Multiple sequence alignment - TraesCS3A01G084600

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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 TraesCS3A01G084600 chr3A 100.000 4484 0 0 1 4484 54670058 54665575 0.000000e+00 8281
1 TraesCS3A01G084600 chr3D 95.513 3499 132 11 1 3487 42748284 42744799 0.000000e+00 5568
2 TraesCS3A01G084600 chr3D 90.587 818 52 7 3484 4294 42744761 42743962 0.000000e+00 1061
3 TraesCS3A01G084600 chr3D 87.171 304 18 9 4200 4484 42743962 42743661 4.330000e-85 326
4 TraesCS3A01G084600 chr3B 97.016 2480 74 0 1008 3487 66588646 66586167 0.000000e+00 4170
5 TraesCS3A01G084600 chr3B 94.662 637 28 5 3484 4116 66586129 66585495 0.000000e+00 983
6 TraesCS3A01G084600 chr1B 92.888 2517 179 0 962 3478 32594787 32592271 0.000000e+00 3657
7 TraesCS3A01G084600 chr1B 80.469 256 38 8 321 571 32595281 32595033 7.660000e-43 185
8 TraesCS3A01G084600 chrUn 91.910 2398 166 10 1092 3484 10169503 10171877 0.000000e+00 3328
9 TraesCS3A01G084600 chrUn 88.693 283 25 6 444 722 10169185 10169464 5.560000e-89 339


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 TraesCS3A01G084600 chr3A 54665575 54670058 4483 True 8281.000000 8281 100.000000 1 4484 1 chr3A.!!$R1 4483
1 TraesCS3A01G084600 chr3D 42743661 42748284 4623 True 2318.333333 5568 91.090333 1 4484 3 chr3D.!!$R1 4483
2 TraesCS3A01G084600 chr3B 66585495 66588646 3151 True 2576.500000 4170 95.839000 1008 4116 2 chr3B.!!$R1 3108
3 TraesCS3A01G084600 chr1B 32592271 32595281 3010 True 1921.000000 3657 86.678500 321 3478 2 chr1B.!!$R1 3157
4 TraesCS3A01G084600 chrUn 10169185 10171877 2692 False 1833.500000 3328 90.301500 444 3484 2 chrUn.!!$F1 3040

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
775 811 0.174845 AATCGATTGGGCTCGTTCGA 59.825 50.0 10.50 12.37 43.82 3.71 F
1005 1041 1.089481 CGGCGCTGGTGAACATGTAT 61.089 55.0 8.83 0.00 0.00 2.29 F
1749 1785 0.819259 TGGGAAGACAAGTGCAGTGC 60.819 55.0 8.58 8.58 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1653 1689 0.251077 CAGCCTCAAGACCAAGCCTT 60.251 55.000 0.00 0.0 0.00 4.35 R
2182 2218 3.067180 CCCGCAATCAGAGCATTTATTGT 59.933 43.478 0.00 0.0 32.99 2.71 R
3506 3588 0.333993 ATGCAAGTCCTGGATTGGCT 59.666 50.000 18.17 0.0 30.67 4.75 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 2.411765 CTTCCCTTGTCCCGCAACCT 62.412 60.000 0.00 0.00 32.90 3.50
54 55 4.572389 ACAAGTGAAGCTCTGTAAGTTGTG 59.428 41.667 0.00 0.00 34.10 3.33
59 60 2.704572 AGCTCTGTAAGTTGTGCCATC 58.295 47.619 0.00 0.00 33.76 3.51
