Multiple sequence alignment - TraesCS7A01G285400

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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 TraesCS7A01G285400 chr7A 100.000 6066 0 0 1 6066 328991546 328985481 0.000000e+00 11202.0
1 TraesCS7A01G285400 chr7A 87.287 527 60 7 12 534 493360448 493359925 4.050000e-166 595.0
2 TraesCS7A01G285400 chr7A 83.819 618 96 4 1 617 628983045 628982431 8.760000e-163 584.0
3 TraesCS7A01G285400 chr7D 96.739 3128 69 11 652 3769 290547935 290544831 0.000000e+00 5180.0
4 TraesCS7A01G285400 chr7D 95.524 1318 49 3 3845 5153 290544794 290543478 0.000000e+00 2098.0
5 TraesCS7A01G285400 chr7D 94.217 830 45 3 5239 6066 290543203 290542375 0.000000e+00 1264.0
6 TraesCS7A01G285400 chr7D 87.261 628 62 7 1 625 586749670 586750282 0.000000e+00 701.0
7 TraesCS7A01G285400 chr7D 90.278 72 5 2 4052 4123 109017068 109016999 6.470000e-15 93.5
8 TraesCS7A01G285400 chr7B 96.742 2210 48 9 1892 4079 361571059 361568852 0.000000e+00 3661.0
9 TraesCS7A01G285400 chr7B 93.707 2034 107 10 4036 6066 361568851 361566836 0.000000e+00 3027.0
10 TraesCS7A01G285400 chr7B 97.392 1112 24 3 790 1900 361573399 361572292 0.000000e+00 1888.0
11 TraesCS7A01G285400 chr7B 87.077 650 72 7 1 641 522546585 522545939 0.000000e+00 725.0
12 TraesCS7A01G285400 chr7B 84.255 705 105 6 5359 6060 68756785 68756084 0.000000e+00 682.0
13 TraesCS7A01G285400 chr7B 84.144 637 92 8 1 633 136320613 136321244 5.200000e-170 608.0
14 TraesCS7A01G285400 chr7B 82.893 643 96 11 1 642 533844542 533845171 3.170000e-157 566.0
15 TraesCS7A01G285400 chr1A 85.681 866 116 8 5207 6066 102377135 102376272 0.000000e+00 905.0
16 TraesCS7A01G285400 chr4A 85.681 866 115 9 5208 6066 140716695 140715832 0.000000e+00 904.0
17 TraesCS7A01G285400 chr4A 79.595 642 75 35 1 638 620559367 620558778 5.660000e-110 409.0
18 TraesCS7A01G285400 chr4A 91.892 37 3 0 784 820 379462539 379462575 1.100000e-02 52.8
19 TraesCS7A01G285400 chr5A 85.352 867 118 9 5206 6066 477718305 477717442 0.000000e+00 889.0
20 TraesCS7A01G285400 chr5A 88.889 621 68 1 1 620 18961686 18962306 0.000000e+00 763.0
21 TraesCS7A01G285400 chr5A 94.118 51 2 1 3697 3746 294714141 294714091 6.520000e-10 76.8
22 TraesCS7A01G285400 chr2D 84.677 868 124 9 5205 6066 73580726 73579862 0.000000e+00 857.0
23 TraesCS7A01G285400 chr2D 95.238 63 2 1 4058 4119 324997839 324997901 1.390000e-16 99.0
24 TraesCS7A01G285400 chr2D 100.000 45 0 0 3702 3746 20772872 20772828 3.900000e-12 84.2
