Multiple sequence alignment - TraesCS3B01G055800

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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 TraesCS3B01G055800 chr3B 100.000 3668 0 0 1 3668 29499628 29495961 0.000000e+00 6774.0
1 TraesCS3B01G055800 chr3B 94.597 1129 18 4 2475 3560 30005917 30004789 0.000000e+00 1707.0
2 TraesCS3B01G055800 chr3B 93.933 923 46 3 717 1630 30016674 30015753 0.000000e+00 1386.0
3 TraesCS3B01G055800 chr3B 95.000 680 23 6 1789 2464 30006808 30006136 0.000000e+00 1057.0
4 TraesCS3B01G055800 chr3B 80.965 767 115 15 2605 3351 29774707 29775462 2.460000e-161 579.0
5 TraesCS3B01G055800 chr3B 78.579 901 151 21 2475 3355 29776785 29777663 1.150000e-154 556.0
6 TraesCS3B01G055800 chr3B 78.532 899 148 29 2475 3355 30498190 30499061 1.930000e-152 549.0
7 TraesCS3B01G055800 chr3B 77.849 939 153 33 2475 3390 30508841 30509747 6.970000e-147 531.0
8 TraesCS3B01G055800 chr3B 78.529 843 146 18 2531 3355 30199926 30200751 4.200000e-144 521.0
9 TraesCS3B01G055800 chr3B 80.456 701 108 15 2657 3338 24928705 24929395 3.270000e-140 508.0
10 TraesCS3B01G055800 chr3B 92.378 328 18 4 1628 1953 30007131 30006809 9.280000e-126 460.0
11 TraesCS3B01G055800 chr3B 97.107 242 7 0 2 243 29505199 29504958 3.410000e-110 409.0
12 TraesCS3B01G055800 chr3B 96.694 242 8 0 2 243 29510826 29510585 1.590000e-108 403.0
13 TraesCS3B01G055800 chr3B 89.600 250 26 0 1036 1285 29689890 29690139 5.910000e-83 318.0
14 TraesCS3B01G055800 chr3B 88.492 252 22 3 763 1013 29689363 29689608 7.700000e-77 298.0
15 TraesCS3B01G055800 chr3B 94.152 171 6 1 536 706 30016891 30016725 1.310000e-64 257.0
16 TraesCS3B01G055800 chr3B 97.436 117 2 1 3552 3668 30003703 30003588 8.030000e-47 198.0
17 TraesCS3B01G055800 chr3B 74.098 305 56 16 2077 2361 30442916 30443217 1.800000e-18 104.0
18 TraesCS3B01G055800 chr3B 89.552 67 7 0 2077 2143 30374878 30374944 6.530000e-13 86.1
19 TraesCS3B01G055800 chr3B 89.552 67 7 0 2077 2143 30508736 30508802 6.530000e-13 86.1
20 TraesCS3B01G055800 chr3B 85.915 71 6 2 2077 2143 29724222 29724292 5.080000e-09 73.1
21 TraesCS3B01G055800 chr3D 91.844 1079 46 20 2570 3618 18815457 18816523 0.000000e+00 1467.0
22 TraesCS3B01G055800 chr3D 85.057 609 60 20 1009 1606 18811677 18812265 3.150000e-165 592.0
23 TraesCS3B01G055800 chr3D 82.889 637 85 8 2652 3270 17538052 17537422 5.350000e-153 551.0
24 TraesCS3B01G055800 chr3D 81.567 651 99 5 2635 3270 17357434 17358078 5.430000e-143 518.0
25 TraesCS3B01G055800 chr3D 80.995 563 83 14 2478 3038 18793085 18793625 3.390000e-115 425.0
