Multiple sequence alignment - TraesCS2D01G465500

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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 TraesCS2D01G465500 chr2D 100.000 5809 0 0 1 5809 571441906 571447714 0.000000e+00 10728.0
1 TraesCS2D01G465500 chr2D 84.691 3338 464 29 1538 4862 571209195 571212498 0.000000e+00 3290.0
2 TraesCS2D01G465500 chr2D 85.195 1486 203 10 3348 4819 571529043 571530525 0.000000e+00 1509.0
3 TraesCS2D01G465500 chr2D 80.328 732 111 21 644 1370 571526328 571527031 1.850000e-144 523.0
4 TraesCS2D01G465500 chr2D 84.906 424 55 6 953 1370 571208678 571209098 2.500000e-113 420.0
5 TraesCS2D01G465500 chr2D 75.330 454 82 19 4853 5284 571213598 571214043 2.140000e-44 191.0
6 TraesCS2D01G465500 chr2D 74.632 544 75 31 7 526 571208175 571208679 1.290000e-41 182.0
7 TraesCS2D01G465500 chr2B 95.402 5850 188 25 1 5809 683158244 683164053 0.000000e+00 9238.0
8 TraesCS2D01G465500 chr2B 85.357 3360 451 17 1538 4862 683128403 683131756 0.000000e+00 3441.0
9 TraesCS2D01G465500 chr2B 84.203 3336 481 27 1538 4862 683067888 683071188 0.000000e+00 3199.0
10 TraesCS2D01G465500 chr2B 86.223 2976 354 25 1547 4488 794694186 794691233 0.000000e+00 3173.0
11 TraesCS2D01G465500 chr2B 86.223 2976 354 25 1547 4488 794803087 794800134 0.000000e+00 3173.0
12 TraesCS2D01G465500 chr2B 84.501 2897 403 32 1538 4415 683043178 683046047 0.000000e+00 2820.0
13 TraesCS2D01G465500 chr2B 85.778 1793 253 2 1538 3329 683054291 683056082 0.000000e+00 1897.0
14 TraesCS2D01G465500 chr2B 83.099 568 78 10 790 1346 683067195 683067755 8.690000e-138 501.0
15 TraesCS2D01G465500 chr2B 81.757 592 93 10 790 1372 683127651 683128236 1.130000e-131 481.0
16 TraesCS2D01G465500 chr2B 80.769 624 84 22 695 1309 683042415 683043011 6.860000e-124 455.0
17 TraesCS2D01G465500 chr2B 86.683 398 53 0 4465 4862 683046070 683046467 5.340000e-120 442.0
18 TraesCS2D01G465500 chr2B 85.645 411 48 8 953 1358 683053771 683054175 6.960000e-114 422.0
19 TraesCS2D01G465500 chr2B 74.639 623 106 37 4878 5461 683133160 683133769 1.630000e-55 228.0
20 TraesCS2D01G465500 chr2B 76.546 469 61 24 7 453 683053253 683053694 1.640000e-50 211.0
21 TraesCS2D01G465500 chr2A 85.923 3353 407 35 1546 4862 710206333 710209656 0.000000e+00 3517.0
22 TraesCS2D01G465500 chr2A 84.636 3339 464 30 1538 4862 710036409 710039712 0.000000e+00 3278.0
23 TraesCS2D01G465500 chr2A 84.648 3335 464 30 1538 4862 710093265 710096561 0.000000e+00 3278.0