25 TraesCS7A01G285400 chr2D 92.593 54 2 2 3703 3755 49185784 49185732 6.520000e-10 76.8
26 TraesCS7A01G285400 chr6B 83.333 822 127 9 5250 6066 9160230 9161046 0.000000e+00 750.0
27 TraesCS7A01G285400 chr6B 95.385 65 2 1 4056 4119 120824210 120824274 1.080000e-17 102.0
28 TraesCS7A01G285400 chr6B 91.667 72 2 4 4055 4123 719933086 719933016 5.000000e-16 97.1
29 TraesCS7A01G285400 chr6B 89.041 73 6 2 4048 4119 620620354 620620425 8.370000e-14 89.8
30 TraesCS7A01G285400 chr6B 85.938 64 5 4 3708 3769 435313263 435313202 1.410000e-06 65.8
31 TraesCS7A01G285400 chr1D 87.344 640 80 1 1 639 1034603 1035242 0.000000e+00 732.0
32 TraesCS7A01G285400 chr1D 80.523 842 148 13 5231 6066 367850541 367851372 3.080000e-177 632.0
33 TraesCS7A01G285400 chr1D 92.754 69 3 2 4056 4122 204510951 204510883 1.390000e-16 99.0
34 TraesCS7A01G285400 chr1D 100.000 44 0 0 3703 3746 85644470 85644513 1.400000e-11 82.4
35 TraesCS7A01G285400 chr2B 87.224 634 70 7 1 633 540811530 540812153 0.000000e+00 712.0
36 TraesCS7A01G285400 chr3B 91.617 167 13 1 476 641 4476398 4476232 4.730000e-56 230.0
37 TraesCS7A01G285400 chr3B 95.349 43 2 0 1856 1898 595693928 595693970 1.090000e-07 69.4
38 TraesCS7A01G285400 chr4D 95.385 65 2 1 4056 4119 503588983 503588919 1.080000e-17 102.0
39 TraesCS7A01G285400 chr4D 87.273 55 6 1 1854 1907 441486821 441486767 1.830000e-05 62.1
40 TraesCS7A01G285400 chr3A 97.826 46 1 0 3701 3746 59953309 59953354 5.040000e-11 80.5
41 TraesCS7A01G285400 chr6D 95.833 48 2 0 3699 3746 78352777 78352730 1.810000e-10 78.7
42 TraesCS7A01G285400 chrUn 93.478 46 2 1 1857 1902 9171300 9171344 3.920000e-07 67.6
43 TraesCS7A01G285400 chrUn 93.478 46 2 1 1857 1902 205600936 205600980 3.920000e-07 67.6
44 TraesCS7A01G285400 chr1B 93.478 46 2 1 1857 1902 680742806 680742850 3.920000e-07 67.6
45 TraesCS7A01G285400 chr1B 93.478 46 2 1 1857 1902 682486158 682486202 3.920000e-07 67.6
46 TraesCS7A01G285400 chr5B 95.122 41 2 0 1858 1898 383528339 383528379 1.410000e-06 65.8
47 TraesCS7A01G285400 chr5D 100.000 28 0 0 794 821 130665061 130665034 1.100000e-02 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 TraesCS7A01G285400 chr7A 328985481 328991546 6065 True 11202.000000 11202 100.000000 1 6066 1 chr7A.!!$R1 6065
1 TraesCS7A01G285400 chr7A 493359925 493360448 523 True 595.000000 595 87.287000 12 534 1 chr7A.!!$R2 522
2 TraesCS7A01G285400 chr7A 628982431 628983045 614 True 584.000000 584 83.819000 1 617 1 chr7A.!!$R3 616
3 TraesCS7A01G285400 chr7D 290542375 290547935 5560 True 2847.333333 5180 95.493333 652 6066 3 chr7D.!!$R2 5414