157 160 3.217681 TGTTGTTCTGGAACCTAACCC 57.782 47.619 10.44 0.00 40.46 4.11
158 161 2.510382 TGTTGTTCTGGAACCTAACCCA 59.490 45.455 10.44 0.00 40.46 4.51
161 164 5.163077 TGTTGTTCTGGAACCTAACCCAATA 60.163 40.000 10.44 0.00 40.46 1.90
162 165 5.789574 TGTTCTGGAACCTAACCCAATAT 57.210 39.130 10.44 0.00 40.46 1.28
163 166 6.147437 TGTTCTGGAACCTAACCCAATATT 57.853 37.500 10.44 0.00 40.46 1.28
164 167 6.557568 TGTTCTGGAACCTAACCCAATATTT 58.442 36.000 10.44 0.00 40.46 1.40
165 168 7.700846 TGTTCTGGAACCTAACCCAATATTTA 58.299 34.615 10.44 0.00 40.46 1.40
174 177 8.934023 ACCTAACCCAATATTTACATGTATGG 57.066 34.615 13.40 13.40 0.00 2.74
176 179 7.669722 CCTAACCCAATATTTACATGTATGGCT 59.330 37.037 14.52 8.10 0.00 4.75
192 195 1.640149 TGGCTGGGGAAAGATTGATGA 59.360 47.619 0.00 0.00 0.00 2.92
194 197 1.680207 GCTGGGGAAAGATTGATGAGC 59.320 52.381 0.00 0.00 0.00 4.26
208 211 9.842775 AAGATTGATGAGCAGATACATTTCTTA 57.157 29.630 0.00 0.00 0.00 2.10
210 213 8.969260 ATTGATGAGCAGATACATTTCTTACA 57.031 30.769 0.00 0.00 0.00 2.41
220 223 8.121086 CAGATACATTTCTTACATGTGCTTCAG 58.879 37.037 9.11 0.00 35.57 3.02
242 245 3.806521 GCTTGATACTGTACTGCTGATGG 59.193 47.826 0.00 0.00 0.00 3.51
254 257 9.113838 CTGTACTGCTGATGGTAATTCTTAATT 57.886 33.333 0.00 0.00 34.90 1.40
273 276 9.187996 TCTTAATTGGCAAGTTCATGATAATCA 57.812 29.630 5.17 0.00 0.00 2.57
275 278 6.778834 ATTGGCAAGTTCATGATAATCACA 57.221 33.333 5.96 0.00 0.00 3.58
290 303 9.618890 ATGATAATCACAATGCTACTTTAGTGT 57.381 29.630 0.00 0.00 0.00 3.55
292 305 6.500684 AATCACAATGCTACTTTAGTGTGG 57.499 37.500 0.00 0.00 37.53 4.17
296 309 4.455877 ACAATGCTACTTTAGTGTGGAAGC 59.544 41.667 0.00 0.00 0.00 3.86
312 325 8.591072 AGTGTGGAAGCTATACTTGTTTAACTA 58.409 33.333 0.00 0.00 39.29 2.24
336 349 1.335964 CGAGTGTTCCGTGTCTGATGT 60.336 52.381 0.00 0.00 0.00 3.06
363 376 5.763204 TGTACTTCTGATGGAAAGTTGGAAC 59.237 40.000 0.00 0.00 33.07 3.62
377 390 1.608055 TGGAACCAATCTGTGTGCTG 58.392 50.000 0.00 0.00 0.00 4.41
393 406 0.877743 GCTGACACTTTTCTGAGGGC 59.122 55.000 0.00 0.00 0.00 5.19
414 427 2.420642 GTATCTCCATGCGATGCACAT 58.579 47.619 0.00 0.00 43.04 3.21
435 449 5.829924 ACATGCCTATTTCTATCCAAAGTGG 59.170 40.000 0.00 0.00 39.43 4.00
437 451 4.145052 GCCTATTTCTATCCAAAGTGGGG 58.855 47.826 0.00 0.00 38.32 4.96
438 452 4.729868 CCTATTTCTATCCAAAGTGGGGG 58.270 47.826 0.00 0.00 38.32 5.40
481 499 8.070171 CAGTTGTTGAACTCGAAAATTCTATGT 58.930 33.333 0.00 0.00 40.68 2.29
611 638 2.028112 TGTCTTTAGGCGCATTCAGACT 60.028 45.455 24.74 9.44 33.28 3.24
