Multiple sequence alignment - TraesCS6D01G212600

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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 TraesCS6D01G212600 chr6D 100.000 4573 0 0 1 4573 301051439 301056011 0.000000e+00 8445.0
1 TraesCS6D01G212600 chr6D 88.090 848 98 3 2723 3567 271086295 271085448 0.000000e+00 1003.0
2 TraesCS6D01G212600 chr6B 93.052 3627 158 46 182 3769 465844634 465848205 0.000000e+00 5216.0
3 TraesCS6D01G212600 chr6B 88.443 848 95 3 2723 3567 431799390 431798543 0.000000e+00 1020.0
4 TraesCS6D01G212600 chr6B 81.206 431 65 7 1368 1784 431805798 431805370 2.640000e-87 333.0
5 TraesCS6D01G212600 chr6B 89.655 58 2 3 49 105 96680503 96680557 2.280000e-08 71.3
6 TraesCS6D01G212600 chr6B 100.000 37 0 0 154 190 465844186 465844222 8.210000e-08 69.4
7 TraesCS6D01G212600 chr6A 96.803 1345 34 5 2464 3808 416539541 416538206 0.000000e+00 2237.0
8 TraesCS6D01G212600 chr6A 95.272 1269 51 7 1152 2415 416540820 416539556 0.000000e+00 2002.0
9 TraesCS6D01G212600 chr6A 93.750 960 40 8 210 1159 416541793 416540844 0.000000e+00 1423.0
10 TraesCS6D01G212600 chr6A 90.038 793 52 10 3805 4573 416378083 416377294 0.000000e+00 1002.0
11 TraesCS6D01G212600 chr6A 87.854 848 100 2 2723 3567 384921533 384922380 0.000000e+00 992.0
12 TraesCS6D01G212600 chr6A 82.110 436 62 10 1363 1784 384915837 384916270 4.350000e-95 359.0
13 TraesCS6D01G212600 chr5A 76.364 715 143 24 2722 3423 572697756 572697055 1.210000e-95 361.0
14 TraesCS6D01G212600 chr5B 75.770 714 151 20 2721 3423 553945678 553946380 1.580000e-89 340.0
15 TraesCS6D01G212600 chr5D 76.135 683 141 22 2752 3423 453421888 453422559 5.670000e-89 339.0


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 TraesCS6D01G212600 chr6D 301051439 301056011 4572 False 8445.000000 8445 100.000 1 4573 1 chr6D.!!$F1 4572
1 TraesCS6D01G212600 chr6D 271085448 271086295 847 True 1003.000000 1003 88.090 2723 3567 1 chr6D.!!$R1 844
2 TraesCS6D01G212600 chr6B 465844186 465848205 4019 False 2642.700000 5216 96.526 154 3769 2 chr6B.!!$F2 3615
3 TraesCS6D01G212600 chr6B 431798543 431799390 847 True 1020.000000 1020 88.443 2723 3567 1 chr6B.!!$R1 844
4 TraesCS6D01G212600 chr6A 416538206 416541793 3587 True 1887.333333 2237 95.275 210 3808 3 chr6A.!!$R2 3598
5 TraesCS6D01G212600 chr6A 416377294 416378083 789 True 1002.000000 1002 90.038 3805 4573 1 chr6A.!!$R1 768
6 TraesCS6D01G212600 chr6A 384921533 384922380 847 False 992.000000 992 87.854 2723 3567 1 chr6A.!!$F2 844
7 TraesCS6D01G212600 chr5A 572697055 572697756 701 True 361.000000 361 76.364 2722 3423 1 chr5A.!!$R1 701
8 TraesCS6D01G212600 chr5B 553945678 553946380 702 False 340.000000 340 75.770 2721 3423 1 chr5B.!!$F1 702
9 TraesCS6D01G212600 chr5D 453421888 453422559 671 False 339.000000 339 76.135 2752 3423 1 chr5D.!!$F1 671

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
