Multiple sequence alignment - TraesCS5B01G475700

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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 TraesCS5B01G475700 chr5B 100.000 3016 0 0 1 3016 648291327 648288312 0.000000e+00 5570
1 TraesCS5B01G475700 chr5B 94.284 1487 82 3 1215 2700 648358771 648360255 0.000000e+00 2272
2 TraesCS5B01G475700 chr5B 92.179 959 30 14 1 934 648742730 648741792 0.000000e+00 1314
3 TraesCS5B01G475700 chr5B 85.401 1096 80 32 184 1220 648357664 648358738 0.000000e+00 1064
4 TraesCS5B01G475700 chr5B 100.000 546 0 0 3317 3862 648288011 648287466 0.000000e+00 1009
5 TraesCS5B01G475700 chr5B 82.134 403 63 9 1394 1790 417805214 417805613 1.720000e-88 337
6 TraesCS5B01G475700 chr5B 93.684 190 10 1 1 188 648357240 648357429 2.270000e-72 283
7 TraesCS5B01G475700 chr5D 92.377 2453 134 22 578 2999 515676358 515673928 0.000000e+00 3445
8 TraesCS5B01G475700 chr5D 82.482 411 61 11 1387 1790 353655444 353655850 2.210000e-92 350
9 TraesCS5B01G475700 chr5D 79.710 207 33 8 454 653 535646325 535646529 1.450000e-29 141
10 TraesCS5B01G475700 chr5A 91.329 2445 149 24 578 2985 643926900 643924482 0.000000e+00 3282
11 TraesCS5B01G475700 chr5A 90.127 395 30 3 3476 3862 643922837 643922444 4.450000e-139 505
12 TraesCS5B01G475700 chr5A 81.707 410 66 9 1387 1790 454704880 454705286 2.220000e-87 333
13 TraesCS5B01G475700 chr5A 90.411 146 12 2 3331 3475 643924406 643924262 1.420000e-44 191
14 TraesCS5B01G475700 chr7B 81.266 395 70 4 1420 1812 522142132 522142524 2.240000e-82 316
15 TraesCS5B01G475700 chr7D 80.928 388 72 2 1420 1806 493203743 493204129 4.850000e-79 305
16 TraesCS5B01G475700 chr7A 80.928 388 72 2 1420 1806 559361843 559362229 4.850000e-79 305
17 TraesCS5B01G475700 chr1D 75.369 406 79 17 3476 3862 484252021 484251618 3.970000e-40 176
18 TraesCS5B01G475700 chr1A 75.062 401 84 15 3476 3862 581434239 581433841 5.130000e-39 172
19 TraesCS5B01G475700 chr1A 73.966 411 80 21 3472 3862 581206709 581206306 1.450000e-29 141
20 TraesCS5B01G475700 chr1A 74.708 257 59 6 3610 3862 581110830 581110576 4.080000e-20 110
21 TraesCS5B01G475700 chr1B 74.378 402 86 15 3476 3862 674495526 674495127 5.170000e-34 156


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 TraesCS5B01G475700 chr5B 648287466 648291327 3861 True 3289.500000 5570 100.000000 1 3862 2 chr5B.!!$R2 3861
