Multiple sequence alignment - TraesCS7A01G208700

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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 TraesCS7A01G208700 chr7A 100.000 5949 0 0 1 5949 171390176 171384228 0.000000e+00 10986
1 TraesCS7A01G208700 chr7A 84.409 1270 188 5 3767 5033 188660697 188661959 0.000000e+00 1240
2 TraesCS7A01G208700 chr7A 86.007 586 70 10 2686 3266 188659472 188660050 8.470000e-173 617
3 TraesCS7A01G208700 chr7A 82.650 317 38 11 1090 1404 188657973 188658274 1.270000e-66 265
4 TraesCS7A01G208700 chr7D 95.202 5440 154 44 550 5949 169391293 169385921 0.000000e+00 8501
5 TraesCS7A01G208700 chr7D 84.691 1215 171 7 3767 4976 183027056 183025852 0.000000e+00 1199
6 TraesCS7A01G208700 chr7D 85.835 593 75 7 2686 3274 183028280 183027693 6.550000e-174 621
7 TraesCS7A01G208700 chr7D 87.766 376 35 9 12 385 169398879 169398513 4.260000e-116 429
8 TraesCS7A01G208700 chr7D 82.173 359 41 15 1048 1404 183030206 183029869 2.710000e-73 287
9 TraesCS7A01G208700 chr7D 90.640 203 9 5 370 564 169391559 169391359 1.640000e-65 261
10 TraesCS7A01G208700 chr7B 95.363 3429 129 9 2543 5949 134561282 134557862 0.000000e+00 5424
11 TraesCS7A01G208700 chr7B 91.811 2027 86 32 550 2544 134563312 134561334 0.000000e+00 2750
12 TraesCS7A01G208700 chr7B 84.022 1283 191 9 3766 5042 151430469 151429195 0.000000e+00 1221
13 TraesCS7A01G208700 chr7B 85.445 584 79 6 2686 3266 151431735 151431155 2.370000e-168 603
14 TraesCS7A01G208700 chr7B 80.903 576 60 31 11 564 134563927 134563380 5.550000e-110 409
15 TraesCS7A01G208700 chr7B 81.564 358 45 11 1048 1404 151433435 151433098 5.870000e-70 276
16 TraesCS7A01G208700 chr6A 84.651 215 23 9 1189 1399 522641440 522641232 7.820000e-49 206
17 TraesCS7A01G208700 chr6D 84.186 215 24 9 1189 1399 381369321 381369113 3.640000e-47 200
18 TraesCS7A01G208700 chr6B 83.721 215 26 8 1190 1399 569820899 569821109 1.690000e-45 195
19 TraesCS7A01G208700 chr3A 77.652 264 51 6 31 289 647454044 647454304 2.870000e-33 154
20 TraesCS7A01G208700 chr3A 75.889 253 48 10 31 275 526544353 526544600 3.770000e-22 117
21 TraesCS7A01G208700 chr1D 76.543 243 48 7 36 277 270617455 270617689 2.250000e-24 124
22 TraesCS7A01G208700 chr1A 75.277 271 60 7 33 300 451356820 451357086 8.100000e-24 122
23 TraesCS7A01G208700 chr4A 83.846 130 15 4 33 157 33647503 33647631 1.050000e-22 119
24 TraesCS7A01G208700 chr3B 75.502 249 52 8 33 277 489983640 489983397 4.870000e-21 113
25 TraesCS7A01G208700 chr4B 77.604 192 37 4 3344 3530 529405167 529405357 1.750000e-20 111
26 TraesCS7A01G208700 chr2D 75.893 224 42 10 41 262 579061710 579061497 2.930000e-18 104
27 TraesCS7A01G208700 chr5B 81.250 128 19 5 33 157 359874141 359874016 1.360000e-16 99


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 TraesCS7A01G208700 chr7A 171384228 171390176 5948 True 10986.000000 10986 100.000000 1 5949 1 chr7A.!!$R1 5948
