Multiple sequence alignment - TraesCS6D01G286000

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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 TraesCS6D01G286000 chr6D 100.000 3559 0 0 1 3559 394620335 394616777 0.000000e+00 6573
1 TraesCS6D01G286000 chr6B 92.983 2836 127 37 339 3148 590669231 590666442 0.000000e+00 4069
2 TraesCS6D01G286000 chr6B 91.275 149 7 2 1 149 590669686 590669544 7.790000e-47 198
3 TraesCS6D01G286000 chr6B 80.321 249 35 11 2993 3239 590666545 590666309 3.650000e-40 176
4 TraesCS6D01G286000 chr6B 93.103 116 7 1 3381 3495 590666169 590666054 6.110000e-38 169
5 TraesCS6D01G286000 chr6B 83.217 143 7 6 3246 3387 590666326 590666200 8.070000e-22 115
6 TraesCS6D01G286000 chr6A 95.169 1511 58 7 1651 3149 540617226 540615719 0.000000e+00 2372
7 TraesCS6D01G286000 chr6A 92.131 1347 44 25 346 1663 540618709 540617396 0.000000e+00 1844
8 TraesCS6D01G286000 chr6A 92.479 359 13 4 1 354 540619228 540618879 5.300000e-138 501
9 TraesCS6D01G286000 chr6A 81.113 503 54 21 2993 3488 540615828 540615360 7.260000e-97 364
10 TraesCS6D01G286000 chr7B 82.593 540 90 4 1994 2531 105559527 105558990 1.160000e-129 473
11 TraesCS6D01G286000 chr7D 82.037 540 93 3 1994 2531 140327753 140327216 1.160000e-124 457
12 TraesCS6D01G286000 chr7A 82.037 540 93 4 1994 2531 142158590 142158053 1.160000e-124 457


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 TraesCS6D01G286000 chr6D 394616777 394620335 3558 True 6573.00 6573 100.0000 1 3559 1 chr6D.!!$R1 3558
1 TraesCS6D01G286000 chr6B 590666054 590669686 3632 True 945.40 4069 88.1798 1 3495 5 chr6B.!!$R1 3494
2 TraesCS6D01G286000 chr6A 540615360 540619228 3868 True 1270.25 2372 90.2230 1 3488 4 chr6A.!!$R1 3487
3 TraesCS6D01G286000 chr7B 105558990 105559527 537 True 473.00 473 82.5930 1994 2531 1 chr7B.!!$R1 537
4 TraesCS6D01G286000 chr7D 140327216 140327753 537 True 457.00 457 82.0370 1994 2531 1 chr7D.!!$R1 537
5 TraesCS6D01G286000 chr7A 142158053 142158590 537 True 457.00 457 82.0370 1994 2531 1 chr7A.!!$R1 537

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
426 768 0.183014 AGGCTGCCGCTCTACTACTA 59.817 55.0 13.96 0.0 36.09 1.82 F
1257 1637 0.040646 TCCTCGCCCTTTCCTGTCTA 59.959 55.0 0.00 0.0 0.00 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1924 1.203050 CCACAGGTCAGGTCCCAAAAT 60.203 52.381 0.00 0.0 0.00 1.82 R
2713 3293 1.173913 GGGACTCCCAAACCAAATCG 58.826 55.000 9.53 0.0 44.65 3.34 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
141 193 1.955080 GGTAGCTGGTAGTGCGTAGAT 59.045 52.381 0.00 0.00 35.28 1.98
166 330 4.513442 TCGGTTGATCCATCTTCGAAATT 58.487 39.130 0.00 0.00 35.57 1.82
167 331 4.570772 TCGGTTGATCCATCTTCGAAATTC 59.429 41.667 0.00 0.00 35.57 2.17