616 1058 0.259647 TGAATGAATGGCCAGGGAGG 59.740 55.0 13.05 0.0 41.84 4.30 F
629 1071 0.327867 AGGGAGGCAGGGATTCATGA 60.328 55.0 0.00 0.0 0.00 3.07 F
1739 2225 1.182667 CATGAGGTACCTGTCACGGA 58.817 55.0 22.10 0.0 0.00 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1857 2344 0.038892 TACCGAGGAGAAACACGCAC 60.039 55.0 0.00 0.0 0.00 5.34 R
1860 2347 0.108945 GGGTACCGAGGAGAAACACG 60.109 60.0 5.65 0.0 40.86 4.49 R
3583 4080 0.753262 TCTCCTCAAGAATAGGCGGC 59.247 55.0 0.00 0.0 33.84 6.53 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
70 71 3.343941 TTTTTGACCCCGAGACCATAG 57.656 47.619 0.00 0.00 0.00 2.23
71 72 2.241281 TTTGACCCCGAGACCATAGA 57.759 50.000 0.00 0.00 0.00 1.98
72 73 2.241281 TTGACCCCGAGACCATAGAA 57.759 50.000 0.00 0.00 0.00 2.10
73 74 1.481871 TGACCCCGAGACCATAGAAC 58.518 55.000 0.00 0.00 0.00 3.01
74 75 1.272816 TGACCCCGAGACCATAGAACA 60.273 52.381 0.00 0.00 0.00 3.18
75 76 1.829222 GACCCCGAGACCATAGAACAA 59.171 52.381 0.00 0.00 0.00 2.83
76 77 2.434702 GACCCCGAGACCATAGAACAAT 59.565 50.000 0.00 0.00 0.00 2.71
77 78 2.844348 ACCCCGAGACCATAGAACAATT 59.156 45.455 0.00 0.00 0.00 2.32
78 79 3.206150 CCCCGAGACCATAGAACAATTG 58.794 50.000 3.24 3.24 0.00 2.32
79 80 3.370527 CCCCGAGACCATAGAACAATTGT 60.371 47.826 4.92 4.92 0.00 2.71
80 81 4.261801 CCCGAGACCATAGAACAATTGTT 58.738 43.478 23.49 23.49 41.64 2.83
203 624 7.205515 AGGATAATCAGTCTTTCAGGTTCAT 57.794 36.000 0.00 0.00 0.00 2.57
205 626 8.428063 AGGATAATCAGTCTTTCAGGTTCATAG 58.572 37.037 0.00 0.00 0.00 2.23
230 651 1.233019 CACTGCACCAGTTCTTGAGG 58.767 55.000 0.00 0.00 42.59 3.86
260 681 2.917701 TCTGTGGTTTAATGCGCATG 57.082 45.000 26.09 8.01 0.00 4.06
315 736 2.428890 CTCTAGTTACTGGTGCTCTGGG 59.571 54.545 0.00 0.00 0.00 4.45
325 746 3.207669 GCTCTGGGCAGCATTCCG 61.208 66.667 0.00 0.00 39.43 4.30
342 763 5.639082 GCATTCCGGAAAATCTTGTCATTTT 59.361 36.000 23.08 0.00 38.43 1.82
359 780 7.551585 TGTCATTTTGTTGTGTCCATAAACTT 58.448 30.769 0.00 0.00 0.00 2.66
461 903 9.249053 CATCATACTATATTCTGTCCTGGTAGT 57.751 37.037 0.00 0.00 0.00 2.73
502 944 8.658499 TTCATATCTGTCATGAGAAGTCATTG 57.342 34.615 0.00 0.00 40.84 2.82
615 1057 1.688772 CTGAATGAATGGCCAGGGAG 58.311 55.000 13.05 0.00 0.00 4.30
616 1058 0.259647 TGAATGAATGGCCAGGGAGG 59.740 55.000 13.05 0.00 41.84 4.30
629 1071 0.327867 AGGGAGGCAGGGATTCATGA 60.328 55.000 0.00 0.00 0.00 3.07
631 1073 1.685148 GGAGGCAGGGATTCATGAAC 58.315 55.000 11.07 4.95 0.00 3.18
781 1223 1.869767 CTGGTCGATCTGCCTTTATGC 59.130 52.381 0.00 0.00 0.00 3.14
941 1387 7.739825 AGATGCCAATACTCTTGCTTATAAGA 58.260 34.615 16.85 0.00 35.51 2.10
1039 1485 2.436087 AAACGTCAGGTGAGCCTCCG 62.436 60.000 0.00 0.00 44.97 4.63
1088 1534 4.592778 AGGGTAAAATTGTTGGCTTGACAT 59.407 37.500 0.00 0.00 0.00 3.06
1089 1535 5.071653 AGGGTAAAATTGTTGGCTTGACATT 59.928 36.000 0.00 0.00 0.00 2.71
1090 1536 5.762711 GGGTAAAATTGTTGGCTTGACATTT 59.237 36.000 0.00 0.00 0.00 2.32
