Multiple sequence alignment - TraesCS5D01G387300

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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 TraesCS5D01G387300 chr5D 100.000 2690 0 0 1 2690 456753057 456750368 0.000000e+00 4968
1 TraesCS5D01G387300 chr5D 81.517 422 70 8 2274 2690 538625970 538625552 9.220000e-90 340
2 TraesCS5D01G387300 chr5D 75.817 459 100 10 831 1282 495030724 495031178 3.490000e-54 222
3 TraesCS5D01G387300 chr5B 96.071 2036 51 11 154 2174 558688172 558686151 0.000000e+00 3290
4 TraesCS5D01G387300 chr5B 80.523 421 76 6 2274 2690 679666795 679666377 4.320000e-83 318
5 TraesCS5D01G387300 chr5B 79.810 421 80 5 2274 2690 496150381 496150800 4.350000e-78 302
6 TraesCS5D01G387300 chr5B 76.803 513 101 8 2195 2690 558685755 558685244 3.410000e-69 272
7 TraesCS5D01G387300 chr5A 93.941 1964 105 4 727 2690 574785875 574783926 0.000000e+00 2955
8 TraesCS5D01G387300 chr5A 94.184 619 15 13 89 698 574786484 574785878 0.000000e+00 924
9 TraesCS5D01G387300 chr5A 74.672 458 107 8 831 1282 619097928 619098382 7.600000e-46 195
10 TraesCS5D01G387300 chr2D 82.270 423 67 6 2274 2690 606149673 606150093 2.550000e-95 359
11 TraesCS5D01G387300 chr2D 73.538 975 195 51 808 1755 112865096 112866034 2.010000e-81 313
12 TraesCS5D01G387300 chr2D 79.903 413 77 6 2274 2683 66864134 66864543 5.630000e-77 298
13 TraesCS5D01G387300 chr2D 78.960 423 81 8 2274 2690 424653190 424653610 5.670000e-72 281
14 TraesCS5D01G387300 chr2A 73.998 973 194 46 808 1755 114300436 114301374 9.220000e-90 340
15 TraesCS5D01G387300 chr2B 80.998 421 76 4 2274 2690 636877587 636878007 5.550000e-87 331
16 TraesCS5D01G387300 chr1A 80.535 411 73 7 2274 2677 491366802 491366392 2.600000e-80 309
17 TraesCS5D01G387300 chr1D 79.335 421 83 4 2274 2690 409762238 409762658 2.620000e-75 292


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 TraesCS5D01G387300 chr5D 456750368 456753057 2689 True 4968.0 4968 100.0000 1 2690 1 chr5D.!!$R1 2689
1 TraesCS5D01G387300 chr5B 558685244 558688172 2928 True 1781.0 3290 86.4370 154 2690 2 chr5B.!!$R2 2536
2 TraesCS5D01G387300 chr5A 574783926 574786484 2558 True 1939.5 2955 94.0625 89 2690 2 chr5A.!!$R1 2601
3 TraesCS5D01G387300 chr2D 112865096 112866034 938 False 313.0 313 73.5380 808 1755 1 chr2D.!!$F2 947
4 TraesCS5D01G387300 chr2A 114300436 114301374 938 False 340.0 340 73.9980 808 1755 1 chr2A.!!$F1 947

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
