Multiple sequence alignment - TraesCS5B01G408200

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 TraesCS5B01G408200 chr5B 100.000 4452 0 0 1 4452 583910437 583914888 0.000000e+00 8222.0
1 TraesCS5B01G408200 chr5B 85.795 176 23 2 2903 3077 562048319 562048493 7.600000e-43 185.0
2 TraesCS5B01G408200 chr5D 93.867 4484 170 51 1 4452 476459653 476464063 0.000000e+00 6660.0
3 TraesCS5B01G408200 chr5D 85.227 176 24 2 2903 3077 458632622 458632796 3.540000e-41 180.0
4 TraesCS5B01G408200 chr5A 91.940 4516 200 69 1 4452 595893297 595897712 0.000000e+00 6172.0
5 TraesCS5B01G408200 chr1B 82.143 280 48 2 3800 4078 678259509 678259787 5.760000e-59 239.0
6 TraesCS5B01G408200 chr1D 81.786 280 49 2 3800 4078 487168521 487168799 2.680000e-57 233.0
7 TraesCS5B01G408200 chr1A 81.786 280 49 2 3800 4078 584676043 584676321 2.680000e-57 233.0
8 TraesCS5B01G408200 chr4A 84.659 176 25 2 2903 3077 532161998 532162172 1.650000e-39 174.0
9 TraesCS5B01G408200 chr7D 84.091 176 26 2 2903 3077 332692750 332692924 7.660000e-38 169.0
10 TraesCS5B01G408200 chr2D 84.393 173 25 2 2906 3077 601056257 601056086 7.660000e-38 169.0
11 TraesCS5B01G408200 chr2D 83.893 149 22 2 2921 3068 616635060 616634913 1.670000e-29 141.0
12 TraesCS5B01G408200 chr2D 91.228 57 4 1 1676 1732 186775037 186774982 4.780000e-10 76.8
13 TraesCS5B01G408200 chr2A 83.893 149 22 2 2921 3068 746852160 746852013 1.670000e-29 141.0


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 TraesCS5B01G408200 chr5B 583910437 583914888 4451 False 8222 8222 100.000 1 4452 1 chr5B.!!$F2 4451
1 TraesCS5B01G408200 chr5D 476459653 476464063 4410 False 6660 6660 93.867 1 4452 1 chr5D.!!$F2 4451
2 TraesCS5B01G408200 chr5A 595893297 595897712 4415 False 6172 6172 91.940 1 4452 1 chr5A.!!$F1 4451

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
921 993 0.174617 CCGTTCTCCTGCTCCTTCTC 59.825 60.0 0.00 0.0 0.0 2.87 F
1358 1439 0.247301 CGGAGCTCGCATTTTCGTTC 60.247 55.0 7.83 0.0 0.0 3.95 F
1433 1522 0.856080 GCGTCGAATTTTACTGCGGC 60.856 55.0 0.00 0.0 0.0 6.53 F
2423 2517 0.313672 GCACGGCAAACATTCTCCAA 59.686 50.0 0.00 0.0 0.0 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2131 0.033366 GCATTTTTCTTGTGGCGGGT 59.967 50.000 0.00 0.0 0.00 5.28 R
2321 2415 0.041238 TCTTGATGGTCTCCTCGGGT 59.959 55.000 0.00 0.0 0.00 5.28 R
3187 3284 1.451028 GCTGTCCATGTCCAGCCTC 60.451 63.158 18.37 0.0 46.55 4.70 R