4 TraesCS7A01G285400 chr7D 586749670 586750282 612 False 701.000000 701 87.261000 1 625 1 chr7D.!!$F1 624
5 TraesCS7A01G285400 chr7B 361566836 361573399 6563 True 2858.666667 3661 95.947000 790 6066 3 chr7B.!!$R3 5276
6 TraesCS7A01G285400 chr7B 522545939 522546585 646 True 725.000000 725 87.077000 1 641 1 chr7B.!!$R2 640
7 TraesCS7A01G285400 chr7B 68756084 68756785 701 True 682.000000 682 84.255000 5359 6060 1 chr7B.!!$R1 701
8 TraesCS7A01G285400 chr7B 136320613 136321244 631 False 608.000000 608 84.144000 1 633 1 chr7B.!!$F1 632
9 TraesCS7A01G285400 chr7B 533844542 533845171 629 False 566.000000 566 82.893000 1 642 1 chr7B.!!$F2 641
10 TraesCS7A01G285400 chr1A 102376272 102377135 863 True 905.000000 905 85.681000 5207 6066 1 chr1A.!!$R1 859
11 TraesCS7A01G285400 chr4A 140715832 140716695 863 True 904.000000 904 85.681000 5208 6066 1 chr4A.!!$R1 858
12 TraesCS7A01G285400 chr4A 620558778 620559367 589 True 409.000000 409 79.595000 1 638 1 chr4A.!!$R2 637
13 TraesCS7A01G285400 chr5A 477717442 477718305 863 True 889.000000 889 85.352000 5206 6066 1 chr5A.!!$R2 860
14 TraesCS7A01G285400 chr5A 18961686 18962306 620 False 763.000000 763 88.889000 1 620 1 chr5A.!!$F1 619
15 TraesCS7A01G285400 chr2D 73579862 73580726 864 True 857.000000 857 84.677000 5205 6066 1 chr2D.!!$R3 861
16 TraesCS7A01G285400 chr6B 9160230 9161046 816 False 750.000000 750 83.333000 5250 6066 1 chr6B.!!$F1 816
17 TraesCS7A01G285400 chr1D 1034603 1035242 639 False 732.000000 732 87.344000 1 639 1 chr1D.!!$F1 638
18 TraesCS7A01G285400 chr1D 367850541 367851372 831 False 632.000000 632 80.523000 5231 6066 1 chr1D.!!$F3 835
19 TraesCS7A01G285400 chr2B 540811530 540812153 623 False 712.000000 712 87.224000 1 633 1 chr2B.!!$F1 632

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
578 631 1.229209 AGGAGGAGGGAGTTTGCGA 60.229 57.895 0.00 0.0 0.00 5.10 F
1182 1240 1.075374 AGAGGTATTTGCCAGGCACAA 59.925 47.619 15.89 12.4 38.71 3.33 F
1881 1940 0.388294 CTCCCTCCGTCCCGAATTAC 59.612 60.000 0.00 0.0 0.00 1.89 F
2947 4250 1.384222 CCTTCTTAATGGCGGGGCAC 61.384 60.000 0.00 0.0 0.00 5.01 F
3011 4314 2.078849 TGTCCAAGACACGCTACATG 57.921 50.000 0.00 0.0 37.67 3.21 F
4287 5657 3.825328 AGTCCAGCAATTCAAGTTCTGT 58.175 40.909 0.00 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1421 1479 1.273327 GTTTCCAAGAACCATGCCCTG 59.727 52.381 0.00 0.00 0.00 4.45 R
2971 4274 1.025812 CTTTGCCAACCGGTGTTACA 58.974 50.000 8.52 0.99 32.09 2.41 R
3011 4314 1.153549 GTGACCCGAGTGGATCAGC 60.154 63.158 0.00 0.00 37.49 4.26 R
