Multiple sequence alignment - TraesCS2A01G254700

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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 TraesCS2A01G254700 chr2A 100.000 2783 0 0 1 2783 388467813 388470595 0.000000e+00 5140
1 TraesCS2A01G254700 chr2A 97.597 874 11 5 1914 2783 92977098 92976231 0.000000e+00 1489
2 TraesCS2A01G254700 chr2A 98.914 829 9 0 1955 2783 395717408 395716580 0.000000e+00 1482
3 TraesCS2A01G254700 chr2D 95.906 1026 30 7 870 1890 307532476 307533494 0.000000e+00 1652
4 TraesCS2A01G254700 chr2D 91.892 518 11 10 205 718 307530273 307530763 0.000000e+00 695
5 TraesCS2A01G254700 chr2D 91.538 260 11 2 1 260 307519207 307519455 5.700000e-92 348
6 TraesCS2A01G254700 chr2D 98.095 105 2 0 710 814 307530941 307531045 1.700000e-42 183
7 TraesCS2A01G254700 chr2B 94.653 1066 39 7 828 1890 360350760 360349710 0.000000e+00 1637
8 TraesCS2A01G254700 chr2B 91.362 683 16 14 156 830 360353148 360352501 0.000000e+00 894
9 TraesCS2A01G254700 chr2B 91.667 96 5 1 1 96 360360450 360360358 2.250000e-26 130
10 TraesCS2A01G254700 chrUn 98.577 843 8 3 1945 2783 41815672 41816514 0.000000e+00 1487
11 TraesCS2A01G254700 chr1A 98.432 829 13 0 1955 2783 458923742 458922914 0.000000e+00 1459
12 TraesCS2A01G254700 chr6B 98.199 833 14 1 1952 2783 57586648 57587480 0.000000e+00 1454
13 TraesCS2A01G254700 chr3A 92.494 866 35 6 1944 2783 35850763 35851624 0.000000e+00 1212
14 TraesCS2A01G254700 chr7B 91.856 835 45 3 1968 2783 520117215 520118045 0.000000e+00 1144
15 TraesCS2A01G254700 chr3B 90.547 878 48 10 1933 2783 532211093 532210224 0.000000e+00 1129
16 TraesCS2A01G254700 chr5B 92.490 719 26 4 2090 2783 480309092 480308377 0.000000e+00 1003
17 TraesCS2A01G254700 chr7A 93.878 49 3 0 1954 2002 40744785 40744833 1.070000e-09 75


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 TraesCS2A01G254700 chr2A 388467813 388470595 2782 False 5140.000000 5140 100.000000 1 2783 1 chr2A.!!$F1 2782
1 TraesCS2A01G254700 chr2A 92976231 92977098 867 True 1489.000000 1489 97.597000 1914 2783 1 chr2A.!!$R1 869
2 TraesCS2A01G254700 chr2A 395716580 395717408 828 True 1482.000000 1482 98.914000 1955 2783 1 chr2A.!!$R2 828
3 TraesCS2A01G254700 chr2D 307530273 307533494 3221 False 843.333333 1652 95.297667 205 1890 3 chr2D.!!$F2 1685
4 TraesCS2A01G254700 chr2B 360349710 360353148 3438 True 1265.500000 1637 93.007500 156 1890 2 chr2B.!!$R2 1734
5 TraesCS2A01G254700 chrUn 41815672 41816514 842 False 1487.000000 1487 98.577000 1945 2783 1 chrUn.!!$F1 838
6 TraesCS2A01G254700 chr1A 458922914 458923742 828 True 1459.000000 1459 98.432000 1955 2783 1 chr1A.!!$R1 828
7 TraesCS2A01G254700 chr6B 57586648 57587480 832 False 1454.000000 1454 98.199000 1952 2783 1 chr6B.!!$F1 831
8 TraesCS2A01G254700 chr3A 35850763 35851624 861 False 1212.000000 1212 92.494000 1944 2783 1 chr3A.!!$F1 839
9 TraesCS2A01G254700 chr7B 520117215 520118045 830 False 1144.000000 1144 91.856000 1968 2783 1 chr7B.!!$F1 815
10 TraesCS2A01G254700 chr3B 532210224 532211093 869 True 1129.000000 1129 90.547000 1933 2783 1 chr3B.!!$R1 850
