Multiple sequence alignment - TraesCS4D01G105500

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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 TraesCS4D01G105500 chr4D 100.000 8004 0 0 1 8004 84268157 84276160 0.000000e+00 14781.0
1 TraesCS4D01G105500 chr4D 95.349 86 4 0 7908 7993 134953846 134953931 3.900000e-28 137.0
2 TraesCS4D01G105500 chr4A 96.931 7200 156 37 790 7938 496997592 497004777 0.000000e+00 12011.0
3 TraesCS4D01G105500 chr4A 90.130 770 66 5 1 767 496996769 496997531 0.000000e+00 992.0
4 TraesCS4D01G105500 chr4A 100.000 28 0 0 881 908 66913653 66913626 1.500000e-02 52.8
5 TraesCS4D01G105500 chr4B 95.107 3331 99 19 1010 4305 119259891 119263192 0.000000e+00 5190.0
6 TraesCS4D01G105500 chr4B 92.768 1756 71 19 5978 7707 119270386 119272111 0.000000e+00 2488.0
7 TraesCS4D01G105500 chr4B 96.933 815 17 3 4313 5122 119263232 119264043 0.000000e+00 1360.0
8 TraesCS4D01G105500 chr4B 88.183 787 67 16 1 785 119258816 119259578 0.000000e+00 915.0
9 TraesCS4D01G105500 chr4B 97.297 518 14 0 5385 5902 119264349 119264866 0.000000e+00 880.0
10 TraesCS4D01G105500 chr4B 81.993 572 88 8 227 789 414186579 414186014 9.400000e-129 472.0
11 TraesCS4D01G105500 chr4B 91.322 242 13 5 5120 5355 119264121 119264360 2.790000e-84 324.0
12 TraesCS4D01G105500 chr4B 89.669 242 19 5 7769 8004 119272157 119272398 3.630000e-78 303.0
13 TraesCS4D01G105500 chr4B 88.517 209 21 2 786 992 119259607 119259814 4.800000e-62 250.0
14 TraesCS4D01G105500 chr4B 72.441 762 148 41 34 767 671779242 671778515 3.810000e-43 187.0
15 TraesCS4D01G105500 chr1D 89.770 2170 191 18 1067 3230 54918727 54916583 0.000000e+00 2748.0
16 TraesCS4D01G105500 chr1D 90.846 1595 93 23 4315 5896 54915461 54913907 0.000000e+00 2087.0
17 TraesCS4D01G105500 chr1D 88.069 989 90 22 6168 7143 54913630 54912657 0.000000e+00 1147.0
18 TraesCS4D01G105500 chr1D 85.078 965 70 31 3327 4231 54916585 54915635 0.000000e+00 917.0
19 TraesCS4D01G105500 chr1D 93.333 90 6 0 5948 6037 54913764 54913675 5.040000e-27 134.0
20 TraesCS4D01G105500 chr1B 89.661 2186 179 26 1067 3235 90418185 90420340 0.000000e+00 2741.0
21 TraesCS4D01G105500 chr1B 91.326 1591 102 21 4315 5894 90421682 90423247 0.000000e+00 2141.0
22 TraesCS4D01G105500 chr1B 86.915 833 79 21 6325 7143 90423886 90424702 0.000000e+00 907.0
23 TraesCS4D01G105500 chr1B 90.416 553 39 5 3683 4232 90420967 90421508 0.000000e+00 715.0
24 TraesCS4D01G105500 chr1B 89.041 73 8 0 3228 3300 428722561 428722489 3.080000e-14 91.6
25 TraesCS4D01G105500 chr1A 89.404 2180 191 22 1067 3235 53910404 53908254 0.000000e+00 2710.0
