Multiple sequence alignment - TraesCS1B01G133700

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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 TraesCS1B01G133700 chr1B 100.000 2595 0 0 804 3398 169025363 169022769 0.000000e+00 4793
1 TraesCS1B01G133700 chr1B 100.000 395 0 0 1 395 169026166 169025772 0.000000e+00 730
2 TraesCS1B01G133700 chr5B 97.402 1347 32 2 1864 3209 655910866 655909522 0.000000e+00 2290
3 TraesCS1B01G133700 chr5B 91.566 166 14 0 1868 2033 239010319 239010154 2.640000e-56 230
4 TraesCS1B01G133700 chr5B 87.302 189 6 1 3210 3398 655906928 655906758 2.070000e-47 200
5 TraesCS1B01G133700 chr1D 95.442 1075 35 11 804 1868 110905585 110904515 0.000000e+00 1701
6 TraesCS1B01G133700 chr1D 97.959 245 5 0 151 395 110905864 110905620 3.130000e-115 425
7 TraesCS1B01G133700 chr7D 91.636 1088 61 17 806 1868 543731834 543730752 0.000000e+00 1478
8 TraesCS1B01G133700 chr7D 83.047 814 122 10 1050 1862 548551106 548550308 0.000000e+00 725
9 TraesCS1B01G133700 chr7D 83.030 825 91 23 1046 1866 530430880 530431659 0.000000e+00 702
10 TraesCS1B01G133700 chr7D 88.889 171 18 1 1868 2038 115822975 115822806 3.440000e-50 209
11 TraesCS1B01G133700 chr7A 90.674 1083 54 23 806 1868 625642574 625641519 0.000000e+00 1397
12 TraesCS1B01G133700 chr7A 91.364 1019 56 13 806 1812 625675352 625674354 0.000000e+00 1365
13 TraesCS1B01G133700 chr7A 85.145 828 88 9 1043 1866 631652570 631653366 0.000000e+00 815
14 TraesCS1B01G133700 chr7A 94.737 247 10 1 151 394 625675642 625675396 6.880000e-102 381
15 TraesCS1B01G133700 chr7A 94.262 244 14 0 151 394 625642861 625642618 1.150000e-99 374
16 TraesCS1B01G133700 chr6B 90.520 1076 63 20 807 1868 694681370 694680320 0.000000e+00 1386
17 TraesCS1B01G133700 chr6B 94.142 239 14 0 151 389 694681658 694681420 6.930000e-97 364
18 TraesCS1B01G133700 chr7B 86.528 772 84 11 1061 1816 569439964 569440731 0.000000e+00 832
19 TraesCS1B01G133700 chr7B 93.724 239 15 0 151 389 587441105 587440867 3.220000e-95 359
20 TraesCS1B01G133700 chr7B 92.887 239 17 0 151 389 587615638 587615400 6.980000e-92 348
21 TraesCS1B01G133700 chr7B 92.562 242 15 1 151 389 587480110 587479869 9.030000e-91 344
22 TraesCS1B01G133700 chr7B 92.562 242 15 1 151 389 587519371 587519130 9.030000e-91 344
23 TraesCS1B01G133700 chr7B 83.333 336 24 14 807 1128 587101912 587101595 7.180000e-72 281
24 TraesCS1B01G133700 chr7B 83.235 340 24 18 804 1126 587479822 587479499 7.180000e-72 281
25 TraesCS1B01G133700 chr7B 91.525 177 15 0 1046 1222 587503748 587503572 9.420000e-61 244
26 TraesCS1B01G133700 chr7B 81.548 336 21 17 807 1128 587267119 587266811 4.380000e-59 239
27 TraesCS1B01G133700 chr7B 90.395 177 17 0 1046 1222 587464469 587464293 2.040000e-57 233
28 TraesCS1B01G133700 chr7B 90.071 141 12 2 1 139 603670487 603670347 7.490000e-42 182
29 TraesCS1B01G133700 chr7B 85.207 169 12 6 807 975 587440817 587440662 9.760000e-36 161
