Multiple sequence alignment - TraesCS4D01G178500

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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 TraesCS4D01G178500 chr4D 100.000 8177 0 0 1 8177 309918249 309926425 0.000000e+00 15101.0
1 TraesCS4D01G178500 chr4D 94.975 816 39 2 1 816 490121065 490121878 0.000000e+00 1279.0
2 TraesCS4D01G178500 chr4A 95.148 7296 200 53 931 8177 164718564 164711374 0.000000e+00 11370.0
3 TraesCS4D01G178500 chr4B 96.574 6129 108 25 816 6910 387376644 387382704 0.000000e+00 10061.0
4 TraesCS4D01G178500 chr4B 98.468 457 5 1 6937 7391 387382959 387383415 0.000000e+00 804.0
5 TraesCS4D01G178500 chr4B 91.822 538 27 8 7380 7916 387386859 387387380 0.000000e+00 734.0
6 TraesCS4D01G178500 chr4B 92.045 176 9 3 8003 8177 387387695 387387866 8.200000e-60 243.0
7 TraesCS4D01G178500 chr4B 94.203 69 3 1 7900 7968 387387393 387387460 4.040000e-18 104.0
8 TraesCS4D01G178500 chr5D 93.750 816 40 7 1 815 449270182 449270987 0.000000e+00 1214.0
9 TraesCS4D01G178500 chr5D 90.542 719 60 8 22 736 410294175 410293461 0.000000e+00 944.0
10 TraesCS4D01G178500 chr5D 84.591 318 42 6 4889 5202 439665661 439665975 7.970000e-80 309.0
11 TraesCS4D01G178500 chr2D 95.690 696 28 2 1 696 566582370 566583063 0.000000e+00 1118.0
12 TraesCS4D01G178500 chr6B 89.567 786 73 7 22 805 662085043 662085821 0.000000e+00 989.0
13 TraesCS4D01G178500 chr3A 88.986 799 75 11 22 815 101940417 101941207 0.000000e+00 976.0
14 TraesCS4D01G178500 chr3A 88.596 798 80 9 22 815 7892359 7893149 0.000000e+00 959.0
15 TraesCS4D01G178500 chr3B 88.510 792 82 5 25 815 812412931 812412148 0.000000e+00 950.0
16 TraesCS4D01G178500 chr3B 80.165 242 38 10 4890 5126 160369413 160369649 1.090000e-38 172.0
17 TraesCS4D01G178500 chr3B 82.927 123 14 3 5223 5338 333469003 333469125 4.040000e-18 104.0
18 TraesCS4D01G178500 chr6A 88.080 797 80 13 25 816 445286937 445286151 0.000000e+00 931.0
19 TraesCS4D01G178500 chr5B 84.591 318 40 8 4889 5202 534338254 534338566 2.870000e-79 307.0
20 TraesCS4D01G178500 chr5B 82.105 190 23 9 4913 5099 550177068 550177249 1.420000e-32 152.0
21 TraesCS4D01G178500 chr5A 83.165 297 32 13 4914 5205 555557335 555557618 1.050000e-63 255.0
22 TraesCS4D01G178500 chr5A 82.979 188 18 10 4913 5098 569453241 569453416 3.060000e-34 158.0
23 TraesCS4D01G178500 chr5A 96.000 50 2 0 5265 5314 493354773 493354822 1.890000e-11 82.4