1 TraesCS7A01G208700 chr7A 188657973 188661959 3986 False 707.333333 1240 84.355333 1090 5033 3 chr7A.!!$F1 3943
2 TraesCS7A01G208700 chr7D 169385921 169391559 5638 True 4381.000000 8501 92.921000 370 5949 2 chr7D.!!$R2 5579
3 TraesCS7A01G208700 chr7D 183025852 183030206 4354 True 702.333333 1199 84.233000 1048 4976 3 chr7D.!!$R3 3928
4 TraesCS7A01G208700 chr7B 134557862 134563927 6065 True 2861.000000 5424 89.359000 11 5949 3 chr7B.!!$R1 5938
5 TraesCS7A01G208700 chr7B 151429195 151433435 4240 True 700.000000 1221 83.677000 1048 5042 3 chr7B.!!$R2 3994

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
980 1090 0.533085 GCGGTATCCTTCCAGAAGCC 60.533 60.000 1.68 0.00 37.11 4.35 F
1497 1618 0.108756 GAGGTCTCGGGGAAAACTCG 60.109 60.000 0.00 0.00 0.00 4.18 F
1694 1823 0.179094 TGAAGAACACGCGAACCTGT 60.179 50.000 15.93 2.93 0.00 4.00 F
1885 2015 0.524816 AACGTGCACGCTACTATCGG 60.525 55.000 37.35 9.32 44.43 4.18 F
1890 2020 1.475280 TGCACGCTACTATCGGAACTT 59.525 47.619 0.00 0.00 0.00 2.66 F
2345 3156 2.094078 GGCTTCATGGCTTGCATGTTTA 60.094 45.455 1.14 0.00 38.32 2.01 F
4151 5685 1.733526 GCACTGTTCCTTTGCGGTT 59.266 52.632 0.00 0.00 0.00 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1942 1.552337 GACAGGAGCTGATGGAAGACA 59.448 52.381 0.00 0.0 35.18 3.41 R
3381 4913 2.299013 AGAGTGACGTGGCTTAATGTGA 59.701 45.455 0.00 0.0 0.00 3.58 R
3395 4927 6.929606 TCCAGCTACTTTTCTTTTAGAGTGAC 59.070 38.462 0.00 0.0 0.00 3.67 R
3787 5319 4.624015 AGTGAACAGCCAAATTGTCAATG 58.376 39.130 0.00 0.0 0.00 2.82 R
3935 5467 1.248486 GAACCAGGGTTTCCTCTTGC 58.752 55.000 4.99 0.0 42.67 4.01 R
4411 5947 1.174712 GCAACTCCTCAGCTGCCAAA 61.175 55.000 9.47 0.0 35.94 3.28 R
5754 7313 0.460284 CGACCGAAGCTGCCATAACT 60.460 55.000 0.00 0.0 0.00 2.24 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
34 35 6.882656 TGAAAACCATGTGGAAAAGATGAAA 58.117 32.000 5.96 0.00 38.94 2.69
62 63 8.634335 TCAAAACAATCTCAATAGAACATGGA 57.366 30.769 0.00 0.00 34.73 3.41
64 65 9.865321 CAAAACAATCTCAATAGAACATGGAAT 57.135 29.630 0.00 0.00 34.73 3.01
84 85 7.235079 TGGAATGTTAAGAGGGTGATGTTTTA 58.765 34.615 0.00 0.00 0.00 1.52
93 94 5.484998 AGAGGGTGATGTTTTATTGCCAAAT 59.515 36.000 0.00 0.00 0.00 2.32
110 111 7.769272 TGCCAAATAAAAGTTCAAGTTCAAG 57.231 32.000 0.00 0.00 0.00 3.02
111 112 6.257630 TGCCAAATAAAAGTTCAAGTTCAAGC 59.742 34.615 0.00 0.00 0.00 4.01
158 159 6.853279 AAATAACAAAATCAGCATCGAACG 57.147 33.333 0.00 0.00 0.00 3.95
160 161 2.151202 ACAAAATCAGCATCGAACGGT 58.849 42.857 0.00 0.00 0.00 4.83
161 162 2.095768 ACAAAATCAGCATCGAACGGTG 60.096 45.455 10.27 10.27 0.00 4.94
162 163 1.808411 AAATCAGCATCGAACGGTGT 58.192 45.000 14.65 3.18 33.61 4.16
164 165 0.802222 ATCAGCATCGAACGGTGTCG 60.802 55.000 14.65 6.44 42.48 4.35
211 212 9.771915 AATTGTTGAATTTGTTGTTTTCATGTC 57.228 25.926 0.00 0.00 0.00 3.06
212 213 8.545229 TTGTTGAATTTGTTGTTTTCATGTCT 57.455 26.923 0.00 0.00 0.00 3.41
213 214 8.183830 TGTTGAATTTGTTGTTTTCATGTCTC 57.816 30.769 0.00 0.00 0.00 3.36
