Multiple sequence alignment - TraesCS1A01G394300

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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 TraesCS1A01G394300 chr1A 100.000 3143 0 0 1 3143 560394699 560397841 0.000000e+00 5805
1 TraesCS1A01G394300 chr6B 94.291 2575 140 5 572 3143 647697196 647699766 0.000000e+00 3934
2 TraesCS1A01G394300 chr6B 87.447 470 59 0 2661 3130 412286010 412285541 2.760000e-150 542
3 TraesCS1A01G394300 chr6B 94.012 334 19 1 128 461 647696541 647696873 3.620000e-139 505
4 TraesCS1A01G394300 chr3D 94.635 932 47 2 2213 3141 598593932 598594863 0.000000e+00 1441
5 TraesCS1A01G394300 chr3D 94.090 863 48 1 474 1336 598584574 598585433 0.000000e+00 1308
6 TraesCS1A01G394300 chr3D 92.118 850 42 8 1333 2182 598592629 598593453 0.000000e+00 1175
7 TraesCS1A01G394300 chr3D 92.733 344 19 2 133 476 598584067 598584404 2.820000e-135 492
8 TraesCS1A01G394300 chr3D 90.141 284 28 0 2853 3136 433507130 433507413 1.380000e-98 370
9 TraesCS1A01G394300 chr3D 88.192 271 31 1 2853 3122 433506860 433507130 3.910000e-84 322
10 TraesCS1A01G394300 chr7B 88.550 952 105 2 2189 3136 580879635 580878684 0.000000e+00 1151
11 TraesCS1A01G394300 chr7B 86.860 586 62 10 2553 3136 210428726 210428154 2.640000e-180 641
12 TraesCS1A01G394300 chr7B 82.353 527 92 1 1664 2190 580880376 580879851 1.030000e-124 457
13 TraesCS1A01G394300 chr7B 83.333 246 37 4 138 381 382621029 382621272 1.130000e-54 224
14 TraesCS1A01G394300 chr7B 81.481 243 41 4 141 381 580883263 580883023 2.470000e-46 196
15 TraesCS1A01G394300 chr2A 85.934 782 106 4 2361 3138 671345297 671344516 0.000000e+00 832
16 TraesCS1A01G394300 chr1B 90.675 504 44 1 2633 3136 321685480 321685980 0.000000e+00 667
17 TraesCS1A01G394300 chr2D 93.706 429 22 2 2541 2968 629196253 629195829 3.420000e-179 638
18 TraesCS1A01G394300 chr2B 78.365 208 45 0 175 382 95488364 95488157 5.470000e-28 135


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 TraesCS1A01G394300 chr1A 560394699 560397841 3142 False 5805.000000 5805 100.0000 1 3143 1 chr1A.!!$F1 3142
1 TraesCS1A01G394300 chr6B 647696541 647699766 3225 False 2219.500000 3934 94.1515 128 3143 2 chr6B.!!$F1 3015
2 TraesCS1A01G394300 chr3D 598592629 598594863 2234 False 1308.000000 1441 93.3765 1333 3141 2 chr3D.!!$F3 1808
3 TraesCS1A01G394300 chr3D 598584067 598585433 1366 False 900.000000 1308 93.4115 133 1336 2 chr3D.!!$F2 1203