1091 1537 6.073276 GGGTAAAATTGTTGGCTTGACATTTC 60.073 38.462 0.00 0.00 0.00 2.17
1092 1538 6.481644 GGTAAAATTGTTGGCTTGACATTTCA 59.518 34.615 0.00 0.00 0.00 2.69
1093 1539 6.607735 AAAATTGTTGGCTTGACATTTCAG 57.392 33.333 0.00 0.00 31.71 3.02
1210 1696 2.923121 TCTCTGCTGCATTACCATTCC 58.077 47.619 1.31 0.00 0.00 3.01
1225 1711 3.244911 ACCATTCCAGGTTTCAGAACGAT 60.245 43.478 0.00 0.00 39.34 3.73
1256 1742 2.818432 CAGCAGTTGAAAGCAATCTCCT 59.182 45.455 0.00 0.00 36.22 3.69
1519 2005 2.100603 CTCTTCGTCGACCCGCTC 59.899 66.667 10.58 0.00 0.00 5.03
1702 2188 1.836802 GGGAGAGGAGAGCTTGTGATT 59.163 52.381 0.00 0.00 0.00 2.57
1739 2225 1.182667 CATGAGGTACCTGTCACGGA 58.817 55.000 22.10 0.00 0.00 4.69
1821 2308 2.416747 TCAGTGCTCTTTCCGTGAATG 58.583 47.619 0.00 0.00 0.00 2.67
1844 2331 5.698089 TGTCAAGAACTGAAATGCTCTGTAG 59.302 40.000 0.00 0.00 35.33 2.74
1855 2342 7.389232 TGAAATGCTCTGTAGAAATCTTCTGA 58.611 34.615 0.00 0.00 40.94 3.27
1857 2344 7.846644 AATGCTCTGTAGAAATCTTCTGAAG 57.153 36.000 11.18 11.18 40.94 3.02
1858 2345 6.352016 TGCTCTGTAGAAATCTTCTGAAGT 57.648 37.500 16.43 2.45 40.94 3.01
1859 2346 6.162079 TGCTCTGTAGAAATCTTCTGAAGTG 58.838 40.000 16.43 0.00 40.94 3.16
1860 2347 5.063312 GCTCTGTAGAAATCTTCTGAAGTGC 59.937 44.000 16.43 2.25 40.94 4.40
1877 2367 0.038892 TGCGTGTTTCTCCTCGGTAC 60.039 55.000 0.00 0.00 0.00 3.34
2213 2703 2.442212 TCTTCGATTGCAACACCGTA 57.558 45.000 0.00 0.00 0.00 4.02
2291 2781 4.868734 CCGGACAATAGTTTCTACCAGTTC 59.131 45.833 0.00 0.00 0.00 3.01
2303 2793 0.322322 ACCAGTTCGGGATTTACGCA 59.678 50.000 0.00 0.00 40.22 5.24
2399 2889 5.966742 AGAACCTCAGGTTTGAAATTAGC 57.033 39.130 11.44 0.00 46.95 3.09
2427 2917 5.746307 CATGCATGCTTGTTACTCTGTAT 57.254 39.130 22.06 0.00 0.00 2.29
2428 2918 6.849588 CATGCATGCTTGTTACTCTGTATA 57.150 37.500 22.06 0.00 0.00 1.47
2430 2920 7.516481 CATGCATGCTTGTTACTCTGTATATC 58.484 38.462 22.06 0.00 0.00 1.63
2431 2921 6.581712 TGCATGCTTGTTACTCTGTATATCA 58.418 36.000 20.33 0.00 0.00 2.15
2432 2922 6.703165 TGCATGCTTGTTACTCTGTATATCAG 59.297 38.462 20.33 0.00 44.85 2.90
2434 2924 7.225538 GCATGCTTGTTACTCTGTATATCAGTT 59.774 37.037 11.37 0.00 43.97 3.16
2435 2925 9.750125 CATGCTTGTTACTCTGTATATCAGTTA 57.250 33.333 0.00 0.00 43.97 2.24
2487 2980 6.206395 TCAGTTACATATTGGCCATGTTTG 57.794 37.500 15.38 10.84 37.74 2.93
2489 2982 6.210385 TCAGTTACATATTGGCCATGTTTGTT 59.790 34.615 15.38 0.00 37.74 2.83
2490 2983 6.873076 CAGTTACATATTGGCCATGTTTGTTT 59.127 34.615 15.38 2.96 37.74 2.83
2494 2987 7.238486 ACATATTGGCCATGTTTGTTTCTAA 57.762 32.000 6.09 0.00 32.72 2.10
2495 2988 7.096551 ACATATTGGCCATGTTTGTTTCTAAC 58.903 34.615 6.09 0.00 32.72 2.34
2496 2989 5.806654 ATTGGCCATGTTTGTTTCTAACT 57.193 34.783 6.09 0.00 0.00 2.24
2497 2990 6.909550 ATTGGCCATGTTTGTTTCTAACTA 57.090 33.333 6.09 0.00 0.00 2.24
2498 2991 5.957842 TGGCCATGTTTGTTTCTAACTAG 57.042 39.130 0.00 0.00 0.00 2.57
