Multiple sequence alignment - TraesCS5B01G216200

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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 TraesCS5B01G216200 chr5B 100.000 3530 0 0 1 3530 389155476 389159005 0.000000e+00 6519
1 TraesCS5B01G216200 chr5B 74.092 633 136 20 1568 2184 631826630 631827250 5.890000e-58 235
2 TraesCS5B01G216200 chr5A 89.513 3652 194 75 6 3530 434133948 434137537 0.000000e+00 4447
3 TraesCS5B01G216200 chr5D 91.486 3312 148 49 6 3236 333052472 333055730 0.000000e+00 4431
4 TraesCS5B01G216200 chr5D 93.525 278 11 3 3257 3530 333055716 333055990 1.180000e-109 407
5 TraesCS5B01G216200 chr5D 73.806 649 142 22 1568 2200 503049168 503049804 7.620000e-57 231
6 TraesCS5B01G216200 chr5D 79.104 201 38 4 206 403 557885499 557885300 6.150000e-28 135
7 TraesCS5B01G216200 chr7B 78.187 353 62 11 6 353 28493613 28493271 9.930000e-51 211
8 TraesCS5B01G216200 chr7D 76.771 353 64 14 6 353 514097486 514097825 7.780000e-42 182
9 TraesCS5B01G216200 chr3A 75.312 401 75 18 6 397 635040195 635039810 1.680000e-38 171
10 TraesCS5B01G216200 chr3A 74.447 407 84 15 6 405 449787342 449787735 1.310000e-34 158
11 TraesCS5B01G216200 chr7A 73.750 400 82 18 6 397 217822364 217821980 6.150000e-28 135
12 TraesCS5B01G216200 chr4B 82.911 158 20 5 200 353 561036481 561036635 6.150000e-28 135
13 TraesCS5B01G216200 chr6A 77.404 208 42 5 1709 1914 613664291 613664087 6.190000e-23 119


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 TraesCS5B01G216200 chr5B 389155476 389159005 3529 False 6519 6519 100.0000 1 3530 1 chr5B.!!$F1 3529
1 TraesCS5B01G216200 chr5B 631826630 631827250 620 False 235 235 74.0920 1568 2184 1 chr5B.!!$F2 616
2 TraesCS5B01G216200 chr5A 434133948 434137537 3589 False 4447 4447 89.5130 6 3530 1 chr5A.!!$F1 3524
3 TraesCS5B01G216200 chr5D 333052472 333055990 3518 False 2419 4431 92.5055 6 3530 2 chr5D.!!$F2 3524
4 TraesCS5B01G216200 chr5D 503049168 503049804 636 False 231 231 73.8060 1568 2200 1 chr5D.!!$F1 632

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
725 733 0.107993 CCCTTCTTCGCTGCATCTGA 60.108 55.0 0.0 0.0 0.00 3.27 F
854 879 0.457851 AATCCTTCGTCTCCAGCTCG 59.542 55.0 0.0 0.0 0.00 5.03 F
2353 2425 0.250901 GCTGCTGGAGGTCCTGAAAA 60.251 55.0 0.0 0.0 37.15 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1746 1802 0.463295 CGATCATGCTGGACTTGCCT 60.463 55.000 0.00 0.0 37.63 4.75 R
2424 2502 1.002792 CTCCAGGGCCCTCTTCTCT 59.997 63.158 25.77 0.0 0.00 3.10 R
3250 3381 0.248296 GCACGACGGCAGAAACAAAA 60.248 50.000 0.00 0.0 0.00 2.44 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
