Multiple sequence alignment - TraesCS1B01G442400

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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 TraesCS1B01G442400 chr1B 100.000 3348 0 0 1 3348 662943311 662939964 0.000000e+00 6183.0
1 TraesCS1B01G442400 chr1B 88.219 1426 133 23 996 2402 664016623 664018032 0.000000e+00 1670.0
2 TraesCS1B01G442400 chr1B 79.070 344 38 13 2060 2402 664082921 664083231 4.380000e-49 206.0
3 TraesCS1B01G442400 chr1B 87.395 119 15 0 1717 1835 659956226 659956108 1.620000e-28 137.0
4 TraesCS1B01G442400 chr1D 92.769 2019 90 22 1357 3348 476592636 476590647 0.000000e+00 2868.0
5 TraesCS1B01G442400 chr1D 88.171 1378 132 21 996 2363 476763569 476764925 0.000000e+00 1613.0
6 TraesCS1B01G442400 chr1D 94.627 335 15 2 961 1292 476592969 476592635 1.780000e-142 516.0
7 TraesCS1B01G442400 chr1D 84.756 492 56 11 33 512 476594047 476593563 3.020000e-130 475.0
8 TraesCS1B01G442400 chr1D 87.500 208 12 7 629 836 476593155 476592962 9.340000e-56 228.0
9 TraesCS1B01G442400 chr1D 88.235 119 14 0 1717 1835 476759008 476758890 3.480000e-30 143.0
10 TraesCS1B01G442400 chr1A 89.316 1900 140 32 770 2638 572361330 572359463 0.000000e+00 2326.0
11 TraesCS1B01G442400 chr1A 87.392 1388 135 25 997 2363 572676237 572677605 0.000000e+00 1557.0
12 TraesCS1B01G442400 chr1A 92.318 729 41 11 2622 3348 572356486 572355771 0.000000e+00 1022.0
13 TraesCS1B01G442400 chr1A 85.986 578 56 16 3 570 572383658 572383096 2.220000e-166 595.0
14 TraesCS1B01G442400 chr1A 84.062 320 31 11 630 946 572383097 572382795 1.180000e-74 291.0
15 TraesCS1B01G442400 chr1A 91.209 182 12 4 38 216 572382330 572382150 9.280000e-61 244.0
16 TraesCS1B01G442400 chr1A 87.578 161 15 5 285 444 572382039 572381883 7.380000e-42 182.0
17 TraesCS1B01G442400 chr1A 89.286 140 12 3 924 1060 572387558 572387419 4.440000e-39 172.0
18 TraesCS1B01G442400 chr1A 95.161 62 3 0 2898 2959 572356578 572356517 7.640000e-17 99.0
19 TraesCS1B01G442400 chr1A 100.000 29 0 0 259 287 546797193 546797221 2.000000e-03 54.7
20 TraesCS1B01G442400 chr5A 89.816 1031 70 18 629 1628 674545657 674544631 0.000000e+00 1290.0
21 TraesCS1B01G442400 chr5A 91.712 929 62 6 1707 2622 674544519 674543593 0.000000e+00 1275.0
22 TraesCS1B01G442400 chr5A 84.074 270 38 4 37 306 674546345 674546081 4.290000e-64 255.0
23 TraesCS1B01G442400 chr5A 95.312 64 2 1 568 630 224157524 224157461 2.130000e-17 100.0
24 TraesCS1B01G442400 chr5A 93.750 64 3 1 567 630 405312040 405312102 9.890000e-16 95.3
25 TraesCS1B01G442400 chr5A 97.674 43 0 1 567 608 555062867 555062909 4.630000e-09 73.1
26 TraesCS1B01G442400 chr4B 87.200 125 16 0 1711 1835 238161266 238161390 3.480000e-30 143.0
27 TraesCS1B01G442400 chr7A 95.385 65 2 1 568 631 453847474 453847538 5.910000e-18 102.0
