Multiple sequence alignment - TraesCS1B01G138200

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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 TraesCS1B01G138200 chr1B 100.000 4255 0 0 1 4255 178095134 178099388 0.000000e+00 7858
1 TraesCS1B01G138200 chr1A 97.103 2002 45 7 1903 3891 127353923 127355924 0.000000e+00 3363
2 TraesCS1B01G138200 chr1A 96.996 1032 16 6 883 1908 127352873 127353895 0.000000e+00 1720
3 TraesCS1B01G138200 chr1A 90.241 871 34 23 1 850 127352036 127352876 0.000000e+00 1090
4 TraesCS1B01G138200 chr1D 95.691 1926 42 16 1 1908 116452823 116454725 0.000000e+00 3059
5 TraesCS1B01G138200 chr1D 95.921 1716 48 11 1903 3601 116454753 116456463 0.000000e+00 2761
6 TraesCS1B01G138200 chr1D 90.110 455 22 6 3588 4036 116480843 116481280 1.720000e-158 569
7 TraesCS1B01G138200 chr1D 88.889 99 10 1 4047 4145 116481342 116481439 2.080000e-23 121


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 TraesCS1B01G138200 chr1B 178095134 178099388 4254 False 7858.000000 7858 100.0000 1 4255 1 chr1B.!!$F1 4254
1 TraesCS1B01G138200 chr1A 127352036 127355924 3888 False 2057.666667 3363 94.7800 1 3891 3 chr1A.!!$F1 3890
2 TraesCS1B01G138200 chr1D 116452823 116456463 3640 False 2910.000000 3059 95.8060 1 3601 2 chr1D.!!$F1 3600
3 TraesCS1B01G138200 chr1D 116480843 116481439 596 False 345.000000 569 89.4995 3588 4145 2 chr1D.!!$F2 557

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
79 82 1.003442 CCTCCCTCACCCATCTCCA 59.997 63.158 0.00 0.0 0.00 3.86 F
622 636 2.439507 AGGTTGTCTGGACATCACAGTT 59.560 45.455 4.19 0.0 41.52 3.16 F
2103 2178 0.552848 TGATGCAGGAATTCTCCCCC 59.447 55.000 5.23 0.0 43.64 5.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1176 1209 0.253160 ATGCAGTGGAAGGACCCCTA 60.253 55.0 0.0 0.0 38.0 3.53 R
2454 2534 0.961019 TTGAACCATGACTTGCCTGC 59.039 50.0 0.0 0.0 0.0 4.85 R
4091 4265 0.027979 CCCGCATTCGTTAGCACATG 59.972 55.0 0.0 0.0 0.0 3.21 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
26 27 2.046988 TCGTACGCGACTCTCCCA 60.047 61.111 15.93 0.00 42.81 4.37
70 73 3.695825 TCCCCTCCCCTCCCTCAC 61.696 72.222 0.00 0.00 0.00 3.51
79 82 1.003442 CCTCCCTCACCCATCTCCA 59.997 63.158 0.00 0.00 0.00 3.86
165 171 4.066490 CGATACGAGTTCATCCTCTACCT 58.934 47.826 0.00 0.00 0.00 3.08
379 391 6.385843 CGGAATAGATGAGAATGTACTCTGG 58.614 44.000 0.00 0.00 37.73 3.86
429 442 7.362574 GGGTTTCCGATGAATCTTGTGATTAAA 60.363 37.037 0.00 0.00 42.43 1.52
433 446 5.200454 CGATGAATCTTGTGATTAAAGGCG 58.800 41.667 0.00 0.00 42.43 5.52
