Multiple sequence alignment - TraesCS4A01G367000

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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 TraesCS4A01G367000 chr4A 100.000 2632 0 0 1 2632 640156157 640153526 0.000000e+00 4861
1 TraesCS4A01G367000 chr4A 79.379 354 58 11 1 344 456468510 456468858 4.380000e-58 235
2 TraesCS4A01G367000 chr6B 93.848 2292 132 5 343 2632 184806123 184808407 0.000000e+00 3443
3 TraesCS4A01G367000 chr6B 98.990 99 1 0 1 99 184805038 184805136 7.490000e-41 178
4 TraesCS4A01G367000 chr1A 89.759 2285 222 6 349 2632 492001028 491998755 0.000000e+00 2913
5 TraesCS4A01G367000 chr1A 94.746 1199 63 0 1434 2632 575003035 575004233 0.000000e+00 1866
6 TraesCS4A01G367000 chr1A 90.850 612 47 1 1434 2045 575036358 575036960 0.000000e+00 811
7 TraesCS4A01G367000 chr1A 90.701 613 47 2 1434 2045 575076927 575077530 0.000000e+00 808
8 TraesCS4A01G367000 chr1A 88.986 345 34 2 1 345 492002187 492002527 8.710000e-115 424
9 TraesCS4A01G367000 chr3B 94.467 1446 77 2 1187 2632 513943182 513944624 0.000000e+00 2224
10 TraesCS4A01G367000 chr3B 94.506 1347 71 2 1286 2632 661544681 661543338 0.000000e+00 2074
11 TraesCS4A01G367000 chr1B 93.165 1112 72 4 1522 2632 266115583 266114475 0.000000e+00 1629
12 TraesCS4A01G367000 chr4D 87.836 1266 140 9 1378 2632 118590139 118588877 0.000000e+00 1472
13 TraesCS4A01G367000 chr3A 91.726 979 81 0 1654 2632 120813948 120814926 0.000000e+00 1360
14 TraesCS4A01G367000 chr3A 79.494 356 55 13 1 344 737276050 737276399 1.220000e-58 237
15 TraesCS4A01G367000 chr3A 79.109 359 52 5 5 341 82458215 82457858 2.640000e-55 226
16 TraesCS4A01G367000 chr7D 92.350 915 65 4 1720 2632 37927814 37926903 0.000000e+00 1297
17 TraesCS4A01G367000 chr6D 85.502 538 41 24 611 1142 455718410 455718916 6.450000e-146 527
18 TraesCS4A01G367000 chr4B 79.009 343 72 0 2 344 614059757 614059415 4.380000e-58 235
19 TraesCS4A01G367000 chr2A 78.977 352 59 11 1 342 293961058 293961404 2.640000e-55 226
20 TraesCS4A01G367000 chr7A 78.884 251 44 8 1 246 42680946 42681192 7.540000e-36 161
21 TraesCS4A01G367000 chr5A 78.884 251 44 8 1 246 674083940 674084186 7.540000e-36 161


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 TraesCS4A01G367000 chr4A 640153526 640156157 2631 True 4861.0 4861 100.000 1 2632 1 chr4A.!!$R1 2631
1 TraesCS4A01G367000 chr6B 184805038 184808407 3369 False 1810.5 3443 96.419 1 2632 2 chr6B.!!$F1 2631
2 TraesCS4A01G367000 chr1A 491998755 492001028 2273 True 2913.0 2913 89.759 349 2632 1 chr1A.!!$R1 2283
