Multiple sequence alignment - TraesCS7D01G094800

Loading Multiple Alignment...

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 TraesCS7D01G094800 chr7D 100.000 3311 0 0 1 3311 56992153 56988843 0.000000e+00 6115.0
1 TraesCS7D01G094800 chr7D 100.000 532 0 0 3615 4146 56988539 56988008 0.000000e+00 983.0
2 TraesCS7D01G094800 chr3D 93.704 2462 120 15 853 3297 545231812 545229369 0.000000e+00 3655.0
3 TraesCS7D01G094800 chr3D 91.794 524 18 6 348 870 545232346 545231847 0.000000e+00 706.0
4 TraesCS7D01G094800 chr3D 96.954 394 10 1 3752 4145 545228983 545228592 0.000000e+00 660.0
5 TraesCS7D01G094800 chr3D 97.863 234 4 1 3 235 545232582 545232349 1.790000e-108 403.0
6 TraesCS7D01G094800 chr3D 96.939 98 3 0 3631 3728 545229071 545228974 9.220000e-37 165.0
7 TraesCS7D01G094800 chr4A 94.485 2339 88 16 990 3310 673975167 673977482 0.000000e+00 3567.0
8 TraesCS7D01G094800 chr4A 86.299 1613 167 26 991 2560 676546358 676547959 0.000000e+00 1705.0
9 TraesCS7D01G094800 chr4A 91.281 734 57 4 990 1717 674350850 674351582 0.000000e+00 994.0
10 TraesCS7D01G094800 chr4A 90.357 757 53 10 2573 3311 674352537 674353291 0.000000e+00 976.0
11 TraesCS7D01G094800 chr4A 96.450 507 18 0 3639 4145 674353484 674353990 0.000000e+00 837.0
12 TraesCS7D01G094800 chr4A 90.280 607 56 2 2706 3310 676548044 676548649 0.000000e+00 791.0
13 TraesCS7D01G094800 chr4A 93.958 480 24 3 3632 4110 673977850 673978325 0.000000e+00 721.0
14 TraesCS7D01G094800 chr4A 85.307 667 94 4 1777 2441 674351797 674352461 0.000000e+00 686.0
15 TraesCS7D01G094800 chr4A 85.938 512 50 9 3642 4145 676548695 676549192 1.020000e-145 527.0
16 TraesCS7D01G094800 chr4A 100.000 30 0 0 4111 4140 673978340 673978369 5.790000e-04 56.5
17 TraesCS7D01G094800 chr7A 92.949 2340 106 19 990 3311 61796473 61794175 0.000000e+00 3352.0
18 TraesCS7D01G094800 chr7A 96.238 505 16 3 3643 4145 61794159 61793656 0.000000e+00 824.0
19 TraesCS7D01G094800 chr6D 92.453 53 2 2 279 331 433769689 433769639 1.600000e-09 75.0
20 TraesCS7D01G094800 chr6B 93.750 48 2 1 279 326 656034953 656034907 2.070000e-08 71.3


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 TraesCS7D01G094800 chr7D 56988008 56992153 4145 True 3549.000000 6115 100.000000 1 4146 2 chr7D.!!$R1 4145
1 TraesCS7D01G094800 chr3D 545228592 545232582 3990 True 1117.800000 3655 95.450800 3 4145 5 chr3D.!!$R1 4142
2 TraesCS7D01G094800 chr4A 673975167 673978369 3202 False 1448.166667 3567 96.147667 990 4140 3 chr4A.!!$F1 3150