4 TraesCS1A01G394300 chr3D 433506860 433507413 553 False 346.000000 370 89.1665 2853 3136 2 chr3D.!!$F1 283
5 TraesCS1A01G394300 chr7B 210428154 210428726 572 True 641.000000 641 86.8600 2553 3136 1 chr7B.!!$R1 583
6 TraesCS1A01G394300 chr7B 580878684 580883263 4579 True 601.333333 1151 84.1280 141 3136 3 chr7B.!!$R2 2995
7 TraesCS1A01G394300 chr2A 671344516 671345297 781 True 832.000000 832 85.9340 2361 3138 1 chr2A.!!$R1 777
8 TraesCS1A01G394300 chr1B 321685480 321685980 500 False 667.000000 667 90.6750 2633 3136 1 chr1B.!!$F1 503

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
85 86 0.324738 TCGCCACCAGAGAGAGGAAT 60.325 55.0 0.0 0.0 0.0 3.01 F
1375 3179 0.040351 TCTGCCTACCAGCTCTGTCT 59.960 55.0 0.0 0.0 41.5 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2043 3851 1.135141 GCAGAGAGATCGCAGTCAAGT 60.135 52.381 0.0 0.0 0.00 3.16 R
2954 5214 0.769247 ACTACCTTTTGGAAGCCCGT 59.231 50.000 0.0 0.0 44.07 5.28 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 2.882927 TGTGTATAGCGGCGAAATCT 57.117 45.000 12.98 0.00 0.00 2.40
22 23 2.100087 TGTGTATAGCGGCGAAATCTCA 59.900 45.455 12.98 3.58 0.00 3.27
25 26 1.583054 ATAGCGGCGAAATCTCAACC 58.417 50.000 12.98 0.00 0.00 3.77
26 27 0.535335 TAGCGGCGAAATCTCAACCT 59.465 50.000 12.98 0.00 0.00 3.50
27 28 1.021390 AGCGGCGAAATCTCAACCTG 61.021 55.000 12.98 0.00 0.00 4.00
28 29 1.019278 GCGGCGAAATCTCAACCTGA 61.019 55.000 12.98 0.00 0.00 3.86
29 30 1.656652 CGGCGAAATCTCAACCTGAT 58.343 50.000 0.00 0.00 0.00 2.90
31 32 2.632377 GGCGAAATCTCAACCTGATCA 58.368 47.619 0.00 0.00 0.00 2.92
32 33 2.611292 GGCGAAATCTCAACCTGATCAG 59.389 50.000 16.24 16.24 0.00 2.90
33 34 3.525537 GCGAAATCTCAACCTGATCAGA 58.474 45.455 24.62 3.22 0.00 3.27
34 35 3.308323 GCGAAATCTCAACCTGATCAGAC 59.692 47.826 24.62 1.89 0.00 3.51
35 36 4.498241 CGAAATCTCAACCTGATCAGACA 58.502 43.478 24.62 3.70 0.00 3.41
36 37 5.114780 CGAAATCTCAACCTGATCAGACAT 58.885 41.667 24.62 6.29 0.00 3.06
37 38 6.276091 CGAAATCTCAACCTGATCAGACATA 58.724 40.000 24.62 6.01 0.00 2.29
39 40 8.084684 CGAAATCTCAACCTGATCAGACATATA 58.915 37.037 24.62 5.80 0.00 0.86
40 41 9.202273 GAAATCTCAACCTGATCAGACATATAC 57.798 37.037 24.62 2.97 0.00 1.47
41 42 7.846101 ATCTCAACCTGATCAGACATATACA 57.154 36.000 24.62 1.32 0.00 2.29
42 43 7.282332 TCTCAACCTGATCAGACATATACAG 57.718 40.000 24.62 6.30 0.00 2.74
