Multiple sequence alignment - TraesCS5A01G236200

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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 TraesCS5A01G236200 chr5A 100.000 3543 0 0 1 3543 451743698 451740156 0.000000e+00 6543
1 TraesCS5A01G236200 chr5A 94.512 164 9 0 1038 1201 376844943 376845106 1.630000e-63 254
2 TraesCS5A01G236200 chr5A 94.012 167 7 3 38 203 451757535 451757371 2.110000e-62 250
3 TraesCS5A01G236200 chr5D 90.571 3256 129 62 1 3135 351406443 351403245 0.000000e+00 4148
4 TraesCS5A01G236200 chr5D 91.667 240 15 4 3143 3378 351403173 351402935 9.480000e-86 327
5 TraesCS5A01G236200 chr5D 84.733 131 8 4 3392 3522 351402957 351402839 1.730000e-23 121
6 TraesCS5A01G236200 chr5B 89.078 3232 132 79 1 3135 412464186 412461079 0.000000e+00 3808
7 TraesCS5A01G236200 chr5B 93.913 230 11 3 3146 3374 412460998 412460771 9.420000e-91 344
8 TraesCS5A01G236200 chr6A 89.117 974 36 16 832 1752 566431372 566432328 0.000000e+00 1147
9 TraesCS5A01G236200 chr6A 88.501 974 43 18 832 1752 487772219 487773176 0.000000e+00 1114
10 TraesCS5A01G236200 chr2B 88.902 874 34 13 915 1752 267901019 267901865 0.000000e+00 1018
11 TraesCS5A01G236200 chr3A 95.122 164 8 0 1038 1201 435354499 435354662 3.510000e-65 259


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 TraesCS5A01G236200 chr5A 451740156 451743698 3542 True 6543 6543 100.000000 1 3543 1 chr5A.!!$R1 3542
1 TraesCS5A01G236200 chr5D 351402839 351406443 3604 True 1532 4148 88.990333 1 3522 3 chr5D.!!$R1 3521
2 TraesCS5A01G236200 chr5B 412460771 412464186 3415 True 2076 3808 91.495500 1 3374 2 chr5B.!!$R1 3373
3 TraesCS5A01G236200 chr6A 566431372 566432328 956 False 1147 1147 89.117000 832 1752 1 chr6A.!!$F2 920
4 TraesCS5A01G236200 chr6A 487772219 487773176 957 False 1114 1114 88.501000 832 1752 1 chr6A.!!$F1 920
5 TraesCS5A01G236200 chr2B 267901019 267901865 846 False 1018 1018 88.902000 915 1752 1 chr2B.!!$F1 837

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
129 136 0.319641 AGCCTCGACCGAGAAAACAC 60.320 55.0 19.70 3.48 44.53 3.32 F
151 158 0.436150 GGACGCGACGGTTTTCTTAC 59.564 55.0 15.93 0.00 0.00 2.34 F
597 639 0.470456 AACACCGGGAGTACAGACCA 60.470 55.0 6.32 0.00 0.00 4.02 F
598 640 0.898789 ACACCGGGAGTACAGACCAG 60.899 60.0 6.32 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1773 1924 0.736325 CGCACTTGAACTCCCCTACG 60.736 60.000 0.0 0.0 0.00 3.51 R
