Multiple sequence alignment - TraesCS2A01G196600

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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 TraesCS2A01G196600 chr2A 100.000 3489 0 0 1 3489 166258813 166262301 0.000000e+00 6444
1 TraesCS2A01G196600 chr2B 93.279 1830 88 22 1 1807 214285960 214287777 0.000000e+00 2665
2 TraesCS2A01G196600 chr2B 91.813 1649 114 14 1853 3489 214287970 214289609 0.000000e+00 2278
3 TraesCS2A01G196600 chr2B 82.461 382 65 2 3102 3482 399821678 399821298 2.010000e-87 333
4 TraesCS2A01G196600 chr2D 95.298 1510 47 9 1 1493 156596844 156598346 0.000000e+00 2374
5 TraesCS2A01G196600 chr2D 92.654 1021 62 11 1690 2706 156600420 156601431 0.000000e+00 1458
6 TraesCS2A01G196600 chr2D 88.550 393 23 8 2706 3076 156601971 156602363 1.140000e-124 457
7 TraesCS2A01G196600 chr2D 84.334 383 54 6 3099 3479 131769684 131769306 1.530000e-98 370
8 TraesCS2A01G196600 chr2D 91.099 191 14 3 1508 1698 156598625 156598812 4.470000e-64 255
9 TraesCS2A01G196600 chr7B 84.184 392 60 2 3099 3489 387156735 387156345 2.540000e-101 379
10 TraesCS2A01G196600 chr5A 84.293 382 57 3 3099 3479 461482053 461482432 1.530000e-98 370
11 TraesCS2A01G196600 chr7D 83.756 394 50 9 3099 3489 390685912 390685530 9.210000e-96 361
12 TraesCS2A01G196600 chr7D 83.290 383 57 5 3099 3479 499533576 499533199 2.580000e-91 346
13 TraesCS2A01G196600 chr7D 81.934 393 67 3 3099 3489 487763757 487764147 2.600000e-86 329
14 TraesCS2A01G196600 chr4B 82.143 392 67 3 3099 3489 22843018 22842629 2.010000e-87 333


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 TraesCS2A01G196600 chr2A 166258813 166262301 3488 False 6444.0 6444 100.00000 1 3489 1 chr2A.!!$F1 3488
1 TraesCS2A01G196600 chr2B 214285960 214289609 3649 False 2471.5 2665 92.54600 1 3489 2 chr2B.!!$F1 3488
2 TraesCS2A01G196600 chr2D 156596844 156602363 5519 False 1136.0 2374 91.90025 1 3076 4 chr2D.!!$F1 3075

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
284 285 0.107214 GGCATTCCATCGAACAGGGA 60.107 55.0 0.0 0.0 0.0 4.20 F
1177 1187 0.468771 CCCATTTCCCTCCCTGCATC 60.469 60.0 0.0 0.0 0.0 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1978 4038 0.110486 TCCCACAAGTTTGAGAGCCC 59.890 55.0 0.0 0.0 0.0 5.19 R
3108 5736 0.322906 CCCCAAACTCCTCTGAAGCC 60.323 60.0 0.0 0.0 0.0 4.35 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
59 60 2.507854 CCGCATCCATCCTACCGGT 61.508 63.158 13.98 13.98 0.00 5.28
202 203 2.835701 GAACACCTCGAGCGCATCCA 62.836 60.000 11.47 0.00 0.00 3.41