30 TraesCS1B01G133700 chr7B 84.127 126 7 8 804 929 587615353 587615241 3.580000e-20 110
31 TraesCS1B01G133700 chr2A 94.561 239 13 0 151 389 701782254 701782492 1.490000e-98 370
32 TraesCS1B01G133700 chr2A 81.707 410 28 22 804 1182 701782708 701783101 7.130000e-77 298
33 TraesCS1B01G133700 chr5D 91.813 171 13 1 1868 2038 514303880 514304049 1.580000e-58 237
34 TraesCS1B01G133700 chr1A 90.000 170 14 2 1867 2033 8119598 8119429 2.050000e-52 217
35 TraesCS1B01G133700 chr5A 88.889 171 18 1 1864 2034 99017063 99016894 3.440000e-50 209
36 TraesCS1B01G133700 chr3D 90.071 141 12 1 1 139 49498604 49498744 7.490000e-42 182
37 TraesCS1B01G133700 chr4B 88.652 141 14 2 1 139 647707931 647708071 1.620000e-38 171
38 TraesCS1B01G133700 chr4A 89.516 124 13 0 1867 1990 201597111 201597234 1.260000e-34 158


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 TraesCS1B01G133700 chr1B 169022769 169026166 3397 True 2761.5 4793 100.0000 1 3398 2 chr1B.!!$R1 3397
1 TraesCS1B01G133700 chr5B 655906758 655910866 4108 True 1245.0 2290 92.3520 1864 3398 2 chr5B.!!$R2 1534
2 TraesCS1B01G133700 chr1D 110904515 110905864 1349 True 1063.0 1701 96.7005 151 1868 2 chr1D.!!$R1 1717
3 TraesCS1B01G133700 chr7D 543730752 543731834 1082 True 1478.0 1478 91.6360 806 1868 1 chr7D.!!$R2 1062
4 TraesCS1B01G133700 chr7D 548550308 548551106 798 True 725.0 725 83.0470 1050 1862 1 chr7D.!!$R3 812
5 TraesCS1B01G133700 chr7D 530430880 530431659 779 False 702.0 702 83.0300 1046 1866 1 chr7D.!!$F1 820
6 TraesCS1B01G133700 chr7A 625641519 625642861 1342 True 885.5 1397 92.4680 151 1868 2 chr7A.!!$R1 1717
7 TraesCS1B01G133700 chr7A 625674354 625675642 1288 True 873.0 1365 93.0505 151 1812 2 chr7A.!!$R2 1661
8 TraesCS1B01G133700 chr7A 631652570 631653366 796 False 815.0 815 85.1450 1043 1866 1 chr7A.!!$F1 823
9 TraesCS1B01G133700 chr6B 694680320 694681658 1338 True 875.0 1386 92.3310 151 1868 2 chr6B.!!$R1 1717
10 TraesCS1B01G133700 chr7B 569439964 569440731 767 False 832.0 832 86.5280 1061 1816 1 chr7B.!!$F1 755
11 TraesCS1B01G133700 chr7B 587479499 587480110 611 True 312.5 344 87.8985 151 1126 2 chr7B.!!$R8 975
12 TraesCS1B01G133700 chr2A 701782254 701783101 847 False 334.0 370 88.1340 151 1182 2 chr2A.!!$F1 1031

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
123 124 0.106066 TGATGGATGGTGGATTGGCC 60.106 55.000 0.00 0.00 37.10 5.36 F
135 136 0.179065 GATTGGCCACCGGTACCTAC 60.179 60.000 22.65 12.28 0.00 3.18 F
140 141 0.684153 GCCACCGGTACCTACCAGTA 60.684 60.000 6.87 0.00 46.80 2.74 F
963 993 1.300853 GTTTGCATGTGCCACACCC 60.301 57.895 0.00 0.00 41.18 4.61 F
2150 2247 0.811616 GACCCAGGTGCGCTAAGATG 60.812 60.000 9.73 0.03 0.00 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1922 2019 0.175989 GTTCCAGAGGGGTGTCGATC 59.824 60.000 0.00 0.00 38.11 3.69 R
1936 2033 1.008194 CTCGTCGAACCACGTTCCA 60.008 57.895 0.00 0.00 39.14 3.53 R
1956 2053 2.304092 AGCGTCCCGAAGATGTATACA 58.696 47.619 8.27 8.27 33.65 2.29 R
