Multiple sequence alignment - TraesCS3D01G436200

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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 TraesCS3D01G436200 chr3D 100.000 3842 0 0 1 3842 548251602 548247761 0.000000e+00 7095
1 TraesCS3D01G436200 chr3D 95.652 161 7 0 1424 1584 54716776 54716936 3.810000e-65 259
2 TraesCS3D01G436200 chr3D 95.652 161 7 0 1424 1584 520650539 520650379 3.810000e-65 259
3 TraesCS3D01G436200 chr3A 93.812 3216 119 36 660 3842 685123570 685120402 0.000000e+00 4763
4 TraesCS3D01G436200 chr3A 91.393 639 48 1 1 639 685124192 685123561 0.000000e+00 869
5 TraesCS3D01G436200 chr3B 95.713 1563 59 3 2281 3842 725709474 725707919 0.000000e+00 2508
6 TraesCS3D01G436200 chr3B 92.839 1536 90 14 663 2184 725711003 725709474 0.000000e+00 2209
7 TraesCS3D01G436200 chr3B 86.486 518 42 16 120 627 725711507 725711008 9.390000e-151 544
8 TraesCS3D01G436200 chr2D 95.465 419 18 1 960 1377 352630722 352631140 0.000000e+00 667
9 TraesCS3D01G436200 chr2D 95.516 223 10 0 1362 1584 352631371 352631593 1.310000e-94 357
10 TraesCS3D01G436200 chr2D 95.652 161 7 0 1424 1584 577120817 577120657 3.810000e-65 259
11 TraesCS3D01G436200 chr6D 95.652 161 7 0 1424 1584 469922876 469922716 3.810000e-65 259
12 TraesCS3D01G436200 chr6D 95.652 161 7 0 1424 1584 469924306 469924146 3.810000e-65 259
13 TraesCS3D01G436200 chr2B 95.652 161 7 0 1424 1584 766560152 766559992 3.810000e-65 259


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 TraesCS3D01G436200 chr3D 548247761 548251602 3841 True 7095.000000 7095 100.000000 1 3842 1 chr3D.!!$R2 3841
1 TraesCS3D01G436200 chr3A 685120402 685124192 3790 True 2816.000000 4763 92.602500 1 3842 2 chr3A.!!$R1 3841
2 TraesCS3D01G436200 chr3B 725707919 725711507 3588 True 1753.666667 2508 91.679333 120 3842 3 chr3B.!!$R1 3722
3 TraesCS3D01G436200 chr2D 352630722 352631593 871 False 512.000000 667 95.490500 960 1584 2 chr2D.!!$F1 624
4 TraesCS3D01G436200 chr6D 469922716 469924306 1590 True 259.000000 259 95.652000 1424 1584 2 chr6D.!!$R1 160

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
722 733 0.095245 CGTGCTGCTTACGTCATTGG 59.905 55.0 0.0 0.0 36.83 3.16 F
962 976 0.247814 CATCGCCGCTGCTACAAAAG 60.248 55.0 0.0 0.0 34.43 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1666 3373 1.361793 AAATCACCATGCAAATGCGC 58.638 45.0 0.00 0.0 45.83 6.09 R
2943 4663 0.033228 ATGAGCTGGCTCGCTATGAC 59.967 55.0 16.33 0.0 45.48 3.06 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