284 285 0.107214 GGCATTCCATCGAACAGGGA 60.107 55.000 0.00 0.00 0.00 4.20
288 289 1.541310 TTCCATCGAACAGGGAGCGT 61.541 55.000 0.00 0.00 31.19 5.07
832 841 4.331906 GCCTGGGCCCTTATAGGA 57.668 61.111 26.56 2.63 37.67 2.94
902 912 3.731264 CGAAGCGTAGAGTGGAAGGTAAG 60.731 52.174 0.00 0.00 0.00 2.34
903 913 2.805194 AGCGTAGAGTGGAAGGTAAGT 58.195 47.619 0.00 0.00 0.00 2.24
904 914 3.960571 AGCGTAGAGTGGAAGGTAAGTA 58.039 45.455 0.00 0.00 0.00 2.24
905 915 4.338879 AGCGTAGAGTGGAAGGTAAGTAA 58.661 43.478 0.00 0.00 0.00 2.24
957 967 3.023735 GTGGGGAGGGGAGCCAAT 61.024 66.667 0.00 0.00 0.00 3.16
962 972 2.830370 GAGGGGAGCCAATTGCCG 60.830 66.667 0.00 0.00 42.71 5.69
1177 1187 0.468771 CCCATTTCCCTCCCTGCATC 60.469 60.000 0.00 0.00 0.00 3.91
1220 1230 2.404995 GCTCGCTTGCTTGCCTCAT 61.405 57.895 0.00 0.00 0.00 2.90
1253 1264 2.234168 GGATCGAATCTTAGCCCCTACC 59.766 54.545 0.00 0.00 0.00 3.18
1292 1303 3.378112 AGGTGTGATTTATTCCACGCATG 59.622 43.478 0.00 0.00 43.40 4.06
1310 1322 4.614946 GCATGGGTGAATTAGAATCTTGC 58.385 43.478 0.00 0.00 0.00 4.01
1323 1338 3.386402 AGAATCTTGCTACCTACCTGCTC 59.614 47.826 0.00 0.00 0.00 4.26
1328 1343 3.486252 CTACCTACCTGCTCGCGCC 62.486 68.421 0.00 0.00 34.43 6.53
1342 1357 1.078143 GCGCCCAGGACAAGATCTT 60.078 57.895 0.88 0.88 0.00 2.40
1418 1446 0.975556 TGCCATAGCCGACTTCCTCA 60.976 55.000 0.00 0.00 38.69 3.86
1487 1518 2.912025 CAACGGTGCTTTGCCCCT 60.912 61.111 0.00 0.00 0.00 4.79
1518 1813 9.686683 ACTAATAATCACCAGAAATGCTAGTTT 57.313 29.630 0.00 0.00 0.00 2.66
1545 1840 4.526650 TGACTTTACTGCTGACCATGTAGA 59.473 41.667 0.00 0.00 0.00 2.59
1547 1842 5.865085 ACTTTACTGCTGACCATGTAGAAA 58.135 37.500 0.00 0.00 0.00 2.52
1556 1851 5.877012 GCTGACCATGTAGAAATTCTCTTGA 59.123 40.000 0.00 0.00 35.41 3.02
1598 1893 5.882557 ACAGTGGAACCATTGCTAGAAATAG 59.117 40.000 14.62 0.00 37.80 1.73
1604 1899 6.015940 GGAACCATTGCTAGAAATAGGGAATG 60.016 42.308 6.79 0.00 38.11 2.67
1619 1914 3.259123 AGGGAATGCCATCAACAAAGTTC 59.741 43.478 0.00 0.00 35.15 3.01
1636 1931 5.661056 AAGTTCTGCTGTAGTATGTGCTA 57.339 39.130 0.00 0.00 0.00 3.49
1714 3627 2.409870 GCAAACCTGGGAGATGCCG 61.410 63.158 0.00 0.00 37.63 5.69
1871 3931 1.569653 AACTAGTTCGCCCCTTAGCT 58.430 50.000 1.12 0.00 0.00 3.32
1872 3932 0.824759 ACTAGTTCGCCCCTTAGCTG 59.175 55.000 0.00 0.00 0.00 4.24
1887 3947 2.215942 AGCTGTGGGTAATGGGAAAC 57.784 50.000 0.00 0.00 0.00 2.78
1918 3978 7.836842 TCAACTAGTTCTGCACAGTTATATCA 58.163 34.615 4.77 0.00 30.28 2.15