2067 2243 2.125269 CCAAAGTACTCCCCGGCG 60.125 66.667 0.0 0.0 0.00 6.46 R
2184 2360 1.491563 CTTGTCGCCGTTCCGAAAG 59.508 57.895 0.0 0.0 39.17 2.62 R
2563 2742 2.222227 AGAGGAAAGGGGCATGTTTC 57.778 50.000 0.0 0.0 32.79 2.78 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
22 23 2.640302 ATCTGCACTCCACGAGCGT 61.640 57.895 0.00 0.00 32.04 5.07
23 24 1.313091 ATCTGCACTCCACGAGCGTA 61.313 55.000 0.00 0.00 32.04 4.42
36 38 5.702209 TCCACGAGCGTATATACATTACTCA 59.298 40.000 13.22 0.00 0.00 3.41
64 66 4.468510 ACCAGTCGTTTCACTCCCATATAA 59.531 41.667 0.00 0.00 0.00 0.98
65 67 5.130477 ACCAGTCGTTTCACTCCCATATAAT 59.870 40.000 0.00 0.00 0.00 1.28
129 136 0.319641 AGCCTCGACCGAGAAAACAC 60.320 55.000 19.70 3.48 44.53 3.32
147 154 2.664436 CCAGGACGCGACGGTTTTC 61.664 63.158 15.93 0.00 0.00 2.29
151 158 0.436150 GGACGCGACGGTTTTCTTAC 59.564 55.000 15.93 0.00 0.00 2.34
155 162 1.629345 GCGACGGTTTTCTTACCCCG 61.629 60.000 0.00 0.00 45.72 5.73
164 171 2.865119 TTCTTACCCCGAAAAGTCCC 57.135 50.000 0.00 0.00 0.00 4.46
180 187 3.370231 CCGCGGTCAAAAAGGGGG 61.370 66.667 19.50 0.00 34.77 5.40
268 275 2.279517 GGCCACAGAGCCGTATCG 60.280 66.667 0.00 0.00 44.57 2.92
269 276 2.962253 GCCACAGAGCCGTATCGC 60.962 66.667 0.00 0.00 0.00 4.58
270 277 2.655364 CCACAGAGCCGTATCGCG 60.655 66.667 0.00 0.00 40.95 5.87
271 278 3.323136 CACAGAGCCGTATCGCGC 61.323 66.667 0.00 0.00 39.71 6.86
272 279 4.907034 ACAGAGCCGTATCGCGCG 62.907 66.667 26.76 26.76 39.71 6.86
359 372 2.809601 CGTCCACCGGAAAGCTCG 60.810 66.667 9.46 0.95 31.38 5.03
423 447 3.159347 CGCACCCTACCCTACCCC 61.159 72.222 0.00 0.00 0.00 4.95
426 450 1.691689 CACCCTACCCTACCCCACC 60.692 68.421 0.00 0.00 0.00 4.61
594 636 1.707106 TCAAACACCGGGAGTACAGA 58.293 50.000 6.32 0.48 0.00 3.41
595 637 1.342174 TCAAACACCGGGAGTACAGAC 59.658 52.381 6.32 0.00 0.00 3.51
596 638 0.683412 AAACACCGGGAGTACAGACC 59.317 55.000 6.32 0.00 0.00 3.85
597 639 0.470456 AACACCGGGAGTACAGACCA 60.470 55.000 6.32 0.00 0.00 4.02
598 640 0.898789 ACACCGGGAGTACAGACCAG 60.899 60.000 6.32 0.00 0.00 4.00
612 654 0.899019 GACCAGACCCTGTCTTCTCC 59.101 60.000 0.00 0.00 41.37 3.71
730 795 3.081409 TGGGGGCGCTAGGAGTTC 61.081 66.667 7.64 0.00 0.00 3.01
927 1033 3.040414 TTCGCGGCTCTCTCTCACG 62.040 63.158 6.13 0.00 0.00 4.35