182 346 8.965172 TCTTCGAAATTCGCAGTTTAGATATAC 58.035 33.333 13.97 0.00 40.21 1.47
183 347 8.867112 TTCGAAATTCGCAGTTTAGATATACT 57.133 30.769 10.93 0.00 40.21 2.12
184 348 9.955208 TTCGAAATTCGCAGTTTAGATATACTA 57.045 29.630 10.93 0.00 40.21 1.82
185 349 9.390795 TCGAAATTCGCAGTTTAGATATACTAC 57.609 33.333 10.93 0.00 40.21 2.73
186 350 9.395707 CGAAATTCGCAGTTTAGATATACTACT 57.604 33.333 1.35 0.00 31.14 2.57
207 371 9.978044 ACTACTTTAGTGATCTAAAACGTCTTT 57.022 29.630 0.00 0.00 42.97 2.52
228 392 1.729284 ATTAGTTTACGGCGGTGGTG 58.271 50.000 13.24 0.00 0.00 4.17
297 461 3.053619 AGAAAGTGGTTCCTGGTCAAGTT 60.054 43.478 0.00 0.00 36.86 2.66
308 472 1.578206 GGTCAAGTTCGGCAGGAAGC 61.578 60.000 0.00 0.00 44.65 3.86
342 506 0.391130 TTCCGTCGCAATCTTCTGGG 60.391 55.000 0.00 0.00 0.00 4.45
410 752 1.069935 GAATGGACTCGGGCTAGGC 59.930 63.158 8.00 8.00 0.00 3.93
411 753 1.383248 AATGGACTCGGGCTAGGCT 60.383 57.895 16.80 0.00 0.00 4.58
420 762 3.227276 GGCTAGGCTGCCGCTCTA 61.227 66.667 13.96 0.00 43.74 2.43
426 768 0.183014 AGGCTGCCGCTCTACTACTA 59.817 55.000 13.96 0.00 36.09 1.82
440 783 5.198965 TCTACTACTACGCAGGAAGGAAAT 58.801 41.667 0.00 0.00 0.00 2.17
441 784 4.388378 ACTACTACGCAGGAAGGAAATC 57.612 45.455 0.00 0.00 0.00 2.17
442 785 4.024670 ACTACTACGCAGGAAGGAAATCT 58.975 43.478 0.00 0.00 0.00 2.40
443 786 3.528597 ACTACGCAGGAAGGAAATCTC 57.471 47.619 0.00 0.00 0.00 2.75
730 1100 0.610687 GCGCCTATATTCCAGCCTCT 59.389 55.000 0.00 0.00 0.00 3.69
731 1101 1.674221 GCGCCTATATTCCAGCCTCTG 60.674 57.143 0.00 0.00 0.00 3.35
1256 1636 1.229209 TCCTCGCCCTTTCCTGTCT 60.229 57.895 0.00 0.00 0.00 3.41
1257 1637 0.040646 TCCTCGCCCTTTCCTGTCTA 59.959 55.000 0.00 0.00 0.00 2.59
1258 1638 1.123928 CCTCGCCCTTTCCTGTCTAT 58.876 55.000 0.00 0.00 0.00 1.98
1259 1639 2.091499 TCCTCGCCCTTTCCTGTCTATA 60.091 50.000 0.00 0.00 0.00 1.31
1260 1640 2.900546 CCTCGCCCTTTCCTGTCTATAT 59.099 50.000 0.00 0.00 0.00 0.86
1261 1641 4.087182 CCTCGCCCTTTCCTGTCTATATA 58.913 47.826 0.00 0.00 0.00 0.86
1536 1924 2.423185 CCGCATTCCACATAGAGCAAAA 59.577 45.455 0.00 0.00 0.00 2.44
1556 1947 0.184933 TTTTGGGACCTGACCTGTGG 59.815 55.000 0.00 0.00 0.00 4.17
1636 2027 1.189752 CTGGAGAGTTGCTCAGCCTA 58.810 55.000 0.00 0.00 45.81 3.93
1660 2233 4.673311 ACGTTTTTGCGTTTATACTTGCTG 59.327 37.500 0.00 0.00 43.04 4.41
1677 2250 6.064717 ACTTGCTGTGGAAGATAAGAAACTT 58.935 36.000 5.86 0.00 0.00 2.66
1699 2272 2.359848 ACCGTTGCTAACAAAGAAACCC 59.640 45.455 0.00 0.00 40.31 4.11
1742 2317 5.508825 CGAGGAGCTGATTCTAGTATTGCTT 60.509 44.000 0.00 0.00 0.00 3.91
1835 2414 9.257651 ACTACACTTTATGTTGACTGAAAGTAC 57.742 33.333 11.15 0.00 45.98 2.73
1862 2441 2.396590 TAGCGTCTCATGGGGAAAAC 57.603 50.000 0.00 0.00 0.00 2.43
1866 2445 1.812571 CGTCTCATGGGGAAAACTTGG 59.187 52.381 0.00 0.00 0.00 3.61