11 TraesCS2A01G254700 chr5B 480308377 480309092 715 True 1003.000000 1003 92.490000 2090 2783 1 chr5B.!!$R1 693

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
414 421 0.1023 CCATGCATACCGTCGACTCA 59.898 55.0 14.7 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1856 5200 0.249741 ATAGGGTGCGTTACGATGCC 60.25 55.0 9.62 6.54 36.96 4.4 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 5.914085 GGACTTTAACCTCATGATCGATG 57.086 43.478 0.54 0.00 0.00 3.84
23 24 4.212214 GGACTTTAACCTCATGATCGATGC 59.788 45.833 0.54 0.00 31.32 3.91
24 25 4.130118 ACTTTAACCTCATGATCGATGCC 58.870 43.478 0.54 0.00 31.32 4.40
25 26 3.836365 TTAACCTCATGATCGATGCCA 57.164 42.857 0.54 0.00 31.32 4.92
26 27 2.945080 AACCTCATGATCGATGCCAT 57.055 45.000 0.54 0.00 31.32 4.40
27 28 2.180432 ACCTCATGATCGATGCCATG 57.820 50.000 17.00 17.00 40.97 3.66
28 29 1.695788 ACCTCATGATCGATGCCATGA 59.304 47.619 21.80 21.80 44.66 3.07
29 30 2.105306 ACCTCATGATCGATGCCATGAA 59.895 45.455 22.78 12.04 45.68 2.57
30 31 3.244805 ACCTCATGATCGATGCCATGAAT 60.245 43.478 22.78 14.92 45.68 2.57
31 32 3.756963 CCTCATGATCGATGCCATGAATT 59.243 43.478 22.78 0.00 45.68 2.17
32 33 4.379499 CCTCATGATCGATGCCATGAATTG 60.379 45.833 22.78 14.89 45.68 2.32
33 34 4.139038 TCATGATCGATGCCATGAATTGT 58.861 39.130 21.26 0.00 44.12 2.71
34 35 4.581409 TCATGATCGATGCCATGAATTGTT 59.419 37.500 21.26 0.00 44.12 2.83
35 36 5.764192 TCATGATCGATGCCATGAATTGTTA 59.236 36.000 21.26 3.76 44.12 2.41
36 37 5.678132 TGATCGATGCCATGAATTGTTAG 57.322 39.130 0.54 0.00 0.00 2.34
37 38 5.367302 TGATCGATGCCATGAATTGTTAGA 58.633 37.500 0.54 0.00 0.00 2.10
38 39 5.821995 TGATCGATGCCATGAATTGTTAGAA 59.178 36.000 0.54 0.00 0.00 2.10
39 40 6.487668 TGATCGATGCCATGAATTGTTAGAAT 59.512 34.615 0.54 0.00 0.00 2.40
40 41 6.698008 TCGATGCCATGAATTGTTAGAATT 57.302 33.333 0.00 0.00 0.00 2.17
41 42 7.099266 TCGATGCCATGAATTGTTAGAATTT 57.901 32.000 0.00 0.00 0.00 1.82
42 43 7.195646 TCGATGCCATGAATTGTTAGAATTTC 58.804 34.615 0.00 0.00 0.00 2.17
43 44 6.974048 CGATGCCATGAATTGTTAGAATTTCA 59.026 34.615 0.00 0.00 0.00 2.69
44 45 7.650504 CGATGCCATGAATTGTTAGAATTTCAT 59.349 33.333 0.00 0.00 0.00 2.57
45 46 9.321562 GATGCCATGAATTGTTAGAATTTCATT 57.678 29.630 0.00 0.00 0.00 2.57
55 56 9.659135 ATTGTTAGAATTTCATTATGGATGGGA 57.341 29.630 0.00 0.00 36.37 4.37
56 57 9.659135 TTGTTAGAATTTCATTATGGATGGGAT 57.341 29.630 0.00 0.00 36.37 3.85
57 58 9.081204 TGTTAGAATTTCATTATGGATGGGATG 57.919 33.333 0.00 0.00 36.37 3.51
58 59 8.526147 GTTAGAATTTCATTATGGATGGGATGG 58.474 37.037 0.00 0.00 36.37 3.51
59 60 5.482878 AGAATTTCATTATGGATGGGATGGC 59.517 40.000 0.00 0.00 36.37 4.40
60 61 2.905415 TCATTATGGATGGGATGGCC 57.095 50.000 0.00 0.00 36.37 5.36
71 72 3.197664 GGATGGCCCTTGAGAAAGG 57.802 57.895 0.00 0.00 39.68 3.11
72 73 1.039785 GGATGGCCCTTGAGAAAGGC 61.040 60.000 0.00 0.00 46.37 4.35
75 76 4.397348 GCCCTTGAGAAAGGCGAA 57.603 55.556 0.00 0.00 38.63 4.70
76 77 1.876664 GCCCTTGAGAAAGGCGAAC 59.123 57.895 0.00 0.00 38.63 3.95
77 78 0.606673 GCCCTTGAGAAAGGCGAACT 60.607 55.000 0.00 0.00 38.63 3.01
78 79 1.160137 CCCTTGAGAAAGGCGAACTG 58.840 55.000 0.00 0.00 38.63 3.16
79 80 1.160137 CCTTGAGAAAGGCGAACTGG 58.840 55.000 0.00 0.00 32.43 4.00
