Multiple sequence alignment - TraesCS7D01G221900

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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 TraesCS7D01G221900 chr7D 100.000 4280 0 0 2093 6372 183029158 183024879 0.000000e+00 7904
1 TraesCS7D01G221900 chr7D 100.000 1705 0 0 1 1705 183031250 183029546 0.000000e+00 3149
2 TraesCS7D01G221900 chr7D 85.477 1205 162 8 4195 5390 169388089 169386889 0.000000e+00 1243
3 TraesCS7D01G221900 chr7D 85.956 591 78 5 2971 3558 169389169 169388581 1.510000e-175 627
4 TraesCS7D01G221900 chr7D 86.996 446 32 9 2 426 598014601 598014161 4.470000e-131 479
5 TraesCS7D01G221900 chr7D 92.163 319 23 1 446 762 42920239 42920557 3.500000e-122 449
6 TraesCS7D01G221900 chr7D 85.235 447 35 11 11 436 37808035 37807599 1.270000e-116 431
7 TraesCS7D01G221900 chr7D 81.717 361 39 19 1045 1382 169390807 169390451 6.290000e-70 276
8 TraesCS7D01G221900 chr7D 83.333 132 21 1 3677 3807 15429800 15429931 3.120000e-23 121
9 TraesCS7D01G221900 chr7A 96.863 4304 102 11 2093 6372 188658586 188662880 0.000000e+00 7169
10 TraesCS7D01G221900 chr7A 94.688 866 29 6 766 1624 188657654 188658509 0.000000e+00 1328
11 TraesCS7D01G221900 chr7A 84.691 1215 171 7 4195 5399 171386410 171385201 0.000000e+00 1199
12 TraesCS7D01G221900 chr7A 85.787 591 79 5 2971 3558 171387491 171386903 7.020000e-174 621
13 TraesCS7D01G221900 chr7A 90.402 323 27 3 446 764 40794556 40794878 7.640000e-114 422
14 TraesCS7D01G221900 chr7A 82.271 361 37 18 1045 1382 171389129 171388773 2.910000e-73 287
15 TraesCS7D01G221900 chr7A 86.014 143 18 2 6230 6372 571693271 571693411 1.110000e-32 152
16 TraesCS7D01G221900 chr7A 84.848 132 18 2 3677 3807 341444423 341444293 1.440000e-26 132
17 TraesCS7D01G221900 chr7A 95.588 68 3 0 1638 1705 188658494 188658561 6.750000e-20 110
18 TraesCS7D01G221900 chr7B 94.241 2483 95 15 3677 6132 151430986 151428525 0.000000e+00 3749
19 TraesCS7D01G221900 chr7B 96.673 1593 39 6 2103 3687 151432607 151431021 0.000000e+00 2636
20 TraesCS7D01G221900 chr7B 95.095 1631 69 5 3 1624 151434485 151432857 0.000000e+00 2558
21 TraesCS7D01G221900 chr7B 84.774 1215 170 9 4195 5399 134560062 134558853 0.000000e+00 1205
22 TraesCS7D01G221900 chr7B 86.294 591 68 11 2975 3558 134561137 134560553 1.170000e-176 630
23 TraesCS7D01G221900 chr7B 81.073 354 44 18 1045 1379 134562827 134562478 1.760000e-65 261
24 TraesCS7D01G221900 chr3D 88.814 447 32 5 2 430 354025594 354026040 3.380000e-147 532