3 TraesCS7D01G094800 chr4A 676546358 676549192 2834 False 1007.666667 1705 87.505667 991 4145 3 chr4A.!!$F3 3154
4 TraesCS7D01G094800 chr4A 674350850 674353990 3140 False 873.250000 994 90.848750 990 4145 4 chr4A.!!$F2 3155
5 TraesCS7D01G094800 chr7A 61793656 61796473 2817 True 2088.000000 3352 94.593500 990 4145 2 chr7A.!!$R1 3155

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
875 926 0.877071 CACCGAAGCTGCATTTCTGT 59.123 50.0 1.02 0.0 0.00 3.41 F
878 929 1.334054 CGAAGCTGCATTTCTGTTGC 58.666 50.0 1.02 0.0 40.55 4.17 F
2121 2384 1.392589 AACTGCAACAACAGGTCAGG 58.607 50.0 0.00 0.0 42.21 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2311 0.251787 AGGCCCTTTGGTGGTTCATC 60.252 55.0 0.0 0.0 0.00 2.92 R
2388 2652 1.075601 TTCCAGCTTCCACCTCCAAT 58.924 50.0 0.0 0.0 0.00 3.16 R
3779 4159 0.107312 GGATGAGTCCATGCTGCTGT 60.107 55.0 0.0 0.0 44.42 4.40 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
68 69 5.181056 GGACGTATTTTCCCGGTAAGAAAAA 59.819 40.000 17.41 8.98 44.09 1.94
269 270 7.400599 ACATGCTCTTCAAATATGTGATTGT 57.599 32.000 0.00 0.00 31.34 2.71
270 271 7.255569 ACATGCTCTTCAAATATGTGATTGTG 58.744 34.615 0.00 0.00 31.34 3.33
271 272 6.822667 TGCTCTTCAAATATGTGATTGTGT 57.177 33.333 0.00 0.00 0.00 3.72
272 273 7.920160 TGCTCTTCAAATATGTGATTGTGTA 57.080 32.000 0.00 0.00 0.00 2.90
273 274 8.510243 TGCTCTTCAAATATGTGATTGTGTAT 57.490 30.769 0.00 0.00 0.00 2.29
274 275 9.612066 TGCTCTTCAAATATGTGATTGTGTATA 57.388 29.630 0.00 0.00 0.00 1.47
275 276 9.869844 GCTCTTCAAATATGTGATTGTGTATAC 57.130 33.333 0.00 0.00 0.00 1.47
316 317 9.997482 TTTTAGATGTGGAAATAGTATTTTCGC 57.003 29.630 17.29 17.29 36.63 4.70
317 318 8.958119 TTAGATGTGGAAATAGTATTTTCGCT 57.042 30.769 22.30 13.07 36.63 4.93
318 319 7.251704 AGATGTGGAAATAGTATTTTCGCTG 57.748 36.000 22.30 0.00 36.63 5.18
319 320 7.047891 AGATGTGGAAATAGTATTTTCGCTGA 58.952 34.615 22.30 8.78 36.63 4.26
320 321 7.552687 AGATGTGGAAATAGTATTTTCGCTGAA 59.447 33.333 22.30 8.21 36.63 3.02
321 322 7.441890 TGTGGAAATAGTATTTTCGCTGAAA 57.558 32.000 22.30 5.42 36.63 2.69
322 323 7.877003 TGTGGAAATAGTATTTTCGCTGAAAA 58.123 30.769 22.30 15.34 44.04 2.29
323 324 8.353684 TGTGGAAATAGTATTTTCGCTGAAAAA 58.646 29.630 22.30 4.54 43.32 1.94
346 347 7.423844 AAAATAAAGGAGCCAAAATAGAGGG 57.576 36.000 0.00 0.00 0.00 4.30
436 438 8.962679 ACGGAAATTTAATTTGTTAGATAGCCA 58.037 29.630 7.72 0.00 31.47 4.75
465 467 6.404734 GGCCTAATCATTACAAGAAACCACAG 60.405 42.308 0.00 0.00 0.00 3.66
