Multiple sequence alignment - TraesCS4B01G220400

Loading Multiple Alignment...

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 TraesCS4B01G220400 chr4B 100.000 4375 0 0 1 4375 463580792 463585166 0.000000e+00 8080.0
1 TraesCS4B01G220400 chr4D 92.054 4455 168 66 1 4321 377826598 377831000 0.000000e+00 6095.0
2 TraesCS4B01G220400 chr4D 94.545 55 3 0 1731 1785 397682344 397682290 7.800000e-13 86.1
3 TraesCS4B01G220400 chr4A 92.752 4125 162 54 1 4051 88084171 88080110 0.000000e+00 5834.0
4 TraesCS4B01G220400 chr4A 84.713 157 4 5 4170 4321 88080027 88079886 5.900000e-29 139.0
5 TraesCS4B01G220400 chr1A 97.959 49 1 0 1735 1783 471324115 471324163 7.800000e-13 86.1
6 TraesCS4B01G220400 chr7A 96.078 51 2 0 1735 1785 271736403 271736453 2.800000e-12 84.2
7 TraesCS4B01G220400 chr7B 96.000 50 2 0 1736 1785 226429685 226429636 1.010000e-11 82.4
8 TraesCS4B01G220400 chr7B 94.231 52 3 0 1735 1786 146819145 146819094 3.630000e-11 80.5
9 TraesCS4B01G220400 chr6B 94.231 52 3 0 1735 1786 574023852 574023801 3.630000e-11 80.5
10 TraesCS4B01G220400 chr3A 94.118 51 3 0 1730 1780 32122347 32122397 1.300000e-10 78.7


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 TraesCS4B01G220400 chr4B 463580792 463585166 4374 False 8080.0 8080 100.0000 1 4375 1 chr4B.!!$F1 4374
1 TraesCS4B01G220400 chr4D 377826598 377831000 4402 False 6095.0 6095 92.0540 1 4321 1 chr4D.!!$F1 4320
2 TraesCS4B01G220400 chr4A 88079886 88084171 4285 True 2986.5 5834 88.7325 1 4321 2 chr4A.!!$R1 4320

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
708 735 0.317160 TTGGATATAGCGGGAGTGCG 59.683 55.000 0.00 0.00 40.67 5.34 F
1339 1369 1.071542 TGACATGGCGGACTCTTCAAA 59.928 47.619 0.00 0.00 0.00 2.69 F
2503 2534 0.178953 AAAGCTTCATGGTGGCCACT 60.179 50.000 33.91 14.25 35.80 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1890 1920 1.135170 GCTTCCTTGCTGATTCCAAGC 60.135 52.381 0.00 0.0 38.63 4.01 R
3058 3129 0.238289 GCTAGCAGCAGAAAAACGCA 59.762 50.000 10.63 0.0 41.89 5.24 R
4151 4310 0.107017 AGGCTACGGCATCAGCAATT 60.107 50.000 5.23 0.0 44.61 2.32 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
24 25 1.542108 GGTGCTCTGTCAAGCTCAACT 60.542 52.381 0.00 0.00 42.94 3.16
37 38 1.691196 CTCAACTTTGGCCAAGTCCA 58.309 50.000 19.48 2.39 45.77 4.02
38 39 2.242043 CTCAACTTTGGCCAAGTCCAT 58.758 47.619 19.48 1.87 45.77 3.41
114 115 3.730761 CGTTGACAGGCCTGCTGC 61.731 66.667 33.06 21.66 40.16 5.25
150 151 2.960129 GCCGTCCAGTTATCGCGG 60.960 66.667 6.13 0.00 44.60 6.46
381 382 3.132289 TCGGAATCCTTGATTCGTTAGCT 59.868 43.478 9.91 0.00 46.47 3.32
389 390 3.520290 TGATTCGTTAGCTTCGATGGT 57.480 42.857 12.94 8.16 37.18 3.55
419 420 3.504863 CGCTGCTTGCTTGATGTTTTAT 58.495 40.909 0.00 0.00 40.11 1.40
426 427 5.289434 GCTTGCTTGATGTTTTATTGCCTAC 59.711 40.000 0.00 0.00 0.00 3.18
430 431 8.292444 TGCTTGATGTTTTATTGCCTACTTAT 57.708 30.769 0.00 0.00 0.00 1.73
508 509 3.056035 GGGTGGTAACCTCTGTAGAACAG 60.056 52.174 0.50 0.50 46.70 3.16