25 TraesCS7D01G221900 chr3D 91.304 322 26 1 446 765 591660980 591660659 7.580000e-119 438
26 TraesCS7D01G221900 chr3D 85.355 437 34 11 11 426 25391104 25391531 5.900000e-115 425
27 TraesCS7D01G221900 chr3D 86.525 141 17 2 6232 6372 26308437 26308299 3.080000e-33 154
28 TraesCS7D01G221900 chr6A 89.109 404 36 4 24 426 373683793 373684189 4.440000e-136 496
29 TraesCS7D01G221900 chr6A 88.811 143 16 0 1236 1378 522641374 522641232 6.570000e-40 176
30 TraesCS7D01G221900 chr6A 87.050 139 14 3 3677 3812 232334215 232334352 3.080000e-33 154
31 TraesCS7D01G221900 chr2D 86.067 445 39 12 1 428 633573841 633574279 2.090000e-124 457
32 TraesCS7D01G221900 chr2D 90.683 322 27 3 446 764 297234158 297233837 5.900000e-115 425
33 TraesCS7D01G221900 chr2D 85.432 405 46 7 2 403 620680308 620679914 5.950000e-110 409
34 TraesCS7D01G221900 chr2D 81.920 448 37 14 2 429 624254027 624253604 7.910000e-89 339
35 TraesCS7D01G221900 chr2D 94.444 72 4 0 3616 3687 426427017 426427088 1.880000e-20 111
36 TraesCS7D01G221900 chr2B 85.777 457 32 9 2 432 711305909 711306358 2.710000e-123 453
37 TraesCS7D01G221900 chr2B 90.741 324 24 4 446 766 4050806 4050486 1.640000e-115 427
38 TraesCS7D01G221900 chr2B 90.741 324 24 4 446 766 4461545 4461225 1.640000e-115 427
39 TraesCS7D01G221900 chr4B 91.615 322 23 2 448 765 427519053 427518732 5.860000e-120 442
40 TraesCS7D01G221900 chr4B 85.161 310 15 15 146 429 609312131 609311827 8.080000e-74 289
41 TraesCS7D01G221900 chr4B 85.227 264 22 4 186 434 427297889 427297628 8.200000e-64 255
42 TraesCS7D01G221900 chr4B 87.218 133 17 0 6240 6372 567437745 567437877 1.110000e-32 152
43 TraesCS7D01G221900 chr4B 89.362 94 9 1 3594 3687 396716004 396716096 4.040000e-22 117
44 TraesCS7D01G221900 chr5A 90.184 326 26 5 446 766 690786096 690785772 2.750000e-113 420
45 TraesCS7D01G221900 chr4A 86.753 385 31 7 1 368 628814200 628813819 1.650000e-110 411
46 TraesCS7D01G221900 chr4A 89.362 94 9 1 3594 3687 154501922 154501830 4.040000e-22 117
47 TraesCS7D01G221900 chr1D 86.111 288 23 4 160 431 216040200 216040486 1.740000e-75 294
48 TraesCS7D01G221900 chr1D 86.525 141 18 1 6228 6368 245970474 245970613 3.080000e-33 154
49 TraesCS7D01G221900 chr6B 82.547 212 29 6 1171 1378 569820902 569821109 5.080000e-41 180
50 TraesCS7D01G221900 chr5B 89.552 134 13 1 6234 6367 527778705 527778573 1.100000e-37 169
51 TraesCS7D01G221900 chr5B 82.877 146 18 6 3677 3818 473082451 473082309 2.410000e-24 124
52 TraesCS7D01G221900 chr5B 83.453 139 17 4 3677 3815 556139162 556139294 2.410000e-24 124
