Multiple sequence alignment - TraesCS1D01G378600

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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 TraesCS1D01G378600 chr1D 100.000 3575 0 0 1 3575 454566150 454562576 0.000000e+00 6602.0
1 TraesCS1D01G378600 chr1B 92.423 2534 116 33 1101 3575 624885297 624887813 0.000000e+00 3546.0
2 TraesCS1D01G378600 chr1B 94.318 264 9 2 795 1052 624884583 624884846 2.000000e-107 399.0
3 TraesCS1D01G378600 chr1A 94.298 2087 74 11 795 2862 548674014 548676074 0.000000e+00 3153.0
4 TraesCS1D01G378600 chr1A 87.918 1854 153 36 1743 3575 548682956 548684759 0.000000e+00 2117.0
5 TraesCS1D01G378600 chr1A 89.857 700 65 6 86 781 531019633 531018936 0.000000e+00 894.0
6 TraesCS1D01G378600 chr1A 79.179 658 77 28 2941 3575 548676091 548676711 5.560000e-108 401.0
7 TraesCS1D01G378600 chr3A 82.652 1516 232 22 1079 2577 482060543 482062044 0.000000e+00 1314.0
8 TraesCS1D01G378600 chr3A 90.585 701 58 4 86 781 150464625 150463928 0.000000e+00 922.0
9 TraesCS1D01G378600 chr3B 83.417 1399 222 6 1181 2577 471475112 471476502 0.000000e+00 1290.0
10 TraesCS1D01G378600 chr3D 82.916 1399 229 6 1181 2577 361737402 361738792 0.000000e+00 1251.0
11 TraesCS1D01G378600 chr3D 94.864 701 27 6 86 782 168369554 168370249 0.000000e+00 1086.0
12 TraesCS1D01G378600 chr3D 89.714 700 64 8 85 781 153087417 153088111 0.000000e+00 887.0
13 TraesCS1D01G378600 chr6D 98.182 605 10 1 177 780 345063444 345064048 0.000000e+00 1055.0
14 TraesCS1D01G378600 chr4D 90.688 698 59 6 86 781 260717656 260718349 0.000000e+00 924.0
15 TraesCS1D01G378600 chr5D 90.558 699 61 5 86 781 420876083 420876779 0.000000e+00 920.0
16 TraesCS1D01G378600 chr5D 90.517 696 58 8 86 778 71910331 71909641 0.000000e+00 913.0
17 TraesCS1D01G378600 chr7A 90.254 708 59 7 84 784 644455286 644455990 0.000000e+00 917.0
18 TraesCS1D01G378600 chr7B 78.846 104 15 4 3375 3475 695361874 695361973 2.980000e-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 TraesCS1D01G378600 chr1D 454562576 454566150 3574 True 6602.0 6602 100.0000 1 3575 1 chr1D.!!$R1 3574
1 TraesCS1D01G378600 chr1B 624884583 624887813 3230 False 1972.5 3546 93.3705 795 3575 2 chr1B.!!$F1 2780
2 TraesCS1D01G378600 chr1A 548682956 548684759 1803 False 2117.0 2117 87.9180 1743 3575 1 chr1A.!!$F1 1832
3 TraesCS1D01G378600 chr1A 548674014 548676711 2697 False 1777.0 3153 86.7385 795 3575 2 chr1A.!!$F2 2780
4 TraesCS1D01G378600 chr1A 531018936 531019633 697 True 894.0 894 89.8570 86 781 1 chr1A.!!$R1 695
5 TraesCS1D01G378600 chr3A 482060543 482062044 1501 False 1314.0 1314 82.6520 1079 2577 1 chr3A.!!$F1 1498
6 TraesCS1D01G378600 chr3A 150463928 150464625 697 True 922.0 922 90.5850 86 781 1 chr3A.!!$R1 695