622 649 4.142816 GCGCATTCAGACTTTTACACTCAT 60.143 41.667 0.30 0.00 0.00 2.90
649 676 3.699038 ACAGTTTAGACAGCTTTTTGCCA 59.301 39.130 0.00 0.00 44.23 4.92
676 703 3.545633 GCTTTACAACTTTCTCACAGCG 58.454 45.455 0.00 0.00 0.00 5.18
718 745 0.693049 ACAGGTACTTCCCCAAGCTG 59.307 55.000 0.00 0.00 42.84 4.24
762 798 2.086869 CCAAACACAGCCTCAATCGAT 58.913 47.619 0.00 0.00 0.00 3.59
775 811 0.174845 AATCGATTGGGCTCGTTCGA 59.825 50.000 10.50 12.37 43.82 3.71
883 919 1.300697 GACCAGTTTGACCTCGCGT 60.301 57.895 5.77 0.00 0.00 6.01
902 938 4.152625 GGTCATGTCAGCGTGCGC 62.153 66.667 8.67 8.67 42.33 6.09
903 939 3.413861 GTCATGTCAGCGTGCGCA 61.414 61.111 18.87 5.66 44.88 6.09
920 956 1.817099 CAAGGCTGGACATCCTCGC 60.817 63.158 0.00 2.17 36.82 5.03
924 960 2.202987 CTGGACATCCTCGCCTGC 60.203 66.667 0.00 0.00 36.82 4.85
1005 1041 1.089481 CGGCGCTGGTGAACATGTAT 61.089 55.000 8.83 0.00 0.00 2.29
1239 1275 1.980765 CTGGATGATGCTAGGGCCTTA 59.019 52.381 13.45 0.00 37.74 2.69
1586 1622 4.410099 AGGAACATTGTCATGTGGAATGT 58.590 39.130 11.49 11.49 43.34 2.71
1615 1651 2.270352 TGGGCTTGTTCGAAATGAGT 57.730 45.000 0.00 0.00 0.00 3.41
1653 1689 6.772233 CCATCCAAATGTTCTGGTATATGACA 59.228 38.462 0.00 0.00 35.30 3.58
1677 1713 2.877300 GCTTGGTCTTGAGGCTGATGAA 60.877 50.000 0.00 0.00 0.00 2.57
1749 1785 0.819259 TGGGAAGACAAGTGCAGTGC 60.819 55.000 8.58 8.58 0.00 4.40
1863 1899 7.168135 GCGAAAACATTATTCAATCTGATTCCC 59.832 37.037 0.00 0.00 0.00 3.97
1874 1910 7.690454 TCAATCTGATTCCCTACAAGGATAA 57.310 36.000 0.00 0.00 37.67 1.75
2001 2037 4.632153 AGGTGTCTTTTGCTACTGTAGTG 58.368 43.478 15.71 3.06 0.00 2.74
2091 2127 4.575236 AGTATCTGCTCAAATCATGCTGTG 59.425 41.667 0.00 0.00 0.00 3.66
2182 2218 7.013369 CACAGGTAGATGCAAGTAGTATAGTCA 59.987 40.741 0.00 0.00 0.00 3.41
2243 2279 9.571810 CAATAGAGATGATGAAGCTATACAGTC 57.428 37.037 0.00 0.00 0.00 3.51
2244 2280 8.876303 ATAGAGATGATGAAGCTATACAGTCA 57.124 34.615 0.00 0.00 0.00 3.41
2255 2291 3.249559 GCTATACAGTCATTTCAGCAGGC 59.750 47.826 0.00 0.00 0.00 4.85
2277 2313 5.432645 GCTCTTAGAGATGGTTTAAAGCCT 58.567 41.667 14.14 4.90 0.00 4.58
2284 2320 2.373335 TGGTTTAAAGCCTTCCAGCA 57.627 45.000 14.49 0.00 34.23 4.41
2313 2349 3.648339 TCAAGCATTCTTTCTGGTTGC 57.352 42.857 9.65 0.00 46.47 4.17
2407 2443 4.739793 TGATTCTTCCCTTGGTGTTTCAT 58.260 39.130 0.00 0.00 0.00 2.57
2410 2446 3.909732 TCTTCCCTTGGTGTTTCATTGT 58.090 40.909 0.00 0.00 0.00 2.71
2448 2484 1.006281 TCCAAAATGCCTGAGGATGCT 59.994 47.619 0.65 0.00 0.00 3.79