214 215 7.816513 TGTTGAATTTGTTGTTTTCATGTCTCA 59.183 29.630 0.00 0.00 0.00 3.27
215 216 7.754069 TGAATTTGTTGTTTTCATGTCTCAC 57.246 32.000 0.00 0.00 0.00 3.51
216 217 7.318893 TGAATTTGTTGTTTTCATGTCTCACA 58.681 30.769 0.00 0.00 0.00 3.58
217 218 7.980662 TGAATTTGTTGTTTTCATGTCTCACAT 59.019 29.630 0.00 0.00 39.91 3.21
218 219 7.935338 ATTTGTTGTTTTCATGTCTCACATC 57.065 32.000 0.00 0.00 36.53 3.06
219 220 6.698008 TTGTTGTTTTCATGTCTCACATCT 57.302 33.333 0.00 0.00 36.53 2.90
220 221 6.698008 TGTTGTTTTCATGTCTCACATCTT 57.302 33.333 0.00 0.00 36.53 2.40
221 222 6.497437 TGTTGTTTTCATGTCTCACATCTTG 58.503 36.000 0.00 0.00 36.53 3.02
222 223 6.095300 TGTTGTTTTCATGTCTCACATCTTGT 59.905 34.615 0.00 0.00 36.53 3.16
223 224 7.281999 TGTTGTTTTCATGTCTCACATCTTGTA 59.718 33.333 0.00 0.00 36.53 2.41
224 225 7.425577 TGTTTTCATGTCTCACATCTTGTAG 57.574 36.000 0.00 0.00 36.53 2.74
225 226 7.216494 TGTTTTCATGTCTCACATCTTGTAGA 58.784 34.615 0.00 0.00 36.53 2.59
226 227 7.386025 TGTTTTCATGTCTCACATCTTGTAGAG 59.614 37.037 0.00 0.00 36.53 2.43
227 228 6.596309 TTCATGTCTCACATCTTGTAGAGT 57.404 37.500 0.00 0.00 36.53 3.24
228 229 5.958955 TCATGTCTCACATCTTGTAGAGTG 58.041 41.667 0.00 0.00 36.53 3.51
229 230 5.478332 TCATGTCTCACATCTTGTAGAGTGT 59.522 40.000 0.00 0.00 36.53 3.55
246 247 9.179909 TGTAGAGTGTTTCAAGTTGGAATTTTA 57.820 29.630 0.00 0.00 0.00 1.52
254 255 8.755018 GTTTCAAGTTGGAATTTTACATGACAG 58.245 33.333 0.00 0.00 0.00 3.51
268 269 9.891828 TTTTACATGACAGTAAAACATCACATC 57.108 29.630 0.00 0.00 44.53 3.06
271 272 7.394016 ACATGACAGTAAAACATCACATCCTA 58.606 34.615 0.00 0.00 0.00 2.94
273 274 7.667043 TGACAGTAAAACATCACATCCTAAC 57.333 36.000 0.00 0.00 0.00 2.34
274 275 7.220740 TGACAGTAAAACATCACATCCTAACA 58.779 34.615 0.00 0.00 0.00 2.41
275 276 7.882791 TGACAGTAAAACATCACATCCTAACAT 59.117 33.333 0.00 0.00 0.00 2.71
276 277 8.268850 ACAGTAAAACATCACATCCTAACATC 57.731 34.615 0.00 0.00 0.00 3.06
277 278 8.103305 ACAGTAAAACATCACATCCTAACATCT 58.897 33.333 0.00 0.00 0.00 2.90
320 321 5.930837 TTTTCTGACTTCCAAACCAACAT 57.069 34.783 0.00 0.00 0.00 2.71
351 355 9.790344 TTTTGAATGTTGGTTTCCATGATATTT 57.210 25.926 0.00 0.00 31.53 1.40
353 357 9.434420 TTGAATGTTGGTTTCCATGATATTTTC 57.566 29.630 0.00 0.00 31.53 2.29
360 364 5.817296 GGTTTCCATGATATTTTCCCAAAGC 59.183 40.000 0.00 0.00 0.00 3.51
408 414 6.115446 TCCTTGCACAACCTATTTCTATGAG 58.885 40.000 0.00 0.00 0.00 2.90
439 445 8.659527 AGGACATTACAAGAAAATTTCCCATTT 58.340 29.630 1.57 0.00 34.90 2.32
440 446 8.720562 GGACATTACAAGAAAATTTCCCATTTG 58.279 33.333 1.57 3.34 30.26 2.32
441 447 9.487790 GACATTACAAGAAAATTTCCCATTTGA 57.512 29.630 10.92 0.00 0.00 2.69
442 448 9.492973 ACATTACAAGAAAATTTCCCATTTGAG 57.507 29.630 10.92 3.25 0.00 3.02
605 706 3.353836 CGACAACGGGGCACAAGG 61.354 66.667 0.00 0.00 35.72 3.61
606 707 2.112297 GACAACGGGGCACAAGGA 59.888 61.111 0.00 0.00 0.00 3.36
607 708 1.303317 GACAACGGGGCACAAGGAT 60.303 57.895 0.00 0.00 0.00 3.24