435 448 5.545658 TGAATCTTGTGATTAAAGGCGAC 57.454 39.130 0.00 0.00 42.43 5.19
452 465 3.058777 GGCGACGGAAAATTCTTTGTGTA 60.059 43.478 0.00 0.00 0.00 2.90
554 568 4.123745 TGGAGGGATTAAGTTATTGGGGT 58.876 43.478 0.00 0.00 0.00 4.95
555 569 4.546605 TGGAGGGATTAAGTTATTGGGGTT 59.453 41.667 0.00 0.00 0.00 4.11
557 571 6.394640 TGGAGGGATTAAGTTATTGGGGTTAT 59.605 38.462 0.00 0.00 0.00 1.89
558 572 7.091261 TGGAGGGATTAAGTTATTGGGGTTATT 60.091 37.037 0.00 0.00 0.00 1.40
559 573 7.232737 GGAGGGATTAAGTTATTGGGGTTATTG 59.767 40.741 0.00 0.00 0.00 1.90
560 574 7.073208 AGGGATTAAGTTATTGGGGTTATTGG 58.927 38.462 0.00 0.00 0.00 3.16
561 575 6.269077 GGGATTAAGTTATTGGGGTTATTGGG 59.731 42.308 0.00 0.00 0.00 4.12
562 576 6.269077 GGATTAAGTTATTGGGGTTATTGGGG 59.731 42.308 0.00 0.00 0.00 4.96
563 577 3.699025 AGTTATTGGGGTTATTGGGGG 57.301 47.619 0.00 0.00 0.00 5.40
622 636 2.439507 AGGTTGTCTGGACATCACAGTT 59.560 45.455 4.19 0.00 41.52 3.16
669 688 2.969628 AAACTATCAGCCACTCTCGG 57.030 50.000 0.00 0.00 0.00 4.63
830 857 5.391312 ACATTTTTCTCAGGTGGCAATAC 57.609 39.130 0.00 0.00 0.00 1.89
1176 1209 2.173519 CCTTGGATGACTGGCAATTGT 58.826 47.619 7.40 0.00 0.00 2.71
1272 1305 2.084610 TGTTGAAGCATCCTGACTCG 57.915 50.000 0.00 0.00 0.00 4.18
1336 1369 2.097304 TGACAAATACACGCATCATGGC 59.903 45.455 0.00 0.00 0.00 4.40
1461 1502 7.125792 ACTGGTGTTATCAACCTATCCTAAG 57.874 40.000 0.00 0.00 0.00 2.18
1462 1503 5.925509 TGGTGTTATCAACCTATCCTAAGC 58.074 41.667 0.00 0.00 0.00 3.09
1463 1504 5.427157 TGGTGTTATCAACCTATCCTAAGCA 59.573 40.000 0.00 0.00 0.00 3.91
1464 1505 6.069905 TGGTGTTATCAACCTATCCTAAGCAA 60.070 38.462 0.00 0.00 0.00 3.91
1465 1506 6.998673 GGTGTTATCAACCTATCCTAAGCAAT 59.001 38.462 0.00 0.00 0.00 3.56
1466 1507 7.173390 GGTGTTATCAACCTATCCTAAGCAATC 59.827 40.741 0.00 0.00 0.00 2.67
1467 1508 7.715249 GTGTTATCAACCTATCCTAAGCAATCA 59.285 37.037 0.00 0.00 0.00 2.57
1468 1509 8.271458 TGTTATCAACCTATCCTAAGCAATCAA 58.729 33.333 0.00 0.00 0.00 2.57
1469 1510 8.560374 GTTATCAACCTATCCTAAGCAATCAAC 58.440 37.037 0.00 0.00 0.00 3.18
1470 1511 6.061022 TCAACCTATCCTAAGCAATCAACA 57.939 37.500 0.00 0.00 0.00 3.33
2103 2178 0.552848 TGATGCAGGAATTCTCCCCC 59.447 55.000 5.23 0.00 43.64 5.40
2273 2353 8.697507 AGAATGTTTGTTCCTTTCTCTATTGT 57.302 30.769 0.00 0.00 0.00 2.71
2290 2370 1.267121 TGTCTCACCTTCCTGTAGCC 58.733 55.000 0.00 0.00 0.00 3.93
2454 2534 6.127897 CCAACTAGCTGGACAAATTTCTTAGG 60.128 42.308 6.28 0.00 38.96 2.69
3088 3202 0.752658 CATGACCGAGATACTGGCCA 59.247 55.000 4.71 4.71 0.00 5.36
3207 3321 6.457528 GCATTCAGAAGAAAGAAGGGATTACG 60.458 42.308 0.00 0.00 37.29 3.18
