Multiple sequence alignment - TraesCS5A01G328800

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 TraesCS5A01G328800 chr5A 100.000 3515 0 0 1 3515 537789114 537785600 0.000000e+00 6492
1 TraesCS5A01G328800 chr5A 82.041 1548 269 6 958 2502 537769245 537767704 0.000000e+00 1310
2 TraesCS5A01G328800 chr5D 96.825 2268 68 4 810 3074 424167094 424164828 0.000000e+00 3786
3 TraesCS5A01G328800 chr5D 82.345 1535 261 6 970 2502 424125812 424124286 0.000000e+00 1325
4 TraesCS5A01G328800 chr5D 94.514 401 21 1 3072 3471 424164576 424164176 4.990000e-173 617
5 TraesCS5A01G328800 chr5D 89.441 483 45 4 293 771 424169702 424169222 3.880000e-169 604
6 TraesCS5A01G328800 chr5D 88.727 275 20 3 3 269 424169967 424169696 3.380000e-85 326
7 TraesCS5A01G328800 chr5B 93.879 2369 119 17 807 3171 512943290 512940944 0.000000e+00 3548
8 TraesCS5A01G328800 chr5B 82.025 1541 264 7 970 2502 512841661 512840126 0.000000e+00 1299
9 TraesCS5A01G328800 chr5B 89.825 285 25 2 202 482 512947780 512947496 2.580000e-96 363
10 TraesCS5A01G328800 chr2A 79.387 1402 267 19 1096 2493 2188238 2186855 0.000000e+00 968


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 TraesCS5A01G328800 chr5A 537785600 537789114 3514 True 6492.00 6492 100.00000 1 3515 1 chr5A.!!$R2 3514
1 TraesCS5A01G328800 chr5A 537767704 537769245 1541 True 1310.00 1310 82.04100 958 2502 1 chr5A.!!$R1 1544
2 TraesCS5A01G328800 chr5D 424164176 424169967 5791 True 1333.25 3786 92.37675 3 3471 4 chr5D.!!$R2 3468
3 TraesCS5A01G328800 chr5D 424124286 424125812 1526 True 1325.00 1325 82.34500 970 2502 1 chr5D.!!$R1 1532
4 TraesCS5A01G328800 chr5B 512940944 512943290 2346 True 3548.00 3548 93.87900 807 3171 1 chr5B.!!$R2 2364
5 TraesCS5A01G328800 chr5B 512840126 512841661 1535 True 1299.00 1299 82.02500 970 2502 1 chr5B.!!$R1 1532
6 TraesCS5A01G328800 chr2A 2186855 2188238 1383 True 968.00 968 79.38700 1096 2493 1 chr2A.!!$R1 1397

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
34 35 0.036388 ATTAGTGTGTGGGCTGTCCG 60.036 55.0 0.0 0.0 38.76 4.79 F
540 549 0.235926 GTTGTCACAAGCGGAAGAGC 59.764 55.0 0.0 0.0 37.41 4.09 F
1138 3254 0.343372 AGTAGGCATCCTCCCTTCCA 59.657 55.0 0.0 0.0 34.61 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 3858 0.392327 TCCATGATGAAGCCGCGAAA 60.392 50.0 8.23 0.0 0.0 3.46 R
2278 4395 1.078709 CGCAGTTGACGTCCATCATT 58.921 50.0 14.12 0.0 0.0 2.57 R
2952 5079 0.623723 GGTTTGGACTATGAGGGGCA 59.376 55.0 0.00 0.0 0.0 5.36 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
26 27 6.147821 AGTCTTTTCATCGAATTAGTGTGTGG 59.852 38.462 0.00 0.00 0.00 4.17
30 31 2.093306 TCGAATTAGTGTGTGGGCTG 57.907 50.000 0.00 0.00 0.00 4.85
32 33 1.732259 CGAATTAGTGTGTGGGCTGTC 59.268 52.381 0.00 0.00 0.00 3.51
33 34 2.084546 GAATTAGTGTGTGGGCTGTCC 58.915 52.381 0.00 0.00 0.00 4.02
34 35 0.036388 ATTAGTGTGTGGGCTGTCCG 60.036 55.000 0.00 0.00 38.76 4.79