472 474 2.654863 ACAAGAAACCACAGGGAGTTG 58.345 47.619 0.00 0.00 38.05 3.16
594 596 3.270027 TCGCACATAATCACTCAAAGGG 58.730 45.455 0.00 0.00 0.00 3.95
603 605 3.423539 TCACTCAAAGGGACAATGAGG 57.576 47.619 6.92 0.00 44.13 3.86
698 700 5.930569 TGCTACATAATCATCACATGAGAGC 59.069 40.000 0.00 0.00 43.53 4.09
706 708 2.936919 TCACATGAGAGCAAGTTGGT 57.063 45.000 7.41 7.41 0.00 3.67
744 746 3.700539 TGGAAGAATATGACCGTTACCGA 59.299 43.478 0.00 0.00 35.63 4.69
745 747 4.160065 TGGAAGAATATGACCGTTACCGAA 59.840 41.667 0.00 0.00 35.63 4.30
746 748 5.111293 GGAAGAATATGACCGTTACCGAAA 58.889 41.667 0.00 0.00 35.63 3.46
747 749 5.756833 GGAAGAATATGACCGTTACCGAAAT 59.243 40.000 0.00 0.00 35.63 2.17
748 750 6.073927 GGAAGAATATGACCGTTACCGAAATC 60.074 42.308 0.00 0.00 35.63 2.17
749 751 6.158023 AGAATATGACCGTTACCGAAATCT 57.842 37.500 0.00 0.00 35.63 2.40
750 752 5.983720 AGAATATGACCGTTACCGAAATCTG 59.016 40.000 0.00 0.00 35.63 2.90
751 753 3.604875 ATGACCGTTACCGAAATCTGT 57.395 42.857 0.00 0.00 35.63 3.41
752 754 3.389925 TGACCGTTACCGAAATCTGTT 57.610 42.857 0.00 0.00 35.63 3.16
753 755 3.731089 TGACCGTTACCGAAATCTGTTT 58.269 40.909 0.00 0.00 35.63 2.83
754 756 3.495377 TGACCGTTACCGAAATCTGTTTG 59.505 43.478 0.00 0.00 35.63 2.93
755 757 3.731089 ACCGTTACCGAAATCTGTTTGA 58.269 40.909 0.00 0.00 35.63 2.69
756 758 3.495753 ACCGTTACCGAAATCTGTTTGAC 59.504 43.478 0.00 0.00 35.63 3.18
757 759 3.422603 CCGTTACCGAAATCTGTTTGACG 60.423 47.826 0.00 0.00 35.63 4.35
758 760 3.426191 CGTTACCGAAATCTGTTTGACGA 59.574 43.478 0.00 0.00 35.63 4.20
759 761 4.090930 CGTTACCGAAATCTGTTTGACGAT 59.909 41.667 0.00 0.00 35.63 3.73
760 762 5.389098 CGTTACCGAAATCTGTTTGACGATT 60.389 40.000 0.00 0.00 35.63 3.34
835 837 5.931146 AGCAGAGCAGGATTAATTAAGATCG 59.069 40.000 3.94 0.00 0.00 3.69
848 850 1.034838 AAGATCGCCTCGACTCAGCT 61.035 55.000 0.00 0.00 39.18 4.24
852 854 2.705821 CGCCTCGACTCAGCTTCCT 61.706 63.158 0.00 0.00 0.00 3.36
857 859 1.005748 CGACTCAGCTTCCTGCACA 60.006 57.895 0.00 0.00 45.94 4.57
875 926 0.877071 CACCGAAGCTGCATTTCTGT 59.123 50.000 1.02 0.00 0.00 3.41
878 929 1.334054 CGAAGCTGCATTTCTGTTGC 58.666 50.000 1.02 0.00 40.55 4.17
956 1007 1.403679 CAACGAGTTTGGGTCTTTGCA 59.596 47.619 0.00 0.00 0.00 4.08
962 1013 4.546570 GAGTTTGGGTCTTTGCAACATAC 58.453 43.478 0.00 0.00 0.00 2.39
968 1019 3.694072 GGGTCTTTGCAACATACAGCATA 59.306 43.478 0.00 0.00 40.94 3.14
978 1029 3.136763 ACATACAGCATAGCACATCTGC 58.863 45.455 0.00 0.00 44.63 4.26
