Multiple sequence alignment - TraesCS2A01G134800

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 TraesCS2A01G134800 chr2A 100.000 3734 0 0 1 3734 81091090 81087357 0.000000e+00 6896.0
1 TraesCS2A01G134800 chr2A 75.848 501 91 20 3236 3712 778779997 778779503 1.040000e-55 228.0
2 TraesCS2A01G134800 chr2A 88.710 62 7 0 2471 2532 607514787 607514726 4.000000e-10 76.8
3 TraesCS2A01G134800 chr2D 92.489 3701 167 47 83 3734 80728781 80725143 0.000000e+00 5192.0
4 TraesCS2A01G134800 chr2D 76.074 163 31 5 2642 2797 176066150 176065989 1.110000e-10 78.7
5 TraesCS2A01G134800 chr2D 88.710 62 7 0 2471 2532 462242210 462242149 4.000000e-10 76.8
6 TraesCS2A01G134800 chr2B 91.367 3417 189 42 66 3419 132340397 132337024 0.000000e+00 4578.0
7 TraesCS2A01G134800 chr2B 95.679 324 14 0 3411 3734 132335681 132335358 4.270000e-144 521.0
8 TraesCS2A01G134800 chr2B 88.710 62 7 0 2471 2532 545154883 545154822 4.000000e-10 76.8
9 TraesCS2A01G134800 chr7A 76.630 552 100 17 3212 3734 672647896 672647345 1.020000e-70 278.0
10 TraesCS2A01G134800 chr3D 76.514 545 99 15 3211 3726 610408604 610408060 1.710000e-68 270.0
11 TraesCS2A01G134800 chr3D 76.128 532 90 22 3226 3723 310686080 310686608 1.040000e-60 244.0
12 TraesCS2A01G134800 chr3D 75.322 543 100 21 3212 3723 606793234 606793773 2.900000e-56 230.0
13 TraesCS2A01G134800 chr3D 77.582 397 74 11 3212 3594 9842500 9842895 3.750000e-55 226.0
14 TraesCS2A01G134800 chr3D 90.000 90 8 1 3017 3106 433174629 433174541 8.470000e-22 115.0
15 TraesCS2A01G134800 chr3D 95.745 47 2 0 1 47 552962325 552962371 4.000000e-10 76.8
16 TraesCS2A01G134800 chr3D 90.244 41 3 1 3 43 126295483 126295522 7.000000e-03 52.8
17 TraesCS2A01G134800 chr3D 90.244 41 3 1 3 43 126310090 126310129 7.000000e-03 52.8
18 TraesCS2A01G134800 chr3A 77.805 401 75 9 3241 3627 738952683 738953083 6.230000e-58 235.0
19 TraesCS2A01G134800 chr3A 90.805 87 6 2 3021 3106 105553331 105553416 8.470000e-22 115.0
20 TraesCS2A01G134800 chr3A 90.805 87 6 2 3021 3106 593310150 593310065 8.470000e-22 115.0
21 TraesCS2A01G134800 chr1D 79.401 267 40 11 3226 3477 435794623 435794357 1.380000e-39 174.0
22 TraesCS2A01G134800 chr1D 92.157 51 4 0 2470 2520 7905763 7905713 5.170000e-09 73.1
23 TraesCS2A01G134800 chr6D 78.641 206 33 8 2627 2824 53590027 53590229 3.920000e-25 126.0
24 TraesCS2A01G134800 chr6D 93.617 47 3 0 1 47 451764440 451764486 1.860000e-08 71.3
25 TraesCS2A01G134800 chr6B 91.860 86 6 1 3021 3106 450074792 450074708 6.550000e-23 119.0
26 TraesCS2A01G134800 chrUn 90.805 87 6 2 3021 3106 345935602 345935687 8.470000e-22 115.0
27 TraesCS2A01G134800 chr7B 90.805 87 6 2 3021 3106 662751441 662751526 8.470000e-22 115.0
28 TraesCS2A01G134800 chr7B 76.812 138 26 5 2698 2831 631550030 631550165 5.170000e-09 73.1
29 TraesCS2A01G134800 chr5A 90.805 87 6 2 3021 3106 559028321 559028406 8.470000e-22 115.0
30 TraesCS2A01G134800 chr5A 97.778 45 1 0 1 45 476687710 476687754 1.110000e-10 78.7
31 TraesCS2A01G134800 chr5A 84.932 73 10 1 2761 2833 62730340 62730269 5.170000e-09 73.1