7 TraesCS1D01G378600 chr3B 471475112 471476502 1390 False 1290.0 1290 83.4170 1181 2577 1 chr3B.!!$F1 1396
8 TraesCS1D01G378600 chr3D 361737402 361738792 1390 False 1251.0 1251 82.9160 1181 2577 1 chr3D.!!$F3 1396
9 TraesCS1D01G378600 chr3D 168369554 168370249 695 False 1086.0 1086 94.8640 86 782 1 chr3D.!!$F2 696
10 TraesCS1D01G378600 chr3D 153087417 153088111 694 False 887.0 887 89.7140 85 781 1 chr3D.!!$F1 696
11 TraesCS1D01G378600 chr6D 345063444 345064048 604 False 1055.0 1055 98.1820 177 780 1 chr6D.!!$F1 603
12 TraesCS1D01G378600 chr4D 260717656 260718349 693 False 924.0 924 90.6880 86 781 1 chr4D.!!$F1 695
13 TraesCS1D01G378600 chr5D 420876083 420876779 696 False 920.0 920 90.5580 86 781 1 chr5D.!!$F1 695
14 TraesCS1D01G378600 chr5D 71909641 71910331 690 True 913.0 913 90.5170 86 778 1 chr5D.!!$R1 692
15 TraesCS1D01G378600 chr7A 644455286 644455990 704 False 917.0 917 90.2540 84 784 1 chr7A.!!$F1 700

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
62 63 1.085091 GCTGTCAAGCTGGTCATGAG 58.915 55.000 0.0 0.0 46.6 2.90 F
63 64 1.338484 GCTGTCAAGCTGGTCATGAGA 60.338 52.381 0.0 0.0 46.6 3.27 F
2058 2510 1.202371 GGATTCGAGATGTGCCGTGTA 60.202 52.381 0.0 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2058 2510 0.389948 GACGATCAACGAGGCCAAGT 60.390 55.0 5.01 0.12 45.77 3.16 R
2142 2594 0.324645 GTGGCTGGAATTGGGTCCAT 60.325 55.0 0.00 0.00 46.66 3.41 R
3045 3523 0.029700 CCACCCGTTGTCGAAAAACC 59.970 55.0 6.65 0.00 39.71 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
22 23 3.682858 ACTGCAAATGCTTGATTGATTGC 59.317 39.130 6.97 0.00 42.49 3.56
23 24 3.932710 CTGCAAATGCTTGATTGATTGCT 59.067 39.130 6.97 0.00 42.59 3.91
24 25 3.682377 TGCAAATGCTTGATTGATTGCTG 59.318 39.130 6.97 0.00 42.59 4.41
25 26 3.485216 GCAAATGCTTGATTGATTGCTGC 60.485 43.478 0.00 0.00 39.87 5.25
26 27 2.596904 ATGCTTGATTGATTGCTGCC 57.403 45.000 0.00 0.00 0.00 4.85
27 28 1.258676 TGCTTGATTGATTGCTGCCA 58.741 45.000 0.00 0.00 0.00 4.92
28 29 1.828595 TGCTTGATTGATTGCTGCCAT 59.171 42.857 0.00 0.00 0.00 4.40
29 30 3.025262 TGCTTGATTGATTGCTGCCATA 58.975 40.909 0.00 0.00 0.00 2.74
30 31 3.639561 TGCTTGATTGATTGCTGCCATAT 59.360 39.130 0.00 0.00 0.00 1.78
31 32 4.100344 TGCTTGATTGATTGCTGCCATATT 59.900 37.500 0.00 0.00 0.00 1.28
32 33 5.054477 GCTTGATTGATTGCTGCCATATTT 58.946 37.500 0.00 0.00 0.00 1.40
33 34 5.176958 GCTTGATTGATTGCTGCCATATTTC 59.823 40.000 0.00 0.00 0.00 2.17
34 35 6.474140 TTGATTGATTGCTGCCATATTTCT 57.526 33.333 0.00 0.00 0.00 2.52
35 36 6.080648 TGATTGATTGCTGCCATATTTCTC 57.919 37.500 0.00 0.00 0.00 2.87
36 37 5.595133 TGATTGATTGCTGCCATATTTCTCA 59.405 36.000 0.00 0.00 0.00 3.27
37 38 5.509716 TTGATTGCTGCCATATTTCTCAG 57.490 39.130 0.00 0.00 0.00 3.35
38 39 4.529897 TGATTGCTGCCATATTTCTCAGT 58.470 39.130 0.00 0.00 0.00 3.41
