Multiple sequence alignment - TraesCS5B01G178600

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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 TraesCS5B01G178600 chr5B 100.000 4117 0 0 999 5115 326575605 326571489 0.000000e+00 7603
1 TraesCS5B01G178600 chr5B 100.000 408 0 0 1 408 326576603 326576196 0.000000e+00 754
2 TraesCS5B01G178600 chr5A 93.023 4185 185 52 999 5115 379356805 379352660 0.000000e+00 6011
3 TraesCS5B01G178600 chr5A 93.448 290 12 4 4 288 379357499 379357212 1.700000e-114 424
4 TraesCS5B01G178600 chr5D 93.554 3444 168 27 999 4418 287444475 287441062 0.000000e+00 5081
5 TraesCS5B01G178600 chr5D 90.909 682 28 10 4439 5115 287440905 287440253 0.000000e+00 885
6 TraesCS5B01G178600 chr5D 93.703 397 9 8 1 386 287444898 287444507 9.550000e-162 580


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 TraesCS5B01G178600 chr5B 326571489 326576603 5114 True 4178.5 7603 100.0000 1 5115 2 chr5B.!!$R1 5114
1 TraesCS5B01G178600 chr5A 379352660 379357499 4839 True 3217.5 6011 93.2355 4 5115 2 chr5A.!!$R1 5111
2 TraesCS5B01G178600 chr5D 287440253 287444898 4645 True 2182.0 5081 92.7220 1 5115 3 chr5D.!!$R1 5114

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
305 312 0.470766 GTCTCCTCTCCTCCTCGCTA 59.529 60.0 0.00 0.0 0.0 4.26 F
1683 1983 1.089481 CGTACGCACAATCCCTGCAT 61.089 55.0 0.52 0.0 34.0 3.96 F
3409 3727 0.243907 CTTCATCTGTGTCGTCCGGT 59.756 55.0 0.00 0.0 0.0 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1906 2206 0.398696 ACAGGACGGGCACATGTTAA 59.601 50.0 0.00 0.00 0.00 2.01 R
3642 3960 0.165944 AGTTGCGCAAACATAGTCGC 59.834 50.0 26.87 9.04 46.78 5.19 R
4234 4560 0.034089 CTCAACTTGGGCCCCTTAGG 60.034 60.0 22.27 3.22 39.47 2.69 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
60 61 1.021202 TGTTGTGGCAAAACTCCTCG 58.979 50.000 20.59 0.00 0.00 4.63
96 97 2.941720 CAGCTGGCAATTAGAGTCCTTC 59.058 50.000 5.57 0.00 0.00 3.46
216 223 1.141665 GCCAATTTGACCATCCGCC 59.858 57.895 0.00 0.00 0.00 6.13
304 311 1.226262 GTCTCCTCTCCTCCTCGCT 59.774 63.158 0.00 0.00 0.00 4.93
305 312 0.470766 GTCTCCTCTCCTCCTCGCTA 59.529 60.000 0.00 0.00 0.00 4.26
306 313 1.134037 GTCTCCTCTCCTCCTCGCTAA 60.134 57.143 0.00 0.00 0.00 3.09
307 314 1.564818 TCTCCTCTCCTCCTCGCTAAA 59.435 52.381 0.00 0.00 0.00 1.85
319 336 2.743179 CGCTAAACCCCCTCCCCTC 61.743 68.421 0.00 0.00 0.00 4.30
