Multiple sequence alignment - TraesCS5B01G518100

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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 TraesCS5B01G518100 chr5B 100.000 4388 0 0 1 4388 681129740 681134127 0.000000e+00 8104.0
1 TraesCS5B01G518100 chr4A 94.268 3437 143 23 582 3983 628928493 628925076 0.000000e+00 5206.0
2 TraesCS5B01G518100 chr4A 90.741 486 34 9 106 585 628929257 628928777 4.790000e-179 638.0
3 TraesCS5B01G518100 chr4A 85.327 443 21 15 3976 4384 628925016 628924584 6.790000e-113 418.0
4 TraesCS5B01G518100 chr4A 95.604 91 4 0 20 110 628929708 628929618 3.540000e-31 147.0
5 TraesCS5B01G518100 chr5D 94.708 3250 110 19 757 3983 539477374 539480584 0.000000e+00 4992.0
6 TraesCS5B01G518100 chr5D 82.483 451 27 23 3973 4382 539480641 539481080 9.030000e-92 348.0
7 TraesCS5B01G518100 chr2A 89.545 660 50 8 3288 3943 24306053 24306697 0.000000e+00 819.0
8 TraesCS5B01G518100 chr2B 89.028 638 60 6 3349 3982 39189881 39189250 0.000000e+00 782.0
9 TraesCS5B01G518100 chr2B 94.637 317 15 1 2608 2922 39196897 39197213 1.420000e-134 490.0
10 TraesCS5B01G518100 chr7B 85.810 747 75 6 1188 1926 744143050 744142327 0.000000e+00 763.0
11 TraesCS5B01G518100 chr7B 85.809 451 44 11 3534 3982 744141602 744141170 1.110000e-125 460.0
12 TraesCS5B01G518100 chr7B 94.079 152 9 0 2134 2285 744141750 744141599 9.490000e-57 231.0
13 TraesCS5B01G518100 chr2D 85.049 515 55 10 3472 3982 22505524 22506020 5.060000e-139 505.0
14 TraesCS5B01G518100 chr2D 88.189 381 21 8 2617 2997 22504769 22505125 2.420000e-117 433.0
15 TraesCS5B01G518100 chr3B 92.778 180 13 0 3225 3404 826703063 826702884 1.210000e-65 261.0
16 TraesCS5B01G518100 chr3B 90.000 200 19 1 3210 3409 826659025 826658827 1.570000e-64 257.0
17 TraesCS5B01G518100 chr3B 86.517 89 12 0 3874 3962 826658419 826658331 1.000000e-16 99.0
18 TraesCS5B01G518100 chr3B 88.889 63 7 0 3407 3469 804851685 804851747 1.310000e-10 78.7
19 TraesCS5B01G518100 chr3D 90.710 183 16 1 3210 3392 612300983 612301164 4.380000e-60 243.0
20 TraesCS5B01G518100 chr3D 87.640 89 11 0 3874 3962 612301610 612301698 2.160000e-18 104.0
21 TraesCS5B01G518100 chr6D 87.432 183 18 3 528 710 421796138 421796315 5.750000e-49 206.0
22 TraesCS5B01G518100 chr6D 88.158 152 14 2 563 714 360337972 360338119 1.250000e-40 178.0
23 TraesCS5B01G518100 chr3A 85.792 183 20 5 528 710 678334515 678334339 5.790000e-44 189.0
24 TraesCS5B01G518100 chr3A 87.013 154 19 1 528 681 692944447 692944599 5.830000e-39 172.0
25 TraesCS5B01G518100 chr3A 80.214 187 27 8 528 712 163684556 163684734 9.900000e-27 132.0
26 TraesCS5B01G518100 chr7A 83.957 187 22 4 529 712 669280594 669280413 5.830000e-39 172.0
