Multiple sequence alignment - TraesCS6D01G152200

Loading Multiple Alignment...

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 TraesCS6D01G152200 chr6D 100.000 5520 0 0 1 5520 125985670 125991189 0.000000e+00 10194.0
1 TraesCS6D01G152200 chr6D 85.526 228 27 1 2762 2989 291716154 291715933 3.320000e-57 233.0
2 TraesCS6D01G152200 chr6D 98.333 60 1 0 103 162 125985715 125985774 7.560000e-19 106.0
3 TraesCS6D01G152200 chr6D 98.333 60 1 0 46 105 125985772 125985831 7.560000e-19 106.0
4 TraesCS6D01G152200 chr6B 96.523 4832 121 16 103 4900 224252719 224257537 0.000000e+00 7949.0
5 TraesCS6D01G152200 chr6B 88.491 643 49 8 4900 5520 224257570 224258209 0.000000e+00 754.0
6 TraesCS6D01G152200 chr6B 97.143 105 2 1 1 105 224252674 224252777 5.680000e-40 176.0
7 TraesCS6D01G152200 chr6A 94.250 2939 125 17 1978 4900 154040766 154037856 0.000000e+00 4451.0
8 TraesCS6D01G152200 chr6A 96.673 1052 33 2 929 1979 154041900 154040850 0.000000e+00 1748.0
9 TraesCS6D01G152200 chr6A 93.214 840 39 9 103 937 154042778 154041952 0.000000e+00 1219.0
10 TraesCS6D01G152200 chr6A 93.087 622 37 5 4900 5520 154037823 154037207 0.000000e+00 905.0
11 TraesCS6D01G152200 chr6A 97.143 105 3 0 1 105 154042823 154042719 1.580000e-40 178.0
12 TraesCS6D01G152200 chr1D 91.463 492 34 2 3483 3970 249618523 249619010 0.000000e+00 669.0
13 TraesCS6D01G152200 chr3A 88.844 493 43 5 3483 3970 434451098 434450613 3.680000e-166 595.0
14 TraesCS6D01G152200 chr1A 92.891 211 11 1 3763 3969 548308448 548308238 2.500000e-78 303.0
15 TraesCS6D01G152200 chr1A 87.879 231 28 0 2759 2989 466042077 466042307 7.050000e-69 272.0
16 TraesCS6D01G152200 chr1A 86.538 104 14 0 5408 5511 572344973 572345076 1.260000e-21 115.0
17 TraesCS6D01G152200 chr7D 89.520 229 24 0 2761 2989 451621763 451621535 1.950000e-74 291.0
18 TraesCS6D01G152200 chr7D 84.211 228 30 1 2762 2989 23078052 23077831 3.350000e-52 217.0
19 TraesCS6D01G152200 chrUn 84.848 231 29 1 2759 2989 96527184 96527408 1.550000e-55 228.0
20 TraesCS6D01G152200 chr5D 84.848 231 29 1 2759 2989 178477709 178477933 1.550000e-55 228.0
21 TraesCS6D01G152200 chr4D 83.830 235 28 2 2759 2989 215190198 215190426 1.200000e-51 215.0
22 TraesCS6D01G152200 chr5A 81.731 208 37 1 4320 4527 36932726 36932932 7.350000e-39 172.0
23 TraesCS6D01G152200 chr1B 87.356 87 11 0 5425 5511 662790147 662790233 3.520000e-17 100.0
24 TraesCS6D01G152200 chr2D 100.000 38 0 0 4863 4900 318561209 318561172 2.760000e-08 71.3
25 TraesCS6D01G152200 chr2A 94.286 35 2 0 4866 4900 7528438 7528404 3.000000e-03 54.7


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 TraesCS6D01G152200 chr6D 125985670 125991189 5519 False 10194.000000 10194 100.000000 1 5520 1 chr6D.!!$F1 5519
1 TraesCS6D01G152200 chr6B 224252674 224258209 5535 False 2959.666667 7949 94.052333 1 5520 3 chr6B.!!$F1 5519