322 339 3.292460 TAAACCCCCTCCCCTCCCC 62.292 68.421 0.00 0.00 0.00 4.81
380 664 4.924187 CTCCGATCCCCTCCGCCT 62.924 72.222 0.00 0.00 0.00 5.52
402 686 3.659092 CGCGAGCTGCCACCAAAA 61.659 61.111 0.00 0.00 42.08 2.44
403 687 2.256461 GCGAGCTGCCACCAAAAG 59.744 61.111 0.00 0.00 37.76 2.27
1151 1435 2.341846 TTTCTTGCCGAAAGTCTGGT 57.658 45.000 0.00 0.00 36.72 4.00
1217 1501 4.870012 GGGGATTTCGGTCCGGGC 62.870 72.222 12.29 0.00 39.26 6.13
1302 1599 9.672086 CGTAAATTTCTAAACTGAAAACATGGA 57.328 29.630 0.00 0.00 39.08 3.41
1367 1664 2.304761 CCTAGGTGTTTGGTCCTTGCTA 59.695 50.000 0.00 0.00 35.51 3.49
1424 1721 6.515862 GCCTGTCATATAATCTCTCGTGTTCT 60.516 42.308 0.00 0.00 0.00 3.01
1440 1739 8.557029 TCTCGTGTTCTTTTTATTTTCTCCTTC 58.443 33.333 0.00 0.00 0.00 3.46
1683 1983 1.089481 CGTACGCACAATCCCTGCAT 61.089 55.000 0.52 0.00 34.00 3.96
1793 2093 6.440647 TCTTCAGAGTTACCACATGTTCCTAT 59.559 38.462 0.00 0.00 0.00 2.57
1906 2206 8.526147 AGAATAAACTGCAATAGCTTGTTCATT 58.474 29.630 0.00 0.00 42.74 2.57
1943 2243 3.748568 CCTGTTCTTAGTTTGCTCTGGAC 59.251 47.826 0.00 0.00 0.00 4.02
2214 2519 6.252967 TGCATTCAAACATACGTTTCTCAT 57.747 33.333 0.00 0.00 43.57 2.90
2230 2535 6.380190 GTTTCTCATAGTCGTGTCAGTTACT 58.620 40.000 0.00 0.00 0.00 2.24
2349 2657 0.672401 CCCCGTGCACGTGAAGTAAT 60.672 55.000 34.81 0.00 37.74 1.89
2354 2663 3.184783 CCGTGCACGTGAAGTAATAACAA 59.815 43.478 34.81 0.00 37.74 2.83
2375 2684 5.422012 ACAATACAAGAATCCCCCAAATCAC 59.578 40.000 0.00 0.00 0.00 3.06
2402 2711 9.182933 GATAAGCTTGGTAAGTATTTACTCTCG 57.817 37.037 9.86 0.00 39.30 4.04
2404 2713 4.507021 GCTTGGTAAGTATTTACTCTCGGC 59.493 45.833 7.92 3.40 39.30 5.54
2446 2755 7.824779 AGACAGGAGAAAACAGTAAATATGTCC 59.175 37.037 0.00 0.00 34.22 4.02
2506 2815 4.540824 GCTTCATCTGACAGTTTTTGGAC 58.459 43.478 1.59 0.00 0.00 4.02
2547 2857 3.010420 GTGGATTAAGTTCAGCACTCCC 58.990 50.000 0.00 0.00 32.94 4.30
2548 2858 2.026262 TGGATTAAGTTCAGCACTCCCC 60.026 50.000 0.00 0.00 32.94 4.81
2549 2859 2.644676 GATTAAGTTCAGCACTCCCCC 58.355 52.381 0.00 0.00 32.94 5.40
2678 2990 5.914085 AATCAGAAGTTTGAGACAACTCG 57.086 39.130 0.00 0.00 45.25 4.18
2722 3034 0.536260 CTCAGGCTCTCAACCAGGAG 59.464 60.000 0.00 0.00 36.21 3.69
2727 3041 1.611936 GGCTCTCAACCAGGAGTTTCC 60.612 57.143 0.00 0.00 36.18 3.13
2759 3073 7.496591 GGGATTTAACATTTCAGTCGGTATGTA 59.503 37.037 0.00 0.00 31.40 2.29
2948 3266 4.482386 CTTGTTGCACAAAGAGATGATGG 58.518 43.478 1.99 0.00 37.69 3.51
