Multiple sequence alignment - TraesCS5D01G400100

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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 TraesCS5D01G400100 chr5D 100.000 6255 0 0 1 6255 465370480 465364226 0.000000e+00 11551.0
1 TraesCS5D01G400100 chr5D 88.406 69 7 1 4092 4160 382510510 382510443 1.450000e-11 82.4
2 TraesCS5D01G400100 chr5A 97.502 3283 63 5 2438 5711 585612211 585608939 0.000000e+00 5590.0
3 TraesCS5D01G400100 chr5A 93.883 2583 90 20 3 2523 585614788 585612212 0.000000e+00 3832.0
4 TraesCS5D01G400100 chr5A 93.738 543 34 0 5713 6255 585608878 585608336 0.000000e+00 815.0
5 TraesCS5D01G400100 chr5B 94.588 2679 93 21 1461 4089 572595176 572592500 0.000000e+00 4096.0
6 TraesCS5D01G400100 chr5B 95.830 1103 41 4 4612 5710 572592091 572590990 0.000000e+00 1777.0
7 TraesCS5D01G400100 chr5B 93.449 519 17 4 941 1458 572595717 572595215 0.000000e+00 754.0
8 TraesCS5D01G400100 chr5B 92.216 501 36 1 5755 6255 572590461 572589964 0.000000e+00 706.0
9 TraesCS5D01G400100 chr5B 91.136 440 14 8 4133 4572 572592502 572592088 1.960000e-159 573.0
10 TraesCS5D01G400100 chr5B 98.016 252 5 0 610 861 572596205 572595954 7.440000e-119 438.0
11 TraesCS5D01G400100 chr5B 76.923 130 18 4 376 495 275314993 275315120 5.230000e-06 63.9
12 TraesCS5D01G400100 chr7D 82.586 580 81 14 2812 3387 405105725 405105162 1.570000e-135 494.0
13 TraesCS5D01G400100 chr7D 82.301 452 57 12 2948 3387 405642757 405642317 2.750000e-98 370.0
14 TraesCS5D01G400100 chr7D 100.000 49 0 0 4091 4139 265172325 265172373 2.400000e-14 91.6
15 TraesCS5D01G400100 chr6A 86.435 317 36 5 3731 4043 4519683 4519370 2.160000e-89 340.0
16 TraesCS5D01G400100 chr6A 85.232 237 26 5 3616 3852 40915049 40914822 1.050000e-57 235.0
17 TraesCS5D01G400100 chr6A 86.486 111 14 1 254 363 431067274 431067384 3.060000e-23 121.0
18 TraesCS5D01G400100 chr6A 92.537 67 3 1 3066 3130 326745119 326745053 1.860000e-15 95.3
19 TraesCS5D01G400100 chr4D 85.232 237 26 5 3616 3852 503516691 503516464 1.050000e-57 235.0
20 TraesCS5D01G400100 chr4D 92.982 57 3 1 4078 4134 426846117 426846062 1.450000e-11 82.4
21 TraesCS5D01G400100 chr7B 83.966 237 30 4 3616 3852 5925370 5925142 2.940000e-53 220.0
22 TraesCS5D01G400100 chr7B 78.158 380 51 24 3729 4080 373663735 373663360 4.910000e-51 213.0
23 TraesCS5D01G400100 chr4A 83.966 237 30 4 3616 3852 641299364 641299592 2.940000e-53 220.0
24 TraesCS5D01G400100 chr1B 83.966 237 30 4 3616 3852 16458113 16457885 2.940000e-53 220.0
