Multiple sequence alignment - TraesCS3A01G511000

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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 TraesCS3A01G511000 chr3A 100.000 3176 0 0 1 3176 730852585 730849410 0.000000e+00 5866.0
1 TraesCS3A01G511000 chr3A 80.594 1381 205 39 963 2295 731844343 731842978 0.000000e+00 1007.0
2 TraesCS3A01G511000 chr3A 80.071 1400 201 46 963 2298 731894420 731893035 0.000000e+00 968.0
3 TraesCS3A01G511000 chr3A 74.404 1090 190 58 1403 2436 730905168 730904112 4.970000e-103 385.0
4 TraesCS3A01G511000 chr3A 83.171 410 53 9 2632 3027 730892488 730892081 8.370000e-96 361.0
5 TraesCS3A01G511000 chr3A 84.211 152 22 1 2444 2595 731842873 731842724 2.550000e-31 147.0
6 TraesCS3A01G511000 chr3A 83.453 139 23 0 2457 2595 731892802 731892664 2.570000e-26 130.0
7 TraesCS3A01G511000 chr3A 89.000 100 3 3 3077 3176 730891958 730891867 2.000000e-22 117.0
8 TraesCS3A01G511000 chr3B 89.230 1597 120 17 632 2203 809437551 809439120 0.000000e+00 1949.0
9 TraesCS3A01G511000 chr3B 88.618 615 49 12 2429 3032 809439450 809440054 0.000000e+00 728.0
10 TraesCS3A01G511000 chr3B 89.597 471 40 5 1 471 809433644 809434105 9.810000e-165 590.0
11 TraesCS3A01G511000 chr3B 86.740 362 41 4 1010 1370 809510194 809509839 2.300000e-106 396.0
12 TraesCS3A01G511000 chr3B 88.500 200 20 3 2695 2891 809349051 809349250 4.090000e-59 239.0
13 TraesCS3A01G511000 chr3B 87.685 203 12 5 2237 2436 809439123 809439315 1.150000e-54 224.0
14 TraesCS3A01G511000 chr3B 93.919 148 6 1 3029 3176 809440139 809440283 1.480000e-53 220.0
15 TraesCS3A01G511000 chr3B 82.222 180 31 1 2458 2637 809463466 809463288 1.530000e-33 154.0
16 TraesCS3A01G511000 chr3B 79.412 170 35 0 2468 2637 809509124 809508955 1.550000e-23 121.0
17 TraesCS3A01G511000 chr3B 89.000 100 5 2 3077 3176 809349567 809349660 5.570000e-23 119.0
18 TraesCS3A01G511000 chr3D 89.881 1344 104 15 890 2203 602235059 602236400 0.000000e+00 1700.0
19 TraesCS3A01G511000 chr3D 91.950 795 35 12 2237 3024 602236403 602237175 0.000000e+00 1086.0
20 TraesCS3A01G511000 chr3D 79.864 1326 215 34 1007 2292 602261537 602260224 0.000000e+00 922.0
21 TraesCS3A01G511000 chr3D 91.579 475 37 3 1 475 602233903 602234374 0.000000e+00 652.0
22 TraesCS3A01G511000 chr3D 87.794 467 55 2 1 467 332234338 332233874 2.150000e-151 545.0
23 TraesCS3A01G511000 chr3D 73.934 1266 213 62 1232 2436 602210864 602212073 4.930000e-108 401.0
24 TraesCS3A01G511000 chr3D 90.347 259 18 4 474 731 602234405 602234657 1.830000e-87 333.0
25 TraesCS3A01G511000 chr3D 96.000 150 4 1 3029 3176 602237281 602237430 3.170000e-60 243.0
26 TraesCS3A01G511000 chr3D 95.902 122 5 0 724 845 602234926 602235047 6.950000e-47 198.0
