248 CCCAAACTGAAAAATATCTTCTAGTTG 57.154 33.333 0.00 7.55 31.02 3.16
1958 1987 3.058432 CCATGCGCCAGATAGAAGAATTG 60.058 47.826 4.18 0.00 0.00 2.32
1993 2022 3.494573 GGTTTTAGGCGAGAGATAAGGGG 60.495 52.174 0.00 0.00 0.00 4.79
2002 2031 1.053424 ACTGTGGGTTTTAGGCGAGA 58.947 50.000 0.00 0.00 0.00 4.04
2003 2032 1.535462 CAACTGTGGGTTTTAGGCGAG 59.465 52.381 0.00 0.00 35.74 5.03
2044 2073 2.668457 CAGGTTTATCACTGCACTCGTC 59.332 50.000 0.00 0.00 0.00 4.20
2105 2135 5.875224 TGTTCAAAGATTGGACATGTCCTA 58.125 37.500 37.92 32.93 44.03 2.94
2191 3010 7.023197 ACAACATATTATTTGGTTAGTCGGC 57.977 36.000 0.00 0.00 0.00 5.54
2233 3052 3.732048 AGGTTTCGGGGACATAATTGT 57.268 42.857 0.00 0.00 39.32 2.71
2452 3271 1.806542 CACCATGTACCAGCAAGTGAC 59.193 52.381 0.00 0.00 32.07 3.67
2491 3310 0.250727 CTGAAACCTCCTCGGCCAAA 60.251 55.000 2.24 0.00 35.61 3.28
2533 3352 4.328169 GCAGTTGCCTTGAAAGCATAAATC 59.672 41.667 0.00 0.00 40.59 2.17
2680 3499 6.202954 CACTTTATCGATCCACTAATCCCAAC 59.797 42.308 0.00 0.00 0.00 3.77
2717 3536 4.891168 ACCCTTGAAACAGACGGTTAAAAT 59.109 37.500 0.00 0.00 39.29 1.82
2768 3587 2.291475 TGTGCTTGCCTTCATATTCCCA 60.291 45.455 0.00 0.00 0.00 4.37
2792 3611 8.839310 AAATTATGTCATCTACCAGTATCAGC 57.161 34.615 0.00 0.00 0.00 4.26
2912 3731 7.067532 TGCTTTCAAATGTAAGTACCATACG 57.932 36.000 2.44 0.00 0.00 3.06
2994 3813 7.230712 ACAAATGACCGAAAATAGAAAGAAGGT 59.769 33.333 0.00 0.00 0.00 3.50
3000 3819 9.496873 TCTAAGACAAATGACCGAAAATAGAAA 57.503 29.630 0.00 0.00 0.00 2.52
3010 3829 6.968131 TGAGAAATCTAAGACAAATGACCG 57.032 37.500 0.00 0.00 0.00 4.79
3041 3860 4.885907 CGGAGAACCATACCTAGTAACAGA 59.114 45.833 0.00 0.00 35.59 3.41
3042 3861 4.885907 TCGGAGAACCATACCTAGTAACAG 59.114 45.833 0.00 0.00 35.59 3.16
3064 3883 8.066595 GTGTATGCTTCAATGTCATCAATAGTC 58.933 37.037 0.00 0.00 0.00 2.59
3282 4102 5.163713 GGATGACACCTTCAAAGTGATTAGC 60.164 44.000 0.00 0.00 37.92 3.09
3426 4246 1.813513 AGGAAATGAGCCTGAACACG 58.186 50.000 0.00 0.00 33.59 4.49
3513 4333 3.085223 CTCAGAGGCCTGCCCTTT 58.915 61.111 12.00 0.00 46.60 3.11
3597 4417 4.023365 GTCAAAGAAGCTGCTCAACATTCT 60.023 41.667 1.00 0.00 30.48 2.40
3632 4452 7.113658 TCTCTACAAATTACCTCAGATGGAC 57.886 40.000 0.00 0.00 0.00 4.02