26 TraesCS3B01G055800 chr3D 79.121 637 100 17 2658 3273 17670800 17670176 3.410000e-110 409.0
27 TraesCS3B01G055800 chr3D 81.742 356 45 15 2056 2403 18814854 18815197 2.790000e-71 279.0
28 TraesCS3B01G055800 chr3D 96.721 61 1 1 2475 2535 18815395 18815454 2.330000e-17 100.0
29 TraesCS3B01G055800 chr3D 93.548 62 4 0 2082 2143 18794670 18794731 3.900000e-15 93.5
30 TraesCS3B01G055800 chr3D 94.545 55 3 0 2657 2711 11332095 11332149 6.530000e-13 86.1
31 TraesCS3B01G055800 chr3D 86.567 67 9 0 2077 2143 18943668 18943734 1.410000e-09 75.0
32 TraesCS3B01G055800 chr3D 97.143 35 1 0 3634 3668 18816507 18816541 3.960000e-05 60.2
33 TraesCS3B01G055800 chr5B 88.561 542 49 8 3 537 546966833 546967368 0.000000e+00 645.0
34 TraesCS3B01G055800 chr5A 88.462 546 39 11 12 535 442715652 442716195 3.990000e-179 638.0
35 TraesCS3B01G055800 chr3A 81.268 694 112 8 2657 3338 19275657 19276344 2.490000e-151 545.0
36 TraesCS3B01G055800 chr3A 80.512 703 117 9 2652 3341 19491546 19490851 4.200000e-144 521.0
37 TraesCS3B01G055800 chr3A 80.000 580 81 17 2657 3220 25993943 25993383 2.650000e-106 396.0
38 TraesCS3B01G055800 chr3A 75.000 824 162 20 2605 3398 26257492 26258301 1.260000e-89 340.0
39 TraesCS3B01G055800 chr3A 93.651 63 4 0 2078 2140 26204124 26204186 1.080000e-15 95.3
40 TraesCS3B01G055800 chr1B 93.243 296 19 1 244 538 600019903 600019608 5.630000e-118 435.0
41 TraesCS3B01G055800 chr1B 97.521 242 6 0 2 243 4119698 4119457 7.330000e-112 414.0
42 TraesCS3B01G055800 chr1B 97.521 242 6 0 2 243 4125349 4125108 7.330000e-112 414.0
43 TraesCS3B01G055800 chr7B 93.151 292 20 0 244 535 165097675 165097966 2.620000e-116 429.0
44 TraesCS3B01G055800 chr6B 92.929 297 16 2 244 535 2005505 2005801 9.410000e-116 427.0
45 TraesCS3B01G055800 chr6B 96.694 242 8 0 2 243 2010674 2010915 1.590000e-108 403.0
46 TraesCS3B01G055800 chr6B 96.694 242 8 0 2 243 2031810 2032051 1.590000e-108 403.0
47 TraesCS3B01G055800 chr6B 96.281 242 9 0 2 243 2022041 2022282 7.380000e-107 398.0
48 TraesCS3B01G055800 chr1D 92.881 295 20 1 244 538 271294004 271293711 9.410000e-116 427.0
49 TraesCS3B01G055800 chr4A 93.151 292 14 3 244 535 736952497 736952782 1.220000e-114 424.0
50 TraesCS3B01G055800 chr2A 92.256 297 21 2 244 539 717838466 717838171 1.580000e-113 420.0
51 TraesCS3B01G055800 chr2B 92.491 293 20 2 244 535 1288313 1288604 5.670000e-113 418.0
52 TraesCS3B01G055800 chr6D 92.203 295 22 1 244 538 367381428 367381135 2.040000e-112 416.0


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 TraesCS3B01G055800 chr3B 29495961 29499628 3667 True 6774.00 6774 100.00000 1 3668 1 chr3B.!!$R1 3667