27 TraesCS3A01G511000 chr3D 86.986 146 13 2 3036 3176 597299428 597299284 3.280000e-35 159.0
28 TraesCS3A01G511000 chr3D 85.612 139 20 0 2457 2595 602260141 602260003 2.550000e-31 147.0
29 TraesCS3A01G511000 chr3D 89.000 100 5 2 3077 3176 602212782 602212875 5.570000e-23 119.0
30 TraesCS3A01G511000 chr2D 91.006 467 40 2 1 467 403382763 403383227 2.080000e-176 628.0
31 TraesCS3A01G511000 chr2D 86.667 150 16 2 476 625 403383270 403383415 2.530000e-36 163.0
32 TraesCS3A01G511000 chr7D 89.316 468 44 6 1 467 242083031 242083493 1.640000e-162 582.0
33 TraesCS3A01G511000 chr7D 88.009 467 49 5 1 467 162113863 162113404 2.150000e-151 545.0
34 TraesCS3A01G511000 chr7D 73.881 1095 224 37 1048 2108 49186880 49187946 6.430000e-102 381.0
35 TraesCS3A01G511000 chr7D 80.110 362 61 7 1011 1371 27228293 27228644 3.140000e-65 259.0
36 TraesCS3A01G511000 chr7D 73.494 664 155 13 1415 2063 26759576 26758919 6.850000e-57 231.0
37 TraesCS3A01G511000 chr7D 78.571 364 65 9 1010 1371 11727506 11727154 8.860000e-56 228.0
38 TraesCS3A01G511000 chr7D 79.310 319 61 5 1048 1365 12168560 12168246 5.330000e-53 219.0
39 TraesCS3A01G511000 chr7D 81.463 205 32 6 1160 1363 49163947 49164146 2.530000e-36 163.0
40 TraesCS3A01G511000 chr7D 87.500 48 4 2 1038 1085 24341715 24341760 2.000000e-03 54.7
41 TraesCS3A01G511000 chr4D 89.079 467 49 2 1 467 77292397 77292861 2.120000e-161 579.0
42 TraesCS3A01G511000 chr4D 87.742 155 14 3 476 630 380279564 380279713 3.260000e-40 176.0
43 TraesCS3A01G511000 chr5D 88.865 467 49 3 1 467 284900285 284900748 3.550000e-159 571.0
44 TraesCS3A01G511000 chr5D 94.286 35 2 0 1043 1077 552051612 552051578 2.000000e-03 54.7
45 TraesCS3A01G511000 chr5D 100.000 28 0 0 1043 1070 552458352 552458325 6.000000e-03 52.8
46 TraesCS3A01G511000 chr6A 88.486 469 48 6 1 467 567346950 567346486 2.140000e-156 562.0
47 TraesCS3A01G511000 chr6A 86.755 151 15 3 476 625 387977171 387977317 2.530000e-36 163.0
48 TraesCS3A01G511000 chr7A 80.247 324 55 5 1048 1371 11230291 11229977 5.300000e-58 235.0
49 TraesCS3A01G511000 chr4A 81.522 276 46 3 1099 1373 725872520 725872791 4.120000e-54 222.0
50 TraesCS3A01G511000 chr4A 80.795 151 26 1 1431 1581 710786212 710786065 7.200000e-22 115.0
51 TraesCS3A01G511000 chr1B 87.500 144 11 5 476 616 149526738 149526599 3.280000e-35 159.0
52 TraesCS3A01G511000 chr7B 85.621 153 17 3 474 625 438369132 438369280 4.240000e-34 156.0
53 TraesCS3A01G511000 chr1D 85.906 149 17 1 476 624 326223738 326223594 4.240000e-34 156.0
54 TraesCS3A01G511000 chrUn 85.333 150 17 3 476 625 28830841 28830697 1.970000e-32 150.0
55 TraesCS3A01G511000 chr6B 86.111 144 15 3 474 617 433040672 433040810 1.970000e-32 150.0