26 TraesCS4D01G105500 chr1A 89.781 1595 115 23 4315 5894 53907177 53905616 0.000000e+00 1999.0
27 TraesCS4D01G105500 chr1A 88.978 871 76 11 6230 7086 53905036 53904172 0.000000e+00 1059.0
28 TraesCS4D01G105500 chr1A 90.545 550 38 5 3686 4232 53907887 53907349 0.000000e+00 715.0
29 TraesCS4D01G105500 chr1A 89.308 159 17 0 5948 6106 53905437 53905279 4.900000e-47 200.0
30 TraesCS4D01G105500 chr6D 84.243 641 87 11 1 634 43553733 43554366 5.310000e-171 612.0
31 TraesCS4D01G105500 chr6D 76.709 790 125 36 3 767 419441926 419441171 1.260000e-102 385.0
32 TraesCS4D01G105500 chr6D 90.909 55 5 0 3245 3299 365847308 365847362 3.100000e-09 75.0
33 TraesCS4D01G105500 chr7B 81.122 731 108 16 1 728 475245365 475246068 7.020000e-155 558.0
34 TraesCS4D01G105500 chr7B 93.443 61 4 0 3240 3300 611724061 611724001 3.080000e-14 91.6
35 TraesCS4D01G105500 chr7B 100.000 28 0 0 886 913 530823777 530823750 1.500000e-02 52.8
36 TraesCS4D01G105500 chr3B 80.183 767 103 17 1 767 481315708 481314991 5.500000e-146 529.0
37 TraesCS4D01G105500 chr3B 87.166 374 30 12 6471 6842 7294731 7294374 7.480000e-110 409.0
38 TraesCS4D01G105500 chr3B 80.952 252 41 5 9 256 414042498 414042250 8.200000e-45 193.0
39 TraesCS4D01G105500 chr5B 79.408 743 102 19 3 724 604293539 604292827 2.020000e-130 477.0
40 TraesCS4D01G105500 chr5B 78.295 129 15 9 797 913 287446813 287446686 4.010000e-08 71.3
41 TraesCS4D01G105500 chr5D 78.695 751 108 29 1 728 40105126 40105847 3.410000e-123 453.0
42 TraesCS4D01G105500 chr5D 90.909 55 4 1 3245 3299 408779742 408779689 1.110000e-08 73.1
43 TraesCS4D01G105500 chr3A 77.986 695 121 18 89 767 219811482 219810804 2.690000e-109 407.0
44 TraesCS4D01G105500 chr5A 74.311 798 147 27 1 767 139687733 139686963 1.310000e-72 285.0
45 TraesCS4D01G105500 chr6B 93.023 86 5 1 7908 7993 85137436 85137352 3.030000e-24 124.0
46 TraesCS4D01G105500 chr6A 92.857 56 4 0 3245 3300 506643253 506643308 1.850000e-11 82.4
47 TraesCS4D01G105500 chr3D 92.857 56 4 0 3245 3300 604669426 604669481 1.850000e-11 82.4
48 TraesCS4D01G105500 chr3D 97.826 46 1 0 3254 3299 73896428 73896383 6.660000e-11 80.5
49 TraesCS4D01G105500 chr7D 91.304 46 4 0 867 912 133237187 133237142 6.710000e-06 63.9
50 TraesCS4D01G105500 chr7D 100.000 29 0 0 881 909 54186318 54186346 4.000000e-03 54.7
51 TraesCS4D01G105500 chr2A 93.023 43 3 0 867 909 372762043 372762001 6.710000e-06 63.9


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 TraesCS4D01G105500 chr4D 84268157 84276160 8003 False 14781.0 14781 100.000000 1 8004 1 chr4D.!!$F1 8003