3025 3061 7.239166 AGAGTAGATCATTATGCGTGTTTTG 57.761 36.000 0.00 0.00 0.00 2.44
3285 3326 0.462581 TAGCCAGAGAAGCAATGCGG 60.463 55.000 0.00 0.00 0.00 5.69
3489 3571 6.006449 AGCTGAAATGTTTACTTGATGAGGT 58.994 36.000 0.00 0.00 0.00 3.85
3506 3588 4.871822 TGAGGTCCTGATGTCATCTTCTA 58.128 43.478 13.90 0.00 0.00 2.10
3523 3605 1.210478 TCTAGCCAATCCAGGACTTGC 59.790 52.381 0.00 0.00 0.00 4.01
3524 3606 0.991146 TAGCCAATCCAGGACTTGCA 59.009 50.000 0.00 0.00 0.00 4.08
3584 3666 6.917477 TGCTTGGTCATATTTATTTGCGATTC 59.083 34.615 0.00 0.00 0.00 2.52
3611 3693 6.707440 TTCTGACCACTTTATTTTCTGCAA 57.293 33.333 0.00 0.00 0.00 4.08
3614 3696 7.725251 TCTGACCACTTTATTTTCTGCAATTT 58.275 30.769 0.00 0.00 0.00 1.82
3697 3779 3.648545 AGGGAGCCTAATTACCTGTGATC 59.351 47.826 0.00 0.00 28.47 2.92
3733 3815 9.545105 TGTTCAGGTTCGTTTCTAGTTTATTTA 57.455 29.630 0.00 0.00 0.00 1.40
3790 3872 2.238521 TCTGAGGGCTCGCAAAATTTT 58.761 42.857 0.00 0.00 0.00 1.82
3833 3915 2.719531 TGGCTTGTGAAGTTACCACA 57.280 45.000 0.00 0.00 42.16 4.17
3854 3938 1.625818 AGGTCAGTCTTGATGTGGGAC 59.374 52.381 0.00 0.00 35.39 4.46
3860 3944 2.358125 TTGATGTGGGACGCGGTG 60.358 61.111 12.47 0.00 45.01 4.94
3861 3945 3.892740 TTGATGTGGGACGCGGTGG 62.893 63.158 12.47 0.00 45.01 4.61
3877 3961 1.003580 GGTGGCAGTGAAGATTCAGGA 59.996 52.381 0.00 0.00 37.98 3.86
3879 3963 1.980765 TGGCAGTGAAGATTCAGGAGT 59.019 47.619 0.00 0.00 37.98 3.85
3938 4022 9.875675 GCTTTTGCATTCATTTTAACACATTTA 57.124 25.926 0.00 0.00 46.58 1.40
4158 4247 6.066690 GCCATCCATCATAAGCCATATACAT 58.933 40.000 0.00 0.00 0.00 2.29
4169 4258 3.117550 AGCCATATACATCACCCAAGCAA 60.118 43.478 0.00 0.00 0.00 3.91
4170 4259 3.828451 GCCATATACATCACCCAAGCAAT 59.172 43.478 0.00 0.00 0.00 3.56
4185 4274 5.294552 CCCAAGCAATAAGTAGACTAGTTGC 59.705 44.000 17.55 17.55 42.12 4.17
4188 4277 7.436673 CCAAGCAATAAGTAGACTAGTTGCTAG 59.563 40.741 23.56 17.66 46.55 3.42
4189 4278 6.508777 AGCAATAAGTAGACTAGTTGCTAGC 58.491 40.000 22.68 8.10 46.00 3.42
4204 4293 1.079819 TAGCGCAGTTCTGCAGGAC 60.080 57.895 18.09 18.09 34.41 3.85
4211 4300 0.957395 AGTTCTGCAGGACATTGCCG 60.957 55.000 26.95 0.00 43.43 5.69
4221 4310 3.317149 CAGGACATTGCCGATTCATGAAT 59.683 43.478 20.85 20.85 0.00 2.57
4261 4350 2.399856 GTGTTCGCACAAGGTTGGA 58.600 52.632 0.00 0.00 46.85 3.53
4283 4466 2.544486 CCAAGTTTCTGCCAGAACTTGC 60.544 50.000 26.83 13.18 39.37 4.01
4295 4478 4.499865 GCCAGAACTTGCATCGAGATACTA 60.500 45.833 0.00 0.00 0.00 1.82
4298 4481 6.442112 CAGAACTTGCATCGAGATACTATCA 58.558 40.000 0.00 0.00 0.00 2.15