53 TraesCS7D01G221900 chr5D 88.462 130 15 0 6243 6372 347476849 347476720 2.380000e-34 158
54 TraesCS7D01G221900 chr5D 85.517 145 17 4 6230 6372 420697336 420697478 1.430000e-31 148
55 TraesCS7D01G221900 chr3B 87.050 139 18 0 6234 6372 155526691 155526553 2.380000e-34 158
56 TraesCS7D01G221900 chr2A 87.591 137 11 4 3677 3807 602696325 602696189 3.080000e-33 154
57 TraesCS7D01G221900 chr3A 80.905 199 27 7 3614 3804 636691349 636691544 5.150000e-31 147
58 TraesCS7D01G221900 chr3A 79.018 224 11 8 3619 3807 739144463 739144241 3.120000e-23 121
59 TraesCS7D01G221900 chr3A 84.259 108 10 6 3608 3711 27877858 27877962 1.460000e-16 99
60 TraesCS7D01G221900 chr6D 87.121 132 12 4 3677 3805 178861473 178861602 1.850000e-30 145
61 TraesCS7D01G221900 chr4D 89.362 94 9 1 3594 3687 319269585 319269677 4.040000e-22 117


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 TraesCS7D01G221900 chr7D 183024879 183031250 6371 True 5526.500000 7904 100.000000 1 6372 2 chr7D.!!$R4 6371
1 TraesCS7D01G221900 chr7D 169386889 169390807 3918 True 715.333333 1243 84.383333 1045 5390 3 chr7D.!!$R3 4345
2 TraesCS7D01G221900 chr7A 188657654 188662880 5226 False 2869.000000 7169 95.713000 766 6372 3 chr7A.!!$F3 5606
3 TraesCS7D01G221900 chr7A 171385201 171389129 3928 True 702.333333 1199 84.249667 1045 5399 3 chr7A.!!$R2 4354
4 TraesCS7D01G221900 chr7B 151428525 151434485 5960 True 2981.000000 3749 95.336333 3 6132 3 chr7B.!!$R2 6129
5 TraesCS7D01G221900 chr7B 134558853 134562827 3974 True 698.666667 1205 84.047000 1045 5399 3 chr7B.!!$R1 4354

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
170 171 0.098552 TTTGATGCATTGCCTACGCG 59.901 50.000 3.53 3.53 38.08 6.01 F
748 755 1.002134 CTCCAATGCACCCGTCCTT 60.002 57.895 0.00 0.00 0.00 3.36 F
1632 1978 1.745232 ACAGGTGTTTCAGTCGCAAA 58.255 45.000 0.00 0.00 0.00 3.68 F
1633 1979 2.088423 ACAGGTGTTTCAGTCGCAAAA 58.912 42.857 0.00 0.00 0.00 2.44 F
1634 1980 2.490115 ACAGGTGTTTCAGTCGCAAAAA 59.510 40.909 0.00 0.00 0.00 1.94 F
2689 3232 2.503356 AGATTCTAGTTCAGTGGCTGGG 59.497 50.000 0.00 0.00 31.51 4.45 F
3785 4377 1.274167 CTGGATTGCTTTGTGCCACAT 59.726 47.619 0.00 0.00 42.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1507 1576 3.675619 ATTACCACGCTCCACGGGC 62.676 63.158 0.0 0.0 46.66 6.13 R
2689 3232 1.405121 CGGGTACTACAGCAAAGGGTC 60.405 57.143 0.0 0.0 0.00 4.46 R
2892 3435 5.091261 AGAGGCAGGTAAGACAAATACAG 57.909 43.478 0.0 0.0 0.00 2.74 R
3647 4192 0.107643 TCGGAGTTGCCATGTGTTCA 59.892 50.000 0.0 0.0 35.94 3.18 R