2155 2252 0.313043 ACAGTCGGTTCACGTACCAG 59.687 55.000 8.20 1.51 44.69 4.00 R
3284 5975 0.107508 AATGGTGGATGCACCTCGAG 60.108 55.000 33.00 5.13 45.21 4.04 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
26 27 9.155975 TCTCTTTTCTGTAAAGCTGACAATATC 57.844 33.333 3.52 0.00 42.47 1.63
27 28 9.160496 CTCTTTTCTGTAAAGCTGACAATATCT 57.840 33.333 3.52 0.00 42.47 1.98
28 29 9.507329 TCTTTTCTGTAAAGCTGACAATATCTT 57.493 29.630 3.52 0.00 42.47 2.40
31 32 9.719355 TTTCTGTAAAGCTGACAATATCTTACA 57.281 29.630 3.52 3.13 0.00 2.41
32 33 9.890629 TTCTGTAAAGCTGACAATATCTTACAT 57.109 29.630 3.52 0.00 0.00 2.29
33 34 9.534565 TCTGTAAAGCTGACAATATCTTACATC 57.465 33.333 3.52 0.00 0.00 3.06
34 35 9.317936 CTGTAAAGCTGACAATATCTTACATCA 57.682 33.333 3.52 0.00 0.00 3.07
35 36 9.317936 TGTAAAGCTGACAATATCTTACATCAG 57.682 33.333 0.00 0.00 37.28 2.90
36 37 9.319143 GTAAAGCTGACAATATCTTACATCAGT 57.681 33.333 0.00 0.00 36.71 3.41
38 39 8.879342 AAGCTGACAATATCTTACATCAGTAC 57.121 34.615 0.00 0.00 36.71 2.73
39 40 8.011844 AGCTGACAATATCTTACATCAGTACA 57.988 34.615 0.00 0.00 36.71 2.90
40 41 8.646004 AGCTGACAATATCTTACATCAGTACAT 58.354 33.333 0.00 0.00 36.71 2.29
41 42 8.706936 GCTGACAATATCTTACATCAGTACATG 58.293 37.037 0.00 0.00 36.71 3.21
42 43 9.755804 CTGACAATATCTTACATCAGTACATGT 57.244 33.333 2.69 2.69 40.28 3.21
54 55 8.818141 ACATCAGTACATGTATTACTATGTGC 57.182 34.615 9.18 14.90 39.30 4.57
55 56 8.421002 ACATCAGTACATGTATTACTATGTGCA 58.579 33.333 9.18 0.00 40.78 4.57
56 57 9.260002 CATCAGTACATGTATTACTATGTGCAA 57.740 33.333 9.18 12.42 40.78 4.08
58 59 9.476202 TCAGTACATGTATTACTATGTGCAATC 57.524 33.333 9.18 0.00 40.78 2.67
59 60 9.481340 CAGTACATGTATTACTATGTGCAATCT 57.519 33.333 9.18 0.00 40.78 2.40
96 97 8.932945 ATAGAGTATATGATATGCACAAACCG 57.067 34.615 3.44 0.00 0.00 4.44
97 98 6.993079 AGAGTATATGATATGCACAAACCGA 58.007 36.000 3.44 0.00 0.00 4.69
98 99 6.868864 AGAGTATATGATATGCACAAACCGAC 59.131 38.462 3.44 0.00 0.00 4.79
99 100 6.521162 AGTATATGATATGCACAAACCGACA 58.479 36.000 3.44 0.00 0.00 4.35
100 101 6.989759 AGTATATGATATGCACAAACCGACAA 59.010 34.615 3.44 0.00 0.00 3.18
101 102 6.691754 ATATGATATGCACAAACCGACAAA 57.308 33.333 0.00 0.00 0.00 2.83
102 103 4.837896 TGATATGCACAAACCGACAAAA 57.162 36.364 0.00 0.00 0.00 2.44
103 104 4.793071 TGATATGCACAAACCGACAAAAG 58.207 39.130 0.00 0.00 0.00 2.27
104 105 4.277174 TGATATGCACAAACCGACAAAAGT 59.723 37.500 0.00 0.00 0.00 2.66
105 106 2.270275 TGCACAAACCGACAAAAGTG 57.730 45.000 0.00 0.00 0.00 3.16
106 107 1.813178 TGCACAAACCGACAAAAGTGA 59.187 42.857 0.00 0.00 0.00 3.41
107 108 2.425312 TGCACAAACCGACAAAAGTGAT 59.575 40.909 0.00 0.00 0.00 3.06
108 109 2.788786 GCACAAACCGACAAAAGTGATG 59.211 45.455 0.00 0.00 0.00 3.07
109 110 3.371168 CACAAACCGACAAAAGTGATGG 58.629 45.455 0.00 0.00 0.00 3.51
110 111 3.066064 CACAAACCGACAAAAGTGATGGA 59.934 43.478 0.00 0.00 0.00 3.41
111 112 3.888930 ACAAACCGACAAAAGTGATGGAT 59.111 39.130 0.00 0.00 0.00 3.41