56 TraesCS3A01G511000 chr5B 76.549 226 44 6 1036 1261 15034226 15034442 7.200000e-22 115.0
57 TraesCS3A01G511000 chr5B 94.286 35 2 0 1043 1077 677812072 677812106 2.000000e-03 54.7
58 TraesCS3A01G511000 chr5B 94.286 35 2 0 1043 1077 699260123 699260157 2.000000e-03 54.7


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 TraesCS3A01G511000 chr3A 730849410 730852585 3175 True 5866.0 5866 100.000000 1 3176 1 chr3A.!!$R1 3175
1 TraesCS3A01G511000 chr3A 731842724 731844343 1619 True 577.0 1007 82.402500 963 2595 2 chr3A.!!$R4 1632
2 TraesCS3A01G511000 chr3A 731892664 731894420 1756 True 549.0 968 81.762000 963 2595 2 chr3A.!!$R5 1632
3 TraesCS3A01G511000 chr3A 730904112 730905168 1056 True 385.0 385 74.404000 1403 2436 1 chr3A.!!$R2 1033
4 TraesCS3A01G511000 chr3A 730891867 730892488 621 True 239.0 361 86.085500 2632 3176 2 chr3A.!!$R3 544
5 TraesCS3A01G511000 chr3B 809433644 809440283 6639 False 742.2 1949 89.809800 1 3176 5 chr3B.!!$F2 3175
6 TraesCS3A01G511000 chr3B 809508955 809510194 1239 True 258.5 396 83.076000 1010 2637 2 chr3B.!!$R2 1627
7 TraesCS3A01G511000 chr3D 602233903 602237430 3527 False 702.0 1700 92.609833 1 3176 6 chr3D.!!$F2 3175
8 TraesCS3A01G511000 chr3D 602260003 602261537 1534 True 534.5 922 82.738000 1007 2595 2 chr3D.!!$R3 1588
9 TraesCS3A01G511000 chr3D 602210864 602212875 2011 False 260.0 401 81.467000 1232 3176 2 chr3D.!!$F1 1944
10 TraesCS3A01G511000 chr2D 403382763 403383415 652 False 395.5 628 88.836500 1 625 2 chr2D.!!$F1 624
11 TraesCS3A01G511000 chr7D 49186880 49187946 1066 False 381.0 381 73.881000 1048 2108 1 chr7D.!!$F4 1060
12 TraesCS3A01G511000 chr7D 26758919 26759576 657 True 231.0 231 73.494000 1415 2063 1 chr7D.!!$R3 648

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
886 4456 0.106318 GCAGGCCCAATCCTCAGAAT 60.106 55.0 0.00 0.0 33.25 2.40 F
1516 5140 0.256752 TGAACCGGACCTCCTCGATA 59.743 55.0 9.46 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 5639 0.038890 TTTCCGGCAATGGGATGACA 59.961 50.0 0.00 0.00 32.58 3.58 R
2490 6378 1.327303 TGGGGCTGTTGTCATTTGAC 58.673 50.0 3.72 3.72 44.97 3.18 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
18 19 3.566261 CGAGGCATCGTTGTTGCT 58.434 55.556 13.51 0.00 44.09 3.91
23 24 1.514678 GGCATCGTTGTTGCTGGTCA 61.515 55.000 0.00 0.00 40.03 4.02
30 31 0.467844 TTGTTGCTGGTCATGGCACT 60.468 50.000 0.00 0.00 38.23 4.40
50 51 1.593787 CACTCGTGATGCTCTGGGT 59.406 57.895 0.00 0.00 0.00 4.51
136 137 1.322538 GGGGCATCGTTTTGGAGCAT 61.323 55.000 0.00 0.00 0.00 3.79
159 160 1.213926 GCTGATTGGAGGGGACAAGAT 59.786 52.381 0.00 0.00 0.00 2.40
232 233 1.144057 GATGCGGAGGTTCGGTGAT 59.856 57.895 0.00 0.00 0.00 3.06
233 234 1.153369 ATGCGGAGGTTCGGTGATG 60.153 57.895 0.00 0.00 0.00 3.07