1874 2453 1.484653 GGGGAAAACTTGGTTTGCAGT 59.515 47.619 5.13 0.00 35.80 4.40
1935 2514 3.826729 AGGCCTTAACAATTCTTGTGGAC 59.173 43.478 0.00 0.00 44.59 4.02
1945 2524 5.531287 ACAATTCTTGTGGACTTTACCTGAC 59.469 40.000 0.00 0.00 43.48 3.51
1955 2535 4.762251 GGACTTTACCTGACAGCTTCATTT 59.238 41.667 0.00 0.00 32.17 2.32
1960 2540 7.277981 ACTTTACCTGACAGCTTCATTTATACG 59.722 37.037 0.00 0.00 32.17 3.06
2210 2790 2.224793 GGCTCTTTACAACCACCCTCTT 60.225 50.000 0.00 0.00 0.00 2.85
2752 3337 7.076446 AGTCCCATCTTGTATCAAGGTATAGT 58.924 38.462 9.18 0.00 0.00 2.12
3062 3647 1.937191 TGATCCACCAGTGAGCTGTA 58.063 50.000 0.00 0.00 41.02 2.74
3063 3648 2.470990 TGATCCACCAGTGAGCTGTAT 58.529 47.619 0.00 0.00 41.02 2.29
3068 3653 2.744202 CCACCAGTGAGCTGTATTGAAC 59.256 50.000 0.00 0.00 41.02 3.18
3078 3663 9.726438 AGTGAGCTGTATTGAACTATAGTTTTT 57.274 29.630 18.96 9.67 38.56 1.94
3115 3701 1.199327 CCAGTGAGCTGTGCTGAAATG 59.801 52.381 0.00 0.00 39.88 2.32
3116 3702 2.148768 CAGTGAGCTGTGCTGAAATGA 58.851 47.619 0.00 0.00 39.88 2.57
3118 3704 3.004002 CAGTGAGCTGTGCTGAAATGAAA 59.996 43.478 0.00 0.00 39.88 2.69
3119 3705 3.825014 AGTGAGCTGTGCTGAAATGAAAT 59.175 39.130 0.00 0.00 39.88 2.17
3157 3791 4.499865 GCTGATCATCATCATTTGCAGCTT 60.500 41.667 0.00 0.00 42.91 3.74
3226 3860 3.075005 GCCGCCAGTCCAGGACTA 61.075 66.667 22.52 0.00 41.37 2.59
3227 3861 2.656069 GCCGCCAGTCCAGGACTAA 61.656 63.158 22.52 0.00 41.37 2.24
3228 3862 1.980052 CCGCCAGTCCAGGACTAAA 59.020 57.895 22.52 0.00 41.37 1.85
3229 3863 0.391263 CCGCCAGTCCAGGACTAAAC 60.391 60.000 22.52 12.91 41.37 2.01
3230 3864 0.608640 CGCCAGTCCAGGACTAAACT 59.391 55.000 22.52 0.00 41.37 2.66
3231 3865 1.673033 CGCCAGTCCAGGACTAAACTG 60.673 57.143 22.52 10.16 41.37 3.16
3232 3866 1.623811 GCCAGTCCAGGACTAAACTGA 59.376 52.381 22.52 0.00 41.37 3.41
3233 3867 2.038557 GCCAGTCCAGGACTAAACTGAA 59.961 50.000 22.52 0.00 41.37 3.02
3234 3868 3.307762 GCCAGTCCAGGACTAAACTGAAT 60.308 47.826 22.52 0.00 41.37 2.57
3235 3869 4.807643 GCCAGTCCAGGACTAAACTGAATT 60.808 45.833 22.52 0.00 41.37 2.17
3236 3870 5.316987 CCAGTCCAGGACTAAACTGAATTT 58.683 41.667 22.52 0.00 41.37 1.82
3237 3871 5.770162 CCAGTCCAGGACTAAACTGAATTTT 59.230 40.000 22.52 0.00 41.37 1.82
3238 3872 6.294176 CCAGTCCAGGACTAAACTGAATTTTG 60.294 42.308 22.52 5.77 41.37 2.44
3239 3873 6.486657 CAGTCCAGGACTAAACTGAATTTTGA 59.513 38.462 22.52 0.00 41.37 2.69
3240 3874 7.175641 CAGTCCAGGACTAAACTGAATTTTGAT 59.824 37.037 22.52 0.00 41.37 2.57
3241 3875 7.391833 AGTCCAGGACTAAACTGAATTTTGATC 59.608 37.037 21.66 0.00 41.51 2.92
3242 3876 7.391833 GTCCAGGACTAAACTGAATTTTGATCT 59.608 37.037 12.94 0.00 38.20 2.75
3243 3877 7.391554 TCCAGGACTAAACTGAATTTTGATCTG 59.608 37.037 0.00 0.00 38.20 2.90