32 TraesCS2A01G134800 chr7D 93.750 48 2 1 1 47 483284553 483284506 1.860000e-08 71.3
33 TraesCS2A01G134800 chr4A 93.617 47 3 0 1 47 560903432 560903386 1.860000e-08 71.3
34 TraesCS2A01G134800 chr1A 90.196 51 5 0 2470 2520 9561824 9561774 2.410000e-07 67.6
35 TraesCS2A01G134800 chr1A 93.182 44 3 0 1 44 33895070 33895113 8.660000e-07 65.8


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 TraesCS2A01G134800 chr2A 81087357 81091090 3733 True 6896.0 6896 100.000 1 3734 1 chr2A.!!$R1 3733
1 TraesCS2A01G134800 chr2D 80725143 80728781 3638 True 5192.0 5192 92.489 83 3734 1 chr2D.!!$R1 3651
2 TraesCS2A01G134800 chr2B 132335358 132340397 5039 True 2549.5 4578 93.523 66 3734 2 chr2B.!!$R2 3668
3 TraesCS2A01G134800 chr7A 672647345 672647896 551 True 278.0 278 76.630 3212 3734 1 chr7A.!!$R1 522
4 TraesCS2A01G134800 chr3D 610408060 610408604 544 True 270.0 270 76.514 3211 3726 1 chr3D.!!$R2 515
5 TraesCS2A01G134800 chr3D 310686080 310686608 528 False 244.0 244 76.128 3226 3723 1 chr3D.!!$F4 497
6 TraesCS2A01G134800 chr3D 606793234 606793773 539 False 230.0 230 75.322 3212 3723 1 chr3D.!!$F6 511

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
686 751 0.520412 CGGCGCAAATACTTCCAACG 60.520 55.000 10.83 0.0 0.0 4.10 F
1482 1577 0.036952 ATGGACGGAACTGCACTCTG 60.037 55.000 0.00 0.0 0.0 3.35 F
1590 1696 1.372623 GGTGTTCGTCGGTGACTCC 60.373 63.158 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2365 2482 0.161658 CACGTTCATCACACGCAGAC 59.838 55.000 0.0 0.00 41.53 3.51 R
2730 2850 1.337384 TGTGAGTATGCAGCCCCGAT 61.337 55.000 0.0 0.00 0.00 4.18 R
3148 3268 1.925847 GTTGTTCACGACGGTGTGTAA 59.074 47.619 0.0 1.19 44.68 2.41 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
20 21 3.149436 GTTCAGACAGCTTGCAAAACA 57.851 42.857 0.00 0.00 0.00 2.83
21 22 3.111098 GTTCAGACAGCTTGCAAAACAG 58.889 45.455 0.00 0.00 0.00 3.16
22 23 2.368439 TCAGACAGCTTGCAAAACAGT 58.632 42.857 0.00 0.00 0.00 3.55
23 24 2.754552 TCAGACAGCTTGCAAAACAGTT 59.245 40.909 0.00 0.00 0.00 3.16
24 25 3.111098 CAGACAGCTTGCAAAACAGTTC 58.889 45.455 0.00 0.00 0.00 3.01
25 26 2.754552 AGACAGCTTGCAAAACAGTTCA 59.245 40.909 0.00 0.00 0.00 3.18
26 27 3.193267 AGACAGCTTGCAAAACAGTTCAA 59.807 39.130 0.00 0.00 0.00 2.69
27 28 3.924144 ACAGCTTGCAAAACAGTTCAAA 58.076 36.364 0.00 0.00 0.00 2.69
28 29 4.314121 ACAGCTTGCAAAACAGTTCAAAA 58.686 34.783 0.00 0.00 0.00 2.44
29 30 4.937015 ACAGCTTGCAAAACAGTTCAAAAT 59.063 33.333 0.00 0.00 0.00 1.82
30 31 5.063817 ACAGCTTGCAAAACAGTTCAAAATC 59.936 36.000 0.00 0.00 0.00 2.17
31 32 5.063691 CAGCTTGCAAAACAGTTCAAAATCA 59.936 36.000 0.00 0.00 0.00 2.57
32 33 5.292589 AGCTTGCAAAACAGTTCAAAATCAG 59.707 36.000 0.00 0.00 0.00 2.90
33 34 5.467902 TTGCAAAACAGTTCAAAATCAGC 57.532 34.783 0.00 0.00 0.00 4.26
34 35 4.757594 TGCAAAACAGTTCAAAATCAGCT 58.242 34.783 0.00 0.00 0.00 4.24
35 36 4.567558 TGCAAAACAGTTCAAAATCAGCTG 59.432 37.500 7.63 7.63 0.00 4.24
36 37 4.567959 GCAAAACAGTTCAAAATCAGCTGT 59.432 37.500 14.67 0.00 41.51 4.40
37 38 5.276536 GCAAAACAGTTCAAAATCAGCTGTC 60.277 40.000 14.67 0.00 39.19 3.51