954 1063 1.880340 GGAGCAGCAAGATCCGTCG 60.880 63.158 0.00 0.00 44.00 5.12
1278 1411 4.154347 CACCTGCTCCTCCTCGCC 62.154 72.222 0.00 0.00 0.00 5.54
1764 1915 4.803426 CAGACCTGCTCCGACGGC 62.803 72.222 9.66 0.00 0.00 5.68
1773 1924 3.127352 CTCCGACGGCAGCTCCTAC 62.127 68.421 9.66 0.00 0.00 3.18
1876 2027 3.798337 GCTTTGATTTGGTCACACTGTTG 59.202 43.478 0.00 0.00 36.32 3.33
1920 2071 8.391106 ACTGTTCGATTGCTTCATTAATAACTC 58.609 33.333 0.00 0.00 0.00 3.01
1934 2085 7.612633 TCATTAATAACTCCCAACAACCTTACC 59.387 37.037 0.00 0.00 0.00 2.85
1936 2087 2.951229 ACTCCCAACAACCTTACCAG 57.049 50.000 0.00 0.00 0.00 4.00
2034 2210 9.489084 AATTTGGTTGCTAATTTCTAACTTTCC 57.511 29.630 0.00 0.00 0.00 3.13
2035 2211 7.589958 TTGGTTGCTAATTTCTAACTTTCCA 57.410 32.000 0.00 0.00 0.00 3.53
2067 2243 1.852942 TCAGAAATGGCGATCGCTAC 58.147 50.000 36.25 22.80 41.60 3.58
2184 2360 0.616891 AGGGGTTCGGAATGTACACC 59.383 55.000 0.00 0.00 41.55 4.16
2262 2438 1.139498 TGCCCCCAACAGATCCTTCA 61.139 55.000 0.00 0.00 0.00 3.02
2271 2447 0.869454 CAGATCCTTCAGTCGAGCGC 60.869 60.000 0.00 0.00 0.00 5.92
2327 2506 3.694697 TCCCTAGGAGCCCTGCCA 61.695 66.667 11.48 0.00 34.61 4.92
2419 2598 4.785453 GCCTTCCACCTGCCGAGG 62.785 72.222 0.00 0.00 46.21 4.63
2563 2742 2.083774 AGTGTGTGTGTGTGTTCAAGG 58.916 47.619 0.00 0.00 0.00 3.61
2601 2780 5.832060 TCCTCTAACTGTACATTAGGGTAGC 59.168 44.000 16.84 0.00 29.40 3.58
2609 2788 3.180891 ACATTAGGGTAGCGAAGAAGC 57.819 47.619 0.00 0.00 37.41 3.86
2627 2806 2.572290 AGCCCAATAACACTAATCGGC 58.428 47.619 0.00 0.00 35.32 5.54
2693 2874 2.936912 GCCTGCTCCGAGTCAGTGT 61.937 63.158 14.72 0.00 0.00 3.55
2783 2965 0.392193 AAACAGCTCAGATCCTGCGG 60.392 55.000 0.00 0.00 32.37 5.69
2817 2999 1.821061 ATCATCATCGGCGGTCCCTC 61.821 60.000 7.21 0.00 0.00 4.30
2904 3090 2.147150 GTGAGCCTTTCCAGTTCAGTC 58.853 52.381 0.00 0.00 0.00 3.51
2921 3107 1.975680 AGTCGCCCTTCTTGGTTCTTA 59.024 47.619 0.00 0.00 0.00 2.10
2944 3131 3.482156 ACCACTTGCTGCATATCCTAG 57.518 47.619 1.84 0.00 0.00 3.02
2993 3180 2.483877 CACATACCACGAATGTGCTTGT 59.516 45.455 3.51 0.00 45.43 3.16
2994 3181 2.483877 ACATACCACGAATGTGCTTGTG 59.516 45.455 0.00 0.00 45.04 3.33
2995 3182 0.871722 TACCACGAATGTGCTTGTGC 59.128 50.000 0.00 0.00 45.04 4.57
2996 3183 0.819259 ACCACGAATGTGCTTGTGCT 60.819 50.000 0.00 0.00 45.04 4.40
2997 3184 0.311790 CCACGAATGTGCTTGTGCTT 59.688 50.000 0.00 0.00 45.04 3.91