4179 5549 2.479566 ATGTGATGGTCACCAGTGTC 57.520 50.000 1.19 0.00 46.40 3.67 R
4622 6001 3.314331 CAGCCCACGACCAGAGGT 61.314 66.667 0.00 0.00 39.44 3.85 R
5665 7238 0.036164 ACAGGTTAAGCACGATGGCA 59.964 50.000 7.52 0.00 35.83 4.92 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
161 162 2.567169 TGACGAAAGAGATGACCACCAT 59.433 45.455 0.00 0.00 38.43 3.55
162 163 3.007940 TGACGAAAGAGATGACCACCATT 59.992 43.478 0.00 0.00 35.17 3.16
229 230 4.918360 ACCACCAGGCCCTCCACA 62.918 66.667 0.00 0.00 39.06 4.17
231 235 3.252284 CACCAGGCCCTCCACACT 61.252 66.667 0.00 0.00 33.74 3.55
342 354 2.187685 CGCTGCTGTCCATGGCTA 59.812 61.111 6.96 0.00 0.00 3.93
508 522 3.782443 GAGATCCCCGCCACCGTT 61.782 66.667 0.00 0.00 0.00 4.44
578 631 1.229209 AGGAGGAGGGAGTTTGCGA 60.229 57.895 0.00 0.00 0.00 5.10
680 736 4.078516 GGTTCTAGGTGGCCGCGT 62.079 66.667 16.80 16.80 0.00 6.01
682 738 2.098831 GTTCTAGGTGGCCGCGTTC 61.099 63.158 17.88 0.00 0.00 3.95
718 774 1.398390 GACCATGTGATTTGGACGAGC 59.602 52.381 0.00 0.00 37.69 5.03
755 811 1.908066 GCTACACGGGAAAGCGTTGG 61.908 60.000 0.00 0.00 0.00 3.77
1103 1161 3.802866 TCCCATTTGTTCTTGGTTTTGC 58.197 40.909 0.00 0.00 0.00 3.68
1182 1240 1.075374 AGAGGTATTTGCCAGGCACAA 59.925 47.619 15.89 12.40 38.71 3.33
1270 1328 5.153950 ACTGTATCTTTCTTCAGGTCACC 57.846 43.478 0.00 0.00 32.92 4.02
1286 1344 3.181485 GGTCACCCGTTTCAAATGTTTGA 60.181 43.478 4.16 4.16 44.78 2.69
1344 1402 8.893219 TTGATGTTTGTGTTTTGGCATAATAA 57.107 26.923 0.00 0.00 0.00 1.40
1421 1479 4.923281 ACTTTGCGATTAACATTTTCCTGC 59.077 37.500 0.00 0.00 0.00 4.85
1440 1498 1.631405 CAGGGCATGGTTCTTGGAAA 58.369 50.000 0.00 0.00 0.00 3.13
1473 1531 6.601613 TCGTTGATATTATGTGGCCTTCTTTT 59.398 34.615 3.32 0.00 0.00 2.27
1881 1940 0.388294 CTCCCTCCGTCCCGAATTAC 59.612 60.000 0.00 0.00 0.00 1.89
1933 3233 7.595819 AATCAAAGTCAACTAATTTGGGACA 57.404 32.000 13.34 0.00 35.69 4.02
2122 3422 7.726033 TTGGGGCAGTACATATTACAAAAAT 57.274 32.000 0.00 0.00 0.00 1.82
2870 4173 2.858787 TGGGGAAGAACCAAAACCTT 57.141 45.000 0.00 0.00 41.20 3.50
2947 4250 1.384222 CCTTCTTAATGGCGGGGCAC 61.384 60.000 0.00 0.00 0.00 5.01
2970 4273 6.261603 CACCACACAGATATATGCAGTCAAAT 59.738 38.462 0.00 0.00 0.00 2.32
2971 4274 6.830324 ACCACACAGATATATGCAGTCAAATT 59.170 34.615 0.00 0.00 0.00 1.82
2973 4276 7.201758 CCACACAGATATATGCAGTCAAATTGT 60.202 37.037 0.00 0.00 0.00 2.71
3011 4314 2.078849 TGTCCAAGACACGCTACATG 57.921 50.000 0.00 0.00 37.67 3.21
3108 4411 6.476378 ACACACTAAAGCATCCAGAACTAAT 58.524 36.000 0.00 0.00 0.00 1.73