27 TraesCS5B01G518100 chr7A 79.762 168 23 8 542 706 511115149 511115308 1.290000e-20 111.0
28 TraesCS5B01G518100 chr7A 77.297 185 31 9 528 710 511114592 511114767 1.000000e-16 99.0
29 TraesCS5B01G518100 chr4D 80.541 185 27 6 542 725 109244610 109244786 2.750000e-27 134.0


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 TraesCS5B01G518100 chr5B 681129740 681134127 4387 False 8104.000000 8104 100.0000 1 4388 1 chr5B.!!$F1 4387
1 TraesCS5B01G518100 chr4A 628924584 628929708 5124 True 1602.250000 5206 91.4850 20 4384 4 chr4A.!!$R1 4364
2 TraesCS5B01G518100 chr5D 539477374 539481080 3706 False 2670.000000 4992 88.5955 757 4382 2 chr5D.!!$F1 3625
3 TraesCS5B01G518100 chr2A 24306053 24306697 644 False 819.000000 819 89.5450 3288 3943 1 chr2A.!!$F1 655
4 TraesCS5B01G518100 chr2B 39189250 39189881 631 True 782.000000 782 89.0280 3349 3982 1 chr2B.!!$R1 633
5 TraesCS5B01G518100 chr7B 744141170 744143050 1880 True 484.666667 763 88.5660 1188 3982 3 chr7B.!!$R1 2794
6 TraesCS5B01G518100 chr2D 22504769 22506020 1251 False 469.000000 505 86.6190 2617 3982 2 chr2D.!!$F1 1365

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
715 1374 0.107017 CGCCATGATGACCTTTCCCT 60.107 55.000 0.00 0.00 0.0 4.20 F
1602 2300 2.434185 ATGTACCACCACGCGCTG 60.434 61.111 5.73 3.55 0.0 5.18 F
1971 2676 0.405973 GCTTCCTTTCCCCAACCTCT 59.594 55.000 0.00 0.00 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1717 2415 1.524621 GGACGCTGTAGGCATGCAT 60.525 57.895 21.36 16.31 41.91 3.96 R
3015 4089 0.752054 CCCCGCCAATAAATGCATGT 59.248 50.000 0.00 0.00 0.00 3.21 R
3950 5365 1.001860 AGAGCCTGACTTCACTTGCTC 59.998 52.381 10.56 10.56 44.17 4.26 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
50 51 9.301897 AGATTAGAAAATTGGCTTACTCTTTGT 57.698 29.630 0.00 0.00 0.00 2.83
122 488 3.766591 TGGATGTTGAAACACAAACCAGT 59.233 39.130 0.00 0.00 42.51 4.00
128 494 5.221342 TGTTGAAACACAAACCAGTTCAACT 60.221 36.000 21.44 0.00 40.36 3.16
129 495 5.054390 TGAAACACAAACCAGTTCAACTC 57.946 39.130 0.00 0.00 0.00 3.01
131 497 1.400494 ACACAAACCAGTTCAACTCGC 59.600 47.619 0.00 0.00 0.00 5.03
142 508 5.812642 CCAGTTCAACTCGCTGATTATACTT 59.187 40.000 0.00 0.00 32.39 2.24
151 517 3.242739 CGCTGATTATACTTGTTGTGCCC 60.243 47.826 0.00 0.00 0.00 5.36
155 521 2.684001 TATACTTGTTGTGCCCTCGG 57.316 50.000 0.00 0.00 0.00 4.63
170 536 3.716006 CGGTGTGGCTTGAGCGTG 61.716 66.667 0.00 0.00 43.26 5.34
191 557 1.165907 TGCTCGACAAAGTGGCCTTG 61.166 55.000 3.32 2.41 0.00 3.61
221 587 3.659786 TCCCGTGATAGCAAATATTCCG 58.340 45.455 0.00 0.00 0.00 4.30