28 TraesCS1B01G442400 chr7A 97.368 38 1 0 249 286 76508918 76508955 7.750000e-07 65.8
29 TraesCS1B01G442400 chr4D 93.750 64 2 1 568 631 89230021 89229960 9.890000e-16 95.3
30 TraesCS1B01G442400 chr4D 94.595 37 2 0 250 286 5828741 5828777 1.300000e-04 58.4
31 TraesCS1B01G442400 chr2B 92.308 65 4 1 568 631 642090615 642090679 1.280000e-14 91.6
32 TraesCS1B01G442400 chr2B 87.692 65 3 5 568 631 535698633 535698693 1.670000e-08 71.3
33 TraesCS1B01G442400 chr2B 100.000 28 0 0 12 39 644165939 644165912 6.000000e-03 52.8
34 TraesCS1B01G442400 chr4A 80.189 106 18 3 205 308 547890086 547889982 3.580000e-10 76.8
35 TraesCS1B01G442400 chr3B 100.000 41 0 0 568 608 760612097 760612137 3.580000e-10 76.8
36 TraesCS1B01G442400 chr7B 100.000 40 0 0 566 605 17215830 17215869 1.290000e-09 75.0
37 TraesCS1B01G442400 chr2A 82.667 75 13 0 1966 2040 69236201 69236127 2.160000e-07 67.6
38 TraesCS1B01G442400 chr5D 94.737 38 2 0 249 286 490928781 490928744 3.610000e-05 60.2
39 TraesCS1B01G442400 chr3A 100.000 29 0 0 258 286 696474277 696474249 2.000000e-03 54.7
40 TraesCS1B01G442400 chr5B 100.000 28 0 0 2604 2631 693199419 693199392 6.000000e-03 52.8


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 TraesCS1B01G442400 chr1B 662939964 662943311 3347 True 6183.00 6183 100.0000 1 3348 1 chr1B.!!$R2 3347
1 TraesCS1B01G442400 chr1B 664016623 664018032 1409 False 1670.00 1670 88.2190 996 2402 1 chr1B.!!$F1 1406
2 TraesCS1B01G442400 chr1D 476763569 476764925 1356 False 1613.00 1613 88.1710 996 2363 1 chr1D.!!$F1 1367
3 TraesCS1B01G442400 chr1D 476590647 476594047 3400 True 1021.75 2868 89.9130 33 3348 4 chr1D.!!$R2 3315
4 TraesCS1B01G442400 chr1A 572676237 572677605 1368 False 1557.00 1557 87.3920 997 2363 1 chr1A.!!$F2 1366
5 TraesCS1B01G442400 chr1A 572355771 572361330 5559 True 1149.00 2326 92.2650 770 3348 3 chr1A.!!$R1 2578
6 TraesCS1B01G442400 chr1A 572381883 572387558 5675 True 296.80 595 87.6242 3 1060 5 chr1A.!!$R2 1057
7 TraesCS1B01G442400 chr5A 674543593 674546345 2752 True 940.00 1290 88.5340 37 2622 3 chr5A.!!$R2 2585

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
794 5128 0.244450 CATGCAGTTGCCCACGAATT 59.756 50.0 1.06 0.0 41.18 2.17 F
1705 6279 0.172352 GGCTCTTCTCTCTGTCCGTG 59.828 60.0 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 6758 1.453015 ACTTGTTCACCAGCGCCAA 60.453 52.632 2.29 0.0 0.0 4.52 R
3171 10838 1.339631 ACCCCATGTGGTGTTCGTATG 60.340 52.381 0.00 0.0 37.2 2.39 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
42 3941 3.010420 GACTTAGCCACACCCTTTGATC 58.990 50.000 0.00 0.00 0.00 2.92
223 4124 6.982141 TCCTAAATTTTTCGATAAGAGCGCTA 59.018 34.615 11.50 0.00 0.00 4.26
240 4141 8.590719 AGAGCGCTATATTACTTAAAAAGTCC 57.409 34.615 11.50 0.00 41.77 3.85