63 66 8.807948 ACTTAATCAACTGTTAACATGGCTAT 57.192 30.769 9.13 0.00 0.00 2.97
124 127 3.070302 TGTGGTAGTACATGACAACTGCA 59.930 43.478 0.00 0.00 30.81 4.41
135 138 3.706698 TGACAACTGCATATAGACTCGC 58.293 45.455 0.00 0.00 0.00 5.03
143 146 6.749139 ACTGCATATAGACTCGCTAAATTCA 58.251 36.000 0.00 0.00 31.66 2.57
154 157 4.732285 CGCTAAATTCATGCGTCCTATT 57.268 40.909 10.25 0.00 44.00 1.73
155 158 5.839262 CGCTAAATTCATGCGTCCTATTA 57.161 39.130 10.25 0.00 44.00 0.98
156 159 5.847715 CGCTAAATTCATGCGTCCTATTAG 58.152 41.667 10.25 0.00 44.00 1.73
157 160 5.633601 CGCTAAATTCATGCGTCCTATTAGA 59.366 40.000 10.25 0.00 44.00 2.10
158 161 6.183360 CGCTAAATTCATGCGTCCTATTAGAG 60.183 42.308 10.25 0.00 44.00 2.43
159 162 5.931441 AAATTCATGCGTCCTATTAGAGC 57.069 39.130 0.00 0.00 0.00 4.09
160 163 3.386768 TTCATGCGTCCTATTAGAGCC 57.613 47.619 0.00 0.00 0.00 4.70
189 192 2.299867 GTTTGCCTCACATGGGTCATTT 59.700 45.455 0.00 0.00 0.00 2.32
194 197 3.196254 GCCTCACATGGGTCATTTTGATT 59.804 43.478 0.00 0.00 0.00 2.57
196 199 5.069516 GCCTCACATGGGTCATTTTGATTAT 59.930 40.000 0.00 0.00 0.00 1.28
279 282 5.852282 AAAGGGAAATTCCATATTCACGG 57.148 39.130 14.68 0.00 38.64 4.94
322 325 0.250553 TCCGTTCCGCCAGAAAACAT 60.251 50.000 0.00 0.00 35.85 2.71
329 332 0.243636 CGCCAGAAAACATGGTTCCC 59.756 55.000 0.00 0.00 40.17 3.97
347 350 1.483316 CCTTTTGTTTCCGTTTCCGC 58.517 50.000 0.00 0.00 0.00 5.54
349 352 0.450983 TTTTGTTTCCGTTTCCGCGT 59.549 45.000 4.92 0.00 0.00 6.01
353 356 1.004079 TGTTTCCGTTTCCGCGTAAAC 60.004 47.619 16.36 16.36 36.26 2.01
359 362 2.602694 CCGTTTCCGCGTAAACATTTGT 60.603 45.455 24.11 0.00 38.93 2.83
366 369 3.420576 CCGCGTAAACATTTGTGTTTCTG 59.579 43.478 4.92 5.69 41.58 3.02
439 445 1.535462 ACGTTTCCGCTCCATTTTCAG 59.465 47.619 0.00 0.00 37.70 3.02
440 446 1.729149 CGTTTCCGCTCCATTTTCAGC 60.729 52.381 0.00 0.00 0.00 4.26
441 447 1.541588 GTTTCCGCTCCATTTTCAGCT 59.458 47.619 0.00 0.00 33.09 4.24
442 448 1.453155 TTCCGCTCCATTTTCAGCTC 58.547 50.000 0.00 0.00 33.09 4.09
480 486 1.649664 TCGTTCCGTTTTCCGTTTCA 58.350 45.000 0.00 0.00 33.66 2.69
481 487 1.327156 TCGTTCCGTTTTCCGTTTCAC 59.673 47.619 0.00 0.00 33.66 3.18
502 508 2.103388 CGAAAAACACGGTTCCGTTTC 58.897 47.619 14.42 13.72 40.97 2.78
503 509 2.453080 GAAAAACACGGTTCCGTTTCC 58.547 47.619 14.42 0.97 40.97 3.13
551 558 5.627135 TCTGTTTTTCTATTTTCTCCCCGT 58.373 37.500 0.00 0.00 0.00 5.28
589 596 4.548156 CGAAAAAGCGGAAAGTTTTTGCTC 60.548 41.667 13.78 3.96 41.39 4.26
590 597 2.119671 AAGCGGAAAGTTTTTGCTCG 57.880 45.000 13.78 4.62 33.10 5.03
591 598 0.317854 AGCGGAAAGTTTTTGCTCGC 60.318 50.000 9.09 10.03 41.64 5.03
