Multiple sequence alignment - TraesCS2B01G343300

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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 TraesCS2B01G343300 chr2B 100.000 3671 0 0 1 3671 489028244 489031914 0.000000e+00 6780.0
1 TraesCS2B01G343300 chr2B 75.195 641 129 22 1320 1944 489015902 489016528 3.610000e-70 276.0
2 TraesCS2B01G343300 chr2B 96.154 130 5 0 3282 3411 680215105 680214976 2.870000e-51 213.0
3 TraesCS2B01G343300 chr2B 95.455 132 6 0 3281 3412 572324704 572324573 1.030000e-50 211.0
4 TraesCS2B01G343300 chr2D 95.126 2585 97 19 715 3284 417210085 417212655 0.000000e+00 4048.0
5 TraesCS2B01G343300 chr2D 89.359 686 32 13 69 718 417209265 417209945 0.000000e+00 824.0
6 TraesCS2B01G343300 chr2D 90.293 443 30 3 157 586 417187327 417187769 5.320000e-158 568.0
7 TraesCS2B01G343300 chr2D 96.604 265 9 0 3407 3671 417212653 417212917 1.210000e-119 440.0
8 TraesCS2B01G343300 chr2D 85.892 241 18 4 2 236 417187111 417187341 3.660000e-60 243.0
9 TraesCS2B01G343300 chr2A 89.456 2627 140 53 716 3284 572708447 572705900 0.000000e+00 3190.0
10 TraesCS2B01G343300 chr2A 83.051 472 43 22 29 484 572709291 572708841 9.560000e-106 394.0
11 TraesCS2B01G343300 chr2A 76.168 642 121 25 1320 1944 572748090 572747464 3.560000e-80 309.0
12 TraesCS2B01G343300 chr2A 94.558 147 8 0 3525 3671 572705811 572705665 1.030000e-55 228.0
13 TraesCS2B01G343300 chr2A 85.714 98 2 5 3407 3492 572705902 572705805 3.900000e-15 93.5
14 TraesCS2B01G343300 chr1B 89.032 620 68 0 1316 1935 41526840 41526221 0.000000e+00 769.0
15 TraesCS2B01G343300 chr1B 87.207 641 68 9 2150 2783 41526059 41525426 0.000000e+00 717.0
16 TraesCS2B01G343300 chr1B 91.139 158 6 8 3263 3415 123955469 123955315 1.340000e-49 207.0
17 TraesCS2B01G343300 chr1B 87.097 155 17 2 1060 1211 41527587 41527433 4.870000e-39 172.0
18 TraesCS2B01G343300 chr6A 90.123 162 12 4 3251 3410 326796424 326796583 1.340000e-49 207.0
19 TraesCS2B01G343300 chr6A 96.875 32 1 0 171 202 78478990 78479021 2.000000e-03 54.7
20 TraesCS2B01G343300 chr4A 93.007 143 9 1 3273 3415 16485462 16485603 1.340000e-49 207.0
21 TraesCS2B01G343300 chr5A 92.414 145 9 2 3273 3416 677949493 677949636 4.810000e-49 206.0
22 TraesCS2B01G343300 chr4D 92.414 145 9 2 3273 3416 497646525 497646668 4.810000e-49 206.0
23 TraesCS2B01G343300 chr1D 93.525 139 8 1 3271 3409 96916525 96916662 4.810000e-49 206.0
24 TraesCS2B01G343300 chr3B 89.308 159 14 3 3260 3417 747533677 747533833 2.890000e-46 196.0


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 TraesCS2B01G343300 chr2B 489028244 489031914 3670 False 6780.000000 6780 100.000000 1 3671 1 chr2B.!!$F2 3670