2499 2992 5.381757 TGGCCATGTTTGTTTCTAACTAGT 58.618 37.500 0.00 0.00 0.00 2.57
2503 2996 9.169592 GGCCATGTTTGTTTCTAACTAGTATAA 57.830 33.333 0.00 0.00 0.00 0.98
2647 3140 5.630121 TGCAAGTAAGATTTCCTTCCTTCA 58.370 37.500 0.00 0.00 29.85 3.02
2648 3141 5.707298 TGCAAGTAAGATTTCCTTCCTTCAG 59.293 40.000 0.00 0.00 29.85 3.02
2649 3142 5.940470 GCAAGTAAGATTTCCTTCCTTCAGA 59.060 40.000 0.00 0.00 29.85 3.27
2650 3143 6.128145 GCAAGTAAGATTTCCTTCCTTCAGAC 60.128 42.308 0.00 0.00 29.85 3.51
2651 3144 6.943899 AGTAAGATTTCCTTCCTTCAGACT 57.056 37.500 0.00 0.00 36.34 3.24
2652 3145 6.941857 AGTAAGATTTCCTTCCTTCAGACTC 58.058 40.000 0.00 0.00 36.34 3.36
2653 3146 6.728632 AGTAAGATTTCCTTCCTTCAGACTCT 59.271 38.462 0.00 0.00 36.34 3.24
2680 3173 6.279123 TCAATCTTGCAGCAAACAATAAACA 58.721 32.000 9.65 0.00 0.00 2.83
2690 3183 7.393327 CAGCAAACAATAAACAAGAAGTTGTG 58.607 34.615 0.00 0.00 46.68 3.33
2921 3414 2.822637 CCTCCCCATGGACATCCGG 61.823 68.421 15.22 4.49 39.43 5.14
3579 4075 7.333423 CGGTGGAACAAGAGATCTAAATTGTAA 59.667 37.037 16.54 7.08 44.16 2.41
3580 4076 8.669243 GGTGGAACAAGAGATCTAAATTGTAAG 58.331 37.037 16.54 0.00 44.16 2.34
3583 4080 7.283354 GGAACAAGAGATCTAAATTGTAAGGGG 59.717 40.741 16.54 0.00 34.92 4.79
3676 4173 2.414994 ACGGACGGACAGATCTTCTA 57.585 50.000 0.00 0.00 0.00 2.10
3684 4181 5.446860 ACGGACAGATCTTCTATTCTACCA 58.553 41.667 0.00 0.00 0.00 3.25
3699 4196 1.263217 CTACCACCAAACGTTGACTGC 59.737 52.381 0.00 0.00 0.00 4.40
3813 4310 0.959372 ATGGCAGCAGCTCACACTTC 60.959 55.000 0.00 0.00 41.70 3.01
3819 4316 0.737715 GCAGCTCACACTTCCTACGG 60.738 60.000 0.00 0.00 0.00 4.02
3883 4381 2.305927 GGGAGGTCAGATGGAGTGAAAA 59.694 50.000 0.00 0.00 0.00 2.29
3885 4383 3.244561 GGAGGTCAGATGGAGTGAAAACA 60.245 47.826 0.00 0.00 0.00 2.83
3897 4395 6.409704 TGGAGTGAAAACAATCTGATCCTAG 58.590 40.000 0.00 0.00 0.00 3.02
3913 4411 0.824759 CTAGTAACCAAGAGCGCCCT 59.175 55.000 2.29 0.00 0.00 5.19
3916 4414 0.461516 GTAACCAAGAGCGCCCTACC 60.462 60.000 2.29 0.00 0.00 3.18
3918 4416 3.083997 CCAAGAGCGCCCTACCCT 61.084 66.667 2.29 0.00 0.00 4.34
3920 4418 1.153349 CAAGAGCGCCCTACCCTTC 60.153 63.158 2.29 0.00 0.00 3.46
3922 4420 4.893601 GAGCGCCCTACCCTTCGC 62.894 72.222 2.29 0.00 46.95 4.70
3928 4426 4.867599 CCTACCCTTCGCGCGTCC 62.868 72.222 30.98 0.00 0.00 4.79
3945 4443 3.542690 CGTCCGTCTTATAGTGATGTCG 58.457 50.000 0.00 0.00 0.00 4.35
3948 4446 3.246936 TCCGTCTTATAGTGATGTCGACG 59.753 47.826 11.62 0.00 41.48 5.12
3968 4466 2.268920 GCTTCCATCCACTCGCCA 59.731 61.111 0.00 0.00 0.00 5.69
3970 4468 1.450312 CTTCCATCCACTCGCCACC 60.450 63.158 0.00 0.00 0.00 4.61
3971 4469 2.184020 CTTCCATCCACTCGCCACCA 62.184 60.000 0.00 0.00 0.00 4.17
3985 4483 2.084546 GCCACCAGACAGTAATTGGTC 58.915 52.381 1.71 0.00 43.11 4.02
3998 4496 2.809861 ATTGGTCGCTGGAGTGGCAG 62.810 60.000 0.00 0.00 0.00 4.85