1 TraesCS5B01G475700 chr5B 648741792 648742730 938 True 1314.000000 1314 92.179000 1 934 1 chr5B.!!$R1 933
2 TraesCS5B01G475700 chr5B 648357240 648360255 3015 False 1206.333333 2272 91.123000 1 2700 3 chr5B.!!$F2 2699
3 TraesCS5B01G475700 chr5D 515673928 515676358 2430 True 3445.000000 3445 92.377000 578 2999 1 chr5D.!!$R1 2421
4 TraesCS5B01G475700 chr5A 643922444 643926900 4456 True 1326.000000 3282 90.622333 578 3862 3 chr5A.!!$R1 3284

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
125 128 0.391130 TCCGTTCTGTAGGTGCATGC 60.391 55.0 11.82 11.82 0.0 4.06 F
1319 1661 0.038166 TCATGCAAGGGAAGGTGGAC 59.962 55.0 0.00 0.00 0.0 4.02 F
1415 1757 0.179000 CGGGGCAGCTCTACAATCTT 59.821 55.0 0.00 0.00 0.0 2.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2018 2360 0.040692 TGAACGTGACGGTCTTCTCG 60.041 55.0 24.28 10.85 44.6 4.04 R
2257 2602 0.318699 TCAGCTTCCAGTCGAACACG 60.319 55.0 0.00 0.00 0.0 4.49 R
3325 3682 0.036952 CGAGGTCTTGTGGTGCTGAT 60.037 55.0 0.00 0.00 0.0 2.90 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
125 128 0.391130 TCCGTTCTGTAGGTGCATGC 60.391 55.000 11.82 11.82 0.00 4.06
129 132 2.094675 GTTCTGTAGGTGCATGCCATT 58.905 47.619 16.68 2.52 0.00 3.16
268 509 3.068560 CCGTCGGTTCAGATTTTTACCA 58.931 45.455 2.08 0.00 0.00 3.25
523 779 1.749258 GCCCGATGGGTTTGTCTCC 60.749 63.158 3.40 0.00 46.51 3.71
577 833 5.258051 TGGGCTGAAACCGTATAAAAAGAT 58.742 37.500 0.00 0.00 0.00 2.40
855 1157 4.571176 GGAGAGTAATTAAACGGCTCCTTG 59.429 45.833 12.41 0.00 40.10 3.61
963 1266 3.706594 CACCTACTAATCTCCAAGCTCCA 59.293 47.826 0.00 0.00 0.00 3.86
994 1297 0.807667 AATACAAGCGAGCTCAGGCG 60.808 55.000 15.40 0.63 44.37 5.52
1051 1355 5.190528 AGTCCAGATTTCATAGGAAGCAGAA 59.809 40.000 0.00 0.00 33.82 3.02
1087 1391 2.774234 ACAGACTGTAGCTATGGCCAAT 59.226 45.455 10.96 0.36 39.73 3.16
1262 1604 1.931635 TGATTGGCCAGGGGTTTAAC 58.068 50.000 5.11 0.00 0.00 2.01
1289 1631 1.675641 ATGGAAGACACAAGGCGGC 60.676 57.895 0.00 0.00 0.00 6.53
1319 1661 0.038166 TCATGCAAGGGAAGGTGGAC 59.962 55.000 0.00 0.00 0.00 4.02
1412 1754 2.911143 CCGGGGCAGCTCTACAAT 59.089 61.111 0.00 0.00 0.00 2.71
1415 1757 0.179000 CGGGGCAGCTCTACAATCTT 59.821 55.000 0.00 0.00 0.00 2.40
1484 1826 0.321346 TCCGCAGCAAGAACATCTCA 59.679 50.000 0.00 0.00 0.00 3.27