3 TraesCS4A01G367000 chr1A 575003035 575004233 1198 False 1866.0 1866 94.746 1434 2632 1 chr1A.!!$F2 1198
4 TraesCS4A01G367000 chr1A 575036358 575036960 602 False 811.0 811 90.850 1434 2045 1 chr1A.!!$F3 611
5 TraesCS4A01G367000 chr1A 575076927 575077530 603 False 808.0 808 90.701 1434 2045 1 chr1A.!!$F4 611
6 TraesCS4A01G367000 chr3B 513943182 513944624 1442 False 2224.0 2224 94.467 1187 2632 1 chr3B.!!$F1 1445
7 TraesCS4A01G367000 chr3B 661543338 661544681 1343 True 2074.0 2074 94.506 1286 2632 1 chr3B.!!$R1 1346
8 TraesCS4A01G367000 chr1B 266114475 266115583 1108 True 1629.0 1629 93.165 1522 2632 1 chr1B.!!$R1 1110
9 TraesCS4A01G367000 chr4D 118588877 118590139 1262 True 1472.0 1472 87.836 1378 2632 1 chr4D.!!$R1 1254
10 TraesCS4A01G367000 chr3A 120813948 120814926 978 False 1360.0 1360 91.726 1654 2632 1 chr3A.!!$F1 978
11 TraesCS4A01G367000 chr7D 37926903 37927814 911 True 1297.0 1297 92.350 1720 2632 1 chr7D.!!$R1 912
12 TraesCS4A01G367000 chr6D 455718410 455718916 506 False 527.0 527 85.502 611 1142 1 chr6D.!!$F1 531

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
269 900 0.032130 TCAGGCACACAAGAGACGTC 59.968 55.0 7.70 7.7 0.00 4.34 F
1071 1858 0.036952 CATGTGCTTCTGGACGTCCT 60.037 55.0 33.39 8.8 37.34 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1201 1988 0.179018 AGGTGCTCCTTGAAACGCTT 60.179 50.0 0.18 0.0 42.12 4.68 R
2330 3142 0.034960 GAGGTCTTCTTGGCCCCTTC 60.035 60.0 0.00 0.0 42.71 3.46 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
99 100 1.815003 CTCCCGTGATGAATGCGCA 60.815 57.895 14.96 14.96 0.00 6.09
101 102 1.159713 TCCCGTGATGAATGCGCATC 61.160 55.000 25.53 17.12 43.84 3.91
103 104 1.438562 CCGTGATGAATGCGCATCCA 61.439 55.000 25.53 19.59 43.10 3.41
104 105 0.041576 CGTGATGAATGCGCATCCAG 60.042 55.000 25.53 0.39 43.10 3.86
105 106 0.309922 GTGATGAATGCGCATCCAGG 59.690 55.000 25.53 0.00 43.10 4.45
106 107 0.820482 TGATGAATGCGCATCCAGGG 60.820 55.000 25.53 0.00 43.10 4.45
115 116 2.032528 CATCCAGGGCGTGTGTGT 59.967 61.111 6.43 0.00 0.00 3.72
117 118 3.589654 ATCCAGGGCGTGTGTGTCG 62.590 63.158 6.43 0.00 0.00 4.35
118 119 4.602259 CCAGGGCGTGTGTGTCGT 62.602 66.667 6.43 0.00 0.00 4.34
119 120 2.587753 CAGGGCGTGTGTGTCGTT 60.588 61.111 0.00 0.00 0.00 3.85
120 121 2.587753 AGGGCGTGTGTGTCGTTG 60.588 61.111 0.00 0.00 0.00 4.10
121 122 4.307908 GGGCGTGTGTGTCGTTGC 62.308 66.667 0.00 0.00 0.00 4.17
122 123 4.307908 GGCGTGTGTGTCGTTGCC 62.308 66.667 0.00 0.00 35.04 4.52
123 124 4.643385 GCGTGTGTGTCGTTGCCG 62.643 66.667 0.00 0.00 0.00 5.69