533 534 8.448615 AGAAGTATTTCGTGTTTACTTAATGCC 58.551 33.333 0.00 0.00 36.55 4.40
565 592 7.438564 GGGTTGGTTTCATGTTTACTTAATGT 58.561 34.615 0.00 0.00 0.00 2.71
642 669 5.122396 GCTTACGAAGAACATCACAAAGGAT 59.878 40.000 0.00 0.00 0.00 3.24
698 725 9.091784 GTGACACATGTAGCATATTGGATATAG 57.908 37.037 0.00 0.00 0.00 1.31
704 731 4.679373 AGCATATTGGATATAGCGGGAG 57.321 45.455 0.00 0.00 0.00 4.30
706 733 4.122776 GCATATTGGATATAGCGGGAGTG 58.877 47.826 0.00 0.00 0.00 3.51
708 735 0.317160 TTGGATATAGCGGGAGTGCG 59.683 55.000 0.00 0.00 40.67 5.34
709 736 1.215647 GGATATAGCGGGAGTGCGG 59.784 63.158 0.00 0.00 40.67 5.69
710 737 1.215647 GATATAGCGGGAGTGCGGG 59.784 63.158 0.00 0.00 40.67 6.13
711 738 1.228769 ATATAGCGGGAGTGCGGGA 60.229 57.895 0.00 0.00 40.67 5.14
712 739 1.533469 ATATAGCGGGAGTGCGGGAC 61.533 60.000 0.00 0.00 40.67 4.46
713 740 2.635787 TATAGCGGGAGTGCGGGACT 62.636 60.000 0.31 0.31 40.67 3.85
714 741 2.635787 ATAGCGGGAGTGCGGGACTA 62.636 60.000 0.88 0.00 40.67 2.59
715 742 4.509737 GCGGGAGTGCGGGACTAC 62.510 72.222 2.81 2.81 33.83 2.73
772 799 1.913778 AATGGTTGCAGCTGTGATCA 58.086 45.000 16.64 11.06 0.00 2.92
783 810 5.361571 TGCAGCTGTGATCATGGATTTTAAT 59.638 36.000 16.64 0.00 0.00 1.40
792 819 9.806203 GTGATCATGGATTTTAATTCAATCACA 57.194 29.630 16.59 7.68 39.62 3.58
812 840 5.408909 TCACATAGCGTTTATGTCCGAAAAA 59.591 36.000 10.51 0.00 36.13 1.94
838 868 2.228822 CTGGCCGTTTAAATCACTGCTT 59.771 45.455 0.00 0.00 0.00 3.91
896 926 8.425577 AGTGCTGACTCATATTGTTATTGTAC 57.574 34.615 0.00 0.00 0.00 2.90
897 927 8.260818 AGTGCTGACTCATATTGTTATTGTACT 58.739 33.333 0.00 0.00 0.00 2.73
898 928 8.883731 GTGCTGACTCATATTGTTATTGTACTT 58.116 33.333 0.00 0.00 0.00 2.24
899 929 9.098355 TGCTGACTCATATTGTTATTGTACTTC 57.902 33.333 0.00 0.00 0.00 3.01
900 930 9.319143 GCTGACTCATATTGTTATTGTACTTCT 57.681 33.333 0.00 0.00 0.00 2.85
1138 1168 8.059502 GGCGTAAGGAAAATGTAAAACTTTTTG 58.940 33.333 7.99 0.00 35.40 2.44
1299 1329 4.067896 GCGATGTTCCAGAATATCACCAT 58.932 43.478 14.87 0.00 38.38 3.55
1339 1369 1.071542 TGACATGGCGGACTCTTCAAA 59.928 47.619 0.00 0.00 0.00 2.69
1348 1378 3.678548 GCGGACTCTTCAAATCGTAAGTT 59.321 43.478 0.00 0.00 39.48 2.66
1524 1554 7.378995 GCTTTTCATGCATGATTGATCTTAGAC 59.621 37.037 29.13 6.65 36.56 2.59
1615 1645 3.974871 TGTACATCATCACATGCATGC 57.025 42.857 26.53 11.82 0.00 4.06
2354 2384 7.705700 ACCTTTGGGTTGTTAAGGATATAACT 58.294 34.615 7.08 0.00 44.73 2.24
2420 2450 3.666274 AGCTATGATGCTCTGAATCAGC 58.334 45.455 5.18 0.00 39.34 4.26
2451 2481 2.721274 TTGTGCACATTCCAAATCCG 57.279 45.000 22.39 0.00 0.00 4.18
2503 2534 0.178953 AAAGCTTCATGGTGGCCACT 60.179 50.000 33.91 14.25 35.80 4.00
2575 2606 4.833390 AGTGGTGCCAGTAAATAGAGTTC 58.167 43.478 0.00 0.00 0.00 3.01
2648 2680 9.631452 GATCATTACTTTGATAGACATCGATCA 57.369 33.333 0.00 1.02 36.48 2.92
2656 2688 5.766222 TGATAGACATCGATCAGTGTGATG 58.234 41.667 16.04 16.04 43.92 3.07
2681 2713 4.588899 TGCAGCATGTGTTTATAGGAGTT 58.411 39.130 0.00 0.00 39.31 3.01
2787 2844 5.393461 GGGCTCCACATTTTATTTCAGTCAG 60.393 44.000 0.00 0.00 0.00 3.51