572 585 0.259065 TACCTTGCACCCACCAAACA 59.741 50.0 0.0 0.0 0.0 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2490 3007 0.766131 ATGGTTGTTACCCGGTGTGA 59.234 50.0 0.0 0.0 44.35 3.58 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
38 39 6.774354 CTGCAAGCTTTTTGACATTAATGT 57.226 33.333 20.93 20.93 45.16 2.71
39 40 7.872163 CTGCAAGCTTTTTGACATTAATGTA 57.128 32.000 20.83 3.97 41.95 2.29
40 41 7.636259 TGCAAGCTTTTTGACATTAATGTAC 57.364 32.000 20.83 14.27 41.95 2.90
41 42 7.432869 TGCAAGCTTTTTGACATTAATGTACT 58.567 30.769 20.83 7.40 41.95 2.73
42 43 7.594758 TGCAAGCTTTTTGACATTAATGTACTC 59.405 33.333 20.83 9.64 41.95 2.59
43 44 7.062255 GCAAGCTTTTTGACATTAATGTACTCC 59.938 37.037 20.83 9.29 41.95 3.85
44 45 7.158099 AGCTTTTTGACATTAATGTACTCCC 57.842 36.000 20.83 8.94 41.95 4.30
45 46 6.948309 AGCTTTTTGACATTAATGTACTCCCT 59.052 34.615 20.83 8.91 41.95 4.20
46 47 7.121315 AGCTTTTTGACATTAATGTACTCCCTC 59.879 37.037 20.83 7.56 41.95 4.30
47 48 6.978343 TTTTGACATTAATGTACTCCCTCG 57.022 37.500 20.83 0.00 41.95 4.63
48 49 5.670792 TTGACATTAATGTACTCCCTCGT 57.329 39.130 20.83 0.00 41.95 4.18
49 50 5.258456 TGACATTAATGTACTCCCTCGTC 57.742 43.478 20.83 5.49 41.95 4.20
50 51 4.098960 TGACATTAATGTACTCCCTCGTCC 59.901 45.833 20.83 5.01 41.95 4.79
51 52 4.028131 ACATTAATGTACTCCCTCGTCCA 58.972 43.478 19.51 0.00 39.68 4.02
52 53 4.142004 ACATTAATGTACTCCCTCGTCCAC 60.142 45.833 19.51 0.00 39.68 4.02
53 54 1.933021 AATGTACTCCCTCGTCCACA 58.067 50.000 0.00 0.00 0.00 4.17
54 55 1.933021 ATGTACTCCCTCGTCCACAA 58.067 50.000 0.00 0.00 0.00 3.33
55 56 1.707106 TGTACTCCCTCGTCCACAAA 58.293 50.000 0.00 0.00 0.00 2.83
56 57 2.253610 TGTACTCCCTCGTCCACAAAT 58.746 47.619 0.00 0.00 0.00 2.32
57 58 3.433343 TGTACTCCCTCGTCCACAAATA 58.567 45.455 0.00 0.00 0.00 1.40
58 59 4.028131 TGTACTCCCTCGTCCACAAATAT 58.972 43.478 0.00 0.00 0.00 1.28
59 60 5.202765 TGTACTCCCTCGTCCACAAATATA 58.797 41.667 0.00 0.00 0.00 0.86
60 61 5.657745 TGTACTCCCTCGTCCACAAATATAA 59.342 40.000 0.00 0.00 0.00 0.98
61 62 5.019785 ACTCCCTCGTCCACAAATATAAC 57.980 43.478 0.00 0.00 0.00 1.89
62 63 4.468510 ACTCCCTCGTCCACAAATATAACA 59.531 41.667 0.00 0.00 0.00 2.41
63 64 5.130477 ACTCCCTCGTCCACAAATATAACAT 59.870 40.000 0.00 0.00 0.00 2.71
64 65 5.364778 TCCCTCGTCCACAAATATAACATG 58.635 41.667 0.00 0.00 0.00 3.21
65 66 5.104693 TCCCTCGTCCACAAATATAACATGT 60.105 40.000 0.00 0.00 0.00 3.21
66 67 5.588648 CCCTCGTCCACAAATATAACATGTT 59.411 40.000 16.68 16.68 0.00 2.71