3324 3440 4.406456 AGAATGAGCATCGATCTAGTCCT 58.594 43.478 0.00 0.00 38.61 3.85
3421 3537 4.523173 ACGTAACTGAGAAGAAGGATGACA 59.477 41.667 0.00 0.00 0.00 3.58
3433 3549 0.254178 GGATGACAGTGATGCCAGGT 59.746 55.000 0.00 0.00 0.00 4.00
3468 3584 1.412710 TCATGTGCCGAGGAGGTTATC 59.587 52.381 0.00 0.00 43.70 1.75
3472 3588 0.325296 TGCCGAGGAGGTTATCAGGT 60.325 55.000 0.00 0.00 43.70 4.00
3564 3680 0.107703 TCTACCGGCTTCTGCATTGG 60.108 55.000 0.00 0.00 41.91 3.16
3579 3695 4.708726 GCATTGGCATTAGTGAGAGTTT 57.291 40.909 0.00 0.00 40.72 2.66
3917 4037 5.221244 GGTGCCTGAGATTTTAGTTTGTGTT 60.221 40.000 0.00 0.00 0.00 3.32
3918 4038 6.016610 GGTGCCTGAGATTTTAGTTTGTGTTA 60.017 38.462 0.00 0.00 0.00 2.41
3936 4056 5.530915 TGTGTTAGTAAGTTTCTGCATTGCT 59.469 36.000 10.49 0.00 0.00 3.91
4007 4127 2.824041 ACGATTGCGGCATCCACC 60.824 61.111 2.28 0.00 43.17 4.61
4026 4189 1.608283 CCGAGGCGAGGAAGAAACTTT 60.608 52.381 0.00 0.00 0.00 2.66
4036 4199 5.395324 CGAGGAAGAAACTTTAGGGCATCTA 60.395 44.000 0.00 0.00 0.00 1.98
4042 4205 5.128827 AGAAACTTTAGGGCATCTACGATGA 59.871 40.000 7.96 0.00 0.00 2.92
4043 4206 5.552870 AACTTTAGGGCATCTACGATGAT 57.447 39.130 7.96 0.00 0.00 2.45
4045 4208 3.961480 TTAGGGCATCTACGATGATGG 57.039 47.619 18.43 6.22 42.82 3.51
4078 4252 1.078988 GTGCCAACGAACGGGGATA 60.079 57.895 10.38 0.00 0.00 2.59
4091 4265 1.175347 GGGGATAGTACGGTCCGGAC 61.175 65.000 27.04 27.04 41.59 4.79
4093 4267 1.613836 GGATAGTACGGTCCGGACAT 58.386 55.000 34.40 23.99 44.03 3.06
4098 4272 1.980232 TACGGTCCGGACATGTGCT 60.980 57.895 34.40 13.68 0.00 4.40
4105 4279 1.206132 TCCGGACATGTGCTAACGAAT 59.794 47.619 15.82 0.00 0.00 3.34
4108 4282 1.267532 GGACATGTGCTAACGAATGCG 60.268 52.381 10.51 0.00 44.79 4.73
4112 4286 2.046796 TGCTAACGAATGCGGGCA 60.047 55.556 0.00 2.01 43.17 5.36
4129 4303 1.299541 GCATGTATCGGTCCACTTGG 58.700 55.000 0.00 0.00 0.00 3.61
4131 4305 0.179084 ATGTATCGGTCCACTTGGCG 60.179 55.000 0.00 0.00 34.44 5.69
4137 4311 3.998672 GTCCACTTGGCGGTCCGA 61.999 66.667 17.49 0.00 34.14 4.55
4139 4313 3.047877 CCACTTGGCGGTCCGAAC 61.048 66.667 17.49 7.51 34.14 3.95
4147 4321 2.660552 CGGTCCGAACGCACACTT 60.661 61.111 4.91 0.00 0.00 3.16
4148 4322 2.241880 CGGTCCGAACGCACACTTT 61.242 57.895 4.91 0.00 0.00 2.66
4149 4323 1.568025 GGTCCGAACGCACACTTTC 59.432 57.895 0.00 0.00 0.00 2.62
4150 4324 1.568025 GTCCGAACGCACACTTTCC 59.432 57.895 0.00 0.00 0.00 3.13
4151 4325 1.595929 TCCGAACGCACACTTTCCC 60.596 57.895 0.00 0.00 0.00 3.97
4152 4326 2.549282 CGAACGCACACTTTCCCG 59.451 61.111 0.00 0.00 0.00 5.14
