Multiple sequence alignment - TraesCS5D01G452100

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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 TraesCS5D01G452100 chr5D 100.000 4056 0 0 1 4056 500128073 500132128 0.000000e+00 7491.0
1 TraesCS5D01G452100 chr5D 89.404 604 49 7 5 605 296364406 296364997 0.000000e+00 747.0
2 TraesCS5D01G452100 chr5A 96.898 1902 45 5 1077 2975 624677838 624679728 0.000000e+00 3173.0
3 TraesCS5D01G452100 chr5A 92.918 819 52 4 3239 4056 624710433 624711246 0.000000e+00 1186.0
4 TraesCS5D01G452100 chr5A 82.712 671 50 15 2271 2935 624683615 624684225 1.660000e-148 536.0
5 TraesCS5D01G452100 chr5B 93.066 1399 68 15 2680 4056 621466923 621468314 0.000000e+00 2019.0
6 TraesCS5D01G452100 chr5B 94.780 1092 42 6 773 1855 621462977 621464062 0.000000e+00 1687.0
7 TraesCS5D01G452100 chr5B 97.262 767 11 3 1855 2611 621464156 621464922 0.000000e+00 1291.0
8 TraesCS5D01G452100 chr5B 95.126 595 18 7 7 600 621461916 621462500 0.000000e+00 928.0
9 TraesCS5D01G452100 chr5B 94.385 374 7 3 2608 2980 621465044 621465404 2.740000e-156 562.0
10 TraesCS5D01G452100 chr5B 80.428 327 46 13 1417 1727 622619239 622618915 2.440000e-57 233.0
11 TraesCS5D01G452100 chr5B 75.172 290 37 19 1029 1285 622619693 622619406 1.990000e-18 104.0
12 TraesCS5D01G452100 chr5B 94.000 50 3 0 741 790 621462912 621462961 4.350000e-10 76.8
13 TraesCS5D01G452100 chr3A 84.600 487 75 0 3570 4056 738244347 738244833 6.100000e-133 484.0
14 TraesCS5D01G452100 chr3A 83.890 509 78 4 3547 4053 738236658 738237164 2.190000e-132 483.0
15 TraesCS5D01G452100 chr3A 84.232 482 76 0 3569 4050 738690687 738691168 1.710000e-128 470.0
16 TraesCS5D01G452100 chr3A 77.293 229 38 11 344 567 90076619 90076838 5.510000e-24 122.0
17 TraesCS5D01G452100 chr3A 75.217 230 42 10 344 567 90114314 90114534 1.200000e-15 95.3
18 TraesCS5D01G452100 chr3A 88.710 62 4 3 254 314 89981137 89981196 5.620000e-09 73.1
19 TraesCS5D01G452100 chr3D 84.536 485 72 3 3570 4053 605632892 605632410 1.020000e-130 477.0
20 TraesCS5D01G452100 chr3D 84.330 485 76 0 3572 4056 606003382 606002898 3.670000e-130 475.0
21 TraesCS5D01G452100 chr3D 82.669 502 87 0 3549 4050 606772219 606772720 2.880000e-121 446.0
22 TraesCS5D01G452100 chr3D 77.500 280 42 19 257 524 462836656 462836926 9.080000e-32 148.0
23 TraesCS5D01G452100 chr3D 95.556 90 4 0 605 694 248538491 248538580 1.170000e-30 145.0
24 TraesCS5D01G452100 chr3D 76.211 227 41 9 344 567 75643271 75643487 1.540000e-19 108.0
25 TraesCS5D01G452100 chr3D 76.364 220 41 11 390 605 575628384 575628172 1.540000e-19 108.0