1018 1069 1.608590 ACATGTGCCAAGGAAGAAACG 59.391 47.619 0.00 0.00 0.00 3.60
1092 1150 2.176889 TGTACTGCTTCCCTACCAGAC 58.823 52.381 0.00 0.00 0.00 3.51
1124 1183 2.517959 TCTCTTCCCTTGCACCAAATG 58.482 47.619 0.00 0.00 0.00 2.32
1251 1312 5.412286 AGCTTCTGAAGAGAAAGCAGAAATC 59.588 40.000 21.06 0.00 45.02 2.17
1254 1315 6.981762 TCTGAAGAGAAAGCAGAAATCATC 57.018 37.500 0.00 0.00 35.87 2.92
1475 1537 2.609747 TGCTGTAACTGAGAAGGAGGT 58.390 47.619 0.00 0.00 0.00 3.85
1478 1540 2.900546 CTGTAACTGAGAAGGAGGTGGT 59.099 50.000 0.00 0.00 0.00 4.16
1530 1595 2.189342 GGCGATCAGAGAAGAAGTTCG 58.811 52.381 0.00 0.00 37.79 3.95
1617 1682 4.405358 AGTGGAGAATCAGAAGGAGATGAC 59.595 45.833 0.00 0.00 36.25 3.06
1624 1689 4.732672 TCAGAAGGAGATGACATGAGTG 57.267 45.455 0.00 0.00 0.00 3.51
1721 1796 2.095161 CACTCCTCGGTAGTCTGTTGTC 60.095 54.545 0.00 0.00 0.00 3.18
1764 1864 8.173130 GCACCAACTACAAAATACAGTACATAC 58.827 37.037 0.00 0.00 0.00 2.39
1840 2098 6.073602 CGCAATGCAGCTAGAAACTATTGATA 60.074 38.462 5.91 0.00 0.00 2.15
1877 2136 4.326826 AGTTGTCCACGAAATCATCATGT 58.673 39.130 0.00 0.00 0.00 3.21
1935 2194 4.553323 CTGTTTCCTTTCAGGCTTCAATG 58.447 43.478 0.00 0.00 34.61 2.82
1939 2198 4.380843 TCCTTTCAGGCTTCAATGGTTA 57.619 40.909 7.43 0.00 34.61 2.85
1968 2227 4.232221 CACTGAAAAACCTGCATCATGAC 58.768 43.478 0.00 0.00 0.00 3.06
2093 2356 5.220931 CCTTCCTGAAATATGTGCTAACTGC 60.221 44.000 0.00 0.00 43.25 4.40
2108 2371 7.335673 TGTGCTAACTGCTAATATTAAACTGCA 59.664 33.333 6.87 6.87 43.37 4.41
2109 2372 8.181573 GTGCTAACTGCTAATATTAAACTGCAA 58.818 33.333 8.09 0.00 43.37 4.08
2121 2384 1.392589 AACTGCAACAACAGGTCAGG 58.607 50.000 0.00 0.00 42.21 3.86
2287 2551 8.966868 TCTTTTATTTTCTAGCCCTGTAATTGG 58.033 33.333 0.00 0.00 0.00 3.16
2315 2579 6.894654 AGGATCTGAAGTCTCTTTCTCATACA 59.105 38.462 0.00 0.00 0.00 2.29
2388 2652 1.466856 GATGGAAAGAGGCATGTGCA 58.533 50.000 7.36 0.00 44.36 4.57
2660 2941 7.106439 TGCAAGTTTGAAATCCTTGAGTTTA 57.894 32.000 11.14 0.00 38.23 2.01
2672 2953 4.947388 TCCTTGAGTTTACACTTTGCAGTT 59.053 37.500 0.00 0.00 31.22 3.16
2713 3007 6.084326 TCTCTAGTGCGCACAATATCATAA 57.916 37.500 39.21 14.39 0.00 1.90
3126 3420 2.152016 GTTACCAAGGACAGAAGCACC 58.848 52.381 0.00 0.00 0.00 5.01
3167 3461 6.542821 TGACTAAGTTCTCACAATTTCCCAT 58.457 36.000 0.00 0.00 0.00 4.00
3261 3561 8.954950 ATTCATATGGTTTTCTCACTACTCAG 57.045 34.615 2.13 0.00 0.00 3.35
3733 4113 8.650143 AACATCATGGGATACTTACAAAAAGT 57.350 30.769 0.00 0.00 30.87 2.66