3058 3376 5.105997 GGAAAAGAGAATGACAATGGAGGTG 60.106 44.000 0.00 0.00 0.00 4.00
3068 3386 2.026822 ACAATGGAGGTGCTAGTTCCAG 60.027 50.000 11.29 4.22 43.71 3.86
3133 3451 3.663995 TGTGGCACCAAGAAATCAATG 57.336 42.857 16.26 0.00 0.00 2.82
3405 3723 2.726760 GTGTGTCTTCATCTGTGTCGTC 59.273 50.000 0.00 0.00 0.00 4.20
3409 3727 0.243907 CTTCATCTGTGTCGTCCGGT 59.756 55.000 0.00 0.00 0.00 5.28
3529 3847 5.430089 AGGTAAAGAAATCCAGGTAGATGCT 59.570 40.000 0.00 0.00 0.00 3.79
3562 3880 5.066375 CCGGATGAATGTTGATGAAAGCTTA 59.934 40.000 0.00 0.00 0.00 3.09
3601 3919 4.080863 ACACCTAGCGATGAAGAAATTCCT 60.081 41.667 0.00 0.00 0.00 3.36
3614 3932 3.703052 AGAAATTCCTGTGGATGCATTCC 59.297 43.478 1.51 5.41 45.69 3.01
3628 3946 0.379669 CATTCCGCAGCCAGATGAAC 59.620 55.000 0.00 0.00 0.00 3.18
3638 3956 1.137086 GCCAGATGAACGAGCTTCCTA 59.863 52.381 0.00 0.00 0.00 2.94
3639 3957 2.224161 GCCAGATGAACGAGCTTCCTAT 60.224 50.000 0.00 0.00 0.00 2.57
3640 3958 3.648009 CCAGATGAACGAGCTTCCTATC 58.352 50.000 0.00 0.00 0.00 2.08
3641 3959 3.304257 CAGATGAACGAGCTTCCTATCG 58.696 50.000 0.00 0.00 44.36 2.92
3642 3960 2.294791 AGATGAACGAGCTTCCTATCGG 59.705 50.000 0.00 0.00 43.12 4.18
3656 3977 1.452025 CTATCGGCGACTATGTTTGCG 59.548 52.381 13.76 0.00 0.00 4.85
3721 4042 7.678218 GCAGATATGTTTCCTGTCAATGACTTC 60.678 40.741 14.97 0.17 33.15 3.01
3736 4057 0.874607 ACTTCGTCGACACAACAGGC 60.875 55.000 17.16 0.00 0.00 4.85
3829 4150 2.825532 TGCAGAACTTAATTGGGAAGGC 59.174 45.455 0.00 0.00 0.00 4.35
3852 4173 2.547007 TCGACTTTGCTTCGATGGAACA 60.547 45.455 4.71 0.00 40.51 3.18
3906 4228 5.695851 TTGAGGTTTTCATCTTTCTGAGC 57.304 39.130 0.00 0.00 35.27 4.26
3979 4302 3.307480 CGGAAATTGTACAGTCTTCCCCT 60.307 47.826 19.27 0.00 33.40 4.79
4051 4376 9.887629 ATGATCATCTAATTCGAATCTGCTATT 57.112 29.630 11.83 0.00 0.00 1.73
4055 4380 9.546428 TCATCTAATTCGAATCTGCTATTGAAA 57.454 29.630 11.83 0.00 0.00 2.69
4072 4397 7.536622 GCTATTGAAATTCATAATGGAAGCTCG 59.463 37.037 0.00 0.00 0.00 5.03
4076 4401 5.852738 AATTCATAATGGAAGCTCGATCG 57.147 39.130 9.36 9.36 0.00 3.69
4078 4403 3.642705 TCATAATGGAAGCTCGATCGTG 58.357 45.455 15.94 14.19 0.00 4.35
4080 4405 1.645034 AATGGAAGCTCGATCGTGTG 58.355 50.000 15.94 7.98 0.00 3.82
4082 4407 0.109272 TGGAAGCTCGATCGTGTGTC 60.109 55.000 15.94 13.14 0.00 3.67
4085 4410 1.914700 GAAGCTCGATCGTGTGTCTTC 59.085 52.381 15.94 15.55 0.00 2.87