1 TraesCS3B01G055800 chr3B 30003588 30007131 3543 True 855.50 1707 94.85275 1628 3668 4 chr3B.!!$R4 2040
2 TraesCS3B01G055800 chr3B 30015753 30016891 1138 True 821.50 1386 94.04250 536 1630 2 chr3B.!!$R5 1094
3 TraesCS3B01G055800 chr3B 29774707 29777663 2956 False 567.50 579 79.77200 2475 3355 2 chr3B.!!$F8 880
4 TraesCS3B01G055800 chr3B 30498190 30499061 871 False 549.00 549 78.53200 2475 3355 1 chr3B.!!$F6 880
5 TraesCS3B01G055800 chr3B 30199926 30200751 825 False 521.00 521 78.52900 2531 3355 1 chr3B.!!$F3 824
6 TraesCS3B01G055800 chr3B 24928705 24929395 690 False 508.00 508 80.45600 2657 3338 1 chr3B.!!$F1 681
7 TraesCS3B01G055800 chr3B 30508736 30509747 1011 False 308.55 531 83.70050 2077 3390 2 chr3B.!!$F9 1313
8 TraesCS3B01G055800 chr3B 29689363 29690139 776 False 308.00 318 89.04600 763 1285 2 chr3B.!!$F7 522
9 TraesCS3B01G055800 chr3D 17537422 17538052 630 True 551.00 551 82.88900 2652 3270 1 chr3D.!!$R1 618
10 TraesCS3B01G055800 chr3D 17357434 17358078 644 False 518.00 518 81.56700 2635 3270 1 chr3D.!!$F2 635
11 TraesCS3B01G055800 chr3D 18811677 18816541 4864 False 499.64 1467 90.50140 1009 3668 5 chr3D.!!$F5 2659
12 TraesCS3B01G055800 chr3D 17670176 17670800 624 True 409.00 409 79.12100 2658 3273 1 chr3D.!!$R2 615
13 TraesCS3B01G055800 chr3D 18793085 18794731 1646 False 259.25 425 87.27150 2082 3038 2 chr3D.!!$F4 956
14 TraesCS3B01G055800 chr5B 546966833 546967368 535 False 645.00 645 88.56100 3 537 1 chr5B.!!$F1 534
15 TraesCS3B01G055800 chr5A 442715652 442716195 543 False 638.00 638 88.46200 12 535 1 chr5A.!!$F1 523
16 TraesCS3B01G055800 chr3A 19275657 19276344 687 False 545.00 545 81.26800 2657 3338 1 chr3A.!!$F1 681
17 TraesCS3B01G055800 chr3A 19490851 19491546 695 True 521.00 521 80.51200 2652 3341 1 chr3A.!!$R1 689
18 TraesCS3B01G055800 chr3A 25993383 25993943 560 True 396.00 396 80.00000 2657 3220 1 chr3A.!!$R2 563
19 TraesCS3B01G055800 chr3A 26257492 26258301 809 False 340.00 340 75.00000 2605 3398 1 chr3A.!!$F3 793

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
121 123 0.389757 GAGGCCTATTGTCCCGACTC 59.610 60.0 4.42 0.0 0.00 3.36 F
1127 1464 0.252742 ACCATCTCCGACCCCTTCTT 60.253 55.0 0.00 0.0 0.00 2.52 F
1637 1991 0.389166 ACTACGAGCAGCTCAGCAAC 60.389 55.0 22.49 0.0 36.85 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 2000 0.035056 GTGGACCCCATGACAAGAGG 60.035 60.000 0.0 0.0 35.28 3.69 R
2404 5066 0.555769 AAGCACTGTTCCTTTGGGGA 59.444 50.000 0.0 0.0 43.41 4.81 R