1535 1877 2.342648 GCCGACAAGAAGGACGGT 59.657 61.111 0.00 0.00 45.91 4.83
1541 1883 3.300765 AAGAAGGACGGTCGCGGT 61.301 61.111 6.13 0.00 0.00 5.68
1814 2156 1.747206 GCCATGGCCAAGATCTACGTT 60.747 52.381 27.24 0.00 34.56 3.99
1981 2323 3.203086 TTGGGAGGATGCGTGGCAA 62.203 57.895 0.00 0.00 43.62 4.52
2006 2348 1.450312 CAAGGCACCCGGTCTGATC 60.450 63.158 0.00 0.00 0.00 2.92
2018 2360 2.111878 CTGATCGGGTGGATGCCC 59.888 66.667 0.00 0.00 45.21 5.36
2054 2396 0.319211 TCATCGACAACCACGACACC 60.319 55.000 0.00 0.00 42.37 4.16
2176 2521 5.335583 GCACACTGCATAACTTCACCATAAA 60.336 40.000 0.00 0.00 44.26 1.40
2217 2562 5.066375 CACACCGGATGTTTGTGATATGAAT 59.934 40.000 15.17 0.00 42.77 2.57
2222 2567 5.903530 CGGATGTTTGTGATATGAATTCACG 59.096 40.000 11.07 0.57 45.14 4.35
2240 2585 1.080772 GGCTACTTGGTTTTGCGCC 60.081 57.895 4.18 0.00 0.00 6.53
2257 2602 1.445582 CCCGCAGTTCTACGACCAC 60.446 63.158 0.00 0.00 0.00 4.16
2695 3049 7.095187 ACTGATATTTCAAACCTTGACGACTTC 60.095 37.037 0.00 0.00 39.87 3.01
2744 3098 7.558161 TGCATCCTATGTATTTTGTCTTCAG 57.442 36.000 0.00 0.00 0.00 3.02
2754 3108 3.502191 TTTGTCTTCAGTTTGTGTGCC 57.498 42.857 0.00 0.00 0.00 5.01
2764 3118 0.827089 TTTGTGTGCCTGGGACCATG 60.827 55.000 16.15 0.00 0.00 3.66
2765 3119 3.064324 GTGTGCCTGGGACCATGC 61.064 66.667 16.15 11.11 37.93 4.06
2794 3148 1.464608 CGGTTGTGTGCATCCTAACTG 59.535 52.381 0.00 0.00 33.40 3.16
2820 3174 4.133078 GGAGGCTTGATAGGAACTCATTG 58.867 47.826 0.00 0.00 41.75 2.82
2821 3175 4.384647 GGAGGCTTGATAGGAACTCATTGT 60.385 45.833 0.00 0.00 41.75 2.71
2822 3176 4.521146 AGGCTTGATAGGAACTCATTGTG 58.479 43.478 0.00 0.00 41.75 3.33
2823 3177 4.225942 AGGCTTGATAGGAACTCATTGTGA 59.774 41.667 0.00 0.00 41.75 3.58
2824 3178 5.104193 AGGCTTGATAGGAACTCATTGTGAT 60.104 40.000 0.00 0.00 41.75 3.06
2825 3179 5.591877 GGCTTGATAGGAACTCATTGTGATT 59.408 40.000 0.00 0.00 41.75 2.57
2826 3180 6.096001 GGCTTGATAGGAACTCATTGTGATTT 59.904 38.462 0.00 0.00 41.75 2.17
2827 3181 6.971184 GCTTGATAGGAACTCATTGTGATTTG 59.029 38.462 0.00 0.00 41.75 2.32
2828 3182 7.362401 GCTTGATAGGAACTCATTGTGATTTGT 60.362 37.037 0.00 0.00 41.75 2.83
2829 3183 9.166173 CTTGATAGGAACTCATTGTGATTTGTA 57.834 33.333 0.00 0.00 41.75 2.41
2830 3184 9.685276 TTGATAGGAACTCATTGTGATTTGTAT 57.315 29.630 0.00 0.00 41.75 2.29
2831 3185 9.330063 TGATAGGAACTCATTGTGATTTGTATC 57.670 33.333 0.00 0.00 41.75 2.24