3883 3992 0.036732 TCAAGCTCATCGCCAAGGTT 59.963 50.000 0.00 0.0 40.39 3.50 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
144 164 1.003839 TGGCATGGACGTTGGTCTC 60.004 57.895 0.00 0.00 42.97 3.36
215 235 0.716108 CCTCTCGTTGTTAGCGCTTG 59.284 55.000 18.68 0.00 0.00 4.01
261 281 3.442625 GGGTTAATCTACTGCCGCTTTTT 59.557 43.478 0.00 0.00 0.00 1.94
336 377 6.711194 TGGTTTACAAATGGAGTAATTGTCGA 59.289 34.615 0.00 0.00 38.22 4.20
346 387 6.513180 TGGAGTAATTGTCGATGAGTTATCC 58.487 40.000 0.00 0.00 31.82 2.59
348 389 6.984474 GGAGTAATTGTCGATGAGTTATCCAA 59.016 38.462 0.00 0.00 31.82 3.53
350 391 9.692749 GAGTAATTGTCGATGAGTTATCCAATA 57.307 33.333 0.00 0.00 31.54 1.90
363 404 9.739276 TGAGTTATCCAATAATCTTGTTGAGTT 57.261 29.630 1.49 0.00 31.84 3.01
431 486 1.671845 ACGCGTTTGGAAACTGCTAAA 59.328 42.857 5.58 0.00 36.77 1.85
454 509 0.618458 TATGTGAGGTGGTTGGGAGC 59.382 55.000 0.00 0.00 0.00 4.70
494 549 4.329545 ACGTGAACGGCCCAGCAT 62.330 61.111 7.86 0.00 44.95 3.79
609 666 3.385384 TGCAGTCGCAGAGAGGGG 61.385 66.667 0.00 0.00 45.36 4.79
659 728 2.362369 TACTCCTCCTGCTGCTGGC 61.362 63.158 19.55 0.00 42.22 4.85
662 731 3.714001 CCTCCTGCTGCTGGCTGA 61.714 66.667 19.55 3.23 41.52 4.26
663 732 2.350134 CTCCTGCTGCTGGCTGAA 59.650 61.111 19.55 2.88 41.52 3.02
664 733 1.077644 CTCCTGCTGCTGGCTGAAT 60.078 57.895 19.55 0.00 41.52 2.57
665 734 1.077930 TCCTGCTGCTGGCTGAATC 60.078 57.895 19.55 0.00 41.52 2.52
666 735 2.119655 CCTGCTGCTGGCTGAATCC 61.120 63.158 12.79 0.00 41.52 3.01
667 736 1.077644 CTGCTGCTGGCTGAATCCT 60.078 57.895 0.00 0.00 41.52 3.24
690 762 8.817876 TCCTAATAAACAAATTAACAAAGGGGG 58.182 33.333 0.00 0.00 0.00 5.40
691 763 8.598916 CCTAATAAACAAATTAACAAAGGGGGT 58.401 33.333 0.00 0.00 0.00 4.95
843 915 5.664294 TTTAACTCCGCACCTAATACAGA 57.336 39.130 0.00 0.00 0.00 3.41
884 956 0.874175 CCATTATTGCGACCGAGCGA 60.874 55.000 1.05 0.00 40.67 4.93
885 957 0.504384 CATTATTGCGACCGAGCGAG 59.496 55.000 1.05 0.00 40.67 5.03
886 958 1.215655 ATTATTGCGACCGAGCGAGC 61.216 55.000 1.05 0.00 40.67 5.03
918 990 2.294078 CCCCGTTCTCCTGCTCCTT 61.294 63.158 0.00 0.00 0.00 3.36
919 991 1.219393 CCCGTTCTCCTGCTCCTTC 59.781 63.158 0.00 0.00 0.00 3.46
920 992 1.261238 CCCGTTCTCCTGCTCCTTCT 61.261 60.000 0.00 0.00 0.00 2.85
921 993 0.174617 CCGTTCTCCTGCTCCTTCTC 59.825 60.000 0.00 0.00 0.00 2.87
962 1034 2.829043 TTCGTCACTCCCCGAATGCG 62.829 60.000 0.00 0.00 38.09 4.73