2 TraesCS6D01G152200 chr6A 154037207 154042823 5616 True 1700.200000 4451 94.873400 1 5520 5 chr6A.!!$R1 5519

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
74 75 0.252761 TCTCATGGCCGATTCAGCAA 59.747 50.000 0.0 0.0 0.00 3.91 F
78 79 0.254178 ATGGCCGATTCAGCAAGACT 59.746 50.000 0.0 0.0 0.00 3.24 F
816 823 1.021202 CAAGCCCACAGAAAACACGA 58.979 50.000 0.0 0.0 0.00 4.35 F
998 1065 3.917988 AGCAAAGAATAGCAAAGGCAAC 58.082 40.909 0.0 0.0 44.61 4.17 F
2211 2364 0.874175 CGACGCTGACAACAACAGGA 60.874 55.000 0.0 0.0 36.09 3.86 F
2957 3126 0.606096 TCTTCCCAATCTTGCGACGA 59.394 50.000 0.0 0.0 0.00 4.20 F
3726 3901 2.421388 CCTGAAGTGAACCAACCAGACA 60.421 50.000 0.0 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1483 1550 0.237498 GGTGCGAACCTTACTGCAAC 59.763 55.000 4.88 0.0 39.34 4.17 R
1719 1787 2.158871 TCTGTTAAGACGCCACAACCTT 60.159 45.455 0.00 0.0 0.00 3.50 R
2211 2364 1.496001 TCAGCATGCAAGTCCCCATAT 59.504 47.619 21.98 0.0 34.76 1.78 R
2283 2436 1.560923 CGATGAGGTAAGCCGTCAAG 58.439 55.000 0.00 0.0 40.50 3.02 R
3466 3641 2.084546 GCGGAAAGTAAATGGCTGAGT 58.915 47.619 0.00 0.0 0.00 3.41 R
4475 4667 1.037579 TCGCCATCTCGGATGACACT 61.038 55.000 13.47 0.0 36.56 3.55 R
5218 5468 0.555769 TTTTTCCTCCTGTGGCTGGT 59.444 50.000 0.00 0.0 0.00 4.00 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
24 25 3.625099 GCCCATCAAGCAGGCAAT 58.375 55.556 0.00 0.00 46.34 3.56
52 53 4.624015 TGAGTTGGGTACGTCTAAACAAG 58.376 43.478 0.00 0.00 0.00 3.16
53 54 3.992427 GAGTTGGGTACGTCTAAACAAGG 59.008 47.826 0.00 0.00 0.00 3.61
54 55 3.642848 AGTTGGGTACGTCTAAACAAGGA 59.357 43.478 0.00 0.00 0.00 3.36
55 56 4.285260 AGTTGGGTACGTCTAAACAAGGAT 59.715 41.667 0.00 0.00 0.00 3.24
56 57 4.460948 TGGGTACGTCTAAACAAGGATC 57.539 45.455 0.00 0.00 0.00 3.36
57 58 4.091549 TGGGTACGTCTAAACAAGGATCT 58.908 43.478 0.00 0.00 0.00 2.75
58 59 4.159135 TGGGTACGTCTAAACAAGGATCTC 59.841 45.833 0.00 0.00 0.00 2.75
59 60 4.159135 GGGTACGTCTAAACAAGGATCTCA 59.841 45.833 0.00 0.00 0.00 3.27
60 61 5.163437 GGGTACGTCTAAACAAGGATCTCAT 60.163 44.000 0.00 0.00 0.00 2.90
61 62 5.749109 GGTACGTCTAAACAAGGATCTCATG 59.251 44.000 0.00 0.00 0.00 3.07
62 63 4.759782 ACGTCTAAACAAGGATCTCATGG 58.240 43.478 0.00 0.00 0.00 3.66
63 64 3.557595 CGTCTAAACAAGGATCTCATGGC 59.442 47.826 0.00 0.00 0.00 4.40
64 65 3.879892 GTCTAAACAAGGATCTCATGGCC 59.120 47.826 0.00 0.00 0.00 5.36
65 66 1.755179 AAACAAGGATCTCATGGCCG 58.245 50.000 0.00 0.00 0.00 6.13
66 67 0.911769 AACAAGGATCTCATGGCCGA 59.088 50.000 0.00 0.00 0.00 5.54
67 68 1.135094 ACAAGGATCTCATGGCCGAT 58.865 50.000 0.00 0.00 0.00 4.18
68 69 1.492176 ACAAGGATCTCATGGCCGATT 59.508 47.619 0.00 0.00 0.00 3.34
69 70 2.149578 CAAGGATCTCATGGCCGATTC 58.850 52.381 0.00 0.00 0.00 2.52
70 71 1.427809 AGGATCTCATGGCCGATTCA 58.572 50.000 0.00 0.00 0.00 2.57
71 72 1.347050 AGGATCTCATGGCCGATTCAG 59.653 52.381 0.00 0.00 0.00 3.02