39 40 5.683681 TGATTGCTGCCATATTTCTCAGTA 58.316 37.500 0.00 0.00 0.00 2.74
40 41 5.761726 TGATTGCTGCCATATTTCTCAGTAG 59.238 40.000 0.00 0.00 0.00 2.57
41 42 4.760530 TGCTGCCATATTTCTCAGTAGT 57.239 40.909 0.00 0.00 0.00 2.73
42 43 5.102953 TGCTGCCATATTTCTCAGTAGTT 57.897 39.130 0.00 0.00 0.00 2.24
43 44 4.877823 TGCTGCCATATTTCTCAGTAGTTG 59.122 41.667 0.00 0.00 0.00 3.16
44 45 4.260948 GCTGCCATATTTCTCAGTAGTTGC 60.261 45.833 0.00 0.00 0.00 4.17
45 46 5.102953 TGCCATATTTCTCAGTAGTTGCT 57.897 39.130 0.00 0.00 0.00 3.91
46 47 4.877823 TGCCATATTTCTCAGTAGTTGCTG 59.122 41.667 0.00 0.00 37.81 4.41
47 48 4.878397 GCCATATTTCTCAGTAGTTGCTGT 59.122 41.667 0.00 0.00 37.70 4.40
48 49 5.007136 GCCATATTTCTCAGTAGTTGCTGTC 59.993 44.000 0.00 0.00 37.70 3.51
49 50 6.108687 CCATATTTCTCAGTAGTTGCTGTCA 58.891 40.000 0.00 0.00 37.70 3.58
50 51 6.595326 CCATATTTCTCAGTAGTTGCTGTCAA 59.405 38.462 0.00 0.00 37.70 3.18
51 52 7.201591 CCATATTTCTCAGTAGTTGCTGTCAAG 60.202 40.741 0.00 0.00 37.70 3.02
61 62 3.238232 GCTGTCAAGCTGGTCATGA 57.762 52.632 0.00 0.00 46.60 3.07
62 63 1.085091 GCTGTCAAGCTGGTCATGAG 58.915 55.000 0.00 0.00 46.60 2.90
63 64 1.338484 GCTGTCAAGCTGGTCATGAGA 60.338 52.381 0.00 0.00 46.60 3.27
64 65 2.873245 GCTGTCAAGCTGGTCATGAGAA 60.873 50.000 0.00 0.00 46.60 2.87
65 66 3.607741 CTGTCAAGCTGGTCATGAGAAT 58.392 45.455 0.00 0.00 0.00 2.40
66 67 3.603532 TGTCAAGCTGGTCATGAGAATC 58.396 45.455 0.00 0.00 0.00 2.52
67 68 2.606725 GTCAAGCTGGTCATGAGAATCG 59.393 50.000 0.00 0.00 38.61 3.34
68 69 2.497273 TCAAGCTGGTCATGAGAATCGA 59.503 45.455 0.00 0.00 38.61 3.59
69 70 2.593346 AGCTGGTCATGAGAATCGAC 57.407 50.000 0.00 0.00 38.61 4.20
70 71 1.827344 AGCTGGTCATGAGAATCGACA 59.173 47.619 0.00 0.00 38.61 4.35
71 72 2.234661 AGCTGGTCATGAGAATCGACAA 59.765 45.455 0.00 0.00 38.61 3.18
72 73 2.349886 GCTGGTCATGAGAATCGACAAC 59.650 50.000 0.00 0.00 38.61 3.32
73 74 3.854666 CTGGTCATGAGAATCGACAACT 58.145 45.455 0.00 0.00 38.61 3.16
74 75 4.248859 CTGGTCATGAGAATCGACAACTT 58.751 43.478 0.00 0.00 38.61 2.66
75 76 4.641396 TGGTCATGAGAATCGACAACTTT 58.359 39.130 0.00 0.00 38.61 2.66
76 77 4.690748 TGGTCATGAGAATCGACAACTTTC 59.309 41.667 0.00 0.00 38.61 2.62
77 78 4.932200 GGTCATGAGAATCGACAACTTTCT 59.068 41.667 0.00 0.00 38.61 2.52
78 79 5.062809 GGTCATGAGAATCGACAACTTTCTC 59.937 44.000 15.62 15.62 43.58 2.87
79 80 5.866633 GTCATGAGAATCGACAACTTTCTCT 59.133 40.000 20.60 8.62 43.64 3.10
80 81 5.866092 TCATGAGAATCGACAACTTTCTCTG 59.134 40.000 20.60 16.60 43.64 3.35
81 82 5.453567 TGAGAATCGACAACTTTCTCTGA 57.546 39.130 20.60 5.00 43.64 3.27
82 83 5.842907 TGAGAATCGACAACTTTCTCTGAA 58.157 37.500 20.60 4.44 43.64 3.02
118 121 2.942879 TGCGTTGCACGGAACATC 59.057 55.556 10.02 0.00 39.47 3.06