26 TraesCS5D01G452100 chr3D 75.983 229 41 13 343 567 75636029 75636247 5.540000e-19 106.0
27 TraesCS5D01G452100 chr3B 82.178 505 90 0 3546 4050 816170890 816171394 6.230000e-118 435.0
28 TraesCS5D01G452100 chr3B 79.295 227 35 11 350 568 615545967 615546189 9.080000e-32 148.0
29 TraesCS5D01G452100 chr3B 87.156 109 9 3 613 716 71400457 71400349 7.120000e-23 119.0
30 TraesCS5D01G452100 chr3B 74.771 218 41 10 353 567 122012681 122012887 7.220000e-13 86.1
31 TraesCS5D01G452100 chr1A 95.604 91 4 0 603 693 586344422 586344512 3.270000e-31 147.0
32 TraesCS5D01G452100 chr1A 79.646 113 18 4 341 449 61000308 61000419 4.350000e-10 76.8
33 TraesCS5D01G452100 chr1D 95.506 89 4 0 605 693 392952245 392952157 4.230000e-30 143.0
34 TraesCS5D01G452100 chr1D 87.069 116 12 3 263 377 276251020 276251133 1.180000e-25 128.0
35 TraesCS5D01G452100 chr7D 94.505 91 4 1 606 695 156525234 156525324 5.470000e-29 139.0
36 TraesCS5D01G452100 chr7D 90.000 90 9 0 605 694 508316733 508316644 2.560000e-22 117.0
37 TraesCS5D01G452100 chr7D 76.016 246 42 14 319 559 34306803 34307036 1.190000e-20 111.0
38 TraesCS5D01G452100 chr4A 90.217 92 8 1 600 691 743181562 743181472 7.120000e-23 119.0
39 TraesCS5D01G452100 chr4A 90.217 92 8 1 600 691 743224707 743224617 7.120000e-23 119.0
40 TraesCS5D01G452100 chr4A 88.095 84 7 3 487 568 704766358 704766276 3.340000e-16 97.1
41 TraesCS5D01G452100 chr2D 76.800 250 35 16 344 588 636446323 636446554 7.120000e-23 119.0
42 TraesCS5D01G452100 chr2D 89.247 93 9 1 603 695 615026977 615026886 9.210000e-22 115.0
43 TraesCS5D01G452100 chr6B 91.176 68 5 1 487 553 204338618 204338685 1.550000e-14 91.6
44 TraesCS5D01G452100 chr6A 75.000 208 41 11 335 538 601363387 601363587 7.220000e-13 86.1
45 TraesCS5D01G452100 chr6A 94.545 55 2 1 487 540 516940897 516940951 2.600000e-12 84.2
46 TraesCS5D01G452100 chr2B 88.235 68 6 2 503 569 84985963 84985897 3.360000e-11 80.5
47 TraesCS5D01G452100 chr1B 81.481 81 12 3 297 377 375425282 375425359 3.380000e-06 63.9


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 TraesCS5D01G452100 chr5D 500128073 500132128 4055 False 7491.000000 7491 100.000000 1 4056 1 chr5D.!!$F2 4055
1 TraesCS5D01G452100 chr5D 296364406 296364997 591 False 747.000000 747 89.404000 5 605 1 chr5D.!!$F1 600
2 TraesCS5D01G452100 chr5A 624677838 624684225 6387 False 1854.500000 3173 89.805000 1077 2975 2 chr5A.!!$F2 1898
3 TraesCS5D01G452100 chr5A 624710433 624711246 813 False 1186.000000 1186 92.918000 3239 4056 1 chr5A.!!$F1 817
4 TraesCS5D01G452100 chr5B 621461916 621468314 6398 False 1093.966667 2019 94.769833 7 4056 6 chr5B.!!$F1 4049