24 TraesCS4D01G178500 chrUn 80.365 219 33 9 4910 5126 90130059 90130269 3.060000e-34 158.0
25 TraesCS4D01G178500 chrUn 83.158 95 11 2 5223 5313 201313944 201314037 1.890000e-11 82.4
26 TraesCS4D01G178500 chr7A 83.158 95 11 2 5223 5313 35271577 35271670 1.890000e-11 82.4
27 TraesCS4D01G178500 chr7A 83.158 95 11 2 5223 5313 35300222 35300315 1.890000e-11 82.4


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 TraesCS4D01G178500 chr4D 309918249 309926425 8176 False 15101.0 15101 100.0000 1 8177 1 chr4D.!!$F1 8176
1 TraesCS4D01G178500 chr4D 490121065 490121878 813 False 1279.0 1279 94.9750 1 816 1 chr4D.!!$F2 815
2 TraesCS4D01G178500 chr4A 164711374 164718564 7190 True 11370.0 11370 95.1480 931 8177 1 chr4A.!!$R1 7246
3 TraesCS4D01G178500 chr4B 387376644 387387866 11222 False 2389.2 10061 94.6224 816 8177 5 chr4B.!!$F1 7361
4 TraesCS4D01G178500 chr5D 449270182 449270987 805 False 1214.0 1214 93.7500 1 815 1 chr5D.!!$F2 814
5 TraesCS4D01G178500 chr5D 410293461 410294175 714 True 944.0 944 90.5420 22 736 1 chr5D.!!$R1 714
6 TraesCS4D01G178500 chr2D 566582370 566583063 693 False 1118.0 1118 95.6900 1 696 1 chr2D.!!$F1 695
7 TraesCS4D01G178500 chr6B 662085043 662085821 778 False 989.0 989 89.5670 22 805 1 chr6B.!!$F1 783
8 TraesCS4D01G178500 chr3A 101940417 101941207 790 False 976.0 976 88.9860 22 815 1 chr3A.!!$F2 793
9 TraesCS4D01G178500 chr3A 7892359 7893149 790 False 959.0 959 88.5960 22 815 1 chr3A.!!$F1 793
10 TraesCS4D01G178500 chr3B 812412148 812412931 783 True 950.0 950 88.5100 25 815 1 chr3B.!!$R1 790
11 TraesCS4D01G178500 chr6A 445286151 445286937 786 True 931.0 931 88.0800 25 816 1 chr6A.!!$R1 791

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
91 92 1.199789 GCTTTCGGTGCACATGAATGA 59.800 47.619 26.85 14.22 0.00 2.57 F
879 891 1.299468 GCGTGCGTCATCCTCTAGG 60.299 63.158 0.00 0.00 0.00 3.02 F
1330 1350 0.109132 GATTGCTCTGGGCGGTTTTG 60.109 55.000 0.00 0.00 45.43 2.44 F
1512 1532 0.110823 CGTTTTCTTCCTCCGCGTTG 60.111 55.000 4.92 0.00 0.00 4.10 F
1964 1998 1.154225 CGAGGAATTTGCCGTGTGC 60.154 57.895 0.00 0.00 41.77 4.57 F
4001 4037 2.983402 CAACACTGCAGAACTCATGG 57.017 50.000 23.35 1.59 0.00 3.66 F
4709 4747 2.095059 GGCAGCATCGAAAGTTGATGTT 60.095 45.455 8.82 0.00 45.95 2.71 F