4087 4412 1.542030 AGCTCGATCGTGTGTCTTCTT 59.458 47.619 15.94 0.00 0.00 2.52
4094 4419 5.571741 TCGATCGTGTGTCTTCTTGTTATTC 59.428 40.000 15.94 0.00 0.00 1.75
4099 4424 5.609696 CGTGTGTCTTCTTGTTATTCGTGTC 60.610 44.000 0.00 0.00 0.00 3.67
4138 4464 7.357532 GCGTTGCTTTATGTGAATATAATGTGC 60.358 37.037 0.00 0.00 0.00 4.57
4156 4482 4.910195 TGTGCTCCTGTCATATTTCAGTT 58.090 39.130 4.04 0.00 0.00 3.16
4160 4486 4.816925 GCTCCTGTCATATTTCAGTTACCC 59.183 45.833 4.04 0.00 0.00 3.69
4229 4555 9.771534 AGTAAGTTCAGAGATAGCCATAATTTC 57.228 33.333 0.00 0.00 0.00 2.17
4243 4570 5.886474 GCCATAATTTCTATACCTAAGGGGC 59.114 44.000 0.00 0.00 39.10 5.80
4251 4578 0.996583 TACCTAAGGGGCCCAAGTTG 59.003 55.000 27.72 11.38 39.10 3.16
4263 4590 0.385390 CCAAGTTGAGGCTGCGTTTT 59.615 50.000 3.87 0.00 0.00 2.43
4269 4596 0.036732 TGAGGCTGCGTTTTCATCCT 59.963 50.000 0.00 0.00 35.47 3.24
4272 4599 1.555075 AGGCTGCGTTTTCATCCTAGA 59.445 47.619 0.00 0.00 31.36 2.43
4275 4602 4.127171 GGCTGCGTTTTCATCCTAGAATA 58.873 43.478 0.00 0.00 0.00 1.75
4276 4603 4.024809 GGCTGCGTTTTCATCCTAGAATAC 60.025 45.833 0.00 0.00 0.00 1.89
4277 4604 4.024809 GCTGCGTTTTCATCCTAGAATACC 60.025 45.833 0.00 0.00 0.00 2.73
4278 4605 5.092554 TGCGTTTTCATCCTAGAATACCA 57.907 39.130 0.00 0.00 0.00 3.25
4279 4606 5.680619 TGCGTTTTCATCCTAGAATACCAT 58.319 37.500 0.00 0.00 0.00 3.55
4281 4608 5.527582 GCGTTTTCATCCTAGAATACCATGT 59.472 40.000 0.00 0.00 0.00 3.21
4282 4609 6.038271 GCGTTTTCATCCTAGAATACCATGTT 59.962 38.462 0.00 0.00 0.00 2.71
4284 4611 9.104965 CGTTTTCATCCTAGAATACCATGTTTA 57.895 33.333 0.00 0.00 0.00 2.01
4300 4627 8.472007 ACCATGTTTAGTTTTCATAAAGGACA 57.528 30.769 0.00 0.00 0.00 4.02
4343 4670 6.524586 GTGTTTAGCATCAACAAATAGCACTC 59.475 38.462 0.00 0.00 35.91 3.51
4372 4703 0.333993 AAGAGGTCATTGCCAGGCAT 59.666 50.000 17.09 0.00 38.76 4.40
4436 4789 8.630054 AATTGTAAGATAAGTTTGCACTACCA 57.370 30.769 0.00 0.00 30.68 3.25
4437 4790 7.429636 TTGTAAGATAAGTTTGCACTACCAC 57.570 36.000 0.00 0.00 30.68 4.16
4445 4912 5.852282 AGTTTGCACTACCACAGAAATTT 57.148 34.783 0.00 0.00 0.00 1.82
4451 4918 4.320494 GCACTACCACAGAAATTTCACCAG 60.320 45.833 19.99 9.19 0.00 4.00
4452 4919 4.821805 CACTACCACAGAAATTTCACCAGT 59.178 41.667 19.99 13.36 0.00 4.00
4480 4948 5.125900 TGTGGAGAATGCCAATTCACTATTG 59.874 40.000 1.64 0.00 44.05 1.90
4520 4992 6.800072 AAAAGGTCCCTACTAATCTGAGAG 57.200 41.667 0.00 0.00 0.00 3.20