243 4144 9.338622 AGCGCTATATTACTTAAAAAGTCCAAT 57.661 29.630 8.99 0.00 41.77 3.16
256 4157 4.503714 AAGTCCAATCATTACATCCGGT 57.496 40.909 0.00 0.00 0.00 5.28
322 4223 9.273016 CTCTCAAAACAGTACATAAGAAAAGGA 57.727 33.333 0.00 0.00 0.00 3.36
444 4357 5.413969 TTGCAGAGCTCGATTTCATTATG 57.586 39.130 8.37 0.00 0.00 1.90
451 4364 3.987868 GCTCGATTTCATTATGTCGGCTA 59.012 43.478 4.35 0.00 35.01 3.93
464 4377 4.492791 TGTCGGCTAAACTTTTAAAGCC 57.507 40.909 4.42 3.87 38.91 4.35
474 4387 7.009265 GCTAAACTTTTAAAGCCCGATTTCATC 59.991 37.037 4.42 0.00 0.00 2.92
481 4394 9.712305 TTTTAAAGCCCGATTTCATCATTTTTA 57.288 25.926 0.00 0.00 0.00 1.52
535 4843 9.896645 AAGAAAGAGATTATACATGAGAAAGCA 57.103 29.630 0.00 0.00 0.00 3.91
539 4847 4.993584 AGATTATACATGAGAAAGCAGCCG 59.006 41.667 0.00 0.00 0.00 5.52
557 4865 1.538419 CCGAGCTTTCCTCCCGTAATC 60.538 57.143 0.00 0.00 37.27 1.75
567 4875 3.398292 TCCTCCCGTAATCTACATCTCCT 59.602 47.826 0.00 0.00 0.00 3.69
568 4876 4.600547 TCCTCCCGTAATCTACATCTCCTA 59.399 45.833 0.00 0.00 0.00 2.94
569 4877 4.701171 CCTCCCGTAATCTACATCTCCTAC 59.299 50.000 0.00 0.00 0.00 3.18
570 4878 5.515184 CCTCCCGTAATCTACATCTCCTACT 60.515 48.000 0.00 0.00 0.00 2.57
571 4879 5.558818 TCCCGTAATCTACATCTCCTACTC 58.441 45.833 0.00 0.00 0.00 2.59
572 4880 4.701171 CCCGTAATCTACATCTCCTACTCC 59.299 50.000 0.00 0.00 0.00 3.85
573 4881 4.701171 CCGTAATCTACATCTCCTACTCCC 59.299 50.000 0.00 0.00 0.00 4.30
574 4882 5.515184 CCGTAATCTACATCTCCTACTCCCT 60.515 48.000 0.00 0.00 0.00 4.20
575 4883 5.644636 CGTAATCTACATCTCCTACTCCCTC 59.355 48.000 0.00 0.00 0.00 4.30
576 4884 4.668138 ATCTACATCTCCTACTCCCTCC 57.332 50.000 0.00 0.00 0.00 4.30
577 4885 2.372504 TCTACATCTCCTACTCCCTCCG 59.627 54.545 0.00 0.00 0.00 4.63
578 4886 0.927767 ACATCTCCTACTCCCTCCGT 59.072 55.000 0.00 0.00 0.00 4.69
579 4887 1.288335 ACATCTCCTACTCCCTCCGTT 59.712 52.381 0.00 0.00 0.00 4.44
580 4888 1.957877 CATCTCCTACTCCCTCCGTTC 59.042 57.143 0.00 0.00 0.00 3.95
581 4889 0.258194 TCTCCTACTCCCTCCGTTCC 59.742 60.000 0.00 0.00 0.00 3.62
582 4890 1.077212 TCCTACTCCCTCCGTTCCG 60.077 63.158 0.00 0.00 0.00 4.30
583 4891 1.077212 CCTACTCCCTCCGTTCCGA 60.077 63.158 0.00 0.00 0.00 4.55
584 4892 0.682209 CCTACTCCCTCCGTTCCGAA 60.682 60.000 0.00 0.00 0.00 4.30
585 4893 1.180029 CTACTCCCTCCGTTCCGAAA 58.820 55.000 0.00 0.00 0.00 3.46
586 4894 1.755380 CTACTCCCTCCGTTCCGAAAT 59.245 52.381 0.00 0.00 0.00 2.17
587 4895 1.856629 ACTCCCTCCGTTCCGAAATA 58.143 50.000 0.00 0.00 0.00 1.40
588 4896 1.755380 ACTCCCTCCGTTCCGAAATAG 59.245 52.381 0.00 0.00 0.00 1.73
589 4897 2.029623 CTCCCTCCGTTCCGAAATAGA 58.970 52.381 0.00 0.00 0.00 1.98
590 4898 2.628657 CTCCCTCCGTTCCGAAATAGAT 59.371 50.000 0.00 0.00 0.00 1.98