38 39 5.841957 AAACAGTTCAAAATCAGCTGTCT 57.158 34.783 14.67 0.00 39.19 3.41
39 40 6.942532 AAACAGTTCAAAATCAGCTGTCTA 57.057 33.333 14.67 0.00 39.19 2.59
40 41 6.942532 AACAGTTCAAAATCAGCTGTCTAA 57.057 33.333 14.67 0.00 39.19 2.10
41 42 6.942532 ACAGTTCAAAATCAGCTGTCTAAA 57.057 33.333 14.67 0.00 35.78 1.85
42 43 7.333528 ACAGTTCAAAATCAGCTGTCTAAAA 57.666 32.000 14.67 0.05 35.78 1.52
43 44 7.196331 ACAGTTCAAAATCAGCTGTCTAAAAC 58.804 34.615 14.67 11.99 35.78 2.43
44 45 6.358030 CAGTTCAAAATCAGCTGTCTAAAACG 59.642 38.462 14.67 6.04 0.00 3.60
45 46 6.038271 AGTTCAAAATCAGCTGTCTAAAACGT 59.962 34.615 14.67 0.00 0.00 3.99
46 47 5.985781 TCAAAATCAGCTGTCTAAAACGTC 58.014 37.500 14.67 0.00 0.00 4.34
47 48 5.525745 TCAAAATCAGCTGTCTAAAACGTCA 59.474 36.000 14.67 0.00 0.00 4.35
48 49 6.037720 TCAAAATCAGCTGTCTAAAACGTCAA 59.962 34.615 14.67 0.00 0.00 3.18
49 50 6.371809 AAATCAGCTGTCTAAAACGTCAAA 57.628 33.333 14.67 0.00 0.00 2.69
50 51 6.560253 AATCAGCTGTCTAAAACGTCAAAT 57.440 33.333 14.67 0.00 0.00 2.32
51 52 5.342806 TCAGCTGTCTAAAACGTCAAATG 57.657 39.130 14.67 0.00 0.00 2.32
52 53 4.213270 TCAGCTGTCTAAAACGTCAAATGG 59.787 41.667 14.67 0.00 0.00 3.16
53 54 4.213270 CAGCTGTCTAAAACGTCAAATGGA 59.787 41.667 5.25 0.00 0.00 3.41
54 55 4.452455 AGCTGTCTAAAACGTCAAATGGAG 59.548 41.667 0.00 0.00 0.00 3.86
55 56 4.378459 GCTGTCTAAAACGTCAAATGGAGG 60.378 45.833 0.00 0.00 37.42 4.30
56 57 4.069304 TGTCTAAAACGTCAAATGGAGGG 58.931 43.478 0.00 0.00 35.71 4.30
57 58 4.202377 TGTCTAAAACGTCAAATGGAGGGA 60.202 41.667 0.00 0.00 35.71 4.20
58 59 4.392138 GTCTAAAACGTCAAATGGAGGGAG 59.608 45.833 0.00 0.00 35.71 4.30
59 60 2.951229 AAACGTCAAATGGAGGGAGT 57.049 45.000 0.00 0.00 35.71 3.85
60 61 4.360951 AAAACGTCAAATGGAGGGAGTA 57.639 40.909 0.00 0.00 35.71 2.59
61 62 3.611766 AACGTCAAATGGAGGGAGTAG 57.388 47.619 0.00 0.00 35.71 2.57
62 63 1.207329 ACGTCAAATGGAGGGAGTAGC 59.793 52.381 0.00 0.00 35.71 3.58
63 64 1.473434 CGTCAAATGGAGGGAGTAGCC 60.473 57.143 0.00 0.00 0.00 3.93
64 65 1.559682 GTCAAATGGAGGGAGTAGCCA 59.440 52.381 0.00 0.00 38.95 4.75
65 66 2.026262 GTCAAATGGAGGGAGTAGCCAA 60.026 50.000 0.00 0.00 38.95 4.52
66 67 2.647299 TCAAATGGAGGGAGTAGCCAAA 59.353 45.455 0.00 0.00 38.95 3.28
67 68 3.075283 TCAAATGGAGGGAGTAGCCAAAA 59.925 43.478 0.00 0.00 38.95 2.44
68 69 3.825908 AATGGAGGGAGTAGCCAAAAA 57.174 42.857 0.00 0.00 38.95 1.94
76 77 4.139038 GGGAGTAGCCAAAAAGTGTTGTA 58.861 43.478 0.00 0.00 38.95 2.41
81 82 2.032924 AGCCAAAAAGTGTTGTACTCGC 59.967 45.455 0.00 0.00 39.18 5.03
132 133 1.371635 GGTGCGAACATTGTGGTGC 60.372 57.895 0.00 0.00 0.00 5.01
223 227 4.709397 AGTGATTTTGGACCAACTTGTTCA 59.291 37.500 6.36 3.32 0.00 3.18
256 293 3.362791 CGAGACGAGGCTACTATAACACG 60.363 52.174 0.00 0.00 0.00 4.49
268 305 6.417044 GCTACTATAACACGACGAAACATGAT 59.583 38.462 0.00 0.00 0.00 2.45
302 339 5.957842 TGGCAGTCGAATAGTTTTTCAAT 57.042 34.783 0.00 0.00 0.00 2.57
318 356 3.507162 TCAATCAGGAAGCCAAAGACA 57.493 42.857 0.00 0.00 0.00 3.41
319 357 3.149196 TCAATCAGGAAGCCAAAGACAC 58.851 45.455 0.00 0.00 0.00 3.67
436 474 1.337817 CGTCATATCTAGCACGCGGC 61.338 60.000 12.47 11.61 45.30 6.53