4299 4482 6.362016 CAGAACTTGCATCGAGATACTATCAC 59.638 42.308 0.00 0.00 0.00 3.06
4302 4485 6.810911 ACTTGCATCGAGATACTATCACTTT 58.189 36.000 0.00 0.00 0.00 2.66
4305 4488 9.249457 CTTGCATCGAGATACTATCACTTTTTA 57.751 33.333 0.00 0.00 0.00 1.52
4332 4530 8.578308 TTTTGTACTGAAATCATGCTTTCTTG 57.422 30.769 19.64 15.05 36.34 3.02
4343 4541 6.389830 TCATGCTTTCTTGCTGAGTTTTTA 57.610 33.333 0.00 0.00 0.00 1.52
4344 4542 6.985117 TCATGCTTTCTTGCTGAGTTTTTAT 58.015 32.000 0.00 0.00 0.00 1.40
4412 4610 6.073873 CGATGGCATAGATCTTTCTTTCAGTC 60.074 42.308 0.00 0.00 33.17 3.51
4418 4616 8.816144 GCATAGATCTTTCTTTCAGTCAGTTAG 58.184 37.037 0.00 0.00 33.17 2.34
4419 4617 9.868277 CATAGATCTTTCTTTCAGTCAGTTAGT 57.132 33.333 0.00 0.00 33.17 2.24
4422 4620 9.699703 AGATCTTTCTTTCAGTCAGTTAGTTAC 57.300 33.333 0.00 0.00 0.00 2.50
4434 4636 5.464389 GTCAGTTAGTTACGTGTTTCACCAT 59.536 40.000 0.00 0.00 0.00 3.55
4441 4643 3.410631 ACGTGTTTCACCATATCCACA 57.589 42.857 0.00 0.00 0.00 4.17
4456 4658 6.373495 CCATATCCACACTGATATTCCACATG 59.627 42.308 0.00 0.00 36.11 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 0.378962 TTGTTTCCGTTCAGGTTGCG 59.621 50.000 0.00 0.00 41.99 4.85
22 23 2.612212 GAGCTTCACTTGTTTCCGTTCA 59.388 45.455 0.00 0.00 0.00 3.18
29 30 5.648092 ACAACTTACAGAGCTTCACTTGTTT 59.352 36.000 0.00 0.00 0.00 2.83
54 55 3.192844 TCGATAACTAAGGATCGGATGGC 59.807 47.826 0.00 0.00 44.01 4.40
59 60 2.820787 AGCCTCGATAACTAAGGATCGG 59.179 50.000 4.62 0.00 44.01 4.18
126 129 8.383175 AGGTTCCAGAACAACAAAATAGATAGA 58.617 33.333 12.32 0.00 42.85 1.98
157 160 6.009589 TCCCCAGCCATACATGTAAATATTG 58.990 40.000 10.14 3.03 0.00 1.90
158 161 6.212840 TCCCCAGCCATACATGTAAATATT 57.787 37.500 10.14 0.00 0.00 1.28
161 164 4.534647 TTCCCCAGCCATACATGTAAAT 57.465 40.909 10.14 0.00 0.00 1.40
162 165 4.017958 TCTTTCCCCAGCCATACATGTAAA 60.018 41.667 10.14 0.00 0.00 2.01
163 166 3.525609 TCTTTCCCCAGCCATACATGTAA 59.474 43.478 10.14 0.00 0.00 2.41
164 167 3.119319 TCTTTCCCCAGCCATACATGTA 58.881 45.455 8.27 8.27 0.00 2.29
165 168 1.922447 TCTTTCCCCAGCCATACATGT 59.078 47.619 2.69 2.69 0.00 3.21
174 177 1.680207 GCTCATCAATCTTTCCCCAGC 59.320 52.381 0.00 0.00 0.00 4.85
176 179 2.577563 TCTGCTCATCAATCTTTCCCCA 59.422 45.455 0.00 0.00 0.00 4.96
192 195 6.118170 AGCACATGTAAGAAATGTATCTGCT 58.882 36.000 0.00 0.00 36.10 4.24
194 197 7.977904 TGAAGCACATGTAAGAAATGTATCTG 58.022 34.615 0.00 0.00 36.10 2.90
208 211 3.688185 CAGTATCAAGCTGAAGCACATGT 59.312 43.478 4.90 0.00 45.16 3.21