2872 2929 7.713734 AACACTGTAGGTATAGTCTGCTAAA 57.286 36.000 0.00 0.00 0.00 1.85
2947 3018 9.273016 GTTGACCATATGTGCTACAAATACTAT 57.727 33.333 1.24 0.00 0.00 2.12
2974 3045 5.122869 TGCTCTAGAAACATGTTTGCAGATC 59.877 40.000 27.85 21.44 32.11 2.75
3058 3129 5.595952 GGAGTAGGCATCCAAAATTCAGAAT 59.404 40.000 0.00 0.00 36.79 2.40
3082 3153 0.321671 TTTTCTGCTGCTAGCCGAGT 59.678 50.000 13.29 0.00 41.51 4.18
3194 3266 7.854422 CGAGAAATGAATTGGTATGATCAGTTG 59.146 37.037 0.09 0.00 31.13 3.16
3326 3398 1.597854 CTTGGAAGTGAGCACGGCA 60.598 57.895 0.00 0.00 36.20 5.69
3375 3447 4.207891 TCATCAACCTTCCTGAAGTAGC 57.792 45.455 6.19 0.00 36.72 3.58
3376 3448 2.743636 TCAACCTTCCTGAAGTAGCG 57.256 50.000 6.19 0.00 36.72 4.26
3385 3457 4.002906 TCCTGAAGTAGCGAATGTTTGT 57.997 40.909 0.00 0.00 0.00 2.83
3429 3501 1.364626 CCTTAGCCTTGCAGCAGTCG 61.365 60.000 0.00 0.00 34.23 4.18
3430 3502 1.364626 CTTAGCCTTGCAGCAGTCGG 61.365 60.000 0.00 0.00 34.23 4.79
3438 3510 1.521681 GCAGCAGTCGGTATGGTCC 60.522 63.158 0.00 0.00 0.00 4.46
3439 3511 1.961180 GCAGCAGTCGGTATGGTCCT 61.961 60.000 0.00 0.00 0.00 3.85
3459 3541 3.371380 CCTCTCCTGCTTCCAATAGCTTT 60.371 47.826 0.00 0.00 41.76 3.51
3460 3542 4.141620 CCTCTCCTGCTTCCAATAGCTTTA 60.142 45.833 0.00 0.00 41.76 1.85
3477 3583 3.633986 GCTTTATCTCAGGGGTGGAAATG 59.366 47.826 0.00 0.00 0.00 2.32
3478 3584 4.628715 GCTTTATCTCAGGGGTGGAAATGA 60.629 45.833 0.00 0.00 0.00 2.57
3479 3585 4.503714 TTATCTCAGGGGTGGAAATGAC 57.496 45.455 0.00 0.00 0.00 3.06
3483 3589 1.351017 TCAGGGGTGGAAATGACAGTC 59.649 52.381 0.00 0.00 0.00 3.51
3587 3714 9.533253 AGGCATTTTCATTGCTGTATTAAATAC 57.467 29.630 0.00 0.00 40.03 1.89
3588 3715 9.311916 GGCATTTTCATTGCTGTATTAAATACA 57.688 29.630 0.00 0.00 42.95 2.29
3641 3770 5.939447 TGACATAAATGGCTATGTGGATCA 58.061 37.500 2.94 0.00 41.54 2.92
3650 3784 5.565509 TGGCTATGTGGATCAAAACACTTA 58.434 37.500 0.00 0.00 38.39 2.24
3668 3806 6.059484 ACACTTATTTTCTTTCGGGTCTCAA 58.941 36.000 0.00 0.00 0.00 3.02
3669 3807 6.017357 ACACTTATTTTCTTTCGGGTCTCAAC 60.017 38.462 0.00 0.00 0.00 3.18
3670 3808 6.017440 CACTTATTTTCTTTCGGGTCTCAACA 60.017 38.462 0.00 0.00 0.00 3.33
3671 3809 6.715264 ACTTATTTTCTTTCGGGTCTCAACAT 59.285 34.615 0.00 0.00 0.00 2.71
3840 3989 1.452145 GGGCCTGCTTTGTCGTTTGA 61.452 55.000 0.84 0.00 0.00 2.69
3874 4023 0.179129 GCTTTGATTGGCCATCACGG 60.179 55.000 6.09 8.81 41.98 4.94
3907 4056 1.705337 CCCGTGACATAAAGCCAGCG 61.705 60.000 0.00 0.00 0.00 5.18
3980 4129 8.023050 ACTATTCGCAGACTATTATCAATTGC 57.977 34.615 0.00 0.00 34.32 3.56
3987 4136 7.095313 CGCAGACTATTATCAATTGCTTGATCT 60.095 37.037 4.58 0.00 46.83 2.75
4047 4196 1.032014 AATGGGCGATTACACATGGC 58.968 50.000 0.00 0.00 0.00 4.40
4051 4200 1.447317 GGCGATTACACATGGCCCAG 61.447 60.000 0.00 0.00 37.00 4.45
4068 4217 2.674420 CCAGGAATAGGGAAGTACGGA 58.326 52.381 0.00 0.00 0.00 4.69
4069 4218 2.628657 CCAGGAATAGGGAAGTACGGAG 59.371 54.545 0.00 0.00 0.00 4.63
4147 4306 0.101219 TGTCTCGTGAGCCGATGATG 59.899 55.000 0.00 0.00 46.23 3.07
