Multiple sequence alignment - TraesCS4A01G123900

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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 TraesCS4A01G123900 chr4A 100.000 7095 0 0 1 7095 156804374 156797280 0.000000e+00 13103.0
1 TraesCS4A01G123900 chr4D 96.132 6748 175 34 220 6922 317948739 317955445 0.000000e+00 10936.0
2 TraesCS4A01G123900 chr4D 97.458 236 4 2 1 236 317948492 317948725 1.110000e-107 401.0
3 TraesCS4A01G123900 chr4D 92.857 84 6 0 6936 7019 238299970 238299887 9.670000e-24 122.0
4 TraesCS4A01G123900 chr4D 93.671 79 3 1 7017 7095 317955444 317955520 4.500000e-22 117.0
5 TraesCS4A01G123900 chr4D 86.598 97 13 0 6923 7019 310388731 310388827 2.710000e-19 108.0
6 TraesCS4A01G123900 chr4B 95.051 3718 129 23 3 3709 395244970 395248643 0.000000e+00 5795.0
7 TraesCS4A01G123900 chr4B 94.747 3255 100 25 3695 6922 395248697 395251907 0.000000e+00 4998.0
8 TraesCS4A01G123900 chr4B 86.139 101 14 0 6919 7019 438876160 438876060 7.520000e-20 110.0
9 TraesCS4A01G123900 chr1A 88.660 97 11 0 6923 7019 451364361 451364265 1.250000e-22 119.0
10 TraesCS4A01G123900 chr3D 87.000 100 13 0 6923 7022 175538902 175538803 5.820000e-21 113.0
11 TraesCS4A01G123900 chr5A 87.912 91 10 1 6934 7024 99555402 99555491 9.730000e-19 106.0
12 TraesCS4A01G123900 chr5A 83.654 104 16 1 6923 7026 569297564 569297666 5.860000e-16 97.1
13 TraesCS4A01G123900 chr5A 84.536 97 13 2 6923 7019 443694692 443694786 2.110000e-15 95.3
14 TraesCS4A01G123900 chr2D 85.567 97 14 0 6923 7019 579827044 579827140 1.260000e-17 102.0


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 TraesCS4A01G123900 chr4A 156797280 156804374 7094 True 13103.0 13103 100.000000 1 7095 1 chr4A.!!$R1 7094
1 TraesCS4A01G123900 chr4D 317948492 317955520 7028 False 3818.0 10936 95.753667 1 7095 3 chr4D.!!$F2 7094
2 TraesCS4A01G123900 chr4B 395244970 395251907 6937 False 5396.5 5795 94.899000 3 6922 2 chr4B.!!$F1 6919

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
546 587 0.594110 TGTTAAGAAAAAGGGCGCGG 59.406 50.00 8.83 0.00 0.00 6.46 F
742 783 1.227999 CGTTTCCAAGAGGCAGCGAA 61.228 55.00 0.00 0.00 33.74 4.70 F
1834 1877 0.107017 ATTTCAGCGATGGGTCCTGG 60.107 55.00 0.00 0.00 0.00 4.45 F
1918 1961 4.078537 TGCCTTGTAAACTGCATATGTGT 58.921 39.13 4.29 1.24 0.00 3.72 F
2684 2727 0.975887 TGCATGTGAGCACCTAGACA 59.024 50.00 0.00 0.00 40.11 3.41 F
3993 4125 0.109342 CGGGCTTCTGGCATTATCCT 59.891 55.00 0.00 0.00 44.01 3.24 F
5316 5449 2.492088 GGTGGTTTCCTTATTGGACTGC 59.508 50.00 0.00 0.00 46.14 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1411 1454 0.693049 CTGCCCTTACCTTGTGGAGT 59.307 55.000 0.00 0.0 37.04 3.85 R