2832 3186 8.682936 ATAGGAACTCATTGTGATTTGTATCC 57.317 34.615 0.00 0.00 41.75 2.59
2833 3187 5.888161 AGGAACTCATTGTGATTTGTATCCC 59.112 40.000 0.00 0.00 0.00 3.85
2834 3188 5.067805 GGAACTCATTGTGATTTGTATCCCC 59.932 44.000 0.00 0.00 0.00 4.81
2946 3301 1.609555 CTTATTAGCGCTCCTCTCCGT 59.390 52.381 16.34 0.00 0.00 4.69
2952 3307 2.636412 CGCTCCTCTCCGTTGACCA 61.636 63.158 0.00 0.00 0.00 4.02
2971 3326 3.843027 ACCACTCATCCAACATCTTCTCT 59.157 43.478 0.00 0.00 0.00 3.10
2985 3342 5.608437 ACATCTTCTCTTAATCCCCTATGCA 59.392 40.000 0.00 0.00 0.00 3.96
2986 3343 6.274200 ACATCTTCTCTTAATCCCCTATGCAT 59.726 38.462 3.79 3.79 0.00 3.96
3001 3358 1.134075 GCATGTGCAGCTCTTCACG 59.866 57.895 0.00 0.00 41.59 4.35
3005 3362 0.958822 TGTGCAGCTCTTCACGTCTA 59.041 50.000 0.00 0.00 36.06 2.59
3006 3363 1.068264 TGTGCAGCTCTTCACGTCTAG 60.068 52.381 0.00 0.00 36.06 2.43
3010 3367 1.067565 CAGCTCTTCACGTCTAGCCAA 60.068 52.381 4.78 0.00 35.54 4.52
3011 3368 1.618837 AGCTCTTCACGTCTAGCCAAA 59.381 47.619 4.78 0.00 35.54 3.28
3012 3369 1.727335 GCTCTTCACGTCTAGCCAAAC 59.273 52.381 0.00 0.00 0.00 2.93
3014 3371 3.390135 CTCTTCACGTCTAGCCAAACAA 58.610 45.455 0.00 0.00 0.00 2.83
3338 3695 0.037975 GCCCAAATCAGCACCACAAG 60.038 55.000 0.00 0.00 0.00 3.16
3340 3697 1.270550 CCCAAATCAGCACCACAAGAC 59.729 52.381 0.00 0.00 0.00 3.01
3341 3698 1.270550 CCAAATCAGCACCACAAGACC 59.729 52.381 0.00 0.00 0.00 3.85
3348 3705 1.374758 CACCACAAGACCTCGAGCC 60.375 63.158 6.99 0.45 0.00 4.70
3417 3774 2.350458 GCCAACGGGGTGCATGATT 61.350 57.895 0.00 0.00 39.65 2.57
3455 3813 2.417652 TGCTCACATATACCCCCACAT 58.582 47.619 0.00 0.00 0.00 3.21
3468 3826 5.966853 ACCCCCACATAAATTATTTTGGG 57.033 39.130 15.51 15.51 35.40 4.12
3469 3827 5.604752 ACCCCCACATAAATTATTTTGGGA 58.395 37.500 21.33 0.00 37.53 4.37
3470 3828 5.427157 ACCCCCACATAAATTATTTTGGGAC 59.573 40.000 21.33 0.00 37.53 4.46
3471 3829 5.452636 CCCCCACATAAATTATTTTGGGACG 60.453 44.000 21.33 10.95 37.53 4.79
3472 3830 5.128008 CCCCACATAAATTATTTTGGGACGT 59.872 40.000 21.33 0.00 37.53 4.34
3473 3831 6.039616 CCCACATAAATTATTTTGGGACGTG 58.960 40.000 16.88 6.32 37.53 4.49
3474 3832 6.350612 CCCACATAAATTATTTTGGGACGTGT 60.351 38.462 16.88 1.42 37.53 4.49
3488 5269 3.681417 GGGACGTGTTGGATTAACTGTAC 59.319 47.826 0.00 0.00 40.05 2.90