48 49 4.401519 GGGCTGTCCGCTAGATATATTACA 59.598 45.833 0.00 0.00 39.13 2.41
80 81 5.822519 ACGATATAAACTACCGGAGTACACA 59.177 40.000 9.46 0.00 37.44 3.72
91 92 1.270147 GGAGTACACACACCCACTCAC 60.270 57.143 0.00 0.00 39.33 3.51
92 93 0.756903 AGTACACACACCCACTCACC 59.243 55.000 0.00 0.00 0.00 4.02
126 128 6.237384 GGACACGTGTACAATATAAACACTCG 60.237 42.308 26.10 0.00 41.03 4.18
128 130 6.525628 ACACGTGTACAATATAAACACTCGAG 59.474 38.462 21.98 11.84 41.03 4.04
210 219 8.088365 TGATGAGTTACCACCGATAATTCATAG 58.912 37.037 3.60 0.00 38.42 2.23
269 278 2.507886 TCATATGTGGTCGGTTGGGAAT 59.492 45.455 1.90 0.00 0.00 3.01
271 280 4.349636 TCATATGTGGTCGGTTGGGAATAT 59.650 41.667 1.90 0.00 0.00 1.28
272 281 2.411628 TGTGGTCGGTTGGGAATATG 57.588 50.000 0.00 0.00 0.00 1.78
273 282 1.631388 TGTGGTCGGTTGGGAATATGT 59.369 47.619 0.00 0.00 0.00 2.29
274 283 2.285977 GTGGTCGGTTGGGAATATGTC 58.714 52.381 0.00 0.00 0.00 3.06
287 296 4.652822 GGAATATGTCCACCATCCTAACC 58.347 47.826 0.00 0.00 46.97 2.85
288 297 4.351111 GGAATATGTCCACCATCCTAACCT 59.649 45.833 0.00 0.00 46.97 3.50
289 298 5.163088 GGAATATGTCCACCATCCTAACCTT 60.163 44.000 0.00 0.00 46.97 3.50
290 299 5.994416 ATATGTCCACCATCCTAACCTTT 57.006 39.130 0.00 0.00 34.86 3.11
291 300 4.675063 ATGTCCACCATCCTAACCTTTT 57.325 40.909 0.00 0.00 0.00 2.27
292 301 4.463050 TGTCCACCATCCTAACCTTTTT 57.537 40.909 0.00 0.00 0.00 1.94
397 406 1.201424 GGTCCGACCTTATTCCACCT 58.799 55.000 10.59 0.00 34.73 4.00
405 414 2.292719 ACCTTATTCCACCTAGACGGGT 60.293 50.000 0.00 0.00 40.73 5.28
444 453 2.368439 TGCCGCTTTATCATTGAAGCT 58.632 42.857 7.13 0.00 44.59 3.74
462 471 7.182817 TGAAGCTAGTATACCAATGTTGACT 57.817 36.000 0.00 0.00 0.00 3.41
482 491 4.385825 ACTGCGGACAAGAAGTAATCAAA 58.614 39.130 0.00 0.00 0.00 2.69
483 492 4.819630 ACTGCGGACAAGAAGTAATCAAAA 59.180 37.500 0.00 0.00 0.00 2.44
499 508 0.250553 AAAACCACGATCTTGCCGGA 60.251 50.000 5.05 0.00 0.00 5.14
509 518 0.248743 TCTTGCCGGACTATAACGCG 60.249 55.000 5.05 3.53 0.00 6.01
523 532 4.715527 ATAACGCGTAGGAGAGAAAGTT 57.284 40.909 14.46 0.00 0.00 2.66
529 538 3.552273 GCGTAGGAGAGAAAGTTGTCACA 60.552 47.826 0.00 0.00 0.00 3.58
531 540 4.681942 CGTAGGAGAGAAAGTTGTCACAAG 59.318 45.833 0.00 0.00 0.00 3.16
532 541 3.471680 AGGAGAGAAAGTTGTCACAAGC 58.528 45.455 0.00 0.00 0.00 4.01
540 549 0.235926 GTTGTCACAAGCGGAAGAGC 59.764 55.000 0.00 0.00 37.41 4.09
544 553 1.597854 CACAAGCGGAAGAGCCACA 60.598 57.895 0.00 0.00 38.01 4.17
552 561 1.339055 CGGAAGAGCCACAGATCCAAA 60.339 52.381 0.00 0.00 35.94 3.28
558 567 3.149196 GAGCCACAGATCCAAAAGTCAA 58.851 45.455 0.00 0.00 0.00 3.18
560 569 3.319122 AGCCACAGATCCAAAAGTCAAAC 59.681 43.478 0.00 0.00 0.00 2.93
586 595 6.480524 TCATTATTTTTCACAGACCTCACG 57.519 37.500 0.00 0.00 0.00 4.35
588 597 1.305201 TTTTTCACAGACCTCACGCC 58.695 50.000 0.00 0.00 0.00 5.68
608 617 2.079158 CGACACTAGAGGTTGTACCGA 58.921 52.381 0.00 0.00 44.90 4.69
613 622 2.079158 CTAGAGGTTGTACCGACGTGA 58.921 52.381 0.00 0.00 44.90 4.35