1 TraesCS4D01G105500 chr4A 496996769 497004777 8008 False 6501.5 12011 93.530500 1 7938 2 chr4A.!!$F1 7937
2 TraesCS4D01G105500 chr4B 119258816 119264866 6050 False 1486.5 5190 92.893167 1 5902 6 chr4B.!!$F1 5901
3 TraesCS4D01G105500 chr4B 119270386 119272398 2012 False 1395.5 2488 91.218500 5978 8004 2 chr4B.!!$F2 2026
4 TraesCS4D01G105500 chr4B 414186014 414186579 565 True 472.0 472 81.993000 227 789 1 chr4B.!!$R1 562
5 TraesCS4D01G105500 chr1D 54912657 54918727 6070 True 1406.6 2748 89.419200 1067 7143 5 chr1D.!!$R1 6076
6 TraesCS4D01G105500 chr1B 90418185 90424702 6517 False 1626.0 2741 89.579500 1067 7143 4 chr1B.!!$F1 6076
7 TraesCS4D01G105500 chr1A 53904172 53910404 6232 True 1336.6 2710 89.603200 1067 7086 5 chr1A.!!$R1 6019
8 TraesCS4D01G105500 chr6D 43553733 43554366 633 False 612.0 612 84.243000 1 634 1 chr6D.!!$F1 633
9 TraesCS4D01G105500 chr6D 419441171 419441926 755 True 385.0 385 76.709000 3 767 1 chr6D.!!$R1 764
10 TraesCS4D01G105500 chr7B 475245365 475246068 703 False 558.0 558 81.122000 1 728 1 chr7B.!!$F1 727
11 TraesCS4D01G105500 chr3B 481314991 481315708 717 True 529.0 529 80.183000 1 767 1 chr3B.!!$R3 766
12 TraesCS4D01G105500 chr5B 604292827 604293539 712 True 477.0 477 79.408000 3 724 1 chr5B.!!$R2 721
13 TraesCS4D01G105500 chr5D 40105126 40105847 721 False 453.0 453 78.695000 1 728 1 chr5D.!!$F1 727
14 TraesCS4D01G105500 chr3A 219810804 219811482 678 True 407.0 407 77.986000 89 767 1 chr3A.!!$R1 678
15 TraesCS4D01G105500 chr5A 139686963 139687733 770 True 285.0 285 74.311000 1 767 1 chr5A.!!$R1 766

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
869 1032 0.814812 GGACCGACCCAAACGAACAA 60.815 55.000 0.00 0.00 0.00 2.83 F
1592 1817 0.697658 TGTGCTGATTGATCCACCCA 59.302 50.000 0.00 0.00 0.00 4.51 F
1916 2145 1.123928 ATCTCTAACGAAGCTGGGGG 58.876 55.000 0.00 0.00 0.00 5.40 F
2907 3143 2.639839 AGTGTGAACTTGTCCCTGCTAT 59.360 45.455 0.00 0.00 0.00 2.97 F
4129 4687 0.618458 TACTGCGCCCAGGAAGATTT 59.382 50.000 4.18 0.00 43.53 2.17 F
5333 6101 0.801251 GTTGAGATGCTCTGTGGTGC 59.199 55.000 0.00 0.00 0.00 5.01 F
6627 7909 1.282817 TTTCCGGATTCATACACGCG 58.717 50.000 4.15 3.53 0.00 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2551 2780 1.133976 GCACTACATCCAGGGCAGAAT 60.134 52.381 0.00 0.0 44.75 2.40 R
3302 3541 0.181114 CTCCATCCGGAATTGCTCCA 59.819 55.000 9.01 0.0 45.74 3.86 R
3367 3607 0.767375 CCATGATACAGGGTGAGGGG 59.233 60.000 0.00 0.0 29.93 4.79 R
4672 5328 0.392998 ACCCACGAATCCATGAGTGC 60.393 55.000 0.00 0.0 33.62 4.40 R