37 38 6.039270 GCCAATGCCATACTGTTAGATAACAA 59.961 38.462 6.85 0.00 44.67 2.83
114 115 3.473113 ACTGGGGATTGTTAAAGGCAT 57.527 42.857 0.00 0.00 0.00 4.40
115 116 3.790126 ACTGGGGATTGTTAAAGGCATT 58.210 40.909 0.00 0.00 0.00 3.56
116 117 3.515104 ACTGGGGATTGTTAAAGGCATTG 59.485 43.478 0.00 0.00 0.00 2.82
117 118 2.836981 TGGGGATTGTTAAAGGCATTGG 59.163 45.455 0.00 0.00 0.00 3.16
118 119 3.103742 GGGGATTGTTAAAGGCATTGGA 58.896 45.455 0.00 0.00 0.00 3.53
161 162 2.037251 ACTACAGAGGAAGCTTTCGCAA 59.963 45.455 11.38 0.00 39.10 4.85
163 164 2.297701 ACAGAGGAAGCTTTCGCAAAA 58.702 42.857 11.38 0.00 39.10 2.44
216 218 8.935614 TGTTATATATAGTGCTGTAGTGGACT 57.064 34.615 0.00 0.00 41.41 3.85
217 219 9.363401 TGTTATATATAGTGCTGTAGTGGACTT 57.637 33.333 0.00 0.00 39.33 3.01
274 284 6.602803 TCAACCAAATAGAAGAATATGCAGCA 59.397 34.615 0.00 0.00 0.00 4.41
291 301 6.756299 TGCAGCACAGATTATTGTATTTGA 57.244 33.333 0.00 0.00 0.00 2.69
326 336 9.647918 TTGCATACCATGGGAATTTTATTAGTA 57.352 29.630 18.09 0.00 0.00 1.82
327 337 9.647918 TGCATACCATGGGAATTTTATTAGTAA 57.352 29.630 18.09 0.00 0.00 2.24
360 370 6.128849 GGCGCGAAATATTTGAATATTGCAAT 60.129 34.615 17.56 17.56 39.89 3.56
405 415 2.052237 CAAGACGCAACACCACGC 60.052 61.111 0.00 0.00 0.00 5.34
431 441 3.447229 TGTATGAGAATTCACGAGGCTCA 59.553 43.478 15.95 0.93 39.61 4.26
434 444 3.264947 TGAGAATTCACGAGGCTCATTG 58.735 45.455 15.95 10.88 31.24 2.82
435 445 3.265791 GAGAATTCACGAGGCTCATTGT 58.734 45.455 15.95 5.02 0.00 2.71
439 449 5.295292 AGAATTCACGAGGCTCATTGTATTG 59.705 40.000 15.95 0.00 0.00 1.90
466 476 8.700644 CATGAGAATTTAGTACGTGTTATAGCC 58.299 37.037 0.00 0.00 0.00 3.93
469 479 3.988379 TTAGTACGTGTTATAGCCCGG 57.012 47.619 0.00 0.00 0.00 5.73
472 482 2.360165 AGTACGTGTTATAGCCCGGAAG 59.640 50.000 0.73 0.00 0.00 3.46
474 484 1.135721 ACGTGTTATAGCCCGGAAGTC 59.864 52.381 0.73 0.00 0.00 3.01
484 494 1.144936 CCGGAAGTCCTCTGATGGC 59.855 63.158 0.00 0.00 31.20 4.40
488 498 3.376935 AAGTCCTCTGATGGCGCGG 62.377 63.158 8.83 0.00 0.00 6.46
496 506 0.734889 CTGATGGCGCGGAATTTCTT 59.265 50.000 8.83 0.00 0.00 2.52
558 569 5.673514 AGGAATGCGATAAATGGCAAAAAT 58.326 33.333 3.71 0.00 44.49 1.82
560 571 5.523188 GGAATGCGATAAATGGCAAAAATGA 59.477 36.000 3.71 0.00 44.49 2.57
579 590 2.743928 CGAACTGCCAGGCCACTC 60.744 66.667 9.64 1.07 0.00 3.51
627 638 6.587206 TGTTTGCATTGTTCCATCTGATAA 57.413 33.333 0.00 0.00 0.00 1.75
628 639 6.389091 TGTTTGCATTGTTCCATCTGATAAC 58.611 36.000 0.00 0.00 0.00 1.89