210 213 3.947868 ACAGTATCAAGCTGAAGCACAT 58.052 40.909 4.90 0.00 45.16 3.21
220 223 3.806521 CCATCAGCAGTACAGTATCAAGC 59.193 47.826 0.00 0.00 0.00 4.01
242 245 9.807649 ATCATGAACTTGCCAATTAAGAATTAC 57.192 29.630 0.00 0.00 0.00 1.89
254 257 6.566141 CATTGTGATTATCATGAACTTGCCA 58.434 36.000 0.00 0.00 0.00 4.92
273 276 4.455877 GCTTCCACACTAAAGTAGCATTGT 59.544 41.667 0.00 0.00 0.00 2.71
275 278 4.911390 AGCTTCCACACTAAAGTAGCATT 58.089 39.130 5.02 0.00 29.56 3.56
312 325 2.035449 TCAGACACGGAACACTCGAAAT 59.965 45.455 0.00 0.00 0.00 2.17
317 330 2.440539 ACATCAGACACGGAACACTC 57.559 50.000 0.00 0.00 0.00 3.51
336 349 6.831353 TCCAACTTTCCATCAGAAGTACAAAA 59.169 34.615 0.00 0.00 35.40 2.44
377 390 2.450609 TACGCCCTCAGAAAAGTGTC 57.549 50.000 0.00 0.00 0.00 3.67
393 406 0.786581 GTGCATCGCATGGAGATACG 59.213 55.000 0.00 0.00 41.91 3.06
414 427 4.386312 CCCCACTTTGGATAGAAATAGGCA 60.386 45.833 0.00 0.00 40.96 4.75
435 449 4.956075 ACTGTATGAACATGAATTTCCCCC 59.044 41.667 0.00 0.00 34.37 5.40
437 451 6.924111 ACAACTGTATGAACATGAATTTCCC 58.076 36.000 0.00 0.00 34.37 3.97
438 452 8.081633 TCAACAACTGTATGAACATGAATTTCC 58.918 33.333 0.00 0.00 34.37 3.13
439 453 9.462174 TTCAACAACTGTATGAACATGAATTTC 57.538 29.630 0.00 0.00 34.37 2.17
611 638 7.386848 GTCTAAACTGTGGCTATGAGTGTAAAA 59.613 37.037 0.00 0.00 0.00 1.52
622 649 4.351874 AAAGCTGTCTAAACTGTGGCTA 57.648 40.909 0.00 0.00 0.00 3.93
649 676 6.872920 TGTGAGAAAGTTGTAAAGCCATTTT 58.127 32.000 0.00 0.00 0.00 1.82
692 719 1.625508 GGGGAAGTACCTGTGGGAGAT 60.626 57.143 0.00 0.00 38.98 2.75
718 745 1.269257 GGCTGTGGCTTGACAGAAAAC 60.269 52.381 13.19 0.00 45.39 2.43
762 798 1.469335 AACCTCTCGAACGAGCCCAA 61.469 55.000 17.71 1.89 41.71 4.12
775 811 2.093447 GGACCATTGACATCGAACCTCT 60.093 50.000 0.00 0.00 0.00 3.69
787 823 0.254747 GGATTCACCCGGACCATTGA 59.745 55.000 0.73 0.00 0.00 2.57
810 846 1.353076 ACGAATAAAGAACCGCCGTC 58.647 50.000 0.00 0.00 0.00 4.79
823 859 3.305897 CGCTTGATGTGCTTGTACGAATA 59.694 43.478 0.00 0.00 0.00 1.75
883 919 2.432456 GCACGCTGACATGACCGA 60.432 61.111 0.00 0.00 0.00 4.69
889 925 3.425713 CCTTGCGCACGCTGACAT 61.426 61.111 11.12 0.00 42.51 3.06
909 945 4.899239 CCGCAGGCGAGGATGTCC 62.899 72.222 16.21 0.00 46.14 4.02
1109 1145 5.134725 AGACAATGCTTCCCCATATCTTT 57.865 39.130 0.00 0.00 0.00 2.52
1239 1275 1.599047 CACCGGCATCCTCTTCAGT 59.401 57.895 0.00 0.00 0.00 3.41
1422 1458 1.137513 GGAACTGTCGACCTTCAACG 58.862 55.000 14.12 0.00 0.00 4.10
1615 1651 4.380843 TTTGGATGGCCTCTTCTTGTAA 57.619 40.909 3.32 0.00 34.31 2.41