1984 2027 2.296471 AGTCCAGACACTACCAAAGTCG 59.704 50.000 0.00 0.0 35.76 4.18 R
2672 2715 2.832733 AGTTTACCCTGTCTAGGTGCTC 59.167 50.000 0.00 0.0 42.96 4.26 R
3544 3587 5.049680 CGTTTAAGTGAAGAGGCTAAAAGCA 60.050 40.000 0.78 0.0 44.75 3.91 R
4052 4184 1.674441 CCATAGTGCATGCCAGACAAG 59.326 52.381 16.68 1.1 32.84 3.16 R
5380 5514 1.000618 TCAATGCATTTTGCTTCCGCA 59.999 42.857 9.83 0.0 45.31 5.69 R
6338 6474 1.082690 GCTACAAGCCTCAGAACAGC 58.917 55.000 0.00 0.0 34.48 4.40 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
113 114 1.375908 GAAGGCACGACATGGAGCA 60.376 57.895 0.00 0.00 0.00 4.26
154 156 6.801575 TCAACAGTAAGAAATGTTTTCACCC 58.198 36.000 3.11 0.00 37.54 4.61
225 227 3.814842 ACATCATCTCGTGCAAAACTTGA 59.185 39.130 0.00 0.00 0.00 3.02
264 296 1.201825 GGCGCGAAAGATATGACGC 59.798 57.895 12.10 0.00 46.08 5.19
334 367 7.315890 CGAGATATATGACATAGAAGGCAACA 58.684 38.462 0.98 0.00 41.41 3.33
417 452 7.608308 GGCAAAGCCTCTCATATATCTAAAG 57.392 40.000 0.00 0.00 46.69 1.85
491 527 5.347364 GCTATTTGTTAAGAAAAATGGCGCA 59.653 36.000 10.83 0.00 39.43 6.09
546 587 0.594110 TGTTAAGAAAAAGGGCGCGG 59.406 50.000 8.83 0.00 0.00 6.46
592 633 8.283699 TCTCATCATCATTTGCTATTTGTCAA 57.716 30.769 0.00 0.00 0.00 3.18
593 634 8.909923 TCTCATCATCATTTGCTATTTGTCAAT 58.090 29.630 0.00 0.00 0.00 2.57
742 783 1.227999 CGTTTCCAAGAGGCAGCGAA 61.228 55.000 0.00 0.00 33.74 4.70
862 905 5.362430 CCAAAGCTGGCCCAAAATAATAGTA 59.638 40.000 0.00 0.00 35.39 1.82
863 906 6.461509 CCAAAGCTGGCCCAAAATAATAGTAG 60.462 42.308 0.00 0.00 35.39 2.57
864 907 5.388599 AGCTGGCCCAAAATAATAGTAGT 57.611 39.130 0.00 0.00 0.00 2.73
1295 1338 1.392510 GCCGTTTGGTCGTATCTTGTC 59.607 52.381 0.00 0.00 37.67 3.18
1322 1365 4.216687 TCGTGCCTAATTTTGGGTAACTTG 59.783 41.667 0.00 0.00 0.00 3.16
1325 1368 6.285224 GTGCCTAATTTTGGGTAACTTGTTT 58.715 36.000 0.00 0.00 0.00 2.83
1326 1369 6.764085 GTGCCTAATTTTGGGTAACTTGTTTT 59.236 34.615 0.00 0.00 0.00 2.43
1411 1454 1.569548 AGGGAGAGGGTCATACTCGAA 59.430 52.381 0.00 0.00 39.90 3.71
1472 1515 1.669440 CAGCTTGCAATGTGGGCTT 59.331 52.632 7.35 0.00 0.00 4.35
1477 1520 2.343101 CTTGCAATGTGGGCTTGAATG 58.657 47.619 0.00 0.00 0.00 2.67
1496 1539 2.380081 CGACCTGTAATCCGGTTGC 58.620 57.895 0.00 0.00 32.62 4.17
1625 1668 2.549349 GGGGTAAGCACTGAACTCGAAA 60.549 50.000 0.00 0.00 0.00 3.46
1685 1728 3.753797 TGATGCTAGGCTGATCTACTACG 59.246 47.826 0.00 0.00 0.00 3.51
1686 1729 2.505405 TGCTAGGCTGATCTACTACGG 58.495 52.381 0.00 0.00 0.00 4.02
1834 1877 0.107017 ATTTCAGCGATGGGTCCTGG 60.107 55.000 0.00 0.00 0.00 4.45