3734 4114 9.747898 AACATCATGGGATACTTACAAAAAGTA 57.252 29.630 0.00 0.47 37.18 2.24
3735 4115 9.920946 ACATCATGGGATACTTACAAAAAGTAT 57.079 29.630 9.55 9.55 43.84 2.12
3737 4117 9.920946 ATCATGGGATACTTACAAAAAGTATGT 57.079 29.630 13.58 3.34 41.91 2.29
3814 4194 5.741011 ACTCATCCGTTAATTTGAAGCCTA 58.259 37.500 0.00 0.00 0.00 3.93
4091 4474 7.506328 AACACCTTACAAACTATGTTCCTTC 57.494 36.000 0.00 0.00 43.63 3.46
4145 4542 8.143835 CACCTTTAAACATTTGGTCTTGAGAAT 58.856 33.333 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.137675 GCCCTTAAATACGTCCGGTCT 59.862 52.381 0.00 0.00 0.00 3.85
127 128 1.065701 CGCTGTCGCTACTTGGAGTAT 59.934 52.381 0.00 0.00 29.08 2.12
149 150 1.856597 CTCGGGCCGTCTTTTATAACG 59.143 52.381 27.32 0.00 38.58 3.18
243 244 9.128404 ACAATCACATATTTGAAGAGCATGTAT 57.872 29.630 0.00 0.00 0.00 2.29
244 245 8.400186 CACAATCACATATTTGAAGAGCATGTA 58.600 33.333 0.00 0.00 0.00 2.29
245 246 7.094075 ACACAATCACATATTTGAAGAGCATGT 60.094 33.333 0.00 0.00 0.00 3.21
246 247 7.255569 ACACAATCACATATTTGAAGAGCATG 58.744 34.615 0.00 0.00 0.00 4.06
247 248 7.400599 ACACAATCACATATTTGAAGAGCAT 57.599 32.000 0.00 0.00 0.00 3.79
248 249 6.822667 ACACAATCACATATTTGAAGAGCA 57.177 33.333 0.00 0.00 0.00 4.26
249 250 9.869844 GTATACACAATCACATATTTGAAGAGC 57.130 33.333 0.00 0.00 0.00 4.09
290 291 9.997482 GCGAAAATACTATTTCCACATCTAAAA 57.003 29.630 0.00 0.00 36.21 1.52
291 292 9.391006 AGCGAAAATACTATTTCCACATCTAAA 57.609 29.630 0.00 0.00 36.21 1.85
292 293 8.826710 CAGCGAAAATACTATTTCCACATCTAA 58.173 33.333 0.00 0.00 36.21 2.10
293 294 8.201464 TCAGCGAAAATACTATTTCCACATCTA 58.799 33.333 0.00 0.00 36.21 1.98
294 295 7.047891 TCAGCGAAAATACTATTTCCACATCT 58.952 34.615 0.00 0.00 36.21 2.90
295 296 7.246674 TCAGCGAAAATACTATTTCCACATC 57.753 36.000 0.00 0.00 36.21 3.06
296 297 7.624360 TTCAGCGAAAATACTATTTCCACAT 57.376 32.000 0.00 0.00 36.21 3.21
297 298 7.441890 TTTCAGCGAAAATACTATTTCCACA 57.558 32.000 0.00 0.00 36.21 4.17
298 299 8.736751 TTTTTCAGCGAAAATACTATTTCCAC 57.263 30.769 14.24 0.00 40.50 4.02
321 322 7.581464 GCCCTCTATTTTGGCTCCTTTATTTTT 60.581 37.037 0.00 0.00 42.01 1.94
322 323 6.127054 GCCCTCTATTTTGGCTCCTTTATTTT 60.127 38.462 0.00 0.00 42.01 1.82
323 324 5.363868 GCCCTCTATTTTGGCTCCTTTATTT 59.636 40.000 0.00 0.00 42.01 1.40
324 325 4.895889 GCCCTCTATTTTGGCTCCTTTATT 59.104 41.667 0.00 0.00 42.01 1.40
325 326 4.474394 GCCCTCTATTTTGGCTCCTTTAT 58.526 43.478 0.00 0.00 42.01 1.40