3647 4467 3.228453 ACTGGACGAGGTTCTCTACAAA 58.772 45.455 0.00 0.00 0.00 2.83
3650 4470 3.938289 AAACTGGACGAGGTTCTCTAC 57.062 47.619 0.00 0.00 0.00 2.59
3653 4473 1.531578 GCAAAACTGGACGAGGTTCTC 59.468 52.381 0.00 0.00 26.21 2.87
3667 4487 5.701290 ACTATCAGTGGTAGTTCAGCAAAAC 59.299 40.000 10.43 0.00 36.14 2.43
3703 4523 3.181516 GCAACAATCTAGCTACTGTGCAC 60.182 47.826 10.75 10.75 34.99 4.57
3706 4526 3.372206 GGTGCAACAATCTAGCTACTGTG 59.628 47.826 0.00 0.00 39.98 3.66
3707 4527 3.007940 TGGTGCAACAATCTAGCTACTGT 59.992 43.478 0.00 0.00 39.98 3.55
3743 4563 3.971245 AGAAGAACTCATCTCACCACC 57.029 47.619 0.00 0.00 37.42 4.61
3794 4618 5.182950 TGTCAAACAAGAGAGCAAAACTTGA 59.817 36.000 15.76 0.00 42.12 3.02
3795 4619 5.401550 TGTCAAACAAGAGAGCAAAACTTG 58.598 37.500 0.00 0.00 44.16 3.16
3805 4635 5.466728 GTGTAAGAGCATGTCAAACAAGAGA 59.533 40.000 0.00 0.00 0.00 3.10
3816 4646 5.760253 GCCATATAACTGTGTAAGAGCATGT 59.240 40.000 0.00 0.00 0.00 3.21
3817 4647 5.759763 TGCCATATAACTGTGTAAGAGCATG 59.240 40.000 0.00 0.00 0.00 4.06
3818 4648 5.928976 TGCCATATAACTGTGTAAGAGCAT 58.071 37.500 0.00 0.00 0.00 3.79
3819 4649 5.351948 TGCCATATAACTGTGTAAGAGCA 57.648 39.130 0.00 0.00 0.00 4.26
3820 4650 4.212214 GCTGCCATATAACTGTGTAAGAGC 59.788 45.833 0.00 0.00 0.00 4.09
3829 4659 3.504906 CAGGGAATGCTGCCATATAACTG 59.495 47.826 0.00 0.00 34.87 3.16
3878 4708 5.594926 CATATCAGGGCCAAATGAAAGAAC 58.405 41.667 6.18 0.00 0.00 3.01
3881 4711 3.385433 TGCATATCAGGGCCAAATGAAAG 59.615 43.478 6.18 1.60 0.00 2.62
3901 4731 4.946784 ACTAATTCGACAAGTGGATTGC 57.053 40.909 0.00 0.00 43.15 3.56
4026 4882 4.152402 CCTCTGGTCATGTTTACAAAGTCG 59.848 45.833 0.00 0.00 0.00 4.18
4151 5007 7.123547 TCAAATTCTCACCTTAGTTGGTTTGTT 59.876 33.333 0.00 0.00 38.45 2.83
4290 5148 3.243201 CCCTCAAAAGAAGTTGCACAGTC 60.243 47.826 0.00 0.00 0.00 3.51
4292 5150 2.951642 TCCCTCAAAAGAAGTTGCACAG 59.048 45.455 0.00 0.00 0.00 3.66
4326 5185 7.913674 ATCTCAAATTAGTTGACCTGAAGTC 57.086 36.000 0.00 0.00 41.47 3.01
4442 5327 6.836577 TTTCCCGCAAAAGAAAATAAACAG 57.163 33.333 0.00 0.00 0.00 3.16
4453 5338 3.059665 GCACAATCTTTTTCCCGCAAAAG 60.060 43.478 1.54 1.54 42.77 2.27
4513 5403 6.481976 GCAATTTTAGGTTTTTAAGGTGTGCT 59.518 34.615 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.