80 81 1.543429 CCTTGAGAAAGGCGAACTGGT 60.543 52.381 0.00 0.00 32.43 4.00
81 82 2.289444 CCTTGAGAAAGGCGAACTGGTA 60.289 50.000 0.00 0.00 32.43 3.25
82 83 3.399330 CTTGAGAAAGGCGAACTGGTAA 58.601 45.455 0.00 0.00 0.00 2.85
83 84 3.040147 TGAGAAAGGCGAACTGGTAAG 57.960 47.619 0.00 0.00 0.00 2.34
84 85 2.289444 TGAGAAAGGCGAACTGGTAAGG 60.289 50.000 0.00 0.00 0.00 2.69
85 86 1.975680 AGAAAGGCGAACTGGTAAGGA 59.024 47.619 0.00 0.00 0.00 3.36
86 87 2.572104 AGAAAGGCGAACTGGTAAGGAT 59.428 45.455 0.00 0.00 0.00 3.24
87 88 2.403252 AAGGCGAACTGGTAAGGATG 57.597 50.000 0.00 0.00 0.00 3.51
88 89 0.541863 AGGCGAACTGGTAAGGATGG 59.458 55.000 0.00 0.00 0.00 3.51
89 90 0.463833 GGCGAACTGGTAAGGATGGG 60.464 60.000 0.00 0.00 0.00 4.00
90 91 0.539986 GCGAACTGGTAAGGATGGGA 59.460 55.000 0.00 0.00 0.00 4.37
91 92 1.473434 GCGAACTGGTAAGGATGGGAG 60.473 57.143 0.00 0.00 0.00 4.30
92 93 2.108168 CGAACTGGTAAGGATGGGAGA 58.892 52.381 0.00 0.00 0.00 3.71
93 94 2.700897 CGAACTGGTAAGGATGGGAGAT 59.299 50.000 0.00 0.00 0.00 2.75
94 95 3.895656 CGAACTGGTAAGGATGGGAGATA 59.104 47.826 0.00 0.00 0.00 1.98
95 96 4.262079 CGAACTGGTAAGGATGGGAGATAC 60.262 50.000 0.00 0.00 0.00 2.24
96 97 3.231818 ACTGGTAAGGATGGGAGATACG 58.768 50.000 0.00 0.00 0.00 3.06
97 98 3.231818 CTGGTAAGGATGGGAGATACGT 58.768 50.000 0.00 0.00 0.00 3.57
98 99 3.641906 CTGGTAAGGATGGGAGATACGTT 59.358 47.826 0.00 0.00 0.00 3.99
99 100 4.035112 TGGTAAGGATGGGAGATACGTTT 58.965 43.478 0.00 0.00 0.00 3.60
100 101 4.100498 TGGTAAGGATGGGAGATACGTTTC 59.900 45.833 0.00 0.00 0.00 2.78
101 102 4.100498 GGTAAGGATGGGAGATACGTTTCA 59.900 45.833 8.74 0.00 0.00 2.69
102 103 5.221661 GGTAAGGATGGGAGATACGTTTCAT 60.222 44.000 8.74 0.00 0.00 2.57
103 104 4.608948 AGGATGGGAGATACGTTTCATC 57.391 45.455 8.74 3.34 0.00 2.92
104 105 3.967326 AGGATGGGAGATACGTTTCATCA 59.033 43.478 8.74 4.06 34.42 3.07
105 106 4.594920 AGGATGGGAGATACGTTTCATCAT 59.405 41.667 8.74 8.22 34.42 2.45
106 107 4.932200 GGATGGGAGATACGTTTCATCATC 59.068 45.833 18.29 18.29 34.42 2.92
107 108 3.977427 TGGGAGATACGTTTCATCATCG 58.023 45.455 8.74 0.00 0.00 3.84
108 109 3.243737 TGGGAGATACGTTTCATCATCGG 60.244 47.826 8.74 0.00 0.00 4.18
109 110 3.318017 GGAGATACGTTTCATCATCGGG 58.682 50.000 8.74 0.00 0.00 5.14
110 111 3.318017 GAGATACGTTTCATCATCGGGG 58.682 50.000 8.74 0.00 0.00 5.73
111 112 2.698797 AGATACGTTTCATCATCGGGGT 59.301 45.455 8.74 0.00 0.00 4.95
112 113 3.893200 AGATACGTTTCATCATCGGGGTA 59.107 43.478 8.74 0.00 0.00 3.69
113 114 2.596904 ACGTTTCATCATCGGGGTAG 57.403 50.000 0.00 0.00 0.00 3.18
114 115 2.104967 ACGTTTCATCATCGGGGTAGA 58.895 47.619 0.00 0.00 0.00 2.59
115 116 2.698797 ACGTTTCATCATCGGGGTAGAT 59.301 45.455 0.00 0.00 0.00 1.98
116 117 3.243771 ACGTTTCATCATCGGGGTAGATC 60.244 47.826 0.00 0.00 0.00 2.75
117 118 3.318017 GTTTCATCATCGGGGTAGATCG 58.682 50.000 0.00 0.00 0.00 3.69
118 119 1.545841 TCATCATCGGGGTAGATCGG 58.454 55.000 0.00 0.00 0.00 4.18
119 120 0.532573 CATCATCGGGGTAGATCGGG 59.467 60.000 0.00 0.00 0.00 5.14
120 121 1.258445 ATCATCGGGGTAGATCGGGC 61.258 60.000 0.00 0.00 0.00 6.13
121 122 2.603776 ATCGGGGTAGATCGGGCC 60.604 66.667 0.00 0.00 0.00 5.80