4148 4307 1.066422 TCTCGTGAGCCGATGATGC 59.934 57.895 0.00 0.00 46.23 3.91
4149 4308 1.067084 CTCGTGAGCCGATGATGCT 59.933 57.895 0.00 0.00 46.23 3.79
4150 4309 1.213733 CTCGTGAGCCGATGATGCTG 61.214 60.000 0.00 0.00 46.23 4.41
4151 4310 1.227060 CGTGAGCCGATGATGCTGA 60.227 57.895 0.00 0.00 39.69 4.26
4152 4311 0.807275 CGTGAGCCGATGATGCTGAA 60.807 55.000 0.00 0.00 39.69 3.02
4153 4312 1.590932 GTGAGCCGATGATGCTGAAT 58.409 50.000 0.00 0.00 39.69 2.57
4154 4313 1.945394 GTGAGCCGATGATGCTGAATT 59.055 47.619 0.00 0.00 39.69 2.17
4173 4332 0.539518 TGCTGATGCCGTAGCCTTTA 59.460 50.000 0.00 0.00 39.15 1.85
4205 4364 4.578871 TGAACAGATGTTGGTCACATAGG 58.421 43.478 2.31 0.00 46.36 2.57
4290 4454 1.333931 CTGCTGGTGCTGCATGATTAG 59.666 52.381 5.27 1.65 37.65 1.73
4314 4478 2.438021 TGTCAGCTACTTTTCACCCACT 59.562 45.455 0.00 0.00 0.00 4.00
4321 4485 5.046520 AGCTACTTTTCACCCACTAACTAGG 60.047 44.000 0.00 0.00 0.00 3.02
4322 4486 5.046807 GCTACTTTTCACCCACTAACTAGGA 60.047 44.000 0.00 0.00 0.00 2.94
4323 4487 5.485209 ACTTTTCACCCACTAACTAGGAG 57.515 43.478 0.00 0.00 0.00 3.69
4324 4488 5.152934 ACTTTTCACCCACTAACTAGGAGA 58.847 41.667 0.00 0.00 0.00 3.71
4325 4489 5.246429 ACTTTTCACCCACTAACTAGGAGAG 59.754 44.000 0.00 0.00 0.00 3.20
4326 4490 3.383698 TCACCCACTAACTAGGAGAGG 57.616 52.381 0.00 0.00 0.00 3.69
4327 4491 2.024273 TCACCCACTAACTAGGAGAGGG 60.024 54.545 20.86 20.86 40.66 4.30
4328 4492 2.009165 ACCCACTAACTAGGAGAGGGT 58.991 52.381 21.86 21.86 42.96 4.34
4329 4493 2.386113 ACCCACTAACTAGGAGAGGGTT 59.614 50.000 21.86 11.39 45.35 4.11
4330 4494 3.599698 ACCCACTAACTAGGAGAGGGTTA 59.400 47.826 21.86 0.17 45.35 2.85
4331 4495 4.046360 ACCCACTAACTAGGAGAGGGTTAA 59.954 45.833 21.86 0.00 45.35 2.01
4332 4496 4.650131 CCCACTAACTAGGAGAGGGTTAAG 59.350 50.000 16.65 0.00 0.00 1.85
4333 4497 4.650131 CCACTAACTAGGAGAGGGTTAAGG 59.350 50.000 0.00 0.00 0.00 2.69
4334 4498 4.099727 CACTAACTAGGAGAGGGTTAAGGC 59.900 50.000 0.00 0.00 0.00 4.35
4335 4499 2.177811 ACTAGGAGAGGGTTAAGGCC 57.822 55.000 0.00 0.00 0.00 5.19
4336 4500 1.652306 ACTAGGAGAGGGTTAAGGCCT 59.348 52.381 0.00 0.00 0.00 5.19
4337 4501 2.046025 ACTAGGAGAGGGTTAAGGCCTT 59.954 50.000 24.18 24.18 0.00 4.35
4338 4502 1.290134 AGGAGAGGGTTAAGGCCTTG 58.710 55.000 28.77 0.00 0.00 3.61
4339 4503 0.992695 GGAGAGGGTTAAGGCCTTGT 59.007 55.000 28.77 4.97 0.00 3.16
4340 4504 1.340114 GGAGAGGGTTAAGGCCTTGTG 60.340 57.143 28.77 0.00 0.00 3.33
4341 4505 1.628846 GAGAGGGTTAAGGCCTTGTGA 59.371 52.381 28.77 11.00 0.00 3.58
4342 4506 2.239907 GAGAGGGTTAAGGCCTTGTGAT 59.760 50.000 28.77 9.92 0.00 3.06
4343 4507 2.239907 AGAGGGTTAAGGCCTTGTGATC 59.760 50.000 28.77 17.75 0.00 2.92
4344 4508 1.285078 AGGGTTAAGGCCTTGTGATCC 59.715 52.381 28.77 21.31 0.00 3.36
4345 4509 1.005450 GGGTTAAGGCCTTGTGATCCA 59.995 52.381 28.77 2.48 0.00 3.41
4346 4510 2.369394 GGTTAAGGCCTTGTGATCCAG 58.631 52.381 28.77 0.00 0.00 3.86
4347 4511 2.369394 GTTAAGGCCTTGTGATCCAGG 58.631 52.381 28.77 0.00 0.00 4.45