241 607 2.508526 GCTAGGTGGAAATGGCTATGG 58.491 52.381 0.00 0.00 0.00 2.74
245 611 4.270317 AGGTGGAAATGGCTATGGATTT 57.730 40.909 0.00 0.00 0.00 2.17
465 832 2.290705 GGAATCTTCCGAAACCTTCCCA 60.291 50.000 0.00 0.00 37.65 4.37
499 866 4.321974 GGGGAAACATCAGTGAAACCATTC 60.322 45.833 0.00 0.00 37.80 2.67
537 906 8.481492 AATAAATGCATCCATGGTCATCTTTA 57.519 30.769 12.58 11.73 0.00 1.85
538 907 6.795144 AAATGCATCCATGGTCATCTTTAA 57.205 33.333 12.58 0.00 0.00 1.52
549 918 6.500684 TGGTCATCTTTAACTCATTGCTTC 57.499 37.500 0.00 0.00 0.00 3.86
576 945 3.285484 AGCAAATTCAGTAGCCCATGAG 58.715 45.455 0.00 0.00 0.00 2.90
577 946 2.223665 GCAAATTCAGTAGCCCATGAGC 60.224 50.000 0.00 0.00 0.00 4.26
579 948 4.454678 CAAATTCAGTAGCCCATGAGCTA 58.545 43.478 4.60 4.60 42.70 3.32
580 949 4.348863 AATTCAGTAGCCCATGAGCTAG 57.651 45.455 9.48 0.00 45.74 3.42
585 1244 3.070159 CAGTAGCCCATGAGCTAGCTAAA 59.930 47.826 19.38 9.84 45.74 1.85
612 1271 8.958119 TCAGTTTTTGTAATAAGTGTGAGACT 57.042 30.769 0.00 0.00 35.94 3.24
622 1281 4.543590 AAGTGTGAGACTAGTTGGATGG 57.456 45.455 0.00 0.00 33.09 3.51
661 1320 6.442541 TCTTAATTCCCCAACTAGTGAACA 57.557 37.500 0.00 0.00 0.00 3.18
679 1338 8.856490 AGTGAACAATGTAATTCTTGTTTGAC 57.144 30.769 12.33 11.87 43.61 3.18
706 1365 9.836864 ATATTAATATAAAGCTCGCCATGATGA 57.163 29.630 6.16 0.00 0.00 2.92
707 1366 5.869753 AATATAAAGCTCGCCATGATGAC 57.130 39.130 0.00 0.00 0.00 3.06
710 1369 0.254178 AAGCTCGCCATGATGACCTT 59.746 50.000 0.00 0.00 0.00 3.50
711 1370 0.254178 AGCTCGCCATGATGACCTTT 59.746 50.000 0.00 0.00 0.00 3.11
713 1372 1.303309 CTCGCCATGATGACCTTTCC 58.697 55.000 0.00 0.00 0.00 3.13
715 1374 0.107017 CGCCATGATGACCTTTCCCT 60.107 55.000 0.00 0.00 0.00 4.20
720 1379 3.564133 CCATGATGACCTTTCCCTCCAAA 60.564 47.826 0.00 0.00 0.00 3.28
721 1380 3.154827 TGATGACCTTTCCCTCCAAAC 57.845 47.619 0.00 0.00 0.00 2.93
725 1395 3.028130 TGACCTTTCCCTCCAAACAAAC 58.972 45.455 0.00 0.00 0.00 2.93
738 1408 7.299586 CCTCCAAACAAACAAATAAATGCATG 58.700 34.615 0.00 0.00 0.00 4.06
739 1409 6.666417 TCCAAACAAACAAATAAATGCATGC 58.334 32.000 11.82 11.82 0.00 4.06
742 1412 5.514059 ACAAACAAATAAATGCATGCGTC 57.486 34.783 13.95 0.00 0.00 5.19
747 1417 2.737467 ATAAATGCATGCGTCGTGAC 57.263 45.000 13.95 0.00 0.00 3.67
783 1454 6.656632 TTCTTGTACAAATAAATGCACCCA 57.343 33.333 10.03 0.00 0.00 4.51
804 1477 4.156556 CCATGGTGACTTTGTCAATGTAGG 59.843 45.833 2.57 0.00 44.49 3.18
806 1479 4.787551 TGGTGACTTTGTCAATGTAGGTT 58.212 39.130 4.21 0.00 44.49 3.50
933 1609 5.668558 AGACGAAAGAAAGTTTGCGTAAT 57.331 34.783 0.00 0.00 31.58 1.89
934 1610 6.056428 AGACGAAAGAAAGTTTGCGTAATT 57.944 33.333 0.00 0.00 31.58 1.40