3280 8410 1.004440 GAGGCACAGGAACTTCGCT 60.004 57.895 0.0 0.0 34.60 4.93 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
23 24 1.548719 ACCAGATCGTCCGTGATGAAA 59.451 47.619 0.81 0.00 31.01 2.69
89 91 2.168496 TCTCCCGTACAGGACTCAAAG 58.832 52.381 0.00 0.00 45.00 2.77
90 92 2.168496 CTCCCGTACAGGACTCAAAGA 58.832 52.381 0.00 0.00 45.00 2.52
110 112 2.363975 TGCGGTTTCGGAGGCCTAT 61.364 57.895 4.42 0.00 36.79 2.57
120 122 1.049289 GGAGGCCTATTGTCCCGACT 61.049 60.000 4.42 0.00 0.00 4.18
121 123 0.389757 GAGGCCTATTGTCCCGACTC 59.610 60.000 4.42 0.00 0.00 3.36
158 160 1.227089 CGGGATGAGGAAGACAGCG 60.227 63.158 0.00 0.00 0.00 5.18
221 225 0.884514 CTGGTGCGTCTCTCTGAGAA 59.115 55.000 8.95 0.00 40.59 2.87
239 243 3.108376 AGAAGAGCGACCTCCCTTTTAT 58.892 45.455 0.00 0.00 38.96 1.40
240 244 4.287552 AGAAGAGCGACCTCCCTTTTATA 58.712 43.478 0.00 0.00 38.96 0.98
241 245 4.342665 AGAAGAGCGACCTCCCTTTTATAG 59.657 45.833 0.00 0.00 38.96 1.31
242 246 2.966516 AGAGCGACCTCCCTTTTATAGG 59.033 50.000 0.00 0.00 44.33 2.57
243 247 2.699321 GAGCGACCTCCCTTTTATAGGT 59.301 50.000 0.00 0.00 46.33 3.08
244 248 3.113043 AGCGACCTCCCTTTTATAGGTT 58.887 45.455 0.00 0.00 43.69 3.50
340 376 2.579201 CTCGCGTGGATGTCCCTT 59.421 61.111 5.77 0.00 35.38 3.95
365 401 4.020307 TGTTCTCATGCTCATACAAGTGGA 60.020 41.667 0.00 0.00 0.00 4.02
397 434 5.340863 CCTCCCTTATAAGGTGGTCCAATTT 60.341 44.000 26.38 0.00 44.98 1.82
399 436 5.494706 TCCCTTATAAGGTGGTCCAATTTCT 59.505 40.000 26.38 0.00 44.98 2.52
555 592 3.665675 CTCTGCCCACGTAGCCACC 62.666 68.421 7.24 0.00 0.00 4.61
556 593 4.778143 CTGCCCACGTAGCCACCC 62.778 72.222 7.24 0.00 0.00 4.61
600 637 2.230508 TGTAACAGTAGCCACCTCTTCG 59.769 50.000 0.00 0.00 0.00 3.79
601 638 1.339097 AACAGTAGCCACCTCTTCGT 58.661 50.000 0.00 0.00 0.00 3.85
602 639 0.603569 ACAGTAGCCACCTCTTCGTG 59.396 55.000 0.00 0.00 0.00 4.35
603 640 0.603569 CAGTAGCCACCTCTTCGTGT 59.396 55.000 0.00 0.00 31.47 4.49
604 641 0.603569 AGTAGCCACCTCTTCGTGTG 59.396 55.000 0.00 0.00 31.47 3.82
683 720 1.483827 CATCTGCCTTACTCTGCCTCA 59.516 52.381 0.00 0.00 0.00 3.86
706 743 1.217244 CCTACAGCCACACGGTACC 59.783 63.158 0.16 0.16 33.28 3.34
707 744 1.217244 CTACAGCCACACGGTACCC 59.783 63.158 6.25 0.00 33.28 3.69
730 807 1.441729 CGGACACCATACGGCATCT 59.558 57.895 0.00 0.00 34.57 2.90
736 813 1.410517 CACCATACGGCATCTGAGACT 59.589 52.381 0.00 0.00 34.57 3.24
770 847 9.745880 ATTCATGATCTTGTCTTGCAATAATTC 57.254 29.630 0.00 0.00 36.36 2.17
816 893 1.703438 GCTTGATCTGCAGCCACTCG 61.703 60.000 9.47 2.44 0.00 4.18
922 1000 1.089920 CCAAAGACTCCATTGCTCCG 58.910 55.000 0.00 0.00 0.00 4.63