591 4899 2.364324 TCCCTCCGTTCCGAAATAGATG 59.636 50.000 0.00 0.00 0.00 2.90
592 4900 2.364324 CCCTCCGTTCCGAAATAGATGA 59.636 50.000 0.00 0.00 0.00 2.92
593 4901 3.381949 CCTCCGTTCCGAAATAGATGAC 58.618 50.000 0.00 0.00 0.00 3.06
594 4902 3.068307 CCTCCGTTCCGAAATAGATGACT 59.932 47.826 0.00 0.00 0.00 3.41
595 4903 4.291783 CTCCGTTCCGAAATAGATGACTC 58.708 47.826 0.00 0.00 0.00 3.36
596 4904 3.697542 TCCGTTCCGAAATAGATGACTCA 59.302 43.478 0.00 0.00 0.00 3.41
597 4905 4.158949 TCCGTTCCGAAATAGATGACTCAA 59.841 41.667 0.00 0.00 0.00 3.02
598 4906 4.267928 CCGTTCCGAAATAGATGACTCAAC 59.732 45.833 0.00 0.00 0.00 3.18
599 4907 5.103000 CGTTCCGAAATAGATGACTCAACT 58.897 41.667 0.00 0.00 0.00 3.16
600 4908 5.577164 CGTTCCGAAATAGATGACTCAACTT 59.423 40.000 0.00 0.00 0.00 2.66
601 4909 6.090898 CGTTCCGAAATAGATGACTCAACTTT 59.909 38.462 0.00 0.00 0.00 2.66
602 4910 6.968131 TCCGAAATAGATGACTCAACTTTG 57.032 37.500 0.00 0.00 0.00 2.77
603 4911 6.464222 TCCGAAATAGATGACTCAACTTTGT 58.536 36.000 0.00 0.00 0.00 2.83
604 4912 7.608153 TCCGAAATAGATGACTCAACTTTGTA 58.392 34.615 0.00 0.00 0.00 2.41
605 4913 8.258007 TCCGAAATAGATGACTCAACTTTGTAT 58.742 33.333 0.00 0.00 0.00 2.29
606 4914 8.883731 CCGAAATAGATGACTCAACTTTGTATT 58.116 33.333 0.00 0.00 0.00 1.89
624 4932 9.769093 CTTTGTATTACTATTTTGAAACGGAGG 57.231 33.333 0.00 0.00 0.00 4.30
625 4933 7.852971 TGTATTACTATTTTGAAACGGAGGG 57.147 36.000 0.00 0.00 0.00 4.30
626 4934 7.622713 TGTATTACTATTTTGAAACGGAGGGA 58.377 34.615 0.00 0.00 0.00 4.20
627 4935 7.767198 TGTATTACTATTTTGAAACGGAGGGAG 59.233 37.037 0.00 0.00 0.00 4.30
641 4949 2.011222 GAGGGAGTACGTCTGAGACTG 58.989 57.143 11.26 6.94 0.00 3.51
768 5089 4.666253 CCACTGCCACCCCACTGG 62.666 72.222 0.00 0.00 41.37 4.00
786 5120 1.080298 GTTGGAGCATGCAGTTGCC 60.080 57.895 21.98 12.87 43.83 4.52
794 5128 0.244450 CATGCAGTTGCCCACGAATT 59.756 50.000 1.06 0.00 41.18 2.17
851 5189 1.234821 GTCACGCCATTTTCACCTCA 58.765 50.000 0.00 0.00 0.00 3.86
894 5232 2.863153 CGCAAGGTCAGGAAAGCG 59.137 61.111 0.00 0.00 39.17 4.68
920 5258 4.514569 CATTGCCGCCGCGTGTAC 62.515 66.667 12.58 0.00 38.08 2.90
921 5259 4.752879 ATTGCCGCCGCGTGTACT 62.753 61.111 12.58 0.00 38.08 2.73
922 5260 3.359515 ATTGCCGCCGCGTGTACTA 62.360 57.895 12.58 0.00 38.08 1.82
929 5267 1.253545 CGCCGCGTGTACTATAAACAC 59.746 52.381 4.92 7.62 43.04 3.32
939 5277 5.983720 GTGTACTATAAACACCGAGCATGAT 59.016 40.000 0.00 0.00 41.10 2.45
986 5324 7.130917 CAGTTCATAATTCTCATAGTGCAAGC 58.869 38.462 0.00 0.00 0.00 4.01
1290 5757 1.375523 CACCAGGTTCCTGTACGCC 60.376 63.158 16.33 0.00 32.56 5.68
1291 5758 1.839747 ACCAGGTTCCTGTACGCCA 60.840 57.895 16.33 0.00 32.56 5.69
1292 5759 1.375523 CCAGGTTCCTGTACGCCAC 60.376 63.158 16.33 0.00 32.56 5.01
1293 5760 1.736645 CAGGTTCCTGTACGCCACG 60.737 63.158 10.40 0.00 0.00 4.94