43 44 6.836007 TCTCAACCTGATCAGACATATACAGT 59.164 38.462 24.62 6.96 0.00 3.55
44 45 7.013750 TCTCAACCTGATCAGACATATACAGTC 59.986 40.741 24.62 0.04 36.26 3.51
45 46 6.836007 TCAACCTGATCAGACATATACAGTCT 59.164 38.462 24.62 4.29 46.72 3.24
52 53 4.471078 AGACATATACAGTCTGGGCCTA 57.529 45.455 4.53 0.00 44.23 3.93
53 54 4.153411 AGACATATACAGTCTGGGCCTAC 58.847 47.826 4.53 2.92 44.23 3.18
54 55 4.140900 AGACATATACAGTCTGGGCCTACT 60.141 45.833 4.53 5.61 44.23 2.57
55 56 3.898123 ACATATACAGTCTGGGCCTACTG 59.102 47.826 27.46 27.46 46.84 2.74
56 57 2.848678 ATACAGTCTGGGCCTACTGA 57.151 50.000 32.56 21.42 44.79 3.41
57 58 2.848678 TACAGTCTGGGCCTACTGAT 57.151 50.000 32.56 22.67 44.79 2.90
60 61 3.658725 ACAGTCTGGGCCTACTGATAAT 58.341 45.455 32.56 16.33 44.79 1.28
61 62 3.643792 ACAGTCTGGGCCTACTGATAATC 59.356 47.826 32.56 1.52 44.79 1.75
64 65 3.057174 GTCTGGGCCTACTGATAATCGAG 60.057 52.174 4.53 0.00 0.00 4.04
65 66 2.232452 CTGGGCCTACTGATAATCGAGG 59.768 54.545 4.53 0.00 0.00 4.63
66 67 2.249139 GGGCCTACTGATAATCGAGGT 58.751 52.381 0.84 0.00 0.00 3.85
67 68 2.231721 GGGCCTACTGATAATCGAGGTC 59.768 54.545 0.84 0.00 0.00 3.85
68 69 2.095161 GGCCTACTGATAATCGAGGTCG 60.095 54.545 0.00 0.00 41.45 4.79
69 70 2.668834 GCCTACTGATAATCGAGGTCGC 60.669 54.545 0.00 0.00 39.60 5.19
70 71 2.095161 CCTACTGATAATCGAGGTCGCC 60.095 54.545 0.00 0.00 39.60 5.54
71 72 1.399714 ACTGATAATCGAGGTCGCCA 58.600 50.000 0.00 0.00 39.60 5.69
73 74 0.387929 TGATAATCGAGGTCGCCACC 59.612 55.000 0.00 0.00 44.19 4.61
74 75 0.387929 GATAATCGAGGTCGCCACCA 59.612 55.000 2.46 0.00 46.68 4.17
75 76 0.389391 ATAATCGAGGTCGCCACCAG 59.611 55.000 2.46 0.00 46.68 4.00
76 77 0.681887 TAATCGAGGTCGCCACCAGA 60.682 55.000 2.46 2.00 46.68 3.86
78 79 2.838748 ATCGAGGTCGCCACCAGAGA 62.839 60.000 2.46 0.00 46.68 3.10
79 80 2.888863 GAGGTCGCCACCAGAGAG 59.111 66.667 2.46 0.00 46.68 3.20
80 81 1.679305 GAGGTCGCCACCAGAGAGA 60.679 63.158 2.46 0.00 46.68 3.10
81 82 1.662438 GAGGTCGCCACCAGAGAGAG 61.662 65.000 2.46 0.00 46.68 3.20
85 86 0.324738 TCGCCACCAGAGAGAGGAAT 60.325 55.000 0.00 0.00 0.00 3.01
86 87 0.539051 CGCCACCAGAGAGAGGAATT 59.461 55.000 0.00 0.00 0.00 2.17
92 93 4.224818 CCACCAGAGAGAGGAATTCTTCTT 59.775 45.833 19.92 10.77 35.87 2.52
93 94 5.280419 CCACCAGAGAGAGGAATTCTTCTTT 60.280 44.000 19.92 15.02 35.87 2.52
94 95 6.237154 CACCAGAGAGAGGAATTCTTCTTTT 58.763 40.000 19.92 12.19 35.87 2.27