6777 6822 0.837272 TAAGGAGGAGGCAAATCGGG 59.163 55.000 0.00 0.00 0.00 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1330 1350 1.022451 TTGGCCTAATCAACGCGGAC 61.022 55.000 12.47 0.00 0.00 4.79 R
2538 2574 2.414293 GCACTGCAGATCAAAGCTCTTG 60.414 50.000 23.35 4.33 0.00 3.02 R
2740 2776 3.321968 TGTGCCTCAGCGACTGAATATAT 59.678 43.478 10.12 0.00 40.18 0.86 R
3765 3801 4.536090 TCATGGATGTAGACAGGTCCTTTT 59.464 41.667 0.00 0.00 0.00 2.27 R
4274 4310 8.210946 ACGGAAGATCATGGAAGAAATAACATA 58.789 33.333 0.00 0.00 0.00 2.29 R
5221 5260 3.149196 GCAAGTCCTCCACTTCATCAAA 58.851 45.455 0.00 0.00 44.14 2.69 R
6841 6886 3.007506 TGAACGGATGTACACAATGGACT 59.992 43.478 0.00 0.00 30.83 3.85 R
7954 11721 1.227823 CCAGCCGTGTGGAAGTTGA 60.228 57.895 0.00 0.00 40.44 3.18 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
91 92 1.199789 GCTTTCGGTGCACATGAATGA 59.800 47.619 26.85 14.22 0.00 2.57
203 208 7.126879 CACCCTAAACCCTAACCTAATCTACTT 59.873 40.741 0.00 0.00 0.00 2.24
279 285 1.965643 AGCATTCAACAAGCACACCAT 59.034 42.857 0.00 0.00 0.00 3.55
711 723 1.412343 GTGGCTGTGGACCAAAACATT 59.588 47.619 0.00 0.00 39.39 2.71
719 731 5.882040 TGTGGACCAAAACATTACATAGGA 58.118 37.500 0.00 0.00 0.00 2.94
736 748 6.583562 ACATAGGATGTTAAGTTGTAGGAGC 58.416 40.000 0.00 0.00 41.63 4.70
742 754 3.649023 TGTTAAGTTGTAGGAGCCCTCAA 59.351 43.478 0.00 0.87 34.61 3.02
761 773 9.377312 GCCCTCAATAATATTTTGCAAGTTTTA 57.623 29.630 0.00 0.00 0.00 1.52
816 828 3.985553 TCTGGGGTGCTATTACCTCTA 57.014 47.619 0.00 0.00 41.99 2.43
817 829 3.845860 TCTGGGGTGCTATTACCTCTAG 58.154 50.000 0.00 0.00 41.99 2.43
818 830 3.206866 TCTGGGGTGCTATTACCTCTAGT 59.793 47.826 0.00 0.00 41.99 2.57
819 831 4.417854 TCTGGGGTGCTATTACCTCTAGTA 59.582 45.833 0.00 0.00 41.99 1.82
820 832 4.477249 TGGGGTGCTATTACCTCTAGTAC 58.523 47.826 0.00 0.00 41.99 2.73
836 848 7.040271 ACCTCTAGTACAAAAGAGACTCAACTC 60.040 40.741 17.00 0.00 41.51 3.01
853 865 2.018670 CGCGAGCGTGAAATGACG 59.981 61.111 0.00 0.00 42.42 4.35
879 891 1.299468 GCGTGCGTCATCCTCTAGG 60.299 63.158 0.00 0.00 0.00 3.02
888 900 1.845791 TCATCCTCTAGGGCATTGCAA 59.154 47.619 11.39 0.00 35.41 4.08
889 901 2.444388 TCATCCTCTAGGGCATTGCAAT 59.556 45.455 5.99 5.99 35.41 3.56
890 902 2.645838 TCCTCTAGGGCATTGCAATC 57.354 50.000 9.53 4.70 35.41 2.67
891 903 2.130193 TCCTCTAGGGCATTGCAATCT 58.870 47.619 9.53 6.66 35.41 2.40
892 904 2.511218 TCCTCTAGGGCATTGCAATCTT 59.489 45.455 9.53 0.00 35.41 2.40
