Multiple sequence alignment - TraesCS3D01G540900

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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 TraesCS3D01G540900 chr3D 100.000 2866 0 0 1 2866 612274375 612271510 0.000000e+00 5293.0
1 TraesCS3D01G540900 chr3A 88.840 2482 125 44 448 2866 746918886 746916494 0.000000e+00 2909.0
2 TraesCS3D01G540900 chr3A 91.346 416 36 0 1 416 746919367 746918952 1.150000e-158 569.0
3 TraesCS3D01G540900 chr3B 89.822 2024 120 35 534 2516 826724603 826726581 0.000000e+00 2518.0
4 TraesCS3D01G540900 chr3B 83.715 1093 92 35 1844 2866 826736390 826737466 0.000000e+00 953.0
5 TraesCS3D01G540900 chr3B 90.123 324 26 5 2546 2866 826727441 826727761 1.590000e-112 416.0
6 TraesCS3D01G540900 chr4D 80.635 630 112 8 1237 1864 476875911 476875290 2.000000e-131 479.0
7 TraesCS3D01G540900 chr4B 80.476 630 113 8 1237 1864 601099539 601098918 9.290000e-130 473.0
8 TraesCS3D01G540900 chr4A 80.063 632 116 8 1237 1866 683617603 683616980 7.240000e-126 460.0
9 TraesCS3D01G540900 chr4A 94.737 38 1 1 403 440 726289358 726289394 1.110000e-04 58.4
10 TraesCS3D01G540900 chr7D 81.061 264 44 5 1549 1809 433876585 433876845 3.740000e-49 206.0
11 TraesCS3D01G540900 chr7B 80.534 262 49 2 1549 1809 451289927 451290187 1.740000e-47 200.0
12 TraesCS3D01G540900 chr7B 81.871 171 20 10 253 418 706120698 706120534 1.790000e-27 134.0
13 TraesCS3D01G540900 chr7A 80.534 262 49 2 1549 1809 484525292 484525552 1.740000e-47 200.0
14 TraesCS3D01G540900 chr6A 83.854 192 31 0 1539 1730 464538529 464538720 1.750000e-42 183.0
15 TraesCS3D01G540900 chr6A 91.566 83 4 2 246 328 376486899 376486978 8.390000e-21 111.0
16 TraesCS3D01G540900 chr5B 81.006 179 31 2 238 416 710199613 710199438 3.850000e-29 139.0
17 TraesCS3D01G540900 chr5D 80.347 173 30 3 245 416 556848366 556848535 8.330000e-26 128.0
18 TraesCS3D01G540900 chr6D 92.771 83 3 2 246 328 265898723 265898802 1.800000e-22 117.0
19 TraesCS3D01G540900 chr6B 90.476 84 5 2 245 328 413389257 413389337 1.090000e-19 108.0
20 TraesCS3D01G540900 chr2D 83.333 120 16 3 258 376 427126851 427126735 1.090000e-19 108.0
21 TraesCS3D01G540900 chr1D 81.188 101 17 2 274 373 75884768 75884867 2.370000e-11 80.5
22 TraesCS3D01G540900 chr1A 100.000 28 0 0 408 435 530256804 530256831 5.000000e-03 52.8