269 270 1.909459 ATACGTGCAGGATGGTGGCA 61.909 55.000 14.38 0.00 35.86 4.92
272 273 1.597797 CGTGCAGGATGGTGGCATTT 61.598 55.000 0.00 0.00 40.05 2.32
320 321 2.046023 CCAGGCAAGGTCGATGCA 60.046 61.111 11.32 0.00 45.60 3.96
447 448 1.789523 TCCGGCTTTAGATGCTAGGT 58.210 50.000 0.00 0.00 32.96 3.08
452 453 4.202223 CCGGCTTTAGATGCTAGGTTTAGA 60.202 45.833 0.00 0.00 0.00 2.10
471 474 9.382244 GGTTTAGATGCGATGTATGTTTAATTC 57.618 33.333 0.00 0.00 0.00 2.17
490 525 9.629878 TTTAATTCTGGTAGGAGTAACAACAAA 57.370 29.630 0.00 0.00 0.00 2.83
515 550 3.708451 TGTCTAGATGGTGGCTTCAGTA 58.292 45.455 0.00 0.00 0.00 2.74
516 551 4.093743 TGTCTAGATGGTGGCTTCAGTAA 58.906 43.478 0.00 0.00 0.00 2.24
517 552 4.160439 TGTCTAGATGGTGGCTTCAGTAAG 59.840 45.833 0.00 0.00 35.68 2.34
518 553 4.402793 GTCTAGATGGTGGCTTCAGTAAGA 59.597 45.833 0.00 0.00 34.37 2.10
519 554 5.069781 GTCTAGATGGTGGCTTCAGTAAGAT 59.930 44.000 0.00 0.00 34.37 2.40
523 558 6.721318 AGATGGTGGCTTCAGTAAGATTTAA 58.279 36.000 0.00 0.00 34.37 1.52
679 3972 1.028130 GAAAGCTATGCTCCTTGCCC 58.972 55.000 0.00 0.00 38.25 5.36
703 3996 9.357652 CCCAGATGTAAACTCAAAATGTTAATG 57.642 33.333 0.00 0.00 0.00 1.90
720 4013 9.533831 AATGTTAATGATTGGAAAGGAGTAACT 57.466 29.630 0.00 0.00 28.64 2.24
845 4415 3.521531 AGGCCCCAAAAGAAACTGAAAAA 59.478 39.130 0.00 0.00 0.00 1.94
846 4416 3.876914 GGCCCCAAAAGAAACTGAAAAAG 59.123 43.478 0.00 0.00 0.00 2.27
847 4417 3.876914 GCCCCAAAAGAAACTGAAAAAGG 59.123 43.478 0.00 0.00 0.00 3.11
848 4418 3.876914 CCCCAAAAGAAACTGAAAAAGGC 59.123 43.478 0.00 0.00 0.00 4.35
849 4419 3.876914 CCCAAAAGAAACTGAAAAAGGCC 59.123 43.478 0.00 0.00 0.00 5.19
850 4420 4.512484 CCAAAAGAAACTGAAAAAGGCCA 58.488 39.130 5.01 0.00 0.00 5.36
852 4422 6.287525 CCAAAAGAAACTGAAAAAGGCCATA 58.712 36.000 5.01 0.00 0.00 2.74
853 4423 6.765512 CCAAAAGAAACTGAAAAAGGCCATAA 59.234 34.615 5.01 0.00 0.00 1.90
854 4424 7.281999 CCAAAAGAAACTGAAAAAGGCCATAAA 59.718 33.333 5.01 0.00 0.00 1.40
855 4425 8.672815 CAAAAGAAACTGAAAAAGGCCATAAAA 58.327 29.630 5.01 0.00 0.00 1.52
856 4426 8.978874 AAAGAAACTGAAAAAGGCCATAAAAT 57.021 26.923 5.01 0.00 0.00 1.82
857 4427 7.967890 AGAAACTGAAAAAGGCCATAAAATG 57.032 32.000 5.01 0.00 0.00 2.32
881 4451 1.959282 CATTTAGCAGGCCCAATCCTC 59.041 52.381 0.00 0.00 33.25 3.71
886 4456 0.106318 GCAGGCCCAATCCTCAGAAT 60.106 55.000 0.00 0.00 33.25 2.40
949 4522 2.978978 TGTGAGTGAATCAGAAAGGGGA 59.021 45.455 0.00 0.00 39.07 4.81
950 4523 3.008375 TGTGAGTGAATCAGAAAGGGGAG 59.992 47.826 0.00 0.00 39.07 4.30
951 4524 3.261897 GTGAGTGAATCAGAAAGGGGAGA 59.738 47.826 0.00 0.00 39.07 3.71
984 4560 1.136828 TGGTAGATCCCCCAATTCCG 58.863 55.000 0.00 0.00 34.77 4.30
1200 4801 2.026734 CTCATCGGCGTGCTCGAT 59.973 61.111 13.13 10.89 46.64 3.59