95 96 6.149142 CACCAGAGAGAGGAATTCTTCTTTTG 59.851 42.308 19.92 16.69 35.87 2.44
96 97 5.647225 CCAGAGAGAGGAATTCTTCTTTTGG 59.353 44.000 19.92 20.50 35.87 3.28
97 98 6.237154 CAGAGAGAGGAATTCTTCTTTTGGT 58.763 40.000 19.92 4.71 35.87 3.67
99 100 7.333174 CAGAGAGAGGAATTCTTCTTTTGGTAC 59.667 40.741 19.92 6.78 35.87 3.34
100 101 6.477253 AGAGAGGAATTCTTCTTTTGGTACC 58.523 40.000 19.92 4.43 35.87 3.34
101 102 6.044404 AGAGAGGAATTCTTCTTTTGGTACCA 59.956 38.462 19.92 11.60 35.87 3.25
103 104 5.953571 AGGAATTCTTCTTTTGGTACCAGT 58.046 37.500 15.65 0.00 0.00 4.00
104 105 7.017254 AGAGGAATTCTTCTTTTGGTACCAGTA 59.983 37.037 15.65 4.62 29.61 2.74
105 106 6.940867 AGGAATTCTTCTTTTGGTACCAGTAC 59.059 38.462 15.65 0.00 35.40 2.73
106 107 6.713450 GGAATTCTTCTTTTGGTACCAGTACA 59.287 38.462 15.65 0.00 37.78 2.90
107 108 7.229907 GGAATTCTTCTTTTGGTACCAGTACAA 59.770 37.037 15.65 3.42 37.78 2.41
108 109 8.706322 AATTCTTCTTTTGGTACCAGTACAAT 57.294 30.769 15.65 5.79 37.78 2.71
109 110 7.739498 TTCTTCTTTTGGTACCAGTACAATC 57.261 36.000 15.65 0.00 37.78 2.67
115 116 5.570205 TTGGTACCAGTACAATCTCCAAA 57.430 39.130 15.65 0.00 37.78 3.28
116 117 5.160607 TGGTACCAGTACAATCTCCAAAG 57.839 43.478 11.60 0.00 37.78 2.77
117 118 4.841813 TGGTACCAGTACAATCTCCAAAGA 59.158 41.667 11.60 0.00 37.78 2.52
118 119 5.487488 TGGTACCAGTACAATCTCCAAAGAT 59.513 40.000 11.60 0.00 37.00 2.40
321 322 2.690510 GCTGGAGGGGAGCTCCTT 60.691 66.667 31.36 20.16 41.39 3.36
367 368 4.742201 CTGCCGGTGTGTAGCGCT 62.742 66.667 17.26 17.26 45.83 5.92
400 401 3.294493 GGTGCTCTTTTGCCGGCA 61.294 61.111 29.03 29.03 0.00 5.69
414 415 4.536687 GGCATGCTGCGCGGTTAC 62.537 66.667 19.23 5.13 46.21 2.50
428 429 4.465512 TTACCTCGGACGCGACGC 62.466 66.667 15.93 10.49 0.00 5.19
457 458 3.349006 AAGGTGCACTTCGCTGCG 61.349 61.111 17.25 17.25 43.06 5.18
535 790 1.750399 ATCAAATCGGCGCCTGCTT 60.750 52.632 26.68 12.94 42.25 3.91
598 865 2.345244 CTGCCGCAGTCTCAAGGT 59.655 61.111 12.54 0.00 0.00 3.50
632 899 2.996395 CCATGCTCCTCCTGCTGT 59.004 61.111 0.00 0.00 0.00 4.40
642 909 1.202627 CCTCCTGCTGTGGATTCTAGC 60.203 57.143 0.00 0.00 35.30 3.42
748 1031 4.143333 GCCCAAGCCGTCGAGCTA 62.143 66.667 8.36 0.00 44.11 3.32
752 1035 1.426621 CAAGCCGTCGAGCTACGTA 59.573 57.895 8.15 0.00 44.11 3.57
758 1050 1.262417 CCGTCGAGCTACGTATGCTTA 59.738 52.381 16.95 8.89 41.30 3.09
784 1076 1.745115 CCTGCGCGAAGGGATTTCA 60.745 57.895 26.78 0.60 46.37 2.69