629 640 6.209192 TGTTTGCATTGTTCCATCTGATAACT 59.791 34.615 5.25 0.00 0.00 2.24
630 641 6.839124 TTGCATTGTTCCATCTGATAACTT 57.161 33.333 5.25 0.00 0.00 2.66
631 642 7.936496 TTGCATTGTTCCATCTGATAACTTA 57.064 32.000 5.25 0.00 0.00 2.24
632 643 7.558161 TGCATTGTTCCATCTGATAACTTAG 57.442 36.000 5.25 0.00 0.00 2.18
633 644 7.112122 TGCATTGTTCCATCTGATAACTTAGT 58.888 34.615 5.25 0.00 0.00 2.24
634 645 7.611467 TGCATTGTTCCATCTGATAACTTAGTT 59.389 33.333 2.32 2.32 0.00 2.24
635 646 7.912250 GCATTGTTCCATCTGATAACTTAGTTG 59.088 37.037 8.00 0.00 0.00 3.16
636 647 8.950210 CATTGTTCCATCTGATAACTTAGTTGT 58.050 33.333 8.00 0.04 0.00 3.32
637 648 8.547967 TTGTTCCATCTGATAACTTAGTTGTC 57.452 34.615 13.72 13.72 34.91 3.18
638 649 7.103641 TGTTCCATCTGATAACTTAGTTGTCC 58.896 38.462 17.01 3.51 33.71 4.02
639 650 6.235231 TCCATCTGATAACTTAGTTGTCCC 57.765 41.667 17.01 0.00 33.71 4.46
640 651 5.130477 TCCATCTGATAACTTAGTTGTCCCC 59.870 44.000 17.01 0.00 33.71 4.81
641 652 5.368989 CATCTGATAACTTAGTTGTCCCCC 58.631 45.833 17.01 0.00 33.71 5.40
642 653 3.449737 TCTGATAACTTAGTTGTCCCCCG 59.550 47.826 17.01 5.63 33.71 5.73
643 654 2.093341 TGATAACTTAGTTGTCCCCCGC 60.093 50.000 17.01 0.00 33.71 6.13
644 655 1.350071 TAACTTAGTTGTCCCCCGCA 58.650 50.000 8.00 0.00 0.00 5.69
645 656 0.475044 AACTTAGTTGTCCCCCGCAA 59.525 50.000 0.00 0.00 0.00 4.85
646 657 0.475044 ACTTAGTTGTCCCCCGCAAA 59.525 50.000 0.00 0.00 0.00 3.68
647 658 1.133730 ACTTAGTTGTCCCCCGCAAAA 60.134 47.619 0.00 0.00 0.00 2.44
648 659 1.268625 CTTAGTTGTCCCCCGCAAAAC 59.731 52.381 0.00 0.00 0.00 2.43
649 660 0.183014 TAGTTGTCCCCCGCAAAACA 59.817 50.000 0.00 0.00 0.00 2.83
650 661 0.684805 AGTTGTCCCCCGCAAAACAA 60.685 50.000 0.00 0.00 0.00 2.83
651 662 0.175989 GTTGTCCCCCGCAAAACAAA 59.824 50.000 0.00 0.00 33.75 2.83
652 663 0.902531 TTGTCCCCCGCAAAACAAAA 59.097 45.000 0.00 0.00 0.00 2.44
653 664 0.461961 TGTCCCCCGCAAAACAAAAG 59.538 50.000 0.00 0.00 0.00 2.27
654 665 0.747852 GTCCCCCGCAAAACAAAAGA 59.252 50.000 0.00 0.00 0.00 2.52
655 666 1.343142 GTCCCCCGCAAAACAAAAGAT 59.657 47.619 0.00 0.00 0.00 2.40
656 667 2.559231 GTCCCCCGCAAAACAAAAGATA 59.441 45.455 0.00 0.00 0.00 1.98
657 668 3.006003 GTCCCCCGCAAAACAAAAGATAA 59.994 43.478 0.00 0.00 0.00 1.75
658 669 3.006003 TCCCCCGCAAAACAAAAGATAAC 59.994 43.478 0.00 0.00 0.00 1.89
665 676 7.096230 CCCGCAAAACAAAAGATAACTTAGTTG 60.096 37.037 8.00 1.42 35.89 3.16
673 684 9.628500 ACAAAAGATAACTTAGTTGTCCTTTCT 57.372 29.630 16.32 3.71 34.17 2.52
677 688 8.196378 AGATAACTTAGTTGTCCTTTCTCTGT 57.804 34.615 16.32 0.00 34.88 3.41