124 125 4.643385 CGTGTGTGTCGTTGCCGC 62.643 66.667 0.00 0.00 0.00 6.53
125 126 4.643385 GTGTGTGTCGTTGCCGCG 62.643 66.667 0.00 0.00 0.00 6.46
141 142 4.135153 CGGACTCGGTCAGCCCAG 62.135 72.222 6.41 0.00 33.68 4.45
142 143 4.459089 GGACTCGGTCAGCCCAGC 62.459 72.222 6.41 0.00 33.68 4.85
143 144 3.386237 GACTCGGTCAGCCCAGCT 61.386 66.667 0.00 0.00 40.77 4.24
152 153 3.897856 AGCCCAGCTGACAGAGTT 58.102 55.556 17.39 0.00 37.57 3.01
153 154 3.073228 AGCCCAGCTGACAGAGTTA 57.927 52.632 17.39 0.00 37.57 2.24
154 155 1.352083 AGCCCAGCTGACAGAGTTAA 58.648 50.000 17.39 0.00 37.57 2.01
155 156 1.912043 AGCCCAGCTGACAGAGTTAAT 59.088 47.619 17.39 0.00 37.57 1.40
164 165 2.197577 GACAGAGTTAATGCGCCTCTC 58.802 52.381 4.18 5.65 33.38 3.20
165 166 1.134670 ACAGAGTTAATGCGCCTCTCC 60.135 52.381 4.18 0.00 33.38 3.71
166 167 1.137872 CAGAGTTAATGCGCCTCTCCT 59.862 52.381 4.18 0.00 33.38 3.69
169 170 1.153168 TTAATGCGCCTCTCCTGCC 60.153 57.895 4.18 0.00 0.00 4.85
190 191 3.864686 CCGCGTCGGCATTGAAGG 61.865 66.667 4.92 0.00 41.17 3.46
191 192 4.520846 CGCGTCGGCATTGAAGGC 62.521 66.667 0.00 0.00 39.92 4.35
197 198 4.543084 GGCATTGAAGGCGAGCGC 62.543 66.667 6.27 6.27 41.06 5.92
198 199 4.876081 GCATTGAAGGCGAGCGCG 62.876 66.667 5.14 5.14 43.06 6.86
199 200 3.490759 CATTGAAGGCGAGCGCGT 61.491 61.111 12.44 6.51 43.06 6.01
219 850 4.399395 CCAGAAGCAGCCTGGCGA 62.399 66.667 13.96 0.00 43.93 5.54
221 852 2.999648 AGAAGCAGCCTGGCGAGA 61.000 61.111 13.96 0.00 39.27 4.04
222 853 2.817396 GAAGCAGCCTGGCGAGAC 60.817 66.667 13.96 4.10 39.27 3.36
259 890 2.665603 GGGGAGTCTCAGGCACAC 59.334 66.667 1.47 0.00 0.00 3.82
260 891 2.217038 GGGGAGTCTCAGGCACACA 61.217 63.158 1.47 0.00 0.00 3.72
261 892 1.754745 GGGAGTCTCAGGCACACAA 59.245 57.895 1.47 0.00 0.00 3.33
262 893 0.321122 GGGAGTCTCAGGCACACAAG 60.321 60.000 1.47 0.00 0.00 3.16
264 895 1.337635 GGAGTCTCAGGCACACAAGAG 60.338 57.143 1.47 0.00 0.00 2.85
265 896 1.615883 GAGTCTCAGGCACACAAGAGA 59.384 52.381 0.00 0.00 34.95 3.10
267 898 0.315251 TCTCAGGCACACAAGAGACG 59.685 55.000 0.00 0.00 32.57 4.18
268 899 0.032678 CTCAGGCACACAAGAGACGT 59.967 55.000 0.00 0.00 0.00 4.34
269 900 0.032130 TCAGGCACACAAGAGACGTC 59.968 55.000 7.70 7.70 0.00 4.34
270 901 0.946221 CAGGCACACAAGAGACGTCC 60.946 60.000 13.01 3.77 0.00 4.79
271 902 1.668151 GGCACACAAGAGACGTCCC 60.668 63.158 13.01 0.00 0.00 4.46
272 903 2.022129 GCACACAAGAGACGTCCCG 61.022 63.158 13.01 0.46 0.00 5.14
274 905 2.338620 CACAAGAGACGTCCCGCA 59.661 61.111 13.01 0.00 0.00 5.69