598 605 4.259810 GGAAAGTTTTTGCTCGCTTTTCAC 60.260 41.667 0.00 0.00 32.14 3.18
606 613 1.600413 GCTCGCTTTTCACCCTTGTTG 60.600 52.381 0.00 0.00 0.00 3.33
628 635 4.086457 GTCAACCATCTACCAAACCCAAT 58.914 43.478 0.00 0.00 0.00 3.16
648 655 2.123018 AGGATCCATATGCAGGTCCA 57.877 50.000 15.82 0.00 32.28 4.02
649 656 2.640651 AGGATCCATATGCAGGTCCAT 58.359 47.619 15.82 0.00 32.28 3.41
689 696 4.161942 CCAGAGTGAAGATCTCTCATGGTT 59.838 45.833 11.37 0.00 39.84 3.67
722 730 1.372087 CCACCCTTCTTCGCTGCATC 61.372 60.000 0.00 0.00 0.00 3.91
723 731 0.392193 CACCCTTCTTCGCTGCATCT 60.392 55.000 0.00 0.00 0.00 2.90
724 732 0.392193 ACCCTTCTTCGCTGCATCTG 60.392 55.000 0.00 0.00 0.00 2.90
725 733 0.107993 CCCTTCTTCGCTGCATCTGA 60.108 55.000 0.00 0.00 0.00 3.27
726 734 1.288350 CCTTCTTCGCTGCATCTGAG 58.712 55.000 0.00 0.00 0.00 3.35
727 735 1.288350 CTTCTTCGCTGCATCTGAGG 58.712 55.000 0.00 0.00 0.00 3.86
728 736 0.742281 TTCTTCGCTGCATCTGAGGC 60.742 55.000 7.45 7.45 0.00 4.70
729 737 2.124983 TTCGCTGCATCTGAGGCC 60.125 61.111 12.15 0.00 0.00 5.19
730 738 2.864378 CTTCGCTGCATCTGAGGCCA 62.864 60.000 12.15 0.00 0.00 5.36
846 871 4.855298 TTTCCCCAATAATCCTTCGTCT 57.145 40.909 0.00 0.00 0.00 4.18
854 879 0.457851 AATCCTTCGTCTCCAGCTCG 59.542 55.000 0.00 0.00 0.00 5.03
917 944 2.370349 TCGCAGGAAAACTTGTCCAAA 58.630 42.857 0.56 0.00 37.65 3.28
922 971 1.487482 GAAAACTTGTCCAAAGCCGC 58.513 50.000 0.00 0.00 0.00 6.53
1434 1490 3.066190 TTCACGCTCCGGATCCGT 61.066 61.111 31.22 20.56 37.81 4.69
1458 1514 1.949847 GCGACAGGGAGAAGCTGCTA 61.950 60.000 0.90 0.00 0.00 3.49
1728 1784 3.372554 GAAGCGCGGCTACCTCCTT 62.373 63.158 8.83 0.00 38.25 3.36
1830 1886 3.072476 ACCGAGGTGAGCAGCAAT 58.928 55.556 0.00 0.00 0.00 3.56
2022 2085 3.492311 GATCACGCTCTCCGGCCTC 62.492 68.421 0.00 0.00 42.52 4.70
2073 2136 2.125106 GGGTCGGAGCGCATCTTT 60.125 61.111 11.47 0.00 0.00 2.52
2085 2148 2.146342 CGCATCTTTGTCTTCACCACT 58.854 47.619 0.00 0.00 0.00 4.00
2202 2265 2.167487 CCTCCTCAAGAACTACCTCTGC 59.833 54.545 0.00 0.00 0.00 4.26
2206 2269 2.167487 CTCAAGAACTACCTCTGCCTCC 59.833 54.545 0.00 0.00 0.00 4.30
2353 2425 0.250901 GCTGCTGGAGGTCCTGAAAA 60.251 55.000 0.00 0.00 37.15 2.29
2424 2502 1.325355 AGGACAACGACGAAGAGGAA 58.675 50.000 0.00 0.00 0.00 3.36
2607 2690 4.467795 TCAAAATTTCCCTGTTTGGTCACA 59.532 37.500 0.00 0.00 33.88 3.58
2640 2731 0.875059 CCTTTTCACTGGAGAACGCC 59.125 55.000 0.00 0.00 0.00 5.68
2694 2788 3.749088 TCCGTTATTCGATGTTTGCAGTT 59.251 39.130 0.00 0.00 42.86 3.16
2696 2790 4.463209 CGTTATTCGATGTTTGCAGTTGT 58.537 39.130 0.00 0.00 42.86 3.32