5 TraesCS5D01G452100 chr3A 738236658 738237164 506 False 483.000000 483 83.890000 3547 4053 1 chr3A.!!$F4 506
6 TraesCS5D01G452100 chr3D 606772219 606772720 501 False 446.000000 446 82.669000 3549 4050 1 chr3D.!!$F5 501
7 TraesCS5D01G452100 chr3B 816170890 816171394 504 False 435.000000 435 82.178000 3546 4050 1 chr3B.!!$F3 504

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
828 1201 0.744771 GCTACAGTGTTAGGCTGGCC 60.745 60.0 0.0 3.0 38.22 5.36 F
1736 2120 0.178953 AACCTCCTGCCTGCAAACAT 60.179 50.0 0.0 0.0 0.00 2.71 F
1737 2121 0.178953 ACCTCCTGCCTGCAAACATT 60.179 50.0 0.0 0.0 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2811 3424 0.894835 TCGTCACAGCCTAGATTGCA 59.105 50.000 0.0 0.0 0.00 4.08 R
2884 3497 0.888285 AGCACCAAGAGCTTCAGTGC 60.888 55.000 19.6 19.6 44.17 4.40 R
3622 8803 2.694628 CAGATCCAGGGAGTGAAGAGAG 59.305 54.545 0.0 0.0 0.00 3.20 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
71 72 7.532682 TGTTTGTACCTTTGAAGAAAAATGC 57.467 32.000 0.00 0.00 0.00 3.56
103 104 8.060020 CATTACAAAATGTTCACGTGTTTCAT 57.940 30.769 16.51 14.70 38.15 2.57
161 163 8.759641 TGCAATGTAAACAAATGTTCATGTAAC 58.240 29.630 0.00 0.00 37.25 2.50
600 603 9.943163 TTTTGGTGAAAAAGAAAACAAAAGAAG 57.057 25.926 0.00 0.00 32.72 2.85
617 620 7.767659 ACAAAAGAAGAAAACTACTAACTCCGT 59.232 33.333 0.00 0.00 0.00 4.69
618 621 7.943413 AAAGAAGAAAACTACTAACTCCGTC 57.057 36.000 0.00 0.00 0.00 4.79
619 622 6.023357 AGAAGAAAACTACTAACTCCGTCC 57.977 41.667 0.00 0.00 0.00 4.79
620 623 4.797800 AGAAAACTACTAACTCCGTCCC 57.202 45.455 0.00 0.00 0.00 4.46
621 624 4.154942 AGAAAACTACTAACTCCGTCCCA 58.845 43.478 0.00 0.00 0.00 4.37
622 625 4.776308 AGAAAACTACTAACTCCGTCCCAT 59.224 41.667 0.00 0.00 0.00 4.00
623 626 5.954150 AGAAAACTACTAACTCCGTCCCATA 59.046 40.000 0.00 0.00 0.00 2.74
624 627 6.438425 AGAAAACTACTAACTCCGTCCCATAA 59.562 38.462 0.00 0.00 0.00 1.90
625 628 6.803366 AAACTACTAACTCCGTCCCATAAT 57.197 37.500 0.00 0.00 0.00 1.28
626 629 7.902920 AAACTACTAACTCCGTCCCATAATA 57.097 36.000 0.00 0.00 0.00 0.98
627 630 8.488308 AAACTACTAACTCCGTCCCATAATAT 57.512 34.615 0.00 0.00 0.00 1.28
628 631 9.592196 AAACTACTAACTCCGTCCCATAATATA 57.408 33.333 0.00 0.00 0.00 0.86
629 632 9.592196 AACTACTAACTCCGTCCCATAATATAA 57.408 33.333 0.00 0.00 0.00 0.98
630 633 9.240734 ACTACTAACTCCGTCCCATAATATAAG 57.759 37.037 0.00 0.00 0.00 1.73
631 634 9.458727 CTACTAACTCCGTCCCATAATATAAGA 57.541 37.037 0.00 0.00 0.00 2.10
632 635 8.716674 ACTAACTCCGTCCCATAATATAAGAA 57.283 34.615 0.00 0.00 0.00 2.52
633 636 8.583296 ACTAACTCCGTCCCATAATATAAGAAC 58.417 37.037 0.00 0.00 0.00 3.01