3999 4497 4.767255 GGTCGCTGGAGTGGCAGG 62.767 72.222 0.00 0.00 0.00 4.85
4065 4563 1.364536 TGCAGGCACAATGTTGCAG 59.635 52.632 7.09 2.32 44.94 4.41
4072 4570 0.993251 CACAATGTTGCAGTGCGTCG 60.993 55.000 11.20 0.00 32.35 5.12
4093 4591 3.003480 GAGCAATCTTACGCCTTGTCTT 58.997 45.455 0.00 0.00 0.00 3.01
4101 4599 1.589803 ACGCCTTGTCTTAAAGCGTT 58.410 45.000 2.06 0.00 36.92 4.84
4104 4602 2.661979 CGCCTTGTCTTAAAGCGTTGAC 60.662 50.000 0.00 0.00 0.00 3.18
4106 4604 2.096417 CCTTGTCTTAAAGCGTTGACGG 60.096 50.000 5.62 0.00 40.23 4.79
4116 4614 1.463444 AGCGTTGACGGCATTAAGTTC 59.537 47.619 0.00 0.00 40.23 3.01
4177 4675 8.373981 ACAGTATGAGAGCTAAATGAAGCATAT 58.626 33.333 2.69 0.00 41.72 1.78
4197 4695 8.139989 AGCATATCAATCTTGGCATTTAAACTC 58.860 33.333 0.00 0.00 0.00 3.01
4246 4744 3.104512 ACCTCCTTCGGTATGTCATTGA 58.895 45.455 0.00 0.00 34.94 2.57
4279 4777 8.373256 GTTGTTCAAAAGCTTCTTTACTTGAAC 58.627 33.333 28.85 28.85 46.51 3.18
4284 4782 7.754924 TCAAAAGCTTCTTTACTTGAACTTGTG 59.245 33.333 0.00 0.00 30.36 3.33
4306 4804 5.415701 GTGTCATGGTCATAAATGTCCACTT 59.584 40.000 10.48 0.00 45.97 3.16
4329 4849 4.515191 TGCAACTCACTCTAACATGTTTCC 59.485 41.667 17.78 0.00 0.00 3.13
4337 4857 7.431249 TCACTCTAACATGTTTCCGGATATAC 58.569 38.462 17.78 4.86 0.00 1.47
4342 4862 8.145767 TCTAACATGTTTCCGGATATACGATTT 58.854 33.333 17.78 1.66 35.47 2.17
4343 4863 9.414295 CTAACATGTTTCCGGATATACGATTTA 57.586 33.333 17.78 2.67 35.47 1.40
4393 4913 2.486191 GCCAACCATCTAGTCCATGAGG 60.486 54.545 0.00 0.00 0.00 3.86
4404 4924 7.496346 TCTAGTCCATGAGGTAGACAATTTT 57.504 36.000 0.00 0.00 35.89 1.82
4447 4967 2.560105 TCCCATGCTCATCTAGATGTCG 59.440 50.000 27.80 21.13 39.72 4.35
4448 4968 2.353505 CCCATGCTCATCTAGATGTCGG 60.354 54.545 27.80 20.68 39.72 4.79
4468 4988 7.747888 TGTCGGTGATAATATGTTGTTTGAAG 58.252 34.615 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 2.907696 TCTATGGTCTCGGGGTCAAAAA 59.092 45.455 0.00 0.00 0.00 1.94
51 52 2.542550 TCTATGGTCTCGGGGTCAAAA 58.457 47.619 0.00 0.00 0.00 2.44
52 53 2.235402 GTTCTATGGTCTCGGGGTCAAA 59.765 50.000 0.00 0.00 0.00 2.69
53 54 1.829222 GTTCTATGGTCTCGGGGTCAA 59.171 52.381 0.00 0.00 0.00 3.18
54 55 1.272816 TGTTCTATGGTCTCGGGGTCA 60.273 52.381 0.00 0.00 0.00 4.02
55 56 1.481871 TGTTCTATGGTCTCGGGGTC 58.518 55.000 0.00 0.00 0.00 4.46
56 57 1.946984 TTGTTCTATGGTCTCGGGGT 58.053 50.000 0.00 0.00 0.00 4.95
57 58 3.206150 CAATTGTTCTATGGTCTCGGGG 58.794 50.000 0.00 0.00 0.00 5.73
58 59 3.873910 ACAATTGTTCTATGGTCTCGGG 58.126 45.455 4.92 0.00 0.00 5.14
127 128 9.868277 GGAATTGGTTGATGTAATATTTGTTGA 57.132 29.630 0.00 0.00 0.00 3.18
128 129 9.874205 AGGAATTGGTTGATGTAATATTTGTTG 57.126 29.630 0.00 0.00 0.00 3.33
203 624 3.324846 AGAACTGGTGCAGTGTTCATCTA 59.675 43.478 20.95 0.00 44.62 1.98
205 626 2.498167 AGAACTGGTGCAGTGTTCATC 58.502 47.619 20.95 2.62 44.62 2.92
213 634 1.233019 CACCTCAAGAACTGGTGCAG 58.767 55.000 0.00 0.00 43.61 4.41