112 113 4.229096 CAAACCGACAAAAGTGATGGATG 58.771 43.478 0.00 0.00 0.00 3.51
113 114 2.436417 ACCGACAAAAGTGATGGATGG 58.564 47.619 0.00 0.00 0.00 3.51
114 115 2.224769 ACCGACAAAAGTGATGGATGGT 60.225 45.455 0.00 0.00 0.00 3.55
115 116 2.162208 CCGACAAAAGTGATGGATGGTG 59.838 50.000 0.00 0.00 0.00 4.17
116 117 2.162208 CGACAAAAGTGATGGATGGTGG 59.838 50.000 0.00 0.00 0.00 4.61
117 118 3.420893 GACAAAAGTGATGGATGGTGGA 58.579 45.455 0.00 0.00 0.00 4.02
118 119 4.019174 GACAAAAGTGATGGATGGTGGAT 58.981 43.478 0.00 0.00 0.00 3.41
119 120 4.419282 ACAAAAGTGATGGATGGTGGATT 58.581 39.130 0.00 0.00 0.00 3.01
120 121 4.221262 ACAAAAGTGATGGATGGTGGATTG 59.779 41.667 0.00 0.00 0.00 2.67
121 122 2.742428 AGTGATGGATGGTGGATTGG 57.258 50.000 0.00 0.00 0.00 3.16
122 123 1.035139 GTGATGGATGGTGGATTGGC 58.965 55.000 0.00 0.00 0.00 4.52
123 124 0.106066 TGATGGATGGTGGATTGGCC 60.106 55.000 0.00 0.00 37.10 5.36
124 125 0.106066 GATGGATGGTGGATTGGCCA 60.106 55.000 0.00 0.00 46.96 5.36
131 132 2.672295 TGGATTGGCCACCGGTAC 59.328 61.111 6.87 1.57 43.33 3.34
132 133 2.124445 GGATTGGCCACCGGTACC 60.124 66.667 17.12 17.12 36.34 3.34
133 134 2.676265 GGATTGGCCACCGGTACCT 61.676 63.158 22.65 7.23 36.34 3.08
134 135 1.339644 GGATTGGCCACCGGTACCTA 61.340 60.000 22.65 17.23 36.34 3.08
135 136 0.179065 GATTGGCCACCGGTACCTAC 60.179 60.000 22.65 12.28 0.00 3.18
136 137 1.629181 ATTGGCCACCGGTACCTACC 61.629 60.000 22.65 13.66 42.98 3.18
137 138 2.684655 GGCCACCGGTACCTACCA 60.685 66.667 6.87 0.00 46.80 3.25
138 139 2.728435 GGCCACCGGTACCTACCAG 61.728 68.421 6.87 0.00 46.80 4.00
139 140 1.986210 GCCACCGGTACCTACCAGT 60.986 63.158 6.87 0.00 46.80 4.00
140 141 0.684153 GCCACCGGTACCTACCAGTA 60.684 60.000 6.87 0.00 46.80 2.74
141 142 1.851304 CCACCGGTACCTACCAGTAA 58.149 55.000 6.87 0.00 46.80 2.24
142 143 1.478105 CCACCGGTACCTACCAGTAAC 59.522 57.143 6.87 0.00 46.80 2.50
143 144 2.450476 CACCGGTACCTACCAGTAACT 58.550 52.381 6.87 0.00 46.80 2.24
144 145 2.827921 CACCGGTACCTACCAGTAACTT 59.172 50.000 6.87 0.00 46.80 2.66
145 146 4.016444 CACCGGTACCTACCAGTAACTTA 58.984 47.826 6.87 0.00 46.80 2.24
146 147 4.096984 CACCGGTACCTACCAGTAACTTAG 59.903 50.000 6.87 0.00 46.80 2.18
147 148 4.263949 ACCGGTACCTACCAGTAACTTAGT 60.264 45.833 4.49 0.00 46.80 2.24
148 149 4.336713 CCGGTACCTACCAGTAACTTAGTC 59.663 50.000 10.90 0.00 46.80 2.59
149 150 4.034510 CGGTACCTACCAGTAACTTAGTCG 59.965 50.000 10.90 0.00 46.80 4.18
872 897 1.539929 CCATTCCAGATCAGTCGGAGC 60.540 57.143 0.00 0.00 31.79 4.70
963 993 1.300853 GTTTGCATGTGCCACACCC 60.301 57.895 0.00 0.00 41.18 4.61
1453 1531 4.373116 GCCGGCCGTTCACAGAGA 62.373 66.667 26.12 0.00 0.00 3.10
1768 1859 2.025321 ACACTGTTCCCAGGACAAAACT 60.025 45.455 0.00 0.00 43.36 2.66
1894 1991 1.604378 CAGAAATCTGGGTCGCCCT 59.396 57.895 14.76 0.00 45.70 5.19
1918 2015 3.767806 GGAACGGGGTCGAGGGTC 61.768 72.222 0.00 0.00 40.11 4.46
1936 2033 3.148279 GCGGATCGACACCCCTCT 61.148 66.667 5.12 0.00 0.00 3.69