634 637 6.022163 ACTCCGTCCCATAATATAAGAACG 57.978 41.667 0.00 0.00 0.00 3.95
635 638 5.537674 ACTCCGTCCCATAATATAAGAACGT 59.462 40.000 0.00 0.00 0.00 3.99
636 639 6.041296 ACTCCGTCCCATAATATAAGAACGTT 59.959 38.462 0.00 0.00 0.00 3.99
637 640 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
638 641 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
639 642 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
685 688 9.512588 AAATGTTCTTATATTATGGAGCAGAGG 57.487 33.333 0.00 0.00 0.00 3.69
686 689 7.009179 TGTTCTTATATTATGGAGCAGAGGG 57.991 40.000 0.00 0.00 0.00 4.30
687 690 6.787458 TGTTCTTATATTATGGAGCAGAGGGA 59.213 38.462 0.00 0.00 0.00 4.20
688 691 7.038729 TGTTCTTATATTATGGAGCAGAGGGAG 60.039 40.741 0.00 0.00 0.00 4.30
727 730 6.663523 AGAAGGAAACAAAGAAAACCAGAGAA 59.336 34.615 0.00 0.00 0.00 2.87
728 731 6.850752 AGGAAACAAAGAAAACCAGAGAAA 57.149 33.333 0.00 0.00 0.00 2.52
729 732 7.239763 AGGAAACAAAGAAAACCAGAGAAAA 57.760 32.000 0.00 0.00 0.00 2.29
730 733 7.097192 AGGAAACAAAGAAAACCAGAGAAAAC 58.903 34.615 0.00 0.00 0.00 2.43
731 734 6.871492 GGAAACAAAGAAAACCAGAGAAAACA 59.129 34.615 0.00 0.00 0.00 2.83
732 735 7.386573 GGAAACAAAGAAAACCAGAGAAAACAA 59.613 33.333 0.00 0.00 0.00 2.83
733 736 8.669946 AAACAAAGAAAACCAGAGAAAACAAA 57.330 26.923 0.00 0.00 0.00 2.83
734 737 7.889589 ACAAAGAAAACCAGAGAAAACAAAG 57.110 32.000 0.00 0.00 0.00 2.77
735 738 7.666623 ACAAAGAAAACCAGAGAAAACAAAGA 58.333 30.769 0.00 0.00 0.00 2.52
736 739 8.147704 ACAAAGAAAACCAGAGAAAACAAAGAA 58.852 29.630 0.00 0.00 0.00 2.52
737 740 8.987890 CAAAGAAAACCAGAGAAAACAAAGAAA 58.012 29.630 0.00 0.00 0.00 2.52
738 741 9.554395 AAAGAAAACCAGAGAAAACAAAGAAAA 57.446 25.926 0.00 0.00 0.00 2.29
739 742 9.554395 AAGAAAACCAGAGAAAACAAAGAAAAA 57.446 25.926 0.00 0.00 0.00 1.94
828 1201 0.744771 GCTACAGTGTTAGGCTGGCC 60.745 60.000 0.00 3.00 38.22 5.36
872 1245 5.552178 AGAATATACGCATTTCCTTCCCTC 58.448 41.667 0.00 0.00 0.00 4.30
876 1249 2.593026 ACGCATTTCCTTCCCTCAAAA 58.407 42.857 0.00 0.00 0.00 2.44
994 1367 2.309528 TCGCTCCATTCCATGTGTAC 57.690 50.000 0.00 0.00 0.00 2.90
1003 1376 4.398044 CCATTCCATGTGTACAAACCCTAC 59.602 45.833 0.00 0.00 0.00 3.18
1105 1485 1.914634 CGAACTTCAGGATGGACGAG 58.085 55.000 0.00 0.00 36.16 4.18
1120 1500 0.383231 ACGAGGACGACGAGTTGTTT 59.617 50.000 0.00 0.00 42.66 2.83
1132 1512 2.129607 GAGTTGTTTCACCGCTACGAA 58.870 47.619 0.00 0.00 0.00 3.85
1342 1722 7.873505 TCATGATTTTGTGCTTTGATTCATTGA 59.126 29.630 0.00 0.00 0.00 2.57
1497 1877 6.600822 ACTTGGTTGTGATGGATAGATCAAAG 59.399 38.462 0.00 0.00 34.11 2.77
1564 1944 4.489771 GGTCCGGACATGCCCCTG 62.490 72.222 34.40 0.00 0.00 4.45