4523 4995 2.894765 GTCCCTACTAATCTGAGAGGGC 59.105 54.545 0.06 0.00 45.69 5.19
4524 4996 1.889829 CCCTACTAATCTGAGAGGGCG 59.110 57.143 0.00 0.00 40.53 6.13
4525 4997 2.489255 CCCTACTAATCTGAGAGGGCGA 60.489 54.545 0.00 0.00 40.53 5.54
4530 5004 5.104259 ACTAATCTGAGAGGGCGAAAAAT 57.896 39.130 0.00 0.00 0.00 1.82
4531 5005 6.235231 ACTAATCTGAGAGGGCGAAAAATA 57.765 37.500 0.00 0.00 0.00 1.40
4650 5124 7.595819 TGAGTAAAATGAAATTGTGGGAAGT 57.404 32.000 0.00 0.00 36.10 3.01
5024 5529 1.511305 GGACGATGAGGCGTTGAGA 59.489 57.895 0.00 0.00 45.72 3.27
5027 5532 0.888619 ACGATGAGGCGTTGAGAAGA 59.111 50.000 0.00 0.00 42.71 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 1.003233 GCTGGGTTGAGTGGGAGTC 60.003 63.158 0.00 0.00 0.00 3.36
119 120 9.809096 TGTTGTTGTCATATTGTTATGTTTTGT 57.191 25.926 0.00 0.00 37.16 2.83
282 289 0.544697 GAGGAGGAGAGGAGACGAGT 59.455 60.000 0.00 0.00 0.00 4.18
304 311 2.462605 GGGAGGGGAGGGGGTTTA 59.537 66.667 0.00 0.00 0.00 2.01
305 312 4.714711 GGGGAGGGGAGGGGGTTT 62.715 72.222 0.00 0.00 0.00 3.27
319 336 2.749621 CTCTGGTTTCTTGATTTCGGGG 59.250 50.000 0.00 0.00 0.00 5.73
322 339 4.390297 GGTCTCTCTGGTTTCTTGATTTCG 59.610 45.833 0.00 0.00 0.00 3.46
386 670 2.256461 CTTTTGGTGGCAGCTCGC 59.744 61.111 18.53 0.00 41.28 5.03
387 671 2.256461 GCTTTTGGTGGCAGCTCG 59.744 61.111 18.53 4.68 0.00 5.03
388 672 2.653115 GGCTTTTGGTGGCAGCTC 59.347 61.111 18.53 2.07 33.76 4.09
389 673 2.919328 GGGCTTTTGGTGGCAGCT 60.919 61.111 18.53 0.00 33.76 4.24
390 674 4.007644 GGGGCTTTTGGTGGCAGC 62.008 66.667 10.30 10.30 0.00 5.25
1151 1435 2.031508 GGAACGATTCACCGCAAAAAGA 60.032 45.455 0.00 0.00 0.00 2.52
1341 1638 2.781174 AGGACCAAACACCTAGGACAAA 59.219 45.455 17.98 0.00 34.47 2.83
1367 1664 0.474660 AAGAGAAGGGGGACTGCAGT 60.475 55.000 21.88 21.88 0.00 4.40
1434 1733 4.377897 ACGGAAAGTGTTAACAGAAGGAG 58.622 43.478 8.98 2.73 0.00 3.69
1440 1739 3.302870 CCACGAACGGAAAGTGTTAACAG 60.303 47.826 8.98 0.00 34.34 3.16
1683 1983 3.129462 TCGTTGCAACCAGAAACAATTGA 59.871 39.130 23.42 7.57 35.29 2.57
1725 2025 4.041321 AGAACAGGGGAAACAGGTAGTAAC 59.959 45.833 0.00 0.00 0.00 2.50
1906 2206 0.398696 ACAGGACGGGCACATGTTAA 59.601 50.000 0.00 0.00 0.00 2.01
1943 2243 1.696336 AGGCACACCCATCATAGCTAG 59.304 52.381 0.00 0.00 36.11 3.42
2042 2347 6.206243 CCGGATGAAAATGAGAGCAAGATTAT 59.794 38.462 0.00 0.00 0.00 1.28