935 1611 6.134061 AGACGAAAGAAAGTTTGCGTAATTC 58.866 36.000 0.00 0.00 31.58 2.17
936 1612 6.018180 AGACGAAAGAAAGTTTGCGTAATTCT 60.018 34.615 0.00 0.00 31.58 2.40
937 1613 5.907391 ACGAAAGAAAGTTTGCGTAATTCTG 59.093 36.000 0.00 0.00 31.14 3.02
944 1627 3.951775 TTTGCGTAATTCTGGGCAAAT 57.048 38.095 5.99 0.00 46.76 2.32
985 1670 3.425858 GTCTCGTCGAGTTCCAAAGAAAG 59.574 47.826 21.15 0.00 32.58 2.62
986 1671 3.067742 TCTCGTCGAGTTCCAAAGAAAGT 59.932 43.478 21.15 0.00 32.58 2.66
987 1672 4.276678 TCTCGTCGAGTTCCAAAGAAAGTA 59.723 41.667 21.15 0.00 32.58 2.24
988 1673 4.935702 TCGTCGAGTTCCAAAGAAAGTAA 58.064 39.130 0.00 0.00 32.58 2.24
989 1674 4.980434 TCGTCGAGTTCCAAAGAAAGTAAG 59.020 41.667 0.00 0.00 32.58 2.34
990 1675 4.980434 CGTCGAGTTCCAAAGAAAGTAAGA 59.020 41.667 0.00 0.00 32.58 2.10
991 1676 5.461078 CGTCGAGTTCCAAAGAAAGTAAGAA 59.539 40.000 0.00 0.00 32.58 2.52
992 1677 6.019318 CGTCGAGTTCCAAAGAAAGTAAGAAA 60.019 38.462 0.00 0.00 32.58 2.52
1026 1711 2.742372 CGACTTCCCGCCACCAAG 60.742 66.667 0.00 0.00 0.00 3.61
1036 1721 2.919494 GCCACCAAGCTCAAACCGG 61.919 63.158 0.00 0.00 0.00 5.28
1037 1722 2.644992 CACCAAGCTCAAACCGGC 59.355 61.111 0.00 0.00 0.00 6.13
1038 1723 2.597510 ACCAAGCTCAAACCGGCC 60.598 61.111 0.00 0.00 0.00 6.13
1602 2300 2.434185 ATGTACCACCACGCGCTG 60.434 61.111 5.73 3.55 0.00 5.18
1717 2415 1.335964 CGCTCTGTCAAGGAAAGTCGA 60.336 52.381 0.00 0.00 0.00 4.20
1749 2454 2.418910 CGTCCGTGCCTCTCTCCAT 61.419 63.158 0.00 0.00 0.00 3.41
1794 2499 1.884464 CGCGCTGCTGGACATGTAT 60.884 57.895 5.56 0.00 0.00 2.29
1881 2586 2.930385 CTTGGAGCGCCATCATCGGT 62.930 60.000 10.98 0.00 45.46 4.69
1971 2676 0.405973 GCTTCCTTTCCCCAACCTCT 59.594 55.000 0.00 0.00 0.00 3.69
2052 2898 3.316283 TCATGTTTTGCTTGCGAAATCC 58.684 40.909 10.71 1.24 0.00 3.01
2415 3489 4.206375 TGGATATGTATGCAAAGTGTGGG 58.794 43.478 0.00 0.00 30.84 4.61
2439 3513 5.218179 AGGATTGATCTCTCCAGACAGATT 58.782 41.667 14.22 0.00 33.75 2.40
2459 3533 2.203470 TTTGATGTCATGCCAGCTCA 57.797 45.000 0.00 0.00 0.00 4.26
2760 3834 1.600957 CAGTTTATCCAGAGCATGCCG 59.399 52.381 15.66 2.92 0.00 5.69
3015 4089 5.325239 TGGATCGAGATAAATGGCTCTCTA 58.675 41.667 0.00 0.00 36.56 2.43
3081 4155 8.926374 CCTGAGATATATCAAGAGCTGGATAAT 58.074 37.037 15.08 0.00 30.43 1.28
3123 4197 1.209621 TGGGTTACCAGGCTGATACC 58.790 55.000 17.94 18.29 43.37 2.73
3480 4878 9.383519 CTTGAATAGTGGAGCATTTAGAACTTA 57.616 33.333 0.00 0.00 0.00 2.24
3568 4967 4.665451 TCCAAAGTGATGGTGTCATGAAT 58.335 39.130 0.00 0.00 41.46 2.57
3583 4983 7.201461 GGTGTCATGAATTCAAAATGAAATCCG 60.201 37.037 13.09 0.00 40.12 4.18
3670 5074 7.913674 AAACAAGATCTGATTCTGTAGGTTC 57.086 36.000 0.00 0.00 0.00 3.62