1 TraesCS2B01G343300 chr2B 489015902 489016528 626 False 276.000000 276 75.195000 1320 1944 1 chr2B.!!$F1 624
2 TraesCS2B01G343300 chr2D 417209265 417212917 3652 False 1770.666667 4048 93.696333 69 3671 3 chr2D.!!$F2 3602
3 TraesCS2B01G343300 chr2D 417187111 417187769 658 False 405.500000 568 88.092500 2 586 2 chr2D.!!$F1 584
4 TraesCS2B01G343300 chr2A 572705665 572709291 3626 True 976.375000 3190 88.194750 29 3671 4 chr2A.!!$R2 3642
5 TraesCS2B01G343300 chr2A 572747464 572748090 626 True 309.000000 309 76.168000 1320 1944 1 chr2A.!!$R1 624
6 TraesCS2B01G343300 chr1B 41525426 41527587 2161 True 552.666667 769 87.778667 1060 2783 3 chr1B.!!$R2 1723

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
694 887 0.096628 GCGAGACGTGACATCGTACT 59.903 55.0 0.00 3.8 44.21 2.73 F
759 1105 0.525311 CAGCGCACAAGAGAGAGAGA 59.475 55.0 11.47 0.0 0.00 3.10 F
767 1113 0.751643 AAGAGAGAGAGAGCTCCCGC 60.752 60.0 10.93 0.0 42.30 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2848 1.220749 GGGAATGTCTACGCTGGCA 59.779 57.895 0.0 0.0 0.0 4.92 R
2541 3491 1.226018 CGCCGTGCCGAAGATTTTC 60.226 57.895 0.0 0.0 0.0 2.29 R
2739 3696 2.223845 GCGCTGTTGGAAATTTTGCATT 59.776 40.909 0.0 0.0 0.0 3.56 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
57 58 3.042887 GTGAACGAAAATGACTTGGTGC 58.957 45.455 0.00 0.00 0.00 5.01
60 61 1.880027 ACGAAAATGACTTGGTGCCTC 59.120 47.619 0.00 0.00 0.00 4.70
67 68 2.125912 CTTGGTGCCTCGGACTCG 60.126 66.667 0.00 0.00 37.82 4.18
154 157 2.755103 CAATACAGGGAAGCTGGAAACC 59.245 50.000 0.00 0.00 0.00 3.27
269 357 7.121315 ACATGACTAATAACTTCTGCTTTTCCC 59.879 37.037 0.00 0.00 0.00 3.97
289 377 4.098044 TCCCTAGTCGCAAATAACAGAGAG 59.902 45.833 0.00 0.00 0.00 3.20
409 499 3.717899 CCGTGGTGGCGACATATG 58.282 61.111 0.00 0.00 46.14 1.78
494 616 2.879907 CCACGGCCTTCATGCAAG 59.120 61.111 0.00 0.00 0.00 4.01
598 731 5.060077 CCAAACGAACTATGTGTAGTGTACG 59.940 44.000 0.00 0.00 40.24 3.67
618 760 3.362838 CGTACGTAAACGGTCGGC 58.637 61.111 7.22 0.00 44.95 5.54
694 887 0.096628 GCGAGACGTGACATCGTACT 59.903 55.000 0.00 3.80 44.21 2.73
696 889 2.845022 GCGAGACGTGACATCGTACTAC 60.845 54.545 0.00 0.00 44.21 2.73
697 890 2.602211 CGAGACGTGACATCGTACTACT 59.398 50.000 0.00 0.00 44.21 2.57
757 1103 1.080230 GCAGCGCACAAGAGAGAGA 60.080 57.895 11.47 0.00 0.00 3.10
758 1104 1.077645 GCAGCGCACAAGAGAGAGAG 61.078 60.000 11.47 0.00 0.00 3.20
759 1105 0.525311 CAGCGCACAAGAGAGAGAGA 59.475 55.000 11.47 0.00 0.00 3.10
760 1106 0.810648 AGCGCACAAGAGAGAGAGAG 59.189 55.000 11.47 0.00 0.00 3.20