3785 4377 2.824936 CCCAAATGATAAGTGCCACACA 59.175 45.455 0.0 0.0 36.74 3.72 R
3995 4587 4.565652 GGTGGATCTGGAAGTAGCAAAAGA 60.566 45.833 0.0 0.0 33.76 2.52 R
5669 6707 0.823460 TGCGTGACTATCATCTGCCA 59.177 50.000 0.0 0.0 0.00 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
67 68 2.240500 GCGATGATGCCTCCACGAC 61.241 63.158 8.49 0.00 0.00 4.34
170 171 0.098552 TTTGATGCATTGCCTACGCG 59.901 50.000 3.53 3.53 38.08 6.01
182 183 1.076332 CCTACGCGTCCTTCCTTTTG 58.924 55.000 18.63 0.00 0.00 2.44
231 232 1.393539 CGAACTGTGGCAAGGTAATCG 59.606 52.381 0.00 0.00 0.00 3.34
309 310 4.879545 TGAATTTATGACGTCTTTAGGGGC 59.120 41.667 17.92 1.13 0.00 5.80
385 386 2.477880 CGAAGGGCCAAAATAGCGT 58.522 52.632 6.18 0.00 0.00 5.07
435 436 2.938451 CGGAAATGCTCTTAGTCATGCA 59.062 45.455 0.00 0.00 39.83 3.96
445 446 2.124570 GTCATGCATGACGCCCCT 60.125 61.111 36.65 0.00 46.46 4.79
625 626 7.066284 ACTCACATGGTTACTTATTTGAGCATC 59.934 37.037 12.49 0.00 33.92 3.91
649 650 8.662369 TCAAAATTTGCACACGTGTAATATAC 57.338 30.769 22.90 7.40 35.24 1.47
659 665 9.020813 GCACACGTGTAATATACATCCATATAG 57.979 37.037 22.90 3.18 41.34 1.31
660 666 9.516314 CACACGTGTAATATACATCCATATAGG 57.484 37.037 22.90 0.00 41.34 2.57
713 720 7.444792 TGAAACTTCAAAATAGCATTTTGGCAT 59.555 29.630 22.68 12.47 39.25 4.40
733 740 6.437162 TGGCATAATTCAAAATATAGGGCTCC 59.563 38.462 0.00 0.00 0.00 4.70
745 752 3.134127 GGCTCCAATGCACCCGTC 61.134 66.667 0.00 0.00 34.04 4.79
748 755 1.002134 CTCCAATGCACCCGTCCTT 60.002 57.895 0.00 0.00 0.00 3.36
769 776 6.545666 TCCTTCAAAGTGACTTTTTGCAGATA 59.454 34.615 8.03 0.00 32.77 1.98
965 976 4.969196 CACGGACGCACTGCACCT 62.969 66.667 1.11 0.00 0.00 4.00
992 1003 3.175240 CTCGTGCAAGCGACCTCG 61.175 66.667 0.00 0.00 43.27 4.63
1507 1576 5.530915 TGAACTTCTGTTGTTATGAAGTGGG 59.469 40.000 8.13 0.00 46.39 4.61
1624 1970 7.383687 AGATCGATTAAGTTACAGGTGTTTCA 58.616 34.615 0.00 0.00 0.00 2.69
1625 1971 7.545965 AGATCGATTAAGTTACAGGTGTTTCAG 59.454 37.037 0.00 0.00 0.00 3.02
1626 1972 6.518493 TCGATTAAGTTACAGGTGTTTCAGT 58.482 36.000 0.00 0.00 0.00 3.41
1627 1973 6.643770 TCGATTAAGTTACAGGTGTTTCAGTC 59.356 38.462 0.00 0.00 0.00 3.51
1628 1974 6.399669 CGATTAAGTTACAGGTGTTTCAGTCG 60.400 42.308 0.00 0.00 0.00 4.18
1629 1975 2.480845 AGTTACAGGTGTTTCAGTCGC 58.519 47.619 0.00 0.00 0.00 5.19
1630 1976 2.159014 AGTTACAGGTGTTTCAGTCGCA 60.159 45.455 0.00 0.00 0.00 5.10
1631 1977 2.605837 TACAGGTGTTTCAGTCGCAA 57.394 45.000 0.00 0.00 0.00 4.85
1632 1978 1.745232 ACAGGTGTTTCAGTCGCAAA 58.255 45.000 0.00 0.00 0.00 3.68