24 TraesCS2D01G465500 chr2A 86.825 2907 334 26 1546 4415 710188159 710191053 0.000000e+00 3201.0
25 TraesCS2D01G465500 chr2A 86.466 399 46 5 953 1346 710035892 710036287 1.160000e-116 431.0
26 TraesCS2D01G465500 chr2A 82.218 523 63 18 866 1370 710205402 710205912 1.940000e-114 424.0
27 TraesCS2D01G465500 chr6A 86.106 2044 237 29 2813 4819 617078172 617080205 0.000000e+00 2158.0
28 TraesCS2D01G465500 chrUn 86.421 1414 168 15 3351 4753 307300441 307301841 0.000000e+00 1526.0
29 TraesCS2D01G465500 chr3B 96.774 62 2 0 1381 1442 779543998 779543937 2.860000e-18 104.0
30 TraesCS2D01G465500 chr5D 96.721 61 2 0 1382 1442 496327568 496327628 1.030000e-17 102.0
31 TraesCS2D01G465500 chr3D 96.721 61 2 0 1382 1442 192151866 192151806 1.030000e-17 102.0
32 TraesCS2D01G465500 chr3A 93.056 72 2 3 1382 1452 724015727 724015796 1.030000e-17 102.0
33 TraesCS2D01G465500 chr1D 95.238 63 3 0 1380 1442 391324145 391324207 3.700000e-17 100.0
34 TraesCS2D01G465500 chr7D 92.754 69 3 1 1381 1449 530760067 530760001 1.330000e-16 99.0
35 TraesCS2D01G465500 chr7B 92.754 69 2 2 1381 1449 570220412 570220347 4.790000e-16 97.1
36 TraesCS2D01G465500 chr6B 95.082 61 3 0 1382 1442 146669562 146669622 4.790000e-16 97.1


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 TraesCS2D01G465500 chr2D 571441906 571447714 5808 False 10728.000000 10728 100.000000 1 5809 1 chr2D.!!$F1 5808
1 TraesCS2D01G465500 chr2D 571208175 571214043 5868 False 1020.750000 3290 79.889750 7 5284 4 chr2D.!!$F2 5277
2 TraesCS2D01G465500 chr2D 571526328 571530525 4197 False 1016.000000 1509 82.761500 644 4819 2 chr2D.!!$F3 4175
3 TraesCS2D01G465500 chr2B 683158244 683164053 5809 False 9238.000000 9238 95.402000 1 5809 1 chr2B.!!$F1 5808
4 TraesCS2D01G465500 chr2B 794691233 794694186 2953 True 3173.000000 3173 86.223000 1547 4488 1 chr2B.!!$R1 2941
5 TraesCS2D01G465500 chr2B 794800134 794803087 2953 True 3173.000000 3173 86.223000 1547 4488 1 chr2B.!!$R2 2941
6 TraesCS2D01G465500 chr2B 683067195 683071188 3993 False 1850.000000 3199 83.651000 790 4862 2 chr2B.!!$F4 4072
7 TraesCS2D01G465500 chr2B 683127651 683133769 6118 False 1383.333333 3441 80.584333 790 5461 3 chr2B.!!$F5 4671
8 TraesCS2D01G465500 chr2B 683042415 683046467 4052 False 1239.000000 2820 83.984333 695 4862 3 chr2B.!!$F2 4167
9 TraesCS2D01G465500 chr2B 683053253 683056082 2829 False 843.333333 1897 82.656333 7 3329 3 chr2B.!!$F3 3322
10 TraesCS2D01G465500 chr2A 710093265 710096561 3296 False 3278.000000 3278 84.648000 1538 4862 1 chr2A.!!$F1 3324