767 1113 0.751643 AAGAGAGAGAGAGCTCCCGC 60.752 60.000 10.93 0.00 42.30 6.13
796 1142 2.675423 CTCCCGACTCGTGACCCA 60.675 66.667 0.00 0.00 0.00 4.51
882 1252 2.104859 CACATGCTCCTGTGCTCCG 61.105 63.158 0.00 0.00 40.03 4.63
884 1254 3.397439 ATGCTCCTGTGCTCCGCT 61.397 61.111 0.00 0.00 0.00 5.52
913 1289 2.511600 CCTGTTCCATCCGTCGCC 60.512 66.667 0.00 0.00 0.00 5.54
948 1324 5.369699 CCCCATAGAGGAGATTTGGTCTTTA 59.630 44.000 0.00 0.00 41.22 1.85
950 1326 6.292150 CCATAGAGGAGATTTGGTCTTTACC 58.708 44.000 0.00 0.00 43.03 2.85
1191 1574 1.589716 GCTTCAATGGCCTCAACGCT 61.590 55.000 3.32 0.00 0.00 5.07
1276 1666 1.202879 ACGGTCATGCCCTTTCTTGAA 60.203 47.619 0.00 0.00 0.00 2.69
1349 2224 2.889617 CTGTCCATCCCGTACGCA 59.110 61.111 10.49 0.00 0.00 5.24
1862 2743 1.669211 GCGCTCGGACTCTACACTTTT 60.669 52.381 0.00 0.00 0.00 2.27
1895 2776 2.146342 CATGCCATATTCCCGACACTC 58.854 52.381 0.00 0.00 0.00 3.51
1957 2838 3.877559 TCACTAATCAATGAGTGGCCTG 58.122 45.455 3.32 0.00 42.77 4.85
1967 2848 5.716228 TCAATGAGTGGCCTGTCATTTTAAT 59.284 36.000 23.15 6.76 40.64 1.40
1975 2856 2.164219 CCTGTCATTTTAATGCCAGCGT 59.836 45.455 7.75 0.00 40.15 5.07
2003 2884 5.452078 TTCCCAAACTGTTCATCATTGTC 57.548 39.130 0.00 0.00 0.00 3.18
2007 2888 6.775142 TCCCAAACTGTTCATCATTGTCTTTA 59.225 34.615 0.00 0.00 0.00 1.85
2030 2911 4.233789 TCTTGGCGTTTTAATGTGCAATC 58.766 39.130 0.00 0.00 0.00 2.67
2048 2966 7.484641 TGTGCAATCGAATTGATACTAAAAAGC 59.515 33.333 10.52 0.00 42.83 3.51
2051 2969 7.698130 GCAATCGAATTGATACTAAAAAGCAGT 59.302 33.333 10.52 0.00 42.83 4.40
2052 2970 9.559958 CAATCGAATTGATACTAAAAAGCAGTT 57.440 29.630 0.00 0.00 42.83 3.16
2163 3113 2.371841 TGGAGTGCATTGACAGGTACTT 59.628 45.455 0.00 0.00 34.60 2.24
2393 3343 2.074230 CTGCTTGCCGGCAACAAGAA 62.074 55.000 37.30 22.02 45.99 2.52
2541 3491 1.522355 CCCGTGCATCTGCTACCTG 60.522 63.158 3.53 0.00 42.66 4.00
2739 3696 0.682532 TGCTTGGTGTTCTGTGGCAA 60.683 50.000 0.00 0.00 0.00 4.52
2860 3822 7.620094 ACAGATAGTTCTACCCTCAAATGTACT 59.380 37.037 0.00 0.00 0.00 2.73
2861 3823 9.132923 CAGATAGTTCTACCCTCAAATGTACTA 57.867 37.037 0.00 0.00 0.00 1.82
2924 3886 5.186198 GGTAACTGAATGCTGTTGTAGGAT 58.814 41.667 6.22 0.00 39.39 3.24
2932 3894 1.742761 CTGTTGTAGGATGGCACTGG 58.257 55.000 0.00 0.00 0.00 4.00
3039 4001 5.881923 TTCCTGTTAAACACTAGTGGAGT 57.118 39.130 26.12 13.15 39.82 3.85
3067 4029 8.732746 AATTGTCTCTTGTACACAAAGTAGTT 57.267 30.769 0.00 0.00 33.84 2.24
3099 4065 7.881142 TGGAGTACATTAAGTCAACCATTTTG 58.119 34.615 0.00 0.00 0.00 2.44
3115 4081 5.183140 ACCATTTTGGGTGAAGTAATTCTCG 59.817 40.000 4.35 0.00 43.37 4.04