25 TraesCS5D01G400100 chr1B 94.545 55 3 0 4092 4146 303240412 303240466 1.120000e-12 86.1
26 TraesCS5D01G400100 chr1B 90.323 62 3 3 4094 4154 406341806 406341865 1.870000e-10 78.7
27 TraesCS5D01G400100 chr3D 88.333 180 19 2 3729 3906 4507614 4507435 1.370000e-51 215.0
28 TraesCS5D01G400100 chr3D 87.218 133 6 5 3001 3130 408324527 408324403 2.350000e-29 141.0
29 TraesCS5D01G400100 chr3D 100.000 49 0 0 4092 4140 435451272 435451320 2.400000e-14 91.6
30 TraesCS5D01G400100 chr3B 83.544 237 31 4 3616 3852 647902820 647903048 1.370000e-51 215.0
31 TraesCS5D01G400100 chr2B 83.544 237 31 4 3616 3852 587236824 587236596 1.370000e-51 215.0
32 TraesCS5D01G400100 chr2B 94.444 54 3 0 4094 4147 682041376 682041323 4.020000e-12 84.2
33 TraesCS5D01G400100 chr7A 80.543 221 32 7 2747 2958 444053661 444053879 6.490000e-35 159.0
34 TraesCS5D01G400100 chr7A 92.982 57 2 1 4078 4134 506285479 506285533 1.450000e-11 82.4
35 TraesCS5D01G400100 chr7A 97.143 35 1 0 371 405 518645663 518645629 6.770000e-05 60.2
36 TraesCS5D01G400100 chr4B 92.537 67 3 1 3066 3130 639443285 639443351 1.860000e-15 95.3
37 TraesCS5D01G400100 chr2D 92.537 67 3 1 3066 3130 47003676 47003610 1.860000e-15 95.3
38 TraesCS5D01G400100 chr1D 92.537 67 3 1 3066 3130 487146861 487146927 1.860000e-15 95.3
39 TraesCS5D01G400100 chr1D 97.143 35 0 1 373 406 134685416 134685450 2.440000e-04 58.4
40 TraesCS5D01G400100 chr1A 76.596 141 20 3 371 499 163376784 163376645 1.460000e-06 65.8
41 TraesCS5D01G400100 chr6B 97.222 36 1 0 371 406 707852993 707853028 1.880000e-05 62.1


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 TraesCS5D01G400100 chr5D 465364226 465370480 6254 True 11551.000000 11551 100.000000 1 6255 1 chr5D.!!$R2 6254
1 TraesCS5D01G400100 chr5A 585608336 585614788 6452 True 3412.333333 5590 95.041000 3 6255 3 chr5A.!!$R1 6252
2 TraesCS5D01G400100 chr5B 572589964 572596205 6241 True 1390.666667 4096 94.205833 610 6255 6 chr5B.!!$R1 5645
3 TraesCS5D01G400100 chr7D 405105162 405105725 563 True 494.000000 494 82.586000 2812 3387 1 chr7D.!!$R1 575

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
408 454 0.039074 GGATATGAGAGGTGCCGACG 60.039 60.0 0.00 0.0 0.00 5.12 F
472 528 0.103572 CCGGTCATTAATCGGGTCGT 59.896 55.0 6.24 0.0 40.07 4.34 F
1501 1758 0.108585 ACCACATCTGAACCGCAGTT 59.891 50.0 0.00 0.0 45.14 3.16 F
1528 1785 0.246635 CAGGCTGTTAGTACCTGCGT 59.753 55.0 6.28 0.0 44.16 5.24 F