456 494 4.722700 CCGTCACCAGCCCCCTTG 62.723 72.222 0.00 0.00 0.00 3.61
460 498 4.305956 CACCAGCCCCCTTGCCTT 62.306 66.667 0.00 0.00 0.00 4.35
461 499 3.984732 ACCAGCCCCCTTGCCTTC 61.985 66.667 0.00 0.00 0.00 3.46
462 500 3.665971 CCAGCCCCCTTGCCTTCT 61.666 66.667 0.00 0.00 0.00 2.85
463 501 2.044551 CAGCCCCCTTGCCTTCTC 60.045 66.667 0.00 0.00 0.00 2.87
464 502 3.342477 AGCCCCCTTGCCTTCTCC 61.342 66.667 0.00 0.00 0.00 3.71
465 503 4.803908 GCCCCCTTGCCTTCTCCG 62.804 72.222 0.00 0.00 0.00 4.63
466 504 4.115199 CCCCCTTGCCTTCTCCGG 62.115 72.222 0.00 0.00 0.00 5.14
467 505 4.115199 CCCCTTGCCTTCTCCGGG 62.115 72.222 0.00 0.00 34.62 5.73
536 594 3.945434 GGCTCCATCGTGCATGCG 61.945 66.667 14.09 0.00 0.00 4.73
584 642 2.436646 GCGTGGCTGGCATGTACT 60.437 61.111 22.31 0.00 0.00 2.73
585 643 2.464459 GCGTGGCTGGCATGTACTC 61.464 63.158 22.31 4.42 0.00 2.59
586 644 1.815421 CGTGGCTGGCATGTACTCC 60.815 63.158 14.69 0.00 0.00 3.85
587 645 1.815421 GTGGCTGGCATGTACTCCG 60.815 63.158 7.33 0.00 0.00 4.63
623 686 3.768215 TCTCATCTCTTCTGACATGTGCT 59.232 43.478 1.15 0.00 0.00 4.40
638 701 0.670162 GTGCTCACAAATGGCAGTGT 59.330 50.000 5.42 3.31 37.07 3.55
647 710 2.859538 CAAATGGCAGTGTCACACAAAC 59.140 45.455 11.40 0.00 36.74 2.93
650 713 1.733526 GCAGTGTCACACAAACCCC 59.266 57.895 11.40 0.00 36.74 4.95
665 730 4.019950 ACAAACCCCAGGTATATATACGCC 60.020 45.833 15.15 4.37 33.12 5.68
686 751 0.520412 CGGCGCAAATACTTCCAACG 60.520 55.000 10.83 0.00 0.00 4.10
802 869 1.199624 GCAACCGAACAACAAAGCAG 58.800 50.000 0.00 0.00 0.00 4.24
823 890 1.133407 CCGTTCTCTCTTCCTTCCTCG 59.867 57.143 0.00 0.00 0.00 4.63
864 931 5.157781 CAACCGTTCTCAAAACACAAGAAA 58.842 37.500 0.00 0.00 31.26 2.52
882 965 6.753744 ACAAGAAACAACAAGAGCAGATTTTC 59.246 34.615 0.00 0.00 0.00 2.29
922 1011 1.248486 CCCAAGCGATCGATCCTCTA 58.752 55.000 21.57 0.00 0.00 2.43
933 1022 1.002684 CGATCCTCTACACTACGTGCC 60.003 57.143 0.00 0.00 36.98 5.01
959 1048 2.863153 GTGACATGCCACGCAGAC 59.137 61.111 0.00 0.00 43.65 3.51
1173 1265 2.430921 GAGGTCAGCGTGGTCGTG 60.431 66.667 0.00 0.00 39.49 4.35
1174 1266 4.664677 AGGTCAGCGTGGTCGTGC 62.665 66.667 0.00 0.00 39.49 5.34
1270 1365 3.009140 CTGATCACGACGGCATGC 58.991 61.111 9.90 9.90 0.00 4.06
1482 1577 0.036952 ATGGACGGAACTGCACTCTG 60.037 55.000 0.00 0.00 0.00 3.35
1584 1690 4.657824 CGGCTGGTGTTCGTCGGT 62.658 66.667 0.00 0.00 0.00 4.69
1590 1696 1.372623 GGTGTTCGTCGGTGACTCC 60.373 63.158 0.00 0.00 0.00 3.85
1635 1741 1.592131 GCTCTGCATGCTCTCCTCG 60.592 63.158 20.33 1.59 0.00 4.63
2199 2315 4.020928 TGAATTTCAGCCATGATTTGCACT 60.021 37.500 0.00 0.00 34.73 4.40
2286 2403 1.450312 CCGGAGCTGAACATGACCC 60.450 63.158 0.00 0.00 0.00 4.46
2365 2482 4.778415 CGTCGTCAGGGACCTGCG 62.778 72.222 21.13 21.13 43.31 5.18
2389 2506 1.544777 CGTGTGATGAACGTGACGCA 61.545 55.000 4.25 0.00 36.31 5.24
2578 2695 2.971915 CGTTCTCTTGACTGACGTGTAC 59.028 50.000 0.00 0.00 0.00 2.90
2640 2757 7.983484 TCCGAAAAGGAGTAATTATTCACCTAC 59.017 37.037 9.86 0.00 45.98 3.18
2720 2840 4.624913 ACTCCTATCCACTTGATGAAGGA 58.375 43.478 0.00 0.00 34.76 3.36