3117 4083 4.627284 TTTGGGTGAAGTAATTCTCGGA 57.373 40.909 4.35 0.00 0.00 4.55
3154 4120 2.710377 TGACTGGTTGTATGCATCCAC 58.290 47.619 0.19 0.00 38.99 4.02
3210 4178 5.496133 GATGTAATCAGCAAAGAGCACAT 57.504 39.130 0.00 0.00 44.70 3.21
3231 4199 5.468072 ACATCAGCAACAACAACAAAAACAA 59.532 32.000 0.00 0.00 0.00 2.83
3237 4206 6.909895 AGCAACAACAACAAAAACAAAAAGAC 59.090 30.769 0.00 0.00 0.00 3.01
3291 4260 9.978336 AAGAACTACTATATATGTACTCCCTCC 57.022 37.037 0.00 0.00 0.00 4.30
3292 4261 8.266473 AGAACTACTATATATGTACTCCCTCCG 58.734 40.741 0.00 0.00 0.00 4.63
3293 4262 7.507797 ACTACTATATATGTACTCCCTCCGT 57.492 40.000 0.00 0.00 0.00 4.69
3294 4263 7.563906 ACTACTATATATGTACTCCCTCCGTC 58.436 42.308 0.00 0.00 0.00 4.79
3295 4264 6.639590 ACTATATATGTACTCCCTCCGTCT 57.360 41.667 0.00 0.00 0.00 4.18
3296 4265 6.416415 ACTATATATGTACTCCCTCCGTCTG 58.584 44.000 0.00 0.00 0.00 3.51
3297 4266 3.878237 ATATGTACTCCCTCCGTCTGA 57.122 47.619 0.00 0.00 0.00 3.27
3298 4267 2.526888 ATGTACTCCCTCCGTCTGAA 57.473 50.000 0.00 0.00 0.00 3.02
3299 4268 2.297698 TGTACTCCCTCCGTCTGAAA 57.702 50.000 0.00 0.00 0.00 2.69
3300 4269 2.600790 TGTACTCCCTCCGTCTGAAAA 58.399 47.619 0.00 0.00 0.00 2.29
3301 4270 3.170717 TGTACTCCCTCCGTCTGAAAAT 58.829 45.455 0.00 0.00 0.00 1.82
3302 4271 4.346730 TGTACTCCCTCCGTCTGAAAATA 58.653 43.478 0.00 0.00 0.00 1.40
3303 4272 3.889520 ACTCCCTCCGTCTGAAAATAC 57.110 47.619 0.00 0.00 0.00 1.89
3304 4273 3.442076 ACTCCCTCCGTCTGAAAATACT 58.558 45.455 0.00 0.00 0.00 2.12
3305 4274 3.838903 ACTCCCTCCGTCTGAAAATACTT 59.161 43.478 0.00 0.00 0.00 2.24
3306 4275 4.184629 CTCCCTCCGTCTGAAAATACTTG 58.815 47.826 0.00 0.00 0.00 3.16
3307 4276 3.581332 TCCCTCCGTCTGAAAATACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
3308 4277 3.933332 CCCTCCGTCTGAAAATACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
3309 4278 4.562757 CCCTCCGTCTGAAAATACTTGTCA 60.563 45.833 0.00 0.00 0.00 3.58
3310 4279 5.178797 CCTCCGTCTGAAAATACTTGTCAT 58.821 41.667 0.00 0.00 0.00 3.06
3311 4280 5.292101 CCTCCGTCTGAAAATACTTGTCATC 59.708 44.000 0.00 0.00 0.00 2.92
3312 4281 5.789521 TCCGTCTGAAAATACTTGTCATCA 58.210 37.500 0.00 0.00 0.00 3.07
3313 4282 6.227522 TCCGTCTGAAAATACTTGTCATCAA 58.772 36.000 0.00 0.00 0.00 2.57
3314 4283 6.708502 TCCGTCTGAAAATACTTGTCATCAAA 59.291 34.615 0.00 0.00 32.87 2.69
3315 4284 7.227711 TCCGTCTGAAAATACTTGTCATCAAAA 59.772 33.333 0.00 0.00 32.87 2.44
3316 4285 8.023128 CCGTCTGAAAATACTTGTCATCAAAAT 58.977 33.333 0.00 0.00 32.87 1.82
3317 4286 8.843733 CGTCTGAAAATACTTGTCATCAAAATG 58.156 33.333 0.00 0.00 32.87 2.32