3512 4815 4.099573 CGTTGGACTCTGTTATGGAGGTAT 59.900 45.833 0.00 0.00 35.34 2.73
3529 4832 6.058833 GGAGGTATTTCTCTTCCTGGATTTC 58.941 44.000 0.00 0.00 34.39 2.17
3582 4886 7.830940 TTGTACAAGTTTCTCAGAAAACGTA 57.169 32.000 3.59 1.27 42.63 3.57
3860 5185 5.419788 TGCATTCCTCAGCATAACTTTTGAT 59.580 36.000 0.00 0.00 35.51 2.57
3920 5245 7.148641 ACGGCAAGTGATTCTAATGTATAGAG 58.851 38.462 0.00 0.00 0.00 2.43
3993 5318 4.040217 AGTGCAGACATTGAGAGACTTCTT 59.960 41.667 0.00 0.00 32.53 2.52
4134 5504 9.057089 AGCCATTTATTTATTCTACACACTAGC 57.943 33.333 0.00 0.00 0.00 3.42
4287 5657 3.825328 AGTCCAGCAATTCAAGTTCTGT 58.175 40.909 0.00 0.00 0.00 3.41
4565 5936 5.130477 ACTCTTAACATCCGGTGTATTGGAT 59.870 40.000 0.00 0.00 45.84 3.41
4641 6020 3.314331 CTCTGGTCGTGGGCTGGT 61.314 66.667 0.00 0.00 0.00 4.00
4704 6083 6.849502 AGTATTGATGACTGTGAAATGCAAG 58.150 36.000 0.00 0.00 0.00 4.01
4981 6360 4.197750 AGATGCAGGCAAAACTAGATCTG 58.802 43.478 5.18 0.00 0.00 2.90
5064 6443 7.769272 TTTCTCTTTTAAAATGCAGTTGGTG 57.231 32.000 0.00 0.00 0.00 4.17
5126 6505 3.058016 AGGTTGAATTGCATTCTCACGTG 60.058 43.478 9.94 9.94 39.96 4.49
5166 6545 4.909880 CAGTACGAAAGCAACTAAAAAGCC 59.090 41.667 0.00 0.00 0.00 4.35
5171 6550 5.240844 ACGAAAGCAACTAAAAAGCCATAGT 59.759 36.000 0.00 0.00 33.89 2.12
5178 6557 6.582672 GCAACTAAAAAGCCATAGTCAAAGTC 59.417 38.462 0.00 0.00 31.31 3.01
5180 6559 8.352942 CAACTAAAAAGCCATAGTCAAAGTCTT 58.647 33.333 0.00 0.00 31.31 3.01
5193 6572 4.847633 TCAAAGTCTTTTGAGCAATCACG 58.152 39.130 0.00 0.00 45.77 4.35
5198 6577 1.200020 CTTTTGAGCAATCACGGGACC 59.800 52.381 0.00 0.00 0.00 4.46
5199 6578 0.953471 TTTGAGCAATCACGGGACCG 60.953 55.000 9.56 9.56 46.03 4.79
5200 6579 2.511600 GAGCAATCACGGGACCGG 60.512 66.667 15.92 0.00 44.69 5.28
5201 6580 4.778143 AGCAATCACGGGACCGGC 62.778 66.667 15.92 8.18 44.69 6.13
5289 6859 4.577283 ACTTAGAGATTACAGCGAGAGGAC 59.423 45.833 0.00 0.00 0.00 3.85
5312 6882 3.803082 CATGCGCCAAGACACGGG 61.803 66.667 4.18 0.00 0.00 5.28
5462 7034 4.100084 CACAGGATGGCGAGGGCA 62.100 66.667 0.00 0.00 43.62 5.36
5567 7140 0.617820 GAGGGACCAGACCTAAGCCA 60.618 60.000 0.00 0.00 38.79 4.75
5624 7197 4.083324 CCTCAAAAGATAAGTTGCAGCGAA 60.083 41.667 0.00 0.00 0.00 4.70
5665 7238 4.451096 GTGATGGTCGTGTGATGTAAGTTT 59.549 41.667 0.00 0.00 0.00 2.66
5737 7311 1.289160 TGATAGGTGCCTTTGAGCCT 58.711 50.000 0.00 0.00 35.28 4.58
5748 7322 2.104963 CCTTTGAGCCTAGATGTACCCC 59.895 54.545 0.00 0.00 0.00 4.95
5781 7355 0.753479 GCTCATGGTCGGAGGAGAGA 60.753 60.000 0.00 0.00 32.96 3.10