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 TraesCS3D01G540900 chr3D 612271510 612274375 2865 True 5293 5293 100.0000 1 2866 1 chr3D.!!$R1 2865
1 TraesCS3D01G540900 chr3A 746916494 746919367 2873 True 1739 2909 90.0930 1 2866 2 chr3A.!!$R1 2865
2 TraesCS3D01G540900 chr3B 826724603 826727761 3158 False 1467 2518 89.9725 534 2866 2 chr3B.!!$F2 2332
3 TraesCS3D01G540900 chr3B 826736390 826737466 1076 False 953 953 83.7150 1844 2866 1 chr3B.!!$F1 1022
4 TraesCS3D01G540900 chr4D 476875290 476875911 621 True 479 479 80.6350 1237 1864 1 chr4D.!!$R1 627
5 TraesCS3D01G540900 chr4B 601098918 601099539 621 True 473 473 80.4760 1237 1864 1 chr4B.!!$R1 627
6 TraesCS3D01G540900 chr4A 683616980 683617603 623 True 460 460 80.0630 1237 1866 1 chr4A.!!$R1 629

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
446 481 0.034756 TCCCATTATGACCGGCATCG 59.965 55.0 13.58 5.59 38.44 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1883 1949 0.107268 TGGCGATGACTGATGGATGG 59.893 55.0 0.0 0.0 0.0 3.51 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
34 35 2.666508 CCTAACCTTGTCGATGACAACG 59.333 50.000 8.21 7.53 45.88 4.10
37 38 3.861276 ACCTTGTCGATGACAACGATA 57.139 42.857 11.15 5.77 45.88 2.92
57 58 5.172591 CGATACATTTTTCATGCATGTGCTC 59.827 40.000 25.43 14.38 42.66 4.26
69 70 2.124529 GTGCTCCTAAGGGCCAGC 60.125 66.667 6.18 6.00 34.27 4.85
100 101 3.259625 TGGTAGTCATCATCGTTGAACCA 59.740 43.478 11.28 11.28 36.07 3.67
131 132 1.745232 TGTTTACCATCCGGTCATGC 58.255 50.000 0.00 0.00 44.71 4.06
132 133 0.655733 GTTTACCATCCGGTCATGCG 59.344 55.000 0.00 0.00 44.71 4.73
137 138 1.153568 CATCCGGTCATGCGACAGT 60.154 57.895 0.00 0.00 44.54 3.55
143 144 2.794910 CCGGTCATGCGACAGTTAATAG 59.205 50.000 0.00 0.00 44.54 1.73
145 146 2.544267 GGTCATGCGACAGTTAATAGGC 59.456 50.000 0.00 0.00 44.54 3.93
191 192 2.699768 GGCATTGCGCTAGTTGGCA 61.700 57.895 9.73 1.85 41.91 4.92
211 212 4.381292 GGCATCCATCTTCTTTGTTTCCAG 60.381 45.833 0.00 0.00 0.00 3.86
216 217 4.584325 CCATCTTCTTTGTTTCCAGTTGGA 59.416 41.667 0.00 0.00 43.73 3.53
220 221 4.981806 TCTTTGTTTCCAGTTGGACAAG 57.018 40.909 0.00 2.05 45.39 3.16
221 222 4.340617 TCTTTGTTTCCAGTTGGACAAGT 58.659 39.130 0.00 0.00 45.39 3.16
227 228 5.355910 TGTTTCCAGTTGGACAAGTCTTAAC 59.644 40.000 0.00 1.27 45.39 2.01
233 234 3.396260 TGGACAAGTCTTAACCTTCCG 57.604 47.619 0.00 0.00 0.00 4.30