2730 2850 6.057533 CCACTTGATGAAGGAGTGCATATTA 58.942 40.000 0.00 0.00 39.48 0.98
2753 2873 0.035056 GGGCTGCATACTCACACCTT 60.035 55.000 0.50 0.00 0.00 3.50
2832 2952 2.108976 CACACACTGGTCCAGCGT 59.891 61.111 19.40 13.07 34.37 5.07
2834 2954 0.037326 CACACACTGGTCCAGCGTAT 60.037 55.000 19.40 1.12 34.37 3.06
2836 2956 1.071699 ACACACTGGTCCAGCGTATTT 59.928 47.619 19.40 0.74 34.37 1.40
2850 2970 1.529438 CGTATTTTCAGTGTGCACCGT 59.471 47.619 15.69 0.00 0.00 4.83
2853 2973 4.563580 CGTATTTTCAGTGTGCACCGTATA 59.436 41.667 15.69 0.00 0.00 1.47
2854 2974 5.233476 CGTATTTTCAGTGTGCACCGTATAT 59.767 40.000 15.69 2.09 0.00 0.86
2882 3002 3.414700 GAGGCCGTCGCAACAGTG 61.415 66.667 0.00 0.00 36.38 3.66
2883 3003 4.988598 AGGCCGTCGCAACAGTGG 62.989 66.667 0.00 0.00 36.38 4.00
2924 3044 1.787155 GCAGGTACTAATGCATCGACG 59.213 52.381 0.00 0.00 42.11 5.12
2926 3046 3.549423 GCAGGTACTAATGCATCGACGTA 60.549 47.826 0.00 0.00 42.11 3.57
2962 3082 2.367202 CGCCACCACCTCCCTACAT 61.367 63.158 0.00 0.00 0.00 2.29
2986 3106 3.000623 CGTTCATCATCACACATCCTTCG 59.999 47.826 0.00 0.00 0.00 3.79
3148 3268 7.124147 CCATACTGGGTAAAAATCTCATTGGTT 59.876 37.037 0.00 0.00 32.67 3.67
3205 3325 3.633525 TCGGTGTAGCGTAGACCATAAAT 59.366 43.478 3.29 0.00 41.91 1.40
3421 4904 2.729491 GGCGCGCAAACTTGAACC 60.729 61.111 34.42 7.22 0.00 3.62
3576 5060 7.342769 ACCTTTAGTGGAATTTTCGACTTTT 57.657 32.000 12.27 0.00 42.49 2.27
3579 5063 9.908152 CCTTTAGTGGAATTTTCGACTTTTAAT 57.092 29.630 12.27 0.00 42.49 1.40
3608 5093 9.496710 TTCTTGTTATTATTACTGGGACCTCTA 57.503 33.333 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.111098 CTGTTTTGCAAGCTGTCTGAAC 58.889 45.455 0.00 0.00 0.00 3.18
1 2 2.754552 ACTGTTTTGCAAGCTGTCTGAA 59.245 40.909 0.00 0.00 0.00 3.02
2 3 2.368439 ACTGTTTTGCAAGCTGTCTGA 58.632 42.857 0.00 0.00 0.00 3.27
3 4 2.857592 ACTGTTTTGCAAGCTGTCTG 57.142 45.000 0.00 0.00 0.00 3.51
4 5 2.754552 TGAACTGTTTTGCAAGCTGTCT 59.245 40.909 13.11 6.73 0.00 3.41
5 6 3.149436 TGAACTGTTTTGCAAGCTGTC 57.851 42.857 13.11 9.15 0.00 3.51
6 7 3.591196 TTGAACTGTTTTGCAAGCTGT 57.409 38.095 0.00 4.64 0.00 4.40
7 8 4.925061 TTTTGAACTGTTTTGCAAGCTG 57.075 36.364 0.00 4.01 0.00 4.24
8 9 5.177326 TGATTTTGAACTGTTTTGCAAGCT 58.823 33.333 0.00 0.00 0.00 3.74
9 10 5.467902 TGATTTTGAACTGTTTTGCAAGC 57.532 34.783 0.00 0.00 0.00 4.01
10 11 5.292589 AGCTGATTTTGAACTGTTTTGCAAG 59.707 36.000 0.00 0.00 0.00 4.01
11 12 5.063691 CAGCTGATTTTGAACTGTTTTGCAA 59.936 36.000 8.42 0.00 0.00 4.08
12 13 4.567558 CAGCTGATTTTGAACTGTTTTGCA 59.432 37.500 8.42 0.00 0.00 4.08
13 14 4.567959 ACAGCTGATTTTGAACTGTTTTGC 59.432 37.500 23.35 0.00 38.38 3.68
14 15 6.038356 AGACAGCTGATTTTGAACTGTTTTG 58.962 36.000 23.35 0.00 41.45 2.44
15 16 6.212888 AGACAGCTGATTTTGAACTGTTTT 57.787 33.333 23.35 0.00 41.45 2.43
16 17 5.841957 AGACAGCTGATTTTGAACTGTTT 57.158 34.783 23.35 0.00 41.45 2.83
17 18 6.942532 TTAGACAGCTGATTTTGAACTGTT 57.057 33.333 23.35 0.00 41.45 3.16
18 19 6.942532 TTTAGACAGCTGATTTTGAACTGT 57.057 33.333 23.35 0.00 43.93 3.55
19 20 6.358030 CGTTTTAGACAGCTGATTTTGAACTG 59.642 38.462 23.35 9.82 0.00 3.16