977 1055 2.043752 TCGTGTATCTCCCCGCCA 60.044 61.111 0.00 0.00 0.00 5.69
1122 1459 2.435693 CCTGACCATCTCCGACCCC 61.436 68.421 0.00 0.00 0.00 4.95
1127 1464 0.252742 ACCATCTCCGACCCCTTCTT 60.253 55.000 0.00 0.00 0.00 2.52
1335 1682 2.783135 CACCTGCCAACTAGTGATGTT 58.217 47.619 0.00 0.00 31.79 2.71
1349 1696 3.389329 AGTGATGTTGAACACCTCTGTCT 59.611 43.478 0.00 0.00 37.69 3.41
1355 1702 4.161565 TGTTGAACACCTCTGTCTAAGTGT 59.838 41.667 0.00 0.00 45.02 3.55
1413 1767 3.088532 TCATCTTGTACAATTGCACCCC 58.911 45.455 9.13 0.00 0.00 4.95
1447 1801 1.739562 GGCTGCAGAACGTCAGGAG 60.740 63.158 20.43 2.21 0.00 3.69
1488 1842 2.432444 CATTAGGTGCGGGAAAGACAA 58.568 47.619 0.00 0.00 0.00 3.18
1534 1888 2.472397 GCGTTACGATGAGACAAGCAAC 60.472 50.000 9.62 0.00 0.00 4.17
1558 1912 1.464376 GCAGCTACGCCATAGAGGGA 61.464 60.000 0.00 0.00 38.09 4.20
1637 1991 0.389166 ACTACGAGCAGCTCAGCAAC 60.389 55.000 22.49 0.00 36.85 4.17
1642 1996 0.738762 GAGCAGCTCAGCAACGATGA 60.739 55.000 18.17 0.00 36.85 2.92
1646 2000 1.392853 CAGCTCAGCAACGATGACTTC 59.607 52.381 0.00 0.00 0.00 3.01
1695 2049 3.055094 ACTGAGTTCACCCGCTTAATCAT 60.055 43.478 0.00 0.00 0.00 2.45
1746 2100 6.629156 AGGATTGAGAACAGGTCTAGGATAT 58.371 40.000 0.00 0.00 36.41 1.63
1751 3575 8.921353 TTGAGAACAGGTCTAGGATATAGTAC 57.079 38.462 0.00 0.00 36.41 2.73
1752 3576 7.160049 TGAGAACAGGTCTAGGATATAGTACG 58.840 42.308 0.00 0.00 36.41 3.67
1760 3584 6.827762 GGTCTAGGATATAGTACGGTGCTATT 59.172 42.308 21.15 10.97 32.15 1.73
1833 3824 1.933765 AGGTAGTCCTGGATGGTCTCT 59.066 52.381 0.00 0.00 43.33 3.10
1937 4386 6.098409 AGGACTAATTAGTGGTACTCATGGTG 59.902 42.308 22.68 0.00 36.50 4.17
1973 4422 8.853077 ACAATCTATCATGTCAAGAAACTTGA 57.147 30.769 9.67 9.67 37.61 3.02
2037 4486 5.779529 ATACGACAGGAACGTTACCATAT 57.220 39.130 6.97 0.00 43.62 1.78
2066 4703 6.900299 GCTGTCAACGTATTTATTTCTGCTAC 59.100 38.462 0.00 0.00 0.00 3.58
2181 4840 8.530311 CACCATGCTCTTCATAATATCTAGTCT 58.470 37.037 0.00 0.00 33.19 3.24
2323 4985 2.358247 CGGCCGGTTGCTACAAGT 60.358 61.111 20.10 0.00 40.92 3.16
2331 4993 1.404315 GGTTGCTACAAGTCCTCCTCG 60.404 57.143 0.00 0.00 0.00 4.63
2366 5028 1.340308 TGCTTCATGCTACTGTGCCAT 60.340 47.619 0.00 0.00 43.37 4.40
2403 5065 4.124238 GGCAACCTGCGTACATCTAATAA 58.876 43.478 0.00 0.00 46.21 1.40
2404 5066 4.755123 GGCAACCTGCGTACATCTAATAAT 59.245 41.667 0.00 0.00 46.21 1.28
2408 5070 4.020485 ACCTGCGTACATCTAATAATCCCC 60.020 45.833 0.00 0.00 0.00 4.81
2412 5074 5.995282 TGCGTACATCTAATAATCCCCAAAG 59.005 40.000 0.00 0.00 0.00 2.77
2429 5091 4.443315 CCCAAAGGAACAGTGCTTCAAAAT 60.443 41.667 0.00 0.00 33.69 1.82