242 243 2.028385 TCTTAACCTTCCGTTCAGGCTC 60.028 50.000 0.00 0.00 40.77 4.70
243 244 1.344065 TAACCTTCCGTTCAGGCTCA 58.656 50.000 0.00 0.00 40.77 4.26
260 261 3.406764 GCTCATCACAATGGGAGGTATC 58.593 50.000 0.00 0.00 35.13 2.24
365 366 7.779754 ATGGCCTCATTTATTGTTATGCATA 57.220 32.000 3.32 1.16 0.00 3.14
394 395 9.982651 ACATACTACTACATCATTTACCATGAC 57.017 33.333 0.00 0.00 0.00 3.06
439 474 9.427821 ACTATCTATGATAGTCCCATTATGACC 57.572 37.037 12.79 0.00 33.09 4.02
440 475 6.775594 TCTATGATAGTCCCATTATGACCG 57.224 41.667 0.00 0.00 33.09 4.79
443 478 1.796017 TAGTCCCATTATGACCGGCA 58.204 50.000 0.00 0.00 33.09 5.69
446 481 0.034756 TCCCATTATGACCGGCATCG 59.965 55.000 13.58 5.59 38.44 3.84
450 485 2.209273 CATTATGACCGGCATCGTTCA 58.791 47.619 13.58 3.73 41.77 3.18
459 494 1.538849 CGGCATCGTTCATCCTCATGA 60.539 52.381 0.00 0.00 37.24 3.07
462 497 2.543012 GCATCGTTCATCCTCATGACTG 59.457 50.000 0.00 0.00 38.86 3.51
463 498 3.790091 CATCGTTCATCCTCATGACTGT 58.210 45.455 0.00 0.00 38.86 3.55
479 514 0.236711 CTGTCCTGCTTGAGTTTGCG 59.763 55.000 0.00 0.00 0.00 4.85
491 526 2.115911 GTTTGCGGGTGTGGTGTGA 61.116 57.895 0.00 0.00 0.00 3.58
498 533 2.415357 GCGGGTGTGGTGTGATTATTTG 60.415 50.000 0.00 0.00 0.00 2.32
506 541 8.303876 GGTGTGGTGTGATTATTTGTCTATTTT 58.696 33.333 0.00 0.00 0.00 1.82
554 589 6.840780 ATTTTGGAAGGTCGATTTTGAGAT 57.159 33.333 0.00 0.00 0.00 2.75
563 598 8.842358 AAGGTCGATTTTGAGATGTAAAAGTA 57.158 30.769 0.00 0.00 31.31 2.24
597 638 8.214721 AGTTTCCTAAACAAAGAAGAGTTGAG 57.785 34.615 5.42 0.00 43.79 3.02
611 652 2.825532 GAGTTGAGCCCTATTTTTGCCA 59.174 45.455 0.00 0.00 0.00 4.92
627 668 1.202867 TGCCACTGCAGACATAACCAA 60.203 47.619 23.35 0.00 44.23 3.67
638 680 6.922957 TGCAGACATAACCAAATTTCTCAAAC 59.077 34.615 0.00 0.00 0.00 2.93
640 682 7.653311 GCAGACATAACCAAATTTCTCAAACTT 59.347 33.333 0.00 0.00 0.00 2.66
785 830 2.363359 GCAATCTGATCCCAATCCCAAC 59.637 50.000 0.00 0.00 0.00 3.77
805 850 4.260355 CAATGGCGATGGCAGGCG 62.260 66.667 1.01 8.02 42.43 5.52
809 854 4.916293 GGCGATGGCAGGCGATGA 62.916 66.667 15.44 0.00 42.47 2.92
830 875 0.102663 TGTGTTGAAGCGGTCGTGTA 59.897 50.000 0.00 0.00 0.00 2.90
856 901 3.799755 CCGTAGCAAGTTGCCCGC 61.800 66.667 24.02 13.10 46.52 6.13
859 904 3.960136 TAGCAAGTTGCCCGCCCA 61.960 61.111 24.02 0.29 46.52 5.36
957 1008 0.820226 TAGCTAGCTGCACAGGACAG 59.180 55.000 27.68 0.00 45.94 3.51