816 1108 3.076104 CAGAGAATGCCATCGCTGT 57.924 52.632 10.22 0.00 40.87 4.40
864 1156 1.076332 GTCGAAATCCGTTCACCTGG 58.924 55.000 0.00 0.00 39.75 4.45
899 1191 4.680237 TGGTCACCGCGCTTGGAG 62.680 66.667 5.56 0.00 0.00 3.86
978 1279 2.997315 CACCCTCGTGCTCCTCCA 60.997 66.667 0.00 0.00 32.04 3.86
1375 3179 0.040351 TCTGCCTACCAGCTCTGTCT 59.960 55.000 0.00 0.00 41.50 3.41
1378 3182 0.898320 GCCTACCAGCTCTGTCTTGA 59.102 55.000 0.00 0.00 0.00 3.02
1433 3237 1.817941 CGATCCGGCCGTCCAAAAT 60.818 57.895 26.12 7.23 0.00 1.82
1476 3280 0.463654 ACCACATCGTGTTGTGCACT 60.464 50.000 19.41 0.00 44.53 4.40
1518 3322 0.685097 CCTTCCCTTCCAGTTCGACA 59.315 55.000 0.00 0.00 0.00 4.35
1607 3411 2.526888 ACACCAGAACCTATCCTCGA 57.473 50.000 0.00 0.00 0.00 4.04
1683 3490 2.884012 TCATGAAGTGACAACGCCAATT 59.116 40.909 0.00 0.00 0.00 2.32
1738 3545 0.108138 GGAGGACACACCCATCTTCG 60.108 60.000 0.00 0.00 40.05 3.79
1849 3656 0.392998 CACCGGCCTACAGCTCATTT 60.393 55.000 0.00 0.00 43.05 2.32
1880 3687 0.941542 CGTCTTCGGGCAAAGAACAA 59.058 50.000 3.47 0.00 37.04 2.83
2106 3914 0.344790 ATCATGGAGGACAGGGAGGT 59.655 55.000 0.00 0.00 0.00 3.85
2182 3990 7.395772 TCTGCTTTGATGTATCCATGGTTTAAA 59.604 33.333 12.58 0.63 0.00 1.52
2332 4588 1.133790 GCTGCAGACCATTGATCCAAC 59.866 52.381 20.43 0.00 0.00 3.77
2548 4807 0.762842 TATGGCCCCACTCGTAGCAT 60.763 55.000 0.00 0.00 0.00 3.79
2946 5206 1.194772 CCGCTTCGAAAACTTCTGGAC 59.805 52.381 0.00 0.00 0.00 4.02
2954 5214 4.884744 TCGAAAACTTCTGGACCAAAATGA 59.115 37.500 0.00 0.00 0.00 2.57
2988 5248 2.906389 AGGTAGTCAGTGATGCTTGGAA 59.094 45.455 0.00 0.00 0.00 3.53
3042 5302 2.075338 GCTCTTCCACAAGCTCAAGAG 58.925 52.381 11.94 11.94 43.23 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.243737 TGAGATTTCGCCGCTATACACAT 60.244 43.478 0.00 0.00 0.00 3.21
2 3 2.739292 TGAGATTTCGCCGCTATACAC 58.261 47.619 0.00 0.00 0.00 2.90
6 7 1.139058 AGGTTGAGATTTCGCCGCTAT 59.861 47.619 0.00 0.00 0.00 2.97
8 9 1.021390 CAGGTTGAGATTTCGCCGCT 61.021 55.000 0.00 0.00 0.00 5.52
9 10 1.019278 TCAGGTTGAGATTTCGCCGC 61.019 55.000 0.00 0.00 0.00 6.53
10 11 1.594862 GATCAGGTTGAGATTTCGCCG 59.405 52.381 0.00 0.00 0.00 6.46
11 12 2.611292 CTGATCAGGTTGAGATTTCGCC 59.389 50.000 15.38 0.00 0.00 5.54
12 13 3.308323 GTCTGATCAGGTTGAGATTTCGC 59.692 47.826 22.42 0.00 0.00 4.70
13 14 4.498241 TGTCTGATCAGGTTGAGATTTCG 58.502 43.478 22.42 0.00 0.00 3.46
14 15 9.202273 GTATATGTCTGATCAGGTTGAGATTTC 57.798 37.037 22.42 2.02 0.00 2.17