20 21 6.038271 ACGTTTTAGACAGCTGATTTTGAACT 59.962 34.615 23.35 8.36 0.00 3.01
21 22 6.199393 ACGTTTTAGACAGCTGATTTTGAAC 58.801 36.000 23.35 15.30 0.00 3.18
22 23 6.037720 TGACGTTTTAGACAGCTGATTTTGAA 59.962 34.615 23.35 4.96 0.00 2.69
23 24 5.525745 TGACGTTTTAGACAGCTGATTTTGA 59.474 36.000 23.35 0.00 0.00 2.69
24 25 5.747565 TGACGTTTTAGACAGCTGATTTTG 58.252 37.500 23.35 4.64 0.00 2.44
25 26 6.371809 TTGACGTTTTAGACAGCTGATTTT 57.628 33.333 23.35 0.00 0.00 1.82
26 27 6.371809 TTTGACGTTTTAGACAGCTGATTT 57.628 33.333 23.35 7.66 0.00 2.17
27 28 6.373779 CATTTGACGTTTTAGACAGCTGATT 58.626 36.000 23.35 10.36 0.00 2.57
28 29 5.106555 CCATTTGACGTTTTAGACAGCTGAT 60.107 40.000 23.35 11.17 0.00 2.90
29 30 4.213270 CCATTTGACGTTTTAGACAGCTGA 59.787 41.667 23.35 0.00 0.00 4.26
30 31 4.213270 TCCATTTGACGTTTTAGACAGCTG 59.787 41.667 13.48 13.48 0.00 4.24
31 32 4.385825 TCCATTTGACGTTTTAGACAGCT 58.614 39.130 0.00 0.00 0.00 4.24
32 33 4.378459 CCTCCATTTGACGTTTTAGACAGC 60.378 45.833 0.00 0.00 0.00 4.40
33 34 4.154195 CCCTCCATTTGACGTTTTAGACAG 59.846 45.833 0.00 0.00 0.00 3.51
34 35 4.069304 CCCTCCATTTGACGTTTTAGACA 58.931 43.478 0.00 0.00 0.00 3.41
35 36 4.320870 TCCCTCCATTTGACGTTTTAGAC 58.679 43.478 0.00 0.00 0.00 2.59
36 37 4.041198 ACTCCCTCCATTTGACGTTTTAGA 59.959 41.667 0.00 0.00 0.00 2.10
37 38 4.324267 ACTCCCTCCATTTGACGTTTTAG 58.676 43.478 0.00 0.00 0.00 1.85
38 39 4.360951 ACTCCCTCCATTTGACGTTTTA 57.639 40.909 0.00 0.00 0.00 1.52
39 40 3.223674 ACTCCCTCCATTTGACGTTTT 57.776 42.857 0.00 0.00 0.00 2.43
40 41 2.951229 ACTCCCTCCATTTGACGTTT 57.049 45.000 0.00 0.00 0.00 3.60
41 42 2.354805 GCTACTCCCTCCATTTGACGTT 60.355 50.000 0.00 0.00 0.00 3.99
42 43 1.207329 GCTACTCCCTCCATTTGACGT 59.793 52.381 0.00 0.00 0.00 4.34
43 44 1.473434 GGCTACTCCCTCCATTTGACG 60.473 57.143 0.00 0.00 0.00 4.35
44 45 1.559682 TGGCTACTCCCTCCATTTGAC 59.440 52.381 0.00 0.00 0.00 3.18
45 46 1.965414 TGGCTACTCCCTCCATTTGA 58.035 50.000 0.00 0.00 0.00 2.69
46 47 2.806945 TTGGCTACTCCCTCCATTTG 57.193 50.000 0.00 0.00 0.00 2.32
47 48 3.825908 TTTTGGCTACTCCCTCCATTT 57.174 42.857 0.00 0.00 0.00 2.32
48 49 3.076032 ACTTTTTGGCTACTCCCTCCATT 59.924 43.478 0.00 0.00 0.00 3.16
49 50 2.649816 ACTTTTTGGCTACTCCCTCCAT 59.350 45.455 0.00 0.00 0.00 3.41
50 51 2.062636 ACTTTTTGGCTACTCCCTCCA 58.937 47.619 0.00 0.00 0.00 3.86
51 52 2.224793 ACACTTTTTGGCTACTCCCTCC 60.225 50.000 0.00 0.00 0.00 4.30
52 53 3.141767 ACACTTTTTGGCTACTCCCTC 57.858 47.619 0.00 0.00 0.00 4.30
53 54 3.222603 CAACACTTTTTGGCTACTCCCT 58.777 45.455 0.00 0.00 0.00 4.20
54 55 2.956333 ACAACACTTTTTGGCTACTCCC 59.044 45.455 0.00 0.00 0.00 4.30
55 56 4.820173 AGTACAACACTTTTTGGCTACTCC 59.180 41.667 0.00 0.00 31.59 3.85
56 57 5.333111 CGAGTACAACACTTTTTGGCTACTC 60.333 44.000 0.00 0.00 37.72 2.59
57 58 4.510340 CGAGTACAACACTTTTTGGCTACT 59.490 41.667 0.00 0.00 37.72 2.57
58 59 4.769215 CGAGTACAACACTTTTTGGCTAC 58.231 43.478 0.00 0.00 37.72 3.58
59 60 3.249080 GCGAGTACAACACTTTTTGGCTA 59.751 43.478 0.00 0.00 37.72 3.93
60 61 2.032924 GCGAGTACAACACTTTTTGGCT 59.967 45.455 0.00 0.00 37.72 4.75