976 1027 3.239861 GAGCCGATCCATTCATCCC 57.760 57.895 0.00 0.00 0.00 3.85
1158 1214 1.831290 GCCCACCCCCATTTCTTTCTT 60.831 52.381 0.00 0.00 0.00 2.52
1194 1250 2.029918 TCGACCGATCATCATGTCATCC 60.030 50.000 5.43 0.00 0.00 3.51
1195 1251 2.288395 CGACCGATCATCATGTCATCCA 60.288 50.000 5.43 0.00 0.00 3.41
1199 1255 4.202388 ACCGATCATCATGTCATCCATCAA 60.202 41.667 0.00 0.00 0.00 2.57
1202 1268 5.107065 CGATCATCATGTCATCCATCAAGTG 60.107 44.000 0.00 0.00 0.00 3.16
1216 1282 1.302511 AAGTGCTGATCGCCGGTTT 60.303 52.632 1.90 0.00 38.05 3.27
1226 1292 4.356442 GCCGGTTTTGCATGGCGT 62.356 61.111 1.90 0.00 37.81 5.68
1227 1293 2.430582 CCGGTTTTGCATGGCGTG 60.431 61.111 1.31 1.31 0.00 5.34
1568 1634 0.103208 AGATCGTCATGACCTTCGGC 59.897 55.000 20.03 4.99 0.00 5.54
1580 1646 1.139095 CTTCGGCCTCGTCTACACC 59.861 63.158 0.00 0.00 37.69 4.16
1583 1649 2.488820 GGCCTCGTCTACACCGTC 59.511 66.667 0.00 0.00 0.00 4.79
1869 1935 1.674817 CCACCGCCGACTACTGAAAAT 60.675 52.381 0.00 0.00 0.00 1.82
1870 1936 2.417651 CCACCGCCGACTACTGAAAATA 60.418 50.000 0.00 0.00 0.00 1.40
1877 1943 5.107453 CGCCGACTACTGAAAATATCAATCC 60.107 44.000 0.00 0.00 37.67 3.01
1878 1944 5.107453 GCCGACTACTGAAAATATCAATCCG 60.107 44.000 0.00 0.00 37.67 4.18
1883 1949 8.608844 ACTACTGAAAATATCAATCCGAATCC 57.391 34.615 0.00 0.00 37.67 3.01
1892 1958 2.710471 TCAATCCGAATCCCATCCATCA 59.290 45.455 0.00 0.00 0.00 3.07
1910 1976 1.406898 TCAGTCATCGCCATGAGAGAC 59.593 52.381 0.00 3.96 39.86 3.36
1917 1983 3.616956 TCGCCATGAGAGACTGAAATT 57.383 42.857 0.00 0.00 0.00 1.82
1925 1991 5.936686 TGAGAGACTGAAATTGCTTCAAG 57.063 39.130 0.00 0.00 43.54 3.02
1928 1994 6.713903 TGAGAGACTGAAATTGCTTCAAGAAT 59.286 34.615 0.00 0.00 43.54 2.40
1929 1995 7.094890 TGAGAGACTGAAATTGCTTCAAGAATC 60.095 37.037 0.00 0.00 43.54 2.52
1930 1996 6.713903 AGAGACTGAAATTGCTTCAAGAATCA 59.286 34.615 0.00 0.00 43.54 2.57
1931 1997 7.230108 AGAGACTGAAATTGCTTCAAGAATCAA 59.770 33.333 2.07 2.07 43.54 2.57
1933 1999 5.924825 ACTGAAATTGCTTCAAGAATCAAGC 59.075 36.000 5.49 0.00 43.54 4.01
1940 2006 3.005155 GCTTCAAGAATCAAGCAGGTGTT 59.995 43.478 0.00 0.00 43.87 3.32
1941 2007 4.216257 GCTTCAAGAATCAAGCAGGTGTTA 59.784 41.667 0.00 0.00 43.87 2.41
1942 2008 5.105997 GCTTCAAGAATCAAGCAGGTGTTAT 60.106 40.000 0.00 0.00 43.87 1.89
1946 2012 3.935203 AGAATCAAGCAGGTGTTATCGTG 59.065 43.478 0.00 0.00 0.00 4.35