122 123 3.161853 ATCGGGGTAGATCGGGCCT 62.162 63.158 0.84 0.00 0.00 5.19
123 124 3.616721 CGGGGTAGATCGGGCCTG 61.617 72.222 4.71 4.71 0.00 4.85
124 125 3.242291 GGGGTAGATCGGGCCTGG 61.242 72.222 12.87 0.00 0.00 4.45
125 126 2.446036 GGGTAGATCGGGCCTGGT 60.446 66.667 12.87 3.42 0.00 4.00
126 127 2.508751 GGGTAGATCGGGCCTGGTC 61.509 68.421 17.89 17.89 0.00 4.02
127 128 1.760875 GGTAGATCGGGCCTGGTCA 60.761 63.158 26.87 10.07 0.00 4.02
128 129 1.442148 GTAGATCGGGCCTGGTCAC 59.558 63.158 26.87 17.69 0.00 3.67
129 130 1.001120 TAGATCGGGCCTGGTCACA 59.999 57.895 26.87 11.26 0.00 3.58
130 131 1.327690 TAGATCGGGCCTGGTCACAC 61.328 60.000 26.87 0.00 0.00 3.82
131 132 2.927856 ATCGGGCCTGGTCACACA 60.928 61.111 12.87 0.00 0.00 3.72
132 133 2.257409 GATCGGGCCTGGTCACACAT 62.257 60.000 20.64 0.00 0.00 3.21
133 134 0.980754 ATCGGGCCTGGTCACACATA 60.981 55.000 12.87 0.00 0.00 2.29
134 135 1.153369 CGGGCCTGGTCACACATAG 60.153 63.158 2.57 0.00 0.00 2.23
135 136 1.899437 CGGGCCTGGTCACACATAGT 61.899 60.000 2.57 0.00 0.00 2.12
136 137 1.200519 GGGCCTGGTCACACATAGTA 58.799 55.000 0.84 0.00 0.00 1.82
137 138 1.134491 GGGCCTGGTCACACATAGTAC 60.134 57.143 0.84 0.00 0.00 2.73
138 139 1.134491 GGCCTGGTCACACATAGTACC 60.134 57.143 0.00 0.00 0.00 3.34
139 140 1.831736 GCCTGGTCACACATAGTACCT 59.168 52.381 0.00 0.00 32.99 3.08
140 141 2.236395 GCCTGGTCACACATAGTACCTT 59.764 50.000 0.00 0.00 32.99 3.50
141 142 3.861840 CCTGGTCACACATAGTACCTTG 58.138 50.000 0.00 0.00 32.99 3.61
142 143 3.369471 CCTGGTCACACATAGTACCTTGG 60.369 52.174 0.00 0.00 32.99 3.61
143 144 3.512496 TGGTCACACATAGTACCTTGGA 58.488 45.455 0.00 0.00 32.99 3.53
144 145 3.513912 TGGTCACACATAGTACCTTGGAG 59.486 47.826 0.00 0.00 32.99 3.86
145 146 3.767673 GGTCACACATAGTACCTTGGAGA 59.232 47.826 0.00 0.00 0.00 3.71
146 147 4.381718 GGTCACACATAGTACCTTGGAGAC 60.382 50.000 0.00 0.00 0.00 3.36
147 148 4.219944 GTCACACATAGTACCTTGGAGACA 59.780 45.833 0.00 0.00 39.83 3.41
203 205 3.770765 AAAATGCTGTATATCGTCGCG 57.229 42.857 0.00 0.00 0.00 5.87
276 278 0.389948 AGTGACGCGGATGAAAGGAC 60.390 55.000 12.47 0.00 0.00 3.85
346 353 1.860950 CTCGTACCACATGCATGCTAC 59.139 52.381 26.53 19.69 0.00 3.58
384 391 2.487934 AGATACCAATCGAGTGCATGC 58.512 47.619 11.82 11.82 37.19 4.06
413 420 1.215655 GCCATGCATACCGTCGACTC 61.216 60.000 14.70 0.00 0.00 3.36
414 421 0.102300 CCATGCATACCGTCGACTCA 59.898 55.000 14.70 0.00 0.00 3.41
451 460 3.056607 GCCATGCAAGGACACTTTTATGT 60.057 43.478 13.26 0.00 33.81 2.29
452 461 4.487948 CCATGCAAGGACACTTTTATGTG 58.512 43.478 0.35 0.00 43.07 3.21
453 462 3.641437 TGCAAGGACACTTTTATGTGC 57.359 42.857 0.00 0.00 41.30 4.57
459 468 4.292977 GGACACTTTTATGTGCTATGGC 57.707 45.455 0.00 0.00 41.30 4.40
508 517 2.930562 GACTGCCACCCTCACCCT 60.931 66.667 0.00 0.00 0.00 4.34
509 518 2.930562 ACTGCCACCCTCACCCTC 60.931 66.667 0.00 0.00 0.00 4.30
510 519 4.087892 CTGCCACCCTCACCCTCG 62.088 72.222 0.00 0.00 0.00 4.63
511 520 4.954118 TGCCACCCTCACCCTCGT 62.954 66.667 0.00 0.00 0.00 4.18
512 521 2.682494 GCCACCCTCACCCTCGTA 60.682 66.667 0.00 0.00 0.00 3.43
513 522 2.722201 GCCACCCTCACCCTCGTAG 61.722 68.421 0.00 0.00 0.00 3.51