991 1063 2.681778 AGAGAGTGTCTGCGGGGG 60.682 66.667 0.00 0.00 32.57 5.40
1108 1189 0.737715 GCAAGCGACTGATCCTCGTT 60.738 55.000 10.59 3.26 33.51 3.85
1109 1190 0.994995 CAAGCGACTGATCCTCGTTG 59.005 55.000 10.59 9.67 33.51 4.10
1110 1191 0.603569 AAGCGACTGATCCTCGTTGT 59.396 50.000 10.59 0.00 33.51 3.32
1111 1192 0.603569 AGCGACTGATCCTCGTTGTT 59.396 50.000 10.59 0.00 33.51 2.83
1162 1243 4.844522 GCGTTCCGTGATCTTTAACTTTTC 59.155 41.667 0.00 0.00 0.00 2.29
1257 1338 2.224867 ACCTTCCATCTCCACAAGGTTG 60.225 50.000 0.00 0.00 45.27 3.77
1294 1375 2.234661 TGTTGTCTCTACTCTGCCATGG 59.765 50.000 7.63 7.63 0.00 3.66
1329 1410 1.762460 CATCCCTCGCCCTGGTAGT 60.762 63.158 0.00 0.00 0.00 2.73
1339 1420 1.065636 GCCCTGGTAGTAACAGTTCCC 60.066 57.143 14.13 0.00 34.16 3.97
1352 1433 1.745489 GTTCCCGGAGCTCGCATTT 60.745 57.895 0.73 0.00 37.59 2.32
1354 1435 1.024579 TTCCCGGAGCTCGCATTTTC 61.025 55.000 0.73 0.00 37.59 2.29
1358 1439 0.247301 CGGAGCTCGCATTTTCGTTC 60.247 55.000 7.83 0.00 0.00 3.95
1359 1440 1.079503 GGAGCTCGCATTTTCGTTCT 58.920 50.000 7.83 0.00 0.00 3.01
1360 1441 1.201965 GGAGCTCGCATTTTCGTTCTG 60.202 52.381 7.83 0.00 0.00 3.02
1361 1442 1.461127 GAGCTCGCATTTTCGTTCTGT 59.539 47.619 0.00 0.00 0.00 3.41
1362 1443 1.873591 AGCTCGCATTTTCGTTCTGTT 59.126 42.857 0.00 0.00 0.00 3.16
1368 1449 3.659444 CGCATTTTCGTTCTGTTTGTCTC 59.341 43.478 0.00 0.00 0.00 3.36
1380 1464 0.894184 TTTGTCTCGCTCTCCGTCCT 60.894 55.000 0.00 0.00 38.35 3.85
1385 1469 3.137459 CGCTCTCCGTCCTCTGCT 61.137 66.667 0.00 0.00 0.00 4.24
1391 1475 2.955660 CTCTCCGTCCTCTGCTAATCTT 59.044 50.000 0.00 0.00 0.00 2.40
1433 1522 0.856080 GCGTCGAATTTTACTGCGGC 60.856 55.000 0.00 0.00 0.00 6.53
1448 1542 2.485426 CTGCGGCTCTTGATCTTGAAAA 59.515 45.455 0.00 0.00 0.00 2.29
1482 1576 1.956477 GGCTGAGGTTGTGTTTGATGT 59.044 47.619 0.00 0.00 0.00 3.06
1535 1629 3.452474 CAAGAAGATCCACGACCTGATC 58.548 50.000 0.00 0.00 38.10 2.92
1799 1893 4.521062 GAGCGCCTCGGCATGTCT 62.521 66.667 2.29 0.00 42.06 3.41
2321 2415 2.094906 CGAGACCGTCATTGTCAACCTA 60.095 50.000 0.40 0.00 35.15 3.08
2423 2517 0.313672 GCACGGCAAACATTCTCCAA 59.686 50.000 0.00 0.00 0.00 3.53
2693 2790 1.522569 GCTGATGGACGCCTACCTT 59.477 57.895 0.00 0.00 0.00 3.50
3211 3308 2.406401 GACATGGACAGCATGCGC 59.594 61.111 13.01 0.00 42.53 6.09
3468 3568 1.228925 GATACCTCCTCCCTCCCCG 60.229 68.421 0.00 0.00 0.00 5.73