61 62 2.032924 AGCGAGTACAACACTTTTTGGC 59.967 45.455 0.00 0.00 37.72 4.52
62 63 3.303791 GGAGCGAGTACAACACTTTTTGG 60.304 47.826 0.00 0.00 37.72 3.28
63 64 3.560068 AGGAGCGAGTACAACACTTTTTG 59.440 43.478 0.00 0.00 37.72 2.44
64 65 3.805207 AGGAGCGAGTACAACACTTTTT 58.195 40.909 0.00 0.00 37.72 1.94
65 66 3.470645 AGGAGCGAGTACAACACTTTT 57.529 42.857 0.00 0.00 37.72 2.27
66 67 3.573110 AGTAGGAGCGAGTACAACACTTT 59.427 43.478 0.00 0.00 37.72 2.66
67 68 3.155501 AGTAGGAGCGAGTACAACACTT 58.844 45.455 0.00 0.00 37.72 3.16
68 69 2.748532 GAGTAGGAGCGAGTACAACACT 59.251 50.000 0.00 0.00 41.47 3.55
76 77 0.820074 CATCGGGAGTAGGAGCGAGT 60.820 60.000 0.00 0.00 0.00 4.18
81 82 2.953284 TACCTCATCGGGAGTAGGAG 57.047 55.000 6.20 0.00 42.40 3.69
112 113 0.238289 CACCACAATGTTCGCACCTC 59.762 55.000 0.00 0.00 0.00 3.85
132 133 2.695666 ACTGTCCCTCTACATCCATTCG 59.304 50.000 0.00 0.00 0.00 3.34
223 227 2.607187 CCTCGTCTCGTGTTTAAGCAT 58.393 47.619 0.00 0.00 0.00 3.79
256 293 3.127548 AGTGCCAATCATCATGTTTCGTC 59.872 43.478 0.00 0.00 0.00 4.20
268 305 0.961019 GACTGCCAAAGTGCCAATCA 59.039 50.000 0.00 0.00 40.07 2.57
286 323 6.128007 GGCTTCCTGATTGAAAAACTATTCGA 60.128 38.462 0.00 0.00 31.80 3.71
287 324 6.030228 GGCTTCCTGATTGAAAAACTATTCG 58.970 40.000 0.00 0.00 31.80 3.34
302 339 0.250295 CCGTGTCTTTGGCTTCCTGA 60.250 55.000 0.00 0.00 0.00 3.86
318 356 2.281692 TGCACATGCTCAAGCCGT 60.282 55.556 5.31 0.00 42.66 5.68
319 357 2.177531 GTGCACATGCTCAAGCCG 59.822 61.111 13.17 0.00 42.66 5.52
383 421 1.381056 AGTCTGGCCGCTCTCATCT 60.381 57.895 0.00 0.00 0.00 2.90
408 446 6.068300 CGTGCTAGATATGACGATATCGATC 58.932 44.000 30.75 21.16 43.74 3.69
439 477 4.722700 CAAGGGGGCTGGTGACGG 62.723 72.222 0.00 0.00 40.79 4.79
448 486 4.803908 CGGAGAAGGCAAGGGGGC 62.804 72.222 0.00 0.00 43.80 5.80
449 487 4.115199 CCGGAGAAGGCAAGGGGG 62.115 72.222 0.00 0.00 0.00 5.40
450 488 4.115199 CCCGGAGAAGGCAAGGGG 62.115 72.222 0.73 0.00 38.44 4.79
458 496 3.391665 ATGCCTTCGCCCGGAGAAG 62.392 63.158 24.02 24.02 43.35 2.85
459 497 3.385749 GATGCCTTCGCCCGGAGAA 62.386 63.158 0.73 7.66 0.00 2.87
460 498 3.849951 GATGCCTTCGCCCGGAGA 61.850 66.667 0.73 0.00 0.00 3.71
570 628 0.973496 TACGGAGTACATGCCAGCCA 60.973 55.000 0.00 0.00 45.11 4.75
623 686 1.675483 GTGTGACACTGCCATTTGTGA 59.325 47.619 8.76 0.00 37.59 3.58
638 701 6.239373 CGTATATATACCTGGGGTTTGTGTGA 60.239 42.308 15.70 0.00 37.09 3.58
647 710 2.100252 CGTGGCGTATATATACCTGGGG 59.900 54.545 15.70 4.30 0.00 4.96
650 713 2.805845 GCCGTGGCGTATATATACCTG 58.194 52.381 15.70 5.56 0.00 4.00
665 730 0.519519 TTGGAAGTATTTGCGCCGTG 59.480 50.000 4.18 0.00 0.00 4.94
728 793 1.578206 GAGGAAACTTGGCGGAGTGC 61.578 60.000 0.00 0.00 44.43 4.40
733 798 0.323629 TAGTGGAGGAAACTTGGCGG 59.676 55.000 0.00 0.00 44.43 6.13
802 869 0.899019 AGGAAGGAAGAGAGAACGGC 59.101 55.000 0.00 0.00 0.00 5.68
864 931 3.003689 CGTGGAAAATCTGCTCTTGTTGT 59.996 43.478 0.00 0.00 0.00 3.32
933 1022 2.259618 GTGGCATGTCACGTAGTAGTG 58.740 52.381 15.79 0.00 41.61 2.74
945 1034 3.043713 CGTGTCTGCGTGGCATGT 61.044 61.111 8.75 0.00 38.13 3.21