1653 1689 0.251077 CAGCCTCAAGACCAAGCCTT 60.251 55.000 0.00 0.00 0.00 4.35
1677 1713 3.093717 AGAACACTGACGAACGTGAAT 57.906 42.857 4.19 0.00 35.23 2.57
1749 1785 3.855379 CCATGCAATTCTTGATTGTCACG 59.145 43.478 0.00 0.00 45.62 4.35
1874 1910 5.792712 ACTATAAGGGCATTCCAGGATACAT 59.207 40.000 0.00 0.00 38.24 2.29
2001 2037 4.913924 GCTCGAATATTGGAACATGCATTC 59.086 41.667 0.00 0.00 39.30 2.67
2091 2127 9.377312 GAATATAAATCAATCAGAGAGCTACCC 57.623 37.037 0.00 0.00 0.00 3.69
2182 2218 3.067180 CCCGCAATCAGAGCATTTATTGT 59.933 43.478 0.00 0.00 32.99 2.71
2243 2279 4.134379 TCTCTAAGAGCCTGCTGAAATG 57.866 45.455 0.00 0.00 0.00 2.32
2244 2280 4.444591 CCATCTCTAAGAGCCTGCTGAAAT 60.445 45.833 0.00 0.00 0.00 2.17
2255 2291 6.540551 GGAAGGCTTTAAACCATCTCTAAGAG 59.459 42.308 0.00 0.00 0.00 2.85
2277 2313 5.465532 TGCTTGAAAATGTAATGCTGGAA 57.534 34.783 0.00 0.00 0.00 3.53
2284 2320 8.370182 ACCAGAAAGAATGCTTGAAAATGTAAT 58.630 29.630 0.00 0.00 33.79 1.89
2313 2349 4.818546 ACAATTGAACTGAGAAGTCCAGTG 59.181 41.667 13.59 0.00 43.42 3.66
2407 2443 6.654959 TGGACTTCAAATATATCCGGAACAA 58.345 36.000 9.01 0.00 31.65 2.83
2410 2446 8.629158 CATTTTGGACTTCAAATATATCCGGAA 58.371 33.333 9.01 0.00 43.95 4.30
2469 2505 3.228188 AGCAGGTTTTTGTGATCTGGA 57.772 42.857 0.00 0.00 0.00 3.86
3025 3061 1.550976 ACCTCGTCCAAGGAGATCAAC 59.449 52.381 0.00 0.00 38.87 3.18
3285 3326 7.387673 CCTGGAAATTTTGTTACTCCATTTTCC 59.612 37.037 0.00 0.00 40.66 3.13
3373 3414 7.888250 TTTCATAGATGCTAAGAGAGTCAGA 57.112 36.000 0.00 0.00 0.00 3.27
3489 3571 3.646534 TGGCTAGAAGATGACATCAGGA 58.353 45.455 17.57 0.00 0.00 3.86
3506 3588 0.333993 ATGCAAGTCCTGGATTGGCT 59.666 50.000 18.17 0.00 30.67 4.75
3523 3605 3.181465 ACCTCGGTAACCAAGCATCTATG 60.181 47.826 0.00 0.00 0.00 2.23
3524 3606 3.039011 ACCTCGGTAACCAAGCATCTAT 58.961 45.455 0.00 0.00 0.00 1.98
3584 3666 7.025963 GCAGAAAATAAAGTGGTCAGAATCAG 58.974 38.462 0.00 0.00 0.00 2.90
3611 3693 3.697542 TGCTGATGCAGTGATGCTAAAAT 59.302 39.130 0.00 0.00 45.31 1.82
3614 3696 2.406596 TGCTGATGCAGTGATGCTAA 57.593 45.000 0.00 0.00 45.31 3.09
3752 3834 6.351881 CCCTCAGAAGCTTACAACCATAGTAA 60.352 42.308 0.00 0.00 0.00 2.24
3753 3835 5.128827 CCCTCAGAAGCTTACAACCATAGTA 59.871 44.000 0.00 0.00 0.00 1.82
3833 3915 2.039084 GTCCCACATCAAGACTGACCTT 59.961 50.000 0.00 0.00 33.30 3.50
3840 3924 2.100631 CCGCGTCCCACATCAAGAC 61.101 63.158 4.92 0.00 0.00 3.01
3854 3938 1.970917 GAATCTTCACTGCCACCGCG 61.971 60.000 0.00 0.00 38.08 6.46