326 327 3.898482 GCCCTCTATTTTGGCTCCTTTA 58.102 45.455 0.00 0.00 42.01 1.85
327 328 2.739943 GCCCTCTATTTTGGCTCCTTT 58.260 47.619 0.00 0.00 42.01 3.11
328 329 2.443958 GCCCTCTATTTTGGCTCCTT 57.556 50.000 0.00 0.00 42.01 3.36
333 334 0.107165 ACGGAGCCCTCTATTTTGGC 60.107 55.000 0.00 0.00 45.70 4.52
334 335 1.668419 CACGGAGCCCTCTATTTTGG 58.332 55.000 0.00 0.00 0.00 3.28
335 336 1.209504 TCCACGGAGCCCTCTATTTTG 59.790 52.381 0.00 0.00 0.00 2.44
336 337 1.486726 CTCCACGGAGCCCTCTATTTT 59.513 52.381 0.00 0.00 35.31 1.82
337 338 1.123928 CTCCACGGAGCCCTCTATTT 58.876 55.000 0.00 0.00 35.31 1.40
338 339 2.827715 CTCCACGGAGCCCTCTATT 58.172 57.895 0.00 0.00 35.31 1.73
339 340 4.609098 CTCCACGGAGCCCTCTAT 57.391 61.111 0.00 0.00 35.31 1.98
436 438 8.058847 TGGTTTCTTGTAATGATTAGGCCTAAT 58.941 33.333 33.54 33.54 38.38 1.73
442 444 6.095440 CCCTGTGGTTTCTTGTAATGATTAGG 59.905 42.308 0.00 0.00 0.00 2.69
465 467 0.107654 AGTTATGCTCGCCAACTCCC 60.108 55.000 1.52 0.00 0.00 4.30
472 474 3.134458 AGCTGAATTAGTTATGCTCGCC 58.866 45.455 0.00 0.00 0.00 5.54
547 549 8.830915 TGGTTATCTAGGAAAATAAATTGCCA 57.169 30.769 0.00 0.00 0.00 4.92
594 596 1.808411 TTTGACTCGCCCTCATTGTC 58.192 50.000 0.00 0.00 0.00 3.18
603 605 9.463443 AATAATTAATTATGCTTTTGACTCGCC 57.537 29.630 19.08 0.00 33.51 5.54
698 700 4.789012 ACCAATTATGCTCACCAACTTG 57.211 40.909 0.00 0.00 0.00 3.16
706 708 5.178096 TCTTCCAGAACCAATTATGCTCA 57.822 39.130 0.00 0.00 0.00 4.26
737 739 4.977741 TCGTCAAACAGATTTCGGTAAC 57.022 40.909 0.00 0.00 0.00 2.50
744 746 6.618287 TCAACAGAATCGTCAAACAGATTT 57.382 33.333 0.00 0.00 37.23 2.17
745 747 6.293626 CCTTCAACAGAATCGTCAAACAGATT 60.294 38.462 0.00 0.00 39.52 2.40
746 748 5.180117 CCTTCAACAGAATCGTCAAACAGAT 59.820 40.000 0.00 0.00 0.00 2.90
747 749 4.511454 CCTTCAACAGAATCGTCAAACAGA 59.489 41.667 0.00 0.00 0.00 3.41
748 750 4.776743 CCTTCAACAGAATCGTCAAACAG 58.223 43.478 0.00 0.00 0.00 3.16
749 751 3.003275 GCCTTCAACAGAATCGTCAAACA 59.997 43.478 0.00 0.00 0.00 2.83
750 752 3.003275 TGCCTTCAACAGAATCGTCAAAC 59.997 43.478 0.00 0.00 0.00 2.93
751 753 3.210227 TGCCTTCAACAGAATCGTCAAA 58.790 40.909 0.00 0.00 0.00 2.69
752 754 2.844946 TGCCTTCAACAGAATCGTCAA 58.155 42.857 0.00 0.00 0.00 3.18
753 755 2.542020 TGCCTTCAACAGAATCGTCA 57.458 45.000 0.00 0.00 0.00 4.35
754 756 3.002791 TGATGCCTTCAACAGAATCGTC 58.997 45.455 0.00 0.00 0.00 4.20
755 757 3.057969 TGATGCCTTCAACAGAATCGT 57.942 42.857 0.00 0.00 0.00 3.73