2963 3341 0.976641 CACCTAAGGCAGAGTCACCA 59.023 55.0 5.14 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1637 1924 1.000274 GTTGTGTGGGTTGATTCAGCC 60.000 52.381 10.86 10.86 33.90 4.85 R
1815 2103 3.016031 CTGGGTGTGCATGTATTAAGCA 58.984 45.455 0.00 0.00 35.63 3.91 R
3336 3714 7.607615 AATAGAAAATAGCCCAAATGCATCT 57.392 32.000 0.00 0.00 0.00 2.90 R
4023 4418 7.561722 TCTGATGAATGTTACTTAGTAGGAGCT 59.438 37.037 0.00 0.00 0.00 4.09 R
5304 5702 0.670546 CCGTCGTGCTGAGAAACCAT 60.671 55.000 0.00 0.00 0.00 3.55 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
29 30 1.971167 GGTGCAATCCTTGTCGGCA 60.971 57.895 0.00 0.00 0.00 5.69
30 31 1.523154 GGTGCAATCCTTGTCGGCAA 61.523 55.000 0.91 0.91 36.08 4.52
31 32 0.387239 GTGCAATCCTTGTCGGCAAC 60.387 55.000 0.00 0.00 36.08 4.17
108 124 2.279784 CGCATCCGCTTCCCTCTC 60.280 66.667 0.00 0.00 35.30 3.20
112 128 1.076632 ATCCGCTTCCCTCTCTCGT 60.077 57.895 0.00 0.00 0.00 4.18
117 133 0.456995 GCTTCCCTCTCTCGTTGTCG 60.457 60.000 0.00 0.00 38.55 4.35
145 161 0.681243 GGTTCCTCTGGGCCATGTTC 60.681 60.000 6.72 0.00 0.00 3.18
147 163 1.075601 TTCCTCTGGGCCATGTTCTT 58.924 50.000 6.72 0.00 0.00 2.52
149 165 0.745845 CCTCTGGGCCATGTTCTTCG 60.746 60.000 6.72 0.00 0.00 3.79
172 188 1.810030 GCATGACGAACCCGAGGAC 60.810 63.158 0.00 0.00 39.50 3.85
200 216 2.738521 CGGACAAGGTGGACGCAG 60.739 66.667 0.00 0.00 0.00 5.18
206 222 3.245668 AAGGTGGACGCAGCCTCTG 62.246 63.158 0.00 0.00 34.12 3.35
217 233 2.813042 GCCTCTGTCGCAGCAGTC 60.813 66.667 0.00 0.00 37.70 3.51
239 255 0.464036 GGGACATGCTGGACGACATA 59.536 55.000 0.00 0.00 0.00 2.29
248 264 1.080025 GGACGACATATAGGGCGGC 60.080 63.158 18.04 14.74 0.00 6.53
273 289 1.380302 GATGGGGAGCAAGTGTGGT 59.620 57.895 0.00 0.00 38.47 4.16
286 302 2.668550 GTGGTGAACGGTGAGGGC 60.669 66.667 0.00 0.00 0.00 5.19
290 306 3.691342 TGAACGGTGAGGGCTCGG 61.691 66.667 0.00 0.00 0.00 4.63
314 331 1.301401 CGAAAGGTTGGAGGACGCA 60.301 57.895 0.00 0.00 0.00 5.24
326 343 4.779733 GACGCAGGAGGAGGGGGA 62.780 72.222 0.00 0.00 0.00 4.81
328 345 3.474570 CGCAGGAGGAGGGGGAAG 61.475 72.222 0.00 0.00 0.00 3.46
337 354 2.043115 GAGGAGGGGGAAGGTTTTGATT 59.957 50.000 0.00 0.00 0.00 2.57
343 360 4.286808 AGGGGGAAGGTTTTGATTGATTTG 59.713 41.667 0.00 0.00 0.00 2.32
344 361 4.565444 GGGGGAAGGTTTTGATTGATTTGG 60.565 45.833 0.00 0.00 0.00 3.28
353 372 7.718753 AGGTTTTGATTGATTTGGTGCAATTTA 59.281 29.630 0.00 0.00 35.05 1.40
360 379 3.692257 TTTGGTGCAATTTATGGTGGG 57.308 42.857 0.00 0.00 0.00 4.61
406 452 1.895798 GATGGATATGAGAGGTGCCGA 59.104 52.381 0.00 0.00 0.00 5.54