1946 4006 2.297701 AGAATGTGACTGGTTTTGCGT 58.702 42.857 0.00 0.00 0.00 5.24
1962 4022 2.479837 TGCGTGGTATGCTATTACTGC 58.520 47.619 0.00 0.00 0.00 4.40
1965 4025 2.779506 GTGGTATGCTATTACTGCCCC 58.220 52.381 0.00 0.00 0.00 5.80
1971 4031 1.202758 TGCTATTACTGCCCCGGAATG 60.203 52.381 0.73 0.00 0.00 2.67
1978 4038 0.457035 CTGCCCCGGAATGTTGATTG 59.543 55.000 0.73 0.00 0.00 2.67
1980 4040 1.675720 GCCCCGGAATGTTGATTGGG 61.676 60.000 0.73 0.00 36.37 4.12
1986 4046 2.726821 GGAATGTTGATTGGGCTCTCA 58.273 47.619 0.00 0.00 0.00 3.27
2003 4063 4.199310 CTCTCAAACTTGTGGGAAGAACA 58.801 43.478 0.00 0.00 0.00 3.18
2008 4068 3.933861 ACTTGTGGGAAGAACAGAGTT 57.066 42.857 0.00 0.00 0.00 3.01
2009 4069 5.367945 AACTTGTGGGAAGAACAGAGTTA 57.632 39.130 0.00 0.00 32.33 2.24
2010 4070 4.962155 ACTTGTGGGAAGAACAGAGTTAG 58.038 43.478 0.00 0.00 0.00 2.34
2011 4071 4.409247 ACTTGTGGGAAGAACAGAGTTAGT 59.591 41.667 0.00 0.00 0.00 2.24
2017 4077 5.950549 TGGGAAGAACAGAGTTAGTAGTAGG 59.049 44.000 0.00 0.00 0.00 3.18
2026 4086 6.541641 ACAGAGTTAGTAGTAGGTTGGATACG 59.458 42.308 0.00 0.00 42.51 3.06
2034 4094 5.479124 AGTAGGTTGGATACGTTTGAACT 57.521 39.130 0.00 0.00 42.51 3.01
2035 4095 5.235516 AGTAGGTTGGATACGTTTGAACTG 58.764 41.667 0.00 0.00 42.51 3.16
2040 4100 5.640357 GGTTGGATACGTTTGAACTGTGATA 59.360 40.000 0.00 0.00 42.51 2.15
2069 4129 2.566913 ACAACCATGCGTGTCTGTTTA 58.433 42.857 4.96 0.00 0.00 2.01
2125 4186 0.605319 TGGCGGTTAAAGCAGGAGTG 60.605 55.000 6.53 0.00 36.08 3.51
2136 4198 0.109597 GCAGGAGTGTGCCAATTTCG 60.110 55.000 0.00 0.00 37.49 3.46
2145 4207 6.038271 GGAGTGTGCCAATTTCGTTAAGATAT 59.962 38.462 0.00 0.00 0.00 1.63
2146 4208 7.225931 GGAGTGTGCCAATTTCGTTAAGATATA 59.774 37.037 0.00 0.00 0.00 0.86
2192 4254 3.623954 CGGTTTATAAGGGAAACTGGGCT 60.624 47.826 0.00 0.00 38.82 5.19
2197 4259 1.704641 AAGGGAAACTGGGCTGAAAC 58.295 50.000 0.00 0.00 0.00 2.78
2229 4291 4.245660 CTGACTCTGAGCGAAAACCAATA 58.754 43.478 4.19 0.00 0.00 1.90
2389 4451 2.359230 ACGAAGAGCAAGCTGGCC 60.359 61.111 10.23 0.89 0.00 5.36
2392 4454 1.002868 GAAGAGCAAGCTGGCCTCA 60.003 57.895 10.23 0.00 0.00 3.86
2492 4554 4.389077 CCTCCGTTTTCAACAACTAGCTAG 59.611 45.833 19.44 19.44 0.00 3.42
2509 4571 9.603189 AACTAGCTAGGCCTAATTATCTAGAAA 57.397 33.333 24.35 2.45 33.07 2.52
2613 4680 3.069443 TGTGTGTGCAGTCAATCAGTCTA 59.931 43.478 0.00 0.00 0.00 2.59
2614 4681 4.248859 GTGTGTGCAGTCAATCAGTCTAT 58.751 43.478 0.00 0.00 0.00 1.98
2627 4694 9.534565 GTCAATCAGTCTATGTGTATGTATGTT 57.465 33.333 0.00 0.00 0.00 2.71