5786 7360 1.938585 TGGTCGGAGGAGAGAAATGT 58.061 50.000 0.00 0.00 0.00 2.71
5804 7378 4.208686 GTAGGCGCACCTCGAGGG 62.209 72.222 34.04 23.21 46.34 4.30
5892 7466 3.216800 AGACAAAACAGATGCAAGCTCA 58.783 40.909 0.00 0.00 0.00 4.26
5893 7467 3.825014 AGACAAAACAGATGCAAGCTCAT 59.175 39.130 0.00 0.00 0.00 2.90
5921 7495 1.071071 CACGTTGGTTAGGAGGTTCCA 59.929 52.381 0.00 0.00 39.61 3.53
5922 7496 1.982958 ACGTTGGTTAGGAGGTTCCAT 59.017 47.619 0.00 0.00 39.61 3.41
6000 7574 0.787084 AGTGAGAGAAGAGGTGGGGA 59.213 55.000 0.00 0.00 0.00 4.81
6027 7602 1.060622 CTACGAGCGGAGTCGACAC 59.939 63.158 19.50 11.89 42.85 3.67
6029 7604 1.632948 TACGAGCGGAGTCGACACAG 61.633 60.000 19.50 13.64 42.85 3.66
6035 7610 1.296715 GGAGTCGACACAGGCCAAT 59.703 57.895 19.50 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 0.465460 TTGCCAGTGAAAACCGAGCT 60.465 50.000 0.00 0.00 0.00 4.09
229 230 3.118454 CAAATCGGCGTCGGCAGT 61.118 61.111 19.59 3.25 42.47 4.40
231 235 2.357638 TTCAAATCGGCGTCGGCA 60.358 55.556 19.59 6.50 42.47 5.69
446 458 2.042639 GGGACCCCTAGGCGTGTA 60.043 66.667 3.11 0.00 36.11 2.90
578 631 3.600898 GAAACCTAGCCACCGCCGT 62.601 63.158 0.00 0.00 34.57 5.68
641 697 1.453633 TAGATAGGTAGACCGCCCCT 58.546 55.000 0.00 0.00 42.08 4.79
642 698 1.891811 GTTAGATAGGTAGACCGCCCC 59.108 57.143 0.00 0.00 42.08 5.80
643 699 1.538950 CGTTAGATAGGTAGACCGCCC 59.461 57.143 0.00 0.00 42.08 6.13
644 700 1.538950 CCGTTAGATAGGTAGACCGCC 59.461 57.143 0.00 0.00 42.08 6.13
645 701 2.225467 ACCGTTAGATAGGTAGACCGC 58.775 52.381 0.00 0.00 39.30 5.68
646 702 4.133078 AGAACCGTTAGATAGGTAGACCG 58.867 47.826 0.00 0.00 40.37 4.79
647 703 5.704978 CCTAGAACCGTTAGATAGGTAGACC 59.295 48.000 0.00 0.00 40.37 3.85
648 704 6.204495 CACCTAGAACCGTTAGATAGGTAGAC 59.796 46.154 16.40 0.00 43.38 2.59
649 705 6.294473 CACCTAGAACCGTTAGATAGGTAGA 58.706 44.000 16.40 0.00 43.38 2.59
650 706 5.472820 CCACCTAGAACCGTTAGATAGGTAG 59.527 48.000 16.40 9.72 43.38 3.18
651 707 5.380043 CCACCTAGAACCGTTAGATAGGTA 58.620 45.833 16.40 0.00 43.38 3.08
652 708 4.213513 CCACCTAGAACCGTTAGATAGGT 58.786 47.826 13.11 13.11 45.54 3.08
653 709 3.005578 GCCACCTAGAACCGTTAGATAGG 59.994 52.174 12.18 12.18 39.16 2.57
654 710 3.005578 GGCCACCTAGAACCGTTAGATAG 59.994 52.174 0.00 0.00 0.00 2.08
655 711 2.961062 GGCCACCTAGAACCGTTAGATA 59.039 50.000 0.00 0.00 0.00 1.98
679 735 4.124970 GGTCCCAATGATTACTACCGAAC 58.875 47.826 0.00 0.00 0.00 3.95
680 736 3.775866 TGGTCCCAATGATTACTACCGAA 59.224 43.478 0.00 0.00 0.00 4.30