3488 3588 2.538333 CGCTGCACATGATAGCTTTCAC 60.538 50.000 9.16 0.00 35.36 3.18
3526 3626 4.154717 GTTCTCTTGATTCTTTGCTTCGC 58.845 43.478 0.00 0.00 0.00 4.70
3615 3715 1.462378 CGTTGTAGCAGTGCACAATCG 60.462 52.381 25.38 23.99 34.33 3.34
3616 3716 0.516877 TTGTAGCAGTGCACAATCGC 59.483 50.000 21.04 15.36 29.82 4.58
3622 3722 0.025898 CAGTGCACAATCGCTCGATG 59.974 55.000 21.04 0.00 34.70 3.84
3623 3723 0.390340 AGTGCACAATCGCTCGATGT 60.390 50.000 21.04 3.98 34.70 3.06
3626 3726 0.025513 GCACAATCGCTCGATGTGTC 59.974 55.000 22.60 16.20 36.72 3.67
3627 3727 1.349234 CACAATCGCTCGATGTGTCA 58.651 50.000 17.99 0.00 34.70 3.58
3628 3728 1.929169 CACAATCGCTCGATGTGTCAT 59.071 47.619 17.99 0.00 34.70 3.06
3629 3729 2.034254 CACAATCGCTCGATGTGTCATC 60.034 50.000 17.99 0.25 34.70 2.92
3631 3731 3.066760 ACAATCGCTCGATGTGTCATCTA 59.933 43.478 5.47 0.00 34.70 1.98
3633 3733 5.048713 ACAATCGCTCGATGTGTCATCTATA 60.049 40.000 5.47 0.00 34.70 1.31
3639 3739 3.057245 TCGATGTGTCATCTATAGCTGGC 60.057 47.826 1.16 1.16 0.00 4.85
3655 3755 2.557056 GCTGGCTAATGCATCATGTCAT 59.443 45.455 0.00 0.00 41.91 3.06
3688 3788 6.849588 AAACAAAATGCTTCATTGTTCTCC 57.150 33.333 13.38 0.00 44.15 3.71
3749 3849 1.605457 GCATGGTCGAGACACTGAACA 60.605 52.381 5.55 0.00 36.03 3.18
3793 3902 0.478072 AATGGCAGTTGTGGTGGAGA 59.522 50.000 0.00 0.00 0.00 3.71
3795 3904 1.344953 TGGCAGTTGTGGTGGAGACT 61.345 55.000 0.00 0.00 0.00 3.24
3808 3917 2.490115 GTGGAGACTGTCTCACCAGTAG 59.510 54.545 32.16 0.00 45.46 2.57
3883 3992 2.910479 ATGATCTCGCGGCCGGTA 60.910 61.111 29.38 10.18 34.56 4.02
4123 4232 1.868251 CTCGCGCACCTTCTCGTAC 60.868 63.158 8.75 0.00 0.00 3.67
4144 4253 3.249189 TCCTTCCGCTTGGCCTGT 61.249 61.111 3.32 0.00 0.00 4.00
4195 4304 3.139469 GACGGACCCTCGAGGACC 61.139 72.222 33.39 29.41 46.10 4.46
4354 4463 1.874562 GTCGACGTAGCACTGGAGT 59.125 57.895 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 39 4.980805 TTTGAACTCGGCGGCGCT 62.981 61.111 32.30 11.73 0.00 5.92
28 40 4.445545 CTTTGAACTCGGCGGCGC 62.446 66.667 28.25 26.17 0.00 6.53
29 41 2.494504 GAACTTTGAACTCGGCGGCG 62.495 60.000 27.15 27.15 0.00 6.46
30 42 1.206831 GAACTTTGAACTCGGCGGC 59.793 57.895 7.21 0.00 0.00 6.53
31 43 0.941542 TTGAACTTTGAACTCGGCGG 59.058 50.000 7.21 0.00 0.00 6.13
32 44 2.748461 TTTGAACTTTGAACTCGGCG 57.252 45.000 0.00 0.00 0.00 6.46
33 45 3.550275 GGTTTTTGAACTTTGAACTCGGC 59.450 43.478 0.00 0.00 0.00 5.54