2438 5100 4.083484 ACAGTGCTTCAAAATTAGTACGGC 60.083 41.667 0.00 0.00 33.02 5.68
2464 5126 1.635663 CCGACAATGACAACGCTCCC 61.636 60.000 0.00 0.00 0.00 4.30
2465 5127 0.948623 CGACAATGACAACGCTCCCA 60.949 55.000 0.00 0.00 0.00 4.37
2466 5128 1.453155 GACAATGACAACGCTCCCAT 58.547 50.000 0.00 0.00 0.00 4.00
2467 5129 2.627945 GACAATGACAACGCTCCCATA 58.372 47.619 0.00 0.00 0.00 2.74
2468 5130 3.206150 GACAATGACAACGCTCCCATAT 58.794 45.455 0.00 0.00 0.00 1.78
2469 5131 3.206150 ACAATGACAACGCTCCCATATC 58.794 45.455 0.00 0.00 0.00 1.63
2470 5132 3.118261 ACAATGACAACGCTCCCATATCT 60.118 43.478 0.00 0.00 0.00 1.98
2471 5133 3.845781 ATGACAACGCTCCCATATCTT 57.154 42.857 0.00 0.00 0.00 2.40
2472 5134 3.179443 TGACAACGCTCCCATATCTTC 57.821 47.619 0.00 0.00 0.00 2.87
2808 7879 2.378547 ACACCAAGGCTTCCATTTCCTA 59.621 45.455 0.00 0.00 0.00 2.94
3253 8375 3.190878 GCTTGCATTGCTAGCGGT 58.809 55.556 25.08 0.00 45.53 5.68
3280 8410 1.072489 TGCCGATACAACACCTCCAAA 59.928 47.619 0.00 0.00 0.00 3.28
3351 8498 0.738975 GCCGGTAAGCCTCCAAATTC 59.261 55.000 1.90 0.00 0.00 2.17
3440 8619 2.237392 GACATGATCTGGGTATAGGGCC 59.763 54.545 0.00 0.00 0.00 5.80
3607 10129 4.810191 ACTTAGTAGCTCCAGAACAAGG 57.190 45.455 0.00 0.00 0.00 3.61
3622 10144 6.073440 CCAGAACAAGGAAATGCATCTTTTTG 60.073 38.462 0.00 6.07 0.00 2.44
3625 10147 7.553760 AGAACAAGGAAATGCATCTTTTTGTTT 59.446 29.630 22.27 14.54 0.00 2.83
3626 10148 7.628769 ACAAGGAAATGCATCTTTTTGTTTT 57.371 28.000 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.324736 GCTGTTTCATCACGGACGATC 59.675 52.381 0.00 0.00 0.00 3.69
23 24 3.633094 CTGCGCGACTACTGGCTGT 62.633 63.158 12.10 1.74 0.00 4.40
89 91 3.119096 GCCTCCGAAACCGCACTC 61.119 66.667 0.00 0.00 0.00 3.51
90 92 4.699522 GGCCTCCGAAACCGCACT 62.700 66.667 0.00 0.00 0.00 4.40
158 160 1.134068 GGTTCCATTCCCTGAGCTACC 60.134 57.143 0.00 0.00 0.00 3.18
168 170 3.131478 CGCCACCGGTTCCATTCC 61.131 66.667 2.97 0.00 0.00 3.01
171 173 3.000819 TCTCGCCACCGGTTCCAT 61.001 61.111 2.97 0.00 34.56 3.41
221 225 2.966516 CCTATAAAAGGGAGGTCGCTCT 59.033 50.000 0.00 0.00 42.32 4.09
239 243 1.679680 CCGAGCCGATGTCTAAACCTA 59.320 52.381 0.00 0.00 0.00 3.08
240 244 0.460311 CCGAGCCGATGTCTAAACCT 59.540 55.000 0.00 0.00 0.00 3.50
241 245 1.152383 GCCGAGCCGATGTCTAAACC 61.152 60.000 0.00 0.00 0.00 3.27
242 246 0.179108 AGCCGAGCCGATGTCTAAAC 60.179 55.000 0.00 0.00 0.00 2.01
243 247 0.102481 GAGCCGAGCCGATGTCTAAA 59.898 55.000 0.00 0.00 0.00 1.85
244 248 1.035385 TGAGCCGAGCCGATGTCTAA 61.035 55.000 0.00 0.00 0.00 2.10