407 453 1.040646 TGGATATGAGAGGTGCCGAC 58.959 55.000 0.00 0.00 0.00 4.79
408 454 0.039074 GGATATGAGAGGTGCCGACG 60.039 60.000 0.00 0.00 0.00 5.12
409 455 0.669077 GATATGAGAGGTGCCGACGT 59.331 55.000 0.00 0.00 0.00 4.34
410 456 1.067212 GATATGAGAGGTGCCGACGTT 59.933 52.381 0.00 0.00 0.00 3.99
420 476 3.110178 CCGACGTTTGAGTCCCGC 61.110 66.667 0.00 0.00 37.85 6.13
472 528 0.103572 CCGGTCATTAATCGGGTCGT 59.896 55.000 6.24 0.00 40.07 4.34
510 566 1.222115 GGCGCCCGCTCTAATAACAG 61.222 60.000 18.11 0.00 41.60 3.16
514 570 2.223876 CGCCCGCTCTAATAACAGGTTA 60.224 50.000 0.00 0.00 0.00 2.85
668 731 0.255890 CCCCTGATTTGTCCACGGAT 59.744 55.000 0.00 0.00 0.00 4.18
867 930 3.477346 GCCCCCGGTCCTCCTAAC 61.477 72.222 0.00 0.00 0.00 2.34
1105 1326 1.739466 CATTTCGCTCTTGCTTGCCTA 59.261 47.619 0.00 0.00 36.97 3.93
1250 1471 4.388499 GGCGACGGGAAGAAGGCA 62.388 66.667 0.00 0.00 0.00 4.75
1286 1507 0.839946 ACTGCAACAAGGACCTGTCT 59.160 50.000 0.00 0.00 0.00 3.41
1495 1752 2.618053 CGGAGTTACCACATCTGAACC 58.382 52.381 0.00 0.00 38.90 3.62
1501 1758 0.108585 ACCACATCTGAACCGCAGTT 59.891 50.000 0.00 0.00 45.14 3.16
1528 1785 0.246635 CAGGCTGTTAGTACCTGCGT 59.753 55.000 6.28 0.00 44.16 5.24
1637 1924 5.954296 AAAGATGAAATGTGACACTCCAG 57.046 39.130 7.20 0.00 0.00 3.86
1755 2043 4.463891 TCAGCTGATGTGTGAACTCAGATA 59.536 41.667 13.74 0.00 38.96 1.98
1768 2056 8.264347 TGTGAACTCAGATAATATGTTTGGCTA 58.736 33.333 0.00 0.00 0.00 3.93
1805 2093 5.316167 ACTCAACCATCTTGATTGCAACTA 58.684 37.500 0.00 0.00 0.00 2.24
1815 2103 6.830912 TCTTGATTGCAACTAGCTATATGGT 58.169 36.000 0.00 0.00 45.94 3.55
1962 2252 6.716934 TTGTTGCATCCTTTAACTTAACCA 57.283 33.333 0.00 0.00 0.00 3.67
2246 2536 4.325084 TCCCCTTCCGGTAATCATTTTT 57.675 40.909 0.00 0.00 0.00 1.94
2455 2831 8.782137 ATTTAGGCTGGAACCAAATATTGTAT 57.218 30.769 0.00 0.00 0.00 2.29
2596 2973 4.997395 TGCACAGATCTGTTCTAAAAGGAC 59.003 41.667 25.84 8.77 42.83 3.85
2963 3341 0.976641 CACCTAAGGCAGAGTCACCA 59.023 55.000 5.14 0.00 0.00 4.17
3412 3790 5.132648 TGCCTTCCCATCAGTAATAATGTCT 59.867 40.000 0.00 0.00 0.00 3.41
3574 3969 5.705902 ACCGTCTGCAAAATATTACCAAAC 58.294 37.500 0.00 0.00 0.00 2.93
4023 4418 4.502105 TCATGGCAGCACCTTATTCTTA 57.498 40.909 0.00 0.00 40.22 2.10
4069 4464 4.952335 CAGATGAAAAGGGCTCCATACTTT 59.048 41.667 0.00 0.00 36.09 2.66
4080 4475 5.221126 GGGCTCCATACTTTCTATTGCTTTG 60.221 44.000 0.00 0.00 0.00 2.77
4165 4560 5.106197 TGCACAAATAGTTCTGCTTGTATGG 60.106 40.000 4.83 0.00 31.00 2.74