5946 6853 3.181491 GCTTGACTGCTTGGTTTGTGTAA 60.181 43.478 0.00 0.0 0.00 2.41 R
6864 8149 1.126846 CGATTGCCGACTTGAAGTGTC 59.873 52.381 0.90 0.0 41.76 3.67 R
7745 9091 0.179073 CTCATCCCGCGATCTGGTTT 60.179 55.000 8.23 0.0 0.00 3.27 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
205 235 3.077556 GGCGCAAGGAGGAGGAGA 61.078 66.667 10.83 0.00 38.28 3.71
362 422 1.736365 TACGTGTGCGAGTGGGTCAA 61.736 55.000 0.00 0.00 42.00 3.18
388 449 2.513895 CCGTCTGGTTTGGGGTGT 59.486 61.111 0.00 0.00 0.00 4.16
685 809 3.768185 GACAGCGCGCCTCCGAATA 62.768 63.158 30.33 0.00 36.29 1.75
769 904 3.261580 GTGGCTGGCATTAATGTTTTCC 58.738 45.455 16.61 12.82 0.00 3.13
808 971 4.657824 CGGGTCAGCGTTGGACGT 62.658 66.667 0.00 0.00 44.73 4.34
815 978 3.110178 GCGTTGGACGTAAGCGCT 61.110 61.111 19.92 2.64 44.73 5.92
817 980 2.726691 CGTTGGACGTAAGCGCTGG 61.727 63.158 12.58 6.21 42.83 4.85
825 988 3.053291 TAAGCGCTGGCCCAAACG 61.053 61.111 12.58 1.59 41.24 3.60
836 999 1.862602 GCCCAAACGTGAAAGCGGAT 61.863 55.000 0.00 0.00 35.98 4.18
852 1015 1.461091 GGATATGAGTGTCCGCCGGA 61.461 60.000 5.05 0.00 0.00 5.14
869 1032 0.814812 GGACCGACCCAAACGAACAA 60.815 55.000 0.00 0.00 0.00 2.83
1157 1381 2.677524 CCGTCACCTCGTACCCCA 60.678 66.667 0.00 0.00 0.00 4.96
1494 1719 9.495754 GTAACATCAGTTCTTGCTATTGAAATC 57.504 33.333 0.00 0.00 39.15 2.17
1529 1754 4.082408 CCGACCTTTGACTGTGTAGATGTA 60.082 45.833 0.00 0.00 0.00 2.29
1592 1817 0.697658 TGTGCTGATTGATCCACCCA 59.302 50.000 0.00 0.00 0.00 4.51
1746 1973 6.619801 AAAACTTTAGCTTACCAGTGTCTG 57.380 37.500 0.00 0.00 0.00 3.51
1794 2023 4.463186 GCTCTGTCTCCTTGTTCTTAGGTA 59.537 45.833 0.00 0.00 34.29 3.08
1905 2134 6.577103 TGTGGACAATGATCTCATCTCTAAC 58.423 40.000 0.00 0.00 35.10 2.34
1916 2145 1.123928 ATCTCTAACGAAGCTGGGGG 58.876 55.000 0.00 0.00 0.00 5.40
1996 2225 6.978343 TTCTTCCCTTCGTGTATAAATGTG 57.022 37.500 0.00 0.00 0.00 3.21
2004 2233 4.185394 TCGTGTATAAATGTGGCGAATGT 58.815 39.130 0.00 0.00 0.00 2.71
2093 2322 2.980233 GACCTTGCCTGCACGCTT 60.980 61.111 9.13 0.00 0.00 4.68
2257 2486 4.202503 ACCATCCAGCCATAATAAGTCAGG 60.203 45.833 0.00 0.00 0.00 3.86
2544 2773 3.332761 TTGTAGTTTTGCGTGCAGAAG 57.667 42.857 0.00 0.00 0.00 2.85
2907 3143 2.639839 AGTGTGAACTTGTCCCTGCTAT 59.360 45.455 0.00 0.00 0.00 2.97
3302 3541 3.767711 TCAGTGCTAGATACATCCGGAT 58.232 45.455 12.38 12.38 0.00 4.18
3387 3627 1.695664 CCCCTCACCCTGTATCATGGA 60.696 57.143 0.00 0.00 0.00 3.41
3726 4283 7.658261 AGTAATAGCTGCTGATTATCAACGTA 58.342 34.615 13.43 0.00 0.00 3.57