3244 3878 7.362401 CCAGGACTAAACTGAATTTTGATCTGG 60.362 40.741 0.00 0.00 38.62 3.86
3278 3912 4.591998 ATTTTGTTTGTTCGTTGCAACC 57.408 36.364 23.42 10.47 0.00 3.77
3279 3913 1.618861 TTGTTTGTTCGTTGCAACCG 58.381 45.000 23.42 17.65 0.00 4.44
3280 3914 0.803117 TGTTTGTTCGTTGCAACCGA 59.197 45.000 23.42 19.52 0.00 4.69
3281 3915 1.185189 GTTTGTTCGTTGCAACCGAC 58.815 50.000 23.42 20.42 33.41 4.79
3411 4084 5.212532 AGATTACTCTATGGCAGCTGAAG 57.787 43.478 20.43 8.64 0.00 3.02
3488 4161 4.762251 GCCTAGAACATGAACCAGAAAGTT 59.238 41.667 0.00 0.00 0.00 2.66
3495 4168 4.709397 ACATGAACCAGAAAGTTGGACAAA 59.291 37.500 0.00 0.00 40.87 2.83
3496 4169 4.981806 TGAACCAGAAAGTTGGACAAAG 57.018 40.909 0.00 0.00 40.87 2.77
3497 4170 3.130340 TGAACCAGAAAGTTGGACAAAGC 59.870 43.478 0.00 0.00 40.87 3.51
3498 4171 3.018423 ACCAGAAAGTTGGACAAAGCT 57.982 42.857 0.00 0.00 40.87 3.74
3499 4172 4.164843 ACCAGAAAGTTGGACAAAGCTA 57.835 40.909 0.00 0.00 40.87 3.32
3500 4173 4.137543 ACCAGAAAGTTGGACAAAGCTAG 58.862 43.478 0.00 0.00 40.87 3.42
3501 4174 3.057946 CCAGAAAGTTGGACAAAGCTAGC 60.058 47.826 6.62 6.62 40.87 3.42
3502 4175 2.808543 AGAAAGTTGGACAAAGCTAGCG 59.191 45.455 9.55 0.00 0.00 4.26
3503 4176 0.875059 AAGTTGGACAAAGCTAGCGC 59.125 50.000 9.55 0.00 0.00 5.92
3504 4177 0.250295 AGTTGGACAAAGCTAGCGCA 60.250 50.000 11.47 0.00 39.10 6.09
3505 4178 0.110192 GTTGGACAAAGCTAGCGCAC 60.110 55.000 11.47 0.00 39.10 5.34
3506 4179 0.533978 TTGGACAAAGCTAGCGCACA 60.534 50.000 11.47 1.38 39.10 4.57
3507 4180 0.533978 TGGACAAAGCTAGCGCACAA 60.534 50.000 11.47 0.00 39.10 3.33
3508 4181 0.110192 GGACAAAGCTAGCGCACAAC 60.110 55.000 11.47 0.00 39.10 3.32
3510 4183 1.154413 CAAAGCTAGCGCACAACGG 60.154 57.895 11.47 0.00 43.93 4.44
3511 4184 1.301401 AAAGCTAGCGCACAACGGA 60.301 52.632 11.47 0.00 43.93 4.69
3512 4185 1.291877 AAAGCTAGCGCACAACGGAG 61.292 55.000 11.47 0.00 43.93 4.63
3513 4186 2.432628 GCTAGCGCACAACGGAGT 60.433 61.111 11.47 0.00 43.93 3.85
3514 4187 2.730672 GCTAGCGCACAACGGAGTG 61.731 63.158 11.47 5.27 43.93 3.51
3515 4188 1.080772 CTAGCGCACAACGGAGTGA 60.081 57.895 11.47 0.00 45.00 3.41
3516 4189 1.344942 CTAGCGCACAACGGAGTGAC 61.345 60.000 11.47 4.70 45.00 3.67
3517 4190 2.758770 TAGCGCACAACGGAGTGACC 62.759 60.000 11.47 3.46 45.00 4.02
3518 4191 3.041940 CGCACAACGGAGTGACCC 61.042 66.667 12.86 0.00 45.00 4.46
3526 4199 3.787394 GGAGTGACCCGACCAAGA 58.213 61.111 0.00 0.00 0.00 3.02
3527 4200 2.287829 GGAGTGACCCGACCAAGAT 58.712 57.895 0.00 0.00 0.00 2.40
3528 4201 0.175989 GGAGTGACCCGACCAAGATC 59.824 60.000 0.00 0.00 0.00 2.75
3529 4202 1.187087 GAGTGACCCGACCAAGATCT 58.813 55.000 0.00 0.00 0.00 2.75
3530 4203 1.135333 GAGTGACCCGACCAAGATCTC 59.865 57.143 0.00 0.00 0.00 2.75
3531 4204 0.179134 GTGACCCGACCAAGATCTCG 60.179 60.000 0.00 0.00 0.00 4.04