4153 4327 2.251371 GAACGCACACTTTCCCGC 59.749 61.111 0.00 0.00 0.00 6.13
4154 4328 2.515057 AACGCACACTTTCCCGCA 60.515 55.556 0.00 0.00 0.00 5.69
4155 4329 2.054140 GAACGCACACTTTCCCGCAA 62.054 55.000 0.00 0.00 0.00 4.85
4156 4330 1.658686 AACGCACACTTTCCCGCAAA 61.659 50.000 0.00 0.00 0.00 3.68
4157 4331 1.657181 CGCACACTTTCCCGCAAAC 60.657 57.895 0.00 0.00 0.00 2.93
4158 4332 1.733526 GCACACTTTCCCGCAAACT 59.266 52.632 0.00 0.00 0.00 2.66
4159 4333 0.594796 GCACACTTTCCCGCAAACTG 60.595 55.000 0.00 0.00 0.00 3.16
4160 4334 1.021202 CACACTTTCCCGCAAACTGA 58.979 50.000 0.00 0.00 0.00 3.41
4161 4335 1.403679 CACACTTTCCCGCAAACTGAA 59.596 47.619 0.00 0.00 0.00 3.02
4162 4336 1.676006 ACACTTTCCCGCAAACTGAAG 59.324 47.619 0.00 0.00 0.00 3.02
4163 4337 1.946768 CACTTTCCCGCAAACTGAAGA 59.053 47.619 0.00 0.00 0.00 2.87
4164 4338 1.947456 ACTTTCCCGCAAACTGAAGAC 59.053 47.619 0.00 0.00 0.00 3.01
4165 4339 1.946768 CTTTCCCGCAAACTGAAGACA 59.053 47.619 0.00 0.00 0.00 3.41
4166 4340 2.045561 TTCCCGCAAACTGAAGACAA 57.954 45.000 0.00 0.00 0.00 3.18
4167 4341 1.593196 TCCCGCAAACTGAAGACAAG 58.407 50.000 0.00 0.00 0.00 3.16
4168 4342 1.140052 TCCCGCAAACTGAAGACAAGA 59.860 47.619 0.00 0.00 0.00 3.02
4169 4343 2.154462 CCCGCAAACTGAAGACAAGAT 58.846 47.619 0.00 0.00 0.00 2.40
4170 4344 3.007506 TCCCGCAAACTGAAGACAAGATA 59.992 43.478 0.00 0.00 0.00 1.98
4171 4345 3.372206 CCCGCAAACTGAAGACAAGATAG 59.628 47.826 0.00 0.00 0.00 2.08
4172 4346 3.181516 CCGCAAACTGAAGACAAGATAGC 60.182 47.826 0.00 0.00 0.00 2.97
4173 4347 3.433274 CGCAAACTGAAGACAAGATAGCA 59.567 43.478 0.00 0.00 0.00 3.49
4174 4348 4.435253 CGCAAACTGAAGACAAGATAGCAG 60.435 45.833 0.00 0.00 0.00 4.24
4175 4349 4.453819 GCAAACTGAAGACAAGATAGCAGT 59.546 41.667 0.00 0.00 38.14 4.40
4176 4350 5.049129 GCAAACTGAAGACAAGATAGCAGTT 60.049 40.000 0.00 0.00 45.36 3.16
4177 4351 6.147821 GCAAACTGAAGACAAGATAGCAGTTA 59.852 38.462 0.00 0.00 43.41 2.24
4178 4352 7.513968 CAAACTGAAGACAAGATAGCAGTTAC 58.486 38.462 0.00 0.00 43.41 2.50
4179 4353 5.403246 ACTGAAGACAAGATAGCAGTTACG 58.597 41.667 0.00 0.00 33.19 3.18
4180 4354 4.744570 TGAAGACAAGATAGCAGTTACGG 58.255 43.478 0.00 0.00 0.00 4.02
4181 4355 4.219944 TGAAGACAAGATAGCAGTTACGGT 59.780 41.667 0.00 0.00 0.00 4.83
4182 4356 4.373348 AGACAAGATAGCAGTTACGGTC 57.627 45.455 0.00 0.00 0.00 4.79
4183 4357 3.130693 AGACAAGATAGCAGTTACGGTCC 59.869 47.826 0.00 0.00 0.00 4.46
4184 4358 2.159282 ACAAGATAGCAGTTACGGTCCG 60.159 50.000 10.48 10.48 0.00 4.79
4185 4359 0.384669 AGATAGCAGTTACGGTCCGC 59.615 55.000 12.28 0.00 0.00 5.54