11 TraesCS2D01G465500 chr2A 710188159 710191053 2894 False 3201.000000 3201 86.825000 1546 4415 1 chr2A.!!$F2 2869
12 TraesCS2D01G465500 chr2A 710205402 710209656 4254 False 1970.500000 3517 84.070500 866 4862 2 chr2A.!!$F4 3996
13 TraesCS2D01G465500 chr2A 710035892 710039712 3820 False 1854.500000 3278 85.551000 953 4862 2 chr2A.!!$F3 3909
14 TraesCS2D01G465500 chr6A 617078172 617080205 2033 False 2158.000000 2158 86.106000 2813 4819 1 chr6A.!!$F1 2006
15 TraesCS2D01G465500 chrUn 307300441 307301841 1400 False 1526.000000 1526 86.421000 3351 4753 1 chrUn.!!$F1 1402

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
111 118 0.178068 TGCCTCCTTCGCCAGATTAC 59.822 55.000 0.00 0.0 0.00 1.89 F
112 119 0.466124 GCCTCCTTCGCCAGATTACT 59.534 55.000 0.00 0.0 0.00 2.24 F
743 786 0.673333 TAGTTCCATGGCTGTGCGTG 60.673 55.000 6.96 0.0 0.00 5.34 F
1638 2078 0.912486 ATGCAGGGAGAGGTTGTACC 59.088 55.000 0.00 0.0 38.99 3.34 F
1925 2371 1.804396 CGCCCCACTGCAACATCAAA 61.804 55.000 0.00 0.0 0.00 2.69 F
2613 3069 2.103042 CCCACTAGCTGCACGAAGC 61.103 63.158 1.02 0.0 43.88 3.86 F
2933 3390 3.850752 TGGGCTTCTTCCAAATGGTTAA 58.149 40.909 0.00 0.0 36.34 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1628 2068 1.741770 CTGGCAGCGGTACAACCTC 60.742 63.158 0.00 0.00 35.66 3.85 R
2052 2498 2.387757 ACCACTGGCAAAACATTCAGT 58.612 42.857 0.00 0.00 40.62 3.41 R
2613 3069 2.805671 TGTATTCAGAAGTGCACCAACG 59.194 45.455 14.63 0.00 0.00 4.10 R
3114 3571 4.217767 GGCCGAACCTTCTGAAGTATTTTT 59.782 41.667 15.72 1.81 34.51 1.94 R
3205 3662 6.973229 ACATTTTGCTTCCTTGCATAAATC 57.027 33.333 0.00 0.00 42.96 2.17 R
4320 4815 4.385825 TCTTTGACAACATGTAGGTCCAC 58.614 43.478 21.29 5.02 0.00 4.02 R
4895 6782 2.180276 GCTCTCTCTTGTTCCCCTGTA 58.820 52.381 0.00 0.00 0.00 2.74 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
110 117 0.908910 TTGCCTCCTTCGCCAGATTA 59.091 50.000 0.00 0.00 0.00 1.75
111 118 0.178068 TGCCTCCTTCGCCAGATTAC 59.822 55.000 0.00 0.00 0.00 1.89
112 119 0.466124 GCCTCCTTCGCCAGATTACT 59.534 55.000 0.00 0.00 0.00 2.24
114 121 2.035632 CCTCCTTCGCCAGATTACTCT 58.964 52.381 0.00 0.00 0.00 3.24
118 125 2.693591 CCTTCGCCAGATTACTCTACCA 59.306 50.000 0.00 0.00 0.00 3.25
126 133 4.141620 CCAGATTACTCTACCAATGGCTGT 60.142 45.833 0.00 0.00 0.00 4.40
129 136 6.040955 CAGATTACTCTACCAATGGCTGTAGA 59.959 42.308 0.00 0.00 40.74 2.59
134 141 5.163364 ACTCTACCAATGGCTGTAGATCAAG 60.163 44.000 0.00 0.00 41.77 3.02