3860 3944 2.027745 TGACTCCTGAATCTTCACTGCC 60.028 50.000 0.00 0.00 32.90 4.85
3861 3945 3.325293 TGACTCCTGAATCTTCACTGC 57.675 47.619 0.00 0.00 32.90 4.40
3877 3961 8.470657 TGAGCATATATGAGTTCTAGTTGACT 57.529 34.615 17.10 0.00 0.00 3.41
3879 3963 7.507277 ACCTGAGCATATATGAGTTCTAGTTGA 59.493 37.037 17.10 0.00 0.00 3.18
3982 4067 8.703604 TTAGACAGGAAATCAAGATTAGAACG 57.296 34.615 0.00 0.00 0.00 3.95
4135 4222 7.228108 GTGATGTATATGGCTTATGATGGATGG 59.772 40.741 3.33 0.00 0.00 3.51
4158 4247 5.720041 ACTAGTCTACTTATTGCTTGGGTGA 59.280 40.000 0.00 0.00 0.00 4.02
4169 4258 5.110940 GCGCTAGCAACTAGTCTACTTAT 57.889 43.478 16.45 0.00 44.35 1.73
4170 4259 4.548991 GCGCTAGCAACTAGTCTACTTA 57.451 45.455 16.45 0.00 44.35 2.24
4196 4285 0.379669 GAATCGGCAATGTCCTGCAG 59.620 55.000 6.78 6.78 44.52 4.41
4204 4293 6.974048 TCAACTAAATTCATGAATCGGCAATG 59.026 34.615 20.95 14.95 0.00 2.82
4211 4300 8.804743 CAGTGCAATCAACTAAATTCATGAATC 58.195 33.333 20.95 5.09 0.00 2.52
4221 4310 4.520111 ACATCAGCAGTGCAATCAACTAAA 59.480 37.500 19.20 0.00 0.00 1.85
4259 4348 1.609072 GTTCTGGCAGAAACTTGGTCC 59.391 52.381 30.06 12.41 35.75 4.46
4261 4350 2.689983 CAAGTTCTGGCAGAAACTTGGT 59.310 45.455 34.82 20.19 38.36 3.67
4305 4488 9.768662 AAGAAAGCATGATTTCAGTACAAAAAT 57.231 25.926 31.61 9.82 40.86 1.82
4316 4514 5.056894 ACTCAGCAAGAAAGCATGATTTC 57.943 39.130 25.27 25.27 39.09 2.17
4332 4530 7.200455 ACCACAGTACAAAATAAAAACTCAGC 58.800 34.615 0.00 0.00 0.00 4.26
4344 4542 9.877178 AACATTCAATTTTACCACAGTACAAAA 57.123 25.926 0.00 0.00 0.00 2.44
4352 4550 7.942341 ACCTCTAGAACATTCAATTTTACCACA 59.058 33.333 0.00 0.00 0.00 4.17
4362 4560 7.330946 CGTTGTATGAACCTCTAGAACATTCAA 59.669 37.037 13.89 12.98 33.29 2.69
4367 4565 5.970317 TCGTTGTATGAACCTCTAGAACA 57.030 39.130 0.00 0.00 0.00 3.18
4383 4581 5.028549 AGAAAGATCTATGCCATCGTTGT 57.971 39.130 0.00 0.00 32.88 3.32
4412 4610 5.917541 ATGGTGAAACACGTAACTAACTG 57.082 39.130 0.00 0.00 39.98 3.16
4418 4616 4.691685 TGTGGATATGGTGAAACACGTAAC 59.308 41.667 0.00 0.00 39.98 2.50
4419 4617 4.691685 GTGTGGATATGGTGAAACACGTAA 59.308 41.667 0.00 0.00 39.98 3.18
4421 4619 3.071479 GTGTGGATATGGTGAAACACGT 58.929 45.455 0.00 0.00 39.98 4.49
4422 4620 3.125146 CAGTGTGGATATGGTGAAACACG 59.875 47.826 0.00 0.00 42.05 4.49
4434 4636 6.327365 AGACATGTGGAATATCAGTGTGGATA 59.673 38.462 1.15 0.00 34.47 2.59
4441 4643 3.960755 TCCGAGACATGTGGAATATCAGT 59.039 43.478 1.15 0.00 0.00 3.41
4456 4658 6.183309 AGCTTCATACAAAAATTCCGAGAC 57.817 37.500 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.