2998 3185 1.664016 CCACGAATGTGCTTGTGCTTC 60.664 52.381 0.00 0.00 45.04 3.86
2999 3186 0.593128 ACGAATGTGCTTGTGCTTCC 59.407 50.000 0.00 0.00 40.48 3.46
3000 3187 0.453282 CGAATGTGCTTGTGCTTCCG 60.453 55.000 0.00 0.00 40.48 4.30
3012 3199 2.670934 CTTCCGCTTGCACCTGCT 60.671 61.111 0.00 0.00 42.66 4.24
3135 3327 4.010349 GGATTGTGAATTTCTTCCGGTCT 58.990 43.478 0.00 0.00 0.00 3.85
3136 3328 4.142600 GGATTGTGAATTTCTTCCGGTCTG 60.143 45.833 0.00 0.00 0.00 3.51
3137 3329 2.778299 TGTGAATTTCTTCCGGTCTGG 58.222 47.619 0.00 0.00 40.09 3.86
3138 3330 2.105821 TGTGAATTTCTTCCGGTCTGGT 59.894 45.455 0.00 0.00 39.52 4.00
3198 3460 2.380660 CACCGTGTTGATTCAAAACCG 58.619 47.619 12.99 9.62 28.42 4.44
3218 3480 1.849976 GCAGCAGCGATTCATAGCCC 61.850 60.000 0.00 0.00 0.00 5.19
3228 3490 3.178611 CATAGCCCTGGGTCCCCC 61.179 72.222 15.56 0.00 45.71 5.40
3324 3590 0.576328 CAATTGCGTTGTTGTGTGCC 59.424 50.000 0.00 0.00 33.01 5.01
3343 3609 1.378762 GGGGGAAGTGCTGTTGCTA 59.621 57.895 0.00 0.00 40.48 3.49
3352 3618 5.121454 GGAAGTGCTGTTGCTATATGCTATC 59.879 44.000 0.00 0.00 43.37 2.08
3353 3619 4.573900 AGTGCTGTTGCTATATGCTATCC 58.426 43.478 0.00 0.00 43.37 2.59
3354 3620 3.369147 GTGCTGTTGCTATATGCTATCCG 59.631 47.826 0.00 0.00 43.37 4.18
3355 3621 3.006859 TGCTGTTGCTATATGCTATCCGT 59.993 43.478 0.00 0.00 43.37 4.69
3356 3622 3.614616 GCTGTTGCTATATGCTATCCGTC 59.385 47.826 0.00 0.00 43.37 4.79
3357 3623 4.177026 CTGTTGCTATATGCTATCCGTCC 58.823 47.826 0.00 0.00 43.37 4.79
3358 3624 3.576550 TGTTGCTATATGCTATCCGTCCA 59.423 43.478 0.00 0.00 43.37 4.02
3359 3625 4.222810 TGTTGCTATATGCTATCCGTCCAT 59.777 41.667 0.00 0.00 43.37 3.41
3360 3626 5.178797 GTTGCTATATGCTATCCGTCCATT 58.821 41.667 0.00 0.00 43.37 3.16
3361 3627 5.420725 TGCTATATGCTATCCGTCCATTT 57.579 39.130 0.00 0.00 43.37 2.32
3362 3628 5.804639 TGCTATATGCTATCCGTCCATTTT 58.195 37.500 0.00 0.00 43.37 1.82
3363 3629 5.643348 TGCTATATGCTATCCGTCCATTTTG 59.357 40.000 0.00 0.00 43.37 2.44
3364 3630 5.643777 GCTATATGCTATCCGTCCATTTTGT 59.356 40.000 0.00 0.00 38.95 2.83
3365 3631 5.947228 ATATGCTATCCGTCCATTTTGTG 57.053 39.130 0.00 0.00 0.00 3.33
3366 3632 9.215771 GCTATATGCTATCCGTCCATTTTGTGG 62.216 44.444 0.00 0.00 43.39 4.17
3381 3647 7.067532 CATTTTGTGGATCATGACCATTTTG 57.932 36.000 16.70 9.25 39.69 2.44