3731 4288 6.459066 AGCTGCTGATTATCAACGTATATGT 58.541 36.000 0.00 0.00 0.00 2.29
4019 4577 5.360591 AGTTATCTCTTAGAATGGTTGCCG 58.639 41.667 0.00 0.00 0.00 5.69
4129 4687 0.618458 TACTGCGCCCAGGAAGATTT 59.382 50.000 4.18 0.00 43.53 2.17
4672 5328 1.410153 AGTTGAGTGCCTTGCTTTTGG 59.590 47.619 0.00 0.00 0.00 3.28
4748 5404 3.181479 TGAGTGCTCTTCGCCGTTATATT 60.181 43.478 0.68 0.00 38.05 1.28
5243 6006 7.041098 AGCAGTGAAAACTAGACTAAAACATGG 60.041 37.037 0.00 0.00 0.00 3.66
5333 6101 0.801251 GTTGAGATGCTCTGTGGTGC 59.199 55.000 0.00 0.00 0.00 5.01
5623 6396 2.436469 ACATTGATGGCTCGCGCA 60.436 55.556 8.75 0.00 38.10 6.09
5624 6397 1.980951 GACATTGATGGCTCGCGCAA 61.981 55.000 8.75 0.00 38.10 4.85
5658 6431 4.214758 AGCAAAAATGAATTTCCTTGCAGC 59.785 37.500 19.61 9.47 41.99 5.25
5946 6853 3.131577 TCTTGTGATTATTAGGCCGTCGT 59.868 43.478 0.00 0.00 0.00 4.34
6193 7101 2.683211 AGTCAAAATTGAGGCCCTGT 57.317 45.000 0.00 0.00 37.98 4.00
6627 7909 1.282817 TTTCCGGATTCATACACGCG 58.717 50.000 4.15 3.53 0.00 6.01
6864 8149 4.160439 TGACATCCCAGAAGTAGCAACTAG 59.840 45.833 0.00 0.00 33.75 2.57
7266 8570 8.777865 TTCTCTTCACTTGGTTATTGTATCTG 57.222 34.615 0.00 0.00 0.00 2.90
7281 8585 2.306341 ATCTGAGCCTGATGTTCACG 57.694 50.000 0.00 0.00 0.00 4.35
7337 8643 2.167487 TGACCTTGCCAAACAAAAGGAC 59.833 45.455 7.64 2.34 42.65 3.85
7355 8661 3.053095 AGGACAAAGGAATCCATGCTGAT 60.053 43.478 0.61 0.00 37.47 2.90
7380 8686 6.682746 AGTTGTACTATGATCTTATCCAGCG 58.317 40.000 0.00 0.00 0.00 5.18
7385 8691 5.542779 ACTATGATCTTATCCAGCGTTTCC 58.457 41.667 0.00 0.00 0.00 3.13
7394 8700 2.670934 AGCGTTTCCTGCAGCTGG 60.671 61.111 17.12 12.16 38.67 4.85
7395 8701 2.669569 GCGTTTCCTGCAGCTGGA 60.670 61.111 16.81 16.81 0.00 3.86
7399 8705 2.083774 CGTTTCCTGCAGCTGGATTTA 58.916 47.619 20.91 4.53 31.78 1.40
7403 8711 5.163663 CGTTTCCTGCAGCTGGATTTATTTA 60.164 40.000 20.91 2.33 31.78 1.40
7513 8821 6.613755 TTTTGTAGTGGTAGCTCTTGAAAC 57.386 37.500 1.33 0.00 0.00 2.78
7566 8888 3.451540 TGCAATACCCGTGGAGTGTATAA 59.548 43.478 0.00 0.00 0.00 0.98
7567 8889 4.101898 TGCAATACCCGTGGAGTGTATAAT 59.898 41.667 0.00 0.00 0.00 1.28
7568 8890 5.061179 GCAATACCCGTGGAGTGTATAATT 58.939 41.667 0.00 0.00 0.00 1.40
7621 8943 4.851558 GTCGTCACACCTATTCAAATTTGC 59.148 41.667 13.54 0.00 0.00 3.68
7650 8972 6.399639 TTTAGACCTGTTCCAAATGAAACC 57.600 37.500 0.00 0.00 33.94 3.27
7653 8976 4.342092 AGACCTGTTCCAAATGAAACCTTG 59.658 41.667 0.00 0.00 33.94 3.61
7707 9030 0.758734 CCAGTAATGGCATCGAGGGA 59.241 55.000 0.00 0.00 0.00 4.20
7708 9031 1.270518 CCAGTAATGGCATCGAGGGAG 60.271 57.143 0.00 0.00 0.00 4.30