1913 1956 4.141287 ACTGTTGCCTTGTAAACTGCATA 58.859 39.130 0.00 0.00 33.08 3.14
1918 1961 4.078537 TGCCTTGTAAACTGCATATGTGT 58.921 39.130 4.29 1.24 0.00 3.72
2430 2473 7.551262 ACTCATAAATGTTTCGCATAGGTAACA 59.449 33.333 0.00 0.00 36.67 2.41
2506 2549 9.233232 GTACTTTTTGAAGTGTGGATGTTTTAG 57.767 33.333 2.25 0.00 34.37 1.85
2658 2701 9.479549 AGTTTGAATATATTGGTCTGGTCAATT 57.520 29.630 1.78 0.00 36.40 2.32
2672 2715 6.089820 GTCTGGTCAATTTGTAATTGCATGTG 59.910 38.462 0.00 0.00 0.00 3.21
2684 2727 0.975887 TGCATGTGAGCACCTAGACA 59.024 50.000 0.00 0.00 40.11 3.41
2922 2965 3.385755 ACAGTTTTGAGCCTTTGCAATCT 59.614 39.130 0.00 0.00 41.13 2.40
3153 3196 8.771920 AAATTGTGATGATTACACGTCTTAGA 57.228 30.769 0.00 0.00 40.61 2.10
3378 3421 7.117092 GGTATTATGGTTTCATTTTTGCGTTGT 59.883 33.333 0.00 0.00 34.96 3.32
3488 3531 3.508012 CAGTGACCTAGATATTCTCCCCG 59.492 52.174 0.00 0.00 0.00 5.73
3651 3714 2.745698 CACTCTGCTGGGCACTCA 59.254 61.111 0.00 0.00 33.79 3.41
3671 3734 7.596621 GCACTCATTCTCATAGATTCGACATTA 59.403 37.037 0.00 0.00 0.00 1.90
3898 4029 7.962995 ATGAAGGTCTAACAATAGTCTCAGA 57.037 36.000 0.00 0.00 0.00 3.27
3899 4030 7.159322 TGAAGGTCTAACAATAGTCTCAGAC 57.841 40.000 0.00 0.00 33.31 3.51
3900 4031 6.948886 TGAAGGTCTAACAATAGTCTCAGACT 59.051 38.462 13.16 13.16 45.54 3.24
3901 4032 7.121463 TGAAGGTCTAACAATAGTCTCAGACTC 59.879 40.741 11.71 0.00 42.40 3.36
3902 4033 6.727394 AGGTCTAACAATAGTCTCAGACTCT 58.273 40.000 11.71 0.00 42.40 3.24
3993 4125 0.109342 CGGGCTTCTGGCATTATCCT 59.891 55.000 0.00 0.00 44.01 3.24
4052 4184 6.695245 CACATTCTGTGTACTTTTTGTTTGC 58.305 36.000 0.00 0.00 43.08 3.68
4108 4240 5.920273 GTGTCATTCGATGTGTTTCCAAAAT 59.080 36.000 0.00 0.00 0.00 1.82
4116 4248 5.858581 CGATGTGTTTCCAAAATCCTTCTTC 59.141 40.000 0.00 0.00 0.00 2.87
4314 4446 9.421399 TGTCTGACTTCTATCCTCAATTGTATA 57.579 33.333 9.51 2.18 0.00 1.47
4677 4809 5.527582 CCTACCTAATTTATGCCACACTGTC 59.472 44.000 0.00 0.00 0.00 3.51
4785 4918 9.757227 GTAGAAGAGTCATGAGTTTAATATGCT 57.243 33.333 4.13 0.00 0.00 3.79
4793 4926 8.840321 GTCATGAGTTTAATATGCTTGGTATGT 58.160 33.333 0.00 0.00 0.00 2.29
4848 4981 5.186256 TGGCATGATGGAGTTTAAACCTA 57.814 39.130 14.72 5.19 0.00 3.08
4989 5122 3.269643 CCTTTTCTATTCCCCTGTTCCCT 59.730 47.826 0.00 0.00 0.00 4.20
5133 5266 4.081752 GGCCATGTTCCATATTGTTTCACA 60.082 41.667 0.00 0.00 0.00 3.58
5220 5353 4.933400 GCTTCATTTGATTTGTTGGCATCT 59.067 37.500 0.00 0.00 0.00 2.90
5251 5384 9.683069 TTAATCTCTCTTTTGCTTTGAAATGAC 57.317 29.630 0.00 0.00 0.00 3.06
5311 5444 4.658063 TGTGTAGGTGGTTTCCTTATTGG 58.342 43.478 0.00 0.00 38.86 3.16
5316 5449 2.492088 GGTGGTTTCCTTATTGGACTGC 59.508 50.000 0.00 0.00 46.14 4.40