1213 4814 1.399089 TGCTCGATGTCGACGACAATA 59.601 47.619 32.17 19.37 45.96 1.90
1392 5011 1.444553 GGAGAGGACGTGCGACTTG 60.445 63.158 0.00 0.00 0.00 3.16
1445 5064 4.612412 GTGCGACCCCGTGTTCCA 62.612 66.667 0.00 0.00 38.24 3.53
1466 5085 2.109799 CTACATCCTGCTGCCCGG 59.890 66.667 0.00 0.00 0.00 5.73
1467 5086 2.687200 TACATCCTGCTGCCCGGT 60.687 61.111 0.00 0.00 0.00 5.28
1516 5140 0.256752 TGAACCGGACCTCCTCGATA 59.743 55.000 9.46 0.00 0.00 2.92
1716 5372 5.298276 GGATGGGCTGTTAAATCGTCAATTA 59.702 40.000 0.00 0.00 0.00 1.40
1770 5426 2.031333 CCTCAACAAGTTGCTTCTGCTC 60.031 50.000 8.04 0.00 40.24 4.26
1773 5429 1.506493 ACAAGTTGCTTCTGCTCGAG 58.494 50.000 8.45 8.45 40.48 4.04
1798 5454 1.759445 GCTCCATGGAGTTCTCTGCTA 59.241 52.381 36.32 2.41 43.70 3.49
1812 5468 2.049627 CTGCTATCAGCCTCCCACCC 62.050 65.000 0.00 0.00 41.51 4.61
1820 5482 2.033602 CCTCCCACCCGAACAACC 59.966 66.667 0.00 0.00 0.00 3.77
1880 5554 2.202987 GCTCGGGATGCTCACTGG 60.203 66.667 0.00 0.00 0.00 4.00
1904 5581 1.305219 AATGACGGGCACAACGATGG 61.305 55.000 0.00 0.00 34.93 3.51
1935 5612 2.953648 TCGGCTCGTGTATTCCATTCTA 59.046 45.455 0.00 0.00 0.00 2.10
1957 5634 2.159114 ACAAACAACCAATGGCACTCAC 60.159 45.455 0.00 0.00 0.00 3.51
1962 5639 2.559668 CAACCAATGGCACTCACAGAAT 59.440 45.455 0.00 0.00 0.00 2.40
1996 5673 4.767928 TGCCGGAAAAGTATGGTGTTATTT 59.232 37.500 5.05 0.00 0.00 1.40
2051 5734 2.017049 GGCATACACCACATCTTCACC 58.983 52.381 0.00 0.00 0.00 4.02
2084 5779 3.139077 GGTTCTTTTCAGTGGACGTCAT 58.861 45.455 18.91 0.00 0.00 3.06
2140 5856 6.370453 TCCTGTAGTGGTGAACTATATGCTA 58.630 40.000 0.00 0.00 43.30 3.49
2142 5858 6.085555 TGTAGTGGTGAACTATATGCTAGC 57.914 41.667 8.10 8.10 43.30 3.42
2143 5859 4.608948 AGTGGTGAACTATATGCTAGCC 57.391 45.455 13.29 0.00 37.36 3.93
2150 5866 2.171840 ACTATATGCTAGCCTCCCACG 58.828 52.381 13.29 0.00 0.00 4.94
2153 5869 1.717032 TATGCTAGCCTCCCACGATT 58.283 50.000 13.29 0.00 0.00 3.34
2186 5902 3.804325 CCAACTATATGAAGCGGTGAGTG 59.196 47.826 0.00 0.00 0.00 3.51
2227 5948 7.739498 TTATTTAACCTCTGGTTTCAGTGTC 57.261 36.000 7.32 0.00 44.33 3.67
2228 5949 2.240493 AACCTCTGGTTTCAGTGTCG 57.760 50.000 0.00 0.00 44.33 4.35
2230 5951 1.202533 ACCTCTGGTTTCAGTGTCGTG 60.203 52.381 0.00 0.00 41.59 4.35
2235 5956 1.436195 GGTTTCAGTGTCGTGCAGCA 61.436 55.000 0.00 0.00 0.00 4.41
2335 6069 5.188327 TGCAGATGTAGCAGTATACTGTC 57.812 43.478 28.95 21.72 45.45 3.51
2336 6070 4.038042 TGCAGATGTAGCAGTATACTGTCC 59.962 45.833 28.95 18.75 45.45 4.02
2409 6144 5.477984 TGCAATTGGAAGCTCATTAAACTCT 59.522 36.000 7.72 0.00 0.00 3.24
2489 6377 8.718102 ATGTAACTTCTGTATGCGTAGAAATT 57.282 30.769 0.00 0.00 32.96 1.82
2490 6378 7.959733 TGTAACTTCTGTATGCGTAGAAATTG 58.040 34.615 0.00 0.00 32.96 2.32