275 906 1.734477 CACAAGAGACGTCCCGCAG 60.734 63.158 13.01 1.38 0.00 5.18
277 908 1.251527 ACAAGAGACGTCCCGCAGAT 61.252 55.000 13.01 0.00 0.00 2.90
278 909 0.526524 CAAGAGACGTCCCGCAGATC 60.527 60.000 13.01 0.82 0.00 2.75
279 910 1.994507 AAGAGACGTCCCGCAGATCG 61.995 60.000 13.01 0.00 38.08 3.69
333 964 2.272146 GCCAAAGCCCGATCCAGA 59.728 61.111 0.00 0.00 0.00 3.86
334 965 1.152881 GCCAAAGCCCGATCCAGAT 60.153 57.895 0.00 0.00 0.00 2.90
336 967 0.536006 CCAAAGCCCGATCCAGATCC 60.536 60.000 2.11 0.00 34.40 3.36
337 968 0.181114 CAAAGCCCGATCCAGATCCA 59.819 55.000 2.11 0.00 34.40 3.41
347 1127 2.388526 TCCAGATCCAGATCCGTCAT 57.611 50.000 4.01 0.00 38.58 3.06
419 1199 3.127533 GACAGTGGTGGCCATCGC 61.128 66.667 22.44 22.44 35.28 4.58
431 1211 2.169789 CCATCGCCGTTCTGCTGAG 61.170 63.158 0.00 0.00 0.00 3.35
451 1231 2.030562 GGGCACGGATATGGGTCG 59.969 66.667 0.00 0.00 0.00 4.79
497 1277 3.279116 GCAAGTGGTGACGCAGCA 61.279 61.111 7.48 7.48 45.56 4.41
640 1420 2.121963 TGCCTCCCCACCTCTGTT 60.122 61.111 0.00 0.00 0.00 3.16
644 1424 2.121963 TCCCCACCTCTGTTGCCT 60.122 61.111 0.00 0.00 0.00 4.75
664 1444 1.064003 ACAACTGTGCTCCCACCATA 58.936 50.000 0.00 0.00 41.35 2.74
668 1448 0.839277 CTGTGCTCCCACCATATCCA 59.161 55.000 0.00 0.00 41.35 3.41
686 1466 0.108898 CACGCTCCAGGAGAAGTGAG 60.109 60.000 28.35 11.86 39.94 3.51
706 1486 4.443266 GCGCCTCTCACCGCTCTT 62.443 66.667 0.00 0.00 46.14 2.85
746 1526 4.012811 TTGCGCCTGCTCTGCTCT 62.013 61.111 4.18 0.00 43.34 4.09
764 1544 2.249413 CTCCGTCCATGCTCCAAGCT 62.249 60.000 0.11 0.00 42.97 3.74
935 1716 2.095252 GCCACTCTTCGAAGACCGC 61.095 63.158 23.74 19.36 34.32 5.68
1071 1858 0.036952 CATGTGCTTCTGGACGTCCT 60.037 55.000 33.39 8.80 37.34 3.85
1079 1866 0.251653 TCTGGACGTCCTAAGGCTGT 60.252 55.000 33.39 0.00 36.82 4.40
1147 1934 1.219124 CTGGTGTGCCGCACTCTAT 59.781 57.895 23.52 0.00 46.86 1.98
1167 1954 1.442526 GCATCGTCAAGGATGGGCAG 61.443 60.000 12.98 0.00 43.19 4.85
1201 1988 2.577059 CCCTGGACGCTTTCGCTA 59.423 61.111 0.00 0.00 39.84 4.26
1218 2005 1.135944 GCTAAGCGTTTCAAGGAGCAC 60.136 52.381 0.00 0.00 0.00 4.40
1233 2020 1.200760 AGCACCTGCCACCAGATGTA 61.201 55.000 0.00 0.00 41.77 2.29
1263 2050 1.442769 TGCGAGGATTGTTCAAGCTC 58.557 50.000 0.00 0.00 0.00 4.09
1266 2053 2.544685 CGAGGATTGTTCAAGCTCGAT 58.455 47.619 13.02 0.00 34.85 3.59
1268 2055 4.112634 CGAGGATTGTTCAAGCTCGATTA 58.887 43.478 13.02 0.00 34.85 1.75
1272 2059 5.882557 AGGATTGTTCAAGCTCGATTACAAT 59.117 36.000 4.71 4.71 38.50 2.71
1323 2110 1.378911 GCATGGAGGTGATGGTGCA 60.379 57.895 0.00 0.00 33.09 4.57