1294 5761 2.205152 AGGTTCCTGTACGCCACGT 61.205 57.895 0.00 0.00 44.35 4.49
1295 5762 1.735559 GGTTCCTGTACGCCACGTC 60.736 63.158 0.00 0.00 41.54 4.34
1296 5763 1.735559 GTTCCTGTACGCCACGTCC 60.736 63.158 0.00 0.00 41.54 4.79
1297 5764 1.904865 TTCCTGTACGCCACGTCCT 60.905 57.895 0.00 0.00 41.54 3.85
1298 5765 1.870055 TTCCTGTACGCCACGTCCTC 61.870 60.000 0.00 0.00 41.54 3.71
1299 5766 2.181021 CTGTACGCCACGTCCTCC 59.819 66.667 0.00 0.00 41.54 4.30
1300 5767 3.678717 CTGTACGCCACGTCCTCCG 62.679 68.421 0.00 0.00 41.54 4.63
1340 5807 4.373116 GTTCGTCAGGAGCCGCCA 62.373 66.667 0.00 0.00 40.02 5.69
1341 5808 4.373116 TTCGTCAGGAGCCGCCAC 62.373 66.667 0.00 0.00 40.02 5.01
1382 5915 1.520787 CCAACTGGATCGGGTACGC 60.521 63.158 0.00 0.00 37.43 4.42
1602 6135 2.200337 GGCCTCCACCCACAACAAC 61.200 63.158 0.00 0.00 0.00 3.32
1644 6177 2.521733 CTAAAATTGCGCGGCACCGT 62.522 55.000 8.83 0.00 38.71 4.83
1699 6246 1.184431 TCAGCTGGCTCTTCTCTCTG 58.816 55.000 15.13 0.00 0.00 3.35
1705 6279 0.172352 GGCTCTTCTCTCTGTCCGTG 59.828 60.000 0.00 0.00 0.00 4.94
2171 6758 2.607750 ATGTGGTGGAGCGGGACT 60.608 61.111 0.00 0.00 0.00 3.85
2190 6777 1.723608 TTGGCGCTGGTGAACAAGTG 61.724 55.000 7.64 0.00 0.00 3.16
2269 6856 2.276740 GGCATGGTGAAGGGGGAG 59.723 66.667 0.00 0.00 0.00 4.30
2350 6949 2.328099 GCCGGTGAGCAAGTGAAGG 61.328 63.158 1.90 0.00 0.00 3.46
2365 6964 0.103208 GAAGGCGACGTCTCCATCAT 59.897 55.000 25.55 9.33 35.80 2.45
2526 7142 5.242838 CCTTTTAATTGCGGGATTATAGCCA 59.757 40.000 0.00 0.00 0.00 4.75
2527 7143 6.239176 CCTTTTAATTGCGGGATTATAGCCAA 60.239 38.462 0.00 0.00 0.00 4.52
2596 7212 1.758862 AGCCTATTTGCATGAAAGCCC 59.241 47.619 0.00 0.00 0.00 5.19
2597 7213 1.758862 GCCTATTTGCATGAAAGCCCT 59.241 47.619 0.00 0.00 0.00 5.19
2599 7215 3.369787 GCCTATTTGCATGAAAGCCCTTT 60.370 43.478 0.00 0.00 35.14 3.11
2600 7216 4.835678 CCTATTTGCATGAAAGCCCTTTT 58.164 39.130 0.00 0.00 32.11 2.27
2601 7217 4.872124 CCTATTTGCATGAAAGCCCTTTTC 59.128 41.667 0.00 0.00 44.45 2.29
2602 7218 2.437200 TTGCATGAAAGCCCTTTTCG 57.563 45.000 0.00 0.00 46.65 3.46
2610 7232 4.906618 TGAAAGCCCTTTTCGAATACTCT 58.093 39.130 0.00 0.00 46.65 3.24
2661 10276 1.991813 TCAACCTGTCATGGGATGGAA 59.008 47.619 0.00 0.00 0.00 3.53
2711 10326 9.378597 CTCAATATCATGACAATTAAAGCTTCG 57.621 33.333 0.00 0.00 0.00 3.79
2848 10464 8.422973 TTTTGTGAGAAATCAAGTTTGGAATG 57.577 30.769 0.00 0.00 0.00 2.67
2977 10593 8.645814 TGGTCGTTATCCACATCTATATAACT 57.354 34.615 0.00 0.00 34.24 2.24
3011 10627 5.063438 GTGCATACGTATATTGCCGATCAAT 59.937 40.000 15.14 7.75 46.48 2.57
3012 10628 5.641636 TGCATACGTATATTGCCGATCAATT 59.358 36.000 15.14 1.40 42.48 2.32
3048 10664 2.084546 ACTTGCCTAAAATCGCCTGAC 58.915 47.619 0.00 0.00 0.00 3.51