682 738 3.830744 TGGTCCCAATGATTACTACCG 57.169 47.619 0.00 0.00 0.00 4.02
742 798 3.161817 CGTACCAACGCTTTCCCG 58.838 61.111 0.00 0.00 43.12 5.14
755 811 7.380431 AGATCTACCTTATGCAGATACGTAC 57.620 40.000 0.00 0.00 0.00 3.67
816 874 3.058501 CACCGTACCATTGACCAGAAAAC 60.059 47.826 0.00 0.00 0.00 2.43
1018 1076 2.744494 GCCAAGATACTCTTCAGGCCAG 60.744 54.545 5.01 0.00 38.75 4.85
1103 1161 5.655532 AGGATTCCTGGAGAAAATGAACATG 59.344 40.000 3.86 0.00 38.21 3.21
1182 1240 9.770097 CATGGTTCATAGTTACACAAGATATCT 57.230 33.333 0.00 0.00 0.00 1.98
1247 1305 6.282199 GGTGACCTGAAGAAAGATACAGTA 57.718 41.667 0.00 0.00 0.00 2.74
1421 1479 1.273327 GTTTCCAAGAACCATGCCCTG 59.727 52.381 0.00 0.00 0.00 4.45
1440 1498 7.417612 GCCACATAATATCAACGAAATTCTGT 58.582 34.615 0.00 0.00 0.00 3.41
1473 1531 5.108517 CAACTAAGTGCTTTTGAAAAGGCA 58.891 37.500 18.30 13.51 46.76 4.75
1527 1585 6.494491 TCATTTGGTTCTTTCCATGAATCTGT 59.506 34.615 0.00 0.00 37.33 3.41
1881 1940 7.642194 GTCTAGATACGACAAATCTGAGTCAAG 59.358 40.741 0.00 0.00 35.36 3.02
2122 3422 3.946558 ACCGTTTAGCAACACCAGTTTAA 59.053 39.130 0.00 0.00 35.28 1.52
2870 4173 3.202906 GTTCAGTACCACTGTTGCTTGA 58.797 45.455 6.23 0.00 46.03 3.02
2947 4250 6.872628 ATTTGACTGCATATATCTGTGTGG 57.127 37.500 0.00 0.00 0.00 4.17
2970 4273 1.405821 CTTTGCCAACCGGTGTTACAA 59.594 47.619 8.52 8.26 32.09 2.41
2971 4274 1.025812 CTTTGCCAACCGGTGTTACA 58.974 50.000 8.52 0.99 32.09 2.41
2973 4276 1.883275 CATCTTTGCCAACCGGTGTTA 59.117 47.619 8.52 0.00 32.09 2.41
3011 4314 1.153549 GTGACCCGAGTGGATCAGC 60.154 63.158 0.00 0.00 37.49 4.26
3108 4411 3.025189 TATTCTGCCGGCGCCTTGA 62.025 57.895 26.68 13.79 0.00 3.02
3496 4799 7.070571 AGGAAGAGAAATACCTCCATAACAGAG 59.929 40.741 0.00 0.00 33.76 3.35
3512 4815 8.760980 TTAAACTTGAAATCCAGGAAGAGAAA 57.239 30.769 0.00 0.00 0.00 2.52
3558 4862 6.730960 ACGTTTTCTGAGAAACTTGTACAA 57.269 33.333 7.21 8.28 37.37 2.41
3582 4886 8.822805 TGACCAAAACTAGACCTGAATAATACT 58.177 33.333 0.00 0.00 0.00 2.12
3860 5185 4.039245 AGCAGTGCAGAAGTTTACAGTCTA 59.961 41.667 19.20 0.00 0.00 2.59
4073 5398 3.723922 GCAGAGGCCGGGGGTTAA 61.724 66.667 2.18 0.00 0.00 2.01
4179 5549 2.479566 ATGTGATGGTCACCAGTGTC 57.520 50.000 1.19 0.00 46.40 3.67
4203 5573 5.180680 GGTTAGAGAAGGCAAATTTGTACGT 59.819 40.000 19.03 10.84 0.00 3.57
4287 5657 5.693769 AGGCTTATACCTTCAAGCTACAA 57.306 39.130 6.30 0.00 45.20 2.41
4368 5738 7.565680 ACGGAGAAATTCAGACACCTAAATAT 58.434 34.615 0.00 0.00 0.00 1.28
4414 5784 5.916883 CGAATTTGTGCTGAACTTCTTCAAT 59.083 36.000 0.00 0.00 35.92 2.57