4348 4512 0.918983 TAAGGCCTTGTGATCCAGGG 59.081 55.000 28.77 7.66 43.13 4.45
4352 4516 3.362040 CCTTGTGATCCAGGGCAAA 57.638 52.632 0.00 0.00 32.96 3.68
4353 4517 0.890683 CCTTGTGATCCAGGGCAAAC 59.109 55.000 0.00 0.00 32.96 2.93
4354 4518 0.890683 CTTGTGATCCAGGGCAAACC 59.109 55.000 0.00 0.00 40.67 3.27
4355 4519 0.187117 TTGTGATCCAGGGCAAACCA 59.813 50.000 0.00 0.00 43.89 3.67
4356 4520 0.539438 TGTGATCCAGGGCAAACCAC 60.539 55.000 0.00 0.00 43.89 4.16
4357 4521 1.076549 TGATCCAGGGCAAACCACC 59.923 57.895 0.00 0.00 43.89 4.61
4358 4522 1.384191 GATCCAGGGCAAACCACCT 59.616 57.895 0.00 0.00 43.89 4.00
4359 4523 0.681243 GATCCAGGGCAAACCACCTC 60.681 60.000 0.00 0.00 43.89 3.85
4360 4524 2.155197 ATCCAGGGCAAACCACCTCC 62.155 60.000 0.00 0.00 43.89 4.30
4361 4525 2.672996 CAGGGCAAACCACCTCCG 60.673 66.667 0.00 0.00 43.89 4.63
4362 4526 3.175710 AGGGCAAACCACCTCCGT 61.176 61.111 0.00 0.00 43.89 4.69
4363 4527 1.844289 AGGGCAAACCACCTCCGTA 60.844 57.895 0.00 0.00 43.89 4.02
4364 4528 1.673337 GGGCAAACCACCTCCGTAC 60.673 63.158 0.00 0.00 39.85 3.67
4365 4529 1.373812 GGCAAACCACCTCCGTACT 59.626 57.895 0.00 0.00 35.26 2.73
4366 4530 0.609662 GGCAAACCACCTCCGTACTA 59.390 55.000 0.00 0.00 35.26 1.82
4367 4531 1.405121 GGCAAACCACCTCCGTACTAG 60.405 57.143 0.00 0.00 35.26 2.57
4368 4532 1.547372 GCAAACCACCTCCGTACTAGA 59.453 52.381 0.00 0.00 0.00 2.43
4369 4533 2.416972 GCAAACCACCTCCGTACTAGAG 60.417 54.545 0.00 3.42 0.00 2.43
4370 4534 3.087031 CAAACCACCTCCGTACTAGAGA 58.913 50.000 10.48 0.00 32.86 3.10
4371 4535 3.446442 AACCACCTCCGTACTAGAGAA 57.554 47.619 10.48 0.00 32.86 2.87
4372 4536 3.446442 ACCACCTCCGTACTAGAGAAA 57.554 47.619 10.48 0.00 32.86 2.52
4373 4537 3.354467 ACCACCTCCGTACTAGAGAAAG 58.646 50.000 10.48 2.78 32.86 2.62
4374 4538 3.009916 ACCACCTCCGTACTAGAGAAAGA 59.990 47.826 10.48 0.00 32.86 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 2.949963 GCCAGATATGGACTTGGCCAAA 60.950 50.000 20.91 4.58 42.16 3.28
37 38 0.833834 CCTCGGGACAGGCCAGATAT 60.834 60.000 5.01 0.00 40.21 1.63
38 39 1.457643 CCTCGGGACAGGCCAGATA 60.458 63.158 5.01 0.00 40.21 1.98
135 136 1.588139 GACCCGCGATAACTGGACG 60.588 63.158 8.23 0.00 0.00 4.79
150 151 3.378427 CAGCTAACCTAAAGCATTGGACC 59.622 47.826 0.00 0.00 42.62 4.46
419 420 4.217550 GCAAACAGTGGAATAAGTAGGCAA 59.782 41.667 0.00 0.00 0.00 4.52
426 427 7.148018 ACCAGAATATGCAAACAGTGGAATAAG 60.148 37.037 13.11 0.00 0.00 1.73
430 431 4.218200 CACCAGAATATGCAAACAGTGGAA 59.782 41.667 13.11 0.00 0.00 3.53
508 509 8.231837 TGGCATTAAGTAAACACGAAATACTTC 58.768 33.333 9.63 0.00 39.74 3.01
533 534 2.298729 ACATGAAACCAACCCCGAATTG 59.701 45.455 0.00 0.00 0.00 2.32
579 606 9.490379 CTTGAACTAAACTACTTTGTCCTGTAT 57.510 33.333 0.00 0.00 0.00 2.29
612 639 7.234187 TGTGATGTTCTTCGTAAGCATAATC 57.766 36.000 0.00 0.00 37.18 1.75
613 640 7.609760 TTGTGATGTTCTTCGTAAGCATAAT 57.390 32.000 0.00 0.00 37.18 1.28
614 641 7.360861 CCTTTGTGATGTTCTTCGTAAGCATAA 60.361 37.037 0.00 0.00 37.18 1.90
698 725 4.509737 GTAGTCCCGCACTCCCGC 62.510 72.222 0.00 0.00 36.43 6.13