2045 2350 3.881688 CCGGATGAAAATGAGAGCAAGAT 59.118 43.478 0.00 0.00 0.00 2.40
2214 2519 2.232399 TGGCAGTAACTGACACGACTA 58.768 47.619 0.00 0.00 42.40 2.59
2230 2535 9.271828 CATCACTACAGTACAAATTATATGGCA 57.728 33.333 0.00 0.00 0.00 4.92
2341 2649 9.403583 GGGGATTCTTGTATTGTTATTACTTCA 57.596 33.333 0.00 0.00 0.00 3.02
2349 2657 7.123547 GTGATTTGGGGGATTCTTGTATTGTTA 59.876 37.037 0.00 0.00 0.00 2.41
2354 2663 4.080015 TCGTGATTTGGGGGATTCTTGTAT 60.080 41.667 0.00 0.00 0.00 2.29
2375 2684 9.182933 GAGAGTAAATACTTACCAAGCTTATCG 57.817 37.037 0.00 0.00 38.59 2.92
2402 2711 3.938963 TGTCTGAAATACATTTCCTCGCC 59.061 43.478 11.22 0.00 44.16 5.54
2404 2713 5.419542 TCCTGTCTGAAATACATTTCCTCG 58.580 41.667 11.22 2.20 44.16 4.63
2486 2795 3.003275 GCGTCCAAAAACTGTCAGATGAA 59.997 43.478 6.91 0.00 0.00 2.57
2506 2815 0.875474 CCAAACCAAACCTGCAAGCG 60.875 55.000 0.00 0.00 0.00 4.68
2547 2857 3.445096 GGAATGTCAATGAAACTGAGGGG 59.555 47.826 0.00 0.00 0.00 4.79
2548 2858 4.338879 AGGAATGTCAATGAAACTGAGGG 58.661 43.478 0.00 0.00 0.00 4.30
2549 2859 5.005740 TGAGGAATGTCAATGAAACTGAGG 58.994 41.667 0.00 0.00 0.00 3.86
2550 2860 6.206243 ACTTGAGGAATGTCAATGAAACTGAG 59.794 38.462 0.00 0.00 35.88 3.35
2554 2864 6.738114 TGAACTTGAGGAATGTCAATGAAAC 58.262 36.000 0.00 0.00 35.88 2.78
2611 2923 8.077836 AGTTATTCTTTTTCTGTGAAGACTCG 57.922 34.615 0.00 0.00 32.01 4.18
2678 2990 4.925646 GCACAATCTCCAAAATCAGAAACC 59.074 41.667 0.00 0.00 0.00 3.27
2722 3034 3.414269 TGTTAAATCCCAGGACGGAAAC 58.586 45.455 0.00 0.00 36.56 2.78
2727 3041 4.700213 ACTGAAATGTTAAATCCCAGGACG 59.300 41.667 0.00 0.00 0.00 4.79
2759 3073 6.998074 TCAAAGACAAGGAACATAAGATGTGT 59.002 34.615 0.00 0.00 44.07 3.72
2792 3106 1.276421 CTCACAGGGGGTAGACACTTG 59.724 57.143 0.00 0.00 0.00 3.16
2822 3136 8.546244 CAGATACACTCATATGAACATTCACAC 58.454 37.037 6.90 0.00 40.49 3.82
2948 3266 2.452767 CCTTCCGCGAACAAGGTAC 58.547 57.895 8.23 0.00 35.34 3.34
3058 3376 3.075148 GGAGGTTTTCACTGGAACTAGC 58.925 50.000 0.00 0.00 31.35 3.42
3133 3451 2.038557 TGGTTGCTTCTTCTCTGTACCC 59.961 50.000 0.00 0.00 0.00 3.69
3405 3723 0.817634 TTGTGCTTTCTGGTCACCGG 60.818 55.000 0.00 0.00 0.00 5.28
3409 3727 1.490490 ACCTCTTGTGCTTTCTGGTCA 59.510 47.619 0.00 0.00 0.00 4.02
3529 3847 1.272425 ACATTCATCCGGCCAAGGAAA 60.272 47.619 2.24 0.00 44.50 3.13
3562 3880 0.668706 GTGTCGATGAGCAGTGCACT 60.669 55.000 15.25 15.25 0.00 4.40