4235 4630 9.030452 ACAAAGAGTATTAGATGTGAGAGAACT 57.970 33.333 0.00 0.00 0.00 3.01
4588 4983 3.505386 ACATTTTGCAGTCCCACCATTA 58.495 40.909 0.00 0.00 0.00 1.90
4787 5182 9.744468 AATAGTAAATCAGGACACAAAACAAAC 57.256 29.630 0.00 0.00 0.00 2.93
4802 5197 5.684550 AAACAAACCGTCCTATGAAACTC 57.315 39.130 0.00 0.00 0.00 3.01
5214 5611 7.033791 GTCGATACGGTTTATGATATGGTGAT 58.966 38.462 0.00 0.00 0.00 3.06
5304 5702 1.631405 CTTGGCCCAGAACCAAATCA 58.369 50.000 0.00 0.00 46.24 2.57
5339 5737 2.370445 CGGAGGCCCAGGTGAGAAT 61.370 63.158 0.00 0.00 0.00 2.40
5375 5773 0.035317 TGACTTGGCTGTAGCAGTGG 59.965 55.000 6.18 0.00 44.36 4.00
5525 5923 1.680735 AGACGCCATTGTTGCTGAAAA 59.319 42.857 0.00 0.00 0.00 2.29
5652 6050 6.339730 GGATTCATGTGCAACCATTCATTTA 58.660 36.000 0.00 0.00 34.36 1.40
5654 6052 7.010738 GGATTCATGTGCAACCATTCATTTAAG 59.989 37.037 0.00 0.00 34.36 1.85
5655 6053 6.343716 TCATGTGCAACCATTCATTTAAGT 57.656 33.333 0.00 0.00 34.36 2.24
5656 6054 6.157904 TCATGTGCAACCATTCATTTAAGTG 58.842 36.000 0.00 0.00 34.36 3.16
5657 6055 5.528043 TGTGCAACCATTCATTTAAGTGT 57.472 34.783 0.00 0.00 34.36 3.55
5658 6056 6.641169 TGTGCAACCATTCATTTAAGTGTA 57.359 33.333 0.00 0.00 34.36 2.90
5659 6057 7.225784 TGTGCAACCATTCATTTAAGTGTAT 57.774 32.000 0.00 0.00 34.36 2.29
5660 6058 7.089538 TGTGCAACCATTCATTTAAGTGTATG 58.910 34.615 9.67 9.67 34.36 2.39
5661 6059 7.040132 TGTGCAACCATTCATTTAAGTGTATGA 60.040 33.333 15.99 1.97 34.36 2.15
5741 6202 3.921677 ACAATCCTTGCATCAAAAGCTG 58.078 40.909 0.00 0.00 0.00 4.24
5744 6205 1.888512 TCCTTGCATCAAAAGCTGTCC 59.111 47.619 0.00 0.00 0.00 4.02
5801 6683 1.602377 GTAGCGTATGGATTTGTGCCC 59.398 52.381 0.00 0.00 0.00 5.36
5805 6687 1.742411 CGTATGGATTTGTGCCCGACT 60.742 52.381 0.00 0.00 0.00 4.18
5816 6698 1.689273 GTGCCCGACTATCTTGATCCT 59.311 52.381 0.00 0.00 0.00 3.24
5830 6712 1.229951 ATCCTCCCACCAGCCTTGA 60.230 57.895 0.00 0.00 0.00 3.02
5831 6713 1.277580 ATCCTCCCACCAGCCTTGAG 61.278 60.000 0.00 0.00 0.00 3.02
5880 6762 1.913403 GCGAATTTCTCCGTTGCAATG 59.087 47.619 11.90 11.90 0.00 2.82
5885 6767 2.361610 CTCCGTTGCAATGGGGCT 60.362 61.111 32.39 0.00 35.72 5.19
5940 6822 2.594303 CAGAACCTGCCGTTGCCA 60.594 61.111 0.00 0.00 33.74 4.92
5957 6839 1.003355 CAACATGCACGAGGAGGGT 60.003 57.895 0.00 0.00 0.00 4.34
6010 6892 0.534873 GAGCTCCTTCCTCCAGACAC 59.465 60.000 0.87 0.00 0.00 3.67
6090 6972 6.412362 AAGAGCTTCTTCTTGTGTAGAGAA 57.588 37.500 0.00 0.00 36.12 2.87
6117 6999 3.378399 GAACCAGAGGCCGAGCTCC 62.378 68.421 8.47 0.00 0.00 4.70