1956 2053 1.008079 GAACGTGGTTCGACGAGGT 60.008 57.895 13.51 0.00 42.10 3.85
1972 2069 2.882761 CGAGGTGTATACATCTTCGGGA 59.117 50.000 19.55 0.00 37.46 5.14
2060 2157 2.642139 TCGTGGTACGAGATTCCAAC 57.358 50.000 0.00 0.00 46.73 3.77
2150 2247 0.811616 GACCCAGGTGCGCTAAGATG 60.812 60.000 9.73 0.03 0.00 2.90
2155 2252 1.523938 GGTGCGCTAAGATGGGTCC 60.524 63.158 9.73 0.00 0.00 4.46
2194 2291 2.332063 ATTTGGGTCGATAGCACCTG 57.668 50.000 0.00 0.00 36.78 4.00
2195 2292 0.392461 TTTGGGTCGATAGCACCTGC 60.392 55.000 0.00 0.00 42.49 4.85
2197 2294 2.279517 GGTCGATAGCACCTGCCG 60.280 66.667 0.00 0.00 43.38 5.69
2370 2467 5.183904 AGGAAAATATCAAGTTCACAGCCAC 59.816 40.000 0.00 0.00 0.00 5.01
2466 2563 4.564406 GGTCCAGTATCCATGATCCATCAC 60.564 50.000 0.00 0.00 40.03 3.06
2487 2584 3.257375 ACGTACTTCATGTACCTGCAAGA 59.743 43.478 13.24 0.00 46.49 3.02
2595 2692 1.877443 GCGGTCTTCTGCCTTTTTGTA 59.123 47.619 0.00 0.00 39.82 2.41
2813 2910 2.709213 GAGCTTGTCTGCATTCTTCCT 58.291 47.619 0.00 0.00 34.99 3.36
2853 2950 9.219603 CTCTTGACATTGTGGATAAAAGAGTAA 57.780 33.333 0.00 0.00 36.33 2.24
3182 3280 6.189859 AGCATTTGTGGAAAGATATTGGAGA 58.810 36.000 0.00 0.00 0.00 3.71
3247 5938 4.920112 CCCACGGTGGTTGCACGA 62.920 66.667 24.70 0.00 35.17 4.35
3251 5942 3.698463 CGGTGGTTGCACGACGTC 61.698 66.667 5.18 5.18 0.00 4.34
3255 5946 2.174969 TGGTTGCACGACGTCCAAC 61.175 57.895 23.45 23.45 38.42 3.77
3267 5958 2.678336 GACGTCCAACAATGATTCCTCC 59.322 50.000 3.51 0.00 0.00 4.30
3277 5968 6.380079 ACAATGATTCCTCCAGTTTCTAGT 57.620 37.500 0.00 0.00 0.00 2.57
3278 5969 6.410540 ACAATGATTCCTCCAGTTTCTAGTC 58.589 40.000 0.00 0.00 0.00 2.59
3279 5970 5.622346 ATGATTCCTCCAGTTTCTAGTCC 57.378 43.478 0.00 0.00 0.00 3.85
3280 5971 3.447586 TGATTCCTCCAGTTTCTAGTCCG 59.552 47.826 0.00 0.00 0.00 4.79
3281 5972 1.183549 TCCTCCAGTTTCTAGTCCGC 58.816 55.000 0.00 0.00 0.00 5.54
3282 5973 0.175989 CCTCCAGTTTCTAGTCCGCC 59.824 60.000 0.00 0.00 0.00 6.13
3283 5974 0.175989 CTCCAGTTTCTAGTCCGCCC 59.824 60.000 0.00 0.00 0.00 6.13
3284 5975 1.221021 CCAGTTTCTAGTCCGCCCC 59.779 63.158 0.00 0.00 0.00 5.80
3285 5976 1.265454 CCAGTTTCTAGTCCGCCCCT 61.265 60.000 0.00 0.00 0.00 4.79
3286 5977 0.175989 CAGTTTCTAGTCCGCCCCTC 59.824 60.000 0.00 0.00 0.00 4.30
3287 5978 1.141234 GTTTCTAGTCCGCCCCTCG 59.859 63.158 0.00 0.00 38.08 4.63
3288 5979 1.000521 TTTCTAGTCCGCCCCTCGA 60.001 57.895 0.00 0.00 41.67 4.04
3289 5980 1.035932 TTTCTAGTCCGCCCCTCGAG 61.036 60.000 5.13 5.13 41.67 4.04
3290 5981 2.905935 TTCTAGTCCGCCCCTCGAGG 62.906 65.000 25.36 25.36 41.67 4.63
3291 5982 3.717924 CTAGTCCGCCCCTCGAGGT 62.718 68.421 29.25 12.03 41.67 3.85
3394 6085 2.168728 ACAATAAGGTCTCCTTCGGCTC 59.831 50.000 4.21 0.00 43.57 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.155975 GATATTGTCAGCTTTACAGAAAAGAGA 57.844 33.333 1.78 0.00 46.44 3.10
1 2 9.160496 AGATATTGTCAGCTTTACAGAAAAGAG 57.840 33.333 1.78 0.00 46.44 2.85
2 3 9.507329 AAGATATTGTCAGCTTTACAGAAAAGA 57.493 29.630 1.78 0.00 46.44 2.52