5361 5495 3.503363 TGCGGATTGATAGGAATTGATGC 59.497 43.478 0.00 0.00 0.00 3.91
5380 5514 6.643388 TGATGCTGTATGTTGTAAGATCTGT 58.357 36.000 0.00 0.00 0.00 3.41
5383 5517 4.259970 GCTGTATGTTGTAAGATCTGTGCG 60.260 45.833 0.00 0.00 0.00 5.34
5450 5585 3.119955 CGGACTTAAGTTTAAGGCTTGCC 60.120 47.826 10.02 2.97 45.91 4.52
5650 5785 3.491934 GTGAAATCACGATTCCGCG 57.508 52.632 0.00 0.00 39.95 6.46
5815 5950 4.164796 TCAGAGCAAGTGGATCATACCATT 59.835 41.667 0.00 0.00 42.17 3.16
6140 6275 6.817641 CCTGTGAATATCCAGATGAGAATAGC 59.182 42.308 0.00 0.00 0.00 2.97
6338 6474 1.021202 TTCATTCGGGCGGCTTATTG 58.979 50.000 9.56 4.46 0.00 1.90
6401 6537 5.436175 ACACAGCATAGCAATTGGTATACA 58.564 37.500 25.42 5.13 36.68 2.29
6465 6601 3.062122 AGGTGTAATGTTTGGTACCCG 57.938 47.619 10.07 0.00 0.00 5.28
6468 6604 0.728542 GTAATGTTTGGTACCCGGCG 59.271 55.000 10.07 0.00 0.00 6.46
6506 6642 2.625737 CCTTGTATGGTCAGAGCTGTG 58.374 52.381 4.05 4.05 0.00 3.66
6635 6772 6.128661 TGTTCATGAGTTGTTATGTAGCGAAC 60.129 38.462 0.00 0.00 0.00 3.95
6694 6832 5.126067 TCTTGCATTATCTTGGGCTTACTC 58.874 41.667 0.00 0.00 0.00 2.59
6883 7042 2.301009 AGCATTTCTTCTTTGGCCAAGG 59.699 45.455 21.15 21.15 32.64 3.61
6937 7096 8.727100 ATATGTATGTTACTCTCTTCATCCCA 57.273 34.615 0.00 0.00 0.00 4.37
6938 7097 6.867519 TGTATGTTACTCTCTTCATCCCAA 57.132 37.500 0.00 0.00 0.00 4.12
6939 7098 7.252612 TGTATGTTACTCTCTTCATCCCAAA 57.747 36.000 0.00 0.00 0.00 3.28
6940 7099 7.685481 TGTATGTTACTCTCTTCATCCCAAAA 58.315 34.615 0.00 0.00 0.00 2.44
6941 7100 8.328758 TGTATGTTACTCTCTTCATCCCAAAAT 58.671 33.333 0.00 0.00 0.00 1.82
6942 7101 9.832445 GTATGTTACTCTCTTCATCCCAAAATA 57.168 33.333 0.00 0.00 0.00 1.40
6944 7103 8.792830 TGTTACTCTCTTCATCCCAAAATAAG 57.207 34.615 0.00 0.00 0.00 1.73
6945 7104 8.383175 TGTTACTCTCTTCATCCCAAAATAAGT 58.617 33.333 0.00 0.00 0.00 2.24
6946 7105 9.232473 GTTACTCTCTTCATCCCAAAATAAGTT 57.768 33.333 0.00 0.00 0.00 2.66
6947 7106 9.807921 TTACTCTCTTCATCCCAAAATAAGTTT 57.192 29.630 0.00 0.00 0.00 2.66
6948 7107 8.341892 ACTCTCTTCATCCCAAAATAAGTTTC 57.658 34.615 0.00 0.00 0.00 2.78
6949 7108 8.166726 ACTCTCTTCATCCCAAAATAAGTTTCT 58.833 33.333 0.00 0.00 0.00 2.52
6950 7109 8.567285 TCTCTTCATCCCAAAATAAGTTTCTC 57.433 34.615 0.00 0.00 0.00 2.87
6951 7110 8.163408 TCTCTTCATCCCAAAATAAGTTTCTCA 58.837 33.333 0.00 0.00 0.00 3.27
6952 7111 8.704849 TCTTCATCCCAAAATAAGTTTCTCAA 57.295 30.769 0.00 0.00 0.00 3.02
6953 7112 8.576442 TCTTCATCCCAAAATAAGTTTCTCAAC 58.424 33.333 0.00 0.00 0.00 3.18
6954 7113 8.477419 TTCATCCCAAAATAAGTTTCTCAACT 57.523 30.769 0.00 0.00 45.89 3.16