3532 4205 0.323087 TGACCCGACCAAGATCTCGA 60.323 55.000 0.00 0.00 31.24 4.04
3533 4206 0.100861 GACCCGACCAAGATCTCGAC 59.899 60.000 0.00 0.00 31.24 4.20
3534 4207 0.611062 ACCCGACCAAGATCTCGACA 60.611 55.000 0.00 0.00 31.24 4.35
3535 4208 0.179134 CCCGACCAAGATCTCGACAC 60.179 60.000 0.00 0.00 31.24 3.67
3536 4209 0.179134 CCGACCAAGATCTCGACACC 60.179 60.000 0.00 0.00 31.24 4.16
3537 4210 0.526211 CGACCAAGATCTCGACACCA 59.474 55.000 0.00 0.00 31.24 4.17
3538 4211 1.067846 CGACCAAGATCTCGACACCAA 60.068 52.381 0.00 0.00 31.24 3.67
3539 4212 2.417379 CGACCAAGATCTCGACACCAAT 60.417 50.000 0.00 0.00 31.24 3.16
3540 4213 3.181490 CGACCAAGATCTCGACACCAATA 60.181 47.826 0.00 0.00 31.24 1.90
3541 4214 4.363999 GACCAAGATCTCGACACCAATAG 58.636 47.826 0.00 0.00 0.00 1.73
3542 4215 3.126831 CCAAGATCTCGACACCAATAGC 58.873 50.000 0.00 0.00 0.00 2.97
3543 4216 3.430790 CCAAGATCTCGACACCAATAGCA 60.431 47.826 0.00 0.00 0.00 3.49
3544 4217 4.183865 CAAGATCTCGACACCAATAGCAA 58.816 43.478 0.00 0.00 0.00 3.91
3545 4218 3.786635 AGATCTCGACACCAATAGCAAC 58.213 45.455 0.00 0.00 0.00 4.17
3546 4219 3.195610 AGATCTCGACACCAATAGCAACA 59.804 43.478 0.00 0.00 0.00 3.33
3547 4220 2.683968 TCTCGACACCAATAGCAACAC 58.316 47.619 0.00 0.00 0.00 3.32
3548 4221 2.036604 TCTCGACACCAATAGCAACACA 59.963 45.455 0.00 0.00 0.00 3.72
3549 4222 2.805671 CTCGACACCAATAGCAACACAA 59.194 45.455 0.00 0.00 0.00 3.33
3550 4223 2.546368 TCGACACCAATAGCAACACAAC 59.454 45.455 0.00 0.00 0.00 3.32
3551 4224 2.350388 CGACACCAATAGCAACACAACC 60.350 50.000 0.00 0.00 0.00 3.77
3552 4225 1.606668 ACACCAATAGCAACACAACCG 59.393 47.619 0.00 0.00 0.00 4.44
3553 4226 1.068610 CACCAATAGCAACACAACCGG 60.069 52.381 0.00 0.00 0.00 5.28
3554 4227 1.202830 ACCAATAGCAACACAACCGGA 60.203 47.619 9.46 0.00 0.00 5.14
3555 4228 2.091541 CCAATAGCAACACAACCGGAT 58.908 47.619 9.46 0.00 0.00 4.18
3556 4229 2.097466 CCAATAGCAACACAACCGGATC 59.903 50.000 9.46 0.00 0.00 3.36
3557 4230 2.746904 CAATAGCAACACAACCGGATCA 59.253 45.455 9.46 0.00 0.00 2.92
3558 4231 2.779755 TAGCAACACAACCGGATCAT 57.220 45.000 9.46 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.662044 ACGACACGTTCCAGTACCC 59.338 57.895 0.00 0.00 36.35 3.69
141 193 4.929819 TCGAAGATGGATCAACCGAATA 57.070 40.909 0.00 0.00 42.61 1.75
207 371 3.260740 CACCACCGCCGTAAACTAATTA 58.739 45.455 0.00 0.00 0.00 1.40
208 372 2.078392 CACCACCGCCGTAAACTAATT 58.922 47.619 0.00 0.00 0.00 1.40
297 461 2.665000 CTCCTTGCTTCCTGCCGA 59.335 61.111 0.00 0.00 42.00 5.54
308 472 1.089920 CGGAACTTGATGGCTCCTTG 58.910 55.000 0.00 0.00 0.00 3.61
362 703 1.164041 CGTTGCTCGTTTGACCCCTT 61.164 55.000 0.00 0.00 34.52 3.95
410 752 0.041135 GCGTAGTAGTAGAGCGGCAG 60.041 60.000 1.45 0.00 0.00 4.85
411 753 0.745486 TGCGTAGTAGTAGAGCGGCA 60.745 55.000 1.45 0.00 0.00 5.69