67 68 6.094881 CCCTCGTCCACAAATATAACATGTTT 59.905 38.462 17.78 7.40 0.00 2.83
68 69 7.362574 CCCTCGTCCACAAATATAACATGTTTT 60.363 37.037 17.78 11.71 0.00 2.43
69 70 7.484641 CCTCGTCCACAAATATAACATGTTTTG 59.515 37.037 17.78 16.58 35.66 2.44
70 71 7.309177 TCGTCCACAAATATAACATGTTTTGG 58.691 34.615 17.78 11.49 34.23 3.28
71 72 7.175119 TCGTCCACAAATATAACATGTTTTGGA 59.825 33.333 17.78 13.38 34.23 3.53
72 73 7.973388 CGTCCACAAATATAACATGTTTTGGAT 59.027 33.333 17.78 6.61 35.43 3.41
94 95 7.812191 TGGATACTTCAATATTTTTGCACACAC 59.188 33.333 0.00 0.00 37.61 3.82
186 188 7.069085 GTGAAAGTTTTCTTAGTTTTACCCCCT 59.931 37.037 6.21 0.00 39.48 4.79
197 202 6.229936 AGTTTTACCCCCTTTTGAAGTTTC 57.770 37.500 0.00 0.00 0.00 2.78
232 237 7.288389 TGGATAGTTCCTATAGCGGTTCTTTTA 59.712 37.037 0.00 0.00 43.07 1.52
396 405 4.691860 AGAAGAAAAGAATGTGCATCGG 57.308 40.909 0.00 0.00 0.00 4.18
572 585 0.259065 TACCTTGCACCCACCAAACA 59.741 50.000 0.00 0.00 0.00 2.83
639 652 1.737236 TGTGCATTAGCGACCATGAAC 59.263 47.619 0.00 0.00 46.23 3.18
651 664 4.318121 GCGACCATGAACTAATTCGATGAC 60.318 45.833 0.00 0.00 37.69 3.06
686 699 2.802719 GCTCCTAAACCCCACAAATGA 58.197 47.619 0.00 0.00 0.00 2.57
687 700 3.365472 GCTCCTAAACCCCACAAATGAT 58.635 45.455 0.00 0.00 0.00 2.45
698 711 6.194235 ACCCCACAAATGATGCTTAGAATTA 58.806 36.000 0.00 0.00 0.00 1.40
699 712 6.840705 ACCCCACAAATGATGCTTAGAATTAT 59.159 34.615 0.00 0.00 0.00 1.28
700 713 7.149973 CCCCACAAATGATGCTTAGAATTATG 58.850 38.462 0.00 0.00 0.00 1.90
701 714 7.149973 CCCACAAATGATGCTTAGAATTATGG 58.850 38.462 0.00 0.00 0.00 2.74
702 715 7.201938 CCCACAAATGATGCTTAGAATTATGGT 60.202 37.037 0.00 0.00 0.00 3.55
703 716 8.849168 CCACAAATGATGCTTAGAATTATGGTA 58.151 33.333 0.00 0.00 0.00 3.25
704 717 9.669353 CACAAATGATGCTTAGAATTATGGTAC 57.331 33.333 0.00 0.00 0.00 3.34
705 718 8.559536 ACAAATGATGCTTAGAATTATGGTACG 58.440 33.333 0.00 0.00 0.00 3.67
706 719 8.559536 CAAATGATGCTTAGAATTATGGTACGT 58.440 33.333 0.00 0.00 0.00 3.57
707 720 7.658179 ATGATGCTTAGAATTATGGTACGTG 57.342 36.000 0.00 0.00 0.00 4.49
708 721 6.578944 TGATGCTTAGAATTATGGTACGTGT 58.421 36.000 0.00 0.00 0.00 4.49
709 722 7.718525 TGATGCTTAGAATTATGGTACGTGTA 58.281 34.615 0.00 0.00 0.00 2.90
710 723 7.650504 TGATGCTTAGAATTATGGTACGTGTAC 59.349 37.037 0.00 1.49 35.40 2.90
721 734 3.641437 GTACGTGTACCACTAACACCA 57.359 47.619 0.00 0.00 43.46 4.17
722 735 3.976169 GTACGTGTACCACTAACACCAA 58.024 45.455 0.00 0.00 43.46 3.67
723 736 2.825205 ACGTGTACCACTAACACCAAC 58.175 47.619 0.00 0.00 43.46 3.77