6129 7011 1.227946 GAGCTCCGGGGAGTACTCT 59.772 63.158 21.88 4.62 43.70 3.24
6178 7060 4.335647 CGGCCTTGCTCCACCTGT 62.336 66.667 0.00 0.00 0.00 4.00
6180 7062 2.113986 GCCTTGCTCCACCTGTGT 59.886 61.111 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.605749 ATTGCACCGTCGGACCAGG 62.606 63.158 20.51 1.45 0.00 4.45
1 2 2.047274 ATTGCACCGTCGGACCAG 60.047 61.111 20.51 5.86 0.00 4.00
29 30 1.379843 GCACCCCATTCATCCCGTT 60.380 57.895 0.00 0.00 0.00 4.44
30 31 2.275418 GCACCCCATTCATCCCGT 59.725 61.111 0.00 0.00 0.00 5.28
31 32 2.901840 CGCACCCCATTCATCCCG 60.902 66.667 0.00 0.00 0.00 5.14
38 39 2.355115 GGAACCTCGCACCCCATT 59.645 61.111 0.00 0.00 0.00 3.16
79 95 1.081556 CGGATGCGGACATGAACGAA 61.082 55.000 15.76 7.35 36.35 3.85
123 139 2.988839 ATGGCCCAGAGGAACCAGC 61.989 63.158 0.00 0.00 33.48 4.85
134 150 2.361104 GCCGAAGAACATGGCCCA 60.361 61.111 0.00 0.00 43.06 5.36
145 161 0.179215 GTTCGTCATGCAAGCCGAAG 60.179 55.000 8.15 0.00 39.67 3.79
147 163 2.032634 GGTTCGTCATGCAAGCCGA 61.033 57.895 0.00 0.00 0.00 5.54
149 165 2.877691 GGGTTCGTCATGCAAGCC 59.122 61.111 0.00 4.87 33.20 4.35
175 191 3.920196 ACCTTGTCCGTCGGCGTT 61.920 61.111 9.28 0.00 36.15 4.84
200 216 2.813042 GACTGCTGCGACAGAGGC 60.813 66.667 12.32 4.40 40.25 4.70
217 233 4.838152 CGTCCAGCATGTCCCCCG 62.838 72.222 0.00 0.00 0.00 5.73
239 255 0.537188 CATCCTTATCGCCGCCCTAT 59.463 55.000 0.00 0.00 0.00 2.57
248 264 1.417890 ACTTGCTCCCCATCCTTATCG 59.582 52.381 0.00 0.00 0.00 2.92
273 289 3.691342 CCGAGCCCTCACCGTTCA 61.691 66.667 0.00 0.00 0.00 3.18
290 306 3.011760 CTCCAACCTTTCGCGCGTC 62.012 63.158 30.98 0.00 0.00 5.19
298 314 1.073199 CCTGCGTCCTCCAACCTTT 59.927 57.895 0.00 0.00 0.00 3.11
314 331 0.103337 AAAACCTTCCCCCTCCTCCT 60.103 55.000 0.00 0.00 0.00 3.69
326 343 5.033589 TGCACCAAATCAATCAAAACCTT 57.966 34.783 0.00 0.00 0.00 3.50
328 345 5.945466 ATTGCACCAAATCAATCAAAACC 57.055 34.783 0.00 0.00 0.00 3.27
337 354 4.323333 CCCACCATAAATTGCACCAAATCA 60.323 41.667 0.00 0.00 0.00 2.57
343 360 1.567357 ACCCCACCATAAATTGCACC 58.433 50.000 0.00 0.00 0.00 5.01
344 361 2.354604 CCAACCCCACCATAAATTGCAC 60.355 50.000 0.00 0.00 0.00 4.57
353 372 1.155155 GACAACCCAACCCCACCAT 59.845 57.895 0.00 0.00 0.00 3.55
387 433 1.620819 GTCGGCACCTCTCATATCCAT 59.379 52.381 0.00 0.00 0.00 3.41
406 452 1.607251 CCTTAAGCGGGACTCAAACGT 60.607 52.381 0.00 0.00 0.00 3.99
407 453 1.076332 CCTTAAGCGGGACTCAAACG 58.924 55.000 0.00 0.00 0.00 3.60
408 454 2.347731 CTCCTTAAGCGGGACTCAAAC 58.652 52.381 0.00 0.00 0.00 2.93