119 122 1.889573 TGCGTTGCACGGAACATCA 60.890 52.632 10.02 0.00 39.47 3.07
180 186 3.483954 GGGGGTCATCTCATGTGTG 57.516 57.895 0.00 0.00 0.00 3.82
262 268 5.531287 GGGTGAATAGTAAATGTAGGCAAGG 59.469 44.000 0.00 0.00 0.00 3.61
327 338 6.647334 TCAACTTGCATCCAAAACTTCATA 57.353 33.333 0.00 0.00 0.00 2.15
556 568 2.705821 CGAGAGCAGCGACCTCCTT 61.706 63.158 6.84 0.00 0.00 3.36
661 675 2.507854 CGTGGAGTGGAGTGTGGGT 61.508 63.158 0.00 0.00 0.00 4.51
662 676 1.837090 GTGGAGTGGAGTGTGGGTT 59.163 57.895 0.00 0.00 0.00 4.11
762 778 2.026915 CACCATCATCACCAACTCAGGA 60.027 50.000 0.00 0.00 0.00 3.86
782 798 9.527157 CTCAGGATTTTATAGGAGTAGAGATCA 57.473 37.037 0.00 0.00 0.00 2.92
790 806 8.642935 TTATAGGAGTAGAGATCATCAGTTGG 57.357 38.462 0.00 0.00 0.00 3.77
791 807 5.136068 AGGAGTAGAGATCATCAGTTGGA 57.864 43.478 0.00 0.00 0.00 3.53
792 808 5.714863 AGGAGTAGAGATCATCAGTTGGAT 58.285 41.667 0.00 0.00 36.39 3.41
793 809 5.774690 AGGAGTAGAGATCATCAGTTGGATC 59.225 44.000 0.00 0.00 40.13 3.36
800 816 4.835056 AGATCATCAGTTGGATCGGATGTA 59.165 41.667 0.00 0.00 43.61 2.29
1046 1072 2.123640 CTCCCCGTCCCTCTCCTC 60.124 72.222 0.00 0.00 0.00 3.71
1971 2423 2.189342 GAGATACTGCAGCAGTTCGAC 58.811 52.381 32.64 19.67 42.59 4.20
2058 2510 1.202371 GGATTCGAGATGTGCCGTGTA 60.202 52.381 0.00 0.00 0.00 2.90
2142 2594 2.211250 ACCGCTACTACAAGTCAGGA 57.789 50.000 3.44 0.00 0.00 3.86
2148 2600 3.181474 GCTACTACAAGTCAGGATGGACC 60.181 52.174 0.00 0.00 38.59 4.46
2472 2924 6.493115 AGATCGACTACCATGATCAGAAGATT 59.507 38.462 0.09 0.00 40.72 2.40
2730 3192 0.522180 AGACTCTTGTAGGCGTGTCG 59.478 55.000 0.00 0.00 38.81 4.35
2880 3343 0.597568 TGGCTTGCTGGAAATGTTCG 59.402 50.000 0.00 0.00 0.00 3.95
2893 3356 3.482156 AATGTTCGCTGCTCTATGGAT 57.518 42.857 0.00 0.00 0.00 3.41
2908 3371 9.143155 TGCTCTATGGATTGTCACTAGTATTTA 57.857 33.333 0.00 0.00 0.00 1.40
2942 3408 7.715265 TCTTCTGAAGTTGTATTTGAGTGAC 57.285 36.000 16.43 0.00 0.00 3.67
2953 3419 3.793797 TTTGAGTGACGACTGACAAGA 57.206 42.857 0.00 0.00 30.16 3.02
2957 3423 3.057946 TGAGTGACGACTGACAAGATGAG 60.058 47.826 0.00 0.00 30.16 2.90
2977 3443 4.141711 TGAGGTTGGATTCAGGTGCTATAC 60.142 45.833 0.00 0.00 0.00 1.47
2978 3444 3.131396 GGTTGGATTCAGGTGCTATACG 58.869 50.000 0.00 0.00 0.00 3.06
3013 3491 4.081087 GGCCTTCCAGTTTACATGAGTCTA 60.081 45.833 0.00 0.00 0.00 2.59
3045 3523 9.906111 GACTTTTTGCTTCTTCATTTTAGTTTG 57.094 29.630 0.00 0.00 0.00 2.93
3052 3540 8.878769 TGCTTCTTCATTTTAGTTTGGTTTTTC 58.121 29.630 0.00 0.00 0.00 2.29
3062 3550 1.461559 TTGGTTTTTCGACAACGGGT 58.538 45.000 0.00 0.00 40.21 5.28
3063 3551 0.733729 TGGTTTTTCGACAACGGGTG 59.266 50.000 0.00 0.00 40.21 4.61
3128 3623 1.002544 CCTGTCCTGAAGGTTCCTCAC 59.997 57.143 0.00 0.00 36.34 3.51
3129 3624 0.679505 TGTCCTGAAGGTTCCTCACG 59.320 55.000 0.00 0.00 36.34 4.35