2718 5324 6.237313 ACGCACAGTTAATAAAAGAAGTCC 57.763 37.500 0.00 0.00 0.00 3.85
2723 5329 6.151144 CACAGTTAATAAAAGAAGTCCCCCTG 59.849 42.308 0.00 0.00 0.00 4.45
2732 5338 2.576648 AGAAGTCCCCCTGATTACCAAC 59.423 50.000 0.00 0.00 0.00 3.77
2746 5353 2.186160 CCAACGCTTGCTGGTGACA 61.186 57.895 4.60 0.00 39.59 3.58
2768 5375 8.373981 TGACATGTAACATCCCAATTTTCAAAT 58.626 29.630 0.00 0.00 0.00 2.32
2796 5403 6.070938 TGGATGTTAACATGCCATTCATTTGA 60.071 34.615 30.03 10.55 43.00 2.69
2996 5624 1.556911 TCATGAGTTGAAGGAGAGGGC 59.443 52.381 0.00 0.00 0.00 5.19
3064 5692 0.320771 ACGGAGATGGTGACTTGCAC 60.321 55.000 0.00 0.00 46.98 4.57
3100 5728 6.128145 GCTATCAAGGAGAAGAAAGGTTGTTC 60.128 42.308 0.00 0.00 33.48 3.18
3106 5734 4.083961 GGAGAAGAAAGGTTGTTCGTAAGC 60.084 45.833 0.00 0.00 37.93 3.09
3108 5736 4.511826 AGAAGAAAGGTTGTTCGTAAGCTG 59.488 41.667 0.00 0.00 38.32 4.24
3183 5812 0.392998 GGTGGTGGAACGATGATGCT 60.393 55.000 0.00 0.00 38.12 3.79
3192 5821 3.462021 GAACGATGATGCTTAGAAGGCT 58.538 45.455 0.00 0.00 0.00 4.58
3197 5826 4.863689 CGATGATGCTTAGAAGGCTATCAG 59.136 45.833 0.00 0.00 34.00 2.90
3198 5827 4.613925 TGATGCTTAGAAGGCTATCAGG 57.386 45.455 0.00 0.00 0.00 3.86
3203 5832 3.258123 GCTTAGAAGGCTATCAGGGAGAG 59.742 52.174 0.00 0.00 0.00 3.20
3204 5833 4.735369 CTTAGAAGGCTATCAGGGAGAGA 58.265 47.826 0.00 0.00 0.00 3.10
3206 5835 4.000928 AGAAGGCTATCAGGGAGAGAAA 57.999 45.455 0.00 0.00 0.00 2.52
3207 5836 4.366267 AGAAGGCTATCAGGGAGAGAAAA 58.634 43.478 0.00 0.00 0.00 2.29
3208 5837 4.785376 AGAAGGCTATCAGGGAGAGAAAAA 59.215 41.667 0.00 0.00 0.00 1.94
3221 5850 7.176340 CAGGGAGAGAAAAAGATTGTTTCAGAT 59.824 37.037 0.00 0.00 37.43 2.90
3255 5884 6.669631 TGGATAGGAGTGTAGACAACATAGA 58.330 40.000 0.00 0.00 41.10 1.98
3269 5898 7.896811 AGACAACATAGAGAAGTACAATGTGA 58.103 34.615 0.00 0.00 31.44 3.58
3280 5909 7.275920 AGAAGTACAATGTGACAAAGAAGACT 58.724 34.615 0.00 0.00 0.00 3.24
3290 5919 2.289002 ACAAAGAAGACTGCAAAGCGAG 59.711 45.455 0.00 0.00 0.00 5.03
3305 5934 1.224069 GCGAGCTGTGAGTGAAGCAA 61.224 55.000 0.00 0.00 42.06 3.91
3306 5935 0.788995 CGAGCTGTGAGTGAAGCAAG 59.211 55.000 0.00 0.00 42.06 4.01
3312 5941 1.762370 TGTGAGTGAAGCAAGGAGTCA 59.238 47.619 0.00 0.00 0.00 3.41
3329 5958 4.892934 GGAGTCAGACATATGAGAACCTCT 59.107 45.833 10.38 0.00 0.00 3.69
3331 5960 6.719370 GGAGTCAGACATATGAGAACCTCTAT 59.281 42.308 10.38 0.00 0.00 1.98
3335 5964 6.208402 TCAGACATATGAGAACCTCTATCAGC 59.792 42.308 10.38 0.00 0.00 4.26
3353 5982 9.210329 TCTATCAGCGTTTAAACATGAAGTAAA 57.790 29.630 20.79 0.00 30.93 2.01