409 455 1.338769 GCTCCTTAAGCGGGACTCAAA 60.339 52.381 0.00 0.00 42.21 2.69
410 456 0.249398 GCTCCTTAAGCGGGACTCAA 59.751 55.000 0.00 0.00 42.21 3.02
420 476 2.287668 CGACTCATACGGGCTCCTTAAG 60.288 54.545 0.00 0.00 0.00 1.85
449 505 1.555992 ACCCGATTAATGACCGGTCAA 59.444 47.619 39.04 24.67 43.58 3.18
455 511 1.861971 GGACGACCCGATTAATGACC 58.138 55.000 0.00 0.00 0.00 4.02
522 585 7.467623 GGTGCAGAACTTGTTATTAGAGAATG 58.532 38.462 0.00 0.00 0.00 2.67
680 743 1.954382 CGTCCATCTGAGGTATCGGAA 59.046 52.381 0.00 0.00 44.04 4.30
709 772 1.393487 TAGTATACTGCCGGCGCCAA 61.393 55.000 28.98 10.51 0.00 4.52
1250 1471 3.386768 CAGTAGTTGCAGTGGTACAGT 57.613 47.619 0.00 0.00 46.79 3.55
1286 1507 1.003118 CACTTGAACCGGATCTTCCCA 59.997 52.381 9.46 0.00 31.13 4.37
1495 1752 2.806244 ACAGCCTGTTAAGTTAACTGCG 59.194 45.455 22.87 20.25 39.98 5.18
1501 1758 6.694447 CAGGTACTAACAGCCTGTTAAGTTA 58.306 40.000 17.43 7.29 41.70 2.24
1528 1785 5.546110 TGGGATGCTAACCATGCTATACTAA 59.454 40.000 0.00 0.00 41.55 2.24
1637 1924 1.000274 GTTGTGTGGGTTGATTCAGCC 60.000 52.381 10.86 10.86 33.90 4.85
1755 2043 8.220559 AGAGAACCATGTATAGCCAAACATATT 58.779 33.333 0.00 0.00 34.61 1.28
1805 2093 6.475504 TGCATGTATTAAGCACCATATAGCT 58.524 36.000 0.00 0.00 44.31 3.32
1815 2103 3.016031 CTGGGTGTGCATGTATTAAGCA 58.984 45.455 0.00 0.00 35.63 3.91
1962 2252 4.842574 AGGTTGTCCTGTTGCAAAATTTT 58.157 34.783 0.00 0.00 43.33 1.82
2246 2536 6.544197 TCAACTGCACAAATTAACAGGTAGAA 59.456 34.615 0.00 0.00 34.40 2.10
2596 2973 9.770503 AACGCTACTGAATATACTGTTATATCG 57.229 33.333 0.00 0.00 30.71 2.92
3336 3714 7.607615 AATAGAAAATAGCCCAAATGCATCT 57.392 32.000 0.00 0.00 0.00 2.90
4023 4418 7.561722 TCTGATGAATGTTACTTAGTAGGAGCT 59.438 37.037 0.00 0.00 0.00 4.09
4069 4464 3.955471 AGCTAGCAACCAAAGCAATAGA 58.045 40.909 18.83 0.00 38.75 1.98
4080 4475 6.636562 TTAGATCACTACTAGCTAGCAACC 57.363 41.667 20.91 4.12 0.00 3.77
4165 4560 5.163550 GGTCTGTTGGGGTTATTAATGAAGC 60.164 44.000 0.00 0.00 0.00 3.86
4235 4630 8.862325 TTAACTGGATGAGAAGCATAGAAAAA 57.138 30.769 0.00 0.00 37.34 1.94
4566 4961 2.666272 TGGTGGGACTGCAAAATGTA 57.334 45.000 0.00 0.00 0.00 2.29
4688 5083 6.670027 ACTCCTTTCTCCTCTTTTGCTCTATA 59.330 38.462 0.00 0.00 0.00 1.31
4787 5182 2.683867 AGTCTCGAGTTTCATAGGACGG 59.316 50.000 13.13 0.00 0.00 4.79
4802 5197 1.550524 TCCAAACTCCCATCAGTCTCG 59.449 52.381 0.00 0.00 0.00 4.04
4950 5345 3.788227 AAGCAATGTCCTTACACTGGA 57.212 42.857 0.00 0.00 38.78 3.86