3614 3932 2.806856 GCTCGTTCATCTGGCTGCG 61.807 63.158 0.00 0.00 0.00 5.18
3638 3956 1.762222 GCGCAAACATAGTCGCCGAT 61.762 55.000 0.30 0.00 41.53 4.18
3639 3957 2.449525 GCGCAAACATAGTCGCCGA 61.450 57.895 0.30 0.00 41.53 5.54
3640 3958 2.021380 GCGCAAACATAGTCGCCG 59.979 61.111 0.30 0.00 41.53 6.46
3641 3959 0.793104 GTTGCGCAAACATAGTCGCC 60.793 55.000 26.87 4.16 46.14 5.54
3642 3960 0.165944 AGTTGCGCAAACATAGTCGC 59.834 50.000 26.87 9.04 46.78 5.19
3656 3977 2.289002 CCAGTGAGAGTTTGTCAGTTGC 59.711 50.000 0.00 0.00 0.00 4.17
3721 4042 2.354188 TCGCCTGTTGTGTCGACG 60.354 61.111 11.62 0.00 0.00 5.12
3852 4173 5.013599 AGGCCTCAAAGTTTCTCTAGTTCAT 59.986 40.000 0.00 0.00 0.00 2.57
3906 4228 1.800586 CACAAACTCACCCTGACATCG 59.199 52.381 0.00 0.00 0.00 3.84
3979 4302 6.814954 AAGGCTCAACCAGATTAATCTAGA 57.185 37.500 17.53 11.83 43.14 2.43
4039 4364 9.338291 CCATTATGAATTTCAATAGCAGATTCG 57.662 33.333 2.68 0.00 31.15 3.34
4051 4376 6.073602 CGATCGAGCTTCCATTATGAATTTCA 60.074 38.462 10.26 0.75 0.00 2.69
4055 4380 4.687948 CACGATCGAGCTTCCATTATGAAT 59.312 41.667 24.34 0.00 0.00 2.57
4072 4397 5.345202 ACGAATAACAAGAAGACACACGATC 59.655 40.000 0.00 0.00 0.00 3.69
4076 4401 5.462398 AGACACGAATAACAAGAAGACACAC 59.538 40.000 0.00 0.00 0.00 3.82
4078 4403 5.690409 TGAGACACGAATAACAAGAAGACAC 59.310 40.000 0.00 0.00 0.00 3.67
4080 4405 6.150318 TCTGAGACACGAATAACAAGAAGAC 58.850 40.000 0.00 0.00 0.00 3.01
4082 4407 7.588143 ATTCTGAGACACGAATAACAAGAAG 57.412 36.000 0.00 0.00 0.00 2.85
4113 4438 7.857389 AGCACATTATATTCACATAAAGCAACG 59.143 33.333 0.00 0.00 0.00 4.10
4118 4444 9.060347 ACAGGAGCACATTATATTCACATAAAG 57.940 33.333 0.00 0.00 0.00 1.85
4122 4448 6.594744 TGACAGGAGCACATTATATTCACAT 58.405 36.000 0.00 0.00 0.00 3.21
4125 4451 9.797642 AAATATGACAGGAGCACATTATATTCA 57.202 29.630 0.00 0.00 0.00 2.57
4156 4482 1.681327 GGACTCCAGAGCACGGGTA 60.681 63.158 0.00 0.00 33.25 3.69
4201 4527 7.898014 TTATGGCTATCTCTGAACTTACTGA 57.102 36.000 0.00 0.00 0.00 3.41
4202 4528 9.553064 AAATTATGGCTATCTCTGAACTTACTG 57.447 33.333 0.00 0.00 0.00 2.74
4204 4530 9.771534 AGAAATTATGGCTATCTCTGAACTTAC 57.228 33.333 0.00 0.00 0.00 2.34
4218 4544 6.297068 GCCCCTTAGGTATAGAAATTATGGCT 60.297 42.308 0.00 0.00 38.26 4.75
4229 4555 2.702748 ACTTGGGCCCCTTAGGTATAG 58.297 52.381 22.27 4.97 38.26 1.31
4231 4557 1.569072 CAACTTGGGCCCCTTAGGTAT 59.431 52.381 22.27 2.43 38.26 2.73