7709 9032 1.414181 CAGTAATGGCATCGAGGGAGT 59.586 52.381 0.00 0.00 0.00 3.85
7710 9033 2.628178 CAGTAATGGCATCGAGGGAGTA 59.372 50.000 0.00 0.00 0.00 2.59
7711 9034 2.628657 AGTAATGGCATCGAGGGAGTAC 59.371 50.000 0.00 0.00 0.00 2.73
7712 9035 0.759346 AATGGCATCGAGGGAGTACC 59.241 55.000 0.00 0.00 40.67 3.34
7713 9036 1.464376 ATGGCATCGAGGGAGTACCG 61.464 60.000 0.00 0.00 46.96 4.02
7715 9038 2.857744 GCATCGAGGGAGTACCGGG 61.858 68.421 6.32 0.00 46.96 5.73
7717 9040 1.150992 ATCGAGGGAGTACCGGGAG 59.849 63.158 6.32 0.00 46.96 4.30
7720 9066 0.969409 CGAGGGAGTACCGGGAGTTT 60.969 60.000 6.32 0.00 46.96 2.66
7722 9068 0.908180 AGGGAGTACCGGGAGTTTGG 60.908 60.000 6.32 0.00 46.96 3.28
7742 9088 4.292178 CCCTGCTCGAGATCCCGC 62.292 72.222 18.75 0.00 0.00 6.13
7743 9089 4.637489 CCTGCTCGAGATCCCGCG 62.637 72.222 18.75 0.00 36.92 6.46
7744 9090 3.586961 CTGCTCGAGATCCCGCGA 61.587 66.667 18.75 0.00 42.09 5.87
7745 9091 3.126074 CTGCTCGAGATCCCGCGAA 62.126 63.158 18.75 0.00 43.56 4.70
7746 9092 2.104331 GCTCGAGATCCCGCGAAA 59.896 61.111 18.75 0.00 43.56 3.46
7747 9093 1.518572 GCTCGAGATCCCGCGAAAA 60.519 57.895 18.75 0.00 43.56 2.29
7748 9094 1.753468 GCTCGAGATCCCGCGAAAAC 61.753 60.000 18.75 0.00 43.56 2.43
7749 9095 1.146358 CTCGAGATCCCGCGAAAACC 61.146 60.000 8.23 0.00 43.56 3.27
7750 9096 1.447140 CGAGATCCCGCGAAAACCA 60.447 57.895 8.23 0.00 37.82 3.67
7764 9110 0.179073 AAACCAGATCGCGGGATGAG 60.179 55.000 20.80 11.30 31.51 2.90
7769 9115 1.666234 GATCGCGGGATGAGAAGGC 60.666 63.158 20.80 0.00 31.51 4.35
7795 9142 5.482878 AGAATCCTCTGCATTTGGTTCAAAT 59.517 36.000 0.54 0.54 43.71 2.32
7895 9247 4.825085 ACTCGCACCTCCTTTTCAAATTAA 59.175 37.500 0.00 0.00 0.00 1.40
7902 9254 7.010460 GCACCTCCTTTTCAAATTAATATGCAC 59.990 37.037 0.00 0.00 0.00 4.57
7906 9258 9.352784 CTCCTTTTCAAATTAATATGCACGAAA 57.647 29.630 0.00 0.00 0.00 3.46
7955 9307 6.542821 TGAACTAATATTTATGGGGCTGGAG 58.457 40.000 0.00 0.00 0.00 3.86
7998 9350 6.262496 ACATAAATAGACGAATGAGACTCGGA 59.738 38.462 0.00 0.00 40.64 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 126 1.311403 CCTCTGCCTCCTGGTCCTA 59.689 63.158 0.00 0.00 35.27 2.94
205 235 3.771160 CGCCTGGTACGCCTCCTT 61.771 66.667 0.00 0.00 35.27 3.36
580 702 2.273912 GGAACGTCGTCTCCCAGGT 61.274 63.158 0.00 0.00 0.00 4.00
622 744 2.029964 GCCGGTGAGGTCGACAAA 59.970 61.111 18.91 0.00 43.70 2.83
769 904 9.825109 ACCCGACCCATAAATATTTTTAAAATG 57.175 29.630 12.62 3.69 31.33 2.32
788 923 3.998672 TCCAACGCTGACCCGACC 61.999 66.667 0.00 0.00 0.00 4.79
808 971 3.053291 CGTTTGGGCCAGCGCTTA 61.053 61.111 7.50 0.00 34.44 3.09