3355 5984 6.140110 TCAGCGTTTAAACATGAAGTAAAGC 58.860 36.000 18.07 8.87 0.00 3.51
3394 6024 0.826715 TGGCCAAGATCGAAGAGAGG 59.173 55.000 0.61 0.00 43.63 3.69
3397 6027 2.482839 GGCCAAGATCGAAGAGAGGAAG 60.483 54.545 0.00 0.00 43.63 3.46
3417 6047 2.915604 AGATGAGGGATGTCAACCAAGT 59.084 45.455 1.08 0.00 0.00 3.16
3481 6112 4.979197 ACGAGAAGATCAAACATAGATCGC 59.021 41.667 0.00 0.00 45.05 4.58
3482 6113 4.978580 CGAGAAGATCAAACATAGATCGCA 59.021 41.667 0.00 0.00 45.05 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 0.462581 CGCTGGTGGACATGTATGCT 60.463 55.000 0.00 0.00 0.00 3.79
42 43 1.300931 CACCGGTAGGATGGATGCG 60.301 63.158 6.87 0.00 41.02 4.73
43 44 1.071471 CCACCGGTAGGATGGATGC 59.929 63.158 6.87 0.00 41.02 3.91
59 60 1.816537 GCTCTCATCACCGCTACCA 59.183 57.895 0.00 0.00 0.00 3.25
161 162 1.478105 ACATGATGCTCAGTGCTCGTA 59.522 47.619 0.00 0.00 43.37 3.43
168 169 2.341257 GTGTTCGACATGATGCTCAGT 58.659 47.619 0.00 0.00 0.00 3.41
284 285 4.357947 ACATGGACGACGCACGCT 62.358 61.111 0.00 0.00 46.94 5.07
521 522 2.642254 ATTCCCTCGCCGTCGTTCA 61.642 57.895 0.00 0.00 36.96 3.18
795 796 0.526739 CCACGTATCATTCGGTCGCA 60.527 55.000 0.00 0.00 0.00 5.10
825 834 7.162973 TCTACTTCCACATCCTCTCCTATAA 57.837 40.000 0.00 0.00 0.00 0.98
828 837 5.671463 ATCTACTTCCACATCCTCTCCTA 57.329 43.478 0.00 0.00 0.00 2.94
829 838 4.551215 ATCTACTTCCACATCCTCTCCT 57.449 45.455 0.00 0.00 0.00 3.69
830 839 4.742138 GCAATCTACTTCCACATCCTCTCC 60.742 50.000 0.00 0.00 0.00 3.71
832 841 3.135530 GGCAATCTACTTCCACATCCTCT 59.864 47.826 0.00 0.00 0.00 3.69
902 912 2.000447 GTCGCTTCTGTCCATGGTTAC 59.000 52.381 12.58 3.89 0.00 2.50
903 913 1.899814 AGTCGCTTCTGTCCATGGTTA 59.100 47.619 12.58 0.80 0.00 2.85
904 914 0.687354 AGTCGCTTCTGTCCATGGTT 59.313 50.000 12.58 0.00 0.00 3.67
905 915 0.687354 AAGTCGCTTCTGTCCATGGT 59.313 50.000 12.58 0.00 0.00 3.55
1065 1075 2.282958 TCGCGGTTCTCCCAGTCT 60.283 61.111 6.13 0.00 0.00 3.24
1177 1187 1.690985 GTGGGGGAGGAGGAAGGAG 60.691 68.421 0.00 0.00 0.00 3.69
1205 1215 1.226211 CGAATGAGGCAAGCAAGCG 60.226 57.895 0.00 0.00 34.64 4.68
1238 1249 1.416772 GAAGCGGTAGGGGCTAAGATT 59.583 52.381 0.00 0.00 40.53 2.40
1253 1264 3.432051 CTAGAGGCGGGTGGAAGCG 62.432 68.421 0.00 0.00 33.03 4.68
1292 1303 5.685728 AGGTAGCAAGATTCTAATTCACCC 58.314 41.667 0.00 0.00 0.00 4.61
1323 1338 2.859273 AAGATCTTGTCCTGGGCGCG 62.859 60.000 7.30 0.00 0.00 6.86
1328 1343 3.433314 CCATGAGGAAGATCTTGTCCTGG 60.433 52.174 18.87 18.01 44.57 4.45