704 731 2.351726 CTGCTATTTTGTAGTCCCGCAC 59.648 50.000 0.00 0.00 0.00 5.34
706 733 2.901249 TCTGCTATTTTGTAGTCCCGC 58.099 47.619 0.00 0.00 0.00 6.13
708 735 9.780186 ACTATAATTCTGCTATTTTGTAGTCCC 57.220 33.333 0.00 0.00 0.00 4.46
746 773 1.273048 CAGCTGCAACCATTAAAGCCA 59.727 47.619 0.00 0.00 34.35 4.75
772 799 8.632679 ACGCTATGTGATTGAATTAAAATCCAT 58.367 29.630 9.67 12.58 33.85 3.41
783 810 5.006261 CGGACATAAACGCTATGTGATTGAA 59.994 40.000 13.80 0.00 38.18 2.69
812 840 5.621329 GCAGTGATTTAAACGGCCAGTTATT 60.621 40.000 12.33 2.57 43.37 1.40
838 868 1.268794 CCGAAACAAATCAACGCCACA 60.269 47.619 0.00 0.00 0.00 4.17
896 926 7.220740 AGTAAAGAAAACAGGAGAAGGAGAAG 58.779 38.462 0.00 0.00 0.00 2.85
897 927 7.138054 AGTAAAGAAAACAGGAGAAGGAGAA 57.862 36.000 0.00 0.00 0.00 2.87
898 928 6.749036 AGTAAAGAAAACAGGAGAAGGAGA 57.251 37.500 0.00 0.00 0.00 3.71
899 929 9.508642 AATTAGTAAAGAAAACAGGAGAAGGAG 57.491 33.333 0.00 0.00 0.00 3.69
900 930 9.862149 AAATTAGTAAAGAAAACAGGAGAAGGA 57.138 29.630 0.00 0.00 0.00 3.36
1165 1195 3.242867 TGATGGTGAGGTCAGAAGAAGT 58.757 45.455 0.00 0.00 0.00 3.01
1339 1369 6.444633 ACATACGCAGCTATAAACTTACGAT 58.555 36.000 0.00 0.00 0.00 3.73
1348 1378 8.301002 TGTTGTCATATACATACGCAGCTATAA 58.699 33.333 0.00 0.00 38.10 0.98
1524 1554 5.543714 TGCCTACATGTTACCATAATACCG 58.456 41.667 2.30 0.00 0.00 4.02
1615 1645 9.677567 GATTTTAGCACTACTGATCTCTCTTAG 57.322 37.037 0.00 0.00 0.00 2.18
1890 1920 1.135170 GCTTCCTTGCTGATTCCAAGC 60.135 52.381 0.00 0.00 38.63 4.01
2420 2450 7.482474 TGGAATGTGCACAAAATGTCTATATG 58.518 34.615 25.72 0.00 0.00 1.78
2451 2481 3.827008 TCTGGCTCCAGTATCATGTTC 57.173 47.619 14.96 0.00 43.96 3.18
2503 2534 6.036735 GCGGTGAAGATAGCAATTAACTAACA 59.963 38.462 0.00 0.00 0.00 2.41
2648 2680 1.340697 ACATGCTGCATCCATCACACT 60.341 47.619 13.10 0.00 0.00 3.55
2656 2688 4.136796 TCCTATAAACACATGCTGCATCC 58.863 43.478 13.10 0.00 0.00 3.51
2721 2753 8.853126 TGCTTCGTAATCTTTATTACTAGGCTA 58.147 33.333 13.89 0.00 42.24 3.93
2722 2754 7.723324 TGCTTCGTAATCTTTATTACTAGGCT 58.277 34.615 13.89 0.00 42.24 4.58
2741 2773 1.265095 ACACTGTTGCATTCTGCTTCG 59.735 47.619 0.34 0.00 45.31 3.79
2825 2882 9.853555 TGTTAATAATCACAAAGCACCAATAAG 57.146 29.630 0.00 0.00 0.00 1.73
2879 2937 7.881232 CCCAGTACTCAACCTTAAAACTCATTA 59.119 37.037 0.00 0.00 0.00 1.90
2880 2938 6.715264 CCCAGTACTCAACCTTAAAACTCATT 59.285 38.462 0.00 0.00 0.00 2.57
2947 3018 6.654582 TCTGCAAACATGTTTCTAGAGCAATA 59.345 34.615 24.68 16.89 29.98 1.90
2974 3045 5.067153 CAGTCCTACTCCTAGTTCACATCTG 59.933 48.000 0.00 0.00 0.00 2.90
3058 3129 0.238289 GCTAGCAGCAGAAAAACGCA 59.762 50.000 10.63 0.00 41.89 5.24
3082 3153 3.878103 GACTAGCACCTGAACTCGATCTA 59.122 47.826 0.00 0.00 0.00 1.98
3114 3185 7.088272 TCAAAAGAGCATCAATGATTCACTTG 58.912 34.615 6.37 5.10 37.82 3.16
3194 3266 2.203401 CAGAGCAGACTTAGCATCAGC 58.797 52.381 0.00 0.00 42.56 4.26
3429 3501 1.414550 GAAGCAGGAGAGGACCATACC 59.585 57.143 0.00 0.00 0.00 2.73
3430 3502 1.414550 GGAAGCAGGAGAGGACCATAC 59.585 57.143 0.00 0.00 0.00 2.39