616 625 2.681848 AGAGGTTGTACCGACGTGATAG 59.318 50.000 0.00 0.00 44.90 2.08
655 664 3.317993 TCAAACTACAAAAGGGAAGCAGC 59.682 43.478 0.00 0.00 0.00 5.25
660 669 0.829182 CAAAAGGGAAGCAGCCACCT 60.829 55.000 5.59 0.38 34.04 4.00
667 676 0.884704 GAAGCAGCCACCTTCAACGA 60.885 55.000 0.00 0.00 38.78 3.85
686 695 0.469144 ACCCGACAAACCCTGCAAAT 60.469 50.000 0.00 0.00 0.00 2.32
688 697 1.247567 CCGACAAACCCTGCAAATCT 58.752 50.000 0.00 0.00 0.00 2.40
699 708 3.420893 CCTGCAAATCTTAACCTCACCA 58.579 45.455 0.00 0.00 0.00 4.17
706 718 5.700402 AATCTTAACCTCACCAGCTACAT 57.300 39.130 0.00 0.00 0.00 2.29
715 727 4.100035 CCTCACCAGCTACATGAATCTACA 59.900 45.833 0.00 0.00 0.00 2.74
721 733 4.268644 CAGCTACATGAATCTACACCAACG 59.731 45.833 0.00 0.00 0.00 4.10
722 734 4.159693 AGCTACATGAATCTACACCAACGA 59.840 41.667 0.00 0.00 0.00 3.85
723 735 4.504461 GCTACATGAATCTACACCAACGAG 59.496 45.833 0.00 0.00 0.00 4.18
724 736 3.262420 ACATGAATCTACACCAACGAGC 58.738 45.455 0.00 0.00 0.00 5.03
726 738 1.621317 TGAATCTACACCAACGAGCCA 59.379 47.619 0.00 0.00 0.00 4.75
734 746 3.276091 CAACGAGCCACAACGCCA 61.276 61.111 0.00 0.00 0.00 5.69
737 749 3.853330 CGAGCCACAACGCCATCG 61.853 66.667 0.00 0.00 42.43 3.84
742 754 2.476051 CACAACGCCATCGCAGAC 59.524 61.111 0.00 0.00 42.51 3.51
743 755 2.030412 ACAACGCCATCGCAGACA 59.970 55.556 0.00 0.00 42.51 3.41
768 780 8.709646 CAATTCTGTAAGCGTTACCTATTATCC 58.290 37.037 5.75 0.00 35.25 2.59
771 783 8.332996 TCTGTAAGCGTTACCTATTATCCTAG 57.667 38.462 5.75 0.00 35.25 3.02
772 784 7.941238 TCTGTAAGCGTTACCTATTATCCTAGT 59.059 37.037 5.75 0.00 35.25 2.57
773 785 9.224267 CTGTAAGCGTTACCTATTATCCTAGTA 57.776 37.037 5.75 0.00 35.25 1.82
774 786 9.224267 TGTAAGCGTTACCTATTATCCTAGTAG 57.776 37.037 0.00 0.00 35.25 2.57
775 787 9.225436 GTAAGCGTTACCTATTATCCTAGTAGT 57.775 37.037 0.00 0.00 0.00 2.73
777 789 9.447157 AAGCGTTACCTATTATCCTAGTAGTAG 57.553 37.037 0.00 0.00 0.00 2.57
792 2900 8.952602 TCCTAGTAGTAGTAGGTGGATATTTCA 58.047 37.037 24.50 4.79 41.17 2.69
799 2907 9.261035 AGTAGTAGGTGGATATTTCATATGGAG 57.739 37.037 2.13 0.00 0.00 3.86
800 2908 9.036980 GTAGTAGGTGGATATTTCATATGGAGT 57.963 37.037 2.13 0.00 0.00 3.85
802 2910 9.261035 AGTAGGTGGATATTTCATATGGAGTAG 57.739 37.037 2.13 0.00 0.00 2.57
803 2911 9.036980 GTAGGTGGATATTTCATATGGAGTAGT 57.963 37.037 2.13 0.00 0.00 2.73
805 2913 9.036980 AGGTGGATATTTCATATGGAGTAGTAC 57.963 37.037 2.13 0.00 0.00 2.73
876 2986 9.435688 ACCTGCCACATTTATTATTTTTCTTTC 57.564 29.630 0.00 0.00 0.00 2.62
978 3088 6.721208 TGCATCTCACTACATCTCCATACATA 59.279 38.462 0.00 0.00 0.00 2.29
981 3091 8.747471 CATCTCACTACATCTCCATACATACAT 58.253 37.037 0.00 0.00 0.00 2.29
1068 3178 9.874205 GTGGTACATGTAGTTATTGTAGGTTTA 57.126 33.333 5.62 0.00 44.52 2.01
1138 3254 0.343372 AGTAGGCATCCTCCCTTCCA 59.657 55.000 0.00 0.00 34.61 3.53
1188 3304 4.027437 ACTACATCTCCTTTGACCTCCTC 58.973 47.826 0.00 0.00 0.00 3.71