3238 3738 8.958119 AATTACTAGATAAAAACATCGAGGCA 57.042 30.769 0.00 0.00 33.41 4.75
3239 3739 9.561069 AATTACTAGATAAAAACATCGAGGCAT 57.439 29.630 0.00 0.00 33.41 4.40
3249 3752 5.741388 AACATCGAGGCATTATTCTTGAC 57.259 39.130 0.00 0.00 0.00 3.18
3259 3762 5.221126 GGCATTATTCTTGACATCTTGGACC 60.221 44.000 0.00 0.00 0.00 4.46
3261 3764 6.459298 GCATTATTCTTGACATCTTGGACCTG 60.459 42.308 0.00 0.00 0.00 4.00
3262 3765 4.916041 ATTCTTGACATCTTGGACCTGA 57.084 40.909 0.00 0.00 0.00 3.86
3288 3791 4.926238 CGCCTATAGATGATCTGTCAAACC 59.074 45.833 4.96 0.00 38.01 3.27
3310 3813 4.099419 CCCACTTTGCACCTTATTTATCCC 59.901 45.833 0.00 0.00 0.00 3.85
3355 3858 4.264352 TGGGAAAATATCAGGTGCTTCCTT 60.264 41.667 0.00 0.00 45.67 3.36
3356 3859 4.339530 GGGAAAATATCAGGTGCTTCCTTC 59.660 45.833 0.00 0.00 45.67 3.46
3391 3903 7.867909 TCTGAAAACTCTGAACTACTACATGTG 59.132 37.037 9.11 0.93 0.00 3.21
3416 3928 1.981256 TGAAAACCTGAACTCCTGCC 58.019 50.000 0.00 0.00 0.00 4.85
3422 3934 1.251251 CCTGAACTCCTGCCAAAAGG 58.749 55.000 0.00 0.00 38.84 3.11
3467 3980 2.800250 CTTCAGCCACTTCTGGGATTT 58.200 47.619 0.00 0.00 38.13 2.17
3480 3993 3.826157 TCTGGGATTTCAACATGGTGAAC 59.174 43.478 25.60 14.91 37.24 3.18
3489 4002 2.045926 ATGGTGAACGGCAGCCTC 60.046 61.111 10.54 1.18 44.28 4.70
3550 4070 1.073897 AGCTTGTTCAGAGTGGGCC 59.926 57.895 0.00 0.00 0.00 5.80
3558 4078 1.118965 TCAGAGTGGGCCAAAGTCGA 61.119 55.000 8.40 5.16 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.682858 GCAATCAATCAAGCATTTGCAGT 59.317 39.130 5.20 0.00 45.16 4.40
1 2 3.932710 AGCAATCAATCAAGCATTTGCAG 59.067 39.130 5.20 0.00 45.16 4.41
2 3 3.682377 CAGCAATCAATCAAGCATTTGCA 59.318 39.130 5.20 0.00 45.16 4.08
3 4 3.485216 GCAGCAATCAATCAAGCATTTGC 60.485 43.478 0.00 0.00 39.68 3.68
4 5 3.063452 GGCAGCAATCAATCAAGCATTTG 59.937 43.478 0.00 0.00 35.57 2.32
5 6 3.267483 GGCAGCAATCAATCAAGCATTT 58.733 40.909 0.00 0.00 0.00 2.32
6 7 2.235155 TGGCAGCAATCAATCAAGCATT 59.765 40.909 0.00 0.00 0.00 3.56
7 8 1.828595 TGGCAGCAATCAATCAAGCAT 59.171 42.857 0.00 0.00 0.00 3.79
8 9 1.258676 TGGCAGCAATCAATCAAGCA 58.741 45.000 0.00 0.00 0.00 3.91
9 10 2.596904 ATGGCAGCAATCAATCAAGC 57.403 45.000 0.00 0.00 0.00 4.01
10 11 6.513180 AGAAATATGGCAGCAATCAATCAAG 58.487 36.000 0.00 0.00 0.00 3.02
11 12 6.097129 TGAGAAATATGGCAGCAATCAATCAA 59.903 34.615 0.00 0.00 0.00 2.57
12 13 5.595133 TGAGAAATATGGCAGCAATCAATCA 59.405 36.000 0.00 0.00 0.00 2.57
13 14 6.080648 TGAGAAATATGGCAGCAATCAATC 57.919 37.500 0.00 0.00 0.00 2.67
14 15 5.597182 ACTGAGAAATATGGCAGCAATCAAT 59.403 36.000 0.00 0.00 31.74 2.57
15 16 4.951715 ACTGAGAAATATGGCAGCAATCAA 59.048 37.500 0.00 0.00 31.74 2.57
16 17 4.529897 ACTGAGAAATATGGCAGCAATCA 58.470 39.130 0.00 0.00 31.74 2.57