5 6 9.719355 TGTAAGATATTGTCAGCTTTACAGAAA 57.281 29.630 0.00 0.00 0.00 2.52
6 7 9.890629 ATGTAAGATATTGTCAGCTTTACAGAA 57.109 29.630 7.63 0.00 0.00 3.02
7 8 9.534565 GATGTAAGATATTGTCAGCTTTACAGA 57.465 33.333 7.63 0.00 0.00 3.41
8 9 9.317936 TGATGTAAGATATTGTCAGCTTTACAG 57.682 33.333 7.63 0.00 0.00 2.74
9 10 9.317936 CTGATGTAAGATATTGTCAGCTTTACA 57.682 33.333 4.76 4.76 0.00 2.41
10 11 9.319143 ACTGATGTAAGATATTGTCAGCTTTAC 57.681 33.333 10.14 0.00 37.25 2.01
12 13 9.319143 GTACTGATGTAAGATATTGTCAGCTTT 57.681 33.333 10.14 0.00 37.25 3.51
13 14 8.478066 TGTACTGATGTAAGATATTGTCAGCTT 58.522 33.333 10.14 0.00 37.25 3.74
14 15 8.011844 TGTACTGATGTAAGATATTGTCAGCT 57.988 34.615 10.14 0.00 37.25 4.24
15 16 8.706936 CATGTACTGATGTAAGATATTGTCAGC 58.293 37.037 10.14 1.79 37.25 4.26
16 17 9.755804 ACATGTACTGATGTAAGATATTGTCAG 57.244 33.333 0.00 9.16 39.09 3.51
28 29 9.908152 GCACATAGTAATACATGTACTGATGTA 57.092 33.333 7.96 8.12 41.83 2.29
29 30 8.421002 TGCACATAGTAATACATGTACTGATGT 58.579 33.333 7.96 10.51 39.87 3.06
30 31 8.816640 TGCACATAGTAATACATGTACTGATG 57.183 34.615 7.96 9.93 33.66 3.07
32 33 9.476202 GATTGCACATAGTAATACATGTACTGA 57.524 33.333 7.96 0.00 33.66 3.41
33 34 9.481340 AGATTGCACATAGTAATACATGTACTG 57.519 33.333 7.96 2.34 33.66 2.74
70 71 9.371136 CGGTTTGTGCATATCATATACTCTATT 57.629 33.333 0.00 0.00 0.00 1.73
71 72 8.749354 TCGGTTTGTGCATATCATATACTCTAT 58.251 33.333 0.00 0.00 0.00 1.98
72 73 8.027189 GTCGGTTTGTGCATATCATATACTCTA 58.973 37.037 0.00 0.00 0.00 2.43
73 74 6.868864 GTCGGTTTGTGCATATCATATACTCT 59.131 38.462 0.00 0.00 0.00 3.24
74 75 6.645003 TGTCGGTTTGTGCATATCATATACTC 59.355 38.462 0.00 0.00 0.00 2.59
75 76 6.521162 TGTCGGTTTGTGCATATCATATACT 58.479 36.000 0.00 0.00 0.00 2.12
76 77 6.779115 TGTCGGTTTGTGCATATCATATAC 57.221 37.500 0.00 0.00 0.00 1.47
77 78 7.793927 TTTGTCGGTTTGTGCATATCATATA 57.206 32.000 0.00 0.00 0.00 0.86
78 79 6.691754 TTTGTCGGTTTGTGCATATCATAT 57.308 33.333 0.00 0.00 0.00 1.78
79 80 6.150307 ACTTTTGTCGGTTTGTGCATATCATA 59.850 34.615 0.00 0.00 0.00 2.15
80 81 5.048083 ACTTTTGTCGGTTTGTGCATATCAT 60.048 36.000 0.00 0.00 0.00 2.45
81 82 4.277174 ACTTTTGTCGGTTTGTGCATATCA 59.723 37.500 0.00 0.00 0.00 2.15
82 83 4.616802 CACTTTTGTCGGTTTGTGCATATC 59.383 41.667 0.00 0.00 0.00 1.63
83 84 4.277174 TCACTTTTGTCGGTTTGTGCATAT 59.723 37.500 0.00 0.00 0.00 1.78
84 85 3.628032 TCACTTTTGTCGGTTTGTGCATA 59.372 39.130 0.00 0.00 0.00 3.14
85 86 2.425312 TCACTTTTGTCGGTTTGTGCAT 59.575 40.909 0.00 0.00 0.00 3.96
86 87 1.813178 TCACTTTTGTCGGTTTGTGCA 59.187 42.857 0.00 0.00 0.00 4.57
87 88 2.553079 TCACTTTTGTCGGTTTGTGC 57.447 45.000 0.00 0.00 0.00 4.57
88 89 3.066064 TCCATCACTTTTGTCGGTTTGTG 59.934 43.478 0.00 0.00 0.00 3.33
89 90 3.283751 TCCATCACTTTTGTCGGTTTGT 58.716 40.909 0.00 0.00 0.00 2.83
90 91 3.980646 TCCATCACTTTTGTCGGTTTG 57.019 42.857 0.00 0.00 0.00 2.93
91 92 3.255642 CCATCCATCACTTTTGTCGGTTT 59.744 43.478 0.00 0.00 0.00 3.27