1634 2014 3.257393 GTTGATGACTCTGCCTGTACTG 58.743 50.000 0.00 0.00 0.00 2.74
1635 2015 2.807676 TGATGACTCTGCCTGTACTGA 58.192 47.619 0.60 0.00 0.00 3.41
1732 2116 1.228552 GGAAACCTCCTGCCTGCAA 60.229 57.895 0.00 0.00 38.88 4.08
1733 2117 0.827507 GGAAACCTCCTGCCTGCAAA 60.828 55.000 0.00 0.00 38.88 3.68
1734 2118 0.315251 GAAACCTCCTGCCTGCAAAC 59.685 55.000 0.00 0.00 0.00 2.93
1735 2119 0.396974 AAACCTCCTGCCTGCAAACA 60.397 50.000 0.00 0.00 0.00 2.83
1736 2120 0.178953 AACCTCCTGCCTGCAAACAT 60.179 50.000 0.00 0.00 0.00 2.71
1737 2121 0.178953 ACCTCCTGCCTGCAAACATT 60.179 50.000 0.00 0.00 0.00 2.71
2060 2542 4.379339 AGTGCGTAAATGTTGTTTGGTT 57.621 36.364 0.00 0.00 0.00 3.67
2811 3424 3.944055 AGCTGTTACGTGAGAATCTGT 57.056 42.857 0.00 0.00 34.92 3.41
2895 3508 1.423056 GACATGCGCACTGAAGCTC 59.577 57.895 14.90 2.53 0.00 4.09
3021 8183 5.183904 GTCAAAAAGGTCTTACTGGATGCAT 59.816 40.000 0.00 0.00 0.00 3.96
3073 8235 9.846248 ATAGAGAAAATACAACTTGTGAAATGC 57.154 29.630 4.57 0.00 0.00 3.56
3103 8277 4.377738 CGATATTTGTCCCTGAATGCATCG 60.378 45.833 0.00 0.00 0.00 3.84
3104 8278 1.462616 TTTGTCCCTGAATGCATCGG 58.537 50.000 0.00 0.78 0.00 4.18
3113 8287 3.382546 CCTGAATGCATCGGAATTTTCCT 59.617 43.478 0.00 0.00 45.33 3.36
3226 8406 9.816354 TTTCTGAAACTTTAGGGAAATCAAAAG 57.184 29.630 0.00 0.00 35.54 2.27
3260 8440 7.764141 ATAATGCATATGCCAGTAATTCACA 57.236 32.000 24.54 1.76 41.18 3.58
3273 8453 7.416664 GCCAGTAATTCACACCACATCATTAAT 60.417 37.037 0.00 0.00 0.00 1.40
3306 8486 5.880332 ACATATAACAAGCACGATTCCAACT 59.120 36.000 0.00 0.00 0.00 3.16
3443 8624 9.787532 AACAAATTATCCATCATTACAAACTCG 57.212 29.630 0.00 0.00 0.00 4.18
3445 8626 9.438291 CAAATTATCCATCATTACAAACTCGAC 57.562 33.333 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 7.327214 TCTTCAAAGGTACAAACATGCTTTTT 58.673 30.769 0.00 0.00 0.00 1.94
592 595 8.139521 ACGGAGTTAGTAGTTTTCTTCTTTTG 57.860 34.615 0.00 0.00 37.78 2.44
612 615 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
613 616 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
614 617 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
659 662 9.512588 CCTCTGCTCCATAATATAAGAACATTT 57.487 33.333 0.00 0.00 0.00 2.32
660 663 8.105829 CCCTCTGCTCCATAATATAAGAACATT 58.894 37.037 0.00 0.00 0.00 2.71
661 664 7.459125 TCCCTCTGCTCCATAATATAAGAACAT 59.541 37.037 0.00 0.00 0.00 2.71
662 665 6.787458 TCCCTCTGCTCCATAATATAAGAACA 59.213 38.462 0.00 0.00 0.00 3.18
663 666 7.038658 ACTCCCTCTGCTCCATAATATAAGAAC 60.039 40.741 0.00 0.00 0.00 3.01
664 667 7.019388 ACTCCCTCTGCTCCATAATATAAGAA 58.981 38.462 0.00 0.00 0.00 2.52