16 17 8.255111 TGTATATGTCTGATCAGGTTGAGATT 57.745 34.615 22.42 3.71 0.00 2.40
17 18 7.508636 ACTGTATATGTCTGATCAGGTTGAGAT 59.491 37.037 22.42 9.80 0.00 2.75
18 19 6.836007 ACTGTATATGTCTGATCAGGTTGAGA 59.164 38.462 22.42 2.39 0.00 3.27
19 20 7.014134 AGACTGTATATGTCTGATCAGGTTGAG 59.986 40.741 22.42 10.01 42.46 3.02
20 21 6.836007 AGACTGTATATGTCTGATCAGGTTGA 59.164 38.462 22.42 6.80 42.46 3.18
31 32 3.336509 AGGCCCAGACTGTATATGTCT 57.663 47.619 0.00 5.78 44.62 3.41
32 33 4.021894 CAGTAGGCCCAGACTGTATATGTC 60.022 50.000 17.87 1.91 38.61 3.06
33 34 3.898123 CAGTAGGCCCAGACTGTATATGT 59.102 47.826 17.87 0.00 38.61 2.29
34 35 4.152647 TCAGTAGGCCCAGACTGTATATG 58.847 47.826 22.71 4.76 43.01 1.78
35 36 4.471078 TCAGTAGGCCCAGACTGTATAT 57.529 45.455 22.71 0.00 43.01 0.86
36 37 3.965470 TCAGTAGGCCCAGACTGTATA 57.035 47.619 22.71 7.57 43.01 1.47
37 38 2.848678 TCAGTAGGCCCAGACTGTAT 57.151 50.000 22.71 0.00 43.01 2.29
39 40 2.848678 TATCAGTAGGCCCAGACTGT 57.151 50.000 22.71 15.32 43.01 3.55
40 41 3.305676 CGATTATCAGTAGGCCCAGACTG 60.306 52.174 19.39 19.39 43.70 3.51
41 42 2.894126 CGATTATCAGTAGGCCCAGACT 59.106 50.000 0.00 0.00 0.00 3.24
42 43 2.891580 TCGATTATCAGTAGGCCCAGAC 59.108 50.000 0.00 0.00 0.00 3.51
43 44 3.157881 CTCGATTATCAGTAGGCCCAGA 58.842 50.000 0.00 0.00 0.00 3.86
44 45 2.232452 CCTCGATTATCAGTAGGCCCAG 59.768 54.545 0.00 0.00 0.00 4.45
45 46 2.248248 CCTCGATTATCAGTAGGCCCA 58.752 52.381 0.00 0.00 0.00 5.36
47 48 2.095161 CGACCTCGATTATCAGTAGGCC 60.095 54.545 0.00 0.00 43.02 5.19
48 49 2.668834 GCGACCTCGATTATCAGTAGGC 60.669 54.545 0.00 0.00 43.02 3.93
49 50 2.095161 GGCGACCTCGATTATCAGTAGG 60.095 54.545 0.00 4.36 43.02 3.18
50 51 2.552743 TGGCGACCTCGATTATCAGTAG 59.447 50.000 0.00 0.00 43.02 2.57
52 53 1.067212 GTGGCGACCTCGATTATCAGT 59.933 52.381 0.00 0.00 43.02 3.41
53 54 1.603172 GGTGGCGACCTCGATTATCAG 60.603 57.143 11.17 0.00 43.02 2.90
54 55 0.387929 GGTGGCGACCTCGATTATCA 59.612 55.000 11.17 0.00 43.02 2.15
55 56 0.387929 TGGTGGCGACCTCGATTATC 59.612 55.000 19.42 0.00 43.58 1.75
56 57 0.389391 CTGGTGGCGACCTCGATTAT 59.611 55.000 19.42 0.00 43.58 1.28
57 58 0.681887 TCTGGTGGCGACCTCGATTA 60.682 55.000 19.42 0.00 43.58 1.75
60 61 3.062466 CTCTGGTGGCGACCTCGA 61.062 66.667 19.42 13.67 43.58 4.04
61 62 3.057547 CTCTCTGGTGGCGACCTCG 62.058 68.421 19.42 10.11 43.58 4.63