610 711 0.680921 CAACGGGGCACAAGGATGAT 60.681 55.000 0.00 0.00 0.00 2.45
613 714 1.614711 GGGGCACAAGGATGATGGA 59.385 57.895 0.00 0.00 0.00 3.41
776 883 3.814268 CACCCATGGCGCTTTCCG 61.814 66.667 6.09 0.00 40.75 4.30
786 893 4.717313 GCTTTCCGCCCGTCCCTT 62.717 66.667 0.00 0.00 0.00 3.95
787 894 2.436115 CTTTCCGCCCGTCCCTTC 60.436 66.667 0.00 0.00 0.00 3.46
788 895 3.971109 CTTTCCGCCCGTCCCTTCC 62.971 68.421 0.00 0.00 0.00 3.46
795 902 3.408853 CCGTCCCTTCCCTTCCCC 61.409 72.222 0.00 0.00 0.00 4.81
873 980 4.284490 GCTGACCAGAGTCCATCCATATAA 59.716 45.833 0.47 0.00 42.81 0.98
881 988 3.511934 AGTCCATCCATATAAGCCGAGAC 59.488 47.826 0.00 0.00 0.00 3.36
980 1090 0.533085 GCGGTATCCTTCCAGAAGCC 60.533 60.000 1.68 0.00 37.11 4.35
1459 1574 2.508743 CGTTGCGACGGTTTCTGTA 58.491 52.632 19.10 0.00 45.32 2.74
1467 1582 0.466543 ACGGTTTCTGTACTGTGCCA 59.533 50.000 0.00 0.00 36.31 4.92
1497 1618 0.108756 GAGGTCTCGGGGAAAACTCG 60.109 60.000 0.00 0.00 0.00 4.18
1558 1685 4.568072 TGCTAAATTTAGGCCTCTGTCA 57.432 40.909 23.37 9.77 0.00 3.58
1601 1728 2.082231 GCATCAGTGACTTGAGCATGT 58.918 47.619 0.00 0.00 0.00 3.21
1649 1777 1.559831 CGTGCGATTCTGCTCACATA 58.440 50.000 0.00 0.00 35.36 2.29
1665 1794 4.371786 TCACATATGCGGATCAGAAGTTC 58.628 43.478 1.58 0.00 0.00 3.01
1666 1795 4.100035 TCACATATGCGGATCAGAAGTTCT 59.900 41.667 1.58 0.00 0.00 3.01
1692 1821 2.601562 GTGAAGAACACGCGAACCT 58.398 52.632 15.93 0.54 39.78 3.50
1694 1823 0.179094 TGAAGAACACGCGAACCTGT 60.179 50.000 15.93 2.93 0.00 4.00
1708 1837 3.619038 CGAACCTGTCAGGCTTAGATTTC 59.381 47.826 19.40 11.68 39.63 2.17
1731 1860 6.925211 TCAGGAGTGTAAAGTCTATGTCAAG 58.075 40.000 0.00 0.00 0.00 3.02
1745 1874 3.606595 TGTCAAGAGCCTCTCAATCAG 57.393 47.619 0.00 0.00 32.06 2.90
1812 1942 4.985538 TGCTAAGGGACACAGAGAATTTT 58.014 39.130 0.00 0.00 0.00 1.82
1842 1972 2.027745 TCAGCTCCTGTCAATTGACCTC 60.028 50.000 30.66 16.78 44.15 3.85
1885 2015 0.524816 AACGTGCACGCTACTATCGG 60.525 55.000 37.35 9.32 44.43 4.18
1890 2020 1.475280 TGCACGCTACTATCGGAACTT 59.525 47.619 0.00 0.00 0.00 2.66
1899 2042 4.857509 ACTATCGGAACTTGAGATAGGC 57.142 45.455 13.93 0.00 44.77 3.93
1912 2055 8.719645 ACTTGAGATAGGCAGATTAATCTAGT 57.280 34.615 17.53 10.35 34.85 2.57
2104 2894 4.993705 ACTTGGGACCACTTTGATCTTA 57.006 40.909 0.00 0.00 0.00 2.10
2174 2971 8.902806 TGACTAAAGAAATGAATGTTGTTCTGT 58.097 29.630 0.00 0.00 30.85 3.41
2345 3156 2.094078 GGCTTCATGGCTTGCATGTTTA 60.094 45.455 1.14 0.00 38.32 2.01
2905 3822 7.099266 TCATTTCCTGGTGCATTTTATACAG 57.901 36.000 0.00 0.00 0.00 2.74
3058 3975 3.181329 TGTCATGGTCTCTGGGTACAAT 58.819 45.455 0.00 0.00 0.00 2.71
3381 4913 7.275920 CCTAAACTGTCTCCTAATGTAGCATT 58.724 38.462 0.00 0.00 0.00 3.56
3395 4927 3.373748 TGTAGCATTCACATTAAGCCACG 59.626 43.478 0.00 0.00 0.00 4.94
3410 4942 4.067972 AGCCACGTCACTCTAAAAGAAA 57.932 40.909 0.00 0.00 0.00 2.52
3507 5039 3.814504 AGACACATCCCTTGGTGAAAT 57.185 42.857 0.00 0.00 38.38 2.17
3566 5098 6.605594 TCAGTTTGTAACTTTCCAAAGGATGT 59.394 34.615 4.13 0.00 40.46 3.06