3438 3510 3.557228 AAGCTATTGGAAGCAGGAGAG 57.443 47.619 0.00 0.00 45.30 3.20
3439 3511 5.367937 AGATAAAGCTATTGGAAGCAGGAGA 59.632 40.000 0.00 0.00 45.30 3.71
3459 3541 3.455910 CTGTCATTTCCACCCCTGAGATA 59.544 47.826 0.00 0.00 0.00 1.98
3460 3542 2.240667 CTGTCATTTCCACCCCTGAGAT 59.759 50.000 0.00 0.00 0.00 2.75
3477 3583 3.249559 CAGAAACTCAGCAAAGGACTGTC 59.750 47.826 0.00 0.00 36.50 3.51
3478 3584 3.209410 CAGAAACTCAGCAAAGGACTGT 58.791 45.455 0.00 0.00 36.50 3.55
3479 3585 3.209410 ACAGAAACTCAGCAAAGGACTG 58.791 45.455 0.00 0.00 36.44 3.51
3483 3589 4.636249 ACTAGACAGAAACTCAGCAAAGG 58.364 43.478 0.00 0.00 0.00 3.11
3555 3661 1.919918 GCAATGAAAATGCCTACACGC 59.080 47.619 0.00 0.00 37.85 5.34
3556 3662 3.173599 CAGCAATGAAAATGCCTACACG 58.826 45.455 0.00 0.00 44.91 4.49
3641 3770 7.067737 TGAGACCCGAAAGAAAATAAGTGTTTT 59.932 33.333 0.00 0.00 34.19 2.43
3650 3784 4.154195 CGATGTTGAGACCCGAAAGAAAAT 59.846 41.667 0.00 0.00 0.00 1.82
3668 3806 1.343142 TGAACTGTACAGCACCGATGT 59.657 47.619 22.90 0.00 35.84 3.06
3669 3807 2.078849 TGAACTGTACAGCACCGATG 57.921 50.000 22.90 0.00 0.00 3.84
3670 3808 2.831685 TTGAACTGTACAGCACCGAT 57.168 45.000 22.90 0.00 0.00 4.18
3671 3809 2.831685 ATTGAACTGTACAGCACCGA 57.168 45.000 22.90 11.71 0.00 4.69
3840 3989 6.819649 CCAATCAAAGCATCACCAACAATTAT 59.180 34.615 0.00 0.00 0.00 1.28
3907 4056 1.351017 TGGACTGACCTGTGAATTCCC 59.649 52.381 2.27 0.00 39.86 3.97
3980 4129 3.930336 TGCTTACACAGACCAGATCAAG 58.070 45.455 0.00 0.00 0.00 3.02
3987 4136 2.358957 GCATCATGCTTACACAGACCA 58.641 47.619 1.02 0.00 40.96 4.02
4047 4196 1.692519 CCGTACTTCCCTATTCCTGGG 59.307 57.143 0.00 0.00 45.90 4.45
4051 4200 4.468713 AGTACTCCGTACTTCCCTATTCC 58.531 47.826 1.03 0.00 45.68 3.01
4062 4211 4.453819 ACGCAGGATATTAGTACTCCGTAC 59.546 45.833 0.00 0.00 39.10 3.67
4064 4213 3.484407 ACGCAGGATATTAGTACTCCGT 58.516 45.455 0.00 0.00 34.13 4.69
4065 4214 3.501062 TGACGCAGGATATTAGTACTCCG 59.499 47.826 0.00 0.00 34.13 4.63
4066 4215 5.049398 CTGACGCAGGATATTAGTACTCC 57.951 47.826 0.00 0.00 0.00 3.85
4090 4245 0.326927 GCAACAGGGTTACAGGCCTA 59.673 55.000 3.98 0.00 0.00 3.93
4092 4247 0.611896 ATGCAACAGGGTTACAGGCC 60.612 55.000 0.00 0.00 0.00 5.19
4098 4253 4.359434 TTCTACACATGCAACAGGGTTA 57.641 40.909 0.00 0.00 0.00 2.85
4101 4256 3.084039 ACATTCTACACATGCAACAGGG 58.916 45.455 0.00 0.00 0.00 4.45
4147 4306 1.003116 CTACGGCATCAGCAATTCAGC 60.003 52.381 0.00 0.00 44.61 4.26
4148 4307 1.003116 GCTACGGCATCAGCAATTCAG 60.003 52.381 0.00 0.00 44.61 3.02
4149 4308 1.016627 GCTACGGCATCAGCAATTCA 58.983 50.000 0.00 0.00 44.61 2.57
4150 4309 0.308993 GGCTACGGCATCAGCAATTC 59.691 55.000 5.23 0.00 44.61 2.17
4151 4310 0.107017 AGGCTACGGCATCAGCAATT 60.107 50.000 5.23 0.00 44.61 2.32
4152 4311 0.107017 AAGGCTACGGCATCAGCAAT 60.107 50.000 5.23 0.00 44.61 3.56
4153 4312 0.322456 AAAGGCTACGGCATCAGCAA 60.322 50.000 5.23 0.00 44.61 3.91
4154 4313 0.539518 TAAAGGCTACGGCATCAGCA 59.460 50.000 5.23 0.00 44.61 4.41