3493 5274 4.916831 CGTGTTGGATTAACTGTACGTGTA 59.083 41.667 0.00 0.00 40.05 2.90
3535 5316 7.565190 ACTACATCTGGTCCATTATGATCAT 57.435 36.000 13.81 13.81 0.00 2.45
3538 5319 9.376075 CTACATCTGGTCCATTATGATCATAAC 57.624 37.037 26.51 16.22 36.24 1.89
3591 5372 9.612620 GTGATCTGTACCTCAAAAACATTAAAG 57.387 33.333 0.00 0.00 0.00 1.85
3634 5423 6.583806 GCATATTGCAAGCAAGATATACAACC 59.416 38.462 13.78 0.00 44.26 3.77
3642 5431 6.506538 AGCAAGATATACAACCATCTCCTT 57.493 37.500 0.00 0.00 31.10 3.36
3649 5438 2.065799 ACAACCATCTCCTTCCACCTT 58.934 47.619 0.00 0.00 0.00 3.50
3656 5445 4.156008 CCATCTCCTTCCACCTTTTTAACG 59.844 45.833 0.00 0.00 0.00 3.18
3662 5451 7.886446 TCTCCTTCCACCTTTTTAACGAAATAT 59.114 33.333 0.00 0.00 0.00 1.28
3691 5480 7.865385 TGTCCAACAACATTTATTGAAAGTAGC 59.135 33.333 0.00 0.00 33.57 3.58
3697 5486 4.457603 ACATTTATTGAAAGTAGCGGCACA 59.542 37.500 1.45 0.00 0.00 4.57
3730 5519 4.455533 TGAAGCAACAAAGCGATGTAGAAT 59.544 37.500 0.00 0.00 40.15 2.40
3762 5551 9.847224 TTTATTTTCCCTAGCTTATTACTCAGG 57.153 33.333 0.00 0.00 0.00 3.86
3811 5600 3.872459 ATGGAGGATGAGGTTCCATTC 57.128 47.619 0.00 0.00 46.81 2.67
3820 5609 0.327924 AGGTTCCATTCGCCATCACA 59.672 50.000 0.00 0.00 0.00 3.58
3821 5610 1.064463 AGGTTCCATTCGCCATCACAT 60.064 47.619 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 7.591426 AGAAGTTAGCAAACGCAAAGATTAAAG 59.409 33.333 0.00 0.00 40.73 1.85
50 53 6.703165 CGATGACATCTCCAAGAATTCACATA 59.297 38.462 13.45 0.00 0.00 2.29
125 128 2.037511 GGCTCAGAGAGGAGATCAATGG 59.962 54.545 0.00 0.00 37.05 3.16
129 132 2.539432 TTGGCTCAGAGAGGAGATCA 57.461 50.000 0.00 0.00 37.05 2.92
268 509 0.818040 GGTGAACCGGCAGTCAAACT 60.818 55.000 0.00 0.00 0.00 2.66
408 663 2.866750 CGCGGCAGCAACAACATA 59.133 55.556 10.08 0.00 45.49 2.29
409 664 4.705519 GCGCGGCAGCAACAACAT 62.706 61.111 8.83 0.00 45.49 2.71
523 779 3.217599 TCTCTCTCGATTTTGTCCACG 57.782 47.619 0.00 0.00 0.00 4.94
547 803 1.353022 ACGGTTTCAGCCCATTAGGAA 59.647 47.619 0.00 0.00 38.24 3.36
855 1157 4.036144 GCTGGCTTCTGAGATAAAATGGAC 59.964 45.833 0.00 0.00 0.00 4.02
963 1266 7.498443 AGCTCGCTTGTATTTATAGGTACTTT 58.502 34.615 0.00 0.00 41.75 2.66
994 1297 1.809567 CTGCTCCTTGGGTTGGCAAC 61.810 60.000 21.92 21.92 32.43 4.17
1004 1308 1.444553 GACCGACGACTGCTCCTTG 60.445 63.158 0.00 0.00 0.00 3.61
1051 1355 4.614112 TGTGCAGTGCAGCTCGCT 62.614 61.111 20.42 2.28 40.08 4.93