97 114 4.015084 CCATATGATCCAGCCATCTTTCC 58.985 47.826 3.65 0.00 0.00 3.13
181 201 3.133721 ACGAGAGGAATGAAGGGAATCTG 59.866 47.826 0.00 0.00 0.00 2.90
261 281 1.228094 TGGATCACGCAACAAGCCA 60.228 52.632 0.00 0.00 41.38 4.75
269 289 1.591703 GGACTGTCTGGATCACGCA 59.408 57.895 7.85 0.00 0.00 5.24
336 377 9.911788 ACTCAACAAGATTATTGGATAACTCAT 57.088 29.630 0.00 0.00 0.00 2.90
346 387 8.993121 ACAGTGTAGAACTCAACAAGATTATTG 58.007 33.333 0.00 0.00 36.83 1.90
350 391 8.958119 TTTACAGTGTAGAACTCAACAAGATT 57.042 30.769 2.68 0.00 36.83 2.40
351 392 8.958119 TTTTACAGTGTAGAACTCAACAAGAT 57.042 30.769 2.68 0.00 36.83 2.40
363 404 5.302360 ACGCCAAGATTTTTACAGTGTAGA 58.698 37.500 2.68 0.00 0.00 2.59
409 451 1.721133 GCAGTTTCCAAACGCGTCG 60.721 57.895 14.44 6.98 43.51 5.12
411 456 1.301423 TTAGCAGTTTCCAAACGCGT 58.699 45.000 5.58 5.58 43.51 6.01
412 457 2.392933 TTTAGCAGTTTCCAAACGCG 57.607 45.000 3.53 3.53 43.51 6.01
431 486 4.344104 CTCCCAACCACCTCACATAAAAT 58.656 43.478 0.00 0.00 0.00 1.82
464 519 0.671163 TTCACGTGTTCGGTATGCCC 60.671 55.000 16.51 0.00 41.85 5.36
609 666 4.315803 TCCTAAACTACAGTTTGAGCAGC 58.684 43.478 15.87 0.00 46.56 5.25
664 733 8.817876 CCCCCTTTGTTAATTTGTTTATTAGGA 58.182 33.333 0.00 0.00 0.00 2.94
665 734 8.598916 ACCCCCTTTGTTAATTTGTTTATTAGG 58.401 33.333 0.00 0.00 0.00 2.69
666 735 9.430623 CACCCCCTTTGTTAATTTGTTTATTAG 57.569 33.333 0.00 0.00 0.00 1.73
667 736 8.376270 CCACCCCCTTTGTTAATTTGTTTATTA 58.624 33.333 0.00 0.00 0.00 0.98
754 826 2.317530 TTTTGGTTTTCTTTGGGCGG 57.682 45.000 0.00 0.00 0.00 6.13
843 915 2.505167 GCCCCTAGTATTCCGGCGT 61.505 63.158 6.01 0.00 0.00 5.68
919 991 4.544689 CTCGGCTCGCGTGGAGAG 62.545 72.222 5.77 7.97 46.23 3.20
935 1007 1.215647 GGAGTGACGAACGGATGCT 59.784 57.895 0.00 0.00 0.00 3.79
962 1034 3.761752 AGACACTCTCTCTTCCAGCTAAC 59.238 47.826 0.00 0.00 0.00 2.34
991 1063 1.592669 CCTGCATCATCCCGACGAC 60.593 63.158 0.00 0.00 0.00 4.34
998 1070 1.228184 CTGCTCCCCTGCATCATCC 60.228 63.158 0.00 0.00 42.48 3.51
1033 1105 4.432741 GGCCACCTCCCTCTTGCC 62.433 72.222 0.00 0.00 0.00 4.52
1034 1106 4.432741 GGGCCACCTCCCTCTTGC 62.433 72.222 4.39 0.00 43.13 4.01
1035 1107 4.101448 CGGGCCACCTCCCTCTTG 62.101 72.222 4.39 0.00 44.30 3.02
1108 1189 2.342279 CCGGCGGAAGAGACAACA 59.658 61.111 24.41 0.00 0.00 3.33
1109 1190 2.434359 CCCGGCGGAAGAGACAAC 60.434 66.667 30.79 0.00 0.00 3.32
1110 1191 4.388499 GCCCGGCGGAAGAGACAA 62.388 66.667 30.79 0.00 0.00 3.18