3318 4287 9.897744 GTCTGAAAATACTTGTCATCAAAATGA 57.102 29.630 0.00 0.00 39.63 2.57
3384 4353 7.983484 ACATCTCCTTTTATTCATTTTGATGGC 59.017 33.333 0.00 0.00 33.92 4.40
3385 4354 7.479352 TCTCCTTTTATTCATTTTGATGGCA 57.521 32.000 0.00 0.00 0.00 4.92
3386 4355 7.905265 TCTCCTTTTATTCATTTTGATGGCAA 58.095 30.769 0.00 0.00 0.00 4.52
3387 4356 8.036575 TCTCCTTTTATTCATTTTGATGGCAAG 58.963 33.333 0.00 0.00 35.04 4.01
3388 4357 7.678837 TCCTTTTATTCATTTTGATGGCAAGT 58.321 30.769 0.00 0.00 35.04 3.16
3389 4358 8.811017 TCCTTTTATTCATTTTGATGGCAAGTA 58.189 29.630 0.00 0.00 35.04 2.24
3390 4359 9.603921 CCTTTTATTCATTTTGATGGCAAGTAT 57.396 29.630 0.00 0.00 35.04 2.12
3394 4363 9.598517 TTATTCATTTTGATGGCAAGTATTTCC 57.401 29.630 0.00 0.00 35.04 3.13
3395 4364 5.649557 TCATTTTGATGGCAAGTATTTCCG 58.350 37.500 0.00 0.00 35.04 4.30
3396 4365 5.417266 TCATTTTGATGGCAAGTATTTCCGA 59.583 36.000 0.00 0.00 35.04 4.55
3397 4366 5.713792 TTTTGATGGCAAGTATTTCCGAA 57.286 34.783 0.00 0.00 35.04 4.30
3398 4367 4.695217 TTGATGGCAAGTATTTCCGAAC 57.305 40.909 0.00 0.00 0.00 3.95
3399 4368 2.675844 TGATGGCAAGTATTTCCGAACG 59.324 45.455 0.00 0.00 0.00 3.95
3400 4369 1.444836 TGGCAAGTATTTCCGAACGG 58.555 50.000 6.94 6.94 0.00 4.44
3401 4370 1.002201 TGGCAAGTATTTCCGAACGGA 59.998 47.619 12.04 12.04 43.52 4.69
3402 4371 1.664151 GGCAAGTATTTCCGAACGGAG 59.336 52.381 15.34 4.35 46.06 4.63
3403 4372 1.664151 GCAAGTATTTCCGAACGGAGG 59.336 52.381 15.34 3.40 46.06 4.30
3404 4373 2.277084 CAAGTATTTCCGAACGGAGGG 58.723 52.381 15.34 0.00 46.06 4.30
3405 4374 1.856629 AGTATTTCCGAACGGAGGGA 58.143 50.000 15.34 7.17 46.06 4.20
3498 4479 6.097554 CCAACTAGGAGGAGCTACATATATGG 59.902 46.154 16.96 1.41 41.22 2.74
3564 4545 0.801251 CTGAAGCCGAAAGAAGCTGG 59.199 55.000 0.00 0.00 39.87 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 0.526211 TTCAGATCACCACGAGTCCG 59.474 55.000 0.00 0.00 42.50 4.79
67 68 4.614535 GCACATGTTTCTTCAGATCACCAC 60.615 45.833 0.00 0.00 0.00 4.16
154 157 4.467198 AAATAACTACGTGACCAGGAGG 57.533 45.455 0.00 0.00 42.21 4.30
236 316 8.759641 GCAGAAGTTATTAGTCATGTCACTATG 58.240 37.037 0.00 0.00 0.00 2.23
244 324 7.337942 AGGGAAAAGCAGAAGTTATTAGTCATG 59.662 37.037 0.00 0.00 0.00 3.07
269 357 4.677584 AGCTCTCTGTTATTTGCGACTAG 58.322 43.478 0.00 0.00 0.00 2.57
409 499 4.283678 CACTGAGCTACTTCTGTATACGC 58.716 47.826 0.00 0.00 0.00 4.42
598 731 1.520368 CCGACCGTTTACGTACGTAC 58.480 55.000 26.83 18.26 39.81 3.67
694 887 4.574674 AAGGATGATGCTGTTTGGAGTA 57.425 40.909 0.00 0.00 0.00 2.59
696 889 3.129988 GGAAAGGATGATGCTGTTTGGAG 59.870 47.826 0.00 0.00 0.00 3.86
697 890 3.091545 GGAAAGGATGATGCTGTTTGGA 58.908 45.455 0.00 0.00 0.00 3.53