1633 1979 2.088423 ACAGGTGTTTCAGTCGCAAAA 58.912 42.857 0.00 0.00 0.00 2.44
1634 1980 2.490115 ACAGGTGTTTCAGTCGCAAAAA 59.510 40.909 0.00 0.00 0.00 1.94
1688 2158 7.161404 ACAGTATTGTGAACTTGCAGATTCTA 58.839 34.615 11.88 1.31 35.83 2.10
1689 2159 7.118390 ACAGTATTGTGAACTTGCAGATTCTAC 59.882 37.037 11.88 9.26 35.83 2.59
2262 2773 7.582667 AAGTGCCACTAAATTTTGTTCTACT 57.417 32.000 0.00 5.03 0.00 2.57
2264 2784 7.425606 AGTGCCACTAAATTTTGTTCTACTTG 58.574 34.615 0.00 0.00 0.00 3.16
2305 2827 5.130311 TGGACCAGCTGCAGAACTTATTATA 59.870 40.000 20.43 0.00 0.00 0.98
2306 2828 6.183361 TGGACCAGCTGCAGAACTTATTATAT 60.183 38.462 20.43 0.00 0.00 0.86
2336 2858 2.768527 AGACACACCCATGATGACTAGG 59.231 50.000 0.00 0.00 0.00 3.02
2519 3042 5.932303 AGCGTTGTTTGTGAAGTGTATATCT 59.068 36.000 0.00 0.00 0.00 1.98
2689 3232 2.503356 AGATTCTAGTTCAGTGGCTGGG 59.497 50.000 0.00 0.00 31.51 4.45
3171 3714 4.168922 TCAAAAGCATGCTGAGTTCATG 57.831 40.909 23.48 12.27 43.02 3.07
3776 4368 3.515602 AAGTCAGGACTGGATTGCTTT 57.484 42.857 2.15 0.00 41.58 3.51
3777 4369 2.787994 AGTCAGGACTGGATTGCTTTG 58.212 47.619 0.22 0.00 40.75 2.77
3785 4377 1.274167 CTGGATTGCTTTGTGCCACAT 59.726 47.619 0.00 0.00 42.00 3.21
3812 4404 5.408299 GTGGCACTTATCATTTGGGAAAAAC 59.592 40.000 11.13 0.00 0.00 2.43
4098 4690 3.947196 GGTTGCCATGATGTCACTAATCA 59.053 43.478 0.00 0.00 38.37 2.57
4575 5591 2.507484 CACTGAGGCATTGTTCCTTCA 58.493 47.619 0.00 0.00 33.24 3.02
4675 5691 9.410556 GAAGTTGTGCATGTATTTTCTAAACAT 57.589 29.630 0.00 0.00 34.22 2.71
4958 5982 2.948115 CCATGAATGCCACCCTTATCA 58.052 47.619 0.00 0.00 0.00 2.15
5151 6175 2.624838 CAAACCTGCCACTTGAAGACAT 59.375 45.455 0.00 0.00 0.00 3.06
5422 6460 1.334869 CGCCCACTTTTATCATCCAGC 59.665 52.381 0.00 0.00 0.00 4.85
5491 6529 2.418628 CGGTACTGCCAATCGTCAATTT 59.581 45.455 0.00 0.00 36.97 1.82
5550 6588 4.976731 GGTAGATGTGTTGTAGTATGCTCG 59.023 45.833 0.00 0.00 0.00 5.03
5560 6598 7.699391 GTGTTGTAGTATGCTCGTTATTAGTCA 59.301 37.037 0.00 0.00 0.00 3.41
5726 6764 8.307921 CAGAGATCTGTACAACCATGATTATG 57.692 38.462 0.00 0.00 39.09 1.90
5751 6789 8.257306 TGTATAGCGGCATGATGATTCTAATAA 58.743 33.333 1.45 0.00 0.00 1.40
5752 6790 9.265901 GTATAGCGGCATGATGATTCTAATAAT 57.734 33.333 1.45 0.00 0.00 1.28
5757 6795 9.869844 GCGGCATGATGATTCTAATAATATAAC 57.130 33.333 0.00 0.00 0.00 1.89
5840 6878 2.697431 TTGATTTGTGTTAGTGCCGC 57.303 45.000 0.00 0.00 0.00 6.53
5916 6954 2.078849 TCACACGCATACAGGTCTTG 57.921 50.000 0.00 0.00 0.00 3.02