151 162 7.437713 AGATCAAGGTTGTCTGGTTATGATA 57.562 36.000 0.00 0.00 0.00 2.15
168 185 8.079809 GGTTATGATATACGTTTGGAAATTGGG 58.920 37.037 0.00 0.00 0.00 4.12
223 242 1.971149 AGGGACACCATCATCCTTGA 58.029 50.000 0.00 0.00 40.13 3.02
258 279 4.574013 CAGCTGTCTTAGATTGGTGGATTC 59.426 45.833 5.25 0.00 0.00 2.52
291 315 3.070018 CAGACTACTGCTGGAGGTTTTG 58.930 50.000 7.84 0.00 37.33 2.44
339 364 5.798434 GCCAAAATTTGTCGATAGGTACAAC 59.202 40.000 4.92 0.00 35.43 3.32
368 393 9.898152 TGTACATACCAATCAGAAACAATCATA 57.102 29.630 0.00 0.00 0.00 2.15
383 408 7.798596 AACAATCATACATCTCAATGAGGAC 57.201 36.000 10.71 0.00 35.67 3.85
523 565 3.048600 TGCTATAGGTCCAATGCCTCTT 58.951 45.455 1.04 0.00 37.54 2.85
633 675 7.801716 TTTTTACAAGACTGACAGCTACATT 57.198 32.000 1.25 0.00 0.00 2.71
634 676 8.896320 TTTTTACAAGACTGACAGCTACATTA 57.104 30.769 1.25 0.00 0.00 1.90
635 677 9.502091 TTTTTACAAGACTGACAGCTACATTAT 57.498 29.630 1.25 0.00 0.00 1.28
636 678 8.479313 TTTACAAGACTGACAGCTACATTATG 57.521 34.615 1.25 0.00 0.00 1.90
637 679 6.042638 ACAAGACTGACAGCTACATTATGT 57.957 37.500 1.25 2.58 0.00 2.29
638 680 6.102663 ACAAGACTGACAGCTACATTATGTC 58.897 40.000 0.00 0.00 42.90 3.06
639 681 6.071108 ACAAGACTGACAGCTACATTATGTCT 60.071 38.462 0.00 0.00 42.99 3.41
640 682 6.142818 AGACTGACAGCTACATTATGTCTC 57.857 41.667 0.00 0.00 42.99 3.36
641 683 5.654209 AGACTGACAGCTACATTATGTCTCA 59.346 40.000 0.00 0.00 42.99 3.27
642 684 6.323482 AGACTGACAGCTACATTATGTCTCAT 59.677 38.462 0.00 0.00 42.99 2.90
669 712 3.430374 GCATTGTACAGTCATACGACCCT 60.430 47.826 0.00 0.00 43.73 4.34
677 720 3.194968 CAGTCATACGACCCTAAACACCT 59.805 47.826 0.00 0.00 43.73 4.00
692 735 8.733458 CCCTAAACACCTTTAATTAGTGTAACC 58.267 37.037 8.83 0.00 43.69 2.85
693 736 9.287373 CCTAAACACCTTTAATTAGTGTAACCA 57.713 33.333 8.83 0.00 43.69 3.67
708 751 3.585289 TGTAACCATGGAGCCAAGACTTA 59.415 43.478 21.47 0.00 0.00 2.24
714 757 3.402628 TGGAGCCAAGACTTAGTTCAC 57.597 47.619 0.49 0.00 0.00 3.18
732 775 2.766263 TCACGAGCTTCCATAGTTCCAT 59.234 45.455 0.00 0.00 30.90 3.41
743 786 0.673333 TAGTTCCATGGCTGTGCGTG 60.673 55.000 6.96 0.00 0.00 5.34
855 906 6.939163 AGTTCTAACTTCATCTCATTTGCTGT 59.061 34.615 0.00 0.00 35.21 4.40
926 981 4.787534 ACTCTCCTTTCCTCTGAATCCATT 59.212 41.667 0.00 0.00 0.00 3.16
949 1005 1.622607 TTGGTATCTCCCCTGTGCCG 61.623 60.000 0.00 0.00 34.77 5.69
1078 1143 4.774124 CATCATTGGGAGCTTCTTCACTA 58.226 43.478 0.00 0.00 0.00 2.74
1194 1259 2.234143 GCTGAGGGAAGGATTATTGGC 58.766 52.381 0.00 0.00 0.00 4.52