4173 4332 7.039011 TGACCAACATCTGTTCAATCTACTAGT 60.039 37.037 0.00 0.00 35.83 2.57
4202 4361 7.458170 GGTTCAATTAGGATATCCTTCTCCCTA 59.542 40.741 29.06 6.82 46.09 3.53
4203 4362 6.273495 GGTTCAATTAGGATATCCTTCTCCCT 59.727 42.308 29.06 6.12 46.09 4.20
4204 4363 6.273495 AGGTTCAATTAGGATATCCTTCTCCC 59.727 42.308 29.06 18.08 46.09 4.30
4205 4364 7.323052 AGGTTCAATTAGGATATCCTTCTCC 57.677 40.000 29.06 19.18 46.09 3.71
4290 4454 3.630312 TGGGTGAAAAGTAGCTGACAAAC 59.370 43.478 0.00 0.00 0.00 2.93
4314 4478 3.274153 AGGCCTTAACCCTCTCCTAGTTA 59.726 47.826 0.00 0.00 0.00 2.24
4321 4485 1.628846 TCACAAGGCCTTAACCCTCTC 59.371 52.381 20.00 0.00 0.00 3.20
4322 4486 1.742308 TCACAAGGCCTTAACCCTCT 58.258 50.000 20.00 0.00 0.00 3.69
4323 4487 2.644676 GATCACAAGGCCTTAACCCTC 58.355 52.381 20.00 8.01 0.00 4.30
4324 4488 1.285078 GGATCACAAGGCCTTAACCCT 59.715 52.381 20.00 1.75 0.00 4.34
4325 4489 1.005450 TGGATCACAAGGCCTTAACCC 59.995 52.381 20.00 15.01 0.00 4.11
4326 4490 2.369394 CTGGATCACAAGGCCTTAACC 58.631 52.381 20.00 16.44 0.00 2.85
4327 4491 2.369394 CCTGGATCACAAGGCCTTAAC 58.631 52.381 20.00 7.76 0.00 2.01
4328 4492 1.284785 CCCTGGATCACAAGGCCTTAA 59.715 52.381 20.00 7.30 0.00 1.85
4329 4493 0.918983 CCCTGGATCACAAGGCCTTA 59.081 55.000 20.00 2.57 0.00 2.69
4330 4494 1.693640 CCCTGGATCACAAGGCCTT 59.306 57.895 13.78 13.78 0.00 4.35
4331 4495 3.419858 CCCTGGATCACAAGGCCT 58.580 61.111 0.00 0.00 0.00 5.19
4334 4498 0.890683 GTTTGCCCTGGATCACAAGG 59.109 55.000 0.00 0.00 33.54 3.61
4335 4499 0.890683 GGTTTGCCCTGGATCACAAG 59.109 55.000 0.00 0.00 0.00 3.16
4336 4500 0.187117 TGGTTTGCCCTGGATCACAA 59.813 50.000 0.00 0.00 0.00 3.33
4337 4501 0.539438 GTGGTTTGCCCTGGATCACA 60.539 55.000 0.00 0.00 0.00 3.58
4338 4502 1.250840 GGTGGTTTGCCCTGGATCAC 61.251 60.000 0.00 0.00 0.00 3.06
4339 4503 1.076549 GGTGGTTTGCCCTGGATCA 59.923 57.895 0.00 0.00 0.00 2.92
4340 4504 0.681243 GAGGTGGTTTGCCCTGGATC 60.681 60.000 0.00 0.00 0.00 3.36
4341 4505 1.384191 GAGGTGGTTTGCCCTGGAT 59.616 57.895 0.00 0.00 0.00 3.41
4342 4506 2.840753 GGAGGTGGTTTGCCCTGGA 61.841 63.158 0.00 0.00 0.00 3.86
4343 4507 2.283173 GGAGGTGGTTTGCCCTGG 60.283 66.667 0.00 0.00 0.00 4.45
4344 4508 2.119484 TACGGAGGTGGTTTGCCCTG 62.119 60.000 0.00 0.00 0.00 4.45
4345 4509 1.844289 TACGGAGGTGGTTTGCCCT 60.844 57.895 0.00 0.00 0.00 5.19
4346 4510 1.673337 GTACGGAGGTGGTTTGCCC 60.673 63.158 0.00 0.00 0.00 5.36
4347 4511 0.609662 TAGTACGGAGGTGGTTTGCC 59.390 55.000 0.00 0.00 0.00 4.52
4348 4512 1.547372 TCTAGTACGGAGGTGGTTTGC 59.453 52.381 0.00 0.00 0.00 3.68
4349 4513 3.087031 TCTCTAGTACGGAGGTGGTTTG 58.913 50.000 15.37 0.00 0.00 2.93
4350 4514 3.446442 TCTCTAGTACGGAGGTGGTTT 57.554 47.619 15.37 0.00 0.00 3.27
4351 4515 3.446442 TTCTCTAGTACGGAGGTGGTT 57.554 47.619 15.37 0.00 0.00 3.67
4352 4516 3.009916 TCTTTCTCTAGTACGGAGGTGGT 59.990 47.826 15.37 0.00 0.00 4.16
4353 4517 3.618351 TCTTTCTCTAGTACGGAGGTGG 58.382 50.000 15.37 8.32 0.00 4.61


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

AutoCloner maintained by Alex Coulton.