1400 2187 1.160137 CTTGCTGTTGCTGTCTACCC 58.840 55.000 0.00 0.00 40.48 3.69
1437 2224 7.539712 TCTTAATGTTAGCACAAGACTATGC 57.460 36.000 3.87 3.87 42.39 3.14
1440 2227 3.334691 TGTTAGCACAAGACTATGCCAC 58.665 45.455 7.78 6.39 43.12 5.01
1482 2270 1.133513 TGGGGTGCTCAATGTGTTTCT 60.134 47.619 0.00 0.00 0.00 2.52
1533 2321 8.150296 CCATGTATCTGTAGTGGATTATGTTCA 58.850 37.037 0.00 0.00 31.59 3.18
1554 2342 6.647334 TCATGTGACCTTTAGAATGCAAAA 57.353 33.333 0.00 0.00 0.00 2.44
1625 2426 6.989169 GGTGCTCTCTGTTTTACATGATAGAT 59.011 38.462 0.00 0.00 0.00 1.98
1664 2465 3.655777 TCAGTTGGAACATAAGGGGTCTT 59.344 43.478 0.00 0.00 39.30 3.01
1680 2481 1.207329 GTCTTAACTGCCTGGACCGAT 59.793 52.381 0.00 0.00 0.00 4.18
1754 2564 2.037251 ACAAGAGACTAAGCTCGGCAAA 59.963 45.455 0.00 0.00 39.87 3.68
1777 2587 1.135859 CGACCAATTCACAGCAGCTTC 60.136 52.381 0.00 0.00 0.00 3.86
1778 2588 1.200948 GACCAATTCACAGCAGCTTCC 59.799 52.381 0.00 0.00 0.00 3.46
1822 2632 0.601576 TTCGCGCAAAGACCTGCTTA 60.602 50.000 8.75 0.00 40.33 3.09
1850 2661 0.685458 GGGGTGGCATCTTGATGCTT 60.685 55.000 27.66 0.00 46.22 3.91
1894 2705 2.391616 TCTTGCATCAGCTTCACGAT 57.608 45.000 0.00 0.00 42.74 3.73
1916 2727 2.215451 ATTGCCTCTCCGCCATGGTT 62.215 55.000 14.67 0.00 39.52 3.67
1986 2797 1.238439 CACGGACCACTCTTGCAAAT 58.762 50.000 0.00 0.00 0.00 2.32
2076 2887 7.242914 GATTTTAACCAAATCTATCGGACGT 57.757 36.000 0.00 0.00 45.30 4.34
2078 2889 1.935933 ACCAAATCTATCGGACGTGC 58.064 50.000 0.00 0.00 0.00 5.34
2092 2903 4.863689 TCGGACGTGCGATAAAAATAAGAA 59.136 37.500 28.70 0.78 0.00 2.52
2123 2934 2.486592 CCGAAGCAGGATAAACCGTTTT 59.513 45.455 0.96 0.00 44.74 2.43
2220 3031 1.398692 GAACCCAACCTTGTGCAAGA 58.601 50.000 12.99 0.00 40.79 3.02
2330 3142 1.203928 CGCTTCTACTTGCCGATGAG 58.796 55.000 0.00 0.00 0.00 2.90
2408 3220 0.602905 GGTTTGACGAGGTGGTCCAG 60.603 60.000 0.00 0.00 36.07 3.86
2413 3225 1.152312 ACGAGGTGGTCCAGAAGGT 60.152 57.895 0.00 0.00 35.89 3.50
2428 3240 0.680061 AAGGTGTGGAACGAGAGGAC 59.320 55.000 0.00 0.00 42.39 3.85
2515 3327 1.755200 TGGAGTAGGGGCCTTTTCTT 58.245 50.000 0.84 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 88 0.820482 CCCTGGATGCGCATTCATCA 60.820 55.000 30.86 20.48 43.44 3.07
99 100 2.347490 GACACACACGCCCTGGAT 59.653 61.111 0.00 0.00 0.00 3.41
101 102 4.602259 ACGACACACACGCCCTGG 62.602 66.667 0.00 0.00 0.00 4.45
103 104 2.587753 CAACGACACACACGCCCT 60.588 61.111 0.00 0.00 0.00 5.19
104 105 4.307908 GCAACGACACACACGCCC 62.308 66.667 0.00 0.00 0.00 6.13