3573 5105 6.484364 AACTTTCCAAAGGATGTGACAATT 57.516 33.333 4.13 0.00 40.31 2.32
3574 5106 7.595819 AACTTTCCAAAGGATGTGACAATTA 57.404 32.000 4.13 0.00 40.31 1.40
3685 5217 5.121142 GCAACTCAATGCTTAAACATGCAAT 59.879 36.000 0.00 0.00 43.06 3.56
3956 5488 2.508526 CAAGAGGAAACCCTGGTTCAG 58.491 52.381 1.29 0.00 37.35 3.02
4151 5685 1.733526 GCACTGTTCCTTTGCGGTT 59.266 52.632 0.00 0.00 0.00 4.44
4223 5757 4.569564 AGTTTACTCGACAACCTGTTGAAC 59.430 41.667 16.41 8.31 40.05 3.18
4808 6344 0.536460 AATCGAGTTTGTTGCCCGGT 60.536 50.000 0.00 0.00 0.00 5.28
4907 6443 2.678336 GTTAGCATAGATAATGGCGGGC 59.322 50.000 0.00 0.00 35.99 6.13
4927 6463 4.531332 GGCTTCTCGCTAAAATATGCAAG 58.469 43.478 0.00 0.00 39.13 4.01
4962 6498 2.750166 AGAGTTGACATCGACGATGACT 59.250 45.455 37.26 29.72 42.09 3.41
4992 6528 0.251341 CCTCCACCTGGAAACCTTGG 60.251 60.000 0.00 0.00 44.91 3.61
5068 6605 6.854496 ATAATACAAAACTCGTGTGTGTGT 57.146 33.333 14.23 10.33 30.79 3.72
5069 6606 2.892373 ACAAAACTCGTGTGTGTGTG 57.108 45.000 6.45 0.00 0.00 3.82
5084 6621 4.565962 GTGTGTGTGCAATGAAAACATTGA 59.434 37.500 21.74 8.35 43.26 2.57
5144 6681 7.499232 GCCACTAAGTTGATCAATATGGTAACT 59.501 37.037 12.12 0.00 37.61 2.24
5204 6741 9.448438 TGAAGCACTCTGTAAATAACATGTTAT 57.552 29.630 22.70 22.70 37.50 1.89
5269 6806 6.758416 TGTATAATGTGTGCAAGAGAGATGTC 59.242 38.462 0.00 0.00 0.00 3.06
5523 7082 9.265901 CTCCTGTATATTGGACAGAAAATACAG 57.734 37.037 11.51 11.51 46.01 2.74
5622 7181 8.402472 GTGGATGAGATATACTCTACAGCATAC 58.598 40.741 0.00 0.00 45.13 2.39
5629 7188 8.001875 AGATATACTCTACAGCATACCCATAGG 58.998 40.741 0.00 0.00 33.24 2.57
5727 7286 9.639601 CTTTCTTCCAATTTGGTTTTCCTATAC 57.360 33.333 14.98 0.00 39.03 1.47
5832 7391 2.969238 CACGGGGCGATCATCTGC 60.969 66.667 0.00 0.00 0.00 4.26
5867 7426 0.670162 AAGTTGACTGCGCAATGCTT 59.330 45.000 13.05 8.91 46.63 3.91
5888 7447 1.413445 TCGAAAGGAAGAACGGAACCA 59.587 47.619 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 6.669125 TCATCTTTTCCACATGGTTTTCAT 57.331 33.333 0.00 0.00 36.31 2.57
62 63 8.034804 GCAATAAAACATCACCCTCTTAACATT 58.965 33.333 0.00 0.00 0.00 2.71
64 65 6.071616 GGCAATAAAACATCACCCTCTTAACA 60.072 38.462 0.00 0.00 0.00 2.41
84 85 8.729805 TTGAACTTGAACTTTTATTTGGCAAT 57.270 26.923 0.00 0.00 0.00 3.56
98 99 7.377766 TCCTGTAATATGCTTGAACTTGAAC 57.622 36.000 0.00 0.00 0.00 3.18
110 111 8.777865 TTTATAGCTCACATCCTGTAATATGC 57.222 34.615 0.00 0.00 0.00 3.14
146 147 1.443702 CGACACCGTTCGATGCTGA 60.444 57.895 0.00 0.00 41.78 4.26
147 148 1.006825 TTCGACACCGTTCGATGCTG 61.007 55.000 2.35 0.00 46.94 4.41
148 149 1.007336 GTTCGACACCGTTCGATGCT 61.007 55.000 2.35 0.00 46.94 3.79
149 150 1.279527 TGTTCGACACCGTTCGATGC 61.280 55.000 2.35 0.98 46.94 3.91
150 151 0.433492 GTGTTCGACACCGTTCGATG 59.567 55.000 6.82 0.00 46.94 3.84
151 152 2.805277 GTGTTCGACACCGTTCGAT 58.195 52.632 6.82 0.00 46.94 3.59
152 153 4.307258 GTGTTCGACACCGTTCGA 57.693 55.556 6.82 0.00 46.12 3.71