64 65 2.716017 CCTCTCTCTGGTGGCGACC 61.716 68.421 11.57 11.57 43.48 4.79
65 66 1.251527 TTCCTCTCTCTGGTGGCGAC 61.252 60.000 0.00 0.00 0.00 5.19
66 67 0.324738 ATTCCTCTCTCTGGTGGCGA 60.325 55.000 0.00 0.00 0.00 5.54
67 68 0.539051 AATTCCTCTCTCTGGTGGCG 59.461 55.000 0.00 0.00 0.00 5.69
68 69 1.836802 AGAATTCCTCTCTCTGGTGGC 59.163 52.381 0.65 0.00 0.00 5.01
69 70 4.135747 GAAGAATTCCTCTCTCTGGTGG 57.864 50.000 0.65 0.00 39.83 4.61
80 81 7.420913 TGTACTGGTACCAAAAGAAGAATTCCT 60.421 37.037 17.11 0.00 39.56 3.36
81 82 6.713450 TGTACTGGTACCAAAAGAAGAATTCC 59.287 38.462 17.11 0.00 39.56 3.01
85 86 7.514721 AGATTGTACTGGTACCAAAAGAAGAA 58.485 34.615 17.11 5.04 35.26 2.52
86 87 7.074653 AGATTGTACTGGTACCAAAAGAAGA 57.925 36.000 17.11 0.00 35.26 2.87
92 93 5.570205 TTGGAGATTGTACTGGTACCAAA 57.430 39.130 17.11 7.68 35.26 3.28
93 94 5.308497 TCTTTGGAGATTGTACTGGTACCAA 59.692 40.000 17.11 0.00 35.26 3.67
94 95 4.841813 TCTTTGGAGATTGTACTGGTACCA 59.158 41.667 15.39 15.39 35.26 3.25
95 96 5.416271 TCTTTGGAGATTGTACTGGTACC 57.584 43.478 4.43 4.43 35.26 3.34
107 108 8.204160 TCGTGTGTATCAATAATCTTTGGAGAT 58.796 33.333 0.00 0.00 44.51 2.75
108 109 7.552459 TCGTGTGTATCAATAATCTTTGGAGA 58.448 34.615 0.00 0.00 36.09 3.71
109 110 7.770801 TCGTGTGTATCAATAATCTTTGGAG 57.229 36.000 0.00 0.00 0.00 3.86
115 116 6.291377 AGCCATTCGTGTGTATCAATAATCT 58.709 36.000 0.00 0.00 0.00 2.40
116 117 6.347725 GGAGCCATTCGTGTGTATCAATAATC 60.348 42.308 0.00 0.00 0.00 1.75
117 118 5.470098 GGAGCCATTCGTGTGTATCAATAAT 59.530 40.000 0.00 0.00 0.00 1.28
118 119 4.814234 GGAGCCATTCGTGTGTATCAATAA 59.186 41.667 0.00 0.00 0.00 1.40
120 121 3.206150 GGAGCCATTCGTGTGTATCAAT 58.794 45.455 0.00 0.00 0.00 2.57
121 122 2.627945 GGAGCCATTCGTGTGTATCAA 58.372 47.619 0.00 0.00 0.00 2.57
123 124 1.134521 TGGGAGCCATTCGTGTGTATC 60.135 52.381 0.00 0.00 0.00 2.24
125 126 0.036765 GTGGGAGCCATTCGTGTGTA 60.037 55.000 0.00 0.00 35.28 2.90
126 127 1.302511 GTGGGAGCCATTCGTGTGT 60.303 57.895 0.00 0.00 35.28 3.72
127 128 2.390599 CGTGGGAGCCATTCGTGTG 61.391 63.158 0.00 0.00 35.28 3.82
129 130 3.499737 GCGTGGGAGCCATTCGTG 61.500 66.667 0.00 0.00 35.28 4.35
130 131 3.665675 GAGCGTGGGAGCCATTCGT 62.666 63.158 0.00 0.00 35.28 3.85
321 322 3.181422 ACCATCCCGGATACACAGATCTA 60.181 47.826 0.73 0.00 38.63 1.98
367 368 4.641645 CCAACACCCGAGGCAGCA 62.642 66.667 0.00 0.00 0.00 4.41
381 382 2.855514 GCCGGCAAAAGAGCACCAA 61.856 57.895 24.80 0.00 35.83 3.67