3056 10672 5.177696 GCCTAAAATCGCCTGACATACTAAG 59.822 44.000 0.00 0.00 0.00 2.18
3122 10788 3.942539 TTCGGCGAATGAATACATGTG 57.057 42.857 19.83 0.00 36.79 3.21
3187 10854 4.432712 TCATCTCATACGAACACCACATG 58.567 43.478 0.00 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 9.947669 GCTAAGTCTTAGTCGACTGATAATTAA 57.052 33.333 28.12 11.16 43.14 1.40
3 4 8.566260 GGCTAAGTCTTAGTCGACTGATAATTA 58.434 37.037 28.12 18.98 43.14 1.40
4 5 7.068348 TGGCTAAGTCTTAGTCGACTGATAATT 59.932 37.037 28.12 18.88 43.14 1.40
12 3911 3.500014 GTGTGGCTAAGTCTTAGTCGAC 58.500 50.000 17.32 7.70 40.70 4.20
199 4099 6.049263 AGCGCTCTTATCGAAAAATTTAGG 57.951 37.500 2.64 0.00 0.00 2.69
236 4137 3.711704 AGACCGGATGTAATGATTGGACT 59.288 43.478 9.46 0.00 0.00 3.85
239 4140 4.060900 CAGAGACCGGATGTAATGATTGG 58.939 47.826 9.46 0.00 0.00 3.16
240 4141 3.496130 GCAGAGACCGGATGTAATGATTG 59.504 47.826 9.46 0.00 0.00 2.67
243 4144 2.107366 TGCAGAGACCGGATGTAATGA 58.893 47.619 9.46 0.00 0.00 2.57
279 4180 0.535335 GAGTGGACATCGGTTGGCTA 59.465 55.000 0.00 0.00 32.03 3.93
409 4316 0.835971 TCTGCAAGCTCACCTACCCA 60.836 55.000 0.00 0.00 0.00 4.51
441 4354 5.124297 GGGCTTTAAAAGTTTAGCCGACATA 59.876 40.000 17.68 0.00 42.82 2.29
444 4357 3.668757 CGGGCTTTAAAAGTTTAGCCGAC 60.669 47.826 17.68 7.58 42.82 4.79
510 4818 9.545105 CTGCTTTCTCATGTATAATCTCTTTCT 57.455 33.333 0.00 0.00 0.00 2.52
513 4821 6.709846 GGCTGCTTTCTCATGTATAATCTCTT 59.290 38.462 0.00 0.00 0.00 2.85
514 4822 6.229733 GGCTGCTTTCTCATGTATAATCTCT 58.770 40.000 0.00 0.00 0.00 3.10
515 4823 5.119898 CGGCTGCTTTCTCATGTATAATCTC 59.880 44.000 0.00 0.00 0.00 2.75
516 4824 4.993584 CGGCTGCTTTCTCATGTATAATCT 59.006 41.667 0.00 0.00 0.00 2.40
517 4825 4.991056 TCGGCTGCTTTCTCATGTATAATC 59.009 41.667 0.00 0.00 0.00 1.75
518 4826 4.960938 TCGGCTGCTTTCTCATGTATAAT 58.039 39.130 0.00 0.00 0.00 1.28
519 4827 4.371786 CTCGGCTGCTTTCTCATGTATAA 58.628 43.478 0.00 0.00 0.00 0.98
520 4828 3.800261 GCTCGGCTGCTTTCTCATGTATA 60.800 47.826 0.00 0.00 0.00 1.47
521 4829 2.831333 CTCGGCTGCTTTCTCATGTAT 58.169 47.619 0.00 0.00 0.00 2.29
535 4843 3.775654 CGGGAGGAAAGCTCGGCT 61.776 66.667 0.00 0.00 42.56 5.52
539 4847 3.383825 TGTAGATTACGGGAGGAAAGCTC 59.616 47.826 0.00 0.00 35.44 4.09
548 4856 5.514484 GGAGTAGGAGATGTAGATTACGGGA 60.514 48.000 0.00 0.00 0.00 5.14
557 4865 2.106857 ACGGAGGGAGTAGGAGATGTAG 59.893 54.545 0.00 0.00 0.00 2.74
577 4885 6.969828 AAGTTGAGTCATCTATTTCGGAAC 57.030 37.500 4.14 0.00 0.00 3.62
578 4886 6.934645 ACAAAGTTGAGTCATCTATTTCGGAA 59.065 34.615 4.14 0.00 0.00 4.30
579 4887 6.464222 ACAAAGTTGAGTCATCTATTTCGGA 58.536 36.000 4.14 0.00 0.00 4.55
580 4888 6.727824 ACAAAGTTGAGTCATCTATTTCGG 57.272 37.500 4.14 0.00 0.00 4.30
598 4906 9.769093 CCTCCGTTTCAAAATAGTAATACAAAG 57.231 33.333 0.00 0.00 0.00 2.77