105 106 4.307908 GGCAACGACACACACGCC 62.308 66.667 0.00 0.00 0.00 5.68
126 127 3.386237 AGCTGGGCTGACCGAGTC 61.386 66.667 0.00 0.00 43.43 3.36
135 136 1.352083 TTAACTCTGTCAGCTGGGCT 58.648 50.000 15.13 0.00 40.77 5.19
136 137 2.012673 CATTAACTCTGTCAGCTGGGC 58.987 52.381 15.13 8.06 0.00 5.36
137 138 2.012673 GCATTAACTCTGTCAGCTGGG 58.987 52.381 15.13 4.92 0.00 4.45
138 139 1.662629 CGCATTAACTCTGTCAGCTGG 59.337 52.381 15.13 0.00 0.00 4.85
139 140 1.061711 GCGCATTAACTCTGTCAGCTG 59.938 52.381 7.63 7.63 0.00 4.24
140 141 1.363744 GCGCATTAACTCTGTCAGCT 58.636 50.000 0.30 0.00 0.00 4.24
141 142 0.375106 GGCGCATTAACTCTGTCAGC 59.625 55.000 10.83 0.00 0.00 4.26
142 143 1.929836 GAGGCGCATTAACTCTGTCAG 59.070 52.381 10.83 0.00 0.00 3.51
143 144 1.550524 AGAGGCGCATTAACTCTGTCA 59.449 47.619 10.83 0.00 39.92 3.58
144 145 2.197577 GAGAGGCGCATTAACTCTGTC 58.802 52.381 16.39 3.70 41.38 3.51
145 146 1.134670 GGAGAGGCGCATTAACTCTGT 60.135 52.381 16.39 0.00 41.38 3.41
146 147 1.137872 AGGAGAGGCGCATTAACTCTG 59.862 52.381 16.39 0.00 41.38 3.35
147 148 1.137872 CAGGAGAGGCGCATTAACTCT 59.862 52.381 10.83 11.64 43.81 3.24
148 149 1.576356 CAGGAGAGGCGCATTAACTC 58.424 55.000 10.83 5.06 0.00 3.01
149 150 0.462759 GCAGGAGAGGCGCATTAACT 60.463 55.000 10.83 0.00 0.00 2.24
150 151 1.440145 GGCAGGAGAGGCGCATTAAC 61.440 60.000 10.83 0.00 0.00 2.01
151 152 1.153168 GGCAGGAGAGGCGCATTAA 60.153 57.895 10.83 0.00 0.00 1.40
152 153 2.505982 GGCAGGAGAGGCGCATTA 59.494 61.111 10.83 0.00 0.00 1.90
153 154 4.496336 GGGCAGGAGAGGCGCATT 62.496 66.667 10.83 0.00 43.01 3.56
176 177 2.802667 CTCGCCTTCAATGCCGACG 61.803 63.158 0.00 0.00 0.00 5.12
181 182 4.876081 CGCGCTCGCCTTCAATGC 62.876 66.667 5.56 0.00 37.98 3.56
183 184 3.490759 CACGCGCTCGCCTTCAAT 61.491 61.111 5.73 0.00 39.84 2.57
204 205 2.999648 TCTCGCCAGGCTGCTTCT 61.000 61.111 10.54 0.00 0.00 2.85
205 206 2.817396 GTCTCGCCAGGCTGCTTC 60.817 66.667 10.54 0.00 0.00 3.86
206 207 4.749310 CGTCTCGCCAGGCTGCTT 62.749 66.667 10.54 0.00 0.00 3.91
241 872 2.607750 TGTGCCTGAGACTCCCCC 60.608 66.667 0.00 0.00 0.00 5.40
242 873 1.768684 TTGTGTGCCTGAGACTCCCC 61.769 60.000 0.00 0.00 0.00 4.81
243 874 0.321122 CTTGTGTGCCTGAGACTCCC 60.321 60.000 0.00 0.00 0.00 4.30
245 876 1.615883 TCTCTTGTGTGCCTGAGACTC 59.384 52.381 0.00 0.00 31.53 3.36
246 877 1.342819 GTCTCTTGTGTGCCTGAGACT 59.657 52.381 12.87 0.00 46.84 3.24
247 878 1.789506 GTCTCTTGTGTGCCTGAGAC 58.210 55.000 6.28 6.28 45.30 3.36
248 879 0.315251 CGTCTCTTGTGTGCCTGAGA 59.685 55.000 0.00 0.00 33.75 3.27