2497 6385 7.463544 TCTGTATGCGTAGAAATTGTCAAATG 58.536 34.615 0.00 0.00 0.00 2.32
2670 6566 6.568869 TGATTTTGGTTGTTTGTCGATTCTT 58.431 32.000 0.00 0.00 0.00 2.52
2704 6600 7.141758 TGAGCTAAACATGAAGGATAAGGAT 57.858 36.000 0.00 0.00 0.00 3.24
2910 6847 4.080695 TCCTCTGCATCTGCTTTATCAAGT 60.081 41.667 3.53 0.00 42.66 3.16
2979 6918 5.720202 TGAATAAATCAGTCAGCGTAGTGT 58.280 37.500 0.00 0.00 33.04 3.55
2989 6929 6.317893 TCAGTCAGCGTAGTGTATTCTTATCA 59.682 38.462 0.00 0.00 0.00 2.15
2995 6935 9.066939 CAGCGTAGTGTATTCTTATCATATGAC 57.933 37.037 7.78 0.00 0.00 3.06
2996 6936 8.793592 AGCGTAGTGTATTCTTATCATATGACA 58.206 33.333 7.78 0.00 0.00 3.58
3012 6959 9.941325 ATCATATGACATCTAGGTTTCTGAATC 57.059 33.333 7.78 0.00 0.00 2.52
3022 6969 5.824904 AGGTTTCTGAATCATATGCACAC 57.175 39.130 0.00 0.00 0.00 3.82
3024 6971 5.124457 AGGTTTCTGAATCATATGCACACAC 59.876 40.000 0.00 0.00 0.00 3.82
3026 6973 5.806366 TTCTGAATCATATGCACACACAG 57.194 39.130 0.00 2.55 0.00 3.66
3027 6974 4.193865 TCTGAATCATATGCACACACAGG 58.806 43.478 0.00 0.00 0.00 4.00
3048 7096 3.763897 GGAATTCACTTACTGGGCAATGT 59.236 43.478 7.93 0.00 0.00 2.71
3119 7167 8.364894 ACATGCAGCAATTGATATATTTGATGT 58.635 29.630 10.34 1.74 37.97 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 1.607801 CCCAGAGCATCACGAGTGGA 61.608 60.000 3.19 0.00 37.82 4.02
136 137 1.133181 TGTCCCCTCCAATCAGCACA 61.133 55.000 0.00 0.00 0.00 4.57
143 144 1.849039 CCTCATCTTGTCCCCTCCAAT 59.151 52.381 0.00 0.00 0.00 3.16
144 145 1.203428 TCCTCATCTTGTCCCCTCCAA 60.203 52.381 0.00 0.00 0.00 3.53
159 160 1.557099 AGATGTAACACCGCTCCTCA 58.443 50.000 0.00 0.00 0.00 3.86
191 192 4.570663 GTCGCCTGGATCCGTCGG 62.571 72.222 16.56 4.39 0.00 4.79
215 216 1.153369 CATCACCGAACCTCCGCAT 60.153 57.895 0.00 0.00 0.00 4.73
269 270 1.070786 ACCACGACGCCAGACAAAT 59.929 52.632 0.00 0.00 0.00 2.32
272 273 4.293648 CCACCACGACGCCAGACA 62.294 66.667 0.00 0.00 0.00 3.41
299 300 1.689233 ATCGACCTTGCCTGGCCTA 60.689 57.895 17.53 3.11 0.00 3.93
442 443 7.715265 AAACATACATCGCATCTAAACCTAG 57.285 36.000 0.00 0.00 0.00 3.02
452 453 6.942532 ACCAGAATTAAACATACATCGCAT 57.057 33.333 0.00 0.00 0.00 4.73
471 474 6.668323 CAACATTTGTTGTTACTCCTACCAG 58.332 40.000 13.95 0.00 46.90 4.00
472 475 6.627395 CAACATTTGTTGTTACTCCTACCA 57.373 37.500 13.95 0.00 46.90 3.25
490 525 3.264193 TGAAGCCACCATCTAGACAACAT 59.736 43.478 0.00 0.00 0.00 2.71
551 586 9.993454 TGCATGCAGCCATTTTATTAATTATTA 57.007 25.926 18.46 0.00 44.83 0.98
703 3996 7.387643 AGTCTAACAGTTACTCCTTTCCAATC 58.612 38.462 0.00 0.00 0.00 2.67
704 3997 7.317722 AGTCTAACAGTTACTCCTTTCCAAT 57.682 36.000 0.00 0.00 0.00 3.16
849 4419 5.291971 GCCTGCTAAATGTCCCATTTTATG 58.708 41.667 7.43 1.63 0.00 1.90