1334 1349 6.316640 GCATATCATCCATGAGGAAGATCTTG 59.683 42.308 14.00 0.00 46.56 3.02
1418 1446 2.108514 CCTCATCGGCAACATGCGT 61.109 57.895 0.00 0.00 46.21 5.24
1487 1518 9.905713 AGCATTTCTGGTGATTATTAGTTAGAA 57.094 29.630 0.00 0.00 0.00 2.10
1518 1813 2.698274 TGGTCAGCAGTAAAGTCACAGA 59.302 45.455 0.00 0.00 0.00 3.41
1529 1824 5.046014 AGAGAATTTCTACATGGTCAGCAGT 60.046 40.000 0.00 0.00 33.23 4.40
1573 1868 4.901197 TTCTAGCAATGGTTCCACTGTA 57.099 40.909 2.38 0.00 0.00 2.74
1575 1870 5.297776 CCTATTTCTAGCAATGGTTCCACTG 59.702 44.000 0.00 0.00 0.00 3.66
1576 1871 5.440610 CCTATTTCTAGCAATGGTTCCACT 58.559 41.667 0.00 0.00 0.00 4.00
1577 1872 4.580580 CCCTATTTCTAGCAATGGTTCCAC 59.419 45.833 0.00 0.00 0.00 4.02
1598 1893 3.259123 AGAACTTTGTTGATGGCATTCCC 59.741 43.478 0.00 0.00 0.00 3.97
1604 1899 2.035066 ACAGCAGAACTTTGTTGATGGC 59.965 45.455 0.00 0.00 32.84 4.40
1636 1931 5.189180 GTGCCAAGAAGAGATAAAGGATGT 58.811 41.667 0.00 0.00 0.00 3.06
1705 3618 2.511600 CAACCGTCCGGCATCTCC 60.512 66.667 5.47 0.00 39.32 3.71
1714 3627 1.227853 ACTGGAAGCACAACCGTCC 60.228 57.895 0.00 0.00 37.60 4.79
1843 3891 2.416972 GGGCGAACTAGTTACACCTCTG 60.417 54.545 8.42 0.00 0.00 3.35
1871 3931 1.065647 TCGGTTTCCCATTACCCACA 58.934 50.000 0.00 0.00 0.00 4.17
1872 3932 2.430248 ATCGGTTTCCCATTACCCAC 57.570 50.000 0.00 0.00 0.00 4.61
1887 3947 3.745975 TGTGCAGAACTAGTTGAAATCGG 59.254 43.478 14.14 0.00 0.00 4.18
1918 3978 7.308589 GCAAAACCAGTCACATTCTAGTTACAT 60.309 37.037 0.00 0.00 0.00 2.29
1937 3997 3.775661 AATAGCATACCACGCAAAACC 57.224 42.857 0.00 0.00 0.00 3.27
1946 4006 1.346395 CGGGGCAGTAATAGCATACCA 59.654 52.381 0.00 0.00 0.00 3.25
1962 4022 1.675720 GCCCAATCAACATTCCGGGG 61.676 60.000 0.00 0.00 37.16 5.73
1965 4025 1.672881 GAGAGCCCAATCAACATTCCG 59.327 52.381 0.00 0.00 0.00 4.30
1971 4031 3.319122 ACAAGTTTGAGAGCCCAATCAAC 59.681 43.478 0.00 0.00 35.25 3.18
1978 4038 0.110486 TCCCACAAGTTTGAGAGCCC 59.890 55.000 0.00 0.00 0.00 5.19
1980 4040 2.851195 TCTTCCCACAAGTTTGAGAGC 58.149 47.619 0.00 0.00 0.00 4.09
1986 4046 4.236527 ACTCTGTTCTTCCCACAAGTTT 57.763 40.909 0.00 0.00 0.00 2.66
2003 4063 6.657875 ACGTATCCAACCTACTACTAACTCT 58.342 40.000 0.00 0.00 0.00 3.24
2008 4068 7.394359 AGTTCAAACGTATCCAACCTACTACTA 59.606 37.037 0.00 0.00 0.00 1.82
2009 4069 6.210185 AGTTCAAACGTATCCAACCTACTACT 59.790 38.462 0.00 0.00 0.00 2.57
2010 4070 6.309737 CAGTTCAAACGTATCCAACCTACTAC 59.690 42.308 0.00 0.00 0.00 2.73
2011 4071 6.015180 ACAGTTCAAACGTATCCAACCTACTA 60.015 38.462 0.00 0.00 0.00 1.82