72 73 1.155042 GATCTCATGGCCGATTCAGC 58.845 55.000 0.00 0.00 0.00 4.26
73 74 0.471191 ATCTCATGGCCGATTCAGCA 59.529 50.000 0.00 0.00 0.00 4.41
74 75 0.252761 TCTCATGGCCGATTCAGCAA 59.747 50.000 0.00 0.00 0.00 3.91
75 76 0.661552 CTCATGGCCGATTCAGCAAG 59.338 55.000 0.00 0.00 0.00 4.01
76 77 0.252761 TCATGGCCGATTCAGCAAGA 59.747 50.000 0.00 0.00 0.00 3.02
77 78 0.379669 CATGGCCGATTCAGCAAGAC 59.620 55.000 0.00 0.00 0.00 3.01
78 79 0.254178 ATGGCCGATTCAGCAAGACT 59.746 50.000 0.00 0.00 0.00 3.24
92 93 2.719798 CAAGACTGCAAAACAAGACGG 58.280 47.619 0.00 0.00 0.00 4.79
93 94 2.325583 AGACTGCAAAACAAGACGGA 57.674 45.000 0.00 0.00 0.00 4.69
94 95 2.639065 AGACTGCAAAACAAGACGGAA 58.361 42.857 0.00 0.00 0.00 4.30
95 96 2.354821 AGACTGCAAAACAAGACGGAAC 59.645 45.455 0.00 0.00 0.00 3.62
96 97 2.354821 GACTGCAAAACAAGACGGAACT 59.645 45.455 0.00 0.00 0.00 3.01
97 98 2.752903 ACTGCAAAACAAGACGGAACTT 59.247 40.909 0.00 0.00 0.00 2.66
98 99 3.181500 ACTGCAAAACAAGACGGAACTTC 60.181 43.478 0.00 0.00 0.00 3.01
99 100 2.750166 TGCAAAACAAGACGGAACTTCA 59.250 40.909 0.00 0.00 0.00 3.02
100 101 3.191581 TGCAAAACAAGACGGAACTTCAA 59.808 39.130 0.00 0.00 0.00 2.69
101 102 4.170256 GCAAAACAAGACGGAACTTCAAA 58.830 39.130 0.00 0.00 0.00 2.69
102 103 4.803613 GCAAAACAAGACGGAACTTCAAAT 59.196 37.500 0.00 0.00 0.00 2.32
103 104 5.974751 GCAAAACAAGACGGAACTTCAAATA 59.025 36.000 0.00 0.00 0.00 1.40
104 105 6.474102 GCAAAACAAGACGGAACTTCAAATAA 59.526 34.615 0.00 0.00 0.00 1.40
105 106 7.009723 GCAAAACAAGACGGAACTTCAAATAAA 59.990 33.333 0.00 0.00 0.00 1.40
106 107 7.980742 AAACAAGACGGAACTTCAAATAAAC 57.019 32.000 0.00 0.00 0.00 2.01
107 108 6.687081 ACAAGACGGAACTTCAAATAAACA 57.313 33.333 0.00 0.00 0.00 2.83
108 109 7.090953 ACAAGACGGAACTTCAAATAAACAA 57.909 32.000 0.00 0.00 0.00 2.83
149 151 2.719798 CAAGACTGCAAAACAAGACGG 58.280 47.619 0.00 0.00 0.00 4.79
586 590 4.872691 ACGATTGCTACAGATTCAAGAAGG 59.127 41.667 0.00 0.00 0.00 3.46
816 823 1.021202 CAAGCCCACAGAAAACACGA 58.979 50.000 0.00 0.00 0.00 4.35
998 1065 3.917988 AGCAAAGAATAGCAAAGGCAAC 58.082 40.909 0.00 0.00 44.61 4.17
1719 1787 6.620877 TCCTTTAAGGTTCTCAATCTGCTA 57.379 37.500 11.13 0.00 36.53 3.49
1964 2032 4.874966 CCTTCAAAAGTTTCAACCATGCAA 59.125 37.500 0.00 0.00 0.00 4.08
2211 2364 0.874175 CGACGCTGACAACAACAGGA 60.874 55.000 0.00 0.00 36.09 3.86
2283 2436 7.986085 TTTCTATATGCTCTTTAATCTGGGC 57.014 36.000 0.00 0.00 0.00 5.36
2286 2439 7.164122 TCTATATGCTCTTTAATCTGGGCTTG 58.836 38.462 0.00 0.00 0.00 4.01
2378 2531 8.201464 TGTATGTTTCTCAACTTACTCACAGAA 58.799 33.333 10.67 0.00 41.20 3.02
2385 2538 6.925718 TCTCAACTTACTCACAGAACATTCAG 59.074 38.462 0.00 0.00 0.00 3.02
2387 2540 6.479990 TCAACTTACTCACAGAACATTCAGTG 59.520 38.462 10.08 10.08 43.49 3.66
2388 2541 5.918608 ACTTACTCACAGAACATTCAGTGT 58.081 37.500 14.50 0.00 42.91 3.55
2389 2542 5.986135 ACTTACTCACAGAACATTCAGTGTC 59.014 40.000 14.50 0.00 42.91 3.67