1960 2035 2.604046 ATCGTGTCATCAGTAAGCCC 57.396 50.000 0.00 0.00 0.00 5.19
1973 2048 4.933400 TCAGTAAGCCCGTTTAGTTTCATC 59.067 41.667 0.00 0.00 0.00 2.92
2015 2098 5.935945 TGAGAAATTCAGGGTAAACAGTGA 58.064 37.500 0.00 0.00 0.00 3.41
2018 2101 5.998363 AGAAATTCAGGGTAAACAGTGAGTC 59.002 40.000 0.00 0.00 0.00 3.36
2056 2154 7.278868 CAGGAATAATCTCTTGTCTTGGTGTAC 59.721 40.741 0.00 0.00 0.00 2.90
2153 2252 4.730657 CAACTTGATGTCTTGCCAATCTC 58.269 43.478 0.00 0.00 0.00 2.75
2204 2304 7.410120 GGATTTTGTCCTGTCCATATTTTCT 57.590 36.000 0.00 0.00 44.16 2.52
2205 2305 8.519799 GGATTTTGTCCTGTCCATATTTTCTA 57.480 34.615 0.00 0.00 44.16 2.10
2206 2306 8.966868 GGATTTTGTCCTGTCCATATTTTCTAA 58.033 33.333 0.00 0.00 44.16 2.10
2345 2472 7.828712 TGTGAGTATGAATGATTGCAAAATGA 58.171 30.769 1.71 0.00 0.00 2.57
2409 2554 5.047188 GGCCACCCAAAATATGTTTAATCG 58.953 41.667 0.00 0.00 0.00 3.34
2437 2582 3.553302 GCCTTTCTAGCCGTTAGATCTCC 60.553 52.174 0.00 0.00 38.19 3.71
2453 2598 5.230759 AGATCTCCATCCAACCCTCTAAAT 58.769 41.667 0.00 0.00 0.00 1.40
2456 2601 3.197983 TCCATCCAACCCTCTAAATGGT 58.802 45.455 0.00 0.00 36.04 3.55
2472 2617 1.408969 TGGTACTCACAGCTCACACA 58.591 50.000 0.00 0.00 0.00 3.72
2509 2658 1.212935 CCCACCCTGTCCCATTCTTAG 59.787 57.143 0.00 0.00 0.00 2.18
2516 2665 3.118223 CCTGTCCCATTCTTAGTCTTCCC 60.118 52.174 0.00 0.00 0.00 3.97
2777 3762 1.154197 GGTTTGACCGGAGTGCTTAC 58.846 55.000 9.46 0.00 0.00 2.34
2844 3829 1.971149 AGGTGGTGAGGATGATGGAA 58.029 50.000 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.151677 ACAAGGTTAGGCCCCTCCA 60.152 57.895 0.00 0.00 38.26 3.86
34 35 5.461078 GGAGCACATGCATGAAAAATGTATC 59.539 40.000 32.75 19.01 45.16 2.24
37 38 3.259876 AGGAGCACATGCATGAAAAATGT 59.740 39.130 32.75 7.43 45.16 2.71
69 70 0.103208 GATGACTACCACTCTGGGCG 59.897 60.000 0.00 0.00 43.37 6.13
131 132 9.256477 TGTCTAATTAATGCCTATTAACTGTCG 57.744 33.333 0.00 0.00 40.51 4.35
162 163 2.738135 GCGCAATGCCCGTAAAATAAT 58.262 42.857 0.30 0.00 37.76 1.28
191 192 5.244626 CCAACTGGAAACAAAGAAGATGGAT 59.755 40.000 0.00 0.00 42.06 3.41
211 212 3.497262 CGGAAGGTTAAGACTTGTCCAAC 59.503 47.826 0.00 2.88 0.00 3.77
216 217 4.377897 CTGAACGGAAGGTTAAGACTTGT 58.622 43.478 0.00 0.00 39.19 3.16
220 221 2.074576 GCCTGAACGGAAGGTTAAGAC 58.925 52.381 2.75 0.00 39.19 3.01