893 905 3.053395 TCCTCTAGGGCATTGCAATCTTT 60.053 43.478 9.53 0.00 35.41 2.52
895 907 4.205587 CTCTAGGGCATTGCAATCTTTCT 58.794 43.478 9.53 7.54 0.00 2.52
897 909 3.881937 AGGGCATTGCAATCTTTCTTC 57.118 42.857 9.53 0.00 0.00 2.87
898 910 2.165030 AGGGCATTGCAATCTTTCTTCG 59.835 45.455 9.53 0.00 0.00 3.79
899 911 2.164219 GGGCATTGCAATCTTTCTTCGA 59.836 45.455 9.53 0.00 0.00 3.71
900 912 3.174375 GGCATTGCAATCTTTCTTCGAC 58.826 45.455 9.53 0.00 0.00 4.20
901 913 3.366273 GGCATTGCAATCTTTCTTCGACA 60.366 43.478 9.53 0.00 0.00 4.35
902 914 4.229096 GCATTGCAATCTTTCTTCGACAA 58.771 39.130 9.53 0.00 0.00 3.18
903 915 4.681025 GCATTGCAATCTTTCTTCGACAAA 59.319 37.500 9.53 0.00 0.00 2.83
904 916 5.175491 GCATTGCAATCTTTCTTCGACAAAA 59.825 36.000 9.53 0.00 0.00 2.44
905 917 6.292274 GCATTGCAATCTTTCTTCGACAAAAA 60.292 34.615 9.53 0.00 0.00 1.94
906 918 6.567769 TTGCAATCTTTCTTCGACAAAAAC 57.432 33.333 0.00 0.00 0.00 2.43
907 919 5.645624 TGCAATCTTTCTTCGACAAAAACA 58.354 33.333 0.00 0.00 0.00 2.83
908 920 5.514914 TGCAATCTTTCTTCGACAAAAACAC 59.485 36.000 0.00 0.00 0.00 3.32
928 940 2.476619 ACAGAGAAAACTCGCGATTGTG 59.523 45.455 10.36 0.00 0.00 3.33
929 941 2.476619 CAGAGAAAACTCGCGATTGTGT 59.523 45.455 10.36 0.00 0.00 3.72
1003 1016 1.606601 CCTCCCTCGTGGACAGTGA 60.607 63.158 4.76 0.00 38.61 3.41
1011 1024 1.373497 GTGGACAGTGACCAGAGCG 60.373 63.158 14.89 0.00 38.14 5.03
1114 1127 2.011947 CATCTTTCTCATCTGCCGCAA 58.988 47.619 0.00 0.00 0.00 4.85
1176 1196 1.575304 AGCTTCTCTCCTCCTCTCCAT 59.425 52.381 0.00 0.00 0.00 3.41
1220 1240 4.463879 CCTCCTCCACAGCGCCAG 62.464 72.222 2.29 0.00 0.00 4.85
1300 1320 2.507471 AGCCAGGTAATTCTCTTCCCTG 59.493 50.000 0.00 0.00 41.89 4.45
1329 1349 1.250840 GGATTGCTCTGGGCGGTTTT 61.251 55.000 0.00 0.00 45.43 2.43
1330 1350 0.109132 GATTGCTCTGGGCGGTTTTG 60.109 55.000 0.00 0.00 45.43 2.44
1466 1486 2.469826 GGGGTTTCTCTTTTGTTTGCG 58.530 47.619 0.00 0.00 0.00 4.85
1473 1493 6.453265 GGTTTCTCTTTTGTTTGCGTTGTTAC 60.453 38.462 0.00 0.00 0.00 2.50
1512 1532 0.110823 CGTTTTCTTCCTCCGCGTTG 60.111 55.000 4.92 0.00 0.00 4.10
1519 1539 3.345808 CCTCCGCGTTGTGGTGTG 61.346 66.667 4.92 0.00 34.40 3.82
1520 1540 4.012895 CTCCGCGTTGTGGTGTGC 62.013 66.667 4.92 0.00 34.40 4.57
1919 1953 2.421424 GTGGCTTGATACTTCTGCTTGG 59.579 50.000 0.00 0.00 0.00 3.61
1958 1992 3.682372 GAGACAATCGAGGAATTTGCC 57.318 47.619 0.00 0.00 0.00 4.52