3382 3648 5.804944 TTTGTGGATCATGACCATTTTGT 57.195 34.783 16.70 0.00 39.69 2.83
3383 3649 4.787260 TGTGGATCATGACCATTTTGTG 57.213 40.909 16.70 0.00 39.69 3.33
3417 3683 6.504398 CATTTTCTGGATCAGGACAATCATG 58.496 40.000 0.00 0.00 31.51 3.07
3418 3684 3.204306 TCTGGATCAGGACAATCATGC 57.796 47.619 0.00 0.00 31.51 4.06
3429 3695 1.344114 ACAATCATGCCACCAACCAAC 59.656 47.619 0.00 0.00 0.00 3.77
3430 3696 0.975887 AATCATGCCACCAACCAACC 59.024 50.000 0.00 0.00 0.00 3.77
3432 3698 0.397675 TCATGCCACCAACCAACCAA 60.398 50.000 0.00 0.00 0.00 3.67
3433 3699 0.686224 CATGCCACCAACCAACCAAT 59.314 50.000 0.00 0.00 0.00 3.16
3434 3700 0.686224 ATGCCACCAACCAACCAATG 59.314 50.000 0.00 0.00 0.00 2.82
3435 3701 0.397675 TGCCACCAACCAACCAATGA 60.398 50.000 0.00 0.00 0.00 2.57
3436 3702 0.975887 GCCACCAACCAACCAATGAT 59.024 50.000 0.00 0.00 0.00 2.45
3437 3703 1.347378 GCCACCAACCAACCAATGATT 59.653 47.619 0.00 0.00 0.00 2.57
3438 3704 2.612721 GCCACCAACCAACCAATGATTC 60.613 50.000 0.00 0.00 0.00 2.52
3439 3705 2.028203 CCACCAACCAACCAATGATTCC 60.028 50.000 0.00 0.00 0.00 3.01
3440 3706 1.892474 ACCAACCAACCAATGATTCCG 59.108 47.619 0.00 0.00 0.00 4.30
3441 3707 1.404047 CCAACCAACCAATGATTCCGC 60.404 52.381 0.00 0.00 0.00 5.54
3446 3712 1.094785 AACCAATGATTCCGCTTCCG 58.905 50.000 0.00 0.00 0.00 4.30
3494 3760 9.990360 TGCTTATATATTCCGTAATGTCAGAAA 57.010 29.630 0.00 0.00 0.00 2.52
3507 3773 6.983906 AATGTCAGAAATCCCCATTATTCC 57.016 37.500 0.00 0.00 0.00 3.01
3513 3779 4.524328 AGAAATCCCCATTATTCCGAATGC 59.476 41.667 3.73 0.00 35.79 3.56
3514 3780 2.286365 TCCCCATTATTCCGAATGCC 57.714 50.000 3.73 0.00 35.79 4.40
3522 3788 1.683943 ATTCCGAATGCCTCATGGTG 58.316 50.000 0.00 0.00 35.27 4.17
3523 3789 0.617935 TTCCGAATGCCTCATGGTGA 59.382 50.000 0.00 0.00 35.27 4.02
3524 3790 0.107703 TCCGAATGCCTCATGGTGAC 60.108 55.000 0.00 0.00 35.27 3.67
3535 3801 3.791640 TGGTGACATGGTCGCTCT 58.208 55.556 9.48 0.00 42.03 4.09
3536 3802 2.057830 TGGTGACATGGTCGCTCTT 58.942 52.632 9.48 0.00 42.03 2.85
3537 3803 1.262417 TGGTGACATGGTCGCTCTTA 58.738 50.000 9.48 0.00 42.03 2.10
3538 3804 1.831106 TGGTGACATGGTCGCTCTTAT 59.169 47.619 9.48 0.00 42.03 1.73
3539 3805 2.159099 TGGTGACATGGTCGCTCTTATC 60.159 50.000 9.48 0.00 42.03 1.75
3540 3806 2.101582 GGTGACATGGTCGCTCTTATCT 59.898 50.000 9.48 0.00 42.03 1.98
3541 3807 3.430929 GGTGACATGGTCGCTCTTATCTT 60.431 47.826 9.48 0.00 42.03 2.40