1195 1260 2.423373 GCTGAGGGAAGGATTATTGGCA 60.423 50.000 0.00 0.00 0.00 4.92
1456 1524 6.043822 TGCAGCCCCTTAGTATAATGTGATTA 59.956 38.462 0.00 0.00 0.00 1.75
1533 1876 1.070914 GCACAGCCCCTTAGACTATCC 59.929 57.143 0.00 0.00 0.00 2.59
1588 2028 3.799366 TCTGCTCAAGTGGTTTTCGTTA 58.201 40.909 0.00 0.00 0.00 3.18
1595 2035 6.687081 TCAAGTGGTTTTCGTTATCTTGTT 57.313 33.333 0.00 0.00 34.43 2.83
1628 2068 4.326826 TGACAGTTTTCTTATGCAGGGAG 58.673 43.478 0.00 0.00 0.00 4.30
1638 2078 0.912486 ATGCAGGGAGAGGTTGTACC 59.088 55.000 0.00 0.00 38.99 3.34
1925 2371 1.804396 CGCCCCACTGCAACATCAAA 61.804 55.000 0.00 0.00 0.00 2.69
1959 2405 6.712095 AGAATATTTGCAGGAATGCTCGATTA 59.288 34.615 1.53 0.00 35.49 1.75
2052 2498 6.159575 TGTTGATAAATGGGGGATCTAGTGAA 59.840 38.462 0.00 0.00 0.00 3.18
2346 2802 4.698201 TGTGTGGGAAGACAAGAACATA 57.302 40.909 0.00 0.00 0.00 2.29
2613 3069 2.103042 CCCACTAGCTGCACGAAGC 61.103 63.158 1.02 0.00 43.88 3.86
2933 3390 3.850752 TGGGCTTCTTCCAAATGGTTAA 58.149 40.909 0.00 0.00 36.34 2.01
3114 3571 5.526111 CAGTTTTCCTAACGAGAGGTTTGAA 59.474 40.000 7.16 0.00 40.09 2.69
3205 3662 8.287503 GCATAAATTTATTAGGGTCCTTACGTG 58.712 37.037 8.01 0.00 0.00 4.49
3594 4081 4.267214 CAGTCGATGAATGAGCTTGTACTG 59.733 45.833 0.00 0.00 28.30 2.74
4176 4663 5.798934 CAGCAAACTCTACATCAAGAAATGC 59.201 40.000 0.00 0.00 32.65 3.56
4268 4763 6.588756 ACTTTGATAAATGATGTTGCAGCAAG 59.411 34.615 8.49 0.00 32.21 4.01
4320 4815 1.528129 GCTCAAGGAGTTGGAGTTGG 58.472 55.000 0.00 0.00 34.09 3.77
4448 4946 4.082026 CCTCTGCAATTTTTACCTTCCCAG 60.082 45.833 0.00 0.00 0.00 4.45
4616 5115 9.113838 AGTATAAGCCAAAGACAGTTGATTATG 57.886 33.333 0.00 0.00 30.02 1.90
4895 6782 0.990374 AAGAGAGCATGGTGAGCCTT 59.010 50.000 0.00 0.00 35.27 4.35
4957 6850 4.590222 AGAACTTTGATTTTGGTCATGCCT 59.410 37.500 7.54 0.00 38.35 4.75
4984 6877 3.620488 TCTTATCACATCCTGCAAACCC 58.380 45.455 0.00 0.00 0.00 4.11
4992 6885 0.676466 TCCTGCAAACCCACATAGCG 60.676 55.000 0.00 0.00 0.00 4.26
5157 7054 5.683876 AAGCTACAGGTCACTATTGATGT 57.316 39.130 0.00 0.00 33.11 3.06
5172 7069 7.918033 CACTATTGATGTCGAGACTGAGTTAAT 59.082 37.037 4.78 1.08 0.00 1.40
5176 7073 6.867550 TGATGTCGAGACTGAGTTAATCAAT 58.132 36.000 4.78 0.00 37.52 2.57
5239 7143 1.583556 TATCAGCACCCTCACCACAT 58.416 50.000 0.00 0.00 0.00 3.21
5328 7237 2.785540 TGCCATCACTAGCACATTCA 57.214 45.000 0.00 0.00 33.08 2.57
5406 7325 3.025322 ACCATGGGTTGAAAGTGACAA 57.975 42.857 18.09 0.00 27.29 3.18