221 222 1.975680 AGCCTGAACGGAAGGTTAAGA 59.024 47.619 2.75 0.00 39.19 2.10
227 228 0.250234 TGATGAGCCTGAACGGAAGG 59.750 55.000 0.00 0.00 37.91 3.46
233 234 1.747355 CCCATTGTGATGAGCCTGAAC 59.253 52.381 0.00 0.00 35.16 3.18
242 243 7.855375 AGTATATGATACCTCCCATTGTGATG 58.145 38.462 0.00 0.00 0.00 3.07
243 244 9.206690 CTAGTATATGATACCTCCCATTGTGAT 57.793 37.037 0.00 0.00 0.00 3.06
325 326 9.759473 AATGAGGCCATTATAATAACAAGCTAT 57.241 29.630 5.01 0.00 40.95 2.97
337 338 9.306777 TGCATAACAATAAATGAGGCCATTATA 57.693 29.630 5.01 0.00 41.84 0.98
341 342 6.675413 ATGCATAACAATAAATGAGGCCAT 57.325 33.333 5.01 0.00 33.66 4.40
372 373 8.704668 TCATGTCATGGTAAATGATGTAGTAGT 58.295 33.333 12.90 0.00 0.00 2.73
416 417 6.325028 CCGGTCATAATGGGACTATCATAGAT 59.675 42.308 0.00 0.00 35.61 1.98
419 454 4.161565 GCCGGTCATAATGGGACTATCATA 59.838 45.833 1.90 0.00 35.61 2.15
420 455 3.055094 GCCGGTCATAATGGGACTATCAT 60.055 47.826 1.90 0.00 35.61 2.45
422 457 2.301870 TGCCGGTCATAATGGGACTATC 59.698 50.000 1.90 0.00 35.61 2.08
424 459 1.796017 TGCCGGTCATAATGGGACTA 58.204 50.000 1.90 0.00 35.61 2.59
426 461 1.523758 GATGCCGGTCATAATGGGAC 58.476 55.000 1.90 0.00 35.05 4.46
428 463 0.250295 ACGATGCCGGTCATAATGGG 60.250 55.000 1.90 0.00 40.78 4.00
439 474 0.863799 CATGAGGATGAACGATGCCG 59.136 55.000 0.00 0.00 42.50 5.69
440 475 1.869767 GTCATGAGGATGAACGATGCC 59.130 52.381 0.00 0.00 40.39 4.40
443 478 3.181471 GGACAGTCATGAGGATGAACGAT 60.181 47.826 2.17 0.00 40.39 3.73
446 481 3.529533 CAGGACAGTCATGAGGATGAAC 58.470 50.000 9.74 0.00 40.39 3.18
450 485 1.876849 AGCAGGACAGTCATGAGGAT 58.123 50.000 19.41 0.00 27.97 3.24
459 494 1.312815 GCAAACTCAAGCAGGACAGT 58.687 50.000 0.00 0.00 0.00 3.55
462 497 1.576421 CCGCAAACTCAAGCAGGAC 59.424 57.895 0.00 0.00 0.00 3.85
463 498 1.600636 CCCGCAAACTCAAGCAGGA 60.601 57.895 0.00 0.00 29.68 3.86
479 514 4.079253 AGACAAATAATCACACCACACCC 58.921 43.478 0.00 0.00 0.00 4.61
528 563 6.374333 TCTCAAAATCGACCTTCCAAAATAGG 59.626 38.462 0.00 0.00 37.56 2.57
529 564 7.377766 TCTCAAAATCGACCTTCCAAAATAG 57.622 36.000 0.00 0.00 0.00 1.73
530 565 7.393234 ACATCTCAAAATCGACCTTCCAAAATA 59.607 33.333 0.00 0.00 0.00 1.40
573 608 6.913132 GCTCAACTCTTCTTTGTTTAGGAAAC 59.087 38.462 0.00 0.00 41.73 2.78
577 612 4.216472 GGGCTCAACTCTTCTTTGTTTAGG 59.784 45.833 0.00 0.00 0.00 2.69
578 613 5.066593 AGGGCTCAACTCTTCTTTGTTTAG 58.933 41.667 0.00 0.00 0.00 1.85