249 880 0.032678 ACGTCTCTTGTGTGCCTGAG 59.967 55.000 0.00 0.00 0.00 3.35
250 881 0.032130 GACGTCTCTTGTGTGCCTGA 59.968 55.000 8.70 0.00 0.00 3.86
253 884 1.668151 GGGACGTCTCTTGTGTGCC 60.668 63.158 16.46 0.36 36.94 5.01
316 947 1.152881 ATCTGGATCGGGCTTTGGC 60.153 57.895 0.00 0.00 37.82 4.52
317 948 0.536006 GGATCTGGATCGGGCTTTGG 60.536 60.000 4.75 0.00 38.69 3.28
318 949 0.181114 TGGATCTGGATCGGGCTTTG 59.819 55.000 4.75 0.00 38.69 2.77
319 950 0.471617 CTGGATCTGGATCGGGCTTT 59.528 55.000 4.75 0.00 38.69 3.51
320 951 0.399091 TCTGGATCTGGATCGGGCTT 60.399 55.000 4.75 0.00 38.69 4.35
321 952 0.178909 ATCTGGATCTGGATCGGGCT 60.179 55.000 4.75 0.00 38.69 5.19
322 953 0.248843 GATCTGGATCTGGATCGGGC 59.751 60.000 10.82 0.00 38.69 6.13
323 954 0.901124 GGATCTGGATCTGGATCGGG 59.099 60.000 16.29 1.21 39.19 5.14
324 955 0.529833 CGGATCTGGATCTGGATCGG 59.470 60.000 16.29 15.83 39.85 4.18
325 956 1.201181 GACGGATCTGGATCTGGATCG 59.799 57.143 19.61 12.25 46.03 3.69
326 957 2.242926 TGACGGATCTGGATCTGGATC 58.757 52.381 19.61 15.25 46.03 3.36
327 958 2.388526 TGACGGATCTGGATCTGGAT 57.611 50.000 19.61 3.93 46.03 3.41
328 959 2.242926 GATGACGGATCTGGATCTGGA 58.757 52.381 19.61 9.18 46.03 3.86
330 961 1.067985 CGGATGACGGATCTGGATCTG 60.068 57.143 15.47 15.47 46.89 2.90
331 962 1.252175 CGGATGACGGATCTGGATCT 58.748 55.000 6.47 0.00 39.42 2.75
333 964 1.668294 GCGGATGACGGATCTGGAT 59.332 57.895 6.47 0.00 44.51 3.41
334 965 2.845550 CGCGGATGACGGATCTGGA 61.846 63.158 6.47 0.00 44.51 3.86
460 1240 2.046507 AGCCAGAGCCTTGAAGCG 60.047 61.111 0.00 0.00 41.25 4.68
497 1277 1.303074 CACCAGCTCCAGCACATGT 60.303 57.895 0.48 0.00 45.16 3.21
499 1279 2.360852 GCACCAGCTCCAGCACAT 60.361 61.111 0.48 0.00 45.16 3.21
640 1420 1.374947 GGGAGCACAGTTGTAGGCA 59.625 57.895 0.00 0.00 0.00 4.75
644 1424 1.064003 ATGGTGGGAGCACAGTTGTA 58.936 50.000 0.00 0.00 0.00 2.41
664 1444 0.616111 ACTTCTCCTGGAGCGTGGAT 60.616 55.000 19.08 0.00 0.00 3.41
668 1448 1.254284 CCTCACTTCTCCTGGAGCGT 61.254 60.000 19.08 14.60 0.00 5.07
727 1507 4.631247 AGCAGAGCAGGCGCAACA 62.631 61.111 10.83 0.00 42.27 3.33
746 1526 2.244117 GAGCTTGGAGCATGGACGGA 62.244 60.000 2.47 0.00 45.56 4.69
764 1544 2.343758 GCAGGTGAGAGCAACGGA 59.656 61.111 0.00 0.00 36.63 4.69
935 1716 1.150081 GGACATGATGGCCTCCTGG 59.850 63.158 10.85 0.00 44.12 4.45
948 1729 1.852157 TGTTGGAGCAGGGGGACAT 60.852 57.895 0.00 0.00 0.00 3.06
992 1778 2.440980 GCCCAGCCATGGTCTTCC 60.441 66.667 14.67 0.00 46.10 3.46
1071 1858 2.359850 CCAGCCGCAACAGCCTTA 60.360 61.111 0.00 0.00 0.00 2.69