230 651 3.782889 AAACCACAGAAAGCAGAACAC 57.217 42.857 0.00 0.00 0.00 3.32
297 718 0.902531 GCCCAGAGCACCAGTAACTA 59.097 55.000 0.00 0.00 42.97 2.24
315 736 2.094545 ACAAGATTTTCCGGAATGCTGC 60.095 45.455 19.62 6.34 0.00 5.25
325 746 7.254421 GGACACAACAAAATGACAAGATTTTCC 60.254 37.037 0.00 0.00 34.05 3.13
342 763 6.238897 GGATGTTGAAGTTTATGGACACAACA 60.239 38.462 0.00 0.00 44.40 3.33
461 903 6.828273 CAGATATGAAGGTGGACATTTTACCA 59.172 38.462 0.00 0.00 36.94 3.25
480 922 9.676861 TTTTCAATGACTTCTCATGACAGATAT 57.323 29.630 4.45 0.00 37.20 1.63
502 944 6.817270 TTTCATACCGCGTATAGAGTTTTC 57.183 37.500 4.92 0.00 0.00 2.29
615 1057 2.725221 AGAGTTCATGAATCCCTGCC 57.275 50.000 12.12 0.00 0.00 4.85
616 1058 3.135530 ACCTAGAGTTCATGAATCCCTGC 59.864 47.826 12.12 0.00 0.00 4.85
617 1059 5.365021 AACCTAGAGTTCATGAATCCCTG 57.635 43.478 12.12 2.94 30.99 4.45
618 1060 6.012508 TCAAAACCTAGAGTTCATGAATCCCT 60.013 38.462 12.12 11.16 37.88 4.20
619 1061 6.180472 TCAAAACCTAGAGTTCATGAATCCC 58.820 40.000 12.12 4.16 37.88 3.85
620 1062 6.183360 GCTCAAAACCTAGAGTTCATGAATCC 60.183 42.308 12.12 6.67 37.88 3.01
621 1063 6.597280 AGCTCAAAACCTAGAGTTCATGAATC 59.403 38.462 12.12 10.09 37.88 2.52
622 1064 6.479884 AGCTCAAAACCTAGAGTTCATGAAT 58.520 36.000 12.12 0.66 37.88 2.57
629 1071 7.719633 TGATGTTTAAGCTCAAAACCTAGAGTT 59.280 33.333 17.40 0.00 41.81 3.01
631 1073 7.604164 TCTGATGTTTAAGCTCAAAACCTAGAG 59.396 37.037 17.40 10.55 36.26 2.43
754 1196 1.139853 GGCAGATCGACCAGAGGAAAT 59.860 52.381 0.00 0.00 0.00 2.17
781 1223 3.131933 AGGGATCTCGTGATTCTTCTGTG 59.868 47.826 5.77 0.00 32.19 3.66
941 1387 5.594725 CACGTATAGAGGCATGGGTAGATAT 59.405 44.000 0.00 0.00 0.00 1.63
1039 1485 1.599542 GCAAGGTGATATTGGTCGAGC 59.400 52.381 7.89 7.89 0.00 5.03
1088 1534 4.319477 CGCGAAAATCCTTGAGAACTGAAA 60.319 41.667 0.00 0.00 0.00 2.69
1089 1535 3.186409 CGCGAAAATCCTTGAGAACTGAA 59.814 43.478 0.00 0.00 0.00 3.02
1090 1536 2.736721 CGCGAAAATCCTTGAGAACTGA 59.263 45.455 0.00 0.00 0.00 3.41
1091 1537 2.480419 ACGCGAAAATCCTTGAGAACTG 59.520 45.455 15.93 0.00 0.00 3.16
1092 1538 2.767505 ACGCGAAAATCCTTGAGAACT 58.232 42.857 15.93 0.00 0.00 3.01
1093 1539 3.537793 AACGCGAAAATCCTTGAGAAC 57.462 42.857 15.93 0.00 0.00 3.01
1133 1585 7.235409 TGGAAACATAGTACAGTTCACTGCAG 61.235 42.308 13.48 13.48 41.12 4.41
1210 1696 3.175152 CTCGAGATCGTTCTGAAACCTG 58.825 50.000 6.58 0.00 40.80 4.00
1225 1711 1.005748 CAACTGCTGCACCTCGAGA 60.006 57.895 15.71 0.00 0.00 4.04
1424 1910 1.079057 GGTCGAAGAAGAGGTGGCC 60.079 63.158 0.00 0.00 39.69 5.36
1430 1916 2.184579 GCGGGGGTCGAAGAAGAG 59.815 66.667 0.00 0.00 39.69 2.85
1519 2005 1.477295 GTTCCGGTGAGGTAGAGGAAG 59.523 57.143 0.00 0.00 41.09 3.46
1702 2188 0.975556 TGGCGATCTTGTAGGGCTGA 60.976 55.000 0.00 0.00 0.00 4.26
1739 2225 4.566488 GGTGATGAGATCAAACCAGAAGGT 60.566 45.833 11.32 0.00 41.90 3.50