815 978 2.840066 CGCTTTCACGTTTGGGCCA 61.840 57.895 0.00 0.00 0.00 5.36
817 980 1.862602 ATCCGCTTTCACGTTTGGGC 61.863 55.000 0.00 0.00 0.00 5.36
825 988 2.866762 GGACACTCATATCCGCTTTCAC 59.133 50.000 0.00 0.00 0.00 3.18
852 1015 1.461559 TTTTGTTCGTTTGGGTCGGT 58.538 45.000 0.00 0.00 0.00 4.69
869 1032 0.604511 ACCCGAACGAAAGGCGATTT 60.605 50.000 0.00 0.00 44.57 2.17
950 1114 7.469870 CGTGGCCAAATAGGATTTGATCATAAA 60.470 37.037 7.24 0.00 41.22 1.40
973 1139 2.669569 CCCCTGTTGTGGAGCGTG 60.670 66.667 0.00 0.00 0.00 5.34
1455 1679 3.812262 TGATGTTACATGGAGCATGGAG 58.188 45.455 12.59 0.00 45.16 3.86
1494 1719 0.108615 AAGGTCGGCTCACAATCGAG 60.109 55.000 0.00 0.00 33.41 4.04
1529 1754 0.038744 CAAGGGGCCACTGTGAGATT 59.961 55.000 9.26 0.00 0.00 2.40
1592 1817 5.049828 GCTTTGTGGCAGTATTGAAAAACT 58.950 37.500 0.00 0.00 0.00 2.66
1746 1973 4.324402 CAGCTGACTTGAACAAAACAACAC 59.676 41.667 8.42 0.00 0.00 3.32
1794 2023 9.429359 CTGTTACTACTTGAAGAAATGAGTGAT 57.571 33.333 0.00 0.00 0.00 3.06
1916 2145 3.084070 CTTTGGCAGTCACAAAGTTCC 57.916 47.619 9.16 0.00 45.94 3.62
2257 2486 3.118261 TCTTACAGGATGGCAATCAGACC 60.118 47.826 2.85 0.00 43.62 3.85
2551 2780 1.133976 GCACTACATCCAGGGCAGAAT 60.134 52.381 0.00 0.00 44.75 2.40
2907 3143 9.973450 AACTAACAAATAAATGTGTGTGCAATA 57.027 25.926 0.00 0.00 32.81 1.90
3235 3474 1.472728 GCGTCATCTAATTCCGGGTGT 60.473 52.381 0.00 0.00 0.00 4.16
3237 3476 1.068741 GAGCGTCATCTAATTCCGGGT 59.931 52.381 0.00 0.00 0.00 5.28
3302 3541 0.181114 CTCCATCCGGAATTGCTCCA 59.819 55.000 9.01 0.00 45.74 3.86
3367 3607 0.767375 CCATGATACAGGGTGAGGGG 59.233 60.000 0.00 0.00 29.93 4.79
3387 3627 9.468532 GAACAAAAGATTGCTCATTTTTCTACT 57.531 29.630 0.00 0.00 40.34 2.57
3757 4314 7.392113 AGTCCTCATCATAGTATAGAGAAACCG 59.608 40.741 7.60 0.00 0.00 4.44
4019 4577 5.877012 TCTCATCCATCAGTTTTAACAGAGC 59.123 40.000 0.00 0.00 0.00 4.09
4329 4981 6.147581 CGTCTCTTAAGTAGCACAAAGTACA 58.852 40.000 1.63 0.00 0.00 2.90
4672 5328 0.392998 ACCCACGAATCCATGAGTGC 60.393 55.000 0.00 0.00 33.62 4.40
4748 5404 8.671028 GGTTGAGTTGAACTTTCTTTTACACTA 58.329 33.333 0.00 0.00 0.00 2.74
5243 6006 6.630444 ACTTCATATCATCCTGAAATGTGC 57.370 37.500 0.00 0.00 31.40 4.57
5658 6431 3.604582 CTGAAAAGCTCAGGACCCTTAG 58.395 50.000 0.00 0.00 46.89 2.18
5946 6853 3.181491 GCTTGACTGCTTGGTTTGTGTAA 60.181 43.478 0.00 0.00 0.00 2.41
6795 8080 8.348507 GCAAATAGTTTATCAGCAAGCTTCTAT 58.651 33.333 0.00 0.00 0.00 1.98
6864 8149 1.126846 CGATTGCCGACTTGAAGTGTC 59.873 52.381 0.90 0.00 41.76 3.67