2390 2543 4.406648 ACTCACAGAACATTCAGTGTCA 57.593 40.909 14.50 0.00 42.91 3.58
2391 2544 4.965814 ACTCACAGAACATTCAGTGTCAT 58.034 39.130 14.50 2.40 42.91 3.06
2392 2545 6.101650 ACTCACAGAACATTCAGTGTCATA 57.898 37.500 14.50 0.00 42.91 2.15
2393 2546 6.524734 ACTCACAGAACATTCAGTGTCATAA 58.475 36.000 14.50 0.00 42.91 1.90
2394 2547 7.164122 ACTCACAGAACATTCAGTGTCATAAT 58.836 34.615 14.50 0.00 42.91 1.28
2395 2548 7.663081 ACTCACAGAACATTCAGTGTCATAATT 59.337 33.333 14.50 0.00 42.91 1.40
2396 2549 7.809665 TCACAGAACATTCAGTGTCATAATTG 58.190 34.615 14.50 0.00 42.91 2.32
2397 2550 7.025365 CACAGAACATTCAGTGTCATAATTGG 58.975 38.462 8.55 0.00 41.14 3.16
2398 2551 6.716628 ACAGAACATTCAGTGTCATAATTGGT 59.283 34.615 0.00 0.00 41.14 3.67
2399 2552 7.231317 ACAGAACATTCAGTGTCATAATTGGTT 59.769 33.333 0.00 0.00 41.14 3.67
2400 2553 7.539710 CAGAACATTCAGTGTCATAATTGGTTG 59.460 37.037 0.00 0.00 41.14 3.77
2422 2575 7.502561 GGTTGGTAGCTATTCATGTCCTTATTT 59.497 37.037 0.00 0.00 0.00 1.40
2423 2576 8.560374 GTTGGTAGCTATTCATGTCCTTATTTC 58.440 37.037 0.00 0.00 0.00 2.17
2456 2618 7.817418 AAAAAGAACAGAAATAGGCTGTACA 57.183 32.000 0.00 0.00 45.27 2.90
2469 2631 2.639839 GGCTGTACATGGATCCCATACT 59.360 50.000 9.90 0.00 43.15 2.12
2526 2688 9.807386 GCACTTTTATTATATACGACATGGTTC 57.193 33.333 0.00 0.00 0.00 3.62
2654 2817 7.604164 TCAACAATTTTAGGCAACAAGAAAACA 59.396 29.630 0.00 0.00 41.41 2.83
2692 2855 1.136252 CAAGGTCTTGCACAATCGACG 60.136 52.381 0.00 0.00 33.45 5.12
2693 2856 1.132640 GGTCTTGCACAATCGACGC 59.867 57.895 0.00 0.00 0.00 5.19
2735 2904 1.754803 TGTTCCACGCCTATAGTCCTG 59.245 52.381 0.00 0.00 0.00 3.86
2957 3126 0.606096 TCTTCCCAATCTTGCGACGA 59.394 50.000 0.00 0.00 0.00 4.20
3206 3375 7.241042 AGCAGTGGTTAGTTTGTTATCTCTA 57.759 36.000 0.00 0.00 0.00 2.43
3353 3522 3.319031 TGCAGAGACTCCCAGATATCA 57.681 47.619 5.32 0.00 0.00 2.15
3361 3530 8.106462 CAGAGACTCCCAGATATCACTAAGATA 58.894 40.741 5.32 0.00 43.11 1.98
3466 3641 6.156256 AGAGGTTGGTGCTCTATGTAACATAA 59.844 38.462 0.00 0.00 0.00 1.90
3726 3901 2.421388 CCTGAAGTGAACCAACCAGACA 60.421 50.000 0.00 0.00 0.00 3.41
4100 4275 2.429930 CAGCCGGGTTCTCCACAA 59.570 61.111 1.64 0.00 34.36 3.33
4234 4409 5.059833 GGTACAGAATGGGAAGCTTATCAG 58.940 45.833 0.00 0.00 43.62 2.90
4262 4437 4.039245 CCTGATTCGCTGGAGGAACTTATA 59.961 45.833 0.00 0.00 41.55 0.98
4341 4530 3.916035 AGCAGAGACCAGATATACACCA 58.084 45.455 0.00 0.00 0.00 4.17
4348 4537 6.895756 AGAGACCAGATATACACCACACTTTA 59.104 38.462 0.00 0.00 0.00 1.85
4398 4590 8.671921 GCACTTCTCTCATCAAATATTTCTTCA 58.328 33.333 0.00 0.00 0.00 3.02
4456 4648 7.036220 CGACAAAAGTGGTCAGTAGAGATTAT 58.964 38.462 0.00 0.00 34.97 1.28
4552 4750 2.890945 GCACAAACCAACCTAACCAGAT 59.109 45.455 0.00 0.00 0.00 2.90
4558 4756 4.467198 ACCAACCTAACCAGATAACTCG 57.533 45.455 0.00 0.00 0.00 4.18
4580 4778 5.594725 TCGTAGAGAGATAAGTGCTCCATTT 59.405 40.000 0.00 0.00 32.82 2.32