5928 6966 3.809905 ACAGGTCTTGTCTTGTTTCCTC 58.190 45.455 0.00 0.00 33.87 3.71
6118 7162 3.010584 ACAATGCCTTGGAGGTGAACTAT 59.989 43.478 6.67 0.00 37.80 2.12
6159 7203 6.978343 TTAATGCTTACAACTACGAATGCT 57.022 33.333 0.00 0.00 0.00 3.79
6308 7352 5.818678 AAATGAGTACAAGAGGTGGTACA 57.181 39.130 0.00 0.00 41.74 2.90
6330 7374 0.249699 ACATGACACGGACGCAAGAA 60.250 50.000 0.00 0.00 43.62 2.52
6333 7377 1.954146 GACACGGACGCAAGAAGCA 60.954 57.895 0.00 0.00 46.13 3.91
6336 7380 1.301716 ACGGACGCAAGAAGCATGT 60.302 52.632 0.00 0.00 46.13 3.21
6345 7389 2.223433 GCAAGAAGCATGTACATGGAGC 60.223 50.000 31.63 20.34 44.79 4.70
6346 7390 2.338577 AGAAGCATGTACATGGAGCC 57.661 50.000 31.63 17.87 39.16 4.70
6352 7396 0.179045 ATGTACATGGAGCCCGAAGC 60.179 55.000 7.78 0.00 44.25 3.86
6361 7405 2.973899 GCCCGAAGCAGAGAGACA 59.026 61.111 0.00 0.00 42.97 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 2.109799 ATCATCGCTCGGGCTTGG 59.890 61.111 5.36 0.00 36.09 3.61
113 114 2.971452 GTCGGACTGGTGGGAGTC 59.029 66.667 0.00 0.00 41.55 3.36
144 145 1.212490 CAATGCATCAAACGGCGGT 59.788 52.632 13.24 0.00 0.00 5.68
146 147 2.160221 GGCAATGCATCAAACGGCG 61.160 57.895 7.79 4.80 0.00 6.46
170 171 0.237498 CGGCGTTCAAAAGGAAGGAC 59.763 55.000 0.00 0.00 44.24 3.85
272 273 8.023128 CGTCATAAATTCAAACTTGTCATTCCT 58.977 33.333 0.00 0.00 0.00 3.36
329 330 1.619332 CCTAGGGGCGATCTAGTTTCC 59.381 57.143 0.00 0.00 34.06 3.13
374 375 2.707039 CGCCCGACGCTATTTTGG 59.293 61.111 0.00 0.00 34.21 3.28
413 414 2.289002 GCATGACTAAGAGCATTTCCGG 59.711 50.000 0.00 0.00 0.00 5.14
435 436 1.280133 CCATATGATCAGGGGCGTCAT 59.720 52.381 3.65 0.00 36.60 3.06
625 626 8.441312 TGTATATTACACGTGTGCAAATTTTG 57.559 30.769 30.83 4.72 32.89 2.44
692 698 9.925268 GAATTATGCCAAAATGCTATTTTGAAG 57.075 29.630 23.97 15.02 40.73 3.02
713 720 7.508636 TGCATTGGAGCCCTATATTTTGAATTA 59.491 33.333 0.00 0.00 0.00 1.40
733 740 0.958091 TTTGAAGGACGGGTGCATTG 59.042 50.000 0.00 0.00 0.00 2.82
745 752 4.997565 TCTGCAAAAAGTCACTTTGAAGG 58.002 39.130 2.78 0.00 39.17 3.46
748 755 6.292865 CGAGTATCTGCAAAAAGTCACTTTGA 60.293 38.462 2.78 0.00 36.12 2.69
769 776 4.094684 GCATGACTAAGCGCGAGT 57.905 55.556 12.10 16.58 0.00 4.18
808 815 1.517257 AGACGCGCCAGATTCTTCG 60.517 57.895 5.73 1.83 0.00 3.79
1041 1055 4.357947 TCCAGCGTCGACCACTGC 62.358 66.667 21.93 14.58 0.00 4.40
1507 1576 3.675619 ATTACCACGCTCCACGGGC 62.676 63.158 0.00 0.00 46.66 6.13
1518 1621 8.227791 CACTGAACATACTGTTAACATTACCAC 58.772 37.037 9.13 2.44 41.28 4.16
1598 1944 8.525316 TGAAACACCTGTAACTTAATCGATCTA 58.475 33.333 0.00 0.00 0.00 1.98