599 4907 8.732531 CCCTCCGTTTCAAAATAGTAATACAAA 58.267 33.333 0.00 0.00 0.00 2.83
600 4908 8.102047 TCCCTCCGTTTCAAAATAGTAATACAA 58.898 33.333 0.00 0.00 0.00 2.41
601 4909 7.622713 TCCCTCCGTTTCAAAATAGTAATACA 58.377 34.615 0.00 0.00 0.00 2.29
602 4910 7.767659 ACTCCCTCCGTTTCAAAATAGTAATAC 59.232 37.037 0.00 0.00 0.00 1.89
603 4911 7.854337 ACTCCCTCCGTTTCAAAATAGTAATA 58.146 34.615 0.00 0.00 0.00 0.98
604 4912 6.718294 ACTCCCTCCGTTTCAAAATAGTAAT 58.282 36.000 0.00 0.00 0.00 1.89
605 4913 6.117975 ACTCCCTCCGTTTCAAAATAGTAA 57.882 37.500 0.00 0.00 0.00 2.24
606 4914 5.750352 ACTCCCTCCGTTTCAAAATAGTA 57.250 39.130 0.00 0.00 0.00 1.82
607 4915 4.635699 ACTCCCTCCGTTTCAAAATAGT 57.364 40.909 0.00 0.00 0.00 2.12
608 4916 4.565564 CGTACTCCCTCCGTTTCAAAATAG 59.434 45.833 0.00 0.00 0.00 1.73
609 4917 4.021192 ACGTACTCCCTCCGTTTCAAAATA 60.021 41.667 0.00 0.00 0.00 1.40
610 4918 3.244318 ACGTACTCCCTCCGTTTCAAAAT 60.244 43.478 0.00 0.00 0.00 1.82
611 4919 2.102925 ACGTACTCCCTCCGTTTCAAAA 59.897 45.455 0.00 0.00 0.00 2.44
612 4920 1.688197 ACGTACTCCCTCCGTTTCAAA 59.312 47.619 0.00 0.00 0.00 2.69
613 4921 1.270550 GACGTACTCCCTCCGTTTCAA 59.729 52.381 0.00 0.00 34.51 2.69
614 4922 0.883833 GACGTACTCCCTCCGTTTCA 59.116 55.000 0.00 0.00 34.51 2.69
615 4923 1.135460 CAGACGTACTCCCTCCGTTTC 60.135 57.143 0.00 0.00 34.51 2.78
616 4924 0.886563 CAGACGTACTCCCTCCGTTT 59.113 55.000 0.00 0.00 34.51 3.60
617 4925 0.037303 TCAGACGTACTCCCTCCGTT 59.963 55.000 0.00 0.00 34.51 4.44
618 4926 0.392729 CTCAGACGTACTCCCTCCGT 60.393 60.000 0.00 0.00 37.56 4.69
619 4927 0.107800 TCTCAGACGTACTCCCTCCG 60.108 60.000 0.00 0.00 0.00 4.63
620 4928 1.065272 AGTCTCAGACGTACTCCCTCC 60.065 57.143 0.00 0.00 37.67 4.30
621 4929 2.011222 CAGTCTCAGACGTACTCCCTC 58.989 57.143 0.00 0.00 37.67 4.30
622 4930 1.351683 ACAGTCTCAGACGTACTCCCT 59.648 52.381 0.00 0.00 37.67 4.20
623 4931 1.469308 CACAGTCTCAGACGTACTCCC 59.531 57.143 0.00 0.00 37.67 4.30
624 4932 2.417239 CTCACAGTCTCAGACGTACTCC 59.583 54.545 0.00 0.00 37.67 3.85
625 4933 2.417239 CCTCACAGTCTCAGACGTACTC 59.583 54.545 0.00 0.00 37.67 2.59
626 4934 2.428491 CCTCACAGTCTCAGACGTACT 58.572 52.381 0.00 0.00 37.67 2.73
627 4935 1.135632 GCCTCACAGTCTCAGACGTAC 60.136 57.143 0.00 0.00 37.67 3.67
641 4949 2.706339 ATCATGTCTTCCAGCCTCAC 57.294 50.000 0.00 0.00 0.00 3.51
768 5089 1.080298 GGCAACTGCATGCTCCAAC 60.080 57.895 20.33 5.66 45.68 3.77
786 5120 3.776644 CACAAACGCGTATTAATTCGTGG 59.223 43.478 25.22 15.70 41.02 4.94
794 5128 3.059702 CACGATGACACAAACGCGTATTA 59.940 43.478 14.46 0.00 0.00 0.98
874 5212 1.576421 CTTTCCTGACCTTGCGTGC 59.424 57.895 0.00 0.00 0.00 5.34
877 5215 2.680913 CCGCTTTCCTGACCTTGCG 61.681 63.158 0.00 0.00 42.52 4.85
883 5221 2.436824 GGCTCCCGCTTTCCTGAC 60.437 66.667 0.00 0.00 36.09 3.51