724 737 2.137523 CGTGTACCACTAACACCAACC 58.862 52.381 1.11 0.00 43.46 3.77
725 738 2.483363 CGTGTACCACTAACACCAACCA 60.483 50.000 1.11 0.00 43.46 3.67
729 742 0.941542 CCACTAACACCAACCACGTG 59.058 55.000 9.08 9.08 37.26 4.49
785 825 2.745884 TCCATGCACGCGGAAAGG 60.746 61.111 12.47 5.74 0.00 3.11
1197 1314 4.024717 AGCAGGATGAGCTCGACA 57.975 55.556 9.64 0.00 38.01 4.35
1758 1879 0.740868 CGGTGATGACGTGCTTCCAT 60.741 55.000 0.00 0.00 0.00 3.41
1922 2043 1.744741 GGAGAGCTCTTGTGGCTGC 60.745 63.158 19.36 1.62 40.40 5.25
1949 2070 2.622436 CTTCGAGAGGGGTGACATTTC 58.378 52.381 0.00 0.00 0.00 2.17
2062 2183 7.218614 TCGGGTGGTTATATATACTGGTTTTG 58.781 38.462 0.00 0.00 0.00 2.44
2065 2186 7.421617 GGGTGGTTATATATACTGGTTTTGGGA 60.422 40.741 0.00 0.00 0.00 4.37
2262 2772 5.923733 ACACCAAAATACTCCAACAACAA 57.076 34.783 0.00 0.00 0.00 2.83
2271 2781 3.156293 ACTCCAACAACAAGCATATGCA 58.844 40.909 28.62 3.75 45.16 3.96
2324 2841 5.804639 TCATAGCAGTACAAAGAACACCAT 58.195 37.500 0.00 0.00 0.00 3.55
2364 2881 1.043673 AGATCCGTCCACCACCTAGC 61.044 60.000 0.00 0.00 0.00 3.42
2372 2889 1.287815 CACCACCTAGCGACGTCAA 59.712 57.895 17.16 0.00 0.00 3.18
2376 2893 1.604693 CCACCTAGCGACGTCAAAAGT 60.605 52.381 17.16 2.88 0.00 2.66
2378 2895 3.508762 CACCTAGCGACGTCAAAAGTAT 58.491 45.455 17.16 0.00 0.00 2.12
2379 2896 3.924686 CACCTAGCGACGTCAAAAGTATT 59.075 43.478 17.16 0.00 0.00 1.89
2389 2906 3.432252 CGTCAAAAGTATTGGAGCGAGTT 59.568 43.478 0.00 0.00 0.00 3.01
2396 2913 1.021390 ATTGGAGCGAGTTGAAGGCG 61.021 55.000 0.00 0.00 0.00 5.52
2490 3007 1.143813 CTAAGGCCCCATGAGACCAT 58.856 55.000 0.00 0.00 0.00 3.55
2492 3009 0.920763 AAGGCCCCATGAGACCATCA 60.921 55.000 0.00 0.00 43.70 3.07
2496 3013 0.107017 CCCCATGAGACCATCACACC 60.107 60.000 0.00 0.00 41.91 4.16
2497 3014 0.462581 CCCATGAGACCATCACACCG 60.463 60.000 0.00 0.00 41.91 4.94
2514 3032 1.913419 ACCGGGTAACAACCATCATCT 59.087 47.619 6.32 0.00 39.74 2.90
2527 3045 9.685276 AACAACCATCATCTATGAATAAAGTCA 57.315 29.630 0.00 0.00 40.69 3.41
2590 3109 6.615088 CACAAATAAGACTGGATCCAAACAG 58.385 40.000 17.00 6.53 40.48 3.16
2607 3126 0.898320 CAGATCCACCGAAGACCAGT 59.102 55.000 0.00 0.00 0.00 4.00
2622 3141 2.169769 GACCAGTACCGATCAAATCCCA 59.830 50.000 0.00 0.00 0.00 4.37
2623 3142 2.093128 ACCAGTACCGATCAAATCCCAC 60.093 50.000 0.00 0.00 0.00 4.61
2631 3150 2.224042 CGATCAAATCCCACGAGATCCA 60.224 50.000 0.00 0.00 33.33 3.41
2632 3151 3.555795 CGATCAAATCCCACGAGATCCAT 60.556 47.826 0.00 0.00 33.33 3.41