1634 1980 6.941857 ACCATTGAAACACCTGTAACTTTTT 58.058 32.000 0.00 0.00 0.00 1.94
1635 1981 6.538945 ACCATTGAAACACCTGTAACTTTT 57.461 33.333 0.00 0.00 0.00 2.27
1636 1982 6.538945 AACCATTGAAACACCTGTAACTTT 57.461 33.333 0.00 0.00 0.00 2.66
1637 1983 6.071051 ACAAACCATTGAAACACCTGTAACTT 60.071 34.615 0.00 0.00 38.94 2.66
1638 1984 5.420739 ACAAACCATTGAAACACCTGTAACT 59.579 36.000 0.00 0.00 38.94 2.24
1639 1985 5.656480 ACAAACCATTGAAACACCTGTAAC 58.344 37.500 0.00 0.00 38.94 2.50
1640 1986 5.923733 ACAAACCATTGAAACACCTGTAA 57.076 34.783 0.00 0.00 38.94 2.41
1641 1987 5.886474 TGTACAAACCATTGAAACACCTGTA 59.114 36.000 0.00 0.00 38.94 2.74
1642 1988 4.707448 TGTACAAACCATTGAAACACCTGT 59.293 37.500 0.00 0.00 38.94 4.00
1643 1989 5.163561 ACTGTACAAACCATTGAAACACCTG 60.164 40.000 0.00 0.00 38.94 4.00
1644 1990 4.953579 ACTGTACAAACCATTGAAACACCT 59.046 37.500 0.00 0.00 38.94 4.00
1645 1991 5.257082 ACTGTACAAACCATTGAAACACC 57.743 39.130 0.00 0.00 38.94 4.16
1646 1992 7.918562 ACAATACTGTACAAACCATTGAAACAC 59.081 33.333 18.07 0.00 39.91 3.32
1647 1993 7.918033 CACAATACTGTACAAACCATTGAAACA 59.082 33.333 18.07 0.00 35.20 2.83
1648 1994 8.132362 TCACAATACTGTACAAACCATTGAAAC 58.868 33.333 18.07 0.00 35.20 2.78
1649 1995 8.226819 TCACAATACTGTACAAACCATTGAAA 57.773 30.769 18.07 8.24 35.20 2.69
1650 1996 7.809546 TCACAATACTGTACAAACCATTGAA 57.190 32.000 18.07 8.47 35.20 2.69
1651 1997 7.500892 AGTTCACAATACTGTACAAACCATTGA 59.499 33.333 18.07 7.28 35.20 2.57
1652 1998 7.648142 AGTTCACAATACTGTACAAACCATTG 58.352 34.615 12.98 12.98 36.73 2.82
1653 1999 7.817418 AGTTCACAATACTGTACAAACCATT 57.183 32.000 0.00 0.00 33.22 3.16
2262 2773 2.361104 GATCAACGCTGGCCCCAA 60.361 61.111 0.00 0.00 0.00 4.12
2264 2784 2.044946 AAGATCAACGCTGGCCCC 60.045 61.111 0.00 0.00 0.00 5.80
2305 2827 4.018506 TCATGGGTGTGTCTACCATTTCAT 60.019 41.667 0.00 0.00 42.08 2.57
2306 2828 3.329225 TCATGGGTGTGTCTACCATTTCA 59.671 43.478 0.00 0.00 42.08 2.69
2689 3232 1.405121 CGGGTACTACAGCAAAGGGTC 60.405 57.143 0.00 0.00 0.00 4.46
2892 3435 5.091261 AGAGGCAGGTAAGACAAATACAG 57.909 43.478 0.00 0.00 0.00 2.74
3647 4192 0.107643 TCGGAGTTGCCATGTGTTCA 59.892 50.000 0.00 0.00 35.94 3.18
3785 4377 2.824936 CCCAAATGATAAGTGCCACACA 59.175 45.455 0.00 0.00 36.74 3.72
3995 4587 4.565652 GGTGGATCTGGAAGTAGCAAAAGA 60.566 45.833 0.00 0.00 33.76 2.52
4310 5325 7.287466 CCCACTATATAGAGGATCATCAGAAGG 59.713 44.444 23.46 5.75 36.32 3.46
4575 5591 4.746309 ATGCAGTGCCATGGCCGT 62.746 61.111 33.44 18.11 41.09 5.68