920 5258 5.333645 GCTTGATCATGCTCGGTGTTTATAG 60.334 44.000 22.66 1.47 0.00 1.31
921 5259 4.511454 GCTTGATCATGCTCGGTGTTTATA 59.489 41.667 22.66 0.00 0.00 0.98
922 5260 3.313526 GCTTGATCATGCTCGGTGTTTAT 59.686 43.478 22.66 0.00 0.00 1.40
929 5267 1.783031 GCTGGCTTGATCATGCTCGG 61.783 60.000 26.99 22.24 0.00 4.63
1010 5351 3.499737 GTCCAACGAGGCGCCATG 61.500 66.667 31.54 22.76 37.29 3.66
1349 5816 3.842925 TTGGACTCCTTGCACCGGC 62.843 63.158 0.00 0.00 41.68 6.13
1350 5817 1.966451 GTTGGACTCCTTGCACCGG 60.966 63.158 0.00 0.00 0.00 5.28
1351 5818 1.071471 AGTTGGACTCCTTGCACCG 59.929 57.895 0.00 0.00 0.00 4.94
1352 5819 0.890996 CCAGTTGGACTCCTTGCACC 60.891 60.000 0.00 0.00 37.39 5.01
1353 5820 0.108585 TCCAGTTGGACTCCTTGCAC 59.891 55.000 0.00 0.00 39.78 4.57
1354 5821 2.538790 TCCAGTTGGACTCCTTGCA 58.461 52.632 0.00 0.00 39.78 4.08
1602 6135 3.020026 CTGCTTTCTGGCGCTGTCG 62.020 63.158 7.64 0.00 39.07 4.35
1637 6170 2.022129 CACTTGACGAGACGGTGCC 61.022 63.158 0.00 0.00 0.00 5.01
1644 6177 2.492088 CTCCATGTACCACTTGACGAGA 59.508 50.000 0.00 0.00 0.00 4.04
1699 6246 3.660111 GCCAACACCTGCACGGAC 61.660 66.667 8.91 0.00 36.31 4.79
1705 6279 2.113986 ACCTCAGCCAACACCTGC 59.886 61.111 0.00 0.00 0.00 4.85
2171 6758 1.453015 ACTTGTTCACCAGCGCCAA 60.453 52.632 2.29 0.00 0.00 4.52
2190 6777 2.879462 CCTTCAGCGCGTCGTACC 60.879 66.667 8.43 0.00 0.00 3.34
2340 6939 1.618640 GAGACGTCGCCTTCACTTGC 61.619 60.000 10.46 0.00 0.00 4.01
2526 7142 4.202101 TGTGCTCGTGGAAACATCATTTTT 60.202 37.500 0.00 0.00 46.14 1.94
2527 7143 3.317711 TGTGCTCGTGGAAACATCATTTT 59.682 39.130 0.00 0.00 46.14 1.82
2596 7212 4.794246 GTGACGGAGAGAGTATTCGAAAAG 59.206 45.833 0.00 0.00 0.00 2.27
2597 7213 4.216902 TGTGACGGAGAGAGTATTCGAAAA 59.783 41.667 0.00 0.00 0.00 2.29
2599 7215 3.340928 TGTGACGGAGAGAGTATTCGAA 58.659 45.455 0.00 0.00 0.00 3.71
2600 7216 2.981898 TGTGACGGAGAGAGTATTCGA 58.018 47.619 0.00 0.00 0.00 3.71
2601 7217 3.972950 ATGTGACGGAGAGAGTATTCG 57.027 47.619 0.00 0.00 0.00 3.34
2638 10253 3.011595 TCCATCCCATGACAGGTTGAAAT 59.988 43.478 0.00 0.00 0.00 2.17
2711 10326 6.759497 AGAAATGAACTTGTGGTATAAGGC 57.241 37.500 0.00 0.00 0.00 4.35
2977 10593 9.279904 GCAATATACGTATGCACAAAACTTAAA 57.720 29.630 18.37 0.00 0.00 1.52
3028 10644 2.084546 GTCAGGCGATTTTAGGCAAGT 58.915 47.619 0.00 0.00 36.55 3.16
3048 10664 9.411801 TCTGATAGCGATTTTAAGCTTAGTATG 57.588 33.333 6.24 0.00 44.15 2.39
3056 10672 5.637104 TTCGTCTGATAGCGATTTTAAGC 57.363 39.130 0.00 0.00 36.97 3.09
3167 10834 3.432186 CCCATGTGGTGTTCGTATGAGAT 60.432 47.826 0.00 0.00 0.00 2.75
3171 10838 1.339631 ACCCCATGTGGTGTTCGTATG 60.340 52.381 0.00 0.00 37.20 2.39
3183 10850 7.814693 AACTAGCTATTCATATACCCCATGT 57.185 36.000 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.