324 360 0.953471 CAAAAGGGACATCCACGCGA 60.953 55.000 15.93 0.00 38.24 5.87
340 376 5.181811 CCACTTGTATGAGCATGAGAACAAA 59.818 40.000 0.00 0.00 0.00 2.83
387 424 5.012664 TGCTAGTTGAGTAGAAATTGGACCA 59.987 40.000 0.00 0.00 0.00 4.02
397 434 4.081642 GTCCCACATTGCTAGTTGAGTAGA 60.082 45.833 0.00 0.00 0.00 2.59
399 436 3.838317 AGTCCCACATTGCTAGTTGAGTA 59.162 43.478 0.00 0.00 0.00 2.59
555 592 0.738975 TAGAGAAGATCACGCCGTGG 59.261 55.000 18.32 0.00 33.87 4.94
556 593 1.402259 AGTAGAGAAGATCACGCCGTG 59.598 52.381 11.80 11.80 34.45 4.94
600 637 1.663643 CACTGGTACACACACACACAC 59.336 52.381 0.00 0.00 0.00 3.82
601 638 1.276705 ACACTGGTACACACACACACA 59.723 47.619 0.00 0.00 0.00 3.72
602 639 2.018542 ACACTGGTACACACACACAC 57.981 50.000 0.00 0.00 0.00 3.82
603 640 5.731957 ATATACACTGGTACACACACACA 57.268 39.130 0.00 0.00 30.94 3.72
604 641 6.623486 TGTATATACACTGGTACACACACAC 58.377 40.000 11.62 0.00 30.94 3.82
639 676 9.933723 ATGAATTCACTGTATATTGATCATCGA 57.066 29.630 11.07 0.00 0.00 3.59
654 691 5.293814 CAGAGTAAGGCAGATGAATTCACTG 59.706 44.000 22.94 22.94 35.14 3.66
708 745 2.510691 CCGTATGGTGTCCGGCAC 60.511 66.667 17.46 17.46 46.97 5.01
711 748 1.594293 GATGCCGTATGGTGTCCGG 60.594 63.158 2.17 0.00 44.46 5.14
712 749 0.875908 CAGATGCCGTATGGTGTCCG 60.876 60.000 2.17 0.00 37.67 4.79
714 751 1.409064 TCTCAGATGCCGTATGGTGTC 59.591 52.381 2.17 1.42 37.67 3.67
715 752 1.137086 GTCTCAGATGCCGTATGGTGT 59.863 52.381 2.17 0.00 37.67 4.16
725 802 4.934001 TGAATTGTCTCAAGTCTCAGATGC 59.066 41.667 10.38 0.00 0.00 3.91
730 807 6.944096 AGATCATGAATTGTCTCAAGTCTCA 58.056 36.000 0.00 3.82 0.00 3.27
770 847 2.932614 CAGGACTTTTCAGCTATGTCGG 59.067 50.000 0.00 0.00 0.00 4.79
816 893 7.042658 GGAAGACATTGGACAAATCTACGATAC 60.043 40.741 0.00 0.00 0.00 2.24
922 1000 4.515191 TGTTCTGCAGAGTGAACCATAAAC 59.485 41.667 17.43 8.09 41.10 2.01
977 1055 4.353191 TCGGAGTATAAGACTATCAGGGGT 59.647 45.833 0.00 0.00 39.06 4.95
1122 1459 0.169672 CCATGTTGGCGAGCAAGAAG 59.830 55.000 0.00 0.00 0.00 2.85
1127 1464 1.375908 GTCTCCATGTTGGCGAGCA 60.376 57.895 0.00 0.00 37.47 4.26
1178 1515 2.300437 GGAGTGTTCCTAGAGCAAGTGT 59.700 50.000 0.00 0.00 40.58 3.55
1335 1682 3.492656 GCACACTTAGACAGAGGTGTTCA 60.493 47.826 0.00 0.00 40.34 3.18
1349 1696 5.005299 CGATCATAAACGACATGCACACTTA 59.995 40.000 0.00 0.00 0.00 2.24
1355 1702 2.863740 GGACGATCATAAACGACATGCA 59.136 45.455 0.00 0.00 0.00 3.96
1427 1781 2.356313 CTGACGTTCTGCAGCCGT 60.356 61.111 24.87 24.87 37.56 5.68
1447 1801 1.458827 CTCGTCTGCACAAGCTCTTTC 59.541 52.381 0.00 0.00 42.74 2.62
1471 1825 0.759959 TGTTGTCTTTCCCGCACCTA 59.240 50.000 0.00 0.00 0.00 3.08