1796 2282 5.592104 TCACGGAAAGAGCACTGAATATA 57.408 39.130 0.00 0.00 0.00 0.86
1797 2283 4.471904 TCACGGAAAGAGCACTGAATAT 57.528 40.909 0.00 0.00 0.00 1.28
1798 2284 3.953712 TCACGGAAAGAGCACTGAATA 57.046 42.857 0.00 0.00 0.00 1.75
1821 2308 5.928839 TCTACAGAGCATTTCAGTTCTTGAC 59.071 40.000 0.00 0.00 34.94 3.18
1844 2331 4.474226 AACACGCACTTCAGAAGATTTC 57.526 40.909 17.56 2.09 0.00 2.17
1855 2342 0.600255 CCGAGGAGAAACACGCACTT 60.600 55.000 0.00 0.00 0.00 3.16
1857 2344 0.038892 TACCGAGGAGAAACACGCAC 60.039 55.000 0.00 0.00 0.00 5.34
1858 2345 0.038892 GTACCGAGGAGAAACACGCA 60.039 55.000 0.00 0.00 0.00 5.24
1859 2346 0.735287 GGTACCGAGGAGAAACACGC 60.735 60.000 0.00 0.00 0.00 5.34
1860 2347 0.108945 GGGTACCGAGGAGAAACACG 60.109 60.000 5.65 0.00 40.86 4.49
2099 2589 0.618458 GGTACCACAATGCTCCCAGA 59.382 55.000 7.15 0.00 0.00 3.86
2213 2703 0.403271 AGATGGTCCTGTTGCTGCTT 59.597 50.000 0.00 0.00 0.00 3.91
2291 2781 3.719214 GCCTCTGCGTAAATCCCG 58.281 61.111 0.00 0.00 0.00 5.14
2303 2793 3.447586 TGAGCTTATAGTTGAACGCCTCT 59.552 43.478 0.00 0.00 0.00 3.69
2309 2799 4.164294 ACGTCGTGAGCTTATAGTTGAAC 58.836 43.478 0.00 0.00 0.00 3.18
2446 2936 8.912988 TGTAACTGATTTTTCCTCTCAACAAAT 58.087 29.630 0.00 0.00 0.00 2.32
2447 2937 8.287439 TGTAACTGATTTTTCCTCTCAACAAA 57.713 30.769 0.00 0.00 0.00 2.83
2448 2938 7.873719 TGTAACTGATTTTTCCTCTCAACAA 57.126 32.000 0.00 0.00 0.00 2.83
2449 2939 9.739276 ATATGTAACTGATTTTTCCTCTCAACA 57.261 29.630 0.00 0.00 0.00 3.33
2452 2942 9.177608 CCAATATGTAACTGATTTTTCCTCTCA 57.822 33.333 0.00 0.00 0.00 3.27
2453 2943 8.131731 GCCAATATGTAACTGATTTTTCCTCTC 58.868 37.037 0.00 0.00 0.00 3.20
2454 2944 7.068716 GGCCAATATGTAACTGATTTTTCCTCT 59.931 37.037 0.00 0.00 0.00 3.69
2455 2945 7.147915 TGGCCAATATGTAACTGATTTTTCCTC 60.148 37.037 0.61 0.00 0.00 3.71
2457 2947 6.872920 TGGCCAATATGTAACTGATTTTTCC 58.127 36.000 0.61 0.00 0.00 3.13
2458 2948 7.981225 ACATGGCCAATATGTAACTGATTTTTC 59.019 33.333 10.96 0.00 37.02 2.29
2494 2987 9.893305 GCAACTGAAACATGTTTTTATACTAGT 57.107 29.630 24.02 15.44 32.11 2.57
2495 2988 9.341899 GGCAACTGAAACATGTTTTTATACTAG 57.658 33.333 24.02 14.93 32.11 2.57
2647 3140 3.055312 TGCTGCAAGATTGATGAGAGTCT 60.055 43.478 0.00 0.00 34.07 3.24
2648 3141 3.268330 TGCTGCAAGATTGATGAGAGTC 58.732 45.455 0.00 0.00 34.07 3.36
2649 3142 3.345508 TGCTGCAAGATTGATGAGAGT 57.654 42.857 0.00 0.00 34.07 3.24
2650 3143 4.082949 TGTTTGCTGCAAGATTGATGAGAG 60.083 41.667 15.39 0.00 34.07 3.20
2651 3144 3.822167 TGTTTGCTGCAAGATTGATGAGA 59.178 39.130 15.39 0.00 34.07 3.27
2652 3145 4.168922 TGTTTGCTGCAAGATTGATGAG 57.831 40.909 15.39 0.00 34.07 2.90
2653 3146 4.587584 TTGTTTGCTGCAAGATTGATGA 57.412 36.364 15.39 0.00 34.07 2.92
2680 3173 4.843728 TGTCAGTTCTTCCACAACTTCTT 58.156 39.130 0.00 0.00 31.40 2.52
3580 4076 1.227973 CTCAAGAATAGGCGGCCCC 60.228 63.158 17.02 0.00 0.00 5.80
3583 4080 0.753262 TCTCCTCAAGAATAGGCGGC 59.247 55.000 0.00 0.00 33.84 6.53