1067 1371 2.988010 TTGGCCATAGCTACAGTCTG 57.012 50.000 6.09 0.00 39.73 3.51
1087 1391 0.964700 CACAGAGAGTGGCAGAGTGA 59.035 55.000 0.00 0.00 44.69 3.41
1262 1604 3.354948 TGTGTCTTCCATGATTCCCAG 57.645 47.619 0.00 0.00 0.00 4.45
1289 1631 2.489329 CCCTTGCATGAACTTGTACCAG 59.511 50.000 0.00 0.00 0.00 4.00
1412 1754 2.353406 GCTGCCGTACTTGGAGTTAAGA 60.353 50.000 0.00 0.00 0.00 2.10
1415 1757 0.108992 CGCTGCCGTACTTGGAGTTA 60.109 55.000 0.00 0.00 0.00 2.24
1535 1877 1.138883 GATGCAGTAGACACCGCGA 59.861 57.895 8.23 0.00 30.15 5.87
1541 1883 1.751351 CCCTCGAAGATGCAGTAGACA 59.249 52.381 0.00 0.00 33.89 3.41
1757 2099 2.954684 AAAGTCGAGGCGCCATCCA 61.955 57.895 31.54 9.23 0.00 3.41
1814 2156 2.243957 CGACGGCTTGCTGTTGTCA 61.244 57.895 8.57 0.00 0.00 3.58
1964 2306 3.645660 TTGCCACGCATCCTCCCA 61.646 61.111 0.00 0.00 38.76 4.37
2018 2360 0.040692 TGAACGTGACGGTCTTCTCG 60.041 55.000 24.28 10.85 44.60 4.04
2072 2414 3.003173 TCTGAGGGGAACGGCCAG 61.003 66.667 2.24 0.00 38.95 4.85
2078 2420 1.056660 TGACCTTGTCTGAGGGGAAC 58.943 55.000 0.00 0.00 41.31 3.62
2176 2521 4.370917 GGTGTGCAGTTTGATGTGAAATT 58.629 39.130 0.00 0.00 0.00 1.82
2217 2562 1.335496 GCAAAACCAAGTAGCCGTGAA 59.665 47.619 0.00 0.00 0.00 3.18
2222 2567 1.080772 GGCGCAAAACCAAGTAGCC 60.081 57.895 10.83 0.00 36.08 3.93
2257 2602 0.318699 TCAGCTTCCAGTCGAACACG 60.319 55.000 0.00 0.00 0.00 4.49
2638 2984 7.255590 CCACATTTCTTCAGGAATAACACAACT 60.256 37.037 0.00 0.00 33.53 3.16
2695 3049 7.531280 TGACAAATACAAAACAAACACATGG 57.469 32.000 0.00 0.00 0.00 3.66
2744 3098 0.827507 ATGGTCCCAGGCACACAAAC 60.828 55.000 0.00 0.00 0.00 2.93
2754 3108 1.378882 CCATCAACGCATGGTCCCAG 61.379 60.000 0.00 0.00 38.92 4.45
2764 3118 2.126888 CACAACCGCCATCAACGC 60.127 61.111 0.00 0.00 0.00 4.84
2765 3119 1.082169 CACACAACCGCCATCAACG 60.082 57.895 0.00 0.00 0.00 4.10
2794 3148 2.237392 AGTTCCTATCAAGCCTCCACAC 59.763 50.000 0.00 0.00 0.00 3.82
2820 3174 6.152661 TGACAAATCAAGGGGATACAAATCAC 59.847 38.462 0.00 0.00 34.28 3.06
2821 3175 6.252233 TGACAAATCAAGGGGATACAAATCA 58.748 36.000 0.00 0.00 34.28 2.57
2822 3176 6.773976 TGACAAATCAAGGGGATACAAATC 57.226 37.500 0.00 0.00 34.28 2.17
2823 3177 7.738437 AATGACAAATCAAGGGGATACAAAT 57.262 32.000 0.00 0.00 38.69 2.32
2824 3178 8.694540 CATAATGACAAATCAAGGGGATACAAA 58.305 33.333 0.00 0.00 38.69 2.83