92 93 2.819608 CCATCCATCACTTTTGTCGGTT 59.180 45.455 0.00 0.00 0.00 4.44
93 94 2.224769 ACCATCCATCACTTTTGTCGGT 60.225 45.455 0.00 0.00 0.00 4.69
94 95 2.162208 CACCATCCATCACTTTTGTCGG 59.838 50.000 0.00 0.00 0.00 4.79
95 96 2.162208 CCACCATCCATCACTTTTGTCG 59.838 50.000 0.00 0.00 0.00 4.35
96 97 3.420893 TCCACCATCCATCACTTTTGTC 58.579 45.455 0.00 0.00 0.00 3.18
97 98 3.524095 TCCACCATCCATCACTTTTGT 57.476 42.857 0.00 0.00 0.00 2.83
98 99 4.382254 CCAATCCACCATCCATCACTTTTG 60.382 45.833 0.00 0.00 0.00 2.44
99 100 3.770933 CCAATCCACCATCCATCACTTTT 59.229 43.478 0.00 0.00 0.00 2.27
100 101 3.368248 CCAATCCACCATCCATCACTTT 58.632 45.455 0.00 0.00 0.00 2.66
101 102 2.951787 GCCAATCCACCATCCATCACTT 60.952 50.000 0.00 0.00 0.00 3.16
102 103 1.410648 GCCAATCCACCATCCATCACT 60.411 52.381 0.00 0.00 0.00 3.41
103 104 1.035139 GCCAATCCACCATCCATCAC 58.965 55.000 0.00 0.00 0.00 3.06
104 105 0.106066 GGCCAATCCACCATCCATCA 60.106 55.000 0.00 0.00 34.01 3.07
105 106 0.106066 TGGCCAATCCACCATCCATC 60.106 55.000 0.61 0.00 40.72 3.51
106 107 2.017604 TGGCCAATCCACCATCCAT 58.982 52.632 0.61 0.00 40.72 3.41
107 108 3.518035 TGGCCAATCCACCATCCA 58.482 55.556 0.61 0.00 40.72 3.41
114 115 2.672295 GTACCGGTGGCCAATCCA 59.328 61.111 19.93 0.00 44.18 3.41
115 116 1.339644 TAGGTACCGGTGGCCAATCC 61.340 60.000 25.44 4.17 0.00 3.01
116 117 0.179065 GTAGGTACCGGTGGCCAATC 60.179 60.000 25.44 1.24 0.00 2.67
117 118 1.629181 GGTAGGTACCGGTGGCCAAT 61.629 60.000 25.44 12.77 36.50 3.16
118 119 2.292559 GGTAGGTACCGGTGGCCAA 61.293 63.158 25.44 1.29 36.50 4.52
119 120 2.684655 GGTAGGTACCGGTGGCCA 60.685 66.667 25.44 0.00 36.50 5.36
127 128 4.336713 CCGACTAAGTTACTGGTAGGTACC 59.663 50.000 2.73 2.73 46.62 3.34
128 129 4.944317 ACCGACTAAGTTACTGGTAGGTAC 59.056 45.833 16.66 0.00 36.28 3.34
129 130 5.179452 ACCGACTAAGTTACTGGTAGGTA 57.821 43.478 16.66 0.00 36.28 3.08
130 131 4.013050 GACCGACTAAGTTACTGGTAGGT 58.987 47.826 17.61 17.61 39.62 3.08
131 132 3.064545 CGACCGACTAAGTTACTGGTAGG 59.935 52.174 13.07 13.07 0.00 3.18
132 133 3.935203 TCGACCGACTAAGTTACTGGTAG 59.065 47.826 0.00 0.00 0.00 3.18
133 134 3.935203 CTCGACCGACTAAGTTACTGGTA 59.065 47.826 0.00 0.00 0.00 3.25
134 135 2.746362 CTCGACCGACTAAGTTACTGGT 59.254 50.000 0.00 0.00 0.00 4.00
135 136 3.005554 TCTCGACCGACTAAGTTACTGG 58.994 50.000 0.00 0.00 0.00 4.00
136 137 4.401714 GTTCTCGACCGACTAAGTTACTG 58.598 47.826 0.00 0.00 0.00 2.74
137 138 3.438434 GGTTCTCGACCGACTAAGTTACT 59.562 47.826 0.00 0.00 39.00 2.24
138 139 3.752731 GGTTCTCGACCGACTAAGTTAC 58.247 50.000 0.00 0.00 39.00 2.50
963 993 4.380841 TGTAGCGTAGTTATGAACAGGG 57.619 45.455 0.00 0.00 0.00 4.45
1014 1055 4.684134 GTGGCCATGGGGTGCTGT 62.684 66.667 9.72 0.00 36.17 4.40
1237 1299 4.821589 CCTCCTCTTGCCGTCGCC 62.822 72.222 0.00 0.00 0.00 5.54
1377 1451 2.031012 TCCAGCACGAGGTTGCAG 59.969 61.111 0.00 0.00 45.62 4.41
1449 1527 3.816524 CGGCGCGTCTCCTTCTCT 61.817 66.667 9.90 0.00 0.00 3.10