3678 5082 5.945784 TCTGATTCTGTAGGTTCCAATTTGG 59.054 40.000 9.28 9.28 39.43 3.28
3703 5107 6.469782 AACCAAGATGACACTGAATTGTTT 57.530 33.333 0.00 0.00 0.00 2.83
3801 5208 8.485976 AGCTAGAATGACACAAATAGAACTTC 57.514 34.615 0.00 0.00 0.00 3.01
3950 5365 5.195940 TCCTGGAGATTAGAAAAGCCAATG 58.804 41.667 0.00 0.00 0.00 2.82
3963 5378 2.157738 AGCCAATGAGCAAGTGAAGTC 58.842 47.619 0.00 0.00 34.23 3.01
3983 5398 4.061596 GTCAGGCTCTTAACCATCATAGC 58.938 47.826 0.00 0.00 0.00 2.97
4031 5517 4.155709 AGAGATCACAGTCAGGAACTTGA 58.844 43.478 0.00 0.00 34.60 3.02
4098 5587 1.865788 GAAGGCGTGCATTTGAGGCA 61.866 55.000 0.00 0.00 39.32 4.75
4209 5730 4.345257 TGTTCCTCTAGTAGATTCCATGGC 59.655 45.833 6.96 0.00 0.00 4.40
4243 5773 2.825836 CCAAGGGGCATCGCACTC 60.826 66.667 0.00 0.00 29.71 3.51
4248 5778 2.107953 GGGCATCGCACTCCTCTC 59.892 66.667 0.00 0.00 0.00 3.20
4323 5853 3.466836 TCATTTCTTCGAAGCAGTGTGT 58.533 40.909 20.56 0.00 0.00 3.72
4324 5854 3.248363 TCATTTCTTCGAAGCAGTGTGTG 59.752 43.478 20.56 11.10 0.00 3.82
4350 5880 7.185318 TGCAGGTGATCCATCAAAATATTTT 57.815 32.000 7.64 7.64 38.75 1.82
4351 5881 7.267128 TGCAGGTGATCCATCAAAATATTTTC 58.733 34.615 10.53 0.00 38.75 2.29
4384 5916 2.929531 TCTGCACGTGATCTCTTCTC 57.070 50.000 22.23 0.00 0.00 2.87
4385 5917 2.441410 TCTGCACGTGATCTCTTCTCT 58.559 47.619 22.23 0.00 0.00 3.10
4386 5918 2.822561 TCTGCACGTGATCTCTTCTCTT 59.177 45.455 22.23 0.00 0.00 2.85
4387 5919 3.256879 TCTGCACGTGATCTCTTCTCTTT 59.743 43.478 22.23 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.848726 TCATTCCGTACTTCCGTTTACC 58.151 45.455 0.00 0.00 0.00 2.85
3 4 5.782047 TCTTTCATTCCGTACTTCCGTTTA 58.218 37.500 0.00 0.00 0.00 2.01
4 5 4.634199 TCTTTCATTCCGTACTTCCGTTT 58.366 39.130 0.00 0.00 0.00 3.60
5 6 4.261578 TCTTTCATTCCGTACTTCCGTT 57.738 40.909 0.00 0.00 0.00 4.44
6 7 3.947910 TCTTTCATTCCGTACTTCCGT 57.052 42.857 0.00 0.00 0.00 4.69
7 8 6.270815 TCTAATCTTTCATTCCGTACTTCCG 58.729 40.000 0.00 0.00 0.00 4.30
8 9 8.488651 TTTCTAATCTTTCATTCCGTACTTCC 57.511 34.615 0.00 0.00 0.00 3.46
12 13 9.503427 CCAATTTTCTAATCTTTCATTCCGTAC 57.497 33.333 0.00 0.00 0.00 3.67
13 14 8.188139 GCCAATTTTCTAATCTTTCATTCCGTA 58.812 33.333 0.00 0.00 0.00 4.02
14 15 7.035612 GCCAATTTTCTAATCTTTCATTCCGT 58.964 34.615 0.00 0.00 0.00 4.69
15 16 7.260603 AGCCAATTTTCTAATCTTTCATTCCG 58.739 34.615 0.00 0.00 0.00 4.30
20 21 9.520515 AGAGTAAGCCAATTTTCTAATCTTTCA 57.479 29.630 0.00 0.00 0.00 2.69
35 36 7.109501 TGCAGAATATACAAAGAGTAAGCCAA 58.890 34.615 0.00 0.00 36.05 4.52
42 43 9.066892 TGAAGTTTTGCAGAATATACAAAGAGT 57.933 29.630 0.00 0.00 34.97 3.24
50 51 7.441890 TTTCGGTGAAGTTTTGCAGAATATA 57.558 32.000 0.00 0.00 0.00 0.86