6973 7132 9.332502 TCTCAACTTTGTATTAACTTTAGCACA 57.667 29.630 0.00 0.00 0.00 4.57
6974 7133 9.944663 CTCAACTTTGTATTAACTTTAGCACAA 57.055 29.630 0.00 0.00 0.00 3.33
6986 7145 9.522804 TTAACTTTAGCACAAAATTGTACCAAG 57.477 29.630 0.00 2.36 39.91 3.61
6987 7146 6.512297 ACTTTAGCACAAAATTGTACCAAGG 58.488 36.000 0.00 0.00 39.91 3.61
6988 7147 6.097696 ACTTTAGCACAAAATTGTACCAAGGT 59.902 34.615 0.00 0.00 39.91 3.50
6989 7148 6.472686 TTAGCACAAAATTGTACCAAGGTT 57.527 33.333 0.00 0.00 39.91 3.50
6990 7149 7.584122 TTAGCACAAAATTGTACCAAGGTTA 57.416 32.000 0.00 0.00 39.91 2.85
6991 7150 6.472686 AGCACAAAATTGTACCAAGGTTAA 57.527 33.333 0.00 0.00 39.91 2.01
6992 7151 6.512297 AGCACAAAATTGTACCAAGGTTAAG 58.488 36.000 0.00 0.00 39.91 1.85
6993 7152 6.322712 AGCACAAAATTGTACCAAGGTTAAGA 59.677 34.615 0.00 0.00 39.91 2.10
6994 7153 6.419710 GCACAAAATTGTACCAAGGTTAAGAC 59.580 38.462 0.00 0.00 39.91 3.01
6995 7154 7.484975 CACAAAATTGTACCAAGGTTAAGACA 58.515 34.615 0.00 0.00 39.91 3.41
6996 7155 7.434013 CACAAAATTGTACCAAGGTTAAGACAC 59.566 37.037 0.00 0.00 39.91 3.67
6997 7156 7.340999 ACAAAATTGTACCAAGGTTAAGACACT 59.659 33.333 0.00 0.00 40.16 3.55
6998 7157 7.891498 AAATTGTACCAAGGTTAAGACACTT 57.109 32.000 0.00 0.00 0.00 3.16
6999 7158 8.983702 AAATTGTACCAAGGTTAAGACACTTA 57.016 30.769 0.00 0.00 0.00 2.24
7000 7159 9.582648 AAATTGTACCAAGGTTAAGACACTTAT 57.417 29.630 0.00 0.00 0.00 1.73
7001 7160 9.582648 AATTGTACCAAGGTTAAGACACTTATT 57.417 29.630 0.00 0.00 0.00 1.40
7002 7161 8.983702 TTGTACCAAGGTTAAGACACTTATTT 57.016 30.769 0.00 0.00 0.00 1.40
7003 7162 8.983702 TGTACCAAGGTTAAGACACTTATTTT 57.016 30.769 0.00 0.00 0.00 1.82
7004 7163 8.842280 TGTACCAAGGTTAAGACACTTATTTTG 58.158 33.333 0.00 0.00 0.00 2.44
7005 7164 9.059260 GTACCAAGGTTAAGACACTTATTTTGA 57.941 33.333 0.00 0.00 0.00 2.69
7006 7165 8.166422 ACCAAGGTTAAGACACTTATTTTGAG 57.834 34.615 0.00 0.00 0.00 3.02
7007 7166 7.996644 ACCAAGGTTAAGACACTTATTTTGAGA 59.003 33.333 0.00 0.00 0.00 3.27
7008 7167 9.014297 CCAAGGTTAAGACACTTATTTTGAGAT 57.986 33.333 0.00 0.00 0.00 2.75
7015 7174 7.979786 AGACACTTATTTTGAGATAGAGGGA 57.020 36.000 0.00 0.00 0.00 4.20
7016 7175 8.017418 AGACACTTATTTTGAGATAGAGGGAG 57.983 38.462 0.00 0.00 0.00 4.30
7086 7245 2.838736 ACAAGATATGCCACATCGTCC 58.161 47.619 0.00 0.00 0.00 4.79
7089 7248 0.396435 GATATGCCACATCGTCCCCA 59.604 55.000 0.00 0.00 0.00 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
99 100 0.523072 ACATTTGCTCCATGTCGTGC 59.477 50.000 0.00 0.00 27.99 5.34
113 114 9.599866 TTACTGTTGATCATCGAGATAACATTT 57.400 29.630 0.00 0.00 37.00 2.32
154 156 1.604604 AATGTGTTCTGTCGGTTGGG 58.395 50.000 0.00 0.00 0.00 4.12