685 696 5.827797 AGTTGTCCTTTCTCTGTTTTATGCA 59.172 36.000 0.00 0.00 0.00 3.96
701 712 7.277539 TGTTTTATGCACTAATAATTGCTTGGC 59.722 33.333 0.00 0.00 39.62 4.52
722 733 0.095245 CGTGCTGCTTACGTCATTGG 59.905 55.000 0.00 0.00 36.83 3.16
740 751 1.643832 GCGGAATGCGCTTTCCTAG 59.356 57.895 37.28 28.33 42.57 3.02
755 766 5.334182 GCTTTCCTAGTTTACAACTGCTCAC 60.334 44.000 0.00 0.00 42.84 3.51
820 831 4.808558 TGCTCCATTTTGTATTCTGCAAC 58.191 39.130 0.00 0.00 0.00 4.17
830 841 9.816354 ATTTTGTATTCTGCAACTGTTTAGTTT 57.184 25.926 0.00 0.00 44.57 2.66
831 842 8.627487 TTTGTATTCTGCAACTGTTTAGTTTG 57.373 30.769 0.00 0.00 44.57 2.93
842 853 7.336975 CAACTGTTTAGTTTGCTTTGTATTGC 58.663 34.615 0.00 0.00 44.57 3.56
873 884 3.000322 CGATTCAGCAATCTGTCGGTTAC 60.000 47.826 0.00 0.00 41.10 2.50
884 895 5.648178 TCTGTCGGTTACTGTTATTGCTA 57.352 39.130 0.00 0.00 0.00 3.49
885 896 5.404946 TCTGTCGGTTACTGTTATTGCTAC 58.595 41.667 0.00 0.00 0.00 3.58
891 902 7.064253 GTCGGTTACTGTTATTGCTACTTCAAT 59.936 37.037 0.00 0.00 39.70 2.57
899 910 9.760660 CTGTTATTGCTACTTCAATGTTAAGTC 57.239 33.333 0.00 0.00 38.18 3.01
904 915 6.530120 TGCTACTTCAATGTTAAGTCCAGAA 58.470 36.000 0.00 0.00 38.18 3.02
962 976 0.247814 CATCGCCGCTGCTACAAAAG 60.248 55.000 0.00 0.00 34.43 2.27
991 1005 6.684897 ATCCTATTCTGAAGGAGGAGATTG 57.315 41.667 21.58 1.03 46.14 2.67
1168 1182 4.025360 TCCAGGTACCGCTCAAATTAGTA 58.975 43.478 6.18 0.00 0.00 1.82
1171 1185 5.465724 CCAGGTACCGCTCAAATTAGTATTC 59.534 44.000 6.18 0.00 0.00 1.75
1666 3373 0.177141 CCCCAATGGCAGCATTTCTG 59.823 55.000 0.00 0.00 45.62 3.02
1697 3404 5.011431 TGCATGGTGATTTTTCCATTGTGTA 59.989 36.000 0.00 0.00 41.79 2.90
1874 3581 1.204146 ATACATCGGCACCAACTCCT 58.796 50.000 0.00 0.00 0.00 3.69
1875 3582 1.855295 TACATCGGCACCAACTCCTA 58.145 50.000 0.00 0.00 0.00 2.94
1882 3589 2.618045 CGGCACCAACTCCTAATTTCCT 60.618 50.000 0.00 0.00 0.00 3.36
1894 3601 7.182060 ACTCCTAATTTCCTTTATTGGCAGAA 58.818 34.615 0.00 0.00 0.00 3.02
1897 3604 6.097412 CCTAATTTCCTTTATTGGCAGAAGCT 59.903 38.462 0.00 0.00 41.70 3.74
1899 3606 7.480760 AATTTCCTTTATTGGCAGAAGCTTA 57.519 32.000 0.00 0.00 41.70 3.09
1902 3609 6.699575 TCCTTTATTGGCAGAAGCTTATTC 57.300 37.500 0.00 0.00 41.70 1.75
1910 3626 5.371526 TGGCAGAAGCTTATTCTCTTATGG 58.628 41.667 0.00 0.00 41.70 2.74
2195 3914 1.074566 ACTGAGCTTCTTCTTTGGGGG 59.925 52.381 0.00 0.00 0.00 5.40
2469 4188 8.088365 GGCATTATTGAATGGGTAAATTCTACC 58.912 37.037 7.79 7.79 42.44 3.18