4581 4779 6.771267 TCGTAGAGAGATAAGTGCTCCATTTA 59.229 38.462 0.00 0.00 32.82 1.40
4582 4780 7.041030 TCGTAGAGAGATAAGTGCTCCATTTAG 60.041 40.741 0.00 0.00 32.82 1.85
4583 4781 7.255312 CGTAGAGAGATAAGTGCTCCATTTAGT 60.255 40.741 0.00 0.00 32.82 2.24
4605 4804 5.889853 AGTGAAAGTAATGGATGCACATGAT 59.110 36.000 0.00 0.00 0.00 2.45
4633 4832 3.167425 CGACTGAAGATGTGAAGACGAG 58.833 50.000 0.00 0.00 31.11 4.18
4767 4966 9.189156 AGCATTTCTTAGTTCCATTTATAGCAA 57.811 29.630 0.00 0.00 0.00 3.91
4787 4986 4.388773 GCAAGTTATGTGTTCGAGTCATGA 59.611 41.667 0.00 0.00 0.00 3.07
4912 5144 1.002069 ATGCAGAACCCCTTCATCCA 58.998 50.000 0.00 0.00 0.00 3.41
5006 5238 1.843206 ACAACCTGTTTGGGCCAAAAT 59.157 42.857 31.94 15.64 39.84 1.82
5015 5247 8.606830 ACCTGTTTGGGCCAAAATAATTATTAA 58.393 29.630 31.94 3.86 41.11 1.40
5025 5257 9.016623 GCCAAAATAATTATTAACCTGTTCGAC 57.983 33.333 11.07 0.00 0.00 4.20
5078 5322 3.083997 AGGCTGGCTTAGACGGGG 61.084 66.667 0.00 0.00 40.39 5.73
5083 5327 0.546598 CTGGCTTAGACGGGGGATTT 59.453 55.000 0.00 0.00 0.00 2.17
5104 5354 3.127425 AGAAGAAACTTCTTGACCCCG 57.873 47.619 9.40 0.00 46.84 5.73
5164 5414 1.600511 TATGGCCAGACAACGCTCGA 61.601 55.000 13.05 0.00 0.00 4.04
5218 5468 6.121776 ACACCTCCTATTTTCACATACACA 57.878 37.500 0.00 0.00 0.00 3.72
5245 5498 3.189287 CCACAGGAGGAAAAACTTCATCG 59.811 47.826 0.00 0.00 32.99 3.84
5262 5515 3.119101 TCATCGGTCAGCTTAAGGAGAAC 60.119 47.826 4.29 0.00 0.00 3.01
5266 5519 3.676324 CGGTCAGCTTAAGGAGAACGATT 60.676 47.826 4.29 0.00 43.39 3.34
5304 5557 6.069440 ATCACAAAGATTTGGAGGATGTCCTA 60.069 38.462 9.91 0.00 42.70 2.94
5321 5574 7.550196 GGATGTCCTATTAAACACTTCGGTAAA 59.450 37.037 0.00 0.00 0.00 2.01
5395 5648 1.348696 TCAACCAGCTTGATCTCAGCA 59.651 47.619 16.82 0.00 33.65 4.41
5410 5663 0.752009 CAGCAGCCTTGATGCCTGAT 60.752 55.000 0.05 0.00 46.90 2.90
5426 5679 1.195442 TGATGGTGTTACGGCCCAGA 61.195 55.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 7.557358 TGTTTAGACGTACCCAACTCATATCTA 59.443 37.037 0.00 0.00 0.00 1.98
52 53 1.805869 CTGAATCGGCCATGAGATCC 58.194 55.000 2.24 0.00 0.00 3.36
53 54 1.155042 GCTGAATCGGCCATGAGATC 58.845 55.000 2.24 0.00 0.00 2.75
54 55 0.471191 TGCTGAATCGGCCATGAGAT 59.529 50.000 12.01 0.00 34.37 2.75
55 56 0.252761 TTGCTGAATCGGCCATGAGA 59.747 50.000 12.01 0.00 34.37 3.27
56 57 0.661552 CTTGCTGAATCGGCCATGAG 59.338 55.000 12.01 0.93 34.37 2.90
57 58 0.252761 TCTTGCTGAATCGGCCATGA 59.747 50.000 12.01 4.29 34.37 3.07
58 59 0.379669 GTCTTGCTGAATCGGCCATG 59.620 55.000 12.01 1.88 34.37 3.66
59 60 0.254178 AGTCTTGCTGAATCGGCCAT 59.746 50.000 12.01 0.00 34.37 4.40
60 61 1.679311 AGTCTTGCTGAATCGGCCA 59.321 52.632 12.01 0.00 34.37 5.36
61 62 4.625800 AGTCTTGCTGAATCGGCC 57.374 55.556 12.01 0.00 34.37 6.13
72 73 2.354510 TCCGTCTTGTTTTGCAGTCTTG 59.645 45.455 0.00 0.00 0.00 3.02
73 74 2.639065 TCCGTCTTGTTTTGCAGTCTT 58.361 42.857 0.00 0.00 0.00 3.01