3542 3808 3.799420 GTGACATGGTCGCTCTTATCTTC 59.201 47.826 0.00 0.00 39.62 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.891056 TGTATATACGCTCGTGGAGTG 57.109 47.619 8.33 4.74 44.67 3.51
22 23 9.961265 CGACTGGTCTTTTGAGTAATGTATATA 57.039 33.333 0.00 0.00 0.00 0.86
23 24 8.475639 ACGACTGGTCTTTTGAGTAATGTATAT 58.524 33.333 0.00 0.00 0.00 0.86
36 38 3.203716 GGAGTGAAACGACTGGTCTTTT 58.796 45.455 5.16 5.16 45.86 2.27
64 66 2.704572 CCGCTTTCTTCTCTGTTGGAT 58.295 47.619 0.00 0.00 0.00 3.41
65 67 1.878102 GCCGCTTTCTTCTCTGTTGGA 60.878 52.381 0.00 0.00 0.00 3.53
129 136 2.663852 AAAACCGTCGCGTCCTGG 60.664 61.111 5.77 6.57 0.00 4.45
147 154 1.022982 GCGGGACTTTTCGGGGTAAG 61.023 60.000 0.00 0.00 0.00 2.34
155 162 0.664224 TTTTGACCGCGGGACTTTTC 59.336 50.000 31.76 17.27 0.00 2.29
164 171 4.050934 GCCCCCTTTTTGACCGCG 62.051 66.667 0.00 0.00 0.00 6.46
521 552 3.295273 CGGCTGGGATCGGATCGA 61.295 66.667 11.62 0.00 41.13 3.59
570 612 0.893727 ACTCCCGGTGTTTGATTGGC 60.894 55.000 0.00 0.00 0.00 4.52
594 636 0.545548 GGGAGAAGACAGGGTCTGGT 60.546 60.000 0.00 0.00 42.59 4.00
595 637 1.268283 GGGGAGAAGACAGGGTCTGG 61.268 65.000 0.00 0.00 42.59 3.86
596 638 1.268283 GGGGGAGAAGACAGGGTCTG 61.268 65.000 0.00 0.00 42.59 3.51
597 639 1.081277 GGGGGAGAAGACAGGGTCT 59.919 63.158 0.00 0.00 45.64 3.85
598 640 0.978667 GAGGGGGAGAAGACAGGGTC 60.979 65.000 0.00 0.00 0.00 4.46
808 877 4.021807 GCTGAGGGGTCTCTTATAACTAGC 60.022 50.000 0.00 0.00 40.58 3.42
888 972 2.123077 AGATCGGAGGGGAGCAGG 60.123 66.667 0.00 0.00 0.00 4.85
934 1040 3.267860 CGGATCTTGCTGCTCCGC 61.268 66.667 13.91 0.00 45.57 5.54
954 1063 1.090052 CGTCCCGCTCCTCAATTTCC 61.090 60.000 0.00 0.00 0.00 3.13
1224 1357 4.098722 AGCAGCAGGAGGAGCAGC 62.099 66.667 0.00 0.00 43.76 5.25
1764 1915 2.721945 CTCCCCTACGTAGGAGCTG 58.278 63.158 37.76 22.63 46.63 4.24
1773 1924 0.736325 CGCACTTGAACTCCCCTACG 60.736 60.000 0.00 0.00 0.00 3.51
1876 2027 4.265073 ACAGTTGCTGAGATATGGAAACC 58.735 43.478 2.91 0.00 35.18 3.27
1920 2071 2.224670 TGCTACTGGTAAGGTTGTTGGG 60.225 50.000 0.00 0.00 0.00 4.12
1934 2085 7.559590 AAGGCTTGAATTATTACTGCTACTG 57.440 36.000 0.00 0.00 0.00 2.74
1936 2087 8.433421 TGTAAGGCTTGAATTATTACTGCTAC 57.567 34.615 10.69 0.00 0.00 3.58
2030 2206 7.621428 TTTCTGAAACAAATTGCAATGGAAA 57.379 28.000 13.82 10.22 0.00 3.13