884 1254 3.177884 AACAGGCAGGGGCACAGA 61.178 61.111 0.00 0.00 43.71 3.41
948 1324 1.608717 CGCCTCCTGTAAGCTCTGGT 61.609 60.000 0.00 0.00 0.00 4.00
950 1326 0.179124 GACGCCTCCTGTAAGCTCTG 60.179 60.000 0.00 0.00 0.00 3.35
984 1364 9.300681 CCAATGGCCATCTTATTCTTATTCTTA 57.699 33.333 21.08 0.00 0.00 2.10
985 1365 7.256083 GCCAATGGCCATCTTATTCTTATTCTT 60.256 37.037 21.08 0.00 44.06 2.52
988 1368 6.350629 GCCAATGGCCATCTTATTCTTATT 57.649 37.500 21.08 0.00 44.06 1.40
1212 1595 2.073816 GGCAACGGAAGAAAGATTCGA 58.926 47.619 0.00 0.00 34.02 3.71
1244 1633 3.006967 GGCATGACCGTACAGGAGATAAT 59.993 47.826 10.17 0.00 45.00 1.28
1245 1634 2.364324 GGCATGACCGTACAGGAGATAA 59.636 50.000 10.17 0.00 45.00 1.75
1382 2257 2.835431 ATGGCGACGAGGAGGAGG 60.835 66.667 0.00 0.00 0.00 4.30
1862 2743 3.133464 GCATGGCCGCAGTAGCAA 61.133 61.111 0.00 0.00 42.27 3.91
1957 2838 4.094294 TGTCTACGCTGGCATTAAAATGAC 59.906 41.667 6.87 4.19 44.87 3.06
1967 2848 1.220749 GGGAATGTCTACGCTGGCA 59.779 57.895 0.00 0.00 0.00 4.92
1975 2856 5.875224 TGATGAACAGTTTGGGAATGTCTA 58.125 37.500 0.00 0.00 0.00 2.59
2003 2884 5.861251 TGCACATTAAAACGCCAAGATAAAG 59.139 36.000 0.00 0.00 0.00 1.85
2007 2888 3.932545 TGCACATTAAAACGCCAAGAT 57.067 38.095 0.00 0.00 0.00 2.40
2058 2980 5.189928 TGTTAGGTCACTGTCACATGTTTT 58.810 37.500 0.00 0.00 0.00 2.43
2123 3073 2.361757 CCAACAGACAGACATGCCAAAA 59.638 45.455 0.00 0.00 0.00 2.44
2163 3113 3.731295 TGCGACGAAGCATATGACA 57.269 47.368 6.97 0.00 42.92 3.58
2541 3491 1.226018 CGCCGTGCCGAAGATTTTC 60.226 57.895 0.00 0.00 0.00 2.29
2739 3696 2.223845 GCGCTGTTGGAAATTTTGCATT 59.776 40.909 0.00 0.00 0.00 3.56
2848 3810 9.599866 TCTCAAACATACATAGTACATTTGAGG 57.400 33.333 25.58 16.43 45.88 3.86
2861 3823 9.896645 ACAGAAATACTCATCTCAAACATACAT 57.103 29.630 0.00 0.00 0.00 2.29
2909 3871 2.094675 GTGCCATCCTACAACAGCATT 58.905 47.619 0.00 0.00 32.11 3.56
2924 3886 3.950794 GAACGCCGATCCAGTGCCA 62.951 63.158 0.00 0.00 0.00 4.92
2932 3894 1.717194 TTTACAGTGGAACGCCGATC 58.283 50.000 0.00 0.00 45.86 3.69
3067 4029 7.335924 GGTTGACTTAATGTACTCCATTGCTTA 59.664 37.037 0.00 0.00 43.63 3.09
3099 4065 3.134081 TCCATCCGAGAATTACTTCACCC 59.866 47.826 0.00 0.00 33.56 4.61
3108 4074 2.104963 GCCTAACCTCCATCCGAGAATT 59.895 50.000 0.00 0.00 41.63 2.17
3115 4081 2.158813 TCAAATCGCCTAACCTCCATCC 60.159 50.000 0.00 0.00 0.00 3.51
3117 4083 2.505819 AGTCAAATCGCCTAACCTCCAT 59.494 45.455 0.00 0.00 0.00 3.41
3154 4120 0.240945 ATTGCGGTTTCTGCCTTTCG 59.759 50.000 0.00 0.00 0.00 3.46
3201 4169 2.300433 TGTTGTTGCTGATGTGCTCTT 58.700 42.857 0.00 0.00 0.00 2.85