1308 3424 1.353022 ACAAACTATCCCAAGGGCGAA 59.647 47.619 0.00 0.00 34.68 4.70
1481 3598 2.587777 AGAGTCTCCTACCCTTCATGGA 59.412 50.000 0.00 0.00 38.35 3.41
1843 3960 8.669946 TGTTTTGTCTAACTATGTCAATGACA 57.330 30.769 19.08 19.08 46.90 3.58
2259 4376 3.433314 GGTCCGACTGTCTGGAGTATAGA 60.433 52.174 17.52 0.00 34.21 1.98
2494 4619 4.202567 TGAAGAATGGGCTTAAGGTGAACT 60.203 41.667 4.29 0.00 0.00 3.01
2710 4835 4.829872 ATTGATAAATATCCCCGCGGTA 57.170 40.909 26.12 12.65 31.71 4.02
2741 4866 3.063588 TGCACATGAAAAACACGTTACGA 59.936 39.130 13.03 0.00 0.00 3.43
2743 4868 3.657625 CACATGAAAAACACGTTACGAGC 59.342 43.478 13.03 0.00 0.00 5.03
2909 5036 3.815809 CCAAGTTTGGTGGTTCACTCTA 58.184 45.455 2.66 0.00 43.43 2.43
2920 5047 7.918076 TGGTGGTTCACTCTATAAGAAGAAAT 58.082 34.615 0.00 0.00 34.40 2.17
2922 5049 9.535878 GGTGGTTCACTCTATAAGAAGAAATAG 57.464 37.037 0.00 0.00 34.40 1.73
2941 5068 2.501261 AGTTAGGAAAACCCGTGAAGC 58.499 47.619 0.00 0.00 40.87 3.86
2952 5079 0.036952 CCGTGAAGCTCACCACTCAT 60.037 55.000 9.71 0.00 44.20 2.90
2954 5081 0.801251 GTGAAGCTCACCACTCATGC 59.199 55.000 5.33 0.00 41.37 4.06
3078 5459 8.470002 GGAGAGGCTGACAAAATATTACAAAAT 58.530 33.333 0.00 0.00 0.00 1.82
3082 5464 9.030452 AGGCTGACAAAATATTACAAAATGGTA 57.970 29.630 0.00 0.00 0.00 3.25
3126 5508 7.781056 TGCTTTTTCCTAATGAAGTTCACTTT 58.219 30.769 7.96 2.20 36.11 2.66
3141 5524 3.469859 TCACTTTCATATGGGAGGGGAA 58.530 45.455 2.13 0.00 0.00 3.97
3193 5576 5.831525 ACCACAATTCAGATGTGCATATCAT 59.168 36.000 23.38 7.10 45.32 2.45
3213 5596 1.580845 GCAGTTCATCTGTGCGGCTT 61.581 55.000 0.00 0.00 45.23 4.35
3259 5642 4.839121 AGTACAAATAATTCCCTCGCACA 58.161 39.130 0.00 0.00 0.00 4.57
3299 5682 9.010029 GGTTCAGTGAAAATAAGTTCTATTCCA 57.990 33.333 7.25 0.00 0.00 3.53
3315 5698 2.509336 CACTCGATGGGTGTCGCC 60.509 66.667 0.00 0.00 41.22 5.54
3355 5738 8.880750 GCTCTTAAACCGTAACAAATCTAGAAT 58.119 33.333 0.00 0.00 0.00 2.40
3486 5870 3.987404 CGGGAGGGTTCTTTGCAG 58.013 61.111 0.00 0.00 0.00 4.41
3487 5871 1.073199 CGGGAGGGTTCTTTGCAGT 59.927 57.895 0.00 0.00 0.00 4.40
3488 5872 0.537371 CGGGAGGGTTCTTTGCAGTT 60.537 55.000 0.00 0.00 0.00 3.16
3489 5873 1.248486 GGGAGGGTTCTTTGCAGTTC 58.752 55.000 0.00 0.00 0.00 3.01
3490 5874 1.478654 GGGAGGGTTCTTTGCAGTTCA 60.479 52.381 0.00 0.00 0.00 3.18
3491 5875 2.306847 GGAGGGTTCTTTGCAGTTCAA 58.693 47.619 0.00 0.00 0.00 2.69
3492 5876 2.693074 GGAGGGTTCTTTGCAGTTCAAA 59.307 45.455 0.00 0.00 42.01 2.69
3493 5877 3.132111 GGAGGGTTCTTTGCAGTTCAAAA 59.868 43.478 0.00 0.00 43.44 2.44
3494 5878 4.202253 GGAGGGTTCTTTGCAGTTCAAAAT 60.202 41.667 0.00 0.00 43.44 1.82
3495 5879 5.357742 AGGGTTCTTTGCAGTTCAAAATT 57.642 34.783 0.00 0.00 43.44 1.82
3496 5880 5.118286 AGGGTTCTTTGCAGTTCAAAATTG 58.882 37.500 0.00 0.00 43.44 2.32
3497 5881 4.875536 GGGTTCTTTGCAGTTCAAAATTGT 59.124 37.500 0.00 0.00 43.44 2.71
3498 5882 5.006649 GGGTTCTTTGCAGTTCAAAATTGTC 59.993 40.000 0.00 0.00 43.44 3.18