457 458 2.071844 AATCCAGCAGCGCATCATGC 62.072 55.000 11.47 11.24 42.87 4.06
598 865 1.293498 GGCTTGACGAAGAGCTCCA 59.707 57.895 10.93 0.00 38.89 3.86
632 899 1.686325 GGGGCACGAGCTAGAATCCA 61.686 60.000 4.48 0.00 41.70 3.41
748 1031 2.894126 CAGGAGGAGGATAAGCATACGT 59.106 50.000 0.00 0.00 0.00 3.57
752 1035 0.683973 CGCAGGAGGAGGATAAGCAT 59.316 55.000 0.00 0.00 0.00 3.79
758 1050 2.759973 TTCGCGCAGGAGGAGGAT 60.760 61.111 8.75 0.00 0.00 3.24
784 1076 4.694509 GCATTCTCTGTCACTGAACTTGAT 59.305 41.667 0.00 0.00 0.00 2.57
816 1108 1.423584 TGCAGTGTCCTTTGAGGAGA 58.576 50.000 0.00 0.00 46.90 3.71
864 1156 1.525535 AATCTGCCGGCATCTGAGC 60.526 57.895 32.87 0.00 0.00 4.26
963 1264 2.801631 GGATGGAGGAGCACGAGGG 61.802 68.421 0.00 0.00 0.00 4.30
978 1279 2.233566 TGGAGCAGCAGGTTGGGAT 61.234 57.895 0.00 0.00 0.00 3.85
1019 1320 4.664677 GGCGCACTGACTGGTCGT 62.665 66.667 10.83 0.00 0.00 4.34
1285 3089 2.039480 TCATTGCAGAGCAGGAAGTCTT 59.961 45.455 0.00 0.00 40.61 3.01
1351 3155 2.681848 CAGAGCTGGTAGGCAGAATTTG 59.318 50.000 0.00 0.00 34.17 2.32
1375 3179 1.888512 GGATCTGCAAAGCCAACTCAA 59.111 47.619 0.00 0.00 0.00 3.02
1378 3182 1.251251 GTGGATCTGCAAAGCCAACT 58.749 50.000 0.00 0.00 31.18 3.16
1433 3237 2.046023 CCTCGCCAACATCCAGCA 60.046 61.111 0.00 0.00 0.00 4.41
1497 3301 1.377333 CGAACTGGAAGGGAAGGCC 60.377 63.158 0.00 0.00 39.30 5.19
1683 3490 1.416401 GCGTGGAAGGAAGGGATATGA 59.584 52.381 0.00 0.00 0.00 2.15
1803 3610 1.609072 GCGAGGGTTTTTCTTCTTGCT 59.391 47.619 0.00 0.00 34.68 3.91
1849 3656 3.858868 GAAGACGCGGACTGTGGCA 62.859 63.158 12.47 0.00 39.17 4.92
1880 3687 2.584064 TGGCGATCGGCATGTTCT 59.416 55.556 36.95 0.00 45.85 3.01
1950 3757 1.742761 TTGCTGCCTCAGTTATCTGC 58.257 50.000 0.00 0.00 41.10 4.26
2043 3851 1.135141 GCAGAGAGATCGCAGTCAAGT 60.135 52.381 0.00 0.00 0.00 3.16
2332 4588 2.223829 CCACCCAGATAAGTAGCGACAG 60.224 54.545 0.00 0.00 0.00 3.51
2528 4787 0.978667 TGCTACGAGTGGGGCCATAA 60.979 55.000 4.39 0.00 0.00 1.90
2617 4877 6.288294 CCGGTATATTTGATTGAAGTCTCCA 58.712 40.000 0.00 0.00 0.00 3.86
2946 5206 0.965439 TTGGAAGCCCGTCATTTTGG 59.035 50.000 0.00 0.00 34.29 3.28
2954 5214 0.769247 ACTACCTTTTGGAAGCCCGT 59.231 50.000 0.00 0.00 44.07 5.28
2988 5248 4.421479 CGTGCCTCGAAGCCTCGT 62.421 66.667 3.02 0.00 45.62 4.18
3042 5302 2.218530 GCACGCAATTTTTGACTTGTCC 59.781 45.455 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.