1162 1243 0.657368 GCCGAGCACGAACACAAAAG 60.657 55.000 4.70 0.00 42.66 2.27
1257 1338 2.362077 ACAACAAGATTCAGCACCAACC 59.638 45.455 0.00 0.00 0.00 3.77
1294 1375 1.409064 GATGGGGAAAAGCGGGAATTC 59.591 52.381 0.00 0.00 0.00 2.17
1329 1410 1.888018 CGAGCTCCGGGAACTGTTA 59.112 57.895 8.47 0.00 33.91 2.41
1339 1420 0.247301 GAACGAAAATGCGAGCTCCG 60.247 55.000 8.47 6.44 42.21 4.63
1352 1433 2.124903 GAGCGAGACAAACAGAACGAA 58.875 47.619 0.00 0.00 0.00 3.85
1354 1435 1.716581 GAGAGCGAGACAAACAGAACG 59.283 52.381 0.00 0.00 0.00 3.95
1358 1439 0.039074 ACGGAGAGCGAGACAAACAG 60.039 55.000 0.00 0.00 0.00 3.16
1359 1440 0.039437 GACGGAGAGCGAGACAAACA 60.039 55.000 0.00 0.00 0.00 2.83
1360 1441 0.733223 GGACGGAGAGCGAGACAAAC 60.733 60.000 0.00 0.00 0.00 2.93
1361 1442 0.894184 AGGACGGAGAGCGAGACAAA 60.894 55.000 0.00 0.00 0.00 2.83
1362 1443 1.303398 AGGACGGAGAGCGAGACAA 60.303 57.895 0.00 0.00 0.00 3.18
1368 1449 1.377366 TTAGCAGAGGACGGAGAGCG 61.377 60.000 0.00 0.00 0.00 5.03
1380 1464 4.794329 GCAGATACGAGCAAGATTAGCAGA 60.794 45.833 0.00 0.00 0.00 4.26
1385 1469 4.142160 ACACAGCAGATACGAGCAAGATTA 60.142 41.667 0.00 0.00 0.00 1.75
1391 1475 1.133216 GAGACACAGCAGATACGAGCA 59.867 52.381 0.00 0.00 0.00 4.26
1433 1522 7.959651 CGGTCACTTTATTTTCAAGATCAAGAG 59.040 37.037 0.00 0.00 0.00 2.85
1448 1542 1.449601 CAGCCGCCGGTCACTTTAT 60.450 57.895 4.45 0.00 0.00 1.40
1472 1566 3.047796 CTGCAAGCAAGACATCAAACAC 58.952 45.455 0.00 0.00 0.00 3.32
1482 1576 4.063529 CGGGAACTGCAAGCAAGA 57.936 55.556 0.00 0.00 37.60 3.02
1535 1629 1.066573 AGGCTCGACTCCTTGTTCATG 60.067 52.381 0.00 0.00 0.00 3.07
1694 1788 4.742201 GCCAGCTCGAACGCCTCA 62.742 66.667 0.00 0.00 0.00 3.86
2037 2131 0.033366 GCATTTTTCTTGTGGCGGGT 59.967 50.000 0.00 0.00 0.00 5.28
2123 2217 2.711311 CTCATGGCCGCAATGACG 59.289 61.111 6.32 0.23 30.94 4.35
2321 2415 0.041238 TCTTGATGGTCTCCTCGGGT 59.959 55.000 0.00 0.00 0.00 5.28
2423 2517 1.992277 ACGGGAAGCCTCTGATGCT 60.992 57.895 1.31 1.31 41.89 3.79
2492 2586 3.621225 CTCGGGATGAGCAGGTCA 58.379 61.111 4.40 4.40 38.03 4.02
2639 2736 4.828925 GCTCGTCTGCTGGCCTCC 62.829 72.222 3.32 0.00 0.00 4.30
2693 2790 4.770362 TCCGTGGCGATCTCCCCA 62.770 66.667 0.00 0.00 0.00 4.96
2891 2988 2.250939 CCTGCACAAAGAACGGCGA 61.251 57.895 16.62 0.00 0.00 5.54
3112 3209 1.604915 GTCTTCCTCTCCTTGGCCC 59.395 63.158 0.00 0.00 0.00 5.80