3499 5883 5.812127 GGTTCTTTGCAGTTCAAAATTGTCT 59.188 36.000 0.00 0.00 43.44 3.41
3500 5884 6.978080 GGTTCTTTGCAGTTCAAAATTGTCTA 59.022 34.615 0.00 0.00 43.44 2.59
3501 5885 7.653311 GGTTCTTTGCAGTTCAAAATTGTCTAT 59.347 33.333 0.00 0.00 43.44 1.98
3502 5886 9.034544 GTTCTTTGCAGTTCAAAATTGTCTATT 57.965 29.630 0.00 0.00 43.44 1.73
3503 5887 8.801715 TCTTTGCAGTTCAAAATTGTCTATTC 57.198 30.769 0.00 0.00 43.44 1.75
3504 5888 8.632679 TCTTTGCAGTTCAAAATTGTCTATTCT 58.367 29.630 0.00 0.00 43.44 2.40
3505 5889 9.252962 CTTTGCAGTTCAAAATTGTCTATTCTT 57.747 29.630 0.00 0.00 43.44 2.52
3506 5890 8.801715 TTGCAGTTCAAAATTGTCTATTCTTC 57.198 30.769 0.00 0.00 0.00 2.87
3507 5891 7.939782 TGCAGTTCAAAATTGTCTATTCTTCA 58.060 30.769 0.00 0.00 0.00 3.02
3508 5892 8.412456 TGCAGTTCAAAATTGTCTATTCTTCAA 58.588 29.630 0.00 0.00 0.00 2.69
3509 5893 8.694394 GCAGTTCAAAATTGTCTATTCTTCAAC 58.306 33.333 0.00 0.00 0.00 3.18
3510 5894 9.185192 CAGTTCAAAATTGTCTATTCTTCAACC 57.815 33.333 0.00 0.00 0.00 3.77
3511 5895 8.076178 AGTTCAAAATTGTCTATTCTTCAACCG 58.924 33.333 0.00 0.00 0.00 4.44
3512 5896 7.737972 TCAAAATTGTCTATTCTTCAACCGA 57.262 32.000 0.00 0.00 0.00 4.69
3513 5897 8.335532 TCAAAATTGTCTATTCTTCAACCGAT 57.664 30.769 0.00 0.00 0.00 4.18
3514 5898 8.792633 TCAAAATTGTCTATTCTTCAACCGATT 58.207 29.630 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.230222 CACACACTAATTCGATGAAAAGACTC 58.770 38.462 0.00 0.00 0.00 3.36
1 2 6.147821 CCACACACTAATTCGATGAAAAGACT 59.852 38.462 0.00 0.00 0.00 3.24
12 13 1.732259 GACAGCCCACACACTAATTCG 59.268 52.381 0.00 0.00 0.00 3.34
13 14 2.084546 GGACAGCCCACACACTAATTC 58.915 52.381 0.00 0.00 34.14 2.17
18 19 4.626081 GCGGACAGCCCACACACT 62.626 66.667 0.00 0.00 40.81 3.55
26 27 7.416890 AAGATGTAATATATCTAGCGGACAGCC 60.417 40.741 0.00 0.00 39.20 4.85
30 31 8.894731 TCTCAAGATGTAATATATCTAGCGGAC 58.105 37.037 0.00 0.00 33.92 4.79
32 33 7.853437 CGTCTCAAGATGTAATATATCTAGCGG 59.147 40.741 0.00 0.00 33.92 5.52
33 34 8.604890 TCGTCTCAAGATGTAATATATCTAGCG 58.395 37.037 0.00 4.47 33.92 4.26
48 49 6.713903 TCCGGTAGTTTATATCGTCTCAAGAT 59.286 38.462 0.00 0.00 0.00 2.40
70 71 0.038526 GAGTGGGTGTGTGTACTCCG 60.039 60.000 0.00 0.00 40.55 4.63
102 103 6.524239 TCGAGTGTTTATATTGTACACGTGTC 59.476 38.462 27.16 16.93 45.12 3.67
107 108 6.309494 TGTGCTCGAGTGTTTATATTGTACAC 59.691 38.462 15.13 8.49 41.82 2.90
108 109 6.309494 GTGTGCTCGAGTGTTTATATTGTACA 59.691 38.462 15.13 0.00 0.00 2.90
126 128 2.169352 ACTCCCATCTATGTGTGTGCTC 59.831 50.000 0.00 0.00 0.00 4.26
128 130 2.698855 ACTCCCATCTATGTGTGTGC 57.301 50.000 0.00 0.00 0.00 4.57
176 178 4.390603 CGGTGGTAACTCATCAATTCGAAA 59.609 41.667 0.00 0.00 37.61 3.46
269 278 5.789574 AAAAGGTTAGGATGGTGGACATA 57.210 39.130 0.00 0.00 40.72 2.29
271 280 4.463050 AAAAAGGTTAGGATGGTGGACA 57.537 40.909 0.00 0.00 0.00 4.02
289 298 8.062065 AGACCTACATGTTCTTTTCACAAAAA 57.938 30.769 2.30 0.00 33.42 1.94