414 756 1.579698 TCCTGCGTAGTAGTAGAGCG 58.420 55.000 0.00 0.00 39.06 5.03
415 757 2.291190 CCTTCCTGCGTAGTAGTAGAGC 59.709 54.545 0.00 0.00 39.06 4.09
417 759 3.920231 TCCTTCCTGCGTAGTAGTAGA 57.080 47.619 0.00 0.00 39.06 2.59
418 760 4.978083 TTTCCTTCCTGCGTAGTAGTAG 57.022 45.455 0.00 0.00 39.06 2.57
419 761 5.198965 AGATTTCCTTCCTGCGTAGTAGTA 58.801 41.667 0.00 0.00 39.06 1.82
420 762 4.024670 AGATTTCCTTCCTGCGTAGTAGT 58.975 43.478 0.00 0.00 39.06 2.73
426 768 2.503356 AGATGAGATTTCCTTCCTGCGT 59.497 45.455 0.00 0.00 0.00 5.24
440 783 3.351794 AGACCACGACAGTAGATGAGA 57.648 47.619 0.00 0.00 0.00 3.27
441 784 3.440522 TGAAGACCACGACAGTAGATGAG 59.559 47.826 0.00 0.00 0.00 2.90
442 785 3.190744 GTGAAGACCACGACAGTAGATGA 59.809 47.826 0.00 0.00 35.86 2.92
443 786 3.502920 GTGAAGACCACGACAGTAGATG 58.497 50.000 0.00 0.00 35.86 2.90
510 867 2.668212 CGGTGGCGATGTTGTGGT 60.668 61.111 0.00 0.00 0.00 4.16
776 1146 0.250727 TTGGAGGACTTTTCAGCGGG 60.251 55.000 0.00 0.00 0.00 6.13
1536 1924 1.203050 CCACAGGTCAGGTCCCAAAAT 60.203 52.381 0.00 0.00 0.00 1.82
1660 2233 6.620089 GCAACGGTAAGTTTCTTATCTTCCAC 60.620 42.308 0.00 0.00 42.02 4.02
1677 2250 3.565063 GGGTTTCTTTGTTAGCAACGGTA 59.435 43.478 0.00 0.00 31.67 4.02
1699 2272 2.617308 TCGCTACTATTTCAGAGGGTCG 59.383 50.000 0.00 0.00 0.00 4.79
1742 2317 5.368145 ACAAATGTACAACTGCTTCTCAGA 58.632 37.500 0.00 0.00 45.72 3.27
1759 2334 7.420002 ACATGCTGTATGCTATTGTACAAATG 58.580 34.615 13.23 9.31 40.59 2.32
1779 2354 5.059833 TCAATTTTGGGGTTTGTAACATGC 58.940 37.500 0.00 0.00 0.00 4.06
1835 2414 2.352651 CCCATGAGACGCTATGTTGTTG 59.647 50.000 0.00 0.00 0.00 3.33
1847 2426 2.876581 ACCAAGTTTTCCCCATGAGAC 58.123 47.619 0.00 0.00 0.00 3.36
1874 2453 4.013728 ACTGCTCGTTAAATTGGGCATTA 58.986 39.130 0.00 0.00 0.00 1.90
1935 2514 7.621991 CGTATAAATGAAGCTGTCAGGTAAAG 58.378 38.462 4.68 0.00 40.43 1.85
1945 2524 6.546395 AGAAACTTGCGTATAAATGAAGCTG 58.454 36.000 0.00 0.00 0.00 4.24
1955 2535 8.830201 TTAACCACTTTAGAAACTTGCGTATA 57.170 30.769 0.00 0.00 0.00 1.47
1973 2553 6.200854 CCTGCAGTTCAAGAAAATTTAACCAC 59.799 38.462 13.81 0.00 0.00 4.16
1987 2567 3.826524 TCACCAATAACCTGCAGTTCAA 58.173 40.909 13.81 0.00 40.05 2.69
2210 2790 1.559682 GTGTCCAGAATAAGGCCCTCA 59.440 52.381 0.00 0.00 0.00 3.86
2423 3003 6.259387 GGACGAAGAAAGGTTGAGAAAAGTTA 59.741 38.462 0.00 0.00 0.00 2.24
2432 3012 3.211045 CCAAAGGACGAAGAAAGGTTGA 58.789 45.455 0.00 0.00 0.00 3.18
2654 3234 7.303182 TCACTATATGAACCAGGACATAAGG 57.697 40.000 12.53 10.90 33.02 2.69
2713 3293 1.173913 GGGACTCCCAAACCAAATCG 58.826 55.000 9.53 0.00 44.65 3.34
2773 3358 3.197766 AGTGGATGCCGAGTATTCTTTCA 59.802 43.478 0.00 0.00 0.00 2.69
2890 3475 1.327303 GAAATGGGCAGGACAACACA 58.673 50.000 0.00 0.00 0.00 3.72