4186 4360 0.933509 GATAGCAGTTACGGTCCGCG 60.934 60.000 12.28 0.00 0.00 6.46
4187 4361 1.660560 ATAGCAGTTACGGTCCGCGT 61.661 55.000 12.28 0.00 0.00 6.01
4188 4362 2.257286 TAGCAGTTACGGTCCGCGTC 62.257 60.000 12.28 1.42 0.00 5.19
4189 4363 2.564975 CAGTTACGGTCCGCGTCT 59.435 61.111 12.28 3.98 0.00 4.18
4190 4364 1.800315 CAGTTACGGTCCGCGTCTG 60.800 63.158 12.28 12.82 0.00 3.51
4191 4365 1.968017 AGTTACGGTCCGCGTCTGA 60.968 57.895 12.28 0.00 0.00 3.27
4192 4366 1.799121 GTTACGGTCCGCGTCTGAC 60.799 63.158 12.28 5.29 0.00 3.51
4193 4367 1.968017 TTACGGTCCGCGTCTGACT 60.968 57.895 12.28 0.00 33.22 3.41
4194 4368 0.673333 TTACGGTCCGCGTCTGACTA 60.673 55.000 12.28 0.00 33.22 2.59
4195 4369 0.673333 TACGGTCCGCGTCTGACTAA 60.673 55.000 12.28 0.00 33.22 2.24
4196 4370 1.513586 CGGTCCGCGTCTGACTAAC 60.514 63.158 4.92 0.00 33.22 2.34
4197 4371 1.153881 GGTCCGCGTCTGACTAACC 60.154 63.158 4.92 4.44 33.22 2.85
4198 4372 1.153881 GTCCGCGTCTGACTAACCC 60.154 63.158 4.92 0.00 0.00 4.11
4199 4373 2.202570 CCGCGTCTGACTAACCCG 60.203 66.667 4.92 1.30 0.00 5.28
4200 4374 2.202570 CGCGTCTGACTAACCCGG 60.203 66.667 6.21 0.00 0.00 5.73
4201 4375 2.968206 GCGTCTGACTAACCCGGT 59.032 61.111 0.00 0.00 0.00 5.28
4202 4376 1.153881 GCGTCTGACTAACCCGGTC 60.154 63.158 0.00 0.00 0.00 4.79
4203 4377 1.593296 GCGTCTGACTAACCCGGTCT 61.593 60.000 0.00 0.00 35.04 3.85
4204 4378 1.742761 CGTCTGACTAACCCGGTCTA 58.257 55.000 0.00 0.00 35.04 2.59
4205 4379 1.399791 CGTCTGACTAACCCGGTCTAC 59.600 57.143 0.00 0.00 35.04 2.59
4206 4380 2.440409 GTCTGACTAACCCGGTCTACA 58.560 52.381 0.00 0.00 35.04 2.74
4207 4381 2.821969 GTCTGACTAACCCGGTCTACAA 59.178 50.000 0.00 0.00 35.04 2.41
4208 4382 3.256631 GTCTGACTAACCCGGTCTACAAA 59.743 47.826 0.00 0.00 35.04 2.83
4209 4383 3.896888 TCTGACTAACCCGGTCTACAAAA 59.103 43.478 0.00 0.00 35.04 2.44
4210 4384 4.344679 TCTGACTAACCCGGTCTACAAAAA 59.655 41.667 0.00 0.00 35.04 1.94
4228 4402 2.436521 AAAAACTCCTTTGCCCCCG 58.563 52.632 0.00 0.00 0.00 5.73
4229 4403 1.754380 AAAAACTCCTTTGCCCCCGC 61.754 55.000 0.00 0.00 0.00 6.13
4230 4404 2.937959 AAAACTCCTTTGCCCCCGCA 62.938 55.000 0.00 0.00 45.49 5.69
4246 4420 4.323477 CACCTTCCCGCCGGAACA 62.323 66.667 5.05 0.00 43.57 3.18
4247 4421 4.016706 ACCTTCCCGCCGGAACAG 62.017 66.667 5.05 0.00 43.57 3.16
4248 4422 4.016706 CCTTCCCGCCGGAACAGT 62.017 66.667 5.05 0.00 43.57 3.55
4249 4423 2.434359 CTTCCCGCCGGAACAGTC 60.434 66.667 5.05 0.00 43.57 3.51
4250 4424 4.367023 TTCCCGCCGGAACAGTCG 62.367 66.667 5.05 0.00 43.57 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 1.881973 CTGTGGATTTGTGGAGGTGTG 59.118 52.381 0.00 0.00 0.00 3.82