3187 3284 1.451028 GCTGTCCATGTCCAGCCTC 60.451 63.158 18.37 0.00 46.55 4.70
3211 3308 4.335647 AGCTCCTGCACCCGGTTG 62.336 66.667 0.00 0.00 42.74 3.77
3294 3391 3.151906 CCGCTCCCTTATCCCCAG 58.848 66.667 0.00 0.00 0.00 4.45
3295 3392 3.168528 GCCGCTCCCTTATCCCCA 61.169 66.667 0.00 0.00 0.00 4.96
3297 3394 4.315941 CCGCCGCTCCCTTATCCC 62.316 72.222 0.00 0.00 0.00 3.85
3298 3395 4.990553 GCCGCCGCTCCCTTATCC 62.991 72.222 0.00 0.00 0.00 2.59
3299 3396 4.235762 TGCCGCCGCTCCCTTATC 62.236 66.667 0.00 0.00 35.36 1.75
3300 3397 4.547367 GTGCCGCCGCTCCCTTAT 62.547 66.667 0.00 0.00 35.36 1.73
3468 3568 2.223433 GGTGAAAGCTATCATGTGCAGC 60.223 50.000 7.56 7.56 35.49 5.25
3488 3588 3.633986 AGAGAACAAAACAAGGAAGCTGG 59.366 43.478 0.00 0.00 0.00 4.85
3526 3626 5.447624 AAACCCCTCGTATTTTCACAAAG 57.552 39.130 0.00 0.00 0.00 2.77
3615 3715 4.165036 CAGCTATAGATGACACATCGAGC 58.835 47.826 12.76 18.80 32.25 5.03
3616 3716 4.731720 CCAGCTATAGATGACACATCGAG 58.268 47.826 19.47 0.00 32.25 4.04
3622 3722 4.629200 GCATTAGCCAGCTATAGATGACAC 59.371 45.833 19.47 8.33 32.25 3.67
3623 3723 4.284234 TGCATTAGCCAGCTATAGATGACA 59.716 41.667 19.47 1.10 41.13 3.58
3626 3726 5.425630 TGATGCATTAGCCAGCTATAGATG 58.574 41.667 11.13 11.13 41.13 2.90
3627 3727 5.688814 TGATGCATTAGCCAGCTATAGAT 57.311 39.130 3.21 0.00 41.13 1.98
3628 3728 5.046087 ACATGATGCATTAGCCAGCTATAGA 60.046 40.000 3.21 0.00 41.13 1.98
3629 3729 5.183969 ACATGATGCATTAGCCAGCTATAG 58.816 41.667 0.00 0.00 41.13 1.31
3631 3731 4.008330 GACATGATGCATTAGCCAGCTAT 58.992 43.478 0.00 0.00 41.13 2.97
3633 3733 2.228059 GACATGATGCATTAGCCAGCT 58.772 47.619 0.00 0.00 41.13 4.24
3639 3739 6.072119 AGCCAACATATGACATGATGCATTAG 60.072 38.462 10.38 0.00 0.00 1.73
3655 3755 6.753180 TGAAGCATTTTGTTTAGCCAACATA 58.247 32.000 0.09 0.00 45.17 2.29
3672 3772 2.042162 AGTGGGGAGAACAATGAAGCAT 59.958 45.455 0.00 0.00 0.00 3.79
3688 3788 3.067601 GGTTTTGGTCTTGTGTAAGTGGG 59.932 47.826 0.00 0.00 35.38 4.61
3749 3849 4.224818 GCATCCATTCCTCTCTTAGCCTAT 59.775 45.833 0.00 0.00 0.00 2.57
3795 3904 0.611062 CGGGGACTACTGGTGAGACA 60.611 60.000 0.00 0.00 0.00 3.41
3883 3992 0.036732 TCAAGCTCATCGCCAAGGTT 59.963 50.000 0.00 0.00 40.39 3.50
4300 4409 4.135153 CTCAGACGAGGCCACCGG 62.135 72.222 19.41 0.00 35.44 5.28
4404 4513 2.466867 GAAATGCTTCGCCGGAGAA 58.533 52.632 19.99 19.99 0.00 2.87


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

AutoCloner maintained by Alex Coulton.