290 299 7.639113 AGACCTACATGTTCTTTTCACAAAA 57.361 32.000 2.30 0.00 0.00 2.44
291 300 8.918202 ATAGACCTACATGTTCTTTTCACAAA 57.082 30.769 2.30 0.00 0.00 2.83
292 301 8.918202 AATAGACCTACATGTTCTTTTCACAA 57.082 30.769 2.30 0.00 0.00 3.33
295 304 9.444600 GGTTAATAGACCTACATGTTCTTTTCA 57.555 33.333 2.30 0.00 36.73 2.69
296 305 9.444600 TGGTTAATAGACCTACATGTTCTTTTC 57.555 33.333 2.30 0.00 40.47 2.29
297 306 9.802039 TTGGTTAATAGACCTACATGTTCTTTT 57.198 29.630 2.30 5.38 40.47 2.27
298 307 9.802039 TTTGGTTAATAGACCTACATGTTCTTT 57.198 29.630 2.30 1.89 40.47 2.52
299 308 9.975218 ATTTGGTTAATAGACCTACATGTTCTT 57.025 29.630 2.30 0.00 40.47 2.52
300 309 9.975218 AATTTGGTTAATAGACCTACATGTTCT 57.025 29.630 2.30 3.41 40.47 3.01
367 376 1.071857 AGGTCGGACCCTTGAAACTTC 59.928 52.381 23.21 0.00 39.75 3.01
372 381 2.237893 GGAATAAGGTCGGACCCTTGAA 59.762 50.000 23.21 5.37 44.57 2.69
373 382 1.835531 GGAATAAGGTCGGACCCTTGA 59.164 52.381 23.21 6.94 44.57 3.02
397 406 3.837578 GAGCCATCGACCCGTCTA 58.162 61.111 0.00 0.00 0.00 2.59
444 453 4.403113 TCCGCAGTCAACATTGGTATACTA 59.597 41.667 2.25 0.00 0.00 1.82
462 471 4.023536 GGTTTTGATTACTTCTTGTCCGCA 60.024 41.667 0.00 0.00 0.00 5.69
482 491 1.375523 GTCCGGCAAGATCGTGGTT 60.376 57.895 10.74 0.00 0.00 3.67
483 492 0.968901 TAGTCCGGCAAGATCGTGGT 60.969 55.000 10.74 0.00 0.00 4.16
499 508 4.880696 ACTTTCTCTCCTACGCGTTATAGT 59.119 41.667 20.78 5.66 0.00 2.12
509 518 4.449405 GCTTGTGACAACTTTCTCTCCTAC 59.551 45.833 0.00 0.00 0.00 3.18
523 532 1.301716 GGCTCTTCCGCTTGTGACA 60.302 57.895 0.00 0.00 0.00 3.58
529 538 0.107945 GATCTGTGGCTCTTCCGCTT 60.108 55.000 0.00 0.00 45.61 4.68
531 540 1.522580 GGATCTGTGGCTCTTCCGC 60.523 63.158 0.00 0.00 45.62 5.54
532 541 0.250234 TTGGATCTGTGGCTCTTCCG 59.750 55.000 0.00 0.00 37.80 4.30
540 549 5.520376 AAGTTTGACTTTTGGATCTGTGG 57.480 39.130 0.00 0.00 34.11 4.17
558 567 8.912988 TGAGGTCTGTGAAAAATAATGAAAGTT 58.087 29.630 0.00 0.00 0.00 2.66
560 569 7.535258 CGTGAGGTCTGTGAAAAATAATGAAAG 59.465 37.037 0.00 0.00 0.00 2.62
563 572 5.106712 GCGTGAGGTCTGTGAAAAATAATGA 60.107 40.000 0.00 0.00 0.00 2.57
586 595 1.135170 GGTACAACCTCTAGTGTCGGC 60.135 57.143 0.00 0.00 34.73 5.54
588 597 2.079158 TCGGTACAACCTCTAGTGTCG 58.921 52.381 0.00 0.00 35.66 4.35
608 617 4.505918 CCTCCTACCTCATCTCTATCACGT 60.506 50.000 0.00 0.00 0.00 4.49
613 622 6.476409 TTGATCCTCCTACCTCATCTCTAT 57.524 41.667 0.00 0.00 0.00 1.98
616 625 4.898861 AGTTTGATCCTCCTACCTCATCTC 59.101 45.833 0.00 0.00 0.00 2.75
655 664 1.666872 GTCGGGTCGTTGAAGGTGG 60.667 63.158 0.00 0.00 0.00 4.61
660 669 0.814812 GGGTTTGTCGGGTCGTTGAA 60.815 55.000 0.00 0.00 0.00 2.69
667 676 0.469144 ATTTGCAGGGTTTGTCGGGT 60.469 50.000 0.00 0.00 0.00 5.28
686 695 4.093743 TCATGTAGCTGGTGAGGTTAAGA 58.906 43.478 0.00 0.00 0.00 2.10
688 697 4.901197 TTCATGTAGCTGGTGAGGTTAA 57.099 40.909 0.00 0.00 0.00 2.01
699 708 4.159693 TCGTTGGTGTAGATTCATGTAGCT 59.840 41.667 0.00 0.00 0.00 3.32