2825 3179 7.287466 CCATAATGACAAATCAAGGGGATACAA 59.713 37.037 0.00 0.00 38.69 2.41
2826 3180 6.777091 CCATAATGACAAATCAAGGGGATACA 59.223 38.462 0.00 0.00 38.69 2.29
2827 3181 6.209391 CCCATAATGACAAATCAAGGGGATAC 59.791 42.308 0.00 0.00 38.69 2.24
2828 3182 6.125919 ACCCATAATGACAAATCAAGGGGATA 60.126 38.462 5.87 0.00 39.35 2.59
2829 3183 5.149976 CCCATAATGACAAATCAAGGGGAT 58.850 41.667 0.00 0.00 38.69 3.85
2830 3184 4.016666 ACCCATAATGACAAATCAAGGGGA 60.017 41.667 5.87 0.00 39.35 4.81
2831 3185 4.289245 ACCCATAATGACAAATCAAGGGG 58.711 43.478 0.00 0.00 39.35 4.79
2832 3186 4.955450 TGACCCATAATGACAAATCAAGGG 59.045 41.667 0.00 0.00 40.17 3.95
2833 3187 6.528537 TTGACCCATAATGACAAATCAAGG 57.471 37.500 0.00 0.00 38.69 3.61
2884 3239 3.868757 TCGATCTCATTCTTCGGTTGT 57.131 42.857 0.00 0.00 33.82 3.32
2892 3247 1.543802 GGAGCCGATCGATCTCATTCT 59.456 52.381 26.79 11.54 0.00 2.40
2946 3301 4.042062 AGAAGATGTTGGATGAGTGGTCAA 59.958 41.667 0.00 0.00 35.88 3.18
2952 3307 7.278875 GGATTAAGAGAAGATGTTGGATGAGT 58.721 38.462 0.00 0.00 0.00 3.41
2985 3342 0.319728 AGACGTGAAGAGCTGCACAT 59.680 50.000 9.18 0.00 34.78 3.21
2986 3343 0.958822 TAGACGTGAAGAGCTGCACA 59.041 50.000 9.18 0.00 34.78 4.57
2993 3350 3.026630 TGTTTGGCTAGACGTGAAGAG 57.973 47.619 0.00 0.00 0.00 2.85
3316 3673 0.609662 GTGGTGCTGATTTGGGCAAT 59.390 50.000 0.00 0.00 40.26 3.56
3317 3674 0.758310 TGTGGTGCTGATTTGGGCAA 60.758 50.000 0.00 0.00 40.26 4.52
3318 3675 0.758310 TTGTGGTGCTGATTTGGGCA 60.758 50.000 0.00 0.00 36.01 5.36
3319 3676 0.037975 CTTGTGGTGCTGATTTGGGC 60.038 55.000 0.00 0.00 0.00 5.36
3320 3677 1.270550 GTCTTGTGGTGCTGATTTGGG 59.729 52.381 0.00 0.00 0.00 4.12
3321 3678 1.270550 GGTCTTGTGGTGCTGATTTGG 59.729 52.381 0.00 0.00 0.00 3.28
3322 3679 2.227388 GAGGTCTTGTGGTGCTGATTTG 59.773 50.000 0.00 0.00 0.00 2.32
3323 3680 2.508526 GAGGTCTTGTGGTGCTGATTT 58.491 47.619 0.00 0.00 0.00 2.17
3324 3681 1.609061 CGAGGTCTTGTGGTGCTGATT 60.609 52.381 0.00 0.00 0.00 2.57
3325 3682 0.036952 CGAGGTCTTGTGGTGCTGAT 60.037 55.000 0.00 0.00 0.00 2.90
3326 3683 1.112916 TCGAGGTCTTGTGGTGCTGA 61.113 55.000 0.00 0.00 0.00 4.26
3329 3686 2.029844 GCTCGAGGTCTTGTGGTGC 61.030 63.158 15.58 0.00 0.00 5.01
3338 3695 2.266055 CCTTGTGGGCTCGAGGTC 59.734 66.667 15.58 0.00 35.01 3.85