2820 4539 1.841302 CTGTGACCCTAGGCAGCCAA 61.841 60.000 15.80 0.00 0.00 4.52
2833 4552 2.089980 GCAGCCAACTCTTCACATCAT 58.910 47.619 0.00 0.00 0.00 2.45
2943 4663 5.412286 CCAATTTTGCCCCATTAGTTTCTTG 59.588 40.000 0.00 0.00 0.00 3.02
2950 4670 4.036852 GCCCCATTAGTTTCTTGTCATAGC 59.963 45.833 0.00 0.00 0.00 2.97
3024 4744 1.755200 TAGGCTTCCCTTTTCACCCT 58.245 50.000 0.00 0.00 42.87 4.34
3122 4844 5.245526 ACTTTTGTAACATCGAGAGGGTAGT 59.754 40.000 0.00 0.00 0.00 2.73
3130 4852 0.320374 CGAGAGGGTAGTGCCAAACA 59.680 55.000 0.00 0.00 39.65 2.83
3171 4893 8.677300 TCTCTACAATTTTAGACATTTGCCATC 58.323 33.333 0.00 0.00 0.00 3.51
3172 4894 7.771183 TCTACAATTTTAGACATTTGCCATCC 58.229 34.615 0.00 0.00 0.00 3.51
3173 4895 6.610075 ACAATTTTAGACATTTGCCATCCT 57.390 33.333 0.00 0.00 0.00 3.24
3314 5036 7.384387 CACTATCATACATGTCATCTGAACTGG 59.616 40.741 0.00 0.00 0.00 4.00
3338 5060 4.578105 CCTCCATTTCTGAATCTAGCCAAC 59.422 45.833 0.00 0.00 0.00 3.77
3456 5178 3.452627 AGATGTCCATGGAGTTGTAGTCC 59.547 47.826 16.81 0.00 38.22 3.85
3596 5318 4.042174 CCAATGTAAAGGTACTCCCCCTA 58.958 47.826 0.00 0.00 38.49 3.53
3600 5322 3.337605 TGTAAAGGTACTCCCCCTAGTGA 59.662 47.826 0.00 0.00 38.49 3.41
3634 5356 3.150458 TGAGTCTTCCTCCGTTCAGTA 57.850 47.619 0.00 0.00 39.65 2.74
3649 5371 4.381612 CGTTCAGTAAGCCCAAGACAGATA 60.382 45.833 0.00 0.00 0.00 1.98
3650 5372 5.112686 GTTCAGTAAGCCCAAGACAGATAG 58.887 45.833 0.00 0.00 0.00 2.08
3651 5373 4.610333 TCAGTAAGCCCAAGACAGATAGA 58.390 43.478 0.00 0.00 0.00 1.98
3652 5374 5.211973 TCAGTAAGCCCAAGACAGATAGAT 58.788 41.667 0.00 0.00 0.00 1.98
3673 5395 7.083062 AGATGATGCATGTAAATAGGAGGAA 57.917 36.000 2.46 0.00 0.00 3.36
3677 5399 7.397221 TGATGCATGTAAATAGGAGGAATAGG 58.603 38.462 2.46 0.00 0.00 2.57
3695 5417 5.803237 ATAGGGGTTAATGGAACTACTCG 57.197 43.478 0.00 0.00 38.21 4.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.134905 GAATGCAGAATTCTTCAACTTTTGTT 57.865 30.769 11.86 0.15 41.38 2.83
114 115 1.489481 TGCAAACCACCAATGTCCAA 58.511 45.000 0.00 0.00 0.00 3.53
115 116 1.411977 CTTGCAAACCACCAATGTCCA 59.588 47.619 0.00 0.00 0.00 4.02
116 117 1.873486 GCTTGCAAACCACCAATGTCC 60.873 52.381 0.00 0.00 0.00 4.02
117 118 1.202510 TGCTTGCAAACCACCAATGTC 60.203 47.619 0.00 0.00 0.00 3.06
118 119 0.829333 TGCTTGCAAACCACCAATGT 59.171 45.000 0.00 0.00 0.00 2.71
161 162 1.538075 CGTCGCCCATACAAAAGGTTT 59.462 47.619 0.00 0.00 0.00 3.27
163 164 0.322322 TCGTCGCCCATACAAAAGGT 59.678 50.000 0.00 0.00 0.00 3.50
274 284 7.800092 AGAGCCTCTCAAATACAATAATCTGT 58.200 34.615 0.00 0.00 32.06 3.41