1550 1904 3.052081 GGCGACGCATCCCTCTAT 58.948 61.111 23.09 0.00 0.00 1.98
1571 1925 4.720902 CCCAGCACCGGCATGACA 62.721 66.667 0.00 0.00 44.61 3.58
1613 1967 1.216710 GAGCTGCTCGTAGTGGCTT 59.783 57.895 14.68 0.00 33.13 4.35
1642 1996 1.630878 GACCCCATGACAAGAGGAAGT 59.369 52.381 0.00 0.00 0.00 3.01
1646 2000 0.035056 GTGGACCCCATGACAAGAGG 60.035 60.000 0.00 0.00 35.28 3.69
1722 2076 4.338795 TCCTAGACCTGTTCTCAATCCT 57.661 45.455 0.00 0.00 35.55 3.24
1771 3595 1.080705 CACTCCGTGACTCGAACCC 60.081 63.158 0.00 0.00 42.86 4.11
1840 3831 6.255887 GGTTCCGAAATAATCCGAGCATATAG 59.744 42.308 0.00 0.00 0.00 1.31
1937 4386 9.045223 TGACATGATAGATTGTTAGTAATGCAC 57.955 33.333 0.00 0.00 0.00 4.57
1973 4422 9.921637 TTTTACTTGAAATAAGAATCGGCATTT 57.078 25.926 0.00 0.00 0.00 2.32
2037 4486 5.703592 AGAAATAAATACGTTGACAGCACCA 59.296 36.000 0.00 0.00 0.00 4.17
2308 4968 1.003718 AGGACTTGTAGCAACCGGC 60.004 57.895 0.00 0.00 45.30 6.13
2311 4971 1.404315 CGAGGAGGACTTGTAGCAACC 60.404 57.143 0.00 0.00 0.00 3.77
2331 4993 1.244019 AAGCATGTTTCCAGGACGGC 61.244 55.000 0.00 0.00 33.14 5.68
2403 5065 0.779997 AGCACTGTTCCTTTGGGGAT 59.220 50.000 0.00 0.00 44.66 3.85
2404 5066 0.555769 AAGCACTGTTCCTTTGGGGA 59.444 50.000 0.00 0.00 43.41 4.81
2408 5070 6.980397 ACTAATTTTGAAGCACTGTTCCTTTG 59.020 34.615 0.00 0.00 0.00 2.77
2412 5074 6.077838 CGTACTAATTTTGAAGCACTGTTCC 58.922 40.000 0.00 0.00 0.00 3.62
2438 5100 2.154963 CGTTGTCATTGTCGGTACAGTG 59.845 50.000 0.00 0.00 42.91 3.66
2467 5129 8.138712 GGAGAAGATAATACAAGTGACGAAGAT 58.861 37.037 0.00 0.00 0.00 2.40
2468 5130 7.416438 GGGAGAAGATAATACAAGTGACGAAGA 60.416 40.741 0.00 0.00 0.00 2.87
2469 5131 6.697892 GGGAGAAGATAATACAAGTGACGAAG 59.302 42.308 0.00 0.00 0.00 3.79
2470 5132 6.153851 TGGGAGAAGATAATACAAGTGACGAA 59.846 38.462 0.00 0.00 0.00 3.85
2471 5133 5.655090 TGGGAGAAGATAATACAAGTGACGA 59.345 40.000 0.00 0.00 0.00 4.20
2472 5134 5.902681 TGGGAGAAGATAATACAAGTGACG 58.097 41.667 0.00 0.00 0.00 4.35
3280 8410 1.004440 GAGGCACAGGAACTTCGCT 60.004 57.895 0.00 0.00 34.60 4.93
3462 8641 7.872138 TCCCTATGTTGAATAGGAACTTCAAT 58.128 34.615 12.10 0.00 42.68 2.57
3607 10129 6.482973 TCCCTCAAAACAAAAAGATGCATTTC 59.517 34.615 0.00 0.00 0.00 2.17
3622 10144 4.260743 GCATTTGCTTGTTTCCCTCAAAAC 60.261 41.667 0.00 0.00 37.56 2.43
3625 10147 2.433604 TGCATTTGCTTGTTTCCCTCAA 59.566 40.909 3.94 0.00 42.66 3.02
3626 10148 2.037901 TGCATTTGCTTGTTTCCCTCA 58.962 42.857 3.94 0.00 42.66 3.86


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

AutoCloner maintained by Alex Coulton.