2633 3152 3.198409 TCAAATCCCACGAGATCCATG 57.802 47.619 0.00 0.00 0.00 3.66
2649 3169 4.627394 TGGAGACACACCTCTGCT 57.373 55.556 0.00 0.00 33.40 4.24
2652 3172 0.901124 GGAGACACACCTCTGCTCAT 59.099 55.000 0.00 0.00 33.79 2.90
2673 3193 2.722548 CCGACGATGCTAGACGCG 60.723 66.667 3.53 3.53 43.27 6.01
2678 3198 2.368105 CGATGCTAGACGCGCCATC 61.368 63.158 5.73 6.92 43.27 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.805971 GCTTGCAGCAAATTCAAACTCTT 59.194 39.130 9.65 0.00 41.89 2.85
1 2 3.069158 AGCTTGCAGCAAATTCAAACTCT 59.931 39.130 9.65 0.00 45.56 3.24
2 3 3.387397 AGCTTGCAGCAAATTCAAACTC 58.613 40.909 9.65 0.00 45.56 3.01
3 4 3.464111 AGCTTGCAGCAAATTCAAACT 57.536 38.095 9.65 0.00 45.56 2.66
4 5 4.541085 AAAGCTTGCAGCAAATTCAAAC 57.459 36.364 9.65 0.00 45.56 2.93
5 6 5.123502 TCAAAAAGCTTGCAGCAAATTCAAA 59.876 32.000 9.65 0.00 45.56 2.69
6 7 4.634883 TCAAAAAGCTTGCAGCAAATTCAA 59.365 33.333 9.65 0.00 45.56 2.69
7 8 4.034279 GTCAAAAAGCTTGCAGCAAATTCA 59.966 37.500 9.65 0.00 45.56 2.57
8 9 4.034279 TGTCAAAAAGCTTGCAGCAAATTC 59.966 37.500 9.65 1.58 45.56 2.17
9 10 3.940221 TGTCAAAAAGCTTGCAGCAAATT 59.060 34.783 9.65 4.38 45.56 1.82
10 11 3.533547 TGTCAAAAAGCTTGCAGCAAAT 58.466 36.364 9.65 0.00 45.56 2.32
11 12 2.969990 TGTCAAAAAGCTTGCAGCAAA 58.030 38.095 9.65 0.00 45.56 3.68
12 13 2.669300 TGTCAAAAAGCTTGCAGCAA 57.331 40.000 7.81 7.81 45.56 3.91
13 14 2.894763 ATGTCAAAAAGCTTGCAGCA 57.105 40.000 0.00 0.00 45.56 4.41
14 15 5.178067 ACATTAATGTCAAAAAGCTTGCAGC 59.822 36.000 15.47 0.47 37.82 5.25
15 16 6.774354 ACATTAATGTCAAAAAGCTTGCAG 57.226 33.333 15.47 0.00 35.87 4.41
16 17 7.432869 AGTACATTAATGTCAAAAAGCTTGCA 58.567 30.769 24.00 0.00 41.97 4.08
17 18 7.062255 GGAGTACATTAATGTCAAAAAGCTTGC 59.938 37.037 24.00 0.29 41.97 4.01
18 19 7.542130 GGGAGTACATTAATGTCAAAAAGCTTG 59.458 37.037 24.00 0.00 41.97 4.01
19 20 7.451566 AGGGAGTACATTAATGTCAAAAAGCTT 59.548 33.333 24.00 0.00 41.97 3.74
20 21 6.948309 AGGGAGTACATTAATGTCAAAAAGCT 59.052 34.615 24.00 11.57 41.97 3.74
21 22 7.158099 AGGGAGTACATTAATGTCAAAAAGC 57.842 36.000 24.00 8.27 41.97 3.51
22 23 7.119262 ACGAGGGAGTACATTAATGTCAAAAAG 59.881 37.037 24.00 12.27 41.97 2.27
23 24 6.938030 ACGAGGGAGTACATTAATGTCAAAAA 59.062 34.615 24.00 4.11 41.97 1.94
24 25 6.469410 ACGAGGGAGTACATTAATGTCAAAA 58.531 36.000 24.00 4.50 41.97 2.44
25 26 6.045072 ACGAGGGAGTACATTAATGTCAAA 57.955 37.500 24.00 4.88 41.97 2.69
26 27 5.394883 GGACGAGGGAGTACATTAATGTCAA 60.395 44.000 24.00 5.65 41.97 3.18