581 616 3.584733 AGGGCTCAACTCTTCTTTGTT 57.415 42.857 0.00 0.00 0.00 2.83
587 628 4.380973 GGCAAAAATAGGGCTCAACTCTTC 60.381 45.833 0.00 0.00 0.00 2.87
592 633 2.562738 AGTGGCAAAAATAGGGCTCAAC 59.437 45.455 0.00 0.00 0.00 3.18
597 638 3.441244 GCAGTGGCAAAAATAGGGC 57.559 52.632 0.00 0.00 40.72 5.19
611 652 5.769662 TGAGAAATTTGGTTATGTCTGCAGT 59.230 36.000 14.67 0.00 0.00 4.40
627 668 4.129380 GGCAGCCAAAAGTTTGAGAAATT 58.871 39.130 6.55 0.00 40.55 1.82
643 685 1.869774 CTTGGTTTCTTTTGGCAGCC 58.130 50.000 3.66 3.66 0.00 4.85
785 830 3.221389 CTGCCATCGCCATTGGGG 61.221 66.667 13.38 13.38 40.85 4.96
805 850 2.474526 CGACCGCTTCAACACAATCATC 60.475 50.000 0.00 0.00 0.00 2.92
809 854 0.586319 CACGACCGCTTCAACACAAT 59.414 50.000 0.00 0.00 0.00 2.71
830 875 3.296709 CTTGCTACGGCCGGTCACT 62.297 63.158 31.76 10.73 37.74 3.41
856 901 0.466922 GGAATGGATGTGAGGCTGGG 60.467 60.000 0.00 0.00 0.00 4.45
859 904 1.528824 CCGGAATGGATGTGAGGCT 59.471 57.895 0.00 0.00 42.00 4.58
957 1008 0.322008 GGGATGAATGGATCGGCTCC 60.322 60.000 0.00 0.00 45.19 4.70
988 1044 4.514569 CGGCATTTTCGACGGGCG 62.515 66.667 0.00 0.00 42.72 6.13
1158 1214 0.036388 GTCGATGCACCAGGAAAGGA 60.036 55.000 0.00 0.00 0.00 3.36
1194 1250 1.640069 CGGCGATCAGCACTTGATG 59.360 57.895 0.00 0.00 46.51 3.07
1228 1294 3.127533 GCTTGCCTGCCAGTACGG 61.128 66.667 0.00 0.06 38.11 4.02
1229 1295 2.046892 AGCTTGCCTGCCAGTACG 60.047 61.111 0.00 0.00 0.00 3.67
1230 1296 1.003355 TCAGCTTGCCTGCCAGTAC 60.003 57.895 0.00 0.00 41.50 2.73
1231 1297 1.003355 GTCAGCTTGCCTGCCAGTA 60.003 57.895 0.00 0.00 41.50 2.74
1232 1298 2.282040 GTCAGCTTGCCTGCCAGT 60.282 61.111 0.00 0.00 41.50 4.00
1568 1634 0.649475 CGTAGACGGTGTAGACGAGG 59.351 60.000 0.00 0.00 35.59 4.63
1835 1901 4.008933 GTGGGGAGCTGCTCGTGT 62.009 66.667 22.25 0.00 0.00 4.49
1869 1935 4.535692 TGATGGATGGGATTCGGATTGATA 59.464 41.667 0.00 0.00 0.00 2.15
1870 1936 3.331591 TGATGGATGGGATTCGGATTGAT 59.668 43.478 0.00 0.00 0.00 2.57
1877 1943 2.916702 TGACTGATGGATGGGATTCG 57.083 50.000 0.00 0.00 0.00 3.34
1878 1944 3.332919 CGATGACTGATGGATGGGATTC 58.667 50.000 0.00 0.00 0.00 2.52
1883 1949 0.107268 TGGCGATGACTGATGGATGG 59.893 55.000 0.00 0.00 0.00 3.51
1892 1958 1.408340 CAGTCTCTCATGGCGATGACT 59.592 52.381 7.38 1.19 37.64 3.41
1910 1976 6.390987 GCTTGATTCTTGAAGCAATTTCAG 57.609 37.500 13.30 4.23 46.01 3.02