122 488 6.649141 ACAACAAGTATAATCAGCGAGTTGAA 59.351 34.615 0.00 0.00 37.74 2.69
128 494 3.621268 GGCACAACAAGTATAATCAGCGA 59.379 43.478 0.00 0.00 0.00 4.93
129 495 3.242739 GGGCACAACAAGTATAATCAGCG 60.243 47.826 0.00 0.00 0.00 5.18
131 497 4.271049 CGAGGGCACAACAAGTATAATCAG 59.729 45.833 0.00 0.00 0.00 2.90
142 508 2.203139 CACACCGAGGGCACAACA 60.203 61.111 0.00 0.00 0.00 3.33
151 517 3.114616 CGCTCAAGCCACACCGAG 61.115 66.667 0.00 0.00 37.91 4.63
155 521 1.499056 CATCACGCTCAAGCCACAC 59.501 57.895 0.00 0.00 37.91 3.82
170 536 0.674895 AGGCCACTTTGTCGAGCATC 60.675 55.000 5.01 0.00 0.00 3.91
191 557 1.000052 GCTATCACGGGAGTAGGAAGC 60.000 57.143 0.00 0.00 44.67 3.86
221 587 2.106511 TCCATAGCCATTTCCACCTAGC 59.893 50.000 0.00 0.00 0.00 3.42
400 767 9.562408 TTTTCTAGTTGGTTTCTTTTGGTTTTT 57.438 25.926 0.00 0.00 0.00 1.94
465 832 5.425217 ACTGATGTTTCCCCTTTCAGTTTTT 59.575 36.000 0.00 0.00 43.24 1.94
513 882 6.989155 AAAGATGACCATGGATGCATTTAT 57.011 33.333 21.47 0.00 0.00 1.40
523 892 5.359009 AGCAATGAGTTAAAGATGACCATGG 59.641 40.000 11.19 11.19 0.00 3.66
524 893 6.446781 AGCAATGAGTTAAAGATGACCATG 57.553 37.500 0.00 0.00 0.00 3.66
525 894 6.096001 GGAAGCAATGAGTTAAAGATGACCAT 59.904 38.462 0.00 0.00 0.00 3.55
549 918 2.159517 GGCTACTGAATTTGCTTCACGG 60.160 50.000 0.00 0.00 38.97 4.94
607 1266 4.407296 AGGTTCATCCATCCAACTAGTCTC 59.593 45.833 0.00 0.00 39.02 3.36
612 1271 3.455910 CAGGAGGTTCATCCATCCAACTA 59.544 47.826 6.29 0.00 42.26 2.24
617 1276 0.475906 CCCAGGAGGTTCATCCATCC 59.524 60.000 6.29 0.00 42.26 3.51
641 1300 6.548321 ACATTGTTCACTAGTTGGGGAATTA 58.452 36.000 0.00 0.00 0.00 1.40
679 1338 9.874215 CATCATGGCGAGCTTTATATTAATATG 57.126 33.333 16.72 3.11 0.00 1.78
682 1341 7.066284 GGTCATCATGGCGAGCTTTATATTAAT 59.934 37.037 7.09 0.00 0.00 1.40
683 1342 6.371548 GGTCATCATGGCGAGCTTTATATTAA 59.628 38.462 7.09 0.00 0.00 1.40
684 1343 5.874810 GGTCATCATGGCGAGCTTTATATTA 59.125 40.000 7.09 0.00 0.00 0.98
685 1344 4.697352 GGTCATCATGGCGAGCTTTATATT 59.303 41.667 7.09 0.00 0.00 1.28
686 1345 4.019860 AGGTCATCATGGCGAGCTTTATAT 60.020 41.667 10.14 0.00 36.62 0.86
687 1346 3.324846 AGGTCATCATGGCGAGCTTTATA 59.675 43.478 10.14 0.00 36.62 0.98
696 1355 0.107017 AGGGAAAGGTCATCATGGCG 60.107 55.000 0.00 0.00 0.00 5.69
706 1365 3.108847 TGTTTGTTTGGAGGGAAAGGT 57.891 42.857 0.00 0.00 0.00 3.50
707 1366 4.479786 TTTGTTTGTTTGGAGGGAAAGG 57.520 40.909 0.00 0.00 0.00 3.11
710 1369 6.484977 GCATTTATTTGTTTGTTTGGAGGGAA 59.515 34.615 0.00 0.00 0.00 3.97
711 1370 5.994668 GCATTTATTTGTTTGTTTGGAGGGA 59.005 36.000 0.00 0.00 0.00 4.20
713 1372 6.857777 TGCATTTATTTGTTTGTTTGGAGG 57.142 33.333 0.00 0.00 0.00 4.30