1964 1998 1.154225 CGAGGAATTTGCCGTGTGC 60.154 57.895 0.00 0.00 41.77 4.57
2127 2161 4.469227 AGTGTTCTAGTTGATGCAGGATCT 59.531 41.667 3.27 0.00 31.55 2.75
2248 2282 3.133003 GGACAGATTTGAGCAGGCTAGTA 59.867 47.826 0.00 0.00 0.00 1.82
2444 2480 6.262273 TCTTGTCAGCTAAGTAAACTTTTGGG 59.738 38.462 0.00 0.00 37.40 4.12
2457 2493 9.628500 AGTAAACTTTTGGGTATTATCTGATCC 57.372 33.333 0.00 0.00 0.00 3.36
2740 2776 3.663176 GCAGCCGCTCACTTTGCA 61.663 61.111 0.00 0.00 34.99 4.08
3221 3257 3.260632 TGCTGATGATATTAGGCGCCTTA 59.739 43.478 37.74 28.19 0.00 2.69
3765 3801 4.561500 TTCGTGATGTTAGAAATGGGGA 57.438 40.909 0.00 0.00 0.00 4.81
4001 4037 2.983402 CAACACTGCAGAACTCATGG 57.017 50.000 23.35 1.59 0.00 3.66
4074 4110 9.004717 GCTGTTCCTTCTCTTTCTAGTTTAATT 57.995 33.333 0.00 0.00 0.00 1.40
4683 4721 6.333416 CACTCTTCGTCATCAAGAAATCCTA 58.667 40.000 0.00 0.00 29.36 2.94
4709 4747 2.095059 GGCAGCATCGAAAGTTGATGTT 60.095 45.455 8.82 0.00 45.95 2.71
4848 4886 2.956333 GCTTATTTGGCCGGTCCTTTAT 59.044 45.455 2.12 3.35 35.26 1.40
5427 5466 4.036734 ACGCAAATTGCACTGGGATTATAG 59.963 41.667 18.65 0.00 45.36 1.31
5556 5595 4.763279 TGATATGCCCACTTGAATATGCAG 59.237 41.667 0.00 0.00 31.53 4.41
5685 5728 4.706962 ACACCTCCATATTTTCTTGCCTTC 59.293 41.667 0.00 0.00 0.00 3.46
6059 6104 7.230108 TCAATAGGCATTTTCTGGAATGATCTC 59.770 37.037 2.04 0.00 38.93 2.75
6567 6612 5.006746 GGTTCAAGGTCTACATTCGCAATAG 59.993 44.000 0.00 0.00 0.00 1.73
6613 6658 4.104383 TGAGGGGAATCCATAGAAATGC 57.896 45.455 0.09 0.00 38.24 3.56
6777 6822 0.837272 TAAGGAGGAGGCAAATCGGG 59.163 55.000 0.00 0.00 0.00 5.14
6931 6976 0.178958 ATAGTCTAGGGGGACAGGCG 60.179 60.000 0.00 0.00 38.57 5.52
7211 7486 8.097791 TGTTTAGGTCTTATTTAGGCTGGTAT 57.902 34.615 0.00 0.00 0.00 2.73
7293 7572 8.140112 AGAGTAAACTGGATCAAACTCACTAT 57.860 34.615 3.12 0.00 36.63 2.12
7466 11201 2.673775 TGGGATGAAGCCAAGTTTGA 57.326 45.000 0.00 0.00 0.00 2.69
7487 11222 3.350219 TCATCTTCAACCCAAGGCTAC 57.650 47.619 0.00 0.00 0.00 3.58
7513 11248 1.614583 GCACTTCTCCCCTTTTCTCCC 60.615 57.143 0.00 0.00 0.00 4.30
7529 11264 2.125106 CCGGAGTAGCAGGTTGCC 60.125 66.667 0.00 0.00 46.52 4.52
7628 11364 7.537596 AAAATAGTTCCCAAATCATCACACA 57.462 32.000 0.00 0.00 0.00 3.72
7671 11407 5.385509 AACACATTTGATTTCGTAAGGGG 57.614 39.130 0.00 0.00 38.47 4.79
7689 11425 2.485479 GGGGCATGTAGTGTAGACCATG 60.485 54.545 5.28 5.28 38.14 3.66