2033 2209 6.375377 CCATTTCTGAAACAAATTGCAATGG 58.625 36.000 13.82 11.09 33.98 3.16
2034 2210 5.854338 GCCATTTCTGAAACAAATTGCAATG 59.146 36.000 13.82 5.51 33.90 2.82
2035 2211 5.334260 CGCCATTTCTGAAACAAATTGCAAT 60.334 36.000 5.99 5.99 33.51 3.56
2067 2243 2.125269 CCAAAGTACTCCCCGGCG 60.125 66.667 0.00 0.00 0.00 6.46
2184 2360 1.491563 CTTGTCGCCGTTCCGAAAG 59.508 57.895 0.00 0.00 39.17 2.62
2271 2447 2.554272 GTTTGTACCTGCACGGCG 59.446 61.111 4.80 4.80 35.61 6.46
2419 2598 4.357947 TGCACCTGCTCGTCGACC 62.358 66.667 10.58 0.00 42.66 4.79
2545 2724 2.481289 TCCTTGAACACACACACACA 57.519 45.000 0.00 0.00 0.00 3.72
2546 2725 3.057876 TGTTTCCTTGAACACACACACAC 60.058 43.478 0.00 0.00 34.77 3.82
2547 2726 3.149981 TGTTTCCTTGAACACACACACA 58.850 40.909 0.00 0.00 34.77 3.72
2548 2727 3.840890 TGTTTCCTTGAACACACACAC 57.159 42.857 0.00 0.00 34.77 3.82
2549 2728 3.428725 GCATGTTTCCTTGAACACACACA 60.429 43.478 0.00 0.00 41.86 3.72
2563 2742 2.222227 AGAGGAAAGGGGCATGTTTC 57.778 50.000 0.00 0.00 32.79 2.78
2601 2780 5.276868 CGATTAGTGTTATTGGGCTTCTTCG 60.277 44.000 0.00 0.00 0.00 3.79
2609 2788 2.800544 CTCGCCGATTAGTGTTATTGGG 59.199 50.000 0.00 0.00 0.00 4.12
2627 2806 2.426183 CGCCGTCGTCTGAAACTCG 61.426 63.158 0.00 0.00 0.00 4.18
2677 2858 0.109365 CTCACACTGACTCGGAGCAG 60.109 60.000 20.48 20.48 38.10 4.24
2693 2874 3.195182 CCTTGTTGCTGATCTCTCTCTCA 59.805 47.826 0.00 0.00 0.00 3.27
2728 2910 3.898509 CAGCTCCGCTCCTCCTCG 61.899 72.222 0.00 0.00 36.40 4.63
2729 2911 2.441164 TCAGCTCCGCTCCTCCTC 60.441 66.667 0.00 0.00 36.40 3.71
2730 2912 2.757917 GTCAGCTCCGCTCCTCCT 60.758 66.667 0.00 0.00 36.40 3.69
2731 2913 2.570582 CTTGTCAGCTCCGCTCCTCC 62.571 65.000 0.00 0.00 36.40 4.30
2804 2986 4.798682 AAGGGAGGGACCGCCGAT 62.799 66.667 5.01 0.00 40.11 4.18
2904 3090 3.626217 GGTAATAAGAACCAAGAAGGGCG 59.374 47.826 0.00 0.00 43.89 6.13
2921 3107 4.443978 AGGATATGCAGCAAGTGGTAAT 57.556 40.909 0.00 0.00 0.00 1.89
2944 3131 1.242076 ATGCACACAGAGAACTTGCC 58.758 50.000 0.00 0.00 31.94 4.52
2995 3182 2.670934 AGCAGGTGCAAGCGGAAG 60.671 61.111 4.48 0.00 45.16 3.46
2996 3183 2.979676 CAGCAGGTGCAAGCGGAA 60.980 61.111 4.48 0.00 45.16 4.30
3012 3199 2.568062 AGATTGGTGCCATGAAAATGCA 59.432 40.909 0.00 0.00 0.00 3.96
3058 3245 2.774799 GGGAATCACCGCACATGGC 61.775 63.158 0.00 0.00 40.11 4.40
3137 3329 0.551396 ATAGGCAGCAAAGGGGGTAC 59.449 55.000 0.00 0.00 0.00 3.34