715 1374 6.565435 CGCATGCATTTATTTGTTTGTTTGGA 60.565 34.615 19.57 0.00 0.00 3.53
720 1379 4.089780 CGACGCATGCATTTATTTGTTTGT 59.910 37.500 19.57 1.81 0.00 2.83
721 1380 4.089780 ACGACGCATGCATTTATTTGTTTG 59.910 37.500 19.57 4.45 0.00 2.93
725 1395 3.238114 GTCACGACGCATGCATTTATTTG 59.762 43.478 19.57 4.98 0.00 2.32
780 1451 2.892852 ACATTGACAAAGTCACCATGGG 59.107 45.455 18.09 5.22 42.60 4.00
783 1454 4.985538 ACCTACATTGACAAAGTCACCAT 58.014 39.130 0.00 0.00 42.60 3.55
933 1609 4.647564 AGAGAGAAGAATTTGCCCAGAA 57.352 40.909 0.00 0.00 0.00 3.02
934 1610 4.647564 AAGAGAGAAGAATTTGCCCAGA 57.352 40.909 0.00 0.00 0.00 3.86
935 1611 4.157472 GGAAAGAGAGAAGAATTTGCCCAG 59.843 45.833 0.00 0.00 0.00 4.45
936 1612 4.082125 GGAAAGAGAGAAGAATTTGCCCA 58.918 43.478 0.00 0.00 0.00 5.36
937 1613 4.339748 AGGAAAGAGAGAAGAATTTGCCC 58.660 43.478 0.00 0.00 0.00 5.36
944 1627 4.746466 AGACCAGAGGAAAGAGAGAAGAA 58.254 43.478 0.00 0.00 0.00 2.52
985 1670 1.268032 CCGCATCGCATGGTTTCTTAC 60.268 52.381 0.00 0.00 0.00 2.34
986 1671 1.013596 CCGCATCGCATGGTTTCTTA 58.986 50.000 0.00 0.00 0.00 2.10
987 1672 1.802636 CCGCATCGCATGGTTTCTT 59.197 52.632 0.00 0.00 0.00 2.52
988 1673 2.764314 GCCGCATCGCATGGTTTCT 61.764 57.895 0.00 0.00 0.00 2.52
989 1674 2.278142 GCCGCATCGCATGGTTTC 60.278 61.111 0.00 0.00 0.00 2.78
990 1675 3.825611 GGCCGCATCGCATGGTTT 61.826 61.111 0.00 0.00 0.00 3.27
1104 1792 2.047274 CATGCGTCGGAAGGTGGT 60.047 61.111 0.00 0.00 0.00 4.16
1292 1989 4.451150 CGGCGTAGAGGGCAAGCA 62.451 66.667 0.00 0.00 0.00 3.91
1339 2036 2.612221 CGAAGGGGAAGGTGTACTTGTC 60.612 54.545 0.00 0.00 40.21 3.18
1717 2415 1.524621 GGACGCTGTAGGCATGCAT 60.525 57.895 21.36 16.31 41.91 3.96
1749 2454 2.847234 AGCACCCCGTCCTTGTCA 60.847 61.111 0.00 0.00 0.00 3.58
1794 2499 1.664873 CAATTCCCCGCACTTTGCA 59.335 52.632 0.00 0.00 45.36 4.08
1881 2586 3.215568 CCGCACACCACAAAGCCA 61.216 61.111 0.00 0.00 0.00 4.75
1971 2676 4.426112 CTGAGAGCGCTGGCGACA 62.426 66.667 18.48 6.53 46.35 4.35
2014 2860 2.177394 TGAAGCTGTTTACCGATGCA 57.823 45.000 0.00 0.00 0.00 3.96
2015 2861 2.420022 ACATGAAGCTGTTTACCGATGC 59.580 45.455 0.00 0.00 0.00 3.91
2052 2898 2.681778 AGGTCAGAGTGGAGGCCG 60.682 66.667 0.00 0.00 0.00 6.13
2415 3489 4.214310 TCTGTCTGGAGAGATCAATCCTC 58.786 47.826 15.09 6.78 36.50 3.71
2439 3513 2.490509 CTGAGCTGGCATGACATCAAAA 59.509 45.455 0.00 0.00 0.00 2.44
2459 3533 9.104713 TCATAGTATTCCATGACACAATATCCT 57.895 33.333 0.00 0.00 0.00 3.24
2610 3684 2.583441 CCCTTCAGTCACGAGCCCA 61.583 63.158 0.00 0.00 0.00 5.36
2760 3834 5.496387 CATACACGAACATCTGCTTTCATC 58.504 41.667 0.00 0.00 0.00 2.92