26 27 1.819305 GCTGTGGATTTGTGGAGGTGT 60.819 52.381 0.00 0.00 0.00 4.16
70 73 1.124477 GGGAGGTAGCTGGAGATGGG 61.124 65.000 0.00 0.00 0.00 4.00
165 171 1.450848 AGACGGGATGACGACGCTA 60.451 57.895 0.00 0.00 37.61 4.26
346 358 6.911250 TTCTCATCTATTCCGCACCTAATA 57.089 37.500 0.00 0.00 0.00 0.98
348 360 5.070446 ACATTCTCATCTATTCCGCACCTAA 59.930 40.000 0.00 0.00 0.00 2.69
349 361 4.588951 ACATTCTCATCTATTCCGCACCTA 59.411 41.667 0.00 0.00 0.00 3.08
350 362 3.389329 ACATTCTCATCTATTCCGCACCT 59.611 43.478 0.00 0.00 0.00 4.00
379 391 2.338228 TCGTTAACGTACACGATTTCGC 59.662 45.455 25.98 0.00 40.43 4.70
429 442 2.031157 CACAAAGAATTTTCCGTCGCCT 60.031 45.455 0.00 0.00 35.03 5.52
433 446 9.673454 ACTATTTTACACAAAGAATTTTCCGTC 57.327 29.630 0.00 0.00 35.03 4.79
561 575 2.417719 TCTAGCCTAAGGATTCCCCC 57.582 55.000 0.00 0.00 34.66 5.40
562 576 4.468153 CACTATCTAGCCTAAGGATTCCCC 59.532 50.000 0.00 0.00 0.00 4.81
563 577 4.468153 CCACTATCTAGCCTAAGGATTCCC 59.532 50.000 0.00 0.00 0.00 3.97
622 636 6.127054 CCATGTACTCAATTAAGAGAGTCCCA 60.127 42.308 13.92 12.49 43.59 4.37
669 688 2.713927 AATGGCACGCAAGCAAACCC 62.714 55.000 0.00 0.00 45.62 4.11
715 734 5.050295 GCTCGGCAAATTCTACTATGTTACC 60.050 44.000 0.00 0.00 0.00 2.85
734 753 2.426738 TGAAATGCCCAATTAAGCTCGG 59.573 45.455 0.00 0.00 0.00 4.63
872 899 7.169140 CCTTTTCCCAAAATACGAAGAAAACTG 59.831 37.037 0.00 0.00 31.82 3.16
1176 1209 0.253160 ATGCAGTGGAAGGACCCCTA 60.253 55.000 0.00 0.00 38.00 3.53
1272 1305 6.763610 AGAAACTTACAGCTCTAATGTATGGC 59.236 38.462 0.00 0.00 34.35 4.40
1336 1369 6.200286 ACAAATGTAACGAGTAGACACAACAG 59.800 38.462 0.00 0.00 0.00 3.16
1543 1584 3.947910 AAATCAAGACACAAGGCCATG 57.052 42.857 5.01 5.77 0.00 3.66
1660 1701 6.185114 AGAAGCCAGCTGATTATCTAACAT 57.815 37.500 17.39 0.00 0.00 2.71
2103 2178 2.061773 GTCATGCGACCATTAGATCCG 58.938 52.381 0.00 0.00 36.02 4.18
2232 2312 8.495949 ACAAACATTCTTCAGTTATAACGACAG 58.504 33.333 9.91 7.18 0.00 3.51
2273 2353 2.024176 TTGGCTACAGGAAGGTGAGA 57.976 50.000 0.00 0.00 0.00 3.27
2454 2534 0.961019 TTGAACCATGACTTGCCTGC 59.039 50.000 0.00 0.00 0.00 4.85
3207 3321 0.924090 CTATTGTCACGCTCGCTTCC 59.076 55.000 0.00 0.00 0.00 3.46
3324 3440 4.735369 TCTCTTTGCTTGTATCCCCAAAA 58.265 39.130 0.00 0.00 0.00 2.44
3564 3680 7.659652 ACAAAGACTAAACTCTCACTAATGC 57.340 36.000 0.00 0.00 0.00 3.56
3868 3988 5.702670 TGAGATTTAGCAAAACCACTCTGAG 59.297 40.000 2.45 2.45 0.00 3.35
3917 4037 3.932710 CCGAGCAATGCAGAAACTTACTA 59.067 43.478 8.35 0.00 0.00 1.82