7711 11447 6.560253 TGGTGAAGCAGAGTAGAATTTTTC 57.440 37.500 0.00 0.00 0.00 2.29
7851 11588 1.159713 TGGTGCACAAACTCAGCTCG 61.160 55.000 20.43 0.00 0.00 5.03
7954 11721 1.994885 ATGAACCCCGGCGGAATGAT 61.995 55.000 30.79 10.16 34.64 2.45
7971 11738 0.798776 GATCAACTTCCACACGGCTG 59.201 55.000 0.00 0.00 0.00 4.85
7987 11754 2.041153 CTGGGGTTTGCACAAGGAC 58.959 57.895 0.00 0.00 0.00 3.85
8026 11993 1.835895 TAACAAGGGGAAGGGACCAA 58.164 50.000 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 92 1.752833 GAGTTGTGGGTCGGTCCTT 59.247 57.895 0.00 0.00 36.25 3.36
203 208 1.228737 GCCTAGTGGGTTTTGGCCA 60.229 57.895 0.00 0.00 37.81 5.36
300 306 3.743636 TCGTCCGCATCAGTCGCA 61.744 61.111 0.00 0.00 0.00 5.10
302 308 2.944557 CGTCGTCCGCATCAGTCG 60.945 66.667 0.00 0.00 0.00 4.18
304 310 2.178521 GTCGTCGTCCGCATCAGT 59.821 61.111 0.00 0.00 36.19 3.41
669 681 2.974698 AGCGTGACAAGTGGCAGC 60.975 61.111 0.00 0.00 30.83 5.25
711 723 7.201974 GGCTCCTACAACTTAACATCCTATGTA 60.202 40.741 0.00 0.00 44.07 2.29
719 731 3.844211 TGAGGGCTCCTACAACTTAACAT 59.156 43.478 0.00 0.00 31.76 2.71
761 773 8.565896 TTGCACAGAATATGATGTTTTAGTCT 57.434 30.769 0.00 0.00 0.00 3.24
816 828 4.299978 GCGAGTTGAGTCTCTTTTGTACT 58.700 43.478 0.65 0.00 32.83 2.73
817 829 3.119792 CGCGAGTTGAGTCTCTTTTGTAC 59.880 47.826 0.00 0.00 32.83 2.90
818 830 3.004002 TCGCGAGTTGAGTCTCTTTTGTA 59.996 43.478 3.71 0.00 32.83 2.41
819 831 2.128035 CGCGAGTTGAGTCTCTTTTGT 58.872 47.619 0.00 0.00 32.83 2.83
820 832 2.394708 TCGCGAGTTGAGTCTCTTTTG 58.605 47.619 3.71 0.00 32.83 2.44
836 848 2.018670 CGTCATTTCACGCTCGCG 59.981 61.111 10.06 10.06 46.03 5.87
853 865 3.295228 ATGACGCACGCTTTGTCGC 62.295 57.895 0.00 0.00 35.40 5.19
863 875 1.068250 GCCCTAGAGGATGACGCAC 59.932 63.158 0.00 0.00 38.24 5.34
879 891 3.174375 GTCGAAGAAAGATTGCAATGCC 58.826 45.455 18.59 2.99 39.69 4.40
888 900 6.538742 TCTCTGTGTTTTTGTCGAAGAAAGAT 59.461 34.615 0.00 0.00 39.69 2.40
889 901 5.872617 TCTCTGTGTTTTTGTCGAAGAAAGA 59.127 36.000 0.00 0.00 39.69 2.52
890 902 6.106877 TCTCTGTGTTTTTGTCGAAGAAAG 57.893 37.500 0.00 0.00 39.69 2.62
891 903 6.489127 TTCTCTGTGTTTTTGTCGAAGAAA 57.511 33.333 0.00 0.00 39.69 2.52
892 904 6.489127 TTTCTCTGTGTTTTTGTCGAAGAA 57.511 33.333 0.00 0.00 39.69 2.52
893 905 6.148811 AGTTTTCTCTGTGTTTTTGTCGAAGA 59.851 34.615 0.00 0.00 0.00 2.87
895 907 6.249035 AGTTTTCTCTGTGTTTTTGTCGAA 57.751 33.333 0.00 0.00 0.00 3.71