27 28 4.098960 GGACGAGGGAGTACATTAATGTCA 59.901 45.833 24.00 8.70 41.97 3.58
28 29 4.098960 TGGACGAGGGAGTACATTAATGTC 59.901 45.833 24.00 15.23 41.97 3.06
29 30 4.028131 TGGACGAGGGAGTACATTAATGT 58.972 43.478 23.80 23.80 44.48 2.71
30 31 4.142026 TGTGGACGAGGGAGTACATTAATG 60.142 45.833 14.01 14.01 37.30 1.90
31 32 4.028131 TGTGGACGAGGGAGTACATTAAT 58.972 43.478 0.00 0.00 37.30 1.40
32 33 3.433343 TGTGGACGAGGGAGTACATTAA 58.567 45.455 0.00 0.00 37.30 1.40
33 34 3.090210 TGTGGACGAGGGAGTACATTA 57.910 47.619 0.00 0.00 37.30 1.90
34 35 1.933021 TGTGGACGAGGGAGTACATT 58.067 50.000 0.00 0.00 37.30 2.71
35 36 1.933021 TTGTGGACGAGGGAGTACAT 58.067 50.000 0.00 0.00 37.30 2.29
36 37 1.707106 TTTGTGGACGAGGGAGTACA 58.293 50.000 0.00 0.00 31.44 2.90
37 38 4.667519 ATATTTGTGGACGAGGGAGTAC 57.332 45.455 0.00 0.00 0.00 2.73
38 39 5.657745 TGTTATATTTGTGGACGAGGGAGTA 59.342 40.000 0.00 0.00 0.00 2.59
39 40 4.468510 TGTTATATTTGTGGACGAGGGAGT 59.531 41.667 0.00 0.00 0.00 3.85
40 41 5.018539 TGTTATATTTGTGGACGAGGGAG 57.981 43.478 0.00 0.00 0.00 4.30
41 42 5.104693 ACATGTTATATTTGTGGACGAGGGA 60.105 40.000 0.00 0.00 0.00 4.20
42 43 5.123227 ACATGTTATATTTGTGGACGAGGG 58.877 41.667 0.00 0.00 0.00 4.30
43 44 6.677781 AACATGTTATATTTGTGGACGAGG 57.322 37.500 9.97 0.00 0.00 4.63
44 45 7.484641 CCAAAACATGTTATATTTGTGGACGAG 59.515 37.037 12.39 0.00 32.29 4.18
45 46 7.175119 TCCAAAACATGTTATATTTGTGGACGA 59.825 33.333 12.39 2.62 32.29 4.20
46 47 7.309177 TCCAAAACATGTTATATTTGTGGACG 58.691 34.615 12.39 0.36 32.29 4.79
63 64 9.770097 TGCAAAAATATTGAAGTATCCAAAACA 57.230 25.926 0.00 0.00 0.00 2.83
65 66 9.770097 TGTGCAAAAATATTGAAGTATCCAAAA 57.230 25.926 0.00 0.00 0.00 2.44
66 67 9.202273 GTGTGCAAAAATATTGAAGTATCCAAA 57.798 29.630 0.00 0.00 0.00 3.28
67 68 8.363390 TGTGTGCAAAAATATTGAAGTATCCAA 58.637 29.630 0.00 0.00 0.00 3.53
68 69 7.812191 GTGTGTGCAAAAATATTGAAGTATCCA 59.188 33.333 0.00 0.00 0.00 3.41
69 70 7.812191 TGTGTGTGCAAAAATATTGAAGTATCC 59.188 33.333 0.00 0.00 0.00 2.59
70 71 8.638565 GTGTGTGTGCAAAAATATTGAAGTATC 58.361 33.333 0.00 0.00 0.00 2.24
71 72 8.359642 AGTGTGTGTGCAAAAATATTGAAGTAT 58.640 29.630 0.00 0.00 0.00 2.12
72 73 7.711846 AGTGTGTGTGCAAAAATATTGAAGTA 58.288 30.769 0.00 0.00 0.00 2.24
73 74 6.572519 AGTGTGTGTGCAAAAATATTGAAGT 58.427 32.000 0.00 0.00 0.00 3.01
74 75 7.436080 AGAAGTGTGTGTGCAAAAATATTGAAG 59.564 33.333 0.00 0.00 0.00 3.02
75 76 7.264221 AGAAGTGTGTGTGCAAAAATATTGAA 58.736 30.769 0.00 0.00 0.00 2.69