4234 4560 0.034089 CTCAACTTGGGCCCCTTAGG 60.034 60.000 22.27 3.22 39.47 2.69
4243 4570 1.455383 AAACGCAGCCTCAACTTGGG 61.455 55.000 0.00 0.00 0.00 4.12
4275 4602 8.472007 TGTCCTTTATGAAAACTAAACATGGT 57.528 30.769 0.00 0.00 0.00 3.55
4276 4603 8.576442 ACTGTCCTTTATGAAAACTAAACATGG 58.424 33.333 0.00 0.00 0.00 3.66
4277 4604 9.965824 AACTGTCCTTTATGAAAACTAAACATG 57.034 29.630 0.00 0.00 0.00 3.21
4294 4621 9.965824 CACATCAAAGTTTATAAAACTGTCCTT 57.034 29.630 5.85 0.00 0.00 3.36
4295 4622 9.131791 ACACATCAAAGTTTATAAAACTGTCCT 57.868 29.630 5.85 0.00 0.00 3.85
4296 4623 9.744468 AACACATCAAAGTTTATAAAACTGTCC 57.256 29.630 5.85 0.00 0.00 4.02
4343 4670 7.761249 CCTGGCAATGACCTCTTTTTATAAAAG 59.239 37.037 10.40 5.72 0.00 2.27
4409 4762 9.908152 GGTAGTGCAAACTTATCTTACAATTTT 57.092 29.630 0.00 0.00 0.00 1.82
4411 4764 8.512138 GTGGTAGTGCAAACTTATCTTACAATT 58.488 33.333 0.00 0.00 0.00 2.32
4413 4766 6.993308 TGTGGTAGTGCAAACTTATCTTACAA 59.007 34.615 0.00 0.00 0.00 2.41
4416 4769 6.999950 TCTGTGGTAGTGCAAACTTATCTTA 58.000 36.000 0.00 0.00 0.00 2.10
4428 4781 3.568007 TGGTGAAATTTCTGTGGTAGTGC 59.432 43.478 18.64 0.00 0.00 4.40
4429 4782 4.821805 ACTGGTGAAATTTCTGTGGTAGTG 59.178 41.667 18.64 3.24 0.00 2.74
4451 4918 1.317613 TTGGCATTCTCCACACACAC 58.682 50.000 0.00 0.00 35.50 3.82
4452 4919 2.291209 ATTGGCATTCTCCACACACA 57.709 45.000 0.00 0.00 35.50 3.72
4515 4987 4.080582 TCTGGATTATTTTTCGCCCTCTCA 60.081 41.667 0.00 0.00 0.00 3.27
4516 4988 4.451900 TCTGGATTATTTTTCGCCCTCTC 58.548 43.478 0.00 0.00 0.00 3.20
4517 4989 4.503714 TCTGGATTATTTTTCGCCCTCT 57.496 40.909 0.00 0.00 0.00 3.69
4518 4990 4.398044 TGTTCTGGATTATTTTTCGCCCTC 59.602 41.667 0.00 0.00 0.00 4.30
4519 4991 4.340617 TGTTCTGGATTATTTTTCGCCCT 58.659 39.130 0.00 0.00 0.00 5.19
4520 4992 4.398044 TCTGTTCTGGATTATTTTTCGCCC 59.602 41.667 0.00 0.00 0.00 6.13
4660 5134 2.338015 GGCGTCTACTGACCACGGA 61.338 63.158 0.00 0.00 39.94 4.69
4661 5135 2.181021 GGCGTCTACTGACCACGG 59.819 66.667 0.00 0.00 39.94 4.94
4712 5187 0.842030 ACTCCATCAAGCTCACCCCA 60.842 55.000 0.00 0.00 0.00 4.96
4841 5316 3.056458 CACCAGCACCACGTAGGA 58.944 61.111 10.46 0.00 41.22 2.94
5012 5517 1.270305 CCACTTCTTCTCAACGCCTCA 60.270 52.381 0.00 0.00 0.00 3.86
5015 5520 1.578206 GGCCACTTCTTCTCAACGCC 61.578 60.000 0.00 0.00 0.00 5.68


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

AutoCloner maintained by Alex Coulton.