213 215 9.490663 GTGTAACTATATGATCAAGTTTTGCAC 57.509 33.333 14.74 15.61 35.23 4.57
225 227 6.590292 GCGCCACTTATGTGTAACTATATGAT 59.410 38.462 0.00 0.00 42.34 2.45
264 296 6.851222 ATGAGAAGCTTTACCGATTGTATG 57.149 37.500 0.00 0.00 0.00 2.39
266 298 8.857098 AGTATATGAGAAGCTTTACCGATTGTA 58.143 33.333 0.00 0.00 0.00 2.41
268 300 8.594881 AAGTATATGAGAAGCTTTACCGATTG 57.405 34.615 0.00 0.00 0.00 2.67
269 301 9.694137 GTAAGTATATGAGAAGCTTTACCGATT 57.306 33.333 0.00 0.00 0.00 3.34
412 447 8.568732 TTTTTCGTGCCATTTTTCTACTTTAG 57.431 30.769 0.00 0.00 0.00 1.85
417 452 7.806014 TCAGTATTTTTCGTGCCATTTTTCTAC 59.194 33.333 0.00 0.00 0.00 2.59
430 465 9.141400 GAGATGTAGACTTTCAGTATTTTTCGT 57.859 33.333 0.00 0.00 0.00 3.85
546 587 7.810658 TGAGATGCAGACTTTCAGTATTTTTC 58.189 34.615 0.00 0.00 0.00 2.29
742 783 2.203437 GGGTTTGGAGTTGGGCGT 60.203 61.111 0.00 0.00 0.00 5.68
862 905 6.038356 CCTCGTGTTTGAATTACGGTATACT 58.962 40.000 2.25 0.00 38.29 2.12
863 906 5.276536 GCCTCGTGTTTGAATTACGGTATAC 60.277 44.000 0.00 0.00 38.29 1.47
864 907 4.805192 GCCTCGTGTTTGAATTACGGTATA 59.195 41.667 0.00 0.00 38.29 1.47
961 1004 2.048503 CCGAGGACGAAGCGGTTT 60.049 61.111 0.00 0.00 42.66 3.27
1031 1074 4.760047 GCTCGGGCTTGCGGAAGA 62.760 66.667 21.87 0.00 35.22 2.87
1295 1338 2.030628 ACCCAAAATTAGGCACGAAACG 60.031 45.455 0.00 0.00 0.00 3.60
1400 1443 3.056749 ACCTTGTGGAGTTCGAGTATGAC 60.057 47.826 0.00 0.00 37.04 3.06
1411 1454 0.693049 CTGCCCTTACCTTGTGGAGT 59.307 55.000 0.00 0.00 37.04 3.85
1472 1515 1.472552 CCGGATTACAGGTCGCATTCA 60.473 52.381 0.00 0.00 0.00 2.57
1477 1520 1.702491 GCAACCGGATTACAGGTCGC 61.702 60.000 9.46 0.00 43.29 5.19
1496 1539 4.682787 TCCATAACTATCTGCAACAGTCG 58.317 43.478 0.00 0.00 32.61 4.18
1625 1668 2.473530 CACAACAAATCGTGCACAGT 57.526 45.000 18.64 0.72 0.00 3.55
1656 1699 2.397597 TCAGCCTAGCATCACACCATA 58.602 47.619 0.00 0.00 0.00 2.74
1834 1877 4.115516 AGCAACTCACATACGATGATCAC 58.884 43.478 0.00 0.00 0.00 3.06
1898 1941 7.761409 ACATAACACATATGCAGTTTACAAGG 58.239 34.615 16.41 6.06 44.46 3.61
1913 1956 6.630203 TGACCCTAACCTAACATAACACAT 57.370 37.500 0.00 0.00 0.00 3.21
1918 1961 3.431207 GCGCTGACCCTAACCTAACATAA 60.431 47.826 0.00 0.00 0.00 1.90
1984 2027 2.296471 AGTCCAGACACTACCAAAGTCG 59.704 50.000 0.00 0.00 35.76 4.18
2246 2289 6.215121 TCTTTATGCCACATCAACAAACAAG 58.785 36.000 0.00 0.00 0.00 3.16
2430 2473 9.479549 TTTAGCAAGATTTCTAATTCCCTGAAT 57.520 29.630 0.00 0.00 33.25 2.57
2483 2526 8.702163 AACTAAAACATCCACACTTCAAAAAG 57.298 30.769 0.00 0.00 38.54 2.27
2506 2549 9.846248 GGAATTGAGGAATATTGTATGCATAAC 57.154 33.333 8.28 3.80 0.00 1.89