160 161 3.852286 AGTGTTGTTACTGTGTTCGACA 58.148 40.909 0.00 0.00 0.00 4.35
161 162 6.520792 AATAGTGTTGTTACTGTGTTCGAC 57.479 37.500 0.00 0.00 32.19 4.20
162 163 8.821147 ATTAATAGTGTTGTTACTGTGTTCGA 57.179 30.769 0.00 0.00 32.19 3.71
190 191 7.816513 TGTGAGACATGAAAACAACAAATTCAA 59.183 29.630 0.00 0.00 36.72 2.69
196 197 6.698008 AGATGTGAGACATGAAAACAACAA 57.302 33.333 0.00 0.00 39.27 2.83
198 199 6.498304 ACAAGATGTGAGACATGAAAACAAC 58.502 36.000 0.00 0.00 39.27 3.32
203 204 6.870439 CACTCTACAAGATGTGAGACATGAAA 59.130 38.462 0.00 0.00 39.27 2.69
204 205 6.015095 ACACTCTACAAGATGTGAGACATGAA 60.015 38.462 0.00 0.00 39.27 2.57
206 207 5.718146 ACACTCTACAAGATGTGAGACATG 58.282 41.667 13.23 0.00 39.27 3.21
207 208 5.991933 ACACTCTACAAGATGTGAGACAT 57.008 39.130 13.23 0.00 42.43 3.06
208 209 5.791336 AACACTCTACAAGATGTGAGACA 57.209 39.130 13.23 0.00 33.15 3.41
209 210 6.216569 TGAAACACTCTACAAGATGTGAGAC 58.783 40.000 13.23 0.00 33.15 3.36
210 211 6.405278 TGAAACACTCTACAAGATGTGAGA 57.595 37.500 13.23 4.34 33.15 3.27
211 212 6.703607 ACTTGAAACACTCTACAAGATGTGAG 59.296 38.462 0.00 5.53 41.16 3.51
212 213 6.582636 ACTTGAAACACTCTACAAGATGTGA 58.417 36.000 0.00 0.00 41.16 3.58
213 214 6.851222 ACTTGAAACACTCTACAAGATGTG 57.149 37.500 0.00 0.00 41.16 3.21
214 215 6.260936 CCAACTTGAAACACTCTACAAGATGT 59.739 38.462 0.00 0.00 41.16 3.06
215 216 6.483307 TCCAACTTGAAACACTCTACAAGATG 59.517 38.462 0.00 0.00 41.16 2.90
216 217 6.591935 TCCAACTTGAAACACTCTACAAGAT 58.408 36.000 0.00 0.00 41.16 2.40
217 218 5.984725 TCCAACTTGAAACACTCTACAAGA 58.015 37.500 0.00 0.00 41.16 3.02
218 219 6.677781 TTCCAACTTGAAACACTCTACAAG 57.322 37.500 0.00 0.00 43.30 3.16
219 220 7.639113 AATTCCAACTTGAAACACTCTACAA 57.361 32.000 0.00 0.00 0.00 2.41
220 221 7.639113 AAATTCCAACTTGAAACACTCTACA 57.361 32.000 0.00 0.00 0.00 2.74
221 222 9.447040 GTAAAATTCCAACTTGAAACACTCTAC 57.553 33.333 0.00 0.00 0.00 2.59
222 223 9.179909 TGTAAAATTCCAACTTGAAACACTCTA 57.820 29.630 0.00 0.00 0.00 2.43
223 224 8.062065 TGTAAAATTCCAACTTGAAACACTCT 57.938 30.769 0.00 0.00 0.00 3.24
224 225 8.755018 CATGTAAAATTCCAACTTGAAACACTC 58.245 33.333 0.00 0.00 0.00 3.51
225 226 8.474025 TCATGTAAAATTCCAACTTGAAACACT 58.526 29.630 0.00 0.00 0.00 3.55
226 227 8.539674 GTCATGTAAAATTCCAACTTGAAACAC 58.460 33.333 0.00 0.00 31.56 3.32
227 228 8.253810 TGTCATGTAAAATTCCAACTTGAAACA 58.746 29.630 0.00 0.00 31.56 2.83
228 229 8.641499 TGTCATGTAAAATTCCAACTTGAAAC 57.359 30.769 0.00 0.00 31.56 2.78
229 230 8.474025 ACTGTCATGTAAAATTCCAACTTGAAA 58.526 29.630 0.00 1.67 31.56 2.69
246 247 6.240894 AGGATGTGATGTTTTACTGTCATGT 58.759 36.000 0.00 0.00 0.00 3.21
254 255 8.946085 TGAAGATGTTAGGATGTGATGTTTTAC 58.054 33.333 0.00 0.00 0.00 2.01
259 260 6.656902 ACATGAAGATGTTAGGATGTGATGT 58.343 36.000 0.00 0.00 40.05 3.06
325 329 9.790344 AAATATCATGGAAACCAACATTCAAAA 57.210 25.926 0.00 0.00 36.95 2.44
339 343 5.721000 ACAGCTTTGGGAAAATATCATGGAA 59.279 36.000 0.00 0.00 0.00 3.53