659 672 2.203401 GCACTCTGCACTGATCTGATC 58.797 52.381 10.72 10.72 44.26 2.92
660 673 2.159071 GCACTCTGCACTGATCTGATCT 60.159 50.000 17.82 0.00 44.26 2.75
661 674 3.449632 CACTCTGCACTGATCTGATCTG 58.550 50.000 19.23 19.23 0.00 2.90
662 675 3.130693 CACTCTGCACTGATCTGATCTGA 59.869 47.826 25.34 4.63 33.12 3.27
663 676 3.962063 ACTCTGCACTGATCTGATCTGAT 59.038 43.478 25.34 14.33 33.12 2.90
858 2800 0.904649 ATTCGTCTCAGCCACCATCA 59.095 50.000 0.00 0.00 0.00 3.07
1488 4829 6.326583 TCTCCTACCACAAGAAGAAGAAGAAA 59.673 38.462 0.00 0.00 0.00 2.52
1706 5047 3.554692 CGACACGGGAAGCATCGC 61.555 66.667 0.00 0.00 35.28 4.58
1736 5080 2.420043 GTCTATTGGCGCCGGCTA 59.580 61.111 26.68 11.94 39.81 3.93
1786 5130 7.537306 TGTTCTTCAACGCATTTAATTAGCTTC 59.463 33.333 0.00 0.00 34.95 3.86
1794 5138 8.662781 ACGCATTTAATTAGCTTCTTGATAGA 57.337 30.769 0.00 0.00 0.00 1.98
1835 5179 4.272504 CGTAGTGCCCAATTAATGTTCGAT 59.727 41.667 0.00 0.00 0.00 3.59
1890 5237 5.277345 CGCACCCTATGTTACTTTGCTTATC 60.277 44.000 0.00 0.00 0.00 1.75
1891 5238 5.823045 GCACCCTATGTTACTTTGCTTATCT 59.177 40.000 0.00 0.00 0.00 1.98
1892 5239 6.318900 GCACCCTATGTTACTTTGCTTATCTT 59.681 38.462 0.00 0.00 0.00 2.40
1893 5240 7.148069 GCACCCTATGTTACTTTGCTTATCTTT 60.148 37.037 0.00 0.00 0.00 2.52
1894 5241 9.391006 CACCCTATGTTACTTTGCTTATCTTTA 57.609 33.333 0.00 0.00 0.00 1.85
2006 5376 4.842091 GCCATACGTCGTCGGCGT 62.842 66.667 28.96 28.96 45.11 5.68
2520 5915 2.214216 ACGAGCTAACACCCCTGCA 61.214 57.895 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.212214 GCATCGATCATGAGGTTAAAGTCC 59.788 45.833 0.09 0.00 33.80 3.85
1 2 4.212214 GGCATCGATCATGAGGTTAAAGTC 59.788 45.833 0.09 0.00 33.80 3.01
2 3 4.130118 GGCATCGATCATGAGGTTAAAGT 58.870 43.478 0.09 0.00 33.80 2.66
7 8 2.105306 TCATGGCATCGATCATGAGGTT 59.895 45.455 20.20 0.00 43.09 3.50
8 9 1.695788 TCATGGCATCGATCATGAGGT 59.304 47.619 20.20 0.00 43.09 3.85
9 10 2.467566 TCATGGCATCGATCATGAGG 57.532 50.000 20.20 0.46 43.09 3.86
10 11 4.215613 ACAATTCATGGCATCGATCATGAG 59.784 41.667 21.93 16.09 46.76 2.90
11 12 4.139038 ACAATTCATGGCATCGATCATGA 58.861 39.130 20.20 20.20 45.31 3.07
12 13 4.499037 ACAATTCATGGCATCGATCATG 57.501 40.909 17.00 17.00 41.35 3.07
13 14 5.999600 TCTAACAATTCATGGCATCGATCAT 59.000 36.000 0.00 0.00 0.00 2.45
14 15 5.367302 TCTAACAATTCATGGCATCGATCA 58.633 37.500 0.00 0.00 0.00 2.92
15 16 5.929697 TCTAACAATTCATGGCATCGATC 57.070 39.130 0.00 0.00 0.00 3.69
16 17 6.889301 ATTCTAACAATTCATGGCATCGAT 57.111 33.333 0.00 0.00 0.00 3.59
17 18 6.698008 AATTCTAACAATTCATGGCATCGA 57.302 33.333 0.00 0.00 0.00 3.59
18 19 6.974048 TGAAATTCTAACAATTCATGGCATCG 59.026 34.615 0.00 0.00 0.00 3.84
19 20 8.882415 ATGAAATTCTAACAATTCATGGCATC 57.118 30.769 0.00 0.00 40.11 3.91
29 30 9.659135 TCCCATCCATAATGAAATTCTAACAAT 57.341 29.630 0.00 0.00 37.87 2.71
30 31 9.659135 ATCCCATCCATAATGAAATTCTAACAA 57.341 29.630 0.00 0.00 37.87 2.83
31 32 9.081204 CATCCCATCCATAATGAAATTCTAACA 57.919 33.333 0.00 0.00 37.87 2.41
32 33 8.526147 CCATCCCATCCATAATGAAATTCTAAC 58.474 37.037 0.00 0.00 37.87 2.34
33 34 7.178983 GCCATCCCATCCATAATGAAATTCTAA 59.821 37.037 0.00 0.00 37.87 2.10
34 35 6.664816 GCCATCCCATCCATAATGAAATTCTA 59.335 38.462 0.00 0.00 37.87 2.10