291 301 2.422519 CCATGGTATGCAAAGAGCCTCT 60.423 50.000 2.57 0.00 44.83 3.69
326 336 5.238432 TCAAATATTTCGCGCCATGACTATT 59.762 36.000 0.00 0.00 0.00 1.73
327 337 4.754618 TCAAATATTTCGCGCCATGACTAT 59.245 37.500 0.00 0.00 0.00 2.12
360 370 3.534357 TGCCTTTTATTTCCCAGACCA 57.466 42.857 0.00 0.00 0.00 4.02
399 409 4.699735 TGAATTCTCATACAATTGCGTGGT 59.300 37.500 5.05 0.00 0.00 4.16
405 415 5.295292 AGCCTCGTGAATTCTCATACAATTG 59.705 40.000 7.05 3.24 33.05 2.32
431 441 9.109393 ACGTACTAAATTCTCATGCAATACAAT 57.891 29.630 0.00 0.00 0.00 2.71
434 444 7.906160 ACACGTACTAAATTCTCATGCAATAC 58.094 34.615 0.00 0.00 0.00 1.89
435 445 8.487313 AACACGTACTAAATTCTCATGCAATA 57.513 30.769 0.00 0.00 0.00 1.90
439 449 8.215132 GCTATAACACGTACTAAATTCTCATGC 58.785 37.037 0.00 0.00 0.00 4.06
466 476 1.144936 GCCATCAGAGGACTTCCGG 59.855 63.158 0.00 0.00 42.08 5.14
469 479 1.880340 CGCGCCATCAGAGGACTTC 60.880 63.158 0.00 0.00 0.00 3.01
472 482 2.650813 ATTCCGCGCCATCAGAGGAC 62.651 60.000 0.00 0.00 37.31 3.85
474 484 1.097547 AAATTCCGCGCCATCAGAGG 61.098 55.000 0.00 0.00 0.00 3.69
484 494 5.108780 CGTTGCAATATTAAGAAATTCCGCG 60.109 40.000 0.59 0.00 0.00 6.46
488 498 6.964934 ACGACCGTTGCAATATTAAGAAATTC 59.035 34.615 0.59 0.00 0.00 2.17
496 506 2.094575 GTGCACGACCGTTGCAATATTA 59.905 45.455 16.53 0.00 40.45 0.98
549 560 1.602668 GCAGTTCGCTCATTTTTGCCA 60.603 47.619 0.00 0.00 37.77 4.92
558 569 4.704833 GGCCTGGCAGTTCGCTCA 62.705 66.667 22.05 0.00 41.91 4.26
627 638 0.475044 TTTGCGGGGGACAACTAAGT 59.525 50.000 0.00 0.00 0.00 2.24
628 639 1.268625 GTTTTGCGGGGGACAACTAAG 59.731 52.381 0.00 0.00 0.00 2.18
629 640 1.320507 GTTTTGCGGGGGACAACTAA 58.679 50.000 0.00 0.00 0.00 2.24
630 641 0.183014 TGTTTTGCGGGGGACAACTA 59.817 50.000 0.00 0.00 0.00 2.24
631 642 0.684805 TTGTTTTGCGGGGGACAACT 60.685 50.000 0.00 0.00 0.00 3.16
632 643 0.175989 TTTGTTTTGCGGGGGACAAC 59.824 50.000 0.00 0.00 32.28 3.32
633 644 0.902531 TTTTGTTTTGCGGGGGACAA 59.097 45.000 0.00 0.00 0.00 3.18
634 645 0.461961 CTTTTGTTTTGCGGGGGACA 59.538 50.000 0.00 0.00 0.00 4.02
635 646 0.747852 TCTTTTGTTTTGCGGGGGAC 59.252 50.000 0.00 0.00 0.00 4.46
636 647 1.710816 ATCTTTTGTTTTGCGGGGGA 58.289 45.000 0.00 0.00 0.00 4.81
637 648 3.006430 AGTTATCTTTTGTTTTGCGGGGG 59.994 43.478 0.00 0.00 0.00 5.40
638 649 4.251543 AGTTATCTTTTGTTTTGCGGGG 57.748 40.909 0.00 0.00 0.00 5.73
639 650 6.443792 ACTAAGTTATCTTTTGTTTTGCGGG 58.556 36.000 0.00 0.00 35.36 6.13