2017 4077 5.607119 ATCACAGTTCAAACGTATCCAAC 57.393 39.130 0.00 0.00 0.00 3.77
2026 4086 6.917477 TGTTGATTTGCTATCACAGTTCAAAC 59.083 34.615 2.16 0.00 30.69 2.93
2034 4094 5.712004 CATGGTTGTTGATTTGCTATCACA 58.288 37.500 2.16 2.58 0.00 3.58
2035 4095 4.563976 GCATGGTTGTTGATTTGCTATCAC 59.436 41.667 0.00 0.51 0.00 3.06
2040 4100 1.340889 ACGCATGGTTGTTGATTTGCT 59.659 42.857 0.00 0.00 0.00 3.91
2069 4129 7.253422 CGAGGATGAATAAGAAAGCAACAAAT 58.747 34.615 0.00 0.00 0.00 2.32
2113 4174 2.584835 ATTGGCACACTCCTGCTTTA 57.415 45.000 0.00 0.00 39.29 1.85
2125 4186 9.997482 TTTTCTATATCTTAACGAAATTGGCAC 57.003 29.630 0.00 0.00 0.00 5.01
2145 4207 7.041644 CGGGTCACTATGTGTTTTCTTTTTCTA 60.042 37.037 0.00 0.00 34.79 2.10
2146 4208 6.238648 CGGGTCACTATGTGTTTTCTTTTTCT 60.239 38.462 0.00 0.00 34.79 2.52
2158 4220 5.054477 CCTTATAAACCGGGTCACTATGTG 58.946 45.833 6.32 0.00 34.45 3.21
2162 4224 3.992999 TCCCTTATAAACCGGGTCACTA 58.007 45.455 6.32 0.00 39.10 2.74
2192 4254 0.541764 GTCAGGCATTGGGGGTTTCA 60.542 55.000 0.00 0.00 0.00 2.69
2197 4259 1.077212 CAGAGTCAGGCATTGGGGG 60.077 63.158 0.00 0.00 0.00 5.40
2261 4323 3.384467 CACATCCCCAAACTTGAGTGTTT 59.616 43.478 0.00 0.00 40.34 2.83
2262 4324 2.958355 CACATCCCCAAACTTGAGTGTT 59.042 45.455 0.00 0.00 0.00 3.32
2269 4331 2.714250 TGTAGTCCACATCCCCAAACTT 59.286 45.455 0.00 0.00 30.04 2.66
2272 4334 2.714250 ACTTGTAGTCCACATCCCCAAA 59.286 45.455 0.00 0.00 36.90 3.28
2389 4451 5.109662 TGTCTAGTTTCTCGTTCAGTGAG 57.890 43.478 0.00 0.00 34.72 3.51
2392 4454 3.305471 GGCTGTCTAGTTTCTCGTTCAGT 60.305 47.826 0.00 0.00 0.00 3.41
2492 4554 7.809546 AGCACTTTTTCTAGATAATTAGGCC 57.190 36.000 0.00 0.00 0.00 5.19
2509 4571 1.738099 CTCCGCGTGCTAGCACTTT 60.738 57.895 37.42 0.00 44.16 2.66
2613 4680 6.869388 TGACACGTACAAACATACATACACAT 59.131 34.615 0.00 0.00 0.00 3.21
2614 4681 6.214399 TGACACGTACAAACATACATACACA 58.786 36.000 0.00 0.00 0.00 3.72
2627 4694 9.642327 ATTAATTGTAGTACATGACACGTACAA 57.358 29.630 13.78 12.58 41.40 2.41
2718 5324 1.094785 CAAGCGTTGGTAATCAGGGG 58.905 55.000 0.00 0.00 0.00 4.79
2723 5329 3.996825 CCAGCAAGCGTTGGTAATC 57.003 52.632 2.87 0.00 39.79 1.75
2732 5338 1.135972 GTTACATGTCACCAGCAAGCG 60.136 52.381 0.00 0.00 0.00 4.68
2768 5375 6.106648 TGAATGGCATGTTAACATCCAAAA 57.893 33.333 28.18 19.39 37.22 2.44
3064 5692 2.693591 TCCTTGATAGCCACCTTACGAG 59.306 50.000 0.00 0.00 0.00 4.18
3100 5728 0.532573 TCCTCTGAAGCCAGCTTACG 59.467 55.000 4.57 0.00 40.20 3.18
3106 5734 1.612726 CCCAAACTCCTCTGAAGCCAG 60.613 57.143 0.00 0.00 41.74 4.85