3202 4170 1.971481 TGTTGTTGCTGATGTGCTCT 58.029 45.000 0.00 0.00 0.00 4.09
3205 4173 2.206815 TGTTGTTGTTGCTGATGTGC 57.793 45.000 0.00 0.00 0.00 4.57
3210 4178 5.991328 TTTGTTTTTGTTGTTGTTGCTGA 57.009 30.435 0.00 0.00 0.00 4.26
3231 4199 0.238289 CGTGGCTGATTGCGTCTTTT 59.762 50.000 0.00 0.00 44.05 2.27
3237 4206 2.099062 GAAGCGTGGCTGATTGCG 59.901 61.111 0.00 0.00 44.05 4.85
3281 4250 3.889520 ATTTTCAGACGGAGGGAGTAC 57.110 47.619 0.00 0.00 0.00 2.73
3282 4251 4.607239 AGTATTTTCAGACGGAGGGAGTA 58.393 43.478 0.00 0.00 0.00 2.59
3283 4252 3.442076 AGTATTTTCAGACGGAGGGAGT 58.558 45.455 0.00 0.00 0.00 3.85
3284 4253 4.184629 CAAGTATTTTCAGACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
3285 4254 3.581332 ACAAGTATTTTCAGACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
3286 4255 3.933332 GACAAGTATTTTCAGACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
3287 4256 4.566004 TGACAAGTATTTTCAGACGGAGG 58.434 43.478 0.00 0.00 0.00 4.30
3288 4257 5.869344 TGATGACAAGTATTTTCAGACGGAG 59.131 40.000 0.00 0.00 0.00 4.63
3289 4258 5.789521 TGATGACAAGTATTTTCAGACGGA 58.210 37.500 0.00 0.00 0.00 4.69
3290 4259 6.480524 TTGATGACAAGTATTTTCAGACGG 57.519 37.500 0.00 0.00 0.00 4.79
3291 4260 8.843733 CATTTTGATGACAAGTATTTTCAGACG 58.156 33.333 0.00 0.00 37.32 4.18
3292 4261 9.897744 TCATTTTGATGACAAGTATTTTCAGAC 57.102 29.630 0.00 0.00 37.32 3.51
3358 4327 7.983484 GCCATCAAAATGAATAAAAGGAGATGT 59.017 33.333 0.00 0.00 34.61 3.06
3359 4328 7.982919 TGCCATCAAAATGAATAAAAGGAGATG 59.017 33.333 0.00 0.00 34.61 2.90
3360 4329 8.081517 TGCCATCAAAATGAATAAAAGGAGAT 57.918 30.769 0.00 0.00 34.61 2.75
3361 4330 7.479352 TGCCATCAAAATGAATAAAAGGAGA 57.521 32.000 0.00 0.00 34.61 3.71
3362 4331 7.820872 ACTTGCCATCAAAATGAATAAAAGGAG 59.179 33.333 0.00 0.00 34.61 3.69
3363 4332 7.678837 ACTTGCCATCAAAATGAATAAAAGGA 58.321 30.769 0.00 0.00 34.61 3.36
3364 4333 7.910441 ACTTGCCATCAAAATGAATAAAAGG 57.090 32.000 0.00 0.00 34.61 3.11
3368 4337 9.598517 GGAAATACTTGCCATCAAAATGAATAA 57.401 29.630 0.00 0.00 34.61 1.40
3369 4338 7.920151 CGGAAATACTTGCCATCAAAATGAATA 59.080 33.333 0.00 0.00 34.61 1.75
3370 4339 6.757947 CGGAAATACTTGCCATCAAAATGAAT 59.242 34.615 0.00 0.00 34.61 2.57
3371 4340 6.071672 TCGGAAATACTTGCCATCAAAATGAA 60.072 34.615 0.00 0.00 34.61 2.57
3372 4341 5.417266 TCGGAAATACTTGCCATCAAAATGA 59.583 36.000 0.00 0.00 34.61 2.57
3373 4342 5.649557 TCGGAAATACTTGCCATCAAAATG 58.350 37.500 0.00 0.00 0.00 2.32
3374 4343 5.913137 TCGGAAATACTTGCCATCAAAAT 57.087 34.783 0.00 0.00 0.00 1.82
3375 4344 5.465935 GTTCGGAAATACTTGCCATCAAAA 58.534 37.500 0.00 0.00 0.00 2.44