706 718 1.621317 TGGCTCGTTGGTGTAGATTCA 59.379 47.619 0.00 0.00 0.00 2.57
715 727 3.276846 GCGTTGTGGCTCGTTGGT 61.277 61.111 0.00 0.00 0.00 3.67
721 733 4.166011 GCGATGGCGTTGTGGCTC 62.166 66.667 0.00 0.00 45.14 4.70
723 735 4.465512 CTGCGATGGCGTTGTGGC 62.466 66.667 0.00 0.00 44.10 5.01
724 736 2.741985 TCTGCGATGGCGTTGTGG 60.742 61.111 0.00 0.00 44.10 4.17
726 738 0.955428 ATTGTCTGCGATGGCGTTGT 60.955 50.000 0.00 0.00 44.10 3.32
742 754 8.709646 GGATAATAGGTAACGCTTACAGAATTG 58.290 37.037 9.18 0.00 46.39 2.32
743 755 8.648693 AGGATAATAGGTAACGCTTACAGAATT 58.351 33.333 9.18 7.77 46.39 2.17
773 785 9.261035 CTCCATATGAAATATCCACCTACTACT 57.739 37.037 3.65 0.00 37.44 2.57
774 786 9.036980 ACTCCATATGAAATATCCACCTACTAC 57.963 37.037 3.65 0.00 37.44 2.73
777 789 9.036980 ACTACTCCATATGAAATATCCACCTAC 57.963 37.037 3.65 0.00 37.44 3.18
780 2888 7.974501 CGTACTACTCCATATGAAATATCCACC 59.025 40.741 3.65 0.00 37.44 4.61
792 2900 4.833380 AGGATTGCACGTACTACTCCATAT 59.167 41.667 0.00 0.00 0.00 1.78
794 2902 3.031736 AGGATTGCACGTACTACTCCAT 58.968 45.455 0.00 0.00 0.00 3.41
801 2909 8.504005 GCATTAATTATAAGGATTGCACGTACT 58.496 33.333 0.00 0.00 0.00 2.73
802 2910 7.477422 CGCATTAATTATAAGGATTGCACGTAC 59.523 37.037 12.84 0.00 0.00 3.67
803 2911 7.360522 CCGCATTAATTATAAGGATTGCACGTA 60.361 37.037 12.84 0.00 0.00 3.57
804 2912 6.370593 CGCATTAATTATAAGGATTGCACGT 58.629 36.000 12.84 0.00 0.00 4.49
805 2913 5.794945 CCGCATTAATTATAAGGATTGCACG 59.205 40.000 12.84 0.00 0.00 5.34
876 2986 5.028375 GGAAACTCTTGTCGTTTTCTTGTG 58.972 41.667 0.00 0.00 34.94 3.33
947 3057 0.894835 TGTAGTGAGATGCAAGCCGA 59.105 50.000 0.00 0.00 0.00 5.54
978 3088 4.897509 TCTTGGAAGAGATGTGTGATGT 57.102 40.909 0.00 0.00 0.00 3.06
981 3091 4.582869 CCATTCTTGGAAGAGATGTGTGA 58.417 43.478 0.00 0.00 46.92 3.58
1188 3304 2.338015 GCTGTGGCCAGATGGTGTG 61.338 63.158 5.11 0.00 41.50 3.82
1308 3424 6.543465 TCATGTCAAAGATTTCGGCATAATCT 59.457 34.615 5.52 5.52 42.58 2.40
1741 3858 0.392327 TCCATGATGAAGCCGCGAAA 60.392 50.000 8.23 0.00 0.00 3.46
2278 4395 1.078709 CGCAGTTGACGTCCATCATT 58.921 50.000 14.12 0.00 0.00 2.57
2393 4518 5.699001 ACATCAAAGTTACACACGATAGCAA 59.301 36.000 0.00 0.00 42.67 3.91
2554 4679 7.390918 ACACGTATTAAGCGATAATGACTTC 57.609 36.000 8.85 0.00 35.77 3.01
2685 4810 5.123227 CCGCGGGGATATTTATCAATACAT 58.877 41.667 20.10 0.00 34.40 2.29
2686 4811 4.020039 ACCGCGGGGATATTTATCAATACA 60.020 41.667 31.76 0.00 36.97 2.29
2687 4812 4.510571 ACCGCGGGGATATTTATCAATAC 58.489 43.478 31.76 0.00 36.97 1.89
2688 4813 4.829872 ACCGCGGGGATATTTATCAATA 57.170 40.909 31.76 0.00 36.97 1.90
2710 4835 4.142204 TGTTTTTCATGTGCATGTGACTGT 60.142 37.500 11.38 0.00 39.72 3.55
2741 4866 3.379372 GCATAGGTCACATGATGTTTGCT 59.621 43.478 0.00 0.00 0.00 3.91
2743 4868 3.695556 TGGCATAGGTCACATGATGTTTG 59.304 43.478 0.00 0.00 0.00 2.93
2830 4956 9.574516 AAGGGACCATGATATTTTATAGAACAC 57.425 33.333 0.00 0.00 0.00 3.32