3918 4038 2.744202 CCGAGCAATGCAGAAACTTACT 59.256 45.455 8.35 0.00 0.00 2.24
3988 4108 1.815421 GTGGATGCCGCAATCGTCT 60.815 57.895 0.00 0.00 33.65 4.18
4001 4121 2.363795 TTCCTCGCCTCGGTGGAT 60.364 61.111 0.00 0.00 38.35 3.41
4004 4124 1.014564 GTTTCTTCCTCGCCTCGGTG 61.015 60.000 0.00 0.00 0.00 4.94
4005 4125 1.186267 AGTTTCTTCCTCGCCTCGGT 61.186 55.000 0.00 0.00 0.00 4.69
4006 4126 0.037232 AAGTTTCTTCCTCGCCTCGG 60.037 55.000 0.00 0.00 0.00 4.63
4007 4127 1.797025 AAAGTTTCTTCCTCGCCTCG 58.203 50.000 0.00 0.00 0.00 4.63
4026 4189 2.889512 ACCATCATCGTAGATGCCCTA 58.110 47.619 12.34 0.00 45.12 3.53
4036 4199 1.731433 CCGGACCGTACCATCATCGT 61.731 60.000 13.94 0.00 0.00 3.73
4042 4205 0.974010 ACATGTCCGGACCGTACCAT 60.974 55.000 31.19 14.40 0.00 3.55
4043 4206 1.607178 ACATGTCCGGACCGTACCA 60.607 57.895 31.19 12.54 0.00 3.25
4045 4208 1.808390 GCACATGTCCGGACCGTAC 60.808 63.158 31.19 18.72 0.00 3.67
4078 4252 1.888018 CACATGTCCGGACCGTACT 59.112 57.895 31.19 8.41 0.00 2.73
4091 4265 0.027979 CCCGCATTCGTTAGCACATG 59.972 55.000 0.00 0.00 0.00 3.21
4093 4267 2.395360 GCCCGCATTCGTTAGCACA 61.395 57.895 0.00 0.00 0.00 4.57
4098 4272 2.139917 GATACATGCCCGCATTCGTTA 58.860 47.619 0.00 0.00 33.90 3.18
4105 4279 2.108157 GACCGATACATGCCCGCA 59.892 61.111 0.00 0.00 0.00 5.69
4108 4282 0.180406 AAGTGGACCGATACATGCCC 59.820 55.000 0.00 0.00 0.00 5.36
4112 4286 0.179084 CGCCAAGTGGACCGATACAT 60.179 55.000 0.18 0.00 37.39 2.29
4131 4305 1.568025 GAAAGTGTGCGTTCGGACC 59.432 57.895 13.51 5.96 0.00 4.46
4137 4311 1.658686 TTTGCGGGAAAGTGTGCGTT 61.659 50.000 0.00 0.00 0.00 4.84
4139 4313 1.657181 GTTTGCGGGAAAGTGTGCG 60.657 57.895 0.00 0.00 0.00 5.34
4145 4319 1.946768 TGTCTTCAGTTTGCGGGAAAG 59.053 47.619 0.00 0.00 0.00 2.62
4146 4320 2.045561 TGTCTTCAGTTTGCGGGAAA 57.954 45.000 0.00 0.00 0.00 3.13
4147 4321 1.946768 CTTGTCTTCAGTTTGCGGGAA 59.053 47.619 0.00 0.00 0.00 3.97
4148 4322 1.140052 TCTTGTCTTCAGTTTGCGGGA 59.860 47.619 0.00 0.00 0.00 5.14
4149 4323 1.593196 TCTTGTCTTCAGTTTGCGGG 58.407 50.000 0.00 0.00 0.00 6.13
4150 4324 3.181516 GCTATCTTGTCTTCAGTTTGCGG 60.182 47.826 0.00 0.00 0.00 5.69
4151 4325 3.433274 TGCTATCTTGTCTTCAGTTTGCG 59.567 43.478 0.00 0.00 0.00 4.85
4152 4326 4.453819 ACTGCTATCTTGTCTTCAGTTTGC 59.546 41.667 0.00 0.00 31.51 3.68
4153 4327 6.551385 AACTGCTATCTTGTCTTCAGTTTG 57.449 37.500 0.00 0.00 40.55 2.93
4154 4328 6.366332 CGTAACTGCTATCTTGTCTTCAGTTT 59.634 38.462 10.14 0.00 42.52 2.66
4155 4329 5.864474 CGTAACTGCTATCTTGTCTTCAGTT 59.136 40.000 9.82 9.82 44.10 3.16
4156 4330 5.403246 CGTAACTGCTATCTTGTCTTCAGT 58.597 41.667 0.00 0.00 36.46 3.41