3052 3637 9.726438 AAAAACTATAGTTCAATACAGCTCACT 57.274 29.630 18.28 0.00 37.25 3.41
3118 3704 9.399797 TGATGATCAGCAGAAACAAAACTATAT 57.600 29.630 10.16 0.00 0.00 0.86
3119 3705 8.791327 TGATGATCAGCAGAAACAAAACTATA 57.209 30.769 10.16 0.00 0.00 1.31
3157 3791 5.064707 GCAGAACTACAGAACTGAAACACAA 59.935 40.000 8.87 0.00 32.90 3.33
3221 3855 6.127619 CCCCAGATCAAAATTCAGTTTAGTCC 60.128 42.308 0.00 0.00 0.00 3.85
3222 3856 6.659242 TCCCCAGATCAAAATTCAGTTTAGTC 59.341 38.462 0.00 0.00 0.00 2.59
3223 3857 6.434340 GTCCCCAGATCAAAATTCAGTTTAGT 59.566 38.462 0.00 0.00 0.00 2.24
3224 3858 6.660949 AGTCCCCAGATCAAAATTCAGTTTAG 59.339 38.462 0.00 0.00 0.00 1.85
3225 3859 6.552008 AGTCCCCAGATCAAAATTCAGTTTA 58.448 36.000 0.00 0.00 0.00 2.01
3226 3860 5.397360 AGTCCCCAGATCAAAATTCAGTTT 58.603 37.500 0.00 0.00 0.00 2.66
3227 3861 5.003096 AGTCCCCAGATCAAAATTCAGTT 57.997 39.130 0.00 0.00 0.00 3.16
3228 3862 4.664688 AGTCCCCAGATCAAAATTCAGT 57.335 40.909 0.00 0.00 0.00 3.41
3229 3863 6.660949 AGTTTAGTCCCCAGATCAAAATTCAG 59.339 38.462 0.00 0.00 0.00 3.02
3230 3864 6.434028 CAGTTTAGTCCCCAGATCAAAATTCA 59.566 38.462 0.00 0.00 0.00 2.57
3231 3865 6.659242 TCAGTTTAGTCCCCAGATCAAAATTC 59.341 38.462 0.00 0.00 0.00 2.17
3232 3866 6.552008 TCAGTTTAGTCCCCAGATCAAAATT 58.448 36.000 0.00 0.00 0.00 1.82
3233 3867 6.139679 TCAGTTTAGTCCCCAGATCAAAAT 57.860 37.500 0.00 0.00 0.00 1.82
3234 3868 5.576563 TCAGTTTAGTCCCCAGATCAAAA 57.423 39.130 0.00 0.00 0.00 2.44
3235 3869 5.576563 TTCAGTTTAGTCCCCAGATCAAA 57.423 39.130 0.00 0.00 0.00 2.69
3236 3870 5.779241 ATTCAGTTTAGTCCCCAGATCAA 57.221 39.130 0.00 0.00 0.00 2.57
3237 3871 5.779241 AATTCAGTTTAGTCCCCAGATCA 57.221 39.130 0.00 0.00 0.00 2.92
3238 3872 6.434340 ACAAAATTCAGTTTAGTCCCCAGATC 59.566 38.462 0.00 0.00 0.00 2.75
3239 3873 6.314917 ACAAAATTCAGTTTAGTCCCCAGAT 58.685 36.000 0.00 0.00 0.00 2.90
3240 3874 5.701224 ACAAAATTCAGTTTAGTCCCCAGA 58.299 37.500 0.00 0.00 0.00 3.86
3241 3875 6.405278 AACAAAATTCAGTTTAGTCCCCAG 57.595 37.500 0.00 0.00 0.00 4.45
3242 3876 6.155393 ACAAACAAAATTCAGTTTAGTCCCCA 59.845 34.615 7.60 0.00 36.28 4.96
3243 3877 6.578944 ACAAACAAAATTCAGTTTAGTCCCC 58.421 36.000 7.60 0.00 36.28 4.81
3244 3878 7.043656 CGAACAAACAAAATTCAGTTTAGTCCC 60.044 37.037 7.60 5.23 36.28 4.46
3281 3915 8.547069 GTTCAGCTATTTACAGATAAGCTTCTG 58.453 37.037 12.89 12.89 46.94 3.02
3488 4161 0.533978 TTGTGCGCTAGCTTTGTCCA 60.534 50.000 13.93 0.00 45.42 4.02
3495 4168 2.125912 CTCCGTTGTGCGCTAGCT 60.126 61.111 13.93 0.00 45.42 3.32
3496 4169 2.432628 ACTCCGTTGTGCGCTAGC 60.433 61.111 9.73 4.06 45.41 3.42
3497 4170 1.080772 TCACTCCGTTGTGCGCTAG 60.081 57.895 9.73 0.00 39.71 3.42
3498 4171 1.372499 GTCACTCCGTTGTGCGCTA 60.372 57.895 9.73 0.00 39.71 4.26