76 77 6.804677 AGAAGTGTGTGTGCAAAAATATTGA 58.195 32.000 0.00 0.00 0.00 2.57
77 78 7.467557 AAGAAGTGTGTGTGCAAAAATATTG 57.532 32.000 0.00 0.00 0.00 1.90
78 79 9.762933 ATAAAGAAGTGTGTGTGCAAAAATATT 57.237 25.926 0.00 0.00 0.00 1.28
81 82 9.762933 AATATAAAGAAGTGTGTGTGCAAAAAT 57.237 25.926 0.00 0.00 0.00 1.82
82 83 9.593134 AAATATAAAGAAGTGTGTGTGCAAAAA 57.407 25.926 0.00 0.00 0.00 1.94
83 84 9.593134 AAAATATAAAGAAGTGTGTGTGCAAAA 57.407 25.926 0.00 0.00 0.00 2.44
84 85 9.593134 AAAAATATAAAGAAGTGTGTGTGCAAA 57.407 25.926 0.00 0.00 0.00 3.68
86 87 9.672086 GTAAAAATATAAAGAAGTGTGTGTGCA 57.328 29.630 0.00 0.00 0.00 4.57
87 88 9.672086 TGTAAAAATATAAAGAAGTGTGTGTGC 57.328 29.630 0.00 0.00 0.00 4.57
132 134 3.198417 GGGGTACTCCGGTTGAAAAGATA 59.802 47.826 0.00 0.00 36.01 1.98
180 182 3.454447 CCAAAGAAACTTCAAAAGGGGGT 59.546 43.478 0.00 0.00 0.00 4.95
181 183 3.454447 ACCAAAGAAACTTCAAAAGGGGG 59.546 43.478 0.00 0.00 0.00 5.40
186 188 6.102897 TCCACAACCAAAGAAACTTCAAAA 57.897 33.333 0.00 0.00 0.00 2.44
250 256 1.265095 CTGCATCGTATTGGACATGGC 59.735 52.381 0.00 0.00 0.00 4.40
257 263 0.659427 CAGGTGCTGCATCGTATTGG 59.341 55.000 5.27 0.00 0.00 3.16
372 381 5.570589 CCGATGCACATTCTTTTCTTCTTTC 59.429 40.000 0.00 0.00 0.00 2.62
396 405 9.155053 CAATAAAGTCACTTTACGACTGTTTTC 57.845 33.333 12.33 0.00 42.90 2.29
588 601 8.714179 AGTTTCGATTATTAATTTGTGTCGTCA 58.286 29.630 0.00 0.00 0.00 4.35
639 652 7.116090 GGTGATCATCAAGAGTCATCGAATTAG 59.884 40.741 0.00 0.00 0.00 1.73
651 664 1.411977 AGGAGCGGTGATCATCAAGAG 59.588 52.381 6.80 0.00 0.00 2.85
686 699 7.941795 GTACACGTACCATAATTCTAAGCAT 57.058 36.000 0.00 0.00 0.00 3.79
706 719 2.483363 CGTGGTTGGTGTTAGTGGTACA 60.483 50.000 0.00 0.00 0.00 2.90
707 720 2.137523 CGTGGTTGGTGTTAGTGGTAC 58.862 52.381 0.00 0.00 0.00 3.34
708 721 1.761784 ACGTGGTTGGTGTTAGTGGTA 59.238 47.619 0.00 0.00 0.00 3.25
709 722 0.542805 ACGTGGTTGGTGTTAGTGGT 59.457 50.000 0.00 0.00 0.00 4.16
710 723 0.941542 CACGTGGTTGGTGTTAGTGG 59.058 55.000 7.95 0.00 0.00 4.00
711 724 0.306533 GCACGTGGTTGGTGTTAGTG 59.693 55.000 18.88 0.00 37.70 2.74
712 725 1.155424 CGCACGTGGTTGGTGTTAGT 61.155 55.000 18.88 0.00 37.70 2.24
713 726 1.567537 CGCACGTGGTTGGTGTTAG 59.432 57.895 18.88 0.00 37.70 2.34
714 727 2.535788 GCGCACGTGGTTGGTGTTA 61.536 57.895 18.88 0.00 37.70 2.41
715 728 3.883180 GCGCACGTGGTTGGTGTT 61.883 61.111 18.88 0.00 37.70 3.32
984 1029 1.381928 CCATCTGCTTGCTGCCGAAT 61.382 55.000 0.00 0.00 38.36 3.34