4157 4331 4.800993 CCGTAACTGCTATCTTGTCTTCAG 59.199 45.833 0.00 0.00 0.00 3.02
4158 4332 4.219944 ACCGTAACTGCTATCTTGTCTTCA 59.780 41.667 0.00 0.00 0.00 3.02
4159 4333 4.745649 ACCGTAACTGCTATCTTGTCTTC 58.254 43.478 0.00 0.00 0.00 2.87
4160 4334 4.381718 GGACCGTAACTGCTATCTTGTCTT 60.382 45.833 0.00 0.00 0.00 3.01
4161 4335 3.130693 GGACCGTAACTGCTATCTTGTCT 59.869 47.826 0.00 0.00 0.00 3.41
4162 4336 3.445857 GGACCGTAACTGCTATCTTGTC 58.554 50.000 0.00 0.00 0.00 3.18
4163 4337 2.159282 CGGACCGTAACTGCTATCTTGT 60.159 50.000 5.48 0.00 0.00 3.16
4164 4338 2.460918 CGGACCGTAACTGCTATCTTG 58.539 52.381 5.48 0.00 0.00 3.02
4165 4339 1.202382 GCGGACCGTAACTGCTATCTT 60.202 52.381 16.73 0.00 36.79 2.40
4166 4340 0.384669 GCGGACCGTAACTGCTATCT 59.615 55.000 16.73 0.00 36.79 1.98
4167 4341 0.933509 CGCGGACCGTAACTGCTATC 60.934 60.000 16.73 0.00 37.48 2.08
4168 4342 1.065273 CGCGGACCGTAACTGCTAT 59.935 57.895 16.73 0.00 37.48 2.97
4169 4343 2.486504 CGCGGACCGTAACTGCTA 59.513 61.111 16.73 0.00 37.48 3.49
4178 4352 1.513586 GTTAGTCAGACGCGGACCG 60.514 63.158 12.47 10.29 44.21 4.79
4179 4353 1.153881 GGTTAGTCAGACGCGGACC 60.154 63.158 12.47 0.00 35.89 4.46
4180 4354 1.153881 GGGTTAGTCAGACGCGGAC 60.154 63.158 12.47 8.63 35.50 4.79
4181 4355 2.693762 CGGGTTAGTCAGACGCGGA 61.694 63.158 12.47 0.00 45.86 5.54
4182 4356 2.202570 CGGGTTAGTCAGACGCGG 60.203 66.667 12.47 0.00 45.86 6.46
4184 4358 1.153881 GACCGGGTTAGTCAGACGC 60.154 63.158 6.32 0.00 34.27 5.19
4185 4359 1.399791 GTAGACCGGGTTAGTCAGACG 59.600 57.143 6.32 0.00 36.68 4.18
4186 4360 2.440409 TGTAGACCGGGTTAGTCAGAC 58.560 52.381 6.32 0.00 36.68 3.51
4187 4361 2.885135 TGTAGACCGGGTTAGTCAGA 57.115 50.000 6.32 0.00 36.68 3.27
4188 4362 3.947910 TTTGTAGACCGGGTTAGTCAG 57.052 47.619 6.32 0.00 36.68 3.51
4189 4363 4.686191 TTTTTGTAGACCGGGTTAGTCA 57.314 40.909 6.32 0.00 36.68 3.41
4210 4384 1.754380 GCGGGGGCAAAGGAGTTTTT 61.754 55.000 0.00 0.00 0.00 1.94
4211 4385 2.207229 GCGGGGGCAAAGGAGTTTT 61.207 57.895 0.00 0.00 0.00 2.43
4212 4386 2.600470 GCGGGGGCAAAGGAGTTT 60.600 61.111 0.00 0.00 0.00 2.66
4213 4387 3.897122 TGCGGGGGCAAAGGAGTT 61.897 61.111 0.00 0.00 0.00 3.01
4214 4388 4.660938 GTGCGGGGGCAAAGGAGT 62.661 66.667 0.00 0.00 0.00 3.85
4217 4391 4.994756 AAGGTGCGGGGGCAAAGG 62.995 66.667 0.00 0.00 0.00 3.11
4218 4392 3.373565 GAAGGTGCGGGGGCAAAG 61.374 66.667 0.00 0.00 0.00 2.77
4219 4393 4.986708 GGAAGGTGCGGGGGCAAA 62.987 66.667 0.00 0.00 0.00 3.68


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

AutoCloner maintained by Alex Coulton.