3499 4172 2.661866 GTCACTCCGTTGTGCGCT 60.662 61.111 9.73 0.00 39.71 5.92
3500 4173 3.712881 GGTCACTCCGTTGTGCGC 61.713 66.667 0.00 0.00 39.71 6.09
3501 4174 3.041940 GGGTCACTCCGTTGTGCG 61.042 66.667 0.83 0.00 37.81 5.34
3502 4175 3.041940 CGGGTCACTCCGTTGTGC 61.042 66.667 0.00 0.00 44.60 4.57
3509 4182 0.175989 GATCTTGGTCGGGTCACTCC 59.824 60.000 0.00 0.00 0.00 3.85
3510 4183 1.135333 GAGATCTTGGTCGGGTCACTC 59.865 57.143 0.00 0.00 0.00 3.51
3511 4184 1.187087 GAGATCTTGGTCGGGTCACT 58.813 55.000 0.00 0.00 0.00 3.41
3512 4185 0.179134 CGAGATCTTGGTCGGGTCAC 60.179 60.000 1.50 0.00 32.40 3.67
3513 4186 0.323087 TCGAGATCTTGGTCGGGTCA 60.323 55.000 10.19 0.00 36.81 4.02
3514 4187 0.100861 GTCGAGATCTTGGTCGGGTC 59.899 60.000 10.19 0.00 36.81 4.46
3515 4188 0.611062 TGTCGAGATCTTGGTCGGGT 60.611 55.000 10.19 0.00 36.81 5.28
3516 4189 0.179134 GTGTCGAGATCTTGGTCGGG 60.179 60.000 10.19 0.00 36.81 5.14
3517 4190 0.179134 GGTGTCGAGATCTTGGTCGG 60.179 60.000 10.19 0.00 36.81 4.79
3518 4191 0.526211 TGGTGTCGAGATCTTGGTCG 59.474 55.000 10.19 2.93 37.54 4.79
3519 4192 2.743636 TTGGTGTCGAGATCTTGGTC 57.256 50.000 10.19 4.89 0.00 4.02
3520 4193 3.430929 GCTATTGGTGTCGAGATCTTGGT 60.431 47.826 10.19 0.00 0.00 3.67
3521 4194 3.126831 GCTATTGGTGTCGAGATCTTGG 58.873 50.000 10.19 0.00 0.00 3.61
3522 4195 3.785486 TGCTATTGGTGTCGAGATCTTG 58.215 45.455 3.24 3.24 0.00 3.02
3523 4196 4.184629 GTTGCTATTGGTGTCGAGATCTT 58.815 43.478 0.00 0.00 0.00 2.40
3524 4197 3.195610 TGTTGCTATTGGTGTCGAGATCT 59.804 43.478 0.00 0.00 0.00 2.75
3525 4198 3.307242 GTGTTGCTATTGGTGTCGAGATC 59.693 47.826 0.00 0.00 0.00 2.75
3526 4199 3.262420 GTGTTGCTATTGGTGTCGAGAT 58.738 45.455 0.00 0.00 0.00 2.75
3527 4200 2.036604 TGTGTTGCTATTGGTGTCGAGA 59.963 45.455 0.00 0.00 0.00 4.04
3528 4201 2.412870 TGTGTTGCTATTGGTGTCGAG 58.587 47.619 0.00 0.00 0.00 4.04
3529 4202 2.535012 TGTGTTGCTATTGGTGTCGA 57.465 45.000 0.00 0.00 0.00 4.20
3530 4203 2.350388 GGTTGTGTTGCTATTGGTGTCG 60.350 50.000 0.00 0.00 0.00 4.35
3531 4204 2.350388 CGGTTGTGTTGCTATTGGTGTC 60.350 50.000 0.00 0.00 0.00 3.67
3532 4205 1.606668 CGGTTGTGTTGCTATTGGTGT 59.393 47.619 0.00 0.00 0.00 4.16
3533 4206 1.068610 CCGGTTGTGTTGCTATTGGTG 60.069 52.381 0.00 0.00 0.00 4.17
3534 4207 1.202830 TCCGGTTGTGTTGCTATTGGT 60.203 47.619 0.00 0.00 0.00 3.67
3535 4208 1.529226 TCCGGTTGTGTTGCTATTGG 58.471 50.000 0.00 0.00 0.00 3.16
3536 4209 2.746904 TGATCCGGTTGTGTTGCTATTG 59.253 45.455 0.00 0.00 0.00 1.90
3537 4210 3.066291 TGATCCGGTTGTGTTGCTATT 57.934 42.857 0.00 0.00 0.00 1.73
3538 4211 2.779755 TGATCCGGTTGTGTTGCTAT 57.220 45.000 0.00 0.00 0.00 2.97
3539 4212 2.779755 ATGATCCGGTTGTGTTGCTA 57.220 45.000 0.00 0.00 0.00 3.49
3540 4213 3.650647 ATGATCCGGTTGTGTTGCT 57.349 47.368 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.