4622 6001 3.314331 CAGCCCACGACCAGAGGT 61.314 66.667 0.00 0.00 39.44 3.85
4641 6020 5.537300 AGAAGTTCTACAACTCTCTTGCA 57.463 39.130 2.75 0.00 42.45 4.08
4704 6083 8.655651 TTGGTTTCTTGTAAACATGAATTTCC 57.344 30.769 0.00 12.86 38.99 3.13
4981 6360 5.934781 AGACTAAACATCTCCATTCCCATC 58.065 41.667 0.00 0.00 0.00 3.51
5064 6443 5.500931 CGATCTTGGAACGATTAAGTCAAGC 60.501 44.000 0.00 0.00 33.68 4.01
5073 6452 5.468746 TCAAAAAGACGATCTTGGAACGATT 59.531 36.000 4.39 0.00 36.71 3.34
5074 6453 4.994852 TCAAAAAGACGATCTTGGAACGAT 59.005 37.500 4.39 0.00 36.71 3.73
5075 6454 4.373527 TCAAAAAGACGATCTTGGAACGA 58.626 39.130 4.39 0.00 36.71 3.85
5166 6545 7.536622 GTGATTGCTCAAAAGACTTTGACTATG 59.463 37.037 0.06 0.00 44.76 2.23
5171 6550 4.261155 CCGTGATTGCTCAAAAGACTTTGA 60.261 41.667 0.06 0.26 46.88 2.69
5178 6557 1.200020 GGTCCCGTGATTGCTCAAAAG 59.800 52.381 0.00 0.00 31.85 2.27
5180 6559 0.953471 CGGTCCCGTGATTGCTCAAA 60.953 55.000 0.00 0.00 31.85 2.69
5212 6591 7.400339 TGACTAATATATTCAGGTGGGGATCTC 59.600 40.741 0.00 0.00 0.00 2.75
5256 6825 6.256757 GCTGTAATCTCTAAGTAACCTGCAAG 59.743 42.308 0.00 0.00 0.00 4.01
5289 6859 0.673333 TGTCTTGGCGCATGTACCTG 60.673 55.000 10.83 0.00 0.00 4.00
5312 6882 2.165234 GACCACGTTAGTAGGGAGGTTC 59.835 54.545 0.00 0.00 0.00 3.62
5567 7140 3.882326 CCTCCTCGGCCCATGCAT 61.882 66.667 0.00 0.00 40.13 3.96
5624 7197 1.071471 CCTTGGTGTCGTCTTGCCT 59.929 57.895 0.00 0.00 0.00 4.75
5651 7224 3.188460 ACGATGGCAAACTTACATCACAC 59.812 43.478 0.00 0.00 40.68 3.82
5665 7238 0.036164 ACAGGTTAAGCACGATGGCA 59.964 50.000 7.52 0.00 35.83 4.92
5691 7264 0.531753 GATCTTCGGCTGGCTTCTCC 60.532 60.000 0.00 0.00 0.00 3.71
5737 7311 1.452953 CTCGCTGCGGGGTACATCTA 61.453 60.000 23.03 0.00 0.00 1.98
5748 7322 0.875040 ATGAGCTTGATCTCGCTGCG 60.875 55.000 17.25 17.25 36.45 5.18
5804 7378 1.891150 TCACCTACTGTTCCTCGTTCC 59.109 52.381 0.00 0.00 0.00 3.62
5892 7466 2.615493 CCTAACCAACGTGGCTTCTGAT 60.615 50.000 0.00 0.00 42.67 2.90
5893 7467 1.270625 CCTAACCAACGTGGCTTCTGA 60.271 52.381 0.00 0.00 42.67 3.27
5921 7495 6.649557 GCATAATGGTTTACTCGCTAACCTAT 59.350 38.462 0.00 0.00 43.36 2.57
5922 7496 5.987347 GCATAATGGTTTACTCGCTAACCTA 59.013 40.000 0.00 0.00 43.36 3.08
6000 7574 3.080319 ACTCCGCTCGTAGAAAACTACT 58.920 45.455 0.00 0.00 34.09 2.57
6027 7602 0.744874 CTGGCTCAATGATTGGCCTG 59.255 55.000 26.57 23.64 43.24 4.85
6029 7604 1.407979 CTTCTGGCTCAATGATTGGCC 59.592 52.381 22.61 22.61 43.18 5.36
6035 7610 2.290514 CCACCTTCTTCTGGCTCAATGA 60.291 50.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.