640 651 7.434013 ACAACTAAGTTATCTTTTGTTTTGCGG 59.566 33.333 0.00 0.00 33.50 5.69
641 652 8.335256 ACAACTAAGTTATCTTTTGTTTTGCG 57.665 30.769 0.00 0.00 33.50 4.85
642 653 8.752254 GGACAACTAAGTTATCTTTTGTTTTGC 58.248 33.333 5.50 1.94 35.83 3.68
647 658 9.628500 AGAAAGGACAACTAAGTTATCTTTTGT 57.372 29.630 0.00 4.12 37.34 2.83
650 661 9.495572 CAGAGAAAGGACAACTAAGTTATCTTT 57.504 33.333 0.00 0.00 35.36 2.52
651 662 8.652290 ACAGAGAAAGGACAACTAAGTTATCTT 58.348 33.333 0.00 0.00 37.65 2.40
652 663 8.196378 ACAGAGAAAGGACAACTAAGTTATCT 57.804 34.615 0.00 0.00 0.00 1.98
653 664 8.834749 AACAGAGAAAGGACAACTAAGTTATC 57.165 34.615 0.00 0.00 0.00 1.75
654 665 9.628500 AAAACAGAGAAAGGACAACTAAGTTAT 57.372 29.630 0.00 0.00 0.00 1.89
656 667 7.939784 AAAACAGAGAAAGGACAACTAAGTT 57.060 32.000 0.00 0.00 0.00 2.66
657 668 9.057089 CATAAAACAGAGAAAGGACAACTAAGT 57.943 33.333 0.00 0.00 0.00 2.24
658 669 8.017946 GCATAAAACAGAGAAAGGACAACTAAG 58.982 37.037 0.00 0.00 0.00 2.18
665 676 5.948992 AGTGCATAAAACAGAGAAAGGAC 57.051 39.130 0.00 0.00 0.00 3.85
685 696 2.687935 CACGGGCCAAGCAATTATTAGT 59.312 45.455 4.39 0.00 0.00 2.24
701 712 1.019278 AATGACGTAAGCAGCACGGG 61.019 55.000 9.82 0.00 43.59 5.28
755 766 5.237344 GGACCGGTTAAATGAGAGATGAATG 59.763 44.000 9.42 0.00 0.00 2.67
800 811 6.017400 ACAGTTGCAGAATACAAAATGGAG 57.983 37.500 0.00 0.00 0.00 3.86
820 831 6.346040 GCAGCAATACAAAGCAAACTAAACAG 60.346 38.462 0.00 0.00 0.00 3.16
873 884 9.760660 GACTTAACATTGAAGTAGCAATAACAG 57.239 33.333 0.00 0.00 37.27 3.16
921 933 9.809096 CGATGCAGACAGATATAACCTAAATAT 57.191 33.333 0.00 0.00 0.00 1.28
933 945 1.300156 GCGGCGATGCAGACAGATA 60.300 57.895 12.98 0.00 34.15 1.98
935 947 3.763356 AGCGGCGATGCAGACAGA 61.763 61.111 12.98 0.00 37.31 3.41
936 948 3.561213 CAGCGGCGATGCAGACAG 61.561 66.667 13.77 0.00 37.31 3.51
962 976 7.945664 TCTCCTCCTTCAGAATAGGATAGTAAC 59.054 40.741 12.68 0.00 40.87 2.50
991 1005 6.073873 GCAAGAATGTCTGACATCTAGTATGC 60.074 42.308 22.47 20.15 37.97 3.14
1096 1110 2.911484 AGAATCTGAATTCCGTCTGCC 58.089 47.619 2.27 0.00 41.97 4.85
1102 1116 5.659463 ACTCTCTGAAGAATCTGAATTCCG 58.341 41.667 2.27 0.00 41.97 4.30
1168 1182 5.016831 ACTGAAATTAAAAGCCCCTCGAAT 58.983 37.500 0.00 0.00 0.00 3.34
1171 1185 3.506067 ACACTGAAATTAAAAGCCCCTCG 59.494 43.478 0.00 0.00 0.00 4.63
1430 1691 4.248058 GAGAAAATTTTGGCACCTCATGG 58.752 43.478 8.47 0.00 39.83 3.66
1531 3238 1.368268 ACCTGGGGAGAAAAGGCCAA 61.368 55.000 5.01 0.00 34.18 4.52
1666 3373 1.361793 AAATCACCATGCAAATGCGC 58.638 45.000 0.00 0.00 45.83 6.09