835 837 1.153667 CAGGAAGCTGAGTCGAGGC 60.154 63.158 0.00 0.00 0.00 4.70
848 850 1.597854 CAGCTTCGGTGTGCAGGAA 60.598 57.895 0.00 0.00 0.00 3.36
857 859 1.267806 CAACAGAAATGCAGCTTCGGT 59.732 47.619 10.13 10.13 33.42 4.69
885 936 6.571150 GCCTGAATTTGTGCAGATTTAACTCT 60.571 38.462 0.00 0.00 34.06 3.24
935 986 1.404035 GCAAAGACCCAAACTCGTTGT 59.596 47.619 0.00 0.00 35.23 3.32
947 998 3.855689 ATGCTGTATGTTGCAAAGACC 57.144 42.857 0.00 0.00 42.74 3.85
978 1029 2.065899 TCAGGTTTGGTTCCCTTGTG 57.934 50.000 0.00 0.00 0.00 3.33
1092 1150 5.189180 CAAGGGAAGAGAAGGGATAGTTTG 58.811 45.833 0.00 0.00 0.00 2.93
1124 1183 1.590932 CATGGCTGGTATCTGCAGAC 58.409 55.000 20.97 7.90 39.25 3.51
1251 1312 3.023946 AGATTCGATCGGCAAGAGATG 57.976 47.619 16.41 0.00 0.00 2.90
1254 1315 2.814269 TCAAGATTCGATCGGCAAGAG 58.186 47.619 16.41 2.31 0.00 2.85
1475 1537 1.207089 CACGAAGGCTATTCTCCACCA 59.793 52.381 0.00 0.00 0.00 4.17
1478 1540 1.899814 ACACACGAAGGCTATTCTCCA 59.100 47.619 0.00 0.00 0.00 3.86
1617 1682 3.900855 GCACTGGAGCCACTCATG 58.099 61.111 0.00 0.00 31.08 3.07
1721 1796 3.327757 TGGTGCTTGGGGCTATTATCTAG 59.672 47.826 0.00 0.00 42.39 2.43
1790 1890 8.393366 CGTGCATGATCATAAAATAGGGATTAG 58.607 37.037 8.15 0.00 0.00 1.73
1840 2098 6.293407 CGTGGACAACTTCTGAACATAACAAT 60.293 38.462 0.00 0.00 0.00 2.71
1851 2109 4.452114 TGATGATTTCGTGGACAACTTCTG 59.548 41.667 0.00 0.00 0.00 3.02
1877 2136 8.780249 GTTTATTAGCTGACAAGTTTTCCAGTA 58.220 33.333 0.00 0.00 0.00 2.74
1935 2194 6.512903 GCAGGTTTTTCAGTGTCTTACTAACC 60.513 42.308 0.00 0.00 41.51 2.85
1939 2198 4.523083 TGCAGGTTTTTCAGTGTCTTACT 58.477 39.130 0.00 0.00 41.36 2.24
1968 2227 2.286872 GCCTGTCTGAGGTCATTGATG 58.713 52.381 0.00 0.00 44.97 3.07
2052 2311 0.251787 AGGCCCTTTGGTGGTTCATC 60.252 55.000 0.00 0.00 0.00 2.92
2093 2356 8.511321 TGACCTGTTGTTGCAGTTTAATATTAG 58.489 33.333 0.00 0.00 34.84 1.73
2108 2371 1.893808 CGCAGCCTGACCTGTTGTT 60.894 57.895 0.00 0.00 35.28 2.83
2109 2372 2.116983 ATCGCAGCCTGACCTGTTGT 62.117 55.000 0.00 0.00 35.28 3.32
2121 2384 1.542544 GAGTTGCAAATGATCGCAGC 58.457 50.000 3.09 0.04 39.75 5.25
2287 2551 5.186797 TGAGAAAGAGACTTCAGATCCTTCC 59.813 44.000 0.00 0.00 0.00 3.46
2315 2579 4.681781 CGACATTGAGCTCTTCCACCTTAT 60.682 45.833 16.19 0.00 0.00 1.73
2388 2652 1.075601 TTCCAGCTTCCACCTCCAAT 58.924 50.000 0.00 0.00 0.00 3.16
2412 2676 5.014202 TCCTGGTTTAGTTCTTTAATGGCC 58.986 41.667 0.00 0.00 0.00 5.36
2672 2953 9.330063 CACTAGAGATGTTTTCCTATTGCATTA 57.670 33.333 0.00 0.00 0.00 1.90