850 4420 4.344968 GGCCTGCTAAATGTCCCATTTTAT 59.655 41.667 7.43 0.00 0.00 1.40
852 4422 2.501316 GGCCTGCTAAATGTCCCATTTT 59.499 45.455 7.43 0.00 0.00 1.82
853 4423 2.110578 GGCCTGCTAAATGTCCCATTT 58.889 47.619 0.00 7.30 0.00 2.32
854 4424 1.689258 GGGCCTGCTAAATGTCCCATT 60.689 52.381 0.84 0.00 34.01 3.16
855 4425 0.106015 GGGCCTGCTAAATGTCCCAT 60.106 55.000 0.84 0.00 34.01 4.00
856 4426 1.306296 GGGCCTGCTAAATGTCCCA 59.694 57.895 0.84 0.00 34.01 4.37
857 4427 0.324275 TTGGGCCTGCTAAATGTCCC 60.324 55.000 4.53 0.00 0.00 4.46
858 4428 1.683385 GATTGGGCCTGCTAAATGTCC 59.317 52.381 4.53 0.00 0.00 4.02
859 4429 1.683385 GGATTGGGCCTGCTAAATGTC 59.317 52.381 4.53 0.00 0.00 3.06
860 4430 1.288932 AGGATTGGGCCTGCTAAATGT 59.711 47.619 4.53 0.00 36.76 2.71
861 4431 1.959282 GAGGATTGGGCCTGCTAAATG 59.041 52.381 4.53 0.00 38.73 2.32
862 4432 1.570501 TGAGGATTGGGCCTGCTAAAT 59.429 47.619 4.53 0.00 38.73 1.40
863 4433 0.998928 TGAGGATTGGGCCTGCTAAA 59.001 50.000 4.53 0.00 38.73 1.85
864 4434 0.548031 CTGAGGATTGGGCCTGCTAA 59.452 55.000 4.53 0.00 38.73 3.09
865 4435 0.326522 TCTGAGGATTGGGCCTGCTA 60.327 55.000 4.53 0.00 38.73 3.49
866 4436 1.210204 TTCTGAGGATTGGGCCTGCT 61.210 55.000 4.53 0.00 38.73 4.24
867 4437 0.106318 ATTCTGAGGATTGGGCCTGC 60.106 55.000 4.53 0.00 38.73 4.85
868 4438 1.688772 CATTCTGAGGATTGGGCCTG 58.311 55.000 4.53 0.00 38.73 4.85
881 4451 1.332997 GCTTCTTCGATGGGCATTCTG 59.667 52.381 10.49 0.00 0.00 3.02
886 4456 1.609635 TACGGCTTCTTCGATGGGCA 61.610 55.000 14.89 0.00 0.00 5.36
1116 4717 1.254975 TGATGAGACGGCGGAAGGAA 61.255 55.000 13.24 0.00 0.00 3.36
1171 4772 2.122989 GATGAGAGGGGGCGGGTA 60.123 66.667 0.00 0.00 0.00 3.69
1200 4801 3.366679 GGAAGAAGGTATTGTCGTCGACA 60.367 47.826 23.70 23.70 41.09 4.35
1213 4814 2.911926 GCTGGGCTGGGAAGAAGGT 61.912 63.158 0.00 0.00 0.00 3.50
1445 5064 2.187946 GCAGCAGGATGTAGCGGT 59.812 61.111 0.00 0.00 39.31 5.68
1716 5372 2.172483 AACAGAAGCATCGGCCGACT 62.172 55.000 33.75 21.99 42.56 4.18
1770 5426 4.193334 TCCATGGAGCGCGTCTCG 62.193 66.667 11.44 9.49 42.82 4.04
1773 5429 2.125512 AACTCCATGGAGCGCGTC 60.126 61.111 36.78 3.87 45.54 5.19
1798 5454 2.285368 TTCGGGTGGGAGGCTGAT 60.285 61.111 0.00 0.00 0.00 2.90
1812 5468 1.275657 GTGACACTGCGGTTGTTCG 59.724 57.895 0.00 0.00 0.00 3.95
1820 5482 5.458452 ACAATAACAAAATTGTGACACTGCG 59.542 36.000 1.62 0.00 45.90 5.18
1880 5554 1.465689 CGTTGTGCCCGTCATTGATTC 60.466 52.381 0.00 0.00 0.00 2.52
1922 5599 7.825331 TGGTTGTTTGTTAGAATGGAATACA 57.175 32.000 0.00 0.00 0.00 2.29
1935 5612 2.499289 TGAGTGCCATTGGTTGTTTGTT 59.501 40.909 4.26 0.00 0.00 2.83
1957 5634 1.335810 CGGCAATGGGATGACATTCTG 59.664 52.381 0.00 0.00 38.94 3.02
1962 5639 0.038890 TTTCCGGCAATGGGATGACA 59.961 50.000 0.00 0.00 32.58 3.58