17 18 5.762218 ACTACTGAGAAATATGGCAGCAATC 59.238 40.000 0.00 0.00 31.74 2.67
18 19 5.688807 ACTACTGAGAAATATGGCAGCAAT 58.311 37.500 0.00 0.00 31.74 3.56
19 20 5.102953 ACTACTGAGAAATATGGCAGCAA 57.897 39.130 0.00 0.00 31.74 3.91
20 21 4.760530 ACTACTGAGAAATATGGCAGCA 57.239 40.909 0.00 0.00 31.74 4.41
21 22 4.260948 GCAACTACTGAGAAATATGGCAGC 60.261 45.833 0.00 0.00 31.74 5.25
22 23 5.007430 CAGCAACTACTGAGAAATATGGCAG 59.993 44.000 0.00 0.00 40.25 4.85
23 24 4.877823 CAGCAACTACTGAGAAATATGGCA 59.122 41.667 0.00 0.00 40.25 4.92
24 25 4.878397 ACAGCAACTACTGAGAAATATGGC 59.122 41.667 0.00 0.00 40.25 4.40
25 26 6.108687 TGACAGCAACTACTGAGAAATATGG 58.891 40.000 0.00 0.00 40.25 2.74
26 27 7.601073 TTGACAGCAACTACTGAGAAATATG 57.399 36.000 0.00 0.00 40.25 1.78
27 28 6.314896 GCTTGACAGCAACTACTGAGAAATAT 59.685 38.462 0.00 0.00 46.49 1.28
28 29 5.639506 GCTTGACAGCAACTACTGAGAAATA 59.360 40.000 0.00 0.00 46.49 1.40
29 30 4.453819 GCTTGACAGCAACTACTGAGAAAT 59.546 41.667 0.00 0.00 46.49 2.17
30 31 3.809832 GCTTGACAGCAACTACTGAGAAA 59.190 43.478 0.00 0.00 46.49 2.52
31 32 3.393800 GCTTGACAGCAACTACTGAGAA 58.606 45.455 0.00 0.00 46.49 2.87
32 33 3.032017 GCTTGACAGCAACTACTGAGA 57.968 47.619 0.00 0.00 46.49 3.27
44 45 2.756840 TCTCATGACCAGCTTGACAG 57.243 50.000 0.00 0.00 0.00 3.51
45 46 3.603532 GATTCTCATGACCAGCTTGACA 58.396 45.455 0.00 0.00 0.00 3.58
46 47 2.606725 CGATTCTCATGACCAGCTTGAC 59.393 50.000 0.00 0.00 0.00 3.18
47 48 2.497273 TCGATTCTCATGACCAGCTTGA 59.503 45.455 0.00 0.00 0.00 3.02
48 49 2.606725 GTCGATTCTCATGACCAGCTTG 59.393 50.000 0.00 0.00 0.00 4.01
49 50 2.234661 TGTCGATTCTCATGACCAGCTT 59.765 45.455 0.00 0.00 0.00 3.74
50 51 1.827344 TGTCGATTCTCATGACCAGCT 59.173 47.619 0.00 0.00 0.00 4.24
51 52 2.299993 TGTCGATTCTCATGACCAGC 57.700 50.000 0.00 0.00 0.00 4.85
52 53 3.854666 AGTTGTCGATTCTCATGACCAG 58.145 45.455 0.00 0.00 0.00 4.00
53 54 3.961480 AGTTGTCGATTCTCATGACCA 57.039 42.857 0.00 0.00 0.00 4.02
54 55 4.932200 AGAAAGTTGTCGATTCTCATGACC 59.068 41.667 0.00 0.00 0.00 4.02
55 56 6.088719 GAGAAAGTTGTCGATTCTCATGAC 57.911 41.667 16.98 0.00 45.30 3.06
60 61 6.587990 TCATTCAGAGAAAGTTGTCGATTCTC 59.412 38.462 14.96 14.96 45.97 2.87
61 62 6.367422 GTCATTCAGAGAAAGTTGTCGATTCT 59.633 38.462 0.00 0.00 36.17 2.40
62 63 6.367422 AGTCATTCAGAGAAAGTTGTCGATTC 59.633 38.462 0.00 0.00 0.00 2.52
63 64 6.226787 AGTCATTCAGAGAAAGTTGTCGATT 58.773 36.000 0.00 0.00 0.00 3.34
64 65 5.788450 AGTCATTCAGAGAAAGTTGTCGAT 58.212 37.500 0.00 0.00 0.00 3.59
65 66 5.201713 AGTCATTCAGAGAAAGTTGTCGA 57.798 39.130 0.00 0.00 0.00 4.20
66 67 6.153067 ACTAGTCATTCAGAGAAAGTTGTCG 58.847 40.000 0.00 0.00 0.00 4.35
67 68 9.134734 CTTACTAGTCATTCAGAGAAAGTTGTC 57.865 37.037 0.00 0.00 0.00 3.18
68 69 8.861086 TCTTACTAGTCATTCAGAGAAAGTTGT 58.139 33.333 0.00 0.00 0.00 3.32