3126 3420 7.102346 ACTTAGTCAGATCCTCATTTGAAGTG 58.898 38.462 0.00 0.00 0.00 3.16
3167 3461 5.459241 GGAACAGGGAGGGATATGTCTAGTA 60.459 48.000 0.00 0.00 0.00 1.82
3261 3561 5.725362 AGTAGCCAGACAAACTAGATTCAC 58.275 41.667 0.00 0.00 0.00 3.18
3669 4014 1.134521 CGTAAGCTGCCCAACATCCTA 60.135 52.381 0.00 0.00 0.00 2.94
3737 4117 9.238368 CCCTGTAAGTATCAAAAGTTCCAAATA 57.762 33.333 0.00 0.00 0.00 1.40
3738 4118 7.728532 ACCCTGTAAGTATCAAAAGTTCCAAAT 59.271 33.333 0.00 0.00 0.00 2.32
3739 4119 7.064229 ACCCTGTAAGTATCAAAAGTTCCAAA 58.936 34.615 0.00 0.00 0.00 3.28
3740 4120 6.607019 ACCCTGTAAGTATCAAAAGTTCCAA 58.393 36.000 0.00 0.00 0.00 3.53
3741 4121 6.195600 ACCCTGTAAGTATCAAAAGTTCCA 57.804 37.500 0.00 0.00 0.00 3.53
3742 4122 6.072119 CCAACCCTGTAAGTATCAAAAGTTCC 60.072 42.308 0.00 0.00 0.00 3.62
3743 4123 6.569801 GCCAACCCTGTAAGTATCAAAAGTTC 60.570 42.308 0.00 0.00 0.00 3.01
3744 4124 5.243060 GCCAACCCTGTAAGTATCAAAAGTT 59.757 40.000 0.00 0.00 0.00 2.66
3745 4125 4.765339 GCCAACCCTGTAAGTATCAAAAGT 59.235 41.667 0.00 0.00 0.00 2.66
3746 4126 4.142687 CGCCAACCCTGTAAGTATCAAAAG 60.143 45.833 0.00 0.00 0.00 2.27
3747 4127 3.754323 CGCCAACCCTGTAAGTATCAAAA 59.246 43.478 0.00 0.00 0.00 2.44
3748 4128 3.244630 ACGCCAACCCTGTAAGTATCAAA 60.245 43.478 0.00 0.00 0.00 2.69
3749 4129 2.303600 ACGCCAACCCTGTAAGTATCAA 59.696 45.455 0.00 0.00 0.00 2.57
3750 4130 1.903860 ACGCCAACCCTGTAAGTATCA 59.096 47.619 0.00 0.00 0.00 2.15
3751 4131 2.676342 CAACGCCAACCCTGTAAGTATC 59.324 50.000 0.00 0.00 0.00 2.24
3752 4132 2.039348 ACAACGCCAACCCTGTAAGTAT 59.961 45.455 0.00 0.00 0.00 2.12
3753 4133 1.417145 ACAACGCCAACCCTGTAAGTA 59.583 47.619 0.00 0.00 0.00 2.24
3754 4134 0.181824 ACAACGCCAACCCTGTAAGT 59.818 50.000 0.00 0.00 0.00 2.24
3755 4135 0.591170 CACAACGCCAACCCTGTAAG 59.409 55.000 0.00 0.00 0.00 2.34
3756 4136 1.448922 GCACAACGCCAACCCTGTAA 61.449 55.000 0.00 0.00 32.94 2.41
3757 4137 1.894756 GCACAACGCCAACCCTGTA 60.895 57.895 0.00 0.00 32.94 2.74
3758 4138 3.216292 GCACAACGCCAACCCTGT 61.216 61.111 0.00 0.00 32.94 4.00
3759 4139 4.326766 CGCACAACGCCAACCCTG 62.327 66.667 0.00 0.00 37.30 4.45
3779 4159 0.107312 GGATGAGTCCATGCTGCTGT 60.107 55.000 0.00 0.00 44.42 4.40
3814 4194 9.283768 TGAGTTTTGACATAATGTATGAGTGTT 57.716 29.630 2.34 0.00 39.45 3.32
4091 4474 6.367695 TCCAGTATTCGTTGTTATGACTGTTG 59.632 38.462 0.00 0.00 0.00 3.33


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

AutoCloner maintained by Alex Coulton.