2649 2692 6.157904 TCACATGCAATTACAAATTGACCAG 58.842 36.000 14.83 5.27 0.00 4.00
2658 2701 3.156293 AGGTGCTCACATGCAATTACAA 58.844 40.909 0.00 0.00 45.12 2.41
2672 2715 2.832733 AGTTTACCCTGTCTAGGTGCTC 59.167 50.000 0.00 0.00 42.96 4.26
2684 2727 6.239800 CCAGTTACAGTCCTTAAGTTTACCCT 60.240 42.308 0.97 0.00 0.00 4.34
3378 3421 7.573710 ACTCAATATGGCTTATCAAGGTACAA 58.426 34.615 0.00 0.00 0.00 2.41
3488 3531 9.875691 ATTAAAATTATGGCCTGAGAAAAACTC 57.124 29.630 3.32 0.00 45.11 3.01
3544 3587 5.049680 CGTTTAAGTGAAGAGGCTAAAAGCA 60.050 40.000 0.78 0.00 44.75 3.91
3993 4125 2.749076 GCCACTATCAGCACATGAACAA 59.251 45.455 0.00 0.00 42.53 2.83
4052 4184 1.674441 CCATAGTGCATGCCAGACAAG 59.326 52.381 16.68 1.10 32.84 3.16
4288 4420 6.611613 ACAATTGAGGATAGAAGTCAGACA 57.388 37.500 13.59 0.00 0.00 3.41
4314 4446 4.098960 CCAACTAGCTGAAAATGGCATCAT 59.901 41.667 0.00 0.00 34.56 2.45
4315 4447 3.444742 CCAACTAGCTGAAAATGGCATCA 59.555 43.478 0.00 0.00 0.00 3.07
4608 4740 5.163550 GCATACCTTGGTCAAAGATAAACCC 60.164 44.000 0.00 0.00 38.24 4.11
4677 4809 3.575687 AGGCAATCAACTTCTTTTGGAGG 59.424 43.478 0.00 0.00 0.00 4.30
4793 4926 7.465900 AGAATAGAAATGGAAGGTATTGGGA 57.534 36.000 0.00 0.00 0.00 4.37
4955 5088 6.071896 GGGAATAGAAAAGGACCAGACAAAAG 60.072 42.308 0.00 0.00 0.00 2.27
5003 5136 9.883142 TCAAATGGAAAAAGTTAACTCAACAAT 57.117 25.926 8.95 0.00 39.81 2.71
5045 5178 5.697473 TCTGTATTTTTGGACGCATCAAA 57.303 34.783 0.00 0.00 32.96 2.69
5051 5184 4.855531 ACAACTTCTGTATTTTTGGACGC 58.144 39.130 0.00 0.00 36.10 5.19
5133 5266 4.253685 CAAGTAACAGATCGATGGGTGTT 58.746 43.478 17.10 17.10 37.00 3.32
5251 5384 6.293244 CCAGTTAAAGTTGGACTTCCGTTAAG 60.293 42.308 0.00 0.00 37.47 1.85
5361 5495 4.268644 CCGCACAGATCTTACAACATACAG 59.731 45.833 0.00 0.00 0.00 2.74
5380 5514 1.000618 TCAATGCATTTTGCTTCCGCA 59.999 42.857 9.83 0.00 45.31 5.69
5383 5517 7.380536 TGGATATATCAATGCATTTTGCTTCC 58.619 34.615 9.83 12.16 45.31 3.46
5435 5569 1.703411 TGCAGGCAAGCCTTAAACTT 58.297 45.000 11.67 0.00 45.70 2.66
5450 5585 2.885266 AGCTGCCTATTCATGAATGCAG 59.115 45.455 34.74 34.74 44.22 4.41
5496 5631 5.178797 ACATCAACACTACTTGTATCCTGC 58.821 41.667 0.00 0.00 37.51 4.85
5719 5854 3.409026 AGGAGAGGTCACAATCAACAC 57.591 47.619 0.00 0.00 0.00 3.32
5908 6043 6.036083 CCTTTCCATAGATGTTGTTAGTGACG 59.964 42.308 0.00 0.00 0.00 4.35
5914 6049 8.792633 CACTTTTCCTTTCCATAGATGTTGTTA 58.207 33.333 0.00 0.00 0.00 2.41
6338 6474 1.082690 GCTACAAGCCTCAGAACAGC 58.917 55.000 0.00 0.00 34.48 4.40
6401 6537 7.947332 TCCTACACTGCTATATCTCTCTCATTT 59.053 37.037 0.00 0.00 0.00 2.32