665 668 6.565974 ACTCCCTCTGCTCCATAATATAAGA 58.434 40.000 0.00 0.00 0.00 2.10
666 669 6.865834 ACTCCCTCTGCTCCATAATATAAG 57.134 41.667 0.00 0.00 0.00 1.73
667 670 7.479579 ACTACTCCCTCTGCTCCATAATATAA 58.520 38.462 0.00 0.00 0.00 0.98
668 671 7.045693 ACTACTCCCTCTGCTCCATAATATA 57.954 40.000 0.00 0.00 0.00 0.86
669 672 5.909760 ACTACTCCCTCTGCTCCATAATAT 58.090 41.667 0.00 0.00 0.00 1.28
670 673 5.340891 ACTACTCCCTCTGCTCCATAATA 57.659 43.478 0.00 0.00 0.00 0.98
671 674 4.206244 ACTACTCCCTCTGCTCCATAAT 57.794 45.455 0.00 0.00 0.00 1.28
672 675 3.689872 ACTACTCCCTCTGCTCCATAA 57.310 47.619 0.00 0.00 0.00 1.90
673 676 3.689872 AACTACTCCCTCTGCTCCATA 57.310 47.619 0.00 0.00 0.00 2.74
674 677 2.559381 AACTACTCCCTCTGCTCCAT 57.441 50.000 0.00 0.00 0.00 3.41
675 678 3.468071 TTAACTACTCCCTCTGCTCCA 57.532 47.619 0.00 0.00 0.00 3.86
676 679 4.505808 GTTTTAACTACTCCCTCTGCTCC 58.494 47.826 0.00 0.00 0.00 4.70
677 680 4.020485 TGGTTTTAACTACTCCCTCTGCTC 60.020 45.833 0.00 0.00 0.00 4.26
678 681 3.908103 TGGTTTTAACTACTCCCTCTGCT 59.092 43.478 0.00 0.00 0.00 4.24
679 682 4.281898 TGGTTTTAACTACTCCCTCTGC 57.718 45.455 0.00 0.00 0.00 4.26
680 683 6.531021 TCTTTGGTTTTAACTACTCCCTCTG 58.469 40.000 0.00 0.00 0.00 3.35
681 684 6.758806 TCTTTGGTTTTAACTACTCCCTCT 57.241 37.500 0.00 0.00 0.00 3.69
682 685 6.430308 CCTTCTTTGGTTTTAACTACTCCCTC 59.570 42.308 0.00 0.00 0.00 4.30
683 686 6.102174 TCCTTCTTTGGTTTTAACTACTCCCT 59.898 38.462 0.00 0.00 0.00 4.20
684 687 6.301486 TCCTTCTTTGGTTTTAACTACTCCC 58.699 40.000 0.00 0.00 0.00 4.30
685 688 7.812690 TTCCTTCTTTGGTTTTAACTACTCC 57.187 36.000 0.00 0.00 0.00 3.85
686 689 8.680001 TGTTTCCTTCTTTGGTTTTAACTACTC 58.320 33.333 0.00 0.00 0.00 2.59
687 690 8.584063 TGTTTCCTTCTTTGGTTTTAACTACT 57.416 30.769 0.00 0.00 0.00 2.57
688 691 9.642327 TTTGTTTCCTTCTTTGGTTTTAACTAC 57.358 29.630 0.00 0.00 0.00 2.73
758 1098 3.674997 TCACCTTTGTAGCATCAGTTCC 58.325 45.455 0.00 0.00 0.00 3.62
759 1099 5.886960 ATTCACCTTTGTAGCATCAGTTC 57.113 39.130 0.00 0.00 0.00 3.01
812 1185 1.715019 TTGGGCCAGCCTAACACTGT 61.715 55.000 6.23 0.00 31.46 3.55
828 1201 6.097915 TCTTATTAGGAACCGCTCTATTGG 57.902 41.667 0.00 0.00 0.00 3.16
943 1316 9.146586 TCCCATCTATATTTTGAATTTCCCAAG 57.853 33.333 0.00 0.00 0.00 3.61
994 1367 2.623239 GGGAGGGGATTTGTAGGGTTTG 60.623 54.545 0.00 0.00 0.00 2.93
1003 1376 0.033109 GGAAGGTGGGAGGGGATTTG 60.033 60.000 0.00 0.00 0.00 2.32
1105 1485 0.857287 GGTGAAACAACTCGTCGTCC 59.143 55.000 0.00 0.00 39.98 4.79
1120 1500 1.592400 CCTCAGGTTCGTAGCGGTGA 61.592 60.000 0.00 0.00 0.00 4.02
1342 1722 5.126061 GGCCATGATCAACAACAACTCTATT 59.874 40.000 0.00 0.00 0.00 1.73