341 345 5.603170 ACAGCTTTGGGAAAATATCATGG 57.397 39.130 0.00 0.00 0.00 3.66
345 349 7.068716 AGGATACAACAGCTTTGGGAAAATATC 59.931 37.037 11.59 8.61 41.41 1.63
351 355 3.420893 CAGGATACAACAGCTTTGGGAA 58.579 45.455 11.59 0.77 41.41 3.97
353 357 2.094675 CCAGGATACAACAGCTTTGGG 58.905 52.381 11.59 1.44 41.41 4.12
360 364 4.096382 GGTAATTGCACCAGGATACAACAG 59.904 45.833 0.00 0.00 38.55 3.16
408 414 7.148804 GGAAATTTTCTTGTAATGTCCTTTCGC 60.149 37.037 8.93 0.00 36.73 4.70
474 485 4.976224 TCGATTTCTGTATGTCGAAGGA 57.024 40.909 0.00 0.00 39.80 3.36
484 495 1.631388 TGCCCCCTTTCGATTTCTGTA 59.369 47.619 0.00 0.00 0.00 2.74
485 496 0.404040 TGCCCCCTTTCGATTTCTGT 59.596 50.000 0.00 0.00 0.00 3.41
486 497 1.098050 CTGCCCCCTTTCGATTTCTG 58.902 55.000 0.00 0.00 0.00 3.02
489 500 2.379005 GAATCTGCCCCCTTTCGATTT 58.621 47.619 0.00 0.00 0.00 2.17
554 571 6.883756 GGTCTGATCTGAAGAATTCCTCTTTT 59.116 38.462 3.59 0.00 46.93 2.27
559 577 4.026744 TCGGTCTGATCTGAAGAATTCCT 58.973 43.478 3.59 0.00 46.93 3.36
560 578 4.116238 GTCGGTCTGATCTGAAGAATTCC 58.884 47.826 3.59 0.00 46.93 3.01
605 706 1.597742 CGTGGGGTTGATCCATCATC 58.402 55.000 0.00 0.00 36.56 2.92
606 707 0.466189 GCGTGGGGTTGATCCATCAT 60.466 55.000 0.00 0.00 36.56 2.45
607 708 1.077787 GCGTGGGGTTGATCCATCA 60.078 57.895 0.00 0.00 36.58 3.07
639 740 3.000724 CAGAATTGATCCGTCGCTTTCTC 59.999 47.826 0.00 0.00 0.00 2.87
646 747 0.179073 AGGGCAGAATTGATCCGTCG 60.179 55.000 0.00 0.00 0.00 5.12
776 883 4.111053 GGAAGGGAAGGGACGGGC 62.111 72.222 0.00 0.00 0.00 6.13
781 888 2.459710 GGAGGGGAAGGGAAGGGA 59.540 66.667 0.00 0.00 0.00 4.20
782 889 2.696504 GGGAGGGGAAGGGAAGGG 60.697 72.222 0.00 0.00 0.00 3.95
783 890 2.696504 GGGGAGGGGAAGGGAAGG 60.697 72.222 0.00 0.00 0.00 3.46
784 891 3.090532 CGGGGAGGGGAAGGGAAG 61.091 72.222 0.00 0.00 0.00 3.46
785 892 4.752594 CCGGGGAGGGGAAGGGAA 62.753 72.222 0.00 0.00 35.97 3.97
898 1005 3.431725 CTTTCTTGGTCGGCGGCC 61.432 66.667 26.28 26.28 0.00 6.13
899 1006 3.431725 CCTTTCTTGGTCGGCGGC 61.432 66.667 7.21 4.32 0.00 6.53
900 1007 3.431725 GCCTTTCTTGGTCGGCGG 61.432 66.667 7.21 0.00 32.22 6.13
901 1008 3.431725 GGCCTTTCTTGGTCGGCG 61.432 66.667 0.00 0.00 43.38 6.46
965 1072 1.414158 CGAGGGCTTCTGGAAGGATA 58.586 55.000 11.61 0.00 38.80 2.59
980 1090 2.341543 CCGGATGGATCTGCGAGG 59.658 66.667 0.00 0.00 37.49 4.63
1558 1685 0.752054 CGGGCATAAAATGGGCACAT 59.248 50.000 0.00 0.00 39.54 3.21
1649 1777 3.340814 ACAAGAACTTCTGATCCGCAT 57.659 42.857 0.00 0.00 0.00 4.73
1665 1794 2.708514 CGTGTTCTTCACTGCAACAAG 58.291 47.619 0.00 0.00 44.16 3.16
1666 1795 1.202132 GCGTGTTCTTCACTGCAACAA 60.202 47.619 0.00 0.00 44.16 2.83
1692 1821 3.840666 ACTCCTGAAATCTAAGCCTGACA 59.159 43.478 0.00 0.00 0.00 3.58
1694 1823 3.840666 ACACTCCTGAAATCTAAGCCTGA 59.159 43.478 0.00 0.00 0.00 3.86
1708 1837 6.925211 TCTTGACATAGACTTTACACTCCTG 58.075 40.000 0.00 0.00 0.00 3.86
1731 1860 4.734398 TCTCTTTCTGATTGAGAGGCTC 57.266 45.455 6.34 6.34 37.95 4.70