2698 2792 5.728049 CGTTATTCGATGTTTGCAGTTGTAG 59.272 40.000 0.00 0.00 42.86 2.74
2699 2793 3.536158 TTCGATGTTTGCAGTTGTAGC 57.464 42.857 0.00 0.00 0.00 3.58
2700 2794 2.488952 TCGATGTTTGCAGTTGTAGCA 58.511 42.857 0.00 0.00 40.85 3.49
2710 2804 5.970317 TGCAGTTGTAGCAAGTACTAGTA 57.030 39.130 0.00 0.00 39.39 1.82
2711 2805 5.950883 TGCAGTTGTAGCAAGTACTAGTAG 58.049 41.667 1.87 0.00 39.39 2.57
2712 2806 5.475909 TGCAGTTGTAGCAAGTACTAGTAGT 59.524 40.000 8.14 8.14 39.39 2.73
2713 2807 6.656270 TGCAGTTGTAGCAAGTACTAGTAGTA 59.344 38.462 10.68 5.90 39.39 1.82
2714 2808 7.361542 TGCAGTTGTAGCAAGTACTAGTAGTAC 60.362 40.741 26.54 26.54 42.89 2.73
2744 2838 7.619698 TGGACCTAGATGAATTCTCTTGAGTTA 59.380 37.037 7.05 0.00 35.79 2.24
2794 2898 4.636249 AGAGATGTTTGAAGACTCACACC 58.364 43.478 0.00 0.00 32.23 4.16
2814 2918 1.802715 GTGTCATTGCGTGGCATGC 60.803 57.895 24.45 24.45 45.63 4.06
2863 2971 2.620112 CCTCCCTGTTGCTTGTGCG 61.620 63.158 0.00 0.00 43.34 5.34
2902 3010 4.456911 CAGTTGGTGCAGATTCAACAGTAT 59.543 41.667 18.16 2.34 42.08 2.12
2944 3057 1.306312 TAGGCCGGCAGGGTTTCTA 60.306 57.895 30.85 15.44 38.44 2.10
2963 3076 1.003839 CGCTTTGTGTAGGGCCTCA 60.004 57.895 10.74 5.30 0.00 3.86
3015 3145 1.865865 ATGTGCACGTTCGTCTCTTT 58.134 45.000 13.13 0.00 0.00 2.52
3045 3175 1.966493 CTGTGGCGCACGTATCCAAC 61.966 60.000 10.83 0.00 37.14 3.77
3113 3243 2.511600 GCCCGTGGAGTTGGATCG 60.512 66.667 0.00 0.00 0.00 3.69
3153 3283 3.466791 CTGTATGAGCCGCCCCCTG 62.467 68.421 0.00 0.00 0.00 4.45
3206 3337 5.159209 ACGGACTAGAAAACGACTGTATTG 58.841 41.667 0.00 0.00 0.00 1.90
3225 3356 2.054363 TGTGTTGTGTTTTGTGCGTTG 58.946 42.857 0.00 0.00 0.00 4.10
3226 3357 2.055100 GTGTTGTGTTTTGTGCGTTGT 58.945 42.857 0.00 0.00 0.00 3.32
3227 3358 2.054363 TGTTGTGTTTTGTGCGTTGTG 58.946 42.857 0.00 0.00 0.00 3.33
3228 3359 1.063806 TTGTGTTTTGTGCGTTGTGC 58.936 45.000 0.00 0.00 46.70 4.57
3229 3360 0.734253 TGTGTTTTGTGCGTTGTGCC 60.734 50.000 0.00 0.00 45.60 5.01
3231 3362 0.179150 TGTTTTGTGCGTTGTGCCTC 60.179 50.000 0.00 0.00 45.60 4.70
3232 3363 1.063327 TTTTGTGCGTTGTGCCTCG 59.937 52.632 0.00 0.00 45.60 4.63
3233 3364 2.329678 TTTTGTGCGTTGTGCCTCGG 62.330 55.000 0.00 0.00 45.60 4.63
3246 3377 1.997669 GCCTCGGCATATAGTAGCAC 58.002 55.000 2.41 0.00 41.49 4.40
3247 3378 1.272490 GCCTCGGCATATAGTAGCACA 59.728 52.381 2.41 0.00 41.49 4.57
3248 3379 2.288825 GCCTCGGCATATAGTAGCACAA 60.289 50.000 2.41 0.00 41.49 3.33
3249 3380 3.318017 CCTCGGCATATAGTAGCACAAC 58.682 50.000 0.00 0.00 0.00 3.32
3250 3381 3.005897 CCTCGGCATATAGTAGCACAACT 59.994 47.826 0.00 0.00 0.00 3.16
3251 3382 4.501571 CCTCGGCATATAGTAGCACAACTT 60.502 45.833 0.00 0.00 0.00 2.66