3676 4173 3.813166 CAGTCAACGTTTGGTGGTAGAAT 59.187 43.478 0.00 0.00 0.00 2.40
3684 4181 1.745232 TTGAGCAGTCAACGTTTGGT 58.255 45.000 0.00 0.00 37.79 3.67
3699 4196 2.669364 GCAGTTTGCAACAGGATTGAG 58.331 47.619 0.00 0.00 44.26 3.02
3819 4316 8.317679 AGATGAATTTACCATATCTGAGTAGGC 58.682 37.037 0.00 0.00 0.00 3.93
3861 4359 0.413434 TCACTCCATCTGACCTCCCA 59.587 55.000 0.00 0.00 0.00 4.37
3883 4381 6.407525 GCTCTTGGTTACTAGGATCAGATTGT 60.408 42.308 0.00 0.00 0.00 2.71
3885 4383 5.221342 CGCTCTTGGTTACTAGGATCAGATT 60.221 44.000 0.00 0.00 0.00 2.40
3897 4395 0.461516 GGTAGGGCGCTCTTGGTTAC 60.462 60.000 18.76 6.90 0.00 2.50
3916 4414 2.931713 ATAAGACGGACGCGCGAAGG 62.932 60.000 39.36 25.08 0.00 3.46
3918 4416 0.316442 CTATAAGACGGACGCGCGAA 60.316 55.000 39.36 10.83 0.00 4.70
3920 4418 1.010350 ACTATAAGACGGACGCGCG 60.010 57.895 30.96 30.96 0.00 6.86
3922 4420 2.286831 ACATCACTATAAGACGGACGCG 60.287 50.000 3.53 3.53 0.00 6.01
3924 4422 3.246936 TCGACATCACTATAAGACGGACG 59.753 47.826 0.00 0.00 0.00 4.79
3933 4431 2.207590 AGCGTCGTCGACATCACTATA 58.792 47.619 24.13 0.00 39.71 1.31
3945 4443 0.802607 GAGTGGATGGAAGCGTCGTC 60.803 60.000 0.00 0.00 0.00 4.20
3948 4446 2.167861 GCGAGTGGATGGAAGCGTC 61.168 63.158 0.00 0.00 0.00 5.19
3968 4466 1.623811 AGCGACCAATTACTGTCTGGT 59.376 47.619 8.41 8.41 46.22 4.00
3970 4468 2.002586 CCAGCGACCAATTACTGTCTG 58.997 52.381 0.00 0.00 0.00 3.51
3971 4469 1.899814 TCCAGCGACCAATTACTGTCT 59.100 47.619 0.00 0.00 0.00 3.41
4003 4501 4.101448 CAACCCCTCCCGGCTCTG 62.101 72.222 0.00 0.00 0.00 3.35
4047 4545 1.364536 CTGCAACATTGTGCCTGCA 59.635 52.632 12.66 12.66 44.26 4.41
4065 4563 0.294887 CGTAAGATTGCTCGACGCAC 59.705 55.000 8.73 0.57 46.21 5.34
4072 4570 2.622436 AGACAAGGCGTAAGATTGCTC 58.378 47.619 0.00 0.00 38.62 4.26
4093 4591 3.068560 ACTTAATGCCGTCAACGCTTTA 58.931 40.909 0.00 0.43 38.18 1.85
4101 4599 7.624360 AATAAAGATGAACTTAATGCCGTCA 57.376 32.000 0.00 0.00 37.93 4.35
4104 4602 9.573133 AAGAAAATAAAGATGAACTTAATGCCG 57.427 29.630 0.00 0.00 37.93 5.69
4177 4675 6.757897 ATCGAGTTTAAATGCCAAGATTGA 57.242 33.333 0.00 0.00 0.00 2.57
4279 4777 5.415389 TGGACATTTATGACCATGACACAAG 59.585 40.000 9.36 0.00 45.20 3.16
4306 4804 4.515191 GGAAACATGTTAGAGTGAGTTGCA 59.485 41.667 12.39 0.00 0.00 4.08
4343 4863 9.638239 AATTTGCACACTATTTTATGTTCGATT 57.362 25.926 0.00 0.00 0.00 3.34
4356 4876 4.526262 TGGTTGGCTAAATTTGCACACTAT 59.474 37.500 0.00 0.00 0.00 2.12
4358 4878 2.697751 TGGTTGGCTAAATTTGCACACT 59.302 40.909 0.00 0.00 0.00 3.55
4364 4884 5.652014 TGGACTAGATGGTTGGCTAAATTTG 59.348 40.000 0.00 0.00 0.00 2.32
4428 4948 2.298446 ACCGACATCTAGATGAGCATGG 59.702 50.000 34.16 26.29 41.20 3.66
4432 4952 3.932545 ATCACCGACATCTAGATGAGC 57.067 47.619 34.16 23.86 41.20 4.26


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

AutoCloner maintained by Alex Coulton.