69 70 9.868277 ATCTTACTAGTCATTCAGAGAAAGTTG 57.132 33.333 0.00 0.00 0.00 3.16
70 71 9.868277 CATCTTACTAGTCATTCAGAGAAAGTT 57.132 33.333 0.00 0.00 0.00 2.66
71 72 7.978975 GCATCTTACTAGTCATTCAGAGAAAGT 59.021 37.037 0.00 0.00 0.00 2.66
72 73 7.437862 GGCATCTTACTAGTCATTCAGAGAAAG 59.562 40.741 0.00 0.00 0.00 2.62
73 74 7.268586 GGCATCTTACTAGTCATTCAGAGAAA 58.731 38.462 0.00 0.00 0.00 2.52
74 75 6.183360 GGGCATCTTACTAGTCATTCAGAGAA 60.183 42.308 0.00 0.00 0.00 2.87
75 76 5.303078 GGGCATCTTACTAGTCATTCAGAGA 59.697 44.000 0.00 0.00 0.00 3.10
76 77 5.537188 GGGCATCTTACTAGTCATTCAGAG 58.463 45.833 0.00 0.00 0.00 3.35
77 78 4.038042 CGGGCATCTTACTAGTCATTCAGA 59.962 45.833 0.00 0.00 0.00 3.27
78 79 4.202161 ACGGGCATCTTACTAGTCATTCAG 60.202 45.833 0.00 0.00 0.00 3.02
79 80 3.704566 ACGGGCATCTTACTAGTCATTCA 59.295 43.478 0.00 0.00 0.00 2.57
80 81 4.051922 CACGGGCATCTTACTAGTCATTC 58.948 47.826 0.00 0.00 0.00 2.67
81 82 3.741388 GCACGGGCATCTTACTAGTCATT 60.741 47.826 3.77 0.00 40.72 2.57
82 83 2.224066 GCACGGGCATCTTACTAGTCAT 60.224 50.000 3.77 0.00 40.72 3.06
118 121 4.730949 ACTCCCTGATCAATGCATTTTG 57.269 40.909 9.83 0.68 0.00 2.44
119 122 4.529377 ACAACTCCCTGATCAATGCATTTT 59.471 37.500 9.83 0.00 0.00 1.82
180 186 8.433421 TCCAAAGAAACCTATCGATATTTGTC 57.567 34.615 18.53 9.52 0.00 3.18
690 706 3.132824 TGATCTACATCCAACGCATCTGT 59.867 43.478 0.00 0.00 0.00 3.41
782 798 5.305386 TCAGATTACATCCGATCCAACTGAT 59.695 40.000 0.00 0.00 36.01 2.90
783 799 4.649218 TCAGATTACATCCGATCCAACTGA 59.351 41.667 0.00 0.00 0.00 3.41
784 800 4.948847 TCAGATTACATCCGATCCAACTG 58.051 43.478 0.00 0.00 0.00 3.16
785 801 5.565637 CGATCAGATTACATCCGATCCAACT 60.566 44.000 4.93 0.00 39.11 3.16
786 802 4.623167 CGATCAGATTACATCCGATCCAAC 59.377 45.833 4.93 0.00 39.11 3.77
787 803 4.522789 TCGATCAGATTACATCCGATCCAA 59.477 41.667 4.93 0.00 39.11 3.53
788 804 4.079253 TCGATCAGATTACATCCGATCCA 58.921 43.478 4.93 0.00 39.11 3.41
789 805 4.703645 TCGATCAGATTACATCCGATCC 57.296 45.455 4.93 0.00 39.11 3.36
790 806 5.461526 TGTTCGATCAGATTACATCCGATC 58.538 41.667 0.00 1.31 38.99 3.69
791 807 5.241728 TCTGTTCGATCAGATTACATCCGAT 59.758 40.000 19.80 0.00 39.20 4.18
792 808 4.578928 TCTGTTCGATCAGATTACATCCGA 59.421 41.667 19.80 0.00 39.20 4.55
793 809 4.677378 GTCTGTTCGATCAGATTACATCCG 59.323 45.833 24.84 0.00 44.59 4.18
800 816 2.881074 CACCGTCTGTTCGATCAGATT 58.119 47.619 24.84 12.53 44.59 2.40
1263 1715 3.807538 TAGCGCTCGTCCGTGGAC 61.808 66.667 16.34 9.04 41.40 4.02
1264 1716 3.807538 GTAGCGCTCGTCCGTGGA 61.808 66.667 16.34 0.00 0.00 4.02
1265 1717 3.736482 GAGTAGCGCTCGTCCGTGG 62.736 68.421 16.34 0.00 34.13 4.94
1890 2342 3.509575 TGAGCGAATTGGCAAGGTAAATT 59.490 39.130 15.20 0.00 34.64 1.82
2058 2510 0.389948 GACGATCAACGAGGCCAAGT 60.390 55.000 5.01 0.12 45.77 3.16