3252 3383 5.018539 TCGGCATATAGTAGCACAACTTT 57.981 39.130 0.00 0.00 0.00 2.66
3253 3384 5.424757 TCGGCATATAGTAGCACAACTTTT 58.575 37.500 0.00 0.00 0.00 2.27
3254 3385 5.293324 TCGGCATATAGTAGCACAACTTTTG 59.707 40.000 0.00 0.00 0.00 2.44
3255 3386 5.064707 CGGCATATAGTAGCACAACTTTTGT 59.935 40.000 0.00 0.00 46.75 2.83
3256 3387 6.403200 CGGCATATAGTAGCACAACTTTTGTT 60.403 38.462 0.00 0.00 43.23 2.83
3275 3406 0.666274 TTCTGCCGTCGTGCACTTAG 60.666 55.000 16.19 5.33 36.04 2.18
3377 3530 0.459899 ATCTACGCATGTTCCTCGCA 59.540 50.000 0.00 0.00 0.00 5.10
3391 3544 1.203928 CTCGCATGACATTCTCCGTC 58.796 55.000 0.00 0.00 0.00 4.79
3429 3582 6.408858 TGCTCGACATTCTCTGTTATTTTC 57.591 37.500 0.00 0.00 38.54 2.29
3436 3592 7.044380 CGACATTCTCTGTTATTTTCTCTCTCG 60.044 40.741 0.00 0.00 38.54 4.04
3471 3644 4.340381 GTGCCTGCAAAATCAGAGGATATT 59.660 41.667 0.00 0.00 36.19 1.28
3475 3649 7.040201 TGCCTGCAAAATCAGAGGATATTTATC 60.040 37.037 0.00 0.00 36.19 1.75
3513 3687 1.490574 GATCCCTGATCCCCCGATAG 58.509 60.000 0.00 0.00 33.37 2.08
3514 3688 0.793617 ATCCCTGATCCCCCGATAGT 59.206 55.000 0.00 0.00 0.00 2.12
3515 3689 1.463531 TCCCTGATCCCCCGATAGTA 58.536 55.000 0.00 0.00 0.00 1.82
3526 3700 4.046231 TCCCCCGATAGTATCTTATTCCCA 59.954 45.833 8.49 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 9.930693 TTAACAGTTGATTAAGTTTGTTGGTTT 57.069 25.926 0.00 0.00 31.84 3.27
81 84 8.202137 ACCACAATACTATGTTAAGTCGCTAAT 58.798 33.333 0.00 0.00 0.00 1.73
114 117 3.381590 AGCGAGTCTATATGCAGTTGTCA 59.618 43.478 0.00 0.00 0.00 3.58
135 138 6.091441 GGCTCTAATAGGACGCATGAATTTAG 59.909 42.308 0.00 0.00 0.00 1.85
143 146 2.320781 ACTGGCTCTAATAGGACGCAT 58.679 47.619 0.00 0.00 0.00 4.73
149 152 5.755861 GCAAACTTCTACTGGCTCTAATAGG 59.244 44.000 0.00 0.00 0.00 2.57
152 155 4.226168 AGGCAAACTTCTACTGGCTCTAAT 59.774 41.667 0.00 0.00 41.73 1.73
153 156 3.583086 AGGCAAACTTCTACTGGCTCTAA 59.417 43.478 0.00 0.00 41.73 2.10
154 157 3.173965 AGGCAAACTTCTACTGGCTCTA 58.826 45.455 0.00 0.00 41.73 2.43
155 158 1.981495 AGGCAAACTTCTACTGGCTCT 59.019 47.619 0.00 0.00 41.73 4.09
156 159 2.481289 AGGCAAACTTCTACTGGCTC 57.519 50.000 0.00 0.00 41.73 4.70
158 161 1.807142 GTGAGGCAAACTTCTACTGGC 59.193 52.381 0.00 0.00 35.96 4.85
159 162 3.126001 TGTGAGGCAAACTTCTACTGG 57.874 47.619 0.00 0.00 0.00 4.00
160 163 3.438087 CCATGTGAGGCAAACTTCTACTG 59.562 47.826 0.00 0.00 0.00 2.74
189 192 7.036996 ACACACAATGACACACAATAATCAA 57.963 32.000 0.00 0.00 0.00 2.57
194 197 7.171678 TCGAATAACACACAATGACACACAATA 59.828 33.333 0.00 0.00 0.00 1.90