3108 5736 0.322906 CCCCAAACTCCTCTGAAGCC 60.323 60.000 0.00 0.00 0.00 4.35
3141 5770 6.265649 ACCAGATATCTTTAGCTTCGCTTCTA 59.734 38.462 1.33 0.00 40.44 2.10
3164 5793 0.392998 AGCATCATCGTTCCACCACC 60.393 55.000 0.00 0.00 0.00 4.61
3183 5812 4.816048 TCTCTCCCTGATAGCCTTCTAA 57.184 45.455 0.00 0.00 0.00 2.10
3192 5821 8.163408 TGAAACAATCTTTTTCTCTCCCTGATA 58.837 33.333 0.00 0.00 34.58 2.15
3197 5826 6.884280 TCTGAAACAATCTTTTTCTCTCCC 57.116 37.500 0.00 0.00 34.58 4.30
3198 5827 6.805760 GCATCTGAAACAATCTTTTTCTCTCC 59.194 38.462 0.00 0.00 34.58 3.71
3203 5832 7.370383 TGTAGGCATCTGAAACAATCTTTTTC 58.630 34.615 0.00 0.00 34.16 2.29
3204 5833 7.288810 TGTAGGCATCTGAAACAATCTTTTT 57.711 32.000 0.00 0.00 0.00 1.94
3206 5835 7.093322 GATGTAGGCATCTGAAACAATCTTT 57.907 36.000 0.80 0.00 45.97 2.52
3207 5836 6.690194 GATGTAGGCATCTGAAACAATCTT 57.310 37.500 0.80 0.00 45.97 2.40
3221 5850 3.234353 CACTCCTATCCAGATGTAGGCA 58.766 50.000 0.00 0.00 37.87 4.75
3255 5884 7.225538 CAGTCTTCTTTGTCACATTGTACTTCT 59.774 37.037 0.00 0.00 0.00 2.85
3269 5898 2.288666 TCGCTTTGCAGTCTTCTTTGT 58.711 42.857 0.00 0.00 0.00 2.83
3280 5909 1.227645 ACTCACAGCTCGCTTTGCA 60.228 52.632 0.34 0.00 0.00 4.08
3290 5919 1.155042 CTCCTTGCTTCACTCACAGC 58.845 55.000 0.00 0.00 36.49 4.40
3305 5934 4.877773 AGGTTCTCATATGTCTGACTCCT 58.122 43.478 9.51 7.57 0.00 3.69
3306 5935 4.892934 AGAGGTTCTCATATGTCTGACTCC 59.107 45.833 9.51 5.80 32.06 3.85
3312 5941 5.182950 CGCTGATAGAGGTTCTCATATGTCT 59.817 44.000 1.90 0.00 32.06 3.41
3329 5958 7.960738 GCTTTACTTCATGTTTAAACGCTGATA 59.039 33.333 18.59 10.22 0.00 2.15
3331 5960 6.140110 GCTTTACTTCATGTTTAAACGCTGA 58.860 36.000 13.45 14.67 0.00 4.26
3335 5964 7.597643 TTTCGCTTTACTTCATGTTTAAACG 57.402 32.000 13.45 0.64 0.00 3.60
3353 5982 5.010012 CCATCTTATAAATGCCCTTTTCGCT 59.990 40.000 0.00 0.00 0.00 4.93
3355 5984 5.222631 GCCATCTTATAAATGCCCTTTTCG 58.777 41.667 0.00 0.00 0.00 3.46
3394 6024 3.634397 TGGTTGACATCCCTCATCTTC 57.366 47.619 0.00 0.00 0.00 2.87
3397 6027 3.274288 GACTTGGTTGACATCCCTCATC 58.726 50.000 0.00 0.00 0.00 2.92
3432 6062 2.836981 ACCAGAAGCTTATCTGCTCTGT 59.163 45.455 9.55 0.63 44.43 3.41
3443 6073 3.194005 TCTCGTTTTCACCAGAAGCTT 57.806 42.857 0.00 0.00 34.71 3.74
3444 6074 2.910688 TCTCGTTTTCACCAGAAGCT 57.089 45.000 0.00 0.00 34.71 3.74
3457 6087 5.460419 GCGATCTATGTTTGATCTTCTCGTT 59.540 40.000 0.00 0.00 38.43 3.85


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

AutoCloner maintained by Alex Coulton.