7266 8570 2.299993 TCATCGTGAACATCAGGCTC 57.700 50.000 0.00 0.00 32.73 4.70
7281 8585 4.217334 TCGGAGCAGATCAGTAGAATCATC 59.783 45.833 0.00 0.00 0.00 2.92
7337 8643 5.359009 ACAACTATCAGCATGGATTCCTTTG 59.641 40.000 3.95 3.29 36.16 2.77
7355 8661 7.447545 ACGCTGGATAAGATCATAGTACAACTA 59.552 37.037 0.00 0.00 34.82 2.24
7373 8679 2.042831 GCTGCAGGAAACGCTGGAT 61.043 57.895 17.12 0.00 32.56 3.41
7380 8686 4.725790 AATAAATCCAGCTGCAGGAAAC 57.274 40.909 18.02 0.00 38.93 2.78
7403 8711 7.508687 AGCTTTCACCAGAACCAAAAATAAAT 58.491 30.769 0.00 0.00 32.39 1.40
7539 8847 0.249120 TCCACGGGTATTGCACAGAG 59.751 55.000 0.00 0.00 0.00 3.35
7540 8848 0.249120 CTCCACGGGTATTGCACAGA 59.751 55.000 0.00 0.00 0.00 3.41
7621 8943 2.422597 TGGAACAGGTCTAAATGTGCG 58.577 47.619 0.00 0.00 0.00 5.34
7707 9030 1.201424 GGATCCAAACTCCCGGTACT 58.799 55.000 6.95 0.00 0.00 2.73
7708 9031 0.179702 GGGATCCAAACTCCCGGTAC 59.820 60.000 15.23 0.00 42.94 3.34
7709 9032 2.611520 GGGATCCAAACTCCCGGTA 58.388 57.895 15.23 0.00 42.94 4.02
7710 9033 3.411700 GGGATCCAAACTCCCGGT 58.588 61.111 15.23 0.00 42.94 5.28
7715 9038 0.537188 TCGAGCAGGGATCCAAACTC 59.463 55.000 15.23 14.59 0.00 3.01
7717 9040 0.537188 TCTCGAGCAGGGATCCAAAC 59.463 55.000 15.23 1.15 0.00 2.93
7742 9088 0.810031 ATCCCGCGATCTGGTTTTCG 60.810 55.000 8.23 0.00 38.37 3.46
7743 9089 0.657840 CATCCCGCGATCTGGTTTTC 59.342 55.000 8.23 0.00 0.00 2.29
7744 9090 0.251916 TCATCCCGCGATCTGGTTTT 59.748 50.000 8.23 0.00 0.00 2.43
7745 9091 0.179073 CTCATCCCGCGATCTGGTTT 60.179 55.000 8.23 0.00 0.00 3.27
7746 9092 1.043116 TCTCATCCCGCGATCTGGTT 61.043 55.000 8.23 0.00 0.00 3.67
7747 9093 1.043116 TTCTCATCCCGCGATCTGGT 61.043 55.000 8.23 0.00 0.00 4.00
7748 9094 0.319383 CTTCTCATCCCGCGATCTGG 60.319 60.000 8.23 0.00 0.00 3.86
7749 9095 0.319383 CCTTCTCATCCCGCGATCTG 60.319 60.000 8.23 0.88 0.00 2.90
7750 9096 2.045280 CCTTCTCATCCCGCGATCT 58.955 57.895 8.23 0.00 0.00 2.75
7764 9110 3.767902 ATGCAGAGGATTCTAGCCTTC 57.232 47.619 0.00 0.00 35.44 3.46
7769 9115 5.188434 TGAACCAAATGCAGAGGATTCTAG 58.812 41.667 8.66 0.00 30.73 2.43
7795 9142 7.944554 ACTTCATCTTTCCTTCTGTTCCATTTA 59.055 33.333 0.00 0.00 0.00 1.40
7861 9213 3.689649 GGAGGTGCGAGTGAATTGTAAAT 59.310 43.478 0.00 0.00 0.00 1.40
7895 9247 9.433317 CGTAAATCAATAACTTTTCGTGCATAT 57.567 29.630 0.00 0.00 0.00 1.78
7902 9254 7.480229 TGTGATGCGTAAATCAATAACTTTTCG 59.520 33.333 0.12 0.00 38.28 3.46
7906 9258 7.139896 TGTGTGATGCGTAAATCAATAACTT 57.860 32.000 0.12 0.00 38.28 2.66


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

AutoCloner maintained by Alex Coulton.