1360 1740 0.982704 TGGGGAACAAATTGGCCATG 59.017 50.000 6.09 4.35 0.00 3.66
1497 1877 1.152368 CATCCCCATGCCTTCTCCC 59.848 63.158 0.00 0.00 0.00 4.30
1732 2116 5.144100 TGGGTCAAACATCTACCAAATGTT 58.856 37.500 0.00 0.00 46.53 2.71
1733 2117 4.735369 TGGGTCAAACATCTACCAAATGT 58.265 39.130 0.00 0.00 38.98 2.71
1734 2118 5.185635 ACATGGGTCAAACATCTACCAAATG 59.814 40.000 0.00 0.00 36.07 2.32
1735 2119 5.332743 ACATGGGTCAAACATCTACCAAAT 58.667 37.500 0.00 0.00 34.83 2.32
1736 2120 4.735369 ACATGGGTCAAACATCTACCAAA 58.265 39.130 0.00 0.00 34.83 3.28
1737 2121 4.380843 ACATGGGTCAAACATCTACCAA 57.619 40.909 0.00 0.00 34.83 3.67
2789 3402 4.449068 CACAGATTCTCACGTAACAGCTTT 59.551 41.667 0.00 0.00 0.00 3.51
2811 3424 0.894835 TCGTCACAGCCTAGATTGCA 59.105 50.000 0.00 0.00 0.00 4.08
2884 3497 0.888285 AGCACCAAGAGCTTCAGTGC 60.888 55.000 19.60 19.60 44.17 4.40
2895 3508 3.420893 TGTTCTTCCCATTAGCACCAAG 58.579 45.455 0.00 0.00 0.00 3.61
2941 3554 7.232534 ACCTAGTAGATTTCTCTGCTCCATTAG 59.767 40.741 0.00 0.00 42.66 1.73
2942 3555 7.069986 ACCTAGTAGATTTCTCTGCTCCATTA 58.930 38.462 0.00 0.00 42.66 1.90
2943 3556 5.902431 ACCTAGTAGATTTCTCTGCTCCATT 59.098 40.000 0.00 0.00 42.66 3.16
3021 8183 2.992543 GTTCAAACAAGCAACTGCAACA 59.007 40.909 4.22 0.00 45.16 3.33
3030 8192 5.060506 TCTCTATTTCCGTTCAAACAAGCA 58.939 37.500 0.00 0.00 0.00 3.91
3031 8193 5.607119 TCTCTATTTCCGTTCAAACAAGC 57.393 39.130 0.00 0.00 0.00 4.01
3070 8232 4.220821 AGGGACAAATATCGATACGAGCAT 59.779 41.667 7.41 0.00 39.91 3.79
3071 8233 3.572682 AGGGACAAATATCGATACGAGCA 59.427 43.478 7.41 0.00 39.91 4.26
3072 8234 3.921021 CAGGGACAAATATCGATACGAGC 59.079 47.826 7.41 0.00 39.91 5.03
3073 8235 5.372547 TCAGGGACAAATATCGATACGAG 57.627 43.478 7.41 2.92 39.91 4.18
3158 8332 9.312904 TGGGAAATTTCAATAGAGAAGAAATGT 57.687 29.630 19.49 0.00 40.11 2.71
3206 8386 9.778741 GATTTCCTTTTGATTTCCCTAAAGTTT 57.221 29.630 0.00 0.00 30.56 2.66
3226 8406 8.472413 ACTGGCATATGCATTATAATGATTTCC 58.528 33.333 28.07 17.61 44.36 3.13
3273 8453 9.758651 ATCGTGCTTGTTATATGTAAACTGATA 57.241 29.630 0.00 0.00 0.00 2.15
3306 8486 6.238897 GGCACCATGATTATATCCGTTTTTCA 60.239 38.462 0.00 0.00 0.00 2.69
3443 8624 4.101942 CGCTTAGATGAGTCTGTTCTGTC 58.898 47.826 0.00 0.00 35.87 3.51
3445 8626 3.856521 CACGCTTAGATGAGTCTGTTCTG 59.143 47.826 0.00 0.00 35.87 3.02
3622 8803 2.694628 CAGATCCAGGGAGTGAAGAGAG 59.305 54.545 0.00 0.00 0.00 3.20
3797 9030 3.786368 TCACAGACATTGTCAATCCCA 57.214 42.857 18.57 0.00 38.16 4.37


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

AutoCloner maintained by Alex Coulton.