897 909 4.723862 CGAGTTTTCTCTGTGTTTTTGTCG 59.276 41.667 0.00 0.00 44.16 4.35
898 910 4.495828 GCGAGTTTTCTCTGTGTTTTTGTC 59.504 41.667 0.00 0.00 44.16 3.18
899 911 4.412207 GCGAGTTTTCTCTGTGTTTTTGT 58.588 39.130 0.00 0.00 44.16 2.83
900 912 3.478516 CGCGAGTTTTCTCTGTGTTTTTG 59.521 43.478 0.00 0.00 44.16 2.44
901 913 3.372822 TCGCGAGTTTTCTCTGTGTTTTT 59.627 39.130 3.71 0.00 44.16 1.94
902 914 2.933906 TCGCGAGTTTTCTCTGTGTTTT 59.066 40.909 3.71 0.00 44.16 2.43
903 915 2.546778 TCGCGAGTTTTCTCTGTGTTT 58.453 42.857 3.71 0.00 44.16 2.83
904 916 2.218953 TCGCGAGTTTTCTCTGTGTT 57.781 45.000 3.71 0.00 44.16 3.32
905 917 2.440539 ATCGCGAGTTTTCTCTGTGT 57.559 45.000 16.66 0.00 44.16 3.72
906 918 2.476619 ACAATCGCGAGTTTTCTCTGTG 59.523 45.455 16.66 0.00 44.16 3.66
907 919 2.476619 CACAATCGCGAGTTTTCTCTGT 59.523 45.455 16.66 0.61 44.16 3.41
908 920 2.476619 ACACAATCGCGAGTTTTCTCTG 59.523 45.455 16.66 0.00 44.16 3.35
928 940 6.428159 TGGCATTTGTTCTCTTCTCTTCTTAC 59.572 38.462 0.00 0.00 0.00 2.34
929 941 6.533730 TGGCATTTGTTCTCTTCTCTTCTTA 58.466 36.000 0.00 0.00 0.00 2.10
1003 1016 3.141488 CCGTAGCCTCGCTCTGGT 61.141 66.667 0.00 0.00 40.44 4.00
1032 1045 1.153881 GGAACCCGACGTGTAGAGC 60.154 63.158 0.00 0.00 0.00 4.09
1176 1196 2.473891 TAGCTGGTCGTCGAGTGGGA 62.474 60.000 0.00 0.00 0.00 4.37
1300 1320 3.424105 AGCAATCCAGGGGAGGGC 61.424 66.667 3.52 3.52 34.05 5.19
1329 1349 1.448893 GGCCTAATCAACGCGGACA 60.449 57.895 12.47 0.00 0.00 4.02
1330 1350 1.022451 TTGGCCTAATCAACGCGGAC 61.022 55.000 12.47 0.00 0.00 4.79
1466 1486 2.322161 TCTTGAGCGCGTAGTAACAAC 58.678 47.619 8.43 0.00 0.00 3.32
1473 1493 1.849219 GAACTGATCTTGAGCGCGTAG 59.151 52.381 8.43 0.29 0.00 3.51
1512 1532 3.544684 TCCATTGATATCAGCACACCAC 58.455 45.455 5.39 0.00 0.00 4.16
1519 1539 5.008415 CCACAAGTTCTCCATTGATATCAGC 59.992 44.000 5.39 0.00 0.00 4.26
1520 1540 6.351711 TCCACAAGTTCTCCATTGATATCAG 58.648 40.000 5.39 0.00 0.00 2.90
1919 1953 5.121768 TGTCTCGCCAAAAAGCTTATAGAAC 59.878 40.000 0.00 0.00 0.00 3.01
2094 2128 4.591498 TCAACTAGAACACTGCTTCCCTAA 59.409 41.667 0.00 0.00 0.00 2.69
2127 2161 7.296628 ACAAAACCAGCAATTAACCTCATAA 57.703 32.000 0.00 0.00 0.00 1.90
2248 2282 5.536161 AGCACACAAATTCACTTCCACTAAT 59.464 36.000 0.00 0.00 0.00 1.73
2397 2433 4.467198 AAGATAACCCGACGTTTCATCT 57.533 40.909 0.00 0.00 35.79 2.90
2538 2574 2.414293 GCACTGCAGATCAAAGCTCTTG 60.414 50.000 23.35 4.33 0.00 3.02