1750 3457 4.501433 AGAGGGATGGCAGAAAGATAGAT 58.499 43.478 0.00 0.00 0.00 1.98
1751 3458 3.933886 AGAGGGATGGCAGAAAGATAGA 58.066 45.455 0.00 0.00 0.00 1.98
1754 3461 3.387962 TGTAGAGGGATGGCAGAAAGAT 58.612 45.455 0.00 0.00 0.00 2.40
1874 3581 7.480760 AAGCTTCTGCCAATAAAGGAAATTA 57.519 32.000 0.00 0.00 40.80 1.40
1875 3582 6.364568 AAGCTTCTGCCAATAAAGGAAATT 57.635 33.333 0.00 0.00 40.80 1.82
1882 3589 7.944729 AAGAGAATAAGCTTCTGCCAATAAA 57.055 32.000 0.00 0.00 40.80 1.40
1894 3601 6.183361 TGAGGCAATCCATAAGAGAATAAGCT 60.183 38.462 0.00 0.00 33.74 3.74
1897 3604 9.425248 AAAATGAGGCAATCCATAAGAGAATAA 57.575 29.630 0.00 0.00 33.74 1.40
1899 3606 7.562454 TGAAAATGAGGCAATCCATAAGAGAAT 59.438 33.333 0.00 0.00 33.74 2.40
1902 3609 6.320672 ACTGAAAATGAGGCAATCCATAAGAG 59.679 38.462 0.00 0.00 33.74 2.85
1910 3626 4.771590 TGTGACTGAAAATGAGGCAATC 57.228 40.909 0.00 0.00 27.36 2.67
2214 3933 7.881775 ATGGAAGTCAAGGGATGTAATTAAC 57.118 36.000 0.00 0.00 0.00 2.01
2215 3934 9.627123 CTAATGGAAGTCAAGGGATGTAATTAA 57.373 33.333 0.00 0.00 0.00 1.40
2469 4188 6.039047 AGGAATTGAACAATCATCAGGAATCG 59.961 38.462 0.45 0.00 34.96 3.34
2833 4552 9.745018 ATAACTTTCCATTCTTCTTCATCTTGA 57.255 29.630 0.00 0.00 0.00 3.02
2943 4663 0.033228 ATGAGCTGGCTCGCTATGAC 59.967 55.000 16.33 0.00 45.48 3.06
2950 4670 1.222766 GCTGATGATGAGCTGGCTCG 61.223 60.000 16.33 3.22 45.48 5.03
3171 4893 7.097192 TGTCAGAAAACACTATGCTACTAAGG 58.903 38.462 0.00 0.00 0.00 2.69
3172 4894 8.534333 TTGTCAGAAAACACTATGCTACTAAG 57.466 34.615 0.00 0.00 0.00 2.18
3173 4895 9.502091 AATTGTCAGAAAACACTATGCTACTAA 57.498 29.630 0.00 0.00 0.00 2.24
3314 5036 3.145286 GGCTAGATTCAGAAATGGAGGC 58.855 50.000 0.00 0.00 0.00 4.70
3338 5060 1.086696 ATTCAGAAATGGTGGTCGCG 58.913 50.000 0.00 0.00 0.00 5.87
3596 5318 5.482908 GACTCATGGTCTATTTGTGTCACT 58.517 41.667 4.27 0.00 41.46 3.41
3634 5356 4.746089 GCATCATCTATCTGTCTTGGGCTT 60.746 45.833 0.00 0.00 0.00 4.35
3649 5371 6.692849 TCCTCCTATTTACATGCATCATCT 57.307 37.500 0.00 0.00 0.00 2.90
3650 5372 7.934855 ATTCCTCCTATTTACATGCATCATC 57.065 36.000 0.00 0.00 0.00 2.92
3651 5373 8.051535 CCTATTCCTCCTATTTACATGCATCAT 58.948 37.037 0.00 0.00 0.00 2.45
3652 5374 7.397221 CCTATTCCTCCTATTTACATGCATCA 58.603 38.462 0.00 0.00 0.00 3.07
3673 5395 5.461327 TCGAGTAGTTCCATTAACCCCTAT 58.539 41.667 0.00 0.00 39.03 2.57
3677 5399 4.629092 GGATCGAGTAGTTCCATTAACCC 58.371 47.826 0.00 0.00 39.03 4.11


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

AutoCloner maintained by Alex Coulton.