35 36 5.482878 GCCATCCCATCCATAATGAAATTCT 59.517 40.000 0.00 0.00 37.87 2.40
36 37 5.337813 GGCCATCCCATCCATAATGAAATTC 60.338 44.000 0.00 0.00 37.87 2.17
37 38 4.533311 GGCCATCCCATCCATAATGAAATT 59.467 41.667 0.00 0.00 41.28 1.82
38 39 4.098894 GGCCATCCCATCCATAATGAAAT 58.901 43.478 0.00 0.00 37.59 2.17
39 40 3.509442 GGCCATCCCATCCATAATGAAA 58.491 45.455 0.00 0.00 37.59 2.69
40 41 3.173953 GGCCATCCCATCCATAATGAA 57.826 47.619 0.00 0.00 37.59 2.57
41 42 2.905415 GGCCATCCCATCCATAATGA 57.095 50.000 0.00 0.00 37.59 2.57
53 54 3.197664 CCTTTCTCAAGGGCCATCC 57.802 57.895 6.18 0.00 45.63 3.51
61 62 1.884235 ACCAGTTCGCCTTTCTCAAG 58.116 50.000 0.00 0.00 0.00 3.02
62 63 3.399330 CTTACCAGTTCGCCTTTCTCAA 58.601 45.455 0.00 0.00 0.00 3.02
63 64 2.289444 CCTTACCAGTTCGCCTTTCTCA 60.289 50.000 0.00 0.00 0.00 3.27
64 65 2.028385 TCCTTACCAGTTCGCCTTTCTC 60.028 50.000 0.00 0.00 0.00 2.87
65 66 1.975680 TCCTTACCAGTTCGCCTTTCT 59.024 47.619 0.00 0.00 0.00 2.52
66 67 2.467566 TCCTTACCAGTTCGCCTTTC 57.532 50.000 0.00 0.00 0.00 2.62
67 68 2.618045 CCATCCTTACCAGTTCGCCTTT 60.618 50.000 0.00 0.00 0.00 3.11
68 69 1.065418 CCATCCTTACCAGTTCGCCTT 60.065 52.381 0.00 0.00 0.00 4.35
69 70 0.541863 CCATCCTTACCAGTTCGCCT 59.458 55.000 0.00 0.00 0.00 5.52
70 71 0.463833 CCCATCCTTACCAGTTCGCC 60.464 60.000 0.00 0.00 0.00 5.54
71 72 0.539986 TCCCATCCTTACCAGTTCGC 59.460 55.000 0.00 0.00 0.00 4.70
72 73 2.108168 TCTCCCATCCTTACCAGTTCG 58.892 52.381 0.00 0.00 0.00 3.95
73 74 4.262079 CGTATCTCCCATCCTTACCAGTTC 60.262 50.000 0.00 0.00 0.00 3.01
74 75 3.641906 CGTATCTCCCATCCTTACCAGTT 59.358 47.826 0.00 0.00 0.00 3.16
75 76 3.231818 CGTATCTCCCATCCTTACCAGT 58.768 50.000 0.00 0.00 0.00 4.00
76 77 3.231818 ACGTATCTCCCATCCTTACCAG 58.768 50.000 0.00 0.00 0.00 4.00
77 78 3.323774 ACGTATCTCCCATCCTTACCA 57.676 47.619 0.00 0.00 0.00 3.25
78 79 4.100498 TGAAACGTATCTCCCATCCTTACC 59.900 45.833 0.00 0.00 0.00 2.85
79 80 5.272283 TGAAACGTATCTCCCATCCTTAC 57.728 43.478 0.00 0.00 0.00 2.34
80 81 5.600898 TGATGAAACGTATCTCCCATCCTTA 59.399 40.000 0.00 0.00 31.93 2.69
81 82 4.408921 TGATGAAACGTATCTCCCATCCTT 59.591 41.667 0.00 0.00 31.93 3.36
82 83 3.967326 TGATGAAACGTATCTCCCATCCT 59.033 43.478 0.00 0.00 31.93 3.24
83 84 4.336889 TGATGAAACGTATCTCCCATCC 57.663 45.455 0.00 0.00 31.93 3.51
84 85 4.623167 CGATGATGAAACGTATCTCCCATC 59.377 45.833 0.00 0.00 0.00 3.51
85 86 4.560128 CGATGATGAAACGTATCTCCCAT 58.440 43.478 0.00 0.00 0.00 4.00
86 87 3.243737 CCGATGATGAAACGTATCTCCCA 60.244 47.826 0.00 0.00 0.00 4.37
87 88 3.318017 CCGATGATGAAACGTATCTCCC 58.682 50.000 0.00 0.00 0.00 4.30
88 89 3.318017 CCCGATGATGAAACGTATCTCC 58.682 50.000 0.00 0.00 0.00 3.71
89 90 3.243771 ACCCCGATGATGAAACGTATCTC 60.244 47.826 0.00 0.00 0.00 2.75
90 91 2.698797 ACCCCGATGATGAAACGTATCT 59.301 45.455 0.00 0.00 0.00 1.98
91 92 3.107642 ACCCCGATGATGAAACGTATC 57.892 47.619 0.00 0.00 0.00 2.24
92 93 3.893200 TCTACCCCGATGATGAAACGTAT 59.107 43.478 0.00 0.00 0.00 3.06
93 94 3.289836 TCTACCCCGATGATGAAACGTA 58.710 45.455 0.00 0.00 0.00 3.57
94 95 2.104967 TCTACCCCGATGATGAAACGT 58.895 47.619 0.00 0.00 0.00 3.99