955 1044 1.734477 CGAGACTTGGCCGTGTCTG 60.734 63.158 27.94 18.26 42.79 3.51
958 1047 2.651361 CTCGAGACTTGGCCGTGT 59.349 61.111 6.58 0.00 0.00 4.49
959 1048 2.811317 GCTCGAGACTTGGCCGTG 60.811 66.667 18.75 0.00 0.00 4.94
1155 1247 2.597805 ACGACCACGCTGACCTCT 60.598 61.111 0.00 0.00 43.96 3.69
1253 1348 0.249031 TAGCATGCCGTCGTGATCAG 60.249 55.000 15.66 0.00 0.00 2.90
1270 1365 2.202570 CCACTCGCCGTCGGTTAG 60.203 66.667 13.94 12.76 36.13 2.34
1317 1412 1.716826 GGCACTCCCTCGAGTCGTAG 61.717 65.000 13.12 8.55 46.90 3.51
1436 1531 4.201679 CATGCCGCCATGGTGCAG 62.202 66.667 27.42 18.62 44.07 4.41
1455 1550 0.984230 AGTTCCGTCCATGACACCAT 59.016 50.000 0.00 0.00 32.09 3.55
1456 1551 0.034756 CAGTTCCGTCCATGACACCA 59.965 55.000 0.00 0.00 32.09 4.17
1457 1552 1.298859 GCAGTTCCGTCCATGACACC 61.299 60.000 0.00 0.00 32.09 4.16
1468 1563 1.581934 TCAAACAGAGTGCAGTTCCG 58.418 50.000 0.00 0.00 0.00 4.30
1584 1690 3.700970 TTGCGCCCGATGGAGTCA 61.701 61.111 4.18 0.00 33.30 3.41
1590 1696 3.803082 CACTGGTTGCGCCCGATG 61.803 66.667 4.18 0.00 36.04 3.84
1947 2053 2.306847 ACCCGAGCAAACATTTCAAGT 58.693 42.857 0.00 0.00 0.00 3.16
1951 2057 1.611491 TGGAACCCGAGCAAACATTTC 59.389 47.619 0.00 0.00 0.00 2.17
1957 2063 1.976474 GCCATGGAACCCGAGCAAA 60.976 57.895 18.40 0.00 0.00 3.68
2365 2482 0.161658 CACGTTCATCACACGCAGAC 59.838 55.000 0.00 0.00 41.53 3.51
2389 2506 3.362399 CTCCTGTGCGCCGTCATCT 62.362 63.158 4.18 0.00 0.00 2.90
2578 2695 4.109766 TCCAAATGCGAAGTAGATGTACG 58.890 43.478 0.00 0.00 33.97 3.67
2615 2732 7.767198 TGTAGGTGAATAATTACTCCTTTTCGG 59.233 37.037 2.97 0.00 33.14 4.30
2691 2811 6.212589 TCATCAAGTGGATAGGAGTAACAACA 59.787 38.462 0.00 0.00 33.95 3.33
2692 2812 6.640518 TCATCAAGTGGATAGGAGTAACAAC 58.359 40.000 0.00 0.00 33.95 3.32
2720 2840 1.611673 GCAGCCCCGATAATATGCACT 60.612 52.381 0.00 0.00 33.92 4.40
2730 2850 1.337384 TGTGAGTATGCAGCCCCGAT 61.337 55.000 0.00 0.00 0.00 4.18
2753 2873 2.969821 AGATGTTGGGCTTTGGTGTA 57.030 45.000 0.00 0.00 0.00 2.90
2832 2952 5.007234 GCATATACGGTGCACACTGAAAATA 59.993 40.000 20.43 10.39 42.08 1.40
2834 2954 3.126171 GCATATACGGTGCACACTGAAAA 59.874 43.478 20.43 2.15 42.08 2.29
2836 2956 2.276201 GCATATACGGTGCACACTGAA 58.724 47.619 20.43 0.63 42.08 3.02
2882 3002 4.336713 GCTCTAAAGATGAATTGGTGGACC 59.663 45.833 0.00 0.00 0.00 4.46
2883 3003 4.943705 TGCTCTAAAGATGAATTGGTGGAC 59.056 41.667 0.00 0.00 0.00 4.02
2900 3020 4.023107 GTCGATGCATTAGTACCTGCTCTA 60.023 45.833 0.00 0.00 39.16 2.43
2962 3082 2.009051 GGATGTGTGATGATGAACGCA 58.991 47.619 0.00 0.00 40.76 5.24
2986 3106 5.054390 TCGAAATCAATAAACTGTTGGGC 57.946 39.130 0.00 0.00 0.00 5.36
3148 3268 1.925847 GTTGTTCACGACGGTGTGTAA 59.074 47.619 0.00 1.19 44.68 2.41
3372 3494 7.502226 TCCAAATAGCGTTCAATCTTTATCCAT 59.498 33.333 0.00 0.00 0.00 3.41
3421 4904 3.052036 CAATCAAGCACCACTTTTTCCG 58.948 45.455 0.00 0.00 36.04 4.30
3579 5063 9.816787 AGGTCCCAGTAATAATAACAAGAAAAA 57.183 29.630 0.00 0.00 0.00 1.94
3608 5093 1.271379 TCTACCATCGCTCACACGTTT 59.729 47.619 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.