1745 1874 8.715191 ATGATGTTGATACAGACTTCTCTTTC 57.285 34.615 0.00 0.00 37.77 2.62
1812 1942 1.552337 GACAGGAGCTGATGGAAGACA 59.448 52.381 0.00 0.00 35.18 3.41
1842 1972 2.033372 TGCATCACCAGCAATAATGGG 58.967 47.619 0.00 0.00 42.48 4.00
1885 2015 9.638239 CTAGATTAATCTGCCTATCTCAAGTTC 57.362 37.037 25.22 0.00 37.76 3.01
1890 2020 7.013220 ACCACTAGATTAATCTGCCTATCTCA 58.987 38.462 25.22 3.75 37.76 3.27
1938 2112 4.283722 ACAGAAAAGACAGAATCTACGGGT 59.716 41.667 0.00 0.00 36.27 5.28
2104 2894 5.746990 ATAGTAAGTTCAACAGCAGGTCT 57.253 39.130 0.00 0.00 0.00 3.85
2345 3156 3.434739 CCTCATTGAGCAGGCTAAGGAAT 60.435 47.826 8.23 0.00 0.00 3.01
2445 3273 3.589495 AACAGAGGTTAGCGGTACTTC 57.411 47.619 0.00 0.00 34.87 3.01
2905 3822 5.598769 AGAGGCGTACAAATTAGATACACC 58.401 41.667 0.00 0.00 0.00 4.16
3058 3975 3.446161 CCGTATCAGTGAACTTCCCTGTA 59.554 47.826 0.00 0.00 0.00 2.74
3321 4853 2.656947 ACCCTACGGCATTGCAATAT 57.343 45.000 12.53 0.85 0.00 1.28
3381 4913 2.299013 AGAGTGACGTGGCTTAATGTGA 59.701 45.455 0.00 0.00 0.00 3.58
3395 4927 6.929606 TCCAGCTACTTTTCTTTTAGAGTGAC 59.070 38.462 0.00 0.00 0.00 3.67
3717 5249 6.908820 GCTGCGGGTATTACTAAATGTTTTAC 59.091 38.462 0.00 0.00 0.00 2.01
3787 5319 4.624015 AGTGAACAGCCAAATTGTCAATG 58.376 39.130 0.00 0.00 0.00 2.82
3935 5467 1.248486 GAACCAGGGTTTCCTCTTGC 58.752 55.000 4.99 0.00 42.67 4.01
4411 5947 1.174712 GCAACTCCTCAGCTGCCAAA 61.175 55.000 9.47 0.00 35.94 3.28
4808 6344 7.418408 TCAAATGCGTTAACAACATTCTGTAA 58.582 30.769 18.88 5.99 33.01 2.41
4894 6430 0.034059 CGAGAAGCCCGCCATTATCT 59.966 55.000 0.00 0.00 0.00 1.98
4907 6443 6.036517 ACAGACTTGCATATTTTAGCGAGAAG 59.963 38.462 8.53 0.00 43.47 2.85
4927 6463 1.876156 CAACTCTTCAGCCCAACAGAC 59.124 52.381 0.00 0.00 0.00 3.51
4962 6498 2.224159 GGTGGAGGGACCTTGCAGA 61.224 63.158 0.00 0.00 39.86 4.26
4992 6528 4.558538 ACTGAATCACAAAAGTGAGTGC 57.441 40.909 3.14 0.00 36.73 4.40
5204 6741 4.449743 GTGCAACTACCAACTATCGAACAA 59.550 41.667 0.00 0.00 0.00 2.83
5206 6743 3.060363 CGTGCAACTACCAACTATCGAAC 59.940 47.826 0.00 0.00 31.75 3.95
5209 6746 1.323534 GCGTGCAACTACCAACTATCG 59.676 52.381 0.00 0.00 31.75 2.92
5237 6774 7.553760 TCTCTTGCACACATTATACATGACATT 59.446 33.333 0.00 0.00 0.00 2.71
5269 6806 2.632028 CCATCATCAGGTAGGTCAGGAG 59.368 54.545 0.00 0.00 0.00 3.69
5549 7108 7.114529 GCATATCAATTTCAAATGAGTAGCAGC 59.885 37.037 0.00 0.00 0.00 5.25
5622 7181 4.000331 CAGAACTCTGCATACCTATGGG 58.000 50.000 0.00 0.00 37.15 4.00
5727 7286 9.807921 ATATAATGGATGTAGTTAAACAAGGGG 57.192 33.333 0.00 0.00 32.02 4.79
5754 7313 0.460284 CGACCGAAGCTGCCATAACT 60.460 55.000 0.00 0.00 0.00 2.24
5755 7314 2.006772 CGACCGAAGCTGCCATAAC 58.993 57.895 0.00 0.00 0.00 1.89
5822 7381 1.153309 TGGCACAGGCAGATGATCG 60.153 57.895 0.00 0.00 43.71 3.69
5867 7426 2.158928 TGGTTCCGTTCTTCCTTTCGAA 60.159 45.455 0.00 0.00 0.00 3.71
5888 7447 0.541296 AGGCCACAGAAAGCAAGCAT 60.541 50.000 5.01 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.