4675 5691 7.265673 GCGGTGCCTAAAATCAGATATATAGA 58.734 38.462 0.00 0.00 0.00 1.98
4958 5982 6.094186 GCTTCATTCTTATTTTCTCTTCCCGT 59.906 38.462 0.00 0.00 0.00 5.28
5151 6175 7.440198 TGCACTTTGATATGTTTTTGATTCCA 58.560 30.769 0.00 0.00 0.00 3.53
5422 6460 5.577164 CGTGGTCCAGAATAACTAAACAGAG 59.423 44.000 0.00 0.00 0.00 3.35
5491 6529 4.698304 GCTTACAGGGTGCTTAAACACATA 59.302 41.667 10.95 0.00 42.55 2.29
5560 6598 5.804944 AGATAGCAGCAACATCACTAGAT 57.195 39.130 0.00 0.00 33.87 1.98
5606 6644 4.836125 ACTTTCAATCGAGCACAACAAT 57.164 36.364 0.00 0.00 0.00 2.71
5669 6707 0.823460 TGCGTGACTATCATCTGCCA 59.177 50.000 0.00 0.00 0.00 4.92
5724 6762 5.095145 AGAATCATCATGCCGCTATACAT 57.905 39.130 0.00 0.00 0.00 2.29
5726 6764 8.648557 TTATTAGAATCATCATGCCGCTATAC 57.351 34.615 0.00 0.00 0.00 1.47
5757 6795 7.749126 AGCGGTCGTTAGAAATTTATCTTTTTG 59.251 33.333 0.00 0.00 0.00 2.44
5758 6796 7.749126 CAGCGGTCGTTAGAAATTTATCTTTTT 59.251 33.333 0.00 0.00 0.00 1.94
5759 6797 7.094933 ACAGCGGTCGTTAGAAATTTATCTTTT 60.095 33.333 0.00 0.00 0.00 2.27
5760 6798 6.370718 ACAGCGGTCGTTAGAAATTTATCTTT 59.629 34.615 0.00 0.00 0.00 2.52
5840 6878 8.863049 GCAAATATTTCACACTTACAATTCCAG 58.137 33.333 0.00 0.00 0.00 3.86
5916 6954 2.061740 AGCGTACGAGGAAACAAGAC 57.938 50.000 21.65 0.00 0.00 3.01
5928 6966 1.920574 CCTGTGATTGAGAAGCGTACG 59.079 52.381 11.84 11.84 0.00 3.67
6176 7220 1.266178 TCGAGAGGGATGCTGAACAA 58.734 50.000 0.00 0.00 0.00 2.83
6223 7267 7.830575 CGTATTCGCGGAAAAATAAGTAGTTA 58.169 34.615 6.13 0.00 0.00 2.24
6280 7324 7.287810 ACCACCTCTTGTACTCATTTTAACTT 58.712 34.615 0.00 0.00 0.00 2.66
6281 7325 6.838382 ACCACCTCTTGTACTCATTTTAACT 58.162 36.000 0.00 0.00 0.00 2.24
6282 7326 7.658575 TGTACCACCTCTTGTACTCATTTTAAC 59.341 37.037 0.00 0.00 38.48 2.01
6286 7330 5.818678 TGTACCACCTCTTGTACTCATTT 57.181 39.130 0.00 0.00 38.48 2.32
6288 7332 4.591498 TGTTGTACCACCTCTTGTACTCAT 59.409 41.667 0.00 0.00 38.48 2.90
6295 7339 3.498397 GTCATGTGTTGTACCACCTCTTG 59.502 47.826 0.00 0.00 34.35 3.02
6308 7352 0.812014 TTGCGTCCGTGTCATGTGTT 60.812 50.000 0.00 0.00 0.00 3.32
6330 7374 1.146930 CGGGCTCCATGTACATGCT 59.853 57.895 27.27 0.00 37.49 3.79
6333 7377 0.179045 GCTTCGGGCTCCATGTACAT 60.179 55.000 1.41 1.41 38.06 2.29
6336 7380 0.975556 TCTGCTTCGGGCTCCATGTA 60.976 55.000 0.00 0.00 42.39 2.29
6345 7389 0.820226 TCATGTCTCTCTGCTTCGGG 59.180 55.000 0.00 0.00 0.00 5.14
6346 7390 1.747924 TCTCATGTCTCTCTGCTTCGG 59.252 52.381 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.