1197 1314 2.742372 GACATGGCCGACACGCTT 60.742 61.111 0.00 0.00 0.00 4.68
1922 2043 1.261238 ACCCCTCTCGAAGCCAAGAG 61.261 60.000 0.00 0.00 39.00 2.85
1949 2070 3.356529 AGGCACCCAAAATCTAGACAG 57.643 47.619 0.00 0.00 0.00 3.51
2062 2183 0.919289 TTCTCCAACCCCCTCATCCC 60.919 60.000 0.00 0.00 0.00 3.85
2065 2186 1.849039 CATCTTCTCCAACCCCCTCAT 59.151 52.381 0.00 0.00 0.00 2.90
2173 2294 4.079970 TGGCATCCACGTACCAATTAAAA 58.920 39.130 0.00 0.00 0.00 1.52
2232 2735 5.309638 TGGAGTATTTTGGTGTTCGAATGA 58.690 37.500 0.00 0.00 0.00 2.57
2262 2772 3.201708 AGGAAGTTTCTCCTGCATATGCT 59.798 43.478 27.13 3.84 44.56 3.79
2305 2822 5.483685 TCTATGGTGTTCTTTGTACTGCT 57.516 39.130 0.00 0.00 0.00 4.24
2349 2866 3.066190 TCGCTAGGTGGTGGACGG 61.066 66.667 0.00 0.00 0.00 4.79
2364 2881 2.222508 CGCTCCAATACTTTTGACGTCG 60.223 50.000 11.62 0.00 0.00 5.12
2372 2889 4.003648 CCTTCAACTCGCTCCAATACTTT 58.996 43.478 0.00 0.00 0.00 2.66
2376 2893 1.739035 CGCCTTCAACTCGCTCCAATA 60.739 52.381 0.00 0.00 0.00 1.90
2378 2895 1.667830 CGCCTTCAACTCGCTCCAA 60.668 57.895 0.00 0.00 0.00 3.53
2379 2896 2.048222 CGCCTTCAACTCGCTCCA 60.048 61.111 0.00 0.00 0.00 3.86
2409 2926 3.239627 TTCCGGTGAGGGAGGAGCT 62.240 63.158 0.00 0.00 41.52 4.09
2490 3007 0.766131 ATGGTTGTTACCCGGTGTGA 59.234 50.000 0.00 0.00 44.35 3.58
2492 3009 0.766131 TGATGGTTGTTACCCGGTGT 59.234 50.000 0.00 0.00 44.35 4.16
2496 3013 4.956085 TCATAGATGATGGTTGTTACCCG 58.044 43.478 0.00 0.00 44.35 5.28
2497 3014 8.918202 TTATTCATAGATGATGGTTGTTACCC 57.082 34.615 0.00 0.00 36.64 3.69
2534 3052 6.011981 TGGGTGTTTATAGGTTTGATCCTTCT 60.012 38.462 0.00 0.00 38.86 2.85
2590 3109 1.136500 GGTACTGGTCTTCGGTGGATC 59.864 57.143 0.00 0.00 36.22 3.36
2607 3126 2.380941 TCTCGTGGGATTTGATCGGTA 58.619 47.619 0.00 0.00 0.00 4.02
2622 3141 1.478510 GTGTGTCTCCATGGATCTCGT 59.521 52.381 16.63 0.00 0.00 4.18
2623 3142 1.202463 GGTGTGTCTCCATGGATCTCG 60.202 57.143 16.63 3.29 0.00 4.04
2631 3150 0.901124 GAGCAGAGGTGTGTCTCCAT 59.099 55.000 0.00 0.00 34.46 3.41
2632 3151 0.469892 TGAGCAGAGGTGTGTCTCCA 60.470 55.000 0.00 0.00 34.46 3.86
2633 3152 0.901124 ATGAGCAGAGGTGTGTCTCC 59.099 55.000 0.00 0.00 34.46 3.71
2646 3166 1.735973 CATCGTCGGAGGATGAGCA 59.264 57.895 27.95 0.00 41.57 4.26
2649 3169 1.202770 TCTAGCATCGTCGGAGGATGA 60.203 52.381 33.15 18.55 41.57 2.92
2652 3172 1.158484 CGTCTAGCATCGTCGGAGGA 61.158 60.000 2.53 2.53 0.00 3.71


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

AutoCloner maintained by Alex Coulton.