1147 1934 1.451927 GCCCATCCTTGACGATGCA 60.452 57.895 0.00 0.00 38.68 3.96
1167 1954 3.503363 GCGGCAGCAGTGACATCC 61.503 66.667 3.18 0.00 44.35 3.51
1201 1988 0.179018 AGGTGCTCCTTGAAACGCTT 60.179 50.000 0.18 0.00 42.12 4.68
1218 2005 1.134401 ACGATTACATCTGGTGGCAGG 60.134 52.381 0.00 0.00 0.00 4.85
1233 2020 0.681733 ATCCTCGCATGGCTACGATT 59.318 50.000 0.00 0.00 37.72 3.34
1263 2050 1.983605 CCCGTAGCGCTATTGTAATCG 59.016 52.381 21.96 16.56 0.00 3.34
1266 2053 3.277652 GCCCGTAGCGCTATTGTAA 57.722 52.632 21.96 0.00 0.00 2.41
1297 2084 0.322366 TCACCTCCATGCGCAATGAA 60.322 50.000 17.11 0.00 38.72 2.57
1352 2139 1.617018 ATTAGCCAGCTGAGCCACGA 61.617 55.000 17.39 3.90 0.00 4.35
1400 2187 3.551846 ACATTAAGAAACTATGGGCCCG 58.448 45.455 19.37 5.25 0.00 6.13
1440 2227 2.025441 CGGGCCAAACACACAACG 59.975 61.111 4.39 0.00 0.00 4.10
1487 2275 1.648720 CACAGGCCAACACAACTCG 59.351 57.895 5.01 0.00 0.00 4.18
1533 2321 6.996509 ACATTTTGCATTCTAAAGGTCACAT 58.003 32.000 0.00 0.00 28.93 3.21
1554 2342 1.474478 TGCAAACGGACACAACAACAT 59.526 42.857 0.00 0.00 0.00 2.71
1664 2465 1.412710 GATCATCGGTCCAGGCAGTTA 59.587 52.381 0.00 0.00 0.00 2.24
1680 2481 4.135747 TCGTTGCATTCACCATAGATCA 57.864 40.909 0.00 0.00 0.00 2.92
1754 2564 1.800805 CTGCTGTGAATTGGTCGACT 58.199 50.000 16.46 0.00 0.00 4.18
1777 2587 3.944250 AATCTGTGCCCGCCCAAGG 62.944 63.158 0.00 0.00 0.00 3.61
1778 2588 2.361610 AATCTGTGCCCGCCCAAG 60.362 61.111 0.00 0.00 0.00 3.61
1822 2632 3.970363 ATGCCACCCCTAGTGCCCT 62.970 63.158 0.00 0.00 45.83 5.19
1916 2727 4.671590 TCAGTCCCTCGCACCCGA 62.672 66.667 0.00 0.00 42.01 5.14
1986 2797 3.146066 ACAACTCGGCAAAGAAAGCATA 58.854 40.909 0.00 0.00 0.00 3.14
2073 2884 8.736751 ACATTTTTCTTATTTTTATCGCACGT 57.263 26.923 0.00 0.00 0.00 4.49
2092 2903 2.582052 TCCTGCTTCGGTTGACATTTT 58.418 42.857 0.00 0.00 0.00 1.82
2123 2934 0.545309 AGCTCTGGAGTGTTGCCCTA 60.545 55.000 0.00 0.00 0.00 3.53
2152 2963 1.341089 GGTTCTGGAGGTGGATTTCCC 60.341 57.143 0.00 0.00 34.29 3.97
2153 2964 1.679032 CGGTTCTGGAGGTGGATTTCC 60.679 57.143 0.00 0.00 0.00 3.13
2236 3047 1.964373 GTGTCCCAATCGGCGTTGT 60.964 57.895 6.85 0.00 0.00 3.32
2330 3142 0.034960 GAGGTCTTCTTGGCCCCTTC 60.035 60.000 0.00 0.00 42.71 3.46
2408 3220 0.966920 TCCTCTCGTTCCACACCTTC 59.033 55.000 0.00 0.00 0.00 3.46
2413 3225 0.959553 GTCAGTCCTCTCGTTCCACA 59.040 55.000 0.00 0.00 0.00 4.17
2428 3240 0.460284 GTATGGCTCGGTGTGGTCAG 60.460 60.000 0.00 0.00 0.00 3.51
2515 3327 2.768527 TGGTGGTGAATTTTTGCCTTCA 59.231 40.909 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.