5407 7326 3.575805 ACCATGGGTTGAAAGTGACAAT 58.424 40.909 18.09 0.00 27.29 2.71
5421 7340 8.402472 TGAAAGTGACAATCTCGTTTTTGTTAT 58.598 29.630 0.00 0.00 36.25 1.89
5470 7390 3.706594 TCTTGTGTCTTCTCTGGTCAGTT 59.293 43.478 0.00 0.00 0.00 3.16
5505 7425 0.527600 TGCTATCGCAAGGTACGCAG 60.528 55.000 0.00 0.00 44.62 5.18
5506 7426 0.527817 GCTATCGCAAGGTACGCAGT 60.528 55.000 0.00 0.00 39.77 4.40
5533 7477 0.307760 CAGTTTTGTCGGTGGCTCAC 59.692 55.000 0.00 0.00 0.00 3.51
5539 7483 4.056125 TCGGTGGCTCACTGCTCG 62.056 66.667 8.75 3.35 40.25 5.03
5542 7486 1.153745 GGTGGCTCACTGCTCGTAG 60.154 63.158 5.48 0.00 42.39 3.51
5663 7607 7.014518 CCAAATTATGCATCCCATCTTCAGTAA 59.985 37.037 0.19 0.00 35.34 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 81 1.921887 GCAACATGTGATGCCAAATCG 59.078 47.619 10.82 0.00 37.80 3.34
110 117 4.290093 TGATCTACAGCCATTGGTAGAGT 58.710 43.478 4.26 1.15 46.43 3.24
111 118 4.944619 TGATCTACAGCCATTGGTAGAG 57.055 45.455 4.26 0.00 46.43 2.43
114 121 3.780294 ACCTTGATCTACAGCCATTGGTA 59.220 43.478 4.26 0.00 0.00 3.25
118 125 4.018960 AGACAACCTTGATCTACAGCCATT 60.019 41.667 0.00 0.00 0.00 3.16
126 133 6.867519 TCATAACCAGACAACCTTGATCTA 57.132 37.500 0.00 0.00 0.00 1.98
129 136 7.872993 CGTATATCATAACCAGACAACCTTGAT 59.127 37.037 0.00 0.00 0.00 2.57
134 141 7.254658 CCAAACGTATATCATAACCAGACAACC 60.255 40.741 0.00 0.00 0.00 3.77
151 162 8.754080 TGATATTTTCCCAATTTCCAAACGTAT 58.246 29.630 0.00 0.00 0.00 3.06
168 185 6.369059 ACTGCTATGCTGTGTGATATTTTC 57.631 37.500 1.47 0.00 39.15 2.29
223 242 1.827969 AGACAGCTGAGGCGTCTATTT 59.172 47.619 23.35 0.00 44.08 1.40
268 292 2.310779 ACCTCCAGCAGTAGTCTGAA 57.689 50.000 0.00 0.00 43.76 3.02
339 364 6.474819 TGTTTCTGATTGGTATGTACAACG 57.525 37.500 0.00 0.00 0.00 4.10
368 393 2.555664 ACTGGGTCCTCATTGAGATGT 58.444 47.619 15.36 2.18 34.77 3.06
383 408 3.600388 CTGTCACTAGGCTTAAACTGGG 58.400 50.000 0.00 0.00 0.00 4.45
523 565 1.834263 GCCTAGAGAGCAGAAAAGGGA 59.166 52.381 0.00 0.00 0.00 4.20
619 661 5.921962 TGAGACATAATGTAGCTGTCAGT 57.078 39.130 0.00 0.00 41.34 3.41
622 664 7.095857 GCACTAATGAGACATAATGTAGCTGTC 60.096 40.741 0.00 0.00 39.63 3.51
623 665 6.703607 GCACTAATGAGACATAATGTAGCTGT 59.296 38.462 0.00 0.00 0.00 4.40
624 666 6.703165 TGCACTAATGAGACATAATGTAGCTG 59.297 38.462 0.00 0.00 0.00 4.24
625 667 6.820335 TGCACTAATGAGACATAATGTAGCT 58.180 36.000 0.00 0.00 0.00 3.32
626 668 7.664082 ATGCACTAATGAGACATAATGTAGC 57.336 36.000 0.00 0.00 0.00 3.58