74 75 2.325583 TCCGTCTTGTTTTGCAGTCT 57.674 45.000 0.00 0.00 0.00 3.24
75 76 2.354821 AGTTCCGTCTTGTTTTGCAGTC 59.645 45.455 0.00 0.00 0.00 3.51
76 77 2.365582 AGTTCCGTCTTGTTTTGCAGT 58.634 42.857 0.00 0.00 0.00 4.40
77 78 3.181501 TGAAGTTCCGTCTTGTTTTGCAG 60.182 43.478 0.00 0.00 0.00 4.41
78 79 2.750166 TGAAGTTCCGTCTTGTTTTGCA 59.250 40.909 0.00 0.00 0.00 4.08
79 80 3.414549 TGAAGTTCCGTCTTGTTTTGC 57.585 42.857 0.00 0.00 0.00 3.68
80 81 7.979115 TTATTTGAAGTTCCGTCTTGTTTTG 57.021 32.000 0.00 0.00 0.00 2.44
81 82 8.030106 TGTTTATTTGAAGTTCCGTCTTGTTTT 58.970 29.630 0.00 0.00 0.00 2.43
82 83 7.540299 TGTTTATTTGAAGTTCCGTCTTGTTT 58.460 30.769 0.00 0.00 0.00 2.83
83 84 7.090953 TGTTTATTTGAAGTTCCGTCTTGTT 57.909 32.000 0.00 0.00 0.00 2.83
84 85 6.687081 TGTTTATTTGAAGTTCCGTCTTGT 57.313 33.333 0.00 0.00 0.00 3.16
85 86 6.636850 CCTTGTTTATTTGAAGTTCCGTCTTG 59.363 38.462 0.00 0.00 0.00 3.02
86 87 6.544564 TCCTTGTTTATTTGAAGTTCCGTCTT 59.455 34.615 0.00 0.00 0.00 3.01
87 88 6.059484 TCCTTGTTTATTTGAAGTTCCGTCT 58.941 36.000 0.00 0.00 0.00 4.18
88 89 6.308371 TCCTTGTTTATTTGAAGTTCCGTC 57.692 37.500 0.00 0.00 0.00 4.79
89 90 6.715264 AGATCCTTGTTTATTTGAAGTTCCGT 59.285 34.615 0.00 0.00 0.00 4.69
90 91 7.094805 TGAGATCCTTGTTTATTTGAAGTTCCG 60.095 37.037 0.00 0.00 0.00 4.30
91 92 8.110860 TGAGATCCTTGTTTATTTGAAGTTCC 57.889 34.615 0.00 0.00 0.00 3.62
92 93 9.565213 CATGAGATCCTTGTTTATTTGAAGTTC 57.435 33.333 0.00 0.00 0.00 3.01
93 94 8.526147 CCATGAGATCCTTGTTTATTTGAAGTT 58.474 33.333 0.00 0.00 0.00 2.66
94 95 7.363268 GCCATGAGATCCTTGTTTATTTGAAGT 60.363 37.037 0.00 0.00 0.00 3.01
95 96 6.976925 GCCATGAGATCCTTGTTTATTTGAAG 59.023 38.462 0.00 0.00 0.00 3.02
96 97 6.664816 AGCCATGAGATCCTTGTTTATTTGAA 59.335 34.615 0.00 0.00 0.00 2.69
97 98 6.095860 CAGCCATGAGATCCTTGTTTATTTGA 59.904 38.462 0.00 0.00 0.00 2.69
98 99 6.095860 TCAGCCATGAGATCCTTGTTTATTTG 59.904 38.462 0.00 0.00 0.00 2.32
99 100 6.189859 TCAGCCATGAGATCCTTGTTTATTT 58.810 36.000 0.00 0.00 0.00 1.40
100 101 5.759059 TCAGCCATGAGATCCTTGTTTATT 58.241 37.500 0.00 0.00 0.00 1.40
101 102 5.378230 TCAGCCATGAGATCCTTGTTTAT 57.622 39.130 0.00 0.00 0.00 1.40
102 103 4.842531 TCAGCCATGAGATCCTTGTTTA 57.157 40.909 0.00 0.00 0.00 2.01
103 104 3.726557 TCAGCCATGAGATCCTTGTTT 57.273 42.857 0.00 0.00 0.00 2.83
104 105 3.947612 ATCAGCCATGAGATCCTTGTT 57.052 42.857 0.00 0.00 39.29 2.83
105 106 3.201487 TGAATCAGCCATGAGATCCTTGT 59.799 43.478 0.00 0.00 39.29 3.16
106 107 3.815962 CTGAATCAGCCATGAGATCCTTG 59.184 47.826 0.00 0.00 39.29 3.61
107 108 4.088056 CTGAATCAGCCATGAGATCCTT 57.912 45.455 0.00 0.00 39.29 3.36
108 109 3.773418 CTGAATCAGCCATGAGATCCT 57.227 47.619 0.00 0.00 39.29 3.24
210 212 3.560025 CCATTAAGGGCTGAACAGACTGT 60.560 47.826 1.07 1.07 36.46 3.55
586 590 2.744741 TCATCGATGACTATCCTCTCGC 59.255 50.000 23.99 0.00 0.00 5.03