3015 4089 0.752054 CCCCGCCAATAAATGCATGT 59.248 50.000 0.00 0.00 0.00 3.21
3123 4197 5.824429 TCAAGATCTTGCAGAACAAAACTG 58.176 37.500 27.45 2.94 40.24 3.16
3480 4878 2.629617 CACCTCAAAGGGCATTCTGTTT 59.370 45.455 0.00 0.00 40.58 2.83
3568 4967 4.862902 TGCCTTCGGATTTCATTTTGAA 57.137 36.364 0.00 0.00 34.03 2.69
3583 4983 4.884164 AGAATAGCACCTTTACATGCCTTC 59.116 41.667 0.00 0.00 43.12 3.46
3670 5074 4.990426 GTGTCATCTTGGTTTCCAAATTGG 59.010 41.667 5.48 5.48 43.44 3.16
3678 5082 6.076981 ACAATTCAGTGTCATCTTGGTTTC 57.923 37.500 0.00 0.00 0.00 2.78
3703 5107 1.064946 CGAAAGCACCAACGCCAAA 59.935 52.632 0.00 0.00 0.00 3.28
3768 5173 4.582869 TGTGTCATTCTAGCTTGATTGCT 58.417 39.130 13.13 0.00 46.11 3.91
3871 5278 6.041865 ACCATTTCATTTCATCAACTGGACAA 59.958 34.615 0.00 0.00 0.00 3.18
3872 5279 5.539574 ACCATTTCATTTCATCAACTGGACA 59.460 36.000 0.00 0.00 0.00 4.02
3950 5365 1.001860 AGAGCCTGACTTCACTTGCTC 59.998 52.381 10.56 10.56 44.17 4.26
3963 5378 4.063689 CTGCTATGATGGTTAAGAGCCTG 58.936 47.826 0.00 0.00 0.00 4.85
4031 5517 1.839994 TCCCAGGAATTTCTCGCTGAT 59.160 47.619 0.00 0.00 0.00 2.90
4062 5548 4.500035 CGCCTTCTCTTCATAGTTAGGGTC 60.500 50.000 0.00 0.00 0.00 4.46
4063 5549 3.385111 CGCCTTCTCTTCATAGTTAGGGT 59.615 47.826 0.00 0.00 0.00 4.34
4098 5587 4.826274 TCTAATAGCTTGTTCCTGCTGT 57.174 40.909 0.00 0.00 40.08 4.40
4101 5590 7.066284 TCAGATTTTCTAATAGCTTGTTCCTGC 59.934 37.037 0.00 0.00 0.00 4.85
4137 5627 6.709145 TGCATAAAAGCACAAGCATTTAAG 57.291 33.333 2.63 0.44 44.17 1.85
4175 5690 1.134438 AGAGGAACAACCCCTGACCC 61.134 60.000 0.00 0.00 40.05 4.46
4209 5730 2.592861 GCTCCAGCGCCAATAGGG 60.593 66.667 2.29 0.00 40.85 3.53
4243 5773 6.036953 CCGAATGAATTCAAAGAAGAGAGAGG 59.963 42.308 13.09 0.14 36.61 3.69
4248 5778 6.073058 TGTCACCGAATGAATTCAAAGAAGAG 60.073 38.462 13.09 0.84 39.72 2.85
4323 5853 0.328926 TTGATGGATCACCTGCAGCA 59.671 50.000 8.66 0.00 40.04 4.41
4324 5854 1.466856 TTTGATGGATCACCTGCAGC 58.533 50.000 8.66 0.00 36.36 5.25
4325 5855 6.401047 AATATTTTGATGGATCACCTGCAG 57.599 37.500 6.78 6.78 36.36 4.41
4326 5856 6.795144 AAATATTTTGATGGATCACCTGCA 57.205 33.333 0.00 0.00 36.36 4.41
4327 5857 7.495055 AGAAAATATTTTGATGGATCACCTGC 58.505 34.615 17.98 0.00 36.36 4.85
4328 5858 8.139989 GGAGAAAATATTTTGATGGATCACCTG 58.860 37.037 17.98 0.00 36.36 4.00
4329 5859 7.288621 GGGAGAAAATATTTTGATGGATCACCT 59.711 37.037 17.98 4.87 36.36 4.00
4330 5860 7.436933 GGGAGAAAATATTTTGATGGATCACC 58.563 38.462 17.98 9.35 36.36 4.02
4331 5861 7.436933 GGGGAGAAAATATTTTGATGGATCAC 58.563 38.462 17.98 7.19 36.36 3.06


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

AutoCloner maintained by Alex Coulton.