196 199 5.294552 TCGAATAACACACAATGACACACAA 59.705 36.000 0.00 0.00 0.00 3.33
279 282 4.494410 CACGGAAACTGAACTTTTCGTTTC 59.506 41.667 18.04 18.04 41.62 2.78
353 356 5.005299 GGAAACGGAAACAGAAACACAAATG 59.995 40.000 0.00 0.00 0.00 2.32
359 362 6.642707 AATATGGAAACGGAAACAGAAACA 57.357 33.333 0.00 0.00 0.00 2.83
366 369 6.510879 AAGAGGAAATATGGAAACGGAAAC 57.489 37.500 0.00 0.00 0.00 2.78
406 412 1.003652 GGAAACGTTCCGCTTTTTCGA 60.004 47.619 0.00 0.00 40.59 3.71
432 438 5.714333 TCTGACAGTAGAGAGAGCTGAAAAT 59.286 40.000 1.59 0.00 34.60 1.82
439 445 5.385509 AAAAGTCTGACAGTAGAGAGAGC 57.614 43.478 10.88 0.00 0.00 4.09
440 446 5.180492 ACGAAAAGTCTGACAGTAGAGAGAG 59.820 44.000 10.88 0.00 0.00 3.20
441 447 5.064558 ACGAAAAGTCTGACAGTAGAGAGA 58.935 41.667 10.88 0.00 0.00 3.10
442 448 5.365403 ACGAAAAGTCTGACAGTAGAGAG 57.635 43.478 10.88 0.00 0.00 3.20
536 543 5.757099 AAGAGAAACGGGGAGAAAATAGA 57.243 39.130 0.00 0.00 0.00 1.98
589 596 1.403679 TGACAACAAGGGTGAAAAGCG 59.596 47.619 0.00 0.00 0.00 4.68
590 597 3.186909 GTTGACAACAAGGGTGAAAAGC 58.813 45.455 13.52 0.00 36.64 3.51
591 598 3.194542 TGGTTGACAACAAGGGTGAAAAG 59.805 43.478 19.58 0.00 36.64 2.27
598 605 3.081804 GGTAGATGGTTGACAACAAGGG 58.918 50.000 19.58 0.00 36.64 3.95
606 613 3.149005 TGGGTTTGGTAGATGGTTGAC 57.851 47.619 0.00 0.00 0.00 3.18
628 635 3.274281 TGGACCTGCATATGGATCCTA 57.726 47.619 14.23 3.34 0.00 2.94
727 735 6.840780 AATTATTGGAAGTATAGGCATGGC 57.159 37.500 12.14 12.14 0.00 4.40
805 826 5.047802 GGAAATGAAAGATGAAGCCTTGTGA 60.048 40.000 0.00 0.00 0.00 3.58
846 871 2.673341 ACGCTGAGACGAGCTGGA 60.673 61.111 1.44 0.00 36.77 3.86
854 879 1.975660 ATAGGAGGAGACGCTGAGAC 58.024 55.000 0.00 0.00 0.00 3.36
1128 1184 2.726351 GCAGTAGGGCGAGAAGGCT 61.726 63.158 0.00 0.00 45.89 4.58
1444 1500 2.060980 CCGGTAGCAGCTTCTCCCT 61.061 63.158 0.00 0.00 0.00 4.20
1458 1514 4.371417 TGGTCGAGGTAGGCCGGT 62.371 66.667 1.90 0.00 39.14 5.28
1519 1575 1.293498 CGTTGGTGTAGAGCAGCCT 59.707 57.895 0.39 0.00 44.44 4.58
1746 1802 0.463295 CGATCATGCTGGACTTGCCT 60.463 55.000 0.00 0.00 37.63 4.75
2022 2085 1.374252 CCCGTCGGTGAAGTTGAGG 60.374 63.158 11.06 0.00 0.00 3.86
2073 2136 3.554129 CGATGTGGTTAGTGGTGAAGACA 60.554 47.826 0.00 0.00 0.00 3.41
2085 2148 2.094182 GTCCAGCTTCTCGATGTGGTTA 60.094 50.000 0.00 0.00 0.00 2.85
2232 2304 1.699054 CGATCCATTCCTCCAGCCCA 61.699 60.000 0.00 0.00 0.00 5.36
2424 2502 1.002792 CTCCAGGGCCCTCTTCTCT 59.997 63.158 25.77 0.00 0.00 3.10
2551 2634 1.268283 CCTCTTCCTGTCCCCCTCAC 61.268 65.000 0.00 0.00 0.00 3.51
2607 2690 6.183347 CAGTGAAAAGGGAGAAGAATATGGT 58.817 40.000 0.00 0.00 0.00 3.55