3348 3705 3.317711 TGTTATGTTTGTCTGCCTTGTGG 59.682 43.478 0.00 0.00 0.00 4.17
3455 3813 6.896021 TCCAACACGTCCCAAAATAATTTA 57.104 33.333 0.00 0.00 0.00 1.40
3468 3826 3.983344 ACGTACAGTTAATCCAACACGTC 59.017 43.478 0.00 0.00 40.98 4.34
3469 3827 3.737266 CACGTACAGTTAATCCAACACGT 59.263 43.478 0.00 0.00 43.80 4.49
3470 3828 3.737266 ACACGTACAGTTAATCCAACACG 59.263 43.478 0.00 0.00 39.81 4.49
3471 3829 6.151691 TCTACACGTACAGTTAATCCAACAC 58.848 40.000 0.00 0.00 39.81 3.32
3472 3830 6.330004 TCTACACGTACAGTTAATCCAACA 57.670 37.500 0.00 0.00 39.81 3.33
3473 3831 7.642071 TTTCTACACGTACAGTTAATCCAAC 57.358 36.000 0.00 0.00 37.41 3.77
3474 3832 9.357652 GTATTTCTACACGTACAGTTAATCCAA 57.642 33.333 0.00 0.00 0.00 3.53
3488 5269 8.390854 AGTTGATTTCTACGTATTTCTACACG 57.609 34.615 0.00 0.00 43.63 4.49
3503 5284 5.762179 TGGACCAGATGTAGTTGATTTCT 57.238 39.130 0.00 0.00 0.00 2.52
3511 5292 7.565190 ATGATCATAATGGACCAGATGTAGT 57.435 36.000 6.36 6.61 0.00 2.73
3518 5299 7.446319 ACACATGTTATGATCATAATGGACCAG 59.554 37.037 26.66 16.82 35.90 4.00
3549 5330 9.877178 GTACAGATCACCCTATATCTTTTATGG 57.123 37.037 0.00 0.00 29.93 2.74
3565 5346 9.612620 CTTTAATGTTTTTGAGGTACAGATCAC 57.387 33.333 0.00 0.00 0.00 3.06
3620 5409 5.703130 GGAAGGAGATGGTTGTATATCTTGC 59.297 44.000 0.00 0.00 33.97 4.01
3621 5410 6.708054 GTGGAAGGAGATGGTTGTATATCTTG 59.292 42.308 0.00 0.00 33.97 3.02
3628 5417 2.915869 AGGTGGAAGGAGATGGTTGTA 58.084 47.619 0.00 0.00 0.00 2.41
3630 5419 2.887151 AAGGTGGAAGGAGATGGTTG 57.113 50.000 0.00 0.00 0.00 3.77
3634 5423 5.001232 TCGTTAAAAAGGTGGAAGGAGATG 58.999 41.667 0.00 0.00 0.00 2.90
3642 5431 8.398878 ACAAGATATTTCGTTAAAAAGGTGGA 57.601 30.769 0.00 0.00 0.00 4.02
3649 5438 9.453325 GTTGTTGGACAAGATATTTCGTTAAAA 57.547 29.630 0.00 0.00 39.00 1.52
3662 5451 8.474025 ACTTTCAATAAATGTTGTTGGACAAGA 58.526 29.630 0.00 0.00 39.00 3.02
3761 5550 8.577296 GCCTTAATATGTAATTTCTTTCTCCCC 58.423 37.037 0.00 0.00 0.00 4.81
3762 5551 9.355916 AGCCTTAATATGTAATTTCTTTCTCCC 57.644 33.333 0.00 0.00 0.00 4.30
3811 5600 1.066002 GGATTTGGTGATGTGATGGCG 59.934 52.381 0.00 0.00 0.00 5.69
3820 5609 6.664816 ACATCTATTGTTGTGGATTTGGTGAT 59.335 34.615 0.00 0.00 33.74 3.06
3821 5610 6.009589 ACATCTATTGTTGTGGATTTGGTGA 58.990 36.000 0.00 0.00 33.74 4.02


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

AutoCloner maintained by Alex Coulton.