6465 6601 1.727857 CGACTTACACATTTTGCCGCC 60.728 52.381 0.00 0.00 0.00 6.13
6468 6604 1.539827 AGGCGACTTACACATTTTGCC 59.460 47.619 0.00 0.00 37.44 4.52
6506 6642 4.096382 CCTACATTTGATGTACCCAGCAAC 59.904 45.833 0.00 0.00 45.92 4.17
6635 6772 3.551454 GCAACATTCATTCATCCGGATGG 60.551 47.826 37.57 24.66 39.24 3.51
6883 7042 4.749245 ACACCGTTTCACATTCAAGATC 57.251 40.909 0.00 0.00 0.00 2.75
6922 7081 9.449719 GAAACTTATTTTGGGATGAAGAGAGTA 57.550 33.333 0.00 0.00 0.00 2.59
6923 7082 8.166726 AGAAACTTATTTTGGGATGAAGAGAGT 58.833 33.333 0.00 0.00 0.00 3.24
6924 7083 8.572855 AGAAACTTATTTTGGGATGAAGAGAG 57.427 34.615 0.00 0.00 0.00 3.20
6925 7084 8.163408 TGAGAAACTTATTTTGGGATGAAGAGA 58.837 33.333 0.00 0.00 0.00 3.10
6926 7085 8.340618 TGAGAAACTTATTTTGGGATGAAGAG 57.659 34.615 0.00 0.00 0.00 2.85
6927 7086 8.576442 GTTGAGAAACTTATTTTGGGATGAAGA 58.424 33.333 0.00 0.00 0.00 2.87
6928 7087 8.579863 AGTTGAGAAACTTATTTTGGGATGAAG 58.420 33.333 0.00 0.00 0.00 3.02
6929 7088 8.477419 AGTTGAGAAACTTATTTTGGGATGAA 57.523 30.769 0.00 0.00 0.00 2.57
6930 7089 8.477419 AAGTTGAGAAACTTATTTTGGGATGA 57.523 30.769 2.11 0.00 40.89 2.92
6931 7090 8.981647 CAAAGTTGAGAAACTTATTTTGGGATG 58.018 33.333 4.40 0.00 41.76 3.51
6932 7091 8.704668 ACAAAGTTGAGAAACTTATTTTGGGAT 58.295 29.630 4.40 0.00 41.76 3.85
6933 7092 8.073467 ACAAAGTTGAGAAACTTATTTTGGGA 57.927 30.769 4.40 0.00 41.76 4.37
6934 7093 9.981114 ATACAAAGTTGAGAAACTTATTTTGGG 57.019 29.630 4.40 0.00 41.76 4.12
6947 7106 9.332502 TGTGCTAAAGTTAATACAAAGTTGAGA 57.667 29.630 0.00 0.00 0.00 3.27
6948 7107 9.944663 TTGTGCTAAAGTTAATACAAAGTTGAG 57.055 29.630 0.00 0.00 0.00 3.02
6978 7137 8.842280 CAAAATAAGTGTCTTAACCTTGGTACA 58.158 33.333 0.00 0.00 0.00 2.90
6979 7138 9.059260 TCAAAATAAGTGTCTTAACCTTGGTAC 57.941 33.333 0.00 0.00 0.00 3.34
6980 7139 9.280174 CTCAAAATAAGTGTCTTAACCTTGGTA 57.720 33.333 0.00 0.00 0.00 3.25
6981 7140 7.996644 TCTCAAAATAAGTGTCTTAACCTTGGT 59.003 33.333 0.00 0.00 0.00 3.67
6982 7141 8.391075 TCTCAAAATAAGTGTCTTAACCTTGG 57.609 34.615 0.00 0.00 0.00 3.61
6989 7148 9.488762 TCCCTCTATCTCAAAATAAGTGTCTTA 57.511 33.333 0.00 0.00 0.00 2.10
6990 7149 8.380742 TCCCTCTATCTCAAAATAAGTGTCTT 57.619 34.615 0.00 0.00 0.00 3.01
6991 7150 7.621683 ACTCCCTCTATCTCAAAATAAGTGTCT 59.378 37.037 0.00 0.00 0.00 3.41
6992 7151 7.787028 ACTCCCTCTATCTCAAAATAAGTGTC 58.213 38.462 0.00 0.00 0.00 3.67
6993 7152 7.741554 ACTCCCTCTATCTCAAAATAAGTGT 57.258 36.000 0.00 0.00 0.00 3.55
7045 7204 9.693739 TCTTGTTATCCCATGCTATTAAAAGAA 57.306 29.630 0.00 0.00 0.00 2.52
7046 7205 9.866655 ATCTTGTTATCCCATGCTATTAAAAGA 57.133 29.630 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.