2142 2594 0.324645 GTGGCTGGAATTGGGTCCAT 60.325 55.000 0.00 0.00 46.66 3.41
2148 2600 0.604578 CCACTTGTGGCTGGAATTGG 59.395 55.000 6.88 0.00 0.00 3.16
2367 2819 2.285368 ATGGTGCCCTCTTCCCGA 60.285 61.111 0.00 0.00 0.00 5.14
2472 2924 1.001764 CTTGCAGGCCATGTCCTCA 60.002 57.895 5.01 0.00 33.25 3.86
2679 3140 7.290014 ACCTACAAGATTTCAAATCAAGGGTTT 59.710 33.333 12.74 0.00 0.00 3.27
2730 3192 2.194868 CCCTAACCATTCCCCGCC 59.805 66.667 0.00 0.00 0.00 6.13
2880 3343 3.191078 AGTGACAATCCATAGAGCAGC 57.809 47.619 0.00 0.00 0.00 5.25
2932 3395 4.322080 TCTTGTCAGTCGTCACTCAAAT 57.678 40.909 0.00 0.00 0.00 2.32
2942 3408 2.029020 TCCAACCTCATCTTGTCAGTCG 60.029 50.000 0.00 0.00 0.00 4.18
2953 3419 1.637553 AGCACCTGAATCCAACCTCAT 59.362 47.619 0.00 0.00 0.00 2.90
2957 3423 3.131396 CGTATAGCACCTGAATCCAACC 58.869 50.000 0.00 0.00 0.00 3.77
3013 3491 4.442706 TGAAGAAGCAAAAAGTCTCGACT 58.557 39.130 0.00 0.00 44.94 4.18
3026 3504 8.785329 AAAAACCAAACTAAAATGAAGAAGCA 57.215 26.923 0.00 0.00 0.00 3.91
3028 3506 9.296400 TCGAAAAACCAAACTAAAATGAAGAAG 57.704 29.630 0.00 0.00 0.00 2.85
3045 3523 0.029700 CCACCCGTTGTCGAAAAACC 59.970 55.000 6.65 0.00 39.71 3.27
3107 3595 0.035915 GAGGAACCTTCAGGACAGGC 60.036 60.000 0.00 0.00 38.94 4.85
3128 3623 3.229156 TTGGGTCGTGCTGGTACCG 62.229 63.158 7.57 3.32 33.89 4.02
3129 3624 1.670083 GTTGGGTCGTGCTGGTACC 60.670 63.158 4.43 4.43 0.00 3.34
3238 3738 6.962182 TCAGGTCCAAGATGTCAAGAATAAT 58.038 36.000 0.00 0.00 0.00 1.28
3239 3739 6.373005 TCAGGTCCAAGATGTCAAGAATAA 57.627 37.500 0.00 0.00 0.00 1.40
3249 3752 1.817099 GCGCCTCAGGTCCAAGATG 60.817 63.158 0.00 0.00 0.00 2.90
3259 3762 3.023119 AGATCATCTATAGGCGCCTCAG 58.977 50.000 36.73 29.67 0.00 3.35
3261 3764 2.757868 ACAGATCATCTATAGGCGCCTC 59.242 50.000 36.73 15.93 0.00 4.70
3262 3765 2.757868 GACAGATCATCTATAGGCGCCT 59.242 50.000 34.85 34.85 0.00 5.52
3288 3791 4.709397 TGGGATAAATAAGGTGCAAAGTGG 59.291 41.667 0.00 0.00 0.00 4.00
3310 3813 1.043116 TCAGACCACCCGCCTATCTG 61.043 60.000 0.00 0.00 38.51 2.90
3355 3858 4.825634 TCAGAGTTTTCAGAGGTAGTTCGA 59.174 41.667 0.00 0.00 0.00 3.71
3356 3859 5.122512 TCAGAGTTTTCAGAGGTAGTTCG 57.877 43.478 0.00 0.00 0.00 3.95
3391 3903 5.106515 GCAGGAGTTCAGGTTTTCATAAGAC 60.107 44.000 0.00 0.00 0.00 3.01
3422 3934 4.560856 ATCGCGTCAGGCTCTCGC 62.561 66.667 18.65 18.65 45.28 5.03
3433 3945 3.127533 GAAGCCCTTGCATCGCGT 61.128 61.111 5.77 0.00 41.13 6.01
3467 3980 1.514678 GCTGCCGTTCACCATGTTGA 61.515 55.000 0.00 0.00 0.00 3.18
3496 4009 0.745486 TTCATGGATCAGTGCAGGCG 60.745 55.000 0.00 0.00 0.00 5.52
3550 4070 2.880822 ATGTTGATGCGTCGACTTTG 57.119 45.000 23.72 0.00 39.17 2.77


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

AutoCloner maintained by Alex Coulton.