95 96 2.882927 TCTACCCCGATGATGAAACG 57.117 50.000 0.00 0.00 0.00 3.60
96 97 3.318017 CGATCTACCCCGATGATGAAAC 58.682 50.000 0.00 0.00 0.00 2.78
97 98 2.299013 CCGATCTACCCCGATGATGAAA 59.701 50.000 0.00 0.00 0.00 2.69
98 99 1.893137 CCGATCTACCCCGATGATGAA 59.107 52.381 0.00 0.00 0.00 2.57
99 100 1.545841 CCGATCTACCCCGATGATGA 58.454 55.000 0.00 0.00 0.00 2.92
100 101 0.532573 CCCGATCTACCCCGATGATG 59.467 60.000 0.00 0.00 0.00 3.07
101 102 1.258445 GCCCGATCTACCCCGATGAT 61.258 60.000 0.00 0.00 0.00 2.45
102 103 1.906824 GCCCGATCTACCCCGATGA 60.907 63.158 0.00 0.00 0.00 2.92
103 104 2.657237 GCCCGATCTACCCCGATG 59.343 66.667 0.00 0.00 0.00 3.84
104 105 2.603776 GGCCCGATCTACCCCGAT 60.604 66.667 0.00 0.00 0.00 4.18
105 106 3.829226 AGGCCCGATCTACCCCGA 61.829 66.667 0.00 0.00 0.00 5.14
106 107 3.616721 CAGGCCCGATCTACCCCG 61.617 72.222 0.00 0.00 0.00 5.73
107 108 3.242291 CCAGGCCCGATCTACCCC 61.242 72.222 0.00 0.00 0.00 4.95
108 109 2.446036 ACCAGGCCCGATCTACCC 60.446 66.667 0.00 0.00 0.00 3.69
109 110 1.760875 TGACCAGGCCCGATCTACC 60.761 63.158 0.00 0.00 0.00 3.18
110 111 1.327690 TGTGACCAGGCCCGATCTAC 61.328 60.000 0.00 0.00 0.00 2.59
111 112 1.001120 TGTGACCAGGCCCGATCTA 59.999 57.895 0.00 0.00 0.00 1.98
112 113 2.284625 TGTGACCAGGCCCGATCT 60.285 61.111 0.00 0.00 0.00 2.75
113 114 2.125106 GTGTGACCAGGCCCGATC 60.125 66.667 0.00 0.00 0.00 3.69
114 115 0.980754 TATGTGTGACCAGGCCCGAT 60.981 55.000 0.00 0.00 0.00 4.18
115 116 1.610967 TATGTGTGACCAGGCCCGA 60.611 57.895 0.00 0.00 0.00 5.14
116 117 1.153369 CTATGTGTGACCAGGCCCG 60.153 63.158 0.00 0.00 0.00 6.13
117 118 1.134491 GTACTATGTGTGACCAGGCCC 60.134 57.143 0.00 0.00 0.00 5.80
118 119 1.134491 GGTACTATGTGTGACCAGGCC 60.134 57.143 0.00 0.00 31.89 5.19
119 120 1.831736 AGGTACTATGTGTGACCAGGC 59.168 52.381 0.00 0.00 36.02 4.85
120 121 3.369471 CCAAGGTACTATGTGTGACCAGG 60.369 52.174 0.00 0.00 38.49 4.45
121 122 3.513912 TCCAAGGTACTATGTGTGACCAG 59.486 47.826 0.00 0.00 38.49 4.00
122 123 3.512496 TCCAAGGTACTATGTGTGACCA 58.488 45.455 0.00 0.00 38.49 4.02
123 124 3.767673 TCTCCAAGGTACTATGTGTGACC 59.232 47.826 0.00 0.00 38.49 4.02
124 125 4.219944 TGTCTCCAAGGTACTATGTGTGAC 59.780 45.833 0.00 4.66 38.49 3.67
125 126 4.412843 TGTCTCCAAGGTACTATGTGTGA 58.587 43.478 0.00 0.00 38.49 3.58
126 127 4.801330 TGTCTCCAAGGTACTATGTGTG 57.199 45.455 0.00 0.00 38.49 3.82
127 128 5.104900 GGATTGTCTCCAAGGTACTATGTGT 60.105 44.000 0.00 0.00 44.26 3.72
128 129 5.360591 GGATTGTCTCCAAGGTACTATGTG 58.639 45.833 0.00 0.00 44.26 3.21
129 130 5.615925 GGATTGTCTCCAAGGTACTATGT 57.384 43.478 0.00 0.00 44.26 2.29
147 148 9.520515 GGGATGATTAATGTACTACAATGGATT 57.479 33.333 0.00 0.00 0.00 3.01
148 149 7.824289 CGGGATGATTAATGTACTACAATGGAT 59.176 37.037 0.00 0.00 0.00 3.41
149 150 7.015779 TCGGGATGATTAATGTACTACAATGGA 59.984 37.037 0.00 0.00 0.00 3.41
150 151 7.158697 TCGGGATGATTAATGTACTACAATGG 58.841 38.462 0.00 0.00 0.00 3.16
151 152 8.777865 ATCGGGATGATTAATGTACTACAATG 57.222 34.615 0.00 0.00 31.57 2.82
152 153 8.593679 TGATCGGGATGATTAATGTACTACAAT 58.406 33.333 0.00 0.00 37.47 2.71
153 154 7.958088 TGATCGGGATGATTAATGTACTACAA 58.042 34.615 0.00 0.00 37.47 2.41