1996 5673 1.228306 CCCCGGCTACACCAAACAA 60.228 57.895 0.00 0.00 39.03 2.83
2031 5708 2.017049 GGTGAAGATGTGGTGTATGCC 58.983 52.381 0.00 0.00 0.00 4.40
2051 5734 5.936956 ACTGAAAAGAACCATAGCTTCTCTG 59.063 40.000 0.00 0.00 0.00 3.35
2084 5779 0.874175 CAACTCGACCTGCAACGTCA 60.874 55.000 12.65 0.00 0.00 4.35
2120 5824 5.244178 AGGCTAGCATATAGTTCACCACTAC 59.756 44.000 18.24 0.00 41.02 2.73
2140 5856 3.807209 GCACATAATAATCGTGGGAGGCT 60.807 47.826 0.00 0.00 0.00 4.58
2142 5858 3.498397 GTGCACATAATAATCGTGGGAGG 59.502 47.826 13.17 0.00 0.00 4.30
2143 5859 3.498397 GGTGCACATAATAATCGTGGGAG 59.502 47.826 20.43 0.00 0.00 4.30
2153 5869 7.117667 CGCTTCATATAGTTGGTGCACATAATA 59.882 37.037 20.43 9.50 0.00 0.98
2212 5933 0.861837 GCACGACACTGAAACCAGAG 59.138 55.000 0.00 0.00 35.67 3.35
2213 5934 0.176910 TGCACGACACTGAAACCAGA 59.823 50.000 0.00 0.00 35.67 3.86
2214 5935 0.583438 CTGCACGACACTGAAACCAG 59.417 55.000 0.00 0.00 37.67 4.00
2219 5940 1.090728 TTTTGCTGCACGACACTGAA 58.909 45.000 0.00 0.00 0.00 3.02
2335 6069 7.340743 TCACCTAAATACCCACAACAATATTGG 59.659 37.037 19.37 5.37 0.00 3.16
2336 6070 8.287439 TCACCTAAATACCCACAACAATATTG 57.713 34.615 14.01 14.01 0.00 1.90
2382 6117 3.308438 AATGAGCTTCCAATTGCACAC 57.692 42.857 0.00 0.00 33.16 3.82
2490 6378 1.327303 TGGGGCTGTTGTCATTTGAC 58.673 50.000 3.72 3.72 44.97 3.18
2497 6385 2.099756 GCAGAAATATGGGGCTGTTGTC 59.900 50.000 0.00 0.00 0.00 3.18
2670 6566 3.038788 TGTTTAGCTCATCGACAGCAA 57.961 42.857 18.06 9.08 39.56 3.91
2910 6847 2.355513 GGAAGATGCAAGAGCTGGAGAA 60.356 50.000 0.00 0.00 42.74 2.87
2950 6889 5.934625 ACGCTGACTGATTTATTCAAGAAGT 59.065 36.000 0.00 0.00 32.78 3.01
2995 6935 7.443272 TGTGCATATGATTCAGAAACCTAGATG 59.557 37.037 6.97 0.00 0.00 2.90
2996 6936 7.443575 GTGTGCATATGATTCAGAAACCTAGAT 59.556 37.037 6.97 0.00 0.00 1.98
3008 6948 5.762825 ATTCCTGTGTGTGCATATGATTC 57.237 39.130 6.97 0.00 0.00 2.52
3011 6958 4.395854 GTGAATTCCTGTGTGTGCATATGA 59.604 41.667 6.97 0.00 0.00 2.15
3012 6959 4.397103 AGTGAATTCCTGTGTGTGCATATG 59.603 41.667 2.27 0.00 0.00 1.78
3015 6962 2.867624 AGTGAATTCCTGTGTGTGCAT 58.132 42.857 2.27 0.00 0.00 3.96
3016 6963 2.346766 AGTGAATTCCTGTGTGTGCA 57.653 45.000 2.27 0.00 0.00 4.57
3022 6969 2.749621 GCCCAGTAAGTGAATTCCTGTG 59.250 50.000 2.27 0.00 0.00 3.66
3024 6971 3.071874 TGCCCAGTAAGTGAATTCCTG 57.928 47.619 2.27 2.48 0.00 3.86
3026 6973 3.763897 ACATTGCCCAGTAAGTGAATTCC 59.236 43.478 2.27 0.00 0.00 3.01
3027 6974 4.458989 TCACATTGCCCAGTAAGTGAATTC 59.541 41.667 0.00 0.00 33.55 2.17
3048 7096 1.367346 TTGCAAGGGGGTGACTATCA 58.633 50.000 0.00 0.00 0.00 2.15
3119 7167 5.005094 GCCTACCAAGTACCACATAACAAA 58.995 41.667 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.