998 1065 5.381174 TTTTGAATGAGCTTGAGTCATGG 57.619 39.130 8.02 0.00 34.78 3.66
1483 1550 0.237498 GGTGCGAACCTTACTGCAAC 59.763 55.000 4.88 0.00 39.34 4.17
1719 1787 2.158871 TCTGTTAAGACGCCACAACCTT 60.159 45.455 0.00 0.00 0.00 3.50
2211 2364 1.496001 TCAGCATGCAAGTCCCCATAT 59.504 47.619 21.98 0.00 34.76 1.78
2283 2436 1.560923 CGATGAGGTAAGCCGTCAAG 58.439 55.000 0.00 0.00 40.50 3.02
2286 2439 1.591863 GCCGATGAGGTAAGCCGTC 60.592 63.158 0.00 0.00 43.70 4.79
2385 2538 7.282224 TGAATAGCTACCAACCAATTATGACAC 59.718 37.037 0.00 0.00 0.00 3.67
2387 2540 7.801716 TGAATAGCTACCAACCAATTATGAC 57.198 36.000 0.00 0.00 0.00 3.06
2388 2541 7.998383 ACATGAATAGCTACCAACCAATTATGA 59.002 33.333 0.00 0.00 0.00 2.15
2389 2542 8.169977 ACATGAATAGCTACCAACCAATTATG 57.830 34.615 0.00 0.00 0.00 1.90
2390 2543 7.448469 GGACATGAATAGCTACCAACCAATTAT 59.552 37.037 0.00 0.00 0.00 1.28
2391 2544 6.770785 GGACATGAATAGCTACCAACCAATTA 59.229 38.462 0.00 0.00 0.00 1.40
2392 2545 5.594317 GGACATGAATAGCTACCAACCAATT 59.406 40.000 0.00 0.00 0.00 2.32
2393 2546 5.103940 AGGACATGAATAGCTACCAACCAAT 60.104 40.000 0.00 0.00 0.00 3.16
2394 2547 4.227300 AGGACATGAATAGCTACCAACCAA 59.773 41.667 0.00 0.00 0.00 3.67
2395 2548 3.780294 AGGACATGAATAGCTACCAACCA 59.220 43.478 0.00 0.00 0.00 3.67
2396 2549 4.423625 AGGACATGAATAGCTACCAACC 57.576 45.455 0.00 3.85 0.00 3.77
2397 2550 8.451908 AAATAAGGACATGAATAGCTACCAAC 57.548 34.615 0.00 0.00 0.00 3.77
2398 2551 7.441157 CGAAATAAGGACATGAATAGCTACCAA 59.559 37.037 0.00 0.00 0.00 3.67
2399 2552 6.929049 CGAAATAAGGACATGAATAGCTACCA 59.071 38.462 0.00 0.00 0.00 3.25
2400 2553 6.128526 GCGAAATAAGGACATGAATAGCTACC 60.129 42.308 0.00 0.00 0.00 3.18
2455 2617 7.442364 CACAACTTTAGTAGTATGGGATCCATG 59.558 40.741 15.23 0.00 44.84 3.66
2456 2618 7.347222 TCACAACTTTAGTAGTATGGGATCCAT 59.653 37.037 15.23 7.94 46.99 3.41
2526 2688 5.048713 GGCTAGGGGATACATTTCATTTTCG 60.049 44.000 0.00 0.00 39.74 3.46
2654 2817 6.774656 AGACCTTGATTCATGTTGTTTTCTCT 59.225 34.615 0.00 0.00 0.00 3.10
2692 2855 7.971455 ACAAGAATGACGGTAACTATTTTAGC 58.029 34.615 0.00 0.00 0.00 3.09
2693 2856 9.968743 GAACAAGAATGACGGTAACTATTTTAG 57.031 33.333 0.00 0.00 0.00 1.85
2900 3069 2.296190 GCTTGAACGGATTCCTTTTGGT 59.704 45.455 0.30 0.00 41.38 3.67
2957 3126 3.342926 ACTCCATGGAAGAGATAGGCT 57.657 47.619 17.00 0.00 35.27 4.58
3206 3375 7.829725 TGCACAAGCTTTGATTCATAACTTAT 58.170 30.769 0.00 0.00 42.74 1.73
3381 3551 9.428097 ACCTGCTTTCAAGAAATTCATTTTATC 57.572 29.630 0.00 0.00 0.00 1.75
3466 3641 2.084546 GCGGAAAGTAAATGGCTGAGT 58.915 47.619 0.00 0.00 0.00 3.41
3664 3839 4.275689 TCAGTTTCTGTACATTGGCACAAG 59.724 41.667 0.00 0.00 36.67 3.16
3726 3901 6.070309 AGGTCATACTTGCTCAAGAATCTTCT 60.070 38.462 15.74 4.63 40.79 2.85
3938 4113 5.195940 TCTTCTTTGTCCATCATTCCATCC 58.804 41.667 0.00 0.00 0.00 3.51
4074 4249 3.281359 AACCCGGCTGCATTTTCGC 62.281 57.895 0.50 0.00 0.00 4.70