154 155 7.533289 TGATCGGGATGATTAATGTACTACA 57.467 36.000 0.00 0.00 37.47 2.74
167 168 3.743521 CATTTTAGGCTGATCGGGATGA 58.256 45.455 3.14 0.00 0.00 2.92
168 169 2.227388 GCATTTTAGGCTGATCGGGATG 59.773 50.000 3.14 0.00 0.00 3.51
169 170 2.107204 AGCATTTTAGGCTGATCGGGAT 59.893 45.455 3.14 0.00 40.80 3.85
170 171 1.490490 AGCATTTTAGGCTGATCGGGA 59.510 47.619 3.14 0.00 40.80 5.14
203 205 5.606348 ACTCTGATCCCAAGATAGTTGAC 57.394 43.478 0.00 0.00 30.90 3.18
276 278 4.149922 CGTATGTGCATGTCTAATTACCGG 59.850 45.833 0.00 0.00 0.00 5.28
346 353 0.647410 CTTGCCTCGTTGCAGATACG 59.353 55.000 3.00 3.00 43.21 3.06
413 420 2.588314 GCTGCCGATGGAGCTCTG 60.588 66.667 14.64 1.31 32.12 3.35
414 421 3.859414 GGCTGCCGATGGAGCTCT 61.859 66.667 14.64 0.00 35.42 4.09
462 471 1.260825 CTGACTCGACATGCATCATGC 59.739 52.381 1.35 1.35 44.80 4.06
463 472 2.538861 GTCTGACTCGACATGCATCATG 59.461 50.000 0.00 5.35 46.18 3.07
464 473 2.797439 CGTCTGACTCGACATGCATCAT 60.797 50.000 6.21 0.00 33.54 2.45
465 474 1.468054 CGTCTGACTCGACATGCATCA 60.468 52.381 6.21 0.00 33.54 3.07
466 475 1.195347 CGTCTGACTCGACATGCATC 58.805 55.000 6.21 0.00 33.54 3.91
508 517 2.482664 CCTGGTCTAGCTACGACTACGA 60.483 54.545 17.34 0.00 42.66 3.43
509 518 1.865970 CCTGGTCTAGCTACGACTACG 59.134 57.143 17.34 0.00 45.75 3.51
510 519 1.603326 GCCTGGTCTAGCTACGACTAC 59.397 57.143 17.34 7.49 0.00 2.73
511 520 1.476471 GGCCTGGTCTAGCTACGACTA 60.476 57.143 17.34 12.98 0.00 2.59
512 521 0.752376 GGCCTGGTCTAGCTACGACT 60.752 60.000 17.34 0.00 0.00 4.18
513 522 1.035932 TGGCCTGGTCTAGCTACGAC 61.036 60.000 3.32 12.34 0.00 4.34
659 672 1.142748 GGGACCGTCTGCAGATCAG 59.857 63.158 21.47 13.87 44.21 2.90
660 673 0.033503 TAGGGACCGTCTGCAGATCA 60.034 55.000 21.47 0.00 0.00 2.92
661 674 0.386113 GTAGGGACCGTCTGCAGATC 59.614 60.000 21.47 13.48 0.00 2.75
662 675 0.324368 TGTAGGGACCGTCTGCAGAT 60.324 55.000 21.47 3.30 0.00 2.90
663 676 0.324368 ATGTAGGGACCGTCTGCAGA 60.324 55.000 13.74 13.74 30.92 4.26
858 2800 2.498885 GTGGACACCTACCGGAGTTATT 59.501 50.000 9.46 0.00 34.02 1.40
901 4242 3.520721 TGAGATGAGAAAGGCTGATGGAA 59.479 43.478 0.00 0.00 0.00 3.53
909 4250 4.199432 TGAGACTTGAGATGAGAAAGGC 57.801 45.455 0.00 0.00 0.00 4.35
963 4304 3.636764 TCCAGAGCAAGCAGACGAATATA 59.363 43.478 0.00 0.00 0.00 0.86
964 4305 2.432146 TCCAGAGCAAGCAGACGAATAT 59.568 45.455 0.00 0.00 0.00 1.28
1152 4493 1.582968 GAACTCGAGTACGTGGGCA 59.417 57.895 20.39 0.00 40.69 5.36
1724 5068 4.501714 CGTAGTAGCCGGCGCCAA 62.502 66.667 28.98 5.54 34.57 4.52
1736 5080 1.604693 GCAAGTATATGCCGCCGTAGT 60.605 52.381 0.00 0.00 40.49 2.73
1786 5130 6.489361 AGGCATTTTGAGGCTAATCTATCAAG 59.511 38.462 0.00 0.00 40.43 3.02
1794 5138 3.004752 ACGAGGCATTTTGAGGCTAAT 57.995 42.857 0.00 0.00 42.47 1.73
1856 5200 0.249741 ATAGGGTGCGTTACGATGCC 60.250 55.000 9.62 6.54 36.96 4.40
1859 5203 2.973694 AACATAGGGTGCGTTACGAT 57.026 45.000 9.62 0.00 0.00 3.73
1868 5215 7.865706 AAGATAAGCAAAGTAACATAGGGTG 57.134 36.000 0.00 0.00 0.00 4.61
1992 5362 2.813100 AAAAACGCCGACGACGTAT 58.187 47.368 10.19 0.00 44.30 3.06
2520 5915 0.396695 CCCAGATTGAGCAAGCCCAT 60.397 55.000 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.