2640 2731 3.470520 TTTTTCCTTGCATCGCGTG 57.529 47.368 5.77 5.06 0.00 5.34
2659 2753 5.826737 TCGAATAACGGAAGAGGAAGACTAT 59.173 40.000 0.00 0.00 42.82 2.12
2660 2754 5.188434 TCGAATAACGGAAGAGGAAGACTA 58.812 41.667 0.00 0.00 42.82 2.59
2661 2755 4.015084 TCGAATAACGGAAGAGGAAGACT 58.985 43.478 0.00 0.00 42.82 3.24
2662 2756 4.367386 TCGAATAACGGAAGAGGAAGAC 57.633 45.455 0.00 0.00 42.82 3.01
2663 2757 4.401519 ACATCGAATAACGGAAGAGGAAGA 59.598 41.667 0.00 0.00 42.82 2.87
2664 2758 4.683832 ACATCGAATAACGGAAGAGGAAG 58.316 43.478 0.00 0.00 42.82 3.46
2704 2798 5.536951 TCTAGGTCCAGGAGTACTACTAGT 58.463 45.833 7.47 0.00 0.00 2.57
2705 2799 6.270463 TCATCTAGGTCCAGGAGTACTACTAG 59.730 46.154 7.47 0.00 0.00 2.57
2706 2800 6.148901 TCATCTAGGTCCAGGAGTACTACTA 58.851 44.000 7.47 0.00 0.00 1.82
2708 2802 5.307544 TCATCTAGGTCCAGGAGTACTAC 57.692 47.826 0.00 0.00 0.00 2.73
2710 2804 4.883021 TTCATCTAGGTCCAGGAGTACT 57.117 45.455 0.00 0.00 0.00 2.73
2711 2805 5.836358 AGAATTCATCTAGGTCCAGGAGTAC 59.164 44.000 8.44 0.00 36.32 2.73
2712 2806 6.031964 AGAATTCATCTAGGTCCAGGAGTA 57.968 41.667 8.44 0.00 36.32 2.59
2713 2807 4.889780 AGAATTCATCTAGGTCCAGGAGT 58.110 43.478 8.44 0.00 36.32 3.85
2714 2808 5.147032 AGAGAATTCATCTAGGTCCAGGAG 58.853 45.833 8.44 0.00 38.96 3.69
2715 2809 5.149584 AGAGAATTCATCTAGGTCCAGGA 57.850 43.478 8.44 0.00 38.96 3.86
2716 2810 5.365025 TCAAGAGAATTCATCTAGGTCCAGG 59.635 44.000 8.44 0.00 38.96 4.45
2717 2811 6.098124 ACTCAAGAGAATTCATCTAGGTCCAG 59.902 42.308 8.44 2.32 38.96 3.86
2718 2812 5.960811 ACTCAAGAGAATTCATCTAGGTCCA 59.039 40.000 8.44 0.00 38.96 4.02
2719 2813 6.478512 ACTCAAGAGAATTCATCTAGGTCC 57.521 41.667 8.44 0.00 38.96 4.46
2720 2814 8.691797 ACTAACTCAAGAGAATTCATCTAGGTC 58.308 37.037 8.44 0.00 38.96 3.85
2721 2815 8.602472 ACTAACTCAAGAGAATTCATCTAGGT 57.398 34.615 8.44 4.78 38.96 3.08
2761 2855 9.871299 GTCTTCAAACATCTCTTTCTTCTTAAC 57.129 33.333 0.00 0.00 0.00 2.01
2762 2856 9.838339 AGTCTTCAAACATCTCTTTCTTCTTAA 57.162 29.630 0.00 0.00 0.00 1.85
2794 2898 2.689785 ATGCCACGCAATGACACCG 61.690 57.895 0.00 0.00 43.62 4.94
2819 2923 1.250328 CCAAACAAGCAGAGCATGGA 58.750 50.000 0.00 0.00 31.12 3.41
2863 2971 2.510768 ACTGAACACGACCTTCTCAC 57.489 50.000 0.00 0.00 0.00 3.51
2902 3010 1.588674 AAACGTGATGTGCCTTCGAA 58.411 45.000 0.00 0.00 0.00 3.71
2944 3057 1.003718 GAGGCCCTACACAAAGCGT 60.004 57.895 0.00 0.00 0.00 5.07
2963 3076 6.824958 TGGTAAGAGGCCATAAACTAATCT 57.175 37.500 5.01 0.00 0.00 2.40
3015 3145 1.304052 CGCCACAGGGGATCCAAAA 60.304 57.895 15.23 0.00 40.01 2.44
3070 3200 3.240631 GCATTATTTTTCTCCGAAAGCGC 59.759 43.478 0.00 0.00 35.83 5.92