2909 5036 9.392259 CGGGTTTTCCTAACTATTTCTTCTTAT 57.608 33.333 0.00 0.00 40.46 1.73
2920 5047 3.325716 AGCTTCACGGGTTTTCCTAACTA 59.674 43.478 0.00 0.00 40.46 2.24
2922 5049 2.483106 GAGCTTCACGGGTTTTCCTAAC 59.517 50.000 0.00 0.00 40.46 2.34
2941 5068 1.222936 GAGGGGCATGAGTGGTGAG 59.777 63.158 0.00 0.00 0.00 3.51
2952 5079 0.623723 GGTTTGGACTATGAGGGGCA 59.376 55.000 0.00 0.00 0.00 5.36
2954 5081 1.139058 CGAGGTTTGGACTATGAGGGG 59.861 57.143 0.00 0.00 0.00 4.79
3046 5173 5.904362 ATTTTGTCAGCCTCTCCAATAAC 57.096 39.130 0.00 0.00 0.00 1.89
3078 5459 6.279882 CAACTTGCTTGGAGAAATTTTACCA 58.720 36.000 11.50 11.50 0.00 3.25
3112 5494 6.604795 CCTCCCATATGAAAGTGAACTTCATT 59.395 38.462 3.65 0.00 34.61 2.57
3126 5508 3.116199 ACTCTCATTCCCCTCCCATATGA 60.116 47.826 3.65 0.00 0.00 2.15
3141 5524 2.417924 GGTGCGTTCAGATGACTCTCAT 60.418 50.000 0.00 0.00 40.34 2.90
3222 5605 2.221169 TGTACTACGACGGTCAAGTGT 58.779 47.619 18.40 7.33 0.00 3.55
3259 5642 2.365617 ACTGAACCGAGACACATGAACT 59.634 45.455 0.00 0.00 0.00 3.01
3299 5682 2.680352 AGGCGACACCCATCGAGT 60.680 61.111 0.00 0.00 45.13 4.18
3313 5696 7.307751 GGTTTAAGAGCATTTTAAAAACCAGGC 60.308 37.037 4.44 4.59 42.40 4.85
3315 5698 7.436970 ACGGTTTAAGAGCATTTTAAAAACCAG 59.563 33.333 4.44 8.70 42.78 4.00
3355 5738 6.871492 TGCATTCTTTTCTATGTCGAACACTA 59.129 34.615 0.00 0.00 0.00 2.74
3471 5855 1.981256 TGAACTGCAAAGAACCCTCC 58.019 50.000 0.00 0.00 0.00 4.30
3472 5856 4.385358 TTTTGAACTGCAAAGAACCCTC 57.615 40.909 0.00 0.00 46.38 4.30
3473 5857 5.118286 CAATTTTGAACTGCAAAGAACCCT 58.882 37.500 0.00 0.00 46.38 4.34
3474 5858 4.875536 ACAATTTTGAACTGCAAAGAACCC 59.124 37.500 0.00 0.00 46.38 4.11
3475 5859 5.812127 AGACAATTTTGAACTGCAAAGAACC 59.188 36.000 0.00 0.00 46.38 3.62
3476 5860 6.892310 AGACAATTTTGAACTGCAAAGAAC 57.108 33.333 0.00 0.00 46.38 3.01
3477 5861 9.248291 GAATAGACAATTTTGAACTGCAAAGAA 57.752 29.630 0.00 0.00 46.38 2.52
3478 5862 8.632679 AGAATAGACAATTTTGAACTGCAAAGA 58.367 29.630 0.00 0.00 46.38 2.52
3479 5863 8.807667 AGAATAGACAATTTTGAACTGCAAAG 57.192 30.769 0.00 0.00 46.38 2.77
3480 5864 9.248291 GAAGAATAGACAATTTTGAACTGCAAA 57.752 29.630 0.00 0.00 44.38 3.68
3481 5865 8.412456 TGAAGAATAGACAATTTTGAACTGCAA 58.588 29.630 0.00 0.00 33.88 4.08
3482 5866 7.939782 TGAAGAATAGACAATTTTGAACTGCA 58.060 30.769 0.00 0.00 0.00 4.41
3483 5867 8.694394 GTTGAAGAATAGACAATTTTGAACTGC 58.306 33.333 0.00 0.00 0.00 4.40
3484 5868 9.185192 GGTTGAAGAATAGACAATTTTGAACTG 57.815 33.333 0.00 0.00 0.00 3.16
3485 5869 8.076178 CGGTTGAAGAATAGACAATTTTGAACT 58.924 33.333 0.00 0.00 0.00 3.01
3486 5870 8.073768 TCGGTTGAAGAATAGACAATTTTGAAC 58.926 33.333 0.00 0.00 0.00 3.18
3487 5871 8.160521 TCGGTTGAAGAATAGACAATTTTGAA 57.839 30.769 0.00 0.00 0.00 2.69
3488 5872 7.737972 TCGGTTGAAGAATAGACAATTTTGA 57.262 32.000 0.00 0.00 0.00 2.69
3489 5873 8.970691 AATCGGTTGAAGAATAGACAATTTTG 57.029 30.769 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.