3376 4345 4.378978 CGTTCGGAAATACTTGCCATCAAA 60.379 41.667 0.00 0.00 0.00 2.69
3377 4346 3.126171 CGTTCGGAAATACTTGCCATCAA 59.874 43.478 0.00 0.00 0.00 2.57
3378 4347 2.675844 CGTTCGGAAATACTTGCCATCA 59.324 45.455 0.00 0.00 0.00 3.07
3379 4348 2.031683 CCGTTCGGAAATACTTGCCATC 59.968 50.000 5.19 0.00 0.00 3.51
3380 4349 2.014128 CCGTTCGGAAATACTTGCCAT 58.986 47.619 5.19 0.00 0.00 4.40
3381 4350 1.002201 TCCGTTCGGAAATACTTGCCA 59.998 47.619 11.66 0.00 0.00 4.92
3382 4351 1.664151 CTCCGTTCGGAAATACTTGCC 59.336 52.381 14.79 0.00 33.41 4.52
3383 4352 1.664151 CCTCCGTTCGGAAATACTTGC 59.336 52.381 14.79 0.00 33.41 4.01
3384 4353 2.093869 TCCCTCCGTTCGGAAATACTTG 60.094 50.000 14.79 1.97 33.41 3.16
3385 4354 2.167900 CTCCCTCCGTTCGGAAATACTT 59.832 50.000 14.79 0.00 33.41 2.24
3386 4355 1.755380 CTCCCTCCGTTCGGAAATACT 59.245 52.381 14.79 0.00 33.41 2.12
3387 4356 1.479730 ACTCCCTCCGTTCGGAAATAC 59.520 52.381 14.79 0.00 33.41 1.89
3388 4357 1.856629 ACTCCCTCCGTTCGGAAATA 58.143 50.000 14.79 2.82 33.41 1.40
3389 4358 1.856629 TACTCCCTCCGTTCGGAAAT 58.143 50.000 14.79 2.39 33.41 2.17
3390 4359 1.856629 ATACTCCCTCCGTTCGGAAA 58.143 50.000 14.79 3.49 33.41 3.13
3391 4360 2.734755 TATACTCCCTCCGTTCGGAA 57.265 50.000 14.79 0.00 33.41 4.30
3392 4361 2.173356 TCTTATACTCCCTCCGTTCGGA 59.827 50.000 13.34 13.34 0.00 4.55
3393 4362 2.579873 TCTTATACTCCCTCCGTTCGG 58.420 52.381 4.74 4.74 0.00 4.30
3394 4363 4.644103 TTTCTTATACTCCCTCCGTTCG 57.356 45.455 0.00 0.00 0.00 3.95
3395 4364 5.358090 CCTTTTCTTATACTCCCTCCGTTC 58.642 45.833 0.00 0.00 0.00 3.95
3396 4365 4.163649 CCCTTTTCTTATACTCCCTCCGTT 59.836 45.833 0.00 0.00 0.00 4.44
3397 4366 3.710165 CCCTTTTCTTATACTCCCTCCGT 59.290 47.826 0.00 0.00 0.00 4.69
3398 4367 3.965347 TCCCTTTTCTTATACTCCCTCCG 59.035 47.826 0.00 0.00 0.00 4.63
3399 4368 4.348461 CCTCCCTTTTCTTATACTCCCTCC 59.652 50.000 0.00 0.00 0.00 4.30
3400 4369 5.217400 TCCTCCCTTTTCTTATACTCCCTC 58.783 45.833 0.00 0.00 0.00 4.30
3401 4370 5.236425 TCCTCCCTTTTCTTATACTCCCT 57.764 43.478 0.00 0.00 0.00 4.20
3402 4371 5.970501 TTCCTCCCTTTTCTTATACTCCC 57.029 43.478 0.00 0.00 0.00 4.30
3403 4372 9.339850 GTAATTTCCTCCCTTTTCTTATACTCC 57.660 37.037 0.00 0.00 0.00 3.85
3404 4373 9.901172 TGTAATTTCCTCCCTTTTCTTATACTC 57.099 33.333 0.00 0.00 0.00 2.59
3405 4374 9.907229 CTGTAATTTCCTCCCTTTTCTTATACT 57.093 33.333 0.00 0.00 0.00 2.12
3478 4459 5.894393 GCTTCCATATATGTAGCTCCTCCTA 59.106 44.000 21.16 0.00 33.44 2.94
3498 4479 0.586802 GTTTCCACCACTCGTGCTTC 59.413 55.000 0.00 0.00 41.53 3.86


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

AutoCloner maintained by Alex Coulton.