2740 2776 3.321968 TGTGCCTCAGCGACTGAATATAT 59.678 43.478 10.12 0.00 40.18 0.86
3765 3801 4.536090 TCATGGATGTAGACAGGTCCTTTT 59.464 41.667 0.00 0.00 0.00 2.27
4274 4310 8.210946 ACGGAAGATCATGGAAGAAATAACATA 58.789 33.333 0.00 0.00 0.00 2.29
4683 4721 0.323725 ACTTTCGATGCTGCCCCAAT 60.324 50.000 0.00 0.00 0.00 3.16
4709 4747 6.566079 AAGATATTTCCAGTGAGACCATCA 57.434 37.500 0.00 0.00 34.79 3.07
4864 4902 6.575162 AACAGTGGCTAAAACAGATTAAGG 57.425 37.500 0.00 0.00 0.00 2.69
5099 5137 6.488006 ACATGCAAGTCCTCCATATAATCAAC 59.512 38.462 0.00 0.00 0.00 3.18
5221 5260 3.149196 GCAAGTCCTCCACTTCATCAAA 58.851 45.455 0.00 0.00 44.14 2.69
5427 5466 7.025963 CCAAGCTTGAGATAAAAGAACATCAC 58.974 38.462 28.05 0.00 0.00 3.06
5685 5728 7.693969 AGACATGGAGAGGTCATTTAAAAAG 57.306 36.000 0.00 0.00 35.24 2.27
6059 6104 9.474920 TTTTAACCAAGAGCAAATGATAAACTG 57.525 29.630 0.00 0.00 0.00 3.16
6567 6612 4.464008 TCATCATTCAACCCTCCATTAGC 58.536 43.478 0.00 0.00 0.00 3.09
6777 6822 5.008613 TGTTTCACTCCAGAAATTAGTGCAC 59.991 40.000 9.40 9.40 40.34 4.57
6841 6886 3.007506 TGAACGGATGTACACAATGGACT 59.992 43.478 0.00 0.00 30.83 3.85
6857 6902 3.489785 GTGCCTATTAGTTCGATGAACGG 59.510 47.826 4.21 1.10 45.96 4.44
7088 7363 1.321474 CACAGGTGCCAACATGAAGT 58.679 50.000 0.00 0.00 40.57 3.01
7293 7572 5.845391 ATTGGTTTCTTTCCGTTCTTTCA 57.155 34.783 0.00 0.00 0.00 2.69
7466 11201 3.682718 CGTAGCCTTGGGTTGAAGATGAT 60.683 47.826 0.00 0.00 0.00 2.45
7487 11222 0.035458 AAGGGGAGAAGTGCTGAACG 59.965 55.000 0.00 0.00 0.00 3.95
7529 11264 5.419542 TGTCCATTCAAAGATAACTCGAGG 58.580 41.667 18.41 0.00 0.00 4.63
7671 11407 3.118775 TCACCATGGTCTACACTACATGC 60.119 47.826 16.53 0.00 39.39 4.06
7689 11425 6.809630 AGAAAAATTCTACTCTGCTTCACC 57.190 37.500 0.00 0.00 38.49 4.02
7818 11554 5.781210 TGTGCACCATTTATTGTTTCAGA 57.219 34.783 15.69 0.00 0.00 3.27
7821 11557 6.478344 TGAGTTTGTGCACCATTTATTGTTTC 59.522 34.615 15.69 0.00 0.00 2.78
7851 11588 7.863877 ACCGAAATATTGAAACTGTTTTGTACC 59.136 33.333 7.28 0.00 0.00 3.34
7954 11721 1.227823 CCAGCCGTGTGGAAGTTGA 60.228 57.895 0.00 0.00 40.44 3.18
7971 11738 2.041153 CAGTCCTTGTGCAAACCCC 58.959 57.895 0.00 0.00 0.00 4.95
8021 11988 3.381590 AGCAGTTTCAGGACTTTTTGGTC 59.618 43.478 0.00 0.00 35.66 4.02
8026 11993 2.378038 TGCAGCAGTTTCAGGACTTTT 58.622 42.857 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.