3138 3330 0.843984 GATAGGCAGCAAAGGGGGTA 59.156 55.000 0.00 0.00 0.00 3.69
3198 3460 1.573436 GCTATGAATCGCTGCTGCC 59.427 57.895 10.24 0.00 35.36 4.85
3228 3490 1.325476 GGAAAATCTGGGGGCAGCAG 61.325 60.000 0.00 0.00 0.00 4.24
3233 3495 1.685765 GGTGGGAAAATCTGGGGGC 60.686 63.158 0.00 0.00 0.00 5.80
3234 3496 0.324645 CTGGTGGGAAAATCTGGGGG 60.325 60.000 0.00 0.00 0.00 5.40
3316 3582 3.494254 ACTTCCCCCGGCACACAA 61.494 61.111 0.00 0.00 0.00 3.33
3324 3590 2.463589 TAGCAACAGCACTTCCCCCG 62.464 60.000 0.00 0.00 0.00 5.73
3343 3609 5.947228 CACAAAATGGACGGATAGCATAT 57.053 39.130 0.00 0.00 0.00 1.78
3357 3623 6.651643 ACAAAATGGTCATGATCCACAAAATG 59.348 34.615 16.20 13.35 37.81 2.32
3358 3624 6.651643 CACAAAATGGTCATGATCCACAAAAT 59.348 34.615 16.20 1.74 37.81 1.82
3359 3625 5.990386 CACAAAATGGTCATGATCCACAAAA 59.010 36.000 16.20 0.00 37.81 2.44
3360 3626 5.511031 CCACAAAATGGTCATGATCCACAAA 60.511 40.000 16.20 0.00 44.46 2.83
3361 3627 4.021280 CCACAAAATGGTCATGATCCACAA 60.021 41.667 16.20 0.00 44.46 3.33
3362 3628 3.510753 CCACAAAATGGTCATGATCCACA 59.489 43.478 16.20 6.92 44.46 4.17
3363 3629 4.114058 CCACAAAATGGTCATGATCCAC 57.886 45.455 16.20 0.00 44.46 4.02
3399 3665 2.228059 GGCATGATTGTCCTGATCCAG 58.772 52.381 0.00 0.00 0.00 3.86
3417 3683 0.975887 ATCATTGGTTGGTTGGTGGC 59.024 50.000 0.00 0.00 0.00 5.01
3418 3684 2.028203 GGAATCATTGGTTGGTTGGTGG 60.028 50.000 0.00 0.00 0.00 4.61
3440 3706 8.484478 TGCAACATATATAATGCAGCGGAAGC 62.484 42.308 16.52 0.00 46.86 3.86
3441 3707 5.106594 TGCAACATATATAATGCAGCGGAAG 60.107 40.000 16.52 0.00 43.32 3.46
3477 3743 4.080015 TGGGGATTTCTGACATTACGGAAT 60.080 41.667 0.00 0.00 35.50 3.01
3478 3744 3.264706 TGGGGATTTCTGACATTACGGAA 59.735 43.478 0.00 0.00 33.98 4.30
3479 3745 2.841266 TGGGGATTTCTGACATTACGGA 59.159 45.455 0.00 0.00 0.00 4.69
3480 3746 3.275617 TGGGGATTTCTGACATTACGG 57.724 47.619 0.00 0.00 0.00 4.02
3481 3747 7.308589 GGAATAATGGGGATTTCTGACATTACG 60.309 40.741 0.00 0.00 36.99 3.18
3482 3748 7.308589 CGGAATAATGGGGATTTCTGACATTAC 60.309 40.741 0.00 0.00 36.99 1.89
3494 3760 2.379907 AGGCATTCGGAATAATGGGGAT 59.620 45.455 2.35 0.00 37.34 3.85
3507 3773 1.671979 ATGTCACCATGAGGCATTCG 58.328 50.000 0.00 0.00 39.06 3.34


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

AutoCloner maintained by Alex Coulton.