5214 5611 1.470632 CGTTGTTGCCCAGCTTTTTCA 60.471 47.619 0.00 0.00 0.00 2.69
5304 5702 0.670546 CCGTCGTGCTGAGAAACCAT 60.671 55.000 0.00 0.00 0.00 3.55
5339 5737 5.070446 CCAAGTCATGTAAGTATAGCCTCCA 59.930 44.000 0.00 0.00 0.00 3.86
5375 5773 8.725148 AGAAATCTGACACAAATCTCAATGTAC 58.275 33.333 0.00 0.00 0.00 2.90
5525 5923 7.871463 CACTATCACATCATCATCACAGTACAT 59.129 37.037 0.00 0.00 0.00 2.29
5652 6050 7.285401 ACTCAAACCAGAACAATTCATACACTT 59.715 33.333 0.00 0.00 0.00 3.16
5654 6052 6.970484 ACTCAAACCAGAACAATTCATACAC 58.030 36.000 0.00 0.00 0.00 2.90
5655 6053 7.519809 CGAACTCAAACCAGAACAATTCATACA 60.520 37.037 0.00 0.00 0.00 2.29
5656 6054 6.797033 CGAACTCAAACCAGAACAATTCATAC 59.203 38.462 0.00 0.00 0.00 2.39
5657 6055 6.485313 ACGAACTCAAACCAGAACAATTCATA 59.515 34.615 0.00 0.00 0.00 2.15
5658 6056 5.299279 ACGAACTCAAACCAGAACAATTCAT 59.701 36.000 0.00 0.00 0.00 2.57
5659 6057 4.638421 ACGAACTCAAACCAGAACAATTCA 59.362 37.500 0.00 0.00 0.00 2.57
5660 6058 5.169836 ACGAACTCAAACCAGAACAATTC 57.830 39.130 0.00 0.00 0.00 2.17
5661 6059 4.260620 CGACGAACTCAAACCAGAACAATT 60.261 41.667 0.00 0.00 0.00 2.32
5666 6064 2.545113 CCTCGACGAACTCAAACCAGAA 60.545 50.000 0.00 0.00 0.00 3.02
5667 6065 1.000607 CCTCGACGAACTCAAACCAGA 60.001 52.381 0.00 0.00 0.00 3.86
5668 6066 1.269621 ACCTCGACGAACTCAAACCAG 60.270 52.381 0.00 0.00 0.00 4.00
5671 6069 3.063045 ACAAAACCTCGACGAACTCAAAC 59.937 43.478 0.00 0.00 0.00 2.93
5744 6205 0.251608 CCACTGGGTGTTTTAGGGGG 60.252 60.000 0.00 0.00 31.21 5.40
5801 6683 2.297597 GGTGGGAGGATCAAGATAGTCG 59.702 54.545 0.00 0.00 36.25 4.18
5805 6687 2.050144 GCTGGTGGGAGGATCAAGATA 58.950 52.381 0.00 0.00 36.25 1.98
5880 6762 0.473326 ATGCAGATGAAGAGAGCCCC 59.527 55.000 0.00 0.00 0.00 5.80
5885 6767 3.429410 CCACGTGTATGCAGATGAAGAGA 60.429 47.826 15.65 0.00 0.00 3.10
5936 6818 1.672030 CTCCTCGTGCATGTTGGCA 60.672 57.895 5.68 0.00 42.53 4.92
5940 6822 1.003355 CACCCTCCTCGTGCATGTT 60.003 57.895 5.68 0.00 0.00 2.71
5957 6839 2.527624 ACTGGGAGCTGCTGGACA 60.528 61.111 7.01 1.88 0.00 4.02
6085 6967 0.251832 TGGTTCGGCCTCTCTTCTCT 60.252 55.000 0.00 0.00 38.35 3.10
6090 6972 1.684049 CCTCTGGTTCGGCCTCTCT 60.684 63.158 0.00 0.00 38.35 3.10
6117 6999 4.208686 GGCGCAGAGTACTCCCCG 62.209 72.222 19.38 20.77 0.00 5.73
6178 7060 1.890041 CCTTCGACACCGCCAAACA 60.890 57.895 0.00 0.00 35.37 2.83
6180 7062 2.975799 GCCTTCGACACCGCCAAA 60.976 61.111 0.00 0.00 35.37 3.28


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

AutoCloner maintained by Alex Coulton.