3166 3297 1.393539 CCGTCCTGCGTGTAGAAAATG 59.606 52.381 0.00 0.00 39.32 2.32
3206 3337 2.055100 ACAACGCACAAAACACAACAC 58.945 42.857 0.00 0.00 0.00 3.32
3227 3358 1.272490 TGTGCTACTATATGCCGAGGC 59.728 52.381 7.26 7.26 42.35 4.70
3228 3359 3.005897 AGTTGTGCTACTATATGCCGAGG 59.994 47.826 0.00 0.00 0.00 4.63
3229 3360 4.244425 AGTTGTGCTACTATATGCCGAG 57.756 45.455 0.00 0.00 0.00 4.63
3231 3362 5.064707 ACAAAAGTTGTGCTACTATATGCCG 59.935 40.000 0.00 0.00 43.48 5.69
3232 3363 6.436843 ACAAAAGTTGTGCTACTATATGCC 57.563 37.500 0.00 0.00 43.48 4.40
3233 3364 8.237267 AGAAACAAAAGTTGTGCTACTATATGC 58.763 33.333 0.00 0.00 44.59 3.14
3234 3365 9.546909 CAGAAACAAAAGTTGTGCTACTATATG 57.453 33.333 0.00 0.00 44.59 1.78
3236 3367 7.308348 GGCAGAAACAAAAGTTGTGCTACTATA 60.308 37.037 12.72 0.00 44.59 1.31
3237 3368 6.438763 GCAGAAACAAAAGTTGTGCTACTAT 58.561 36.000 0.00 0.00 44.59 2.12
3238 3369 5.220970 GGCAGAAACAAAAGTTGTGCTACTA 60.221 40.000 12.72 0.00 44.59 1.82
3239 3370 4.440112 GGCAGAAACAAAAGTTGTGCTACT 60.440 41.667 12.72 0.00 44.59 2.57
3240 3371 3.796717 GGCAGAAACAAAAGTTGTGCTAC 59.203 43.478 12.72 0.00 44.59 3.58
3241 3372 3.488384 CGGCAGAAACAAAAGTTGTGCTA 60.488 43.478 12.72 0.00 44.59 3.49
3242 3373 2.735126 CGGCAGAAACAAAAGTTGTGCT 60.735 45.455 12.72 0.00 44.59 4.40
3243 3374 1.587946 CGGCAGAAACAAAAGTTGTGC 59.412 47.619 0.00 7.18 44.59 4.57
3244 3375 2.851824 GACGGCAGAAACAAAAGTTGTG 59.148 45.455 0.00 0.00 44.59 3.33
3246 3377 2.108700 CGACGGCAGAAACAAAAGTTG 58.891 47.619 0.00 0.00 0.00 3.16
3247 3378 1.741145 ACGACGGCAGAAACAAAAGTT 59.259 42.857 0.00 0.00 0.00 2.66
3248 3379 1.063469 CACGACGGCAGAAACAAAAGT 59.937 47.619 0.00 0.00 0.00 2.66
3249 3380 1.741993 CACGACGGCAGAAACAAAAG 58.258 50.000 0.00 0.00 0.00 2.27
3250 3381 0.248296 GCACGACGGCAGAAACAAAA 60.248 50.000 0.00 0.00 0.00 2.44
3251 3382 1.353804 GCACGACGGCAGAAACAAA 59.646 52.632 0.00 0.00 0.00 2.83
3252 3383 1.815840 TGCACGACGGCAGAAACAA 60.816 52.632 6.88 0.00 39.25 2.83
3253 3384 2.202946 TGCACGACGGCAGAAACA 60.203 55.556 6.88 0.00 39.25 2.83
3254 3385 1.772063 AAGTGCACGACGGCAGAAAC 61.772 55.000 12.01 1.16 45.96 2.78
3255 3386 0.249531 TAAGTGCACGACGGCAGAAA 60.250 50.000 12.01 0.00 45.96 2.52
3256 3387 0.666274 CTAAGTGCACGACGGCAGAA 60.666 55.000 12.01 0.84 45.96 3.02
3391 3544 4.214119 TGTCGAGCAAGAGAAGGAAAAATG 59.786 41.667 0.00 0.00 0.00 2.32
3429 3582 1.336440 ACATGGAATCGAGCGAGAGAG 59.664 52.381 0.00 0.00 0.00 3.20
3436 3592 2.020131 CAGGCACATGGAATCGAGC 58.980 57.895 0.00 0.00 0.00 5.03


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

AutoCloner maintained by Alex Coulton.