627 669 9.049523 ACAATGCACTAATGAGACATAATGTAG 57.950 33.333 0.00 0.00 0.00 2.74
628 670 8.962884 ACAATGCACTAATGAGACATAATGTA 57.037 30.769 0.00 0.00 0.00 2.29
629 671 7.870509 ACAATGCACTAATGAGACATAATGT 57.129 32.000 0.00 0.00 0.00 2.71
630 672 8.829612 TGTACAATGCACTAATGAGACATAATG 58.170 33.333 0.00 0.00 0.00 1.90
631 673 8.962884 TGTACAATGCACTAATGAGACATAAT 57.037 30.769 0.00 0.00 0.00 1.28
632 674 8.040727 ACTGTACAATGCACTAATGAGACATAA 58.959 33.333 0.00 0.00 0.00 1.90
633 675 7.555965 ACTGTACAATGCACTAATGAGACATA 58.444 34.615 0.00 0.00 0.00 2.29
634 676 6.409704 ACTGTACAATGCACTAATGAGACAT 58.590 36.000 0.00 0.00 0.00 3.06
635 677 5.793817 ACTGTACAATGCACTAATGAGACA 58.206 37.500 0.00 0.00 0.00 3.41
636 678 5.869344 TGACTGTACAATGCACTAATGAGAC 59.131 40.000 0.00 0.00 0.00 3.36
637 679 6.036577 TGACTGTACAATGCACTAATGAGA 57.963 37.500 0.00 0.00 0.00 3.27
638 680 6.915544 ATGACTGTACAATGCACTAATGAG 57.084 37.500 0.00 0.00 0.00 2.90
639 681 6.475402 CGTATGACTGTACAATGCACTAATGA 59.525 38.462 0.00 0.00 0.00 2.57
640 682 6.475402 TCGTATGACTGTACAATGCACTAATG 59.525 38.462 0.00 0.00 0.00 1.90
641 683 6.475727 GTCGTATGACTGTACAATGCACTAAT 59.524 38.462 7.88 0.00 42.08 1.73
642 684 5.803461 GTCGTATGACTGTACAATGCACTAA 59.197 40.000 7.88 0.00 42.08 2.24
677 720 6.486056 TGGCTCCATGGTTACACTAATTAAA 58.514 36.000 12.58 0.00 0.00 1.52
692 735 3.686726 GTGAACTAAGTCTTGGCTCCATG 59.313 47.826 0.00 0.00 0.00 3.66
693 736 3.617531 CGTGAACTAAGTCTTGGCTCCAT 60.618 47.826 0.00 0.00 0.00 3.41
708 751 3.368531 GGAACTATGGAAGCTCGTGAACT 60.369 47.826 0.00 0.00 0.00 3.01
743 786 3.756727 GGCAGCTCAAAGCAGGGC 61.757 66.667 1.29 1.95 45.56 5.19
926 981 1.633432 CACAGGGGAGATACCAAACCA 59.367 52.381 0.00 0.00 41.20 3.67
949 1005 2.283460 AGGAGCAAAAGCAGGCCC 60.283 61.111 0.00 0.00 0.00 5.80
1194 1259 3.071874 TGGGACAGAGGCTTATTGTTG 57.928 47.619 0.00 0.00 0.00 3.33
1435 1503 7.770897 CCTCATAATCACATTATACTAAGGGGC 59.229 40.741 0.00 0.00 33.86 5.80
1588 2028 6.773638 ACTGTCAGTTATTCAGGAACAAGAT 58.226 36.000 0.00 0.00 34.02 2.40
1595 2035 9.219603 CATAAGAAAACTGTCAGTTATTCAGGA 57.780 33.333 25.61 17.30 37.47 3.86
1628 2068 1.741770 CTGGCAGCGGTACAACCTC 60.742 63.158 0.00 0.00 35.66 3.85
1638 2078 3.059120 CAGAATTATCATCACTGGCAGCG 60.059 47.826 15.89 5.01 0.00 5.18
1925 2371 6.244552 TCCTGCAAATATTCTGACTCTCAT 57.755 37.500 0.00 0.00 0.00 2.90
2052 2498 2.387757 ACCACTGGCAAAACATTCAGT 58.612 42.857 0.00 0.00 40.62 3.41
2301 2757 4.870426 TCGTCCAATACAAGCAGAAATCTC 59.130 41.667 0.00 0.00 0.00 2.75