4100 4275 5.590259 CCTTGATATGTTTTCGGATGTCCTT 59.410 40.000 0.00 0.00 0.00 3.36
4188 4363 6.041637 ACCGTAGAACCTATTGCATTATGAGA 59.958 38.462 0.00 0.00 0.00 3.27
4201 4376 3.956199 CCCATTCTGTACCGTAGAACCTA 59.044 47.826 0.00 0.00 37.03 3.08
4234 4409 3.207669 CCAGCGAATCAGGCAGGC 61.208 66.667 0.00 0.00 30.05 4.85
4243 4418 7.881775 ATTTTTATAAGTTCCTCCAGCGAAT 57.118 32.000 0.00 0.00 0.00 3.34
4262 4437 8.504812 AACATTTTCACTTACTGCCAATTTTT 57.495 26.923 0.00 0.00 0.00 1.94
4398 4590 3.327757 TGGAAACTTCTGTCCTGCATAGT 59.672 43.478 0.00 0.00 34.77 2.12
4475 4667 1.037579 TCGCCATCTCGGATGACACT 61.038 55.000 13.47 0.00 36.56 3.55
4523 4721 8.056400 TGGTTAGGTTGGTTTGTGCTATATATT 58.944 33.333 0.00 0.00 0.00 1.28
4552 4750 5.759273 GGAGCACTTATCTCTCTACGAGTTA 59.241 44.000 0.00 0.00 40.75 2.24
4558 4756 7.865385 CACTAAATGGAGCACTTATCTCTCTAC 59.135 40.741 0.00 0.00 0.00 2.59
4565 4763 7.617041 ACTTTCACTAAATGGAGCACTTATC 57.383 36.000 0.00 0.00 0.00 1.75
4580 4778 6.413892 TCATGTGCATCCATTACTTTCACTA 58.586 36.000 0.00 0.00 0.00 2.74
4581 4779 5.255687 TCATGTGCATCCATTACTTTCACT 58.744 37.500 0.00 0.00 0.00 3.41
4582 4780 5.565592 TCATGTGCATCCATTACTTTCAC 57.434 39.130 0.00 0.00 0.00 3.18
4583 4781 5.068067 CCATCATGTGCATCCATTACTTTCA 59.932 40.000 0.00 0.00 0.00 2.69
4633 4832 9.573133 CTATTTGTAAGAATGTCAAAATGTCCC 57.427 33.333 0.00 0.00 35.28 4.46
4767 4966 4.220821 ACCTCATGACTCGAACACATAACT 59.779 41.667 0.00 0.00 0.00 2.24
4787 4986 4.861102 CCGGTCGGTAATAAGATTACCT 57.139 45.455 20.69 0.00 41.66 3.08
4815 5014 9.533253 AGTCAAAACAAACAATAAAGATCAAGG 57.467 29.630 0.00 0.00 0.00 3.61
4912 5144 4.458989 TGTTTCTGAGTTTGCAGTTGAAGT 59.541 37.500 0.00 0.00 37.20 3.01
4971 5203 4.105697 ACAGGTTGTTCTTTTATCCCTCCA 59.894 41.667 0.00 0.00 0.00 3.86
5061 5293 3.083997 CCCCGTCTAAGCCAGCCT 61.084 66.667 0.00 0.00 0.00 4.58
5062 5294 4.176752 CCCCCGTCTAAGCCAGCC 62.177 72.222 0.00 0.00 0.00 4.85
5078 5322 6.151312 GGGGTCAAGAAGTTTCTTCTAAATCC 59.849 42.308 11.60 11.59 45.23 3.01
5083 5327 3.556423 GCGGGGTCAAGAAGTTTCTTCTA 60.556 47.826 11.60 0.00 45.23 2.10
5112 5362 2.552315 CGAGCAAAGCCCAAGAAGTTAA 59.448 45.455 0.00 0.00 0.00 2.01
5113 5363 2.151202 CGAGCAAAGCCCAAGAAGTTA 58.849 47.619 0.00 0.00 0.00 2.24
5218 5468 0.555769 TTTTTCCTCCTGTGGCTGGT 59.444 50.000 0.00 0.00 0.00 4.00
5245 5498 3.528597 ATCGTTCTCCTTAAGCTGACC 57.471 47.619 0.00 0.00 0.00 4.02
5266 5519 4.384940 TCTTTGTGATTTGTCACGATCCA 58.615 39.130 4.34 0.00 43.12 3.41
5298 5551 8.149647 TCTTTTACCGAAGTGTTTAATAGGACA 58.850 33.333 0.00 0.00 0.00 4.02
5304 5557 7.524065 CCGATTCTTTTACCGAAGTGTTTAAT 58.476 34.615 0.00 0.00 0.00 1.40
5321 5574 1.056660 ATATGGGTCGGCCGATTCTT 58.943 50.000 33.58 23.79 34.86 2.52
5410 5663 2.589157 CCTCTGGGCCGTAACACCA 61.589 63.158 0.00 0.00 0.00 4.17
5426 5679 2.097110 TCCGGTATGATAAGGCACCT 57.903 50.000 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.