1563 1654 1.295357 CGCATAACTTCACCACGCCA 61.295 55.000 0.00 0.00 0.00 5.69
1576 1667 2.499205 CAGCCCGAGGTCGCATAA 59.501 61.111 0.00 0.00 38.18 1.90
1679 1770 3.482809 CGAGCTCGTCGTAGTCCA 58.517 61.111 27.79 0.00 44.20 4.02
1768 1859 2.750637 GAGGAGCTGGTCGACCGA 60.751 66.667 28.70 16.89 39.43 4.69
1894 1991 2.993264 GACCCCGTTCCTCGACCA 60.993 66.667 0.00 0.00 42.86 4.02
1899 1996 3.459063 CCCTCGACCCCGTTCCTC 61.459 72.222 0.00 0.00 37.05 3.71
1918 2015 4.570663 GAGGGGTGTCGATCCGCG 62.571 72.222 16.44 0.00 41.75 6.46
1922 2019 0.175989 GTTCCAGAGGGGTGTCGATC 59.824 60.000 0.00 0.00 38.11 3.69
1923 2020 1.605058 CGTTCCAGAGGGGTGTCGAT 61.605 60.000 0.00 0.00 38.11 3.59
1936 2033 1.008194 CTCGTCGAACCACGTTCCA 60.008 57.895 0.00 0.00 39.14 3.53
1956 2053 2.304092 AGCGTCCCGAAGATGTATACA 58.696 47.619 8.27 8.27 33.65 2.29
1972 2069 2.493030 CACGTCCCCGATTAGCGT 59.507 61.111 0.00 0.00 38.67 5.07
1981 2078 3.843117 GATCGCGATCCACGTCCCC 62.843 68.421 33.80 10.19 44.60 4.81
2060 2157 2.750815 GGTCATCGACCCAACTTCG 58.249 57.895 1.47 0.00 46.19 3.79
2150 2247 1.294459 GGTTCACGTACCAGGACCC 59.706 63.158 2.50 0.00 38.12 4.46
2155 2252 0.313043 ACAGTCGGTTCACGTACCAG 59.687 55.000 8.20 1.51 44.69 4.00
2216 2313 3.181445 TGGGCATGTATGGGATTCAGTAC 60.181 47.826 0.00 0.00 0.00 2.73
2339 2436 8.293867 TGTGAACTTGATATTTTCCTTTAACCG 58.706 33.333 0.00 0.00 0.00 4.44
2419 2516 1.046204 TGCTGCCATCGATCATCTCT 58.954 50.000 0.00 0.00 0.00 3.10
2595 2692 3.814504 ATGGATGAAGGAACACAACCT 57.185 42.857 0.00 0.00 39.69 3.50
2813 2910 9.905713 ACAATGTCAAGAGGAATAAGCTTAATA 57.094 29.630 10.85 0.00 0.00 0.98
2853 2950 3.118956 CGGCTGAGAGAAATTGGAGTACT 60.119 47.826 0.00 0.00 0.00 2.73
2882 2979 4.417426 TTTGTCCCAGCCTATTAGTAGC 57.583 45.455 0.00 0.00 0.00 3.58
2883 2980 5.990668 AGTTTTGTCCCAGCCTATTAGTAG 58.009 41.667 0.00 0.00 0.00 2.57
3067 3164 4.194640 TGCCAAGATAGCAGAAGATGAAC 58.805 43.478 0.00 0.00 34.69 3.18
3182 3280 6.322126 TGCCCTTTGCCCTAAATATTATGAT 58.678 36.000 0.00 0.00 40.16 2.45
3247 5938 2.039746 TGGAGGAATCATTGTTGGACGT 59.960 45.455 0.00 0.00 0.00 4.34
3251 5942 4.768968 AGAAACTGGAGGAATCATTGTTGG 59.231 41.667 0.00 0.00 0.00 3.77
3255 5946 5.819901 GGACTAGAAACTGGAGGAATCATTG 59.180 44.000 0.00 0.00 0.00 2.82
3267 5958 0.175989 GAGGGGCGGACTAGAAACTG 59.824 60.000 0.00 0.00 0.00 3.16
3281 5972 3.083349 TGGATGCACCTCGAGGGG 61.083 66.667 34.04 32.24 43.01 4.79
3282 5973 2.187946 GTGGATGCACCTCGAGGG 59.812 66.667 34.04 23.21 40.27 4.30
3283 5974 1.976132 ATGGTGGATGCACCTCGAGG 61.976 60.000 33.00 30.11 45.21 4.63
3284 5975 0.107508 AATGGTGGATGCACCTCGAG 60.108 55.000 33.00 5.13 45.21 4.04
3285 5976 0.392863 CAATGGTGGATGCACCTCGA 60.393 55.000 33.00 16.80 45.21 4.04
3286 5977 2.100846 CAATGGTGGATGCACCTCG 58.899 57.895 33.00 19.12 45.21 4.63
3308 5999 1.635663 CCATCCGACCTCAACGTTGC 61.636 60.000 23.47 8.42 0.00 4.17


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

AutoCloner maintained by Alex Coulton.