2346 2802 4.706962 GCCAAGAGTTTAATCCATCCACTT 59.293 41.667 0.00 0.00 0.00 3.16
2452 2908 5.491982 ACCACTCAATCTAACTTCATCCAC 58.508 41.667 0.00 0.00 0.00 4.02
2613 3069 2.805671 TGTATTCAGAAGTGCACCAACG 59.194 45.455 14.63 0.00 0.00 4.10
2933 3390 7.870509 AAATCATGCATAACATAGTGTGAGT 57.129 32.000 0.00 0.00 36.64 3.41
3114 3571 4.217767 GGCCGAACCTTCTGAAGTATTTTT 59.782 41.667 15.72 1.81 34.51 1.94
3205 3662 6.973229 ACATTTTGCTTCCTTGCATAAATC 57.027 33.333 0.00 0.00 42.96 2.17
3594 4081 8.606602 ACAATTTGAAGTTGAGAAATTTCAAGC 58.393 29.630 19.99 9.75 39.74 4.01
3760 4247 8.365647 AGTTATTTCTAGAGTTTTGAGGTTCGA 58.634 33.333 0.00 0.00 0.00 3.71
4320 4815 4.385825 TCTTTGACAACATGTAGGTCCAC 58.614 43.478 21.29 5.02 0.00 4.02
4448 4946 7.888250 AGATGTCCAATTTTCTTTATCTCCC 57.112 36.000 0.00 0.00 0.00 4.30
4616 5115 5.064452 CAGCACACTCAACTCATTAGATTCC 59.936 44.000 0.00 0.00 0.00 3.01
4895 6782 2.180276 GCTCTCTCTTGTTCCCCTGTA 58.820 52.381 0.00 0.00 0.00 2.74
4957 6850 4.026052 TGCAGGATGTGATAAGAGACTCA 58.974 43.478 5.02 0.00 39.31 3.41
4984 6877 4.048378 TCCTTGGAGGTCACGCTATGTG 62.048 54.545 0.00 0.00 41.39 3.21
4992 6885 2.113243 AACCGCTCCTTGGAGGTCAC 62.113 60.000 17.33 1.08 38.40 3.67
5157 7054 6.680625 GCCACTATTGATTAACTCAGTCTCGA 60.681 42.308 0.00 0.00 34.68 4.04
5172 7069 5.720041 AGTGTACCTAAGAAGCCACTATTGA 59.280 40.000 0.00 0.00 31.80 2.57
5176 7073 4.021916 GGAGTGTACCTAAGAAGCCACTA 58.978 47.826 0.00 0.00 33.60 2.74
5239 7143 7.335422 GGATCAATTAGTTCAAGCAAGAAGAGA 59.665 37.037 0.00 0.00 0.00 3.10
5406 7325 3.694566 GCCCCTCATAACAAAAACGAGAT 59.305 43.478 0.00 0.00 0.00 2.75
5407 7326 3.078837 GCCCCTCATAACAAAAACGAGA 58.921 45.455 0.00 0.00 0.00 4.04
5421 7340 0.482446 AAAGGTCACAATGCCCCTCA 59.518 50.000 0.00 0.00 0.00 3.86
5470 7390 1.879575 AGCATACCTTACTGCCAGGA 58.120 50.000 0.00 0.00 39.22 3.86
5505 7425 2.076863 CCGACAAAACTGATCAGGGAC 58.923 52.381 26.08 11.70 0.00 4.46
5506 7426 1.697432 ACCGACAAAACTGATCAGGGA 59.303 47.619 26.08 0.00 0.00 4.20
5533 7477 0.666274 TCGCCAACAACTACGAGCAG 60.666 55.000 0.00 0.00 0.00 4.24
5539 7483 4.634443 AGGAACAATATCGCCAACAACTAC 59.366 41.667 0.00 0.00 0.00 2.73
5542 7486 4.156008 AGAAGGAACAATATCGCCAACAAC 59.844 41.667 0.00 0.00 0.00 3.32
5605 7549 9.601217 GAAAACAGACTAGCTAGATTATTTCCA 57.399 33.333 27.45 0.00 0.00 3.53
5663 7607 5.149239 TCATATGCATGGGGTGATGAATTT 58.851 37.500 10.16 0.00 32.61 1.82


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

AutoCloner maintained by Alex Coulton.