1925 1991 3.684788 ACACGATAACACCTGCTTGATTC 59.315 43.478 0.00 0.00 0.00 2.52
1928 1994 2.036604 TGACACGATAACACCTGCTTGA 59.963 45.455 0.00 0.00 0.00 3.02
1929 1995 2.412870 TGACACGATAACACCTGCTTG 58.587 47.619 0.00 0.00 0.00 4.01
1930 1996 2.831685 TGACACGATAACACCTGCTT 57.168 45.000 0.00 0.00 0.00 3.91
1931 1997 2.233676 TGATGACACGATAACACCTGCT 59.766 45.455 0.00 0.00 0.00 4.24
1933 1999 3.849911 ACTGATGACACGATAACACCTG 58.150 45.455 0.00 0.00 0.00 4.00
1934 2000 5.651530 CTTACTGATGACACGATAACACCT 58.348 41.667 0.00 0.00 0.00 4.00
1935 2001 4.267928 GCTTACTGATGACACGATAACACC 59.732 45.833 0.00 0.00 0.00 4.16
1936 2002 4.267928 GGCTTACTGATGACACGATAACAC 59.732 45.833 0.00 0.00 0.00 3.32
1937 2003 4.430007 GGCTTACTGATGACACGATAACA 58.570 43.478 0.00 0.00 0.00 2.41
1940 2006 2.034179 CGGGCTTACTGATGACACGATA 59.966 50.000 0.00 0.00 0.00 2.92
1941 2007 1.202417 CGGGCTTACTGATGACACGAT 60.202 52.381 0.00 0.00 0.00 3.73
1942 2008 0.172578 CGGGCTTACTGATGACACGA 59.827 55.000 0.00 0.00 0.00 4.35
1946 2012 3.858247 ACTAAACGGGCTTACTGATGAC 58.142 45.455 0.00 0.00 0.00 3.06
1960 2035 5.632959 AGAGAGAGACGATGAAACTAAACG 58.367 41.667 0.00 0.00 0.00 3.60
1973 2048 4.454161 TCTCAAAGACAAGAGAGAGAGACG 59.546 45.833 0.00 0.00 36.05 4.18
2015 2098 2.666272 TCCTGACTGACTGACTGACT 57.334 50.000 0.00 0.00 0.00 3.41
2018 2101 6.096705 AGAGATTATTCCTGACTGACTGACTG 59.903 42.308 0.00 0.00 0.00 3.51
2056 2154 4.745125 AGCATTCATAATTGAGGACGTACG 59.255 41.667 15.01 15.01 32.27 3.67
2211 2311 9.332502 TGCTTACCATACATATTATGTCGTTTT 57.667 29.630 12.50 0.00 43.67 2.43
2212 2312 8.896320 TGCTTACCATACATATTATGTCGTTT 57.104 30.769 12.50 0.47 43.67 3.60
2213 2313 9.502091 AATGCTTACCATACATATTATGTCGTT 57.498 29.630 12.50 1.99 43.67 3.85
2316 2443 6.185852 TGCAATCATTCATACTCACAAGTG 57.814 37.500 0.00 0.00 36.92 3.16
2345 2472 8.973835 TTTTAGTCATTGTCTTTTCGTTTTGT 57.026 26.923 0.00 0.00 0.00 2.83
2437 2582 5.104527 TGAGTACCATTTAGAGGGTTGGATG 60.105 44.000 0.00 0.00 41.02 3.51
2453 2598 1.408969 TGTGTGAGCTGTGAGTACCA 58.591 50.000 0.00 0.00 0.00 3.25
2456 2601 4.988540 GTGTTAATGTGTGAGCTGTGAGTA 59.011 41.667 0.00 0.00 0.00 2.59
2472 2617 0.891904 GGGGTGCGTGGTGTGTTAAT 60.892 55.000 0.00 0.00 0.00 1.40
2499 2644 3.388913 AGGAGGGAAGACTAAGAATGGG 58.611 50.000 0.00 0.00 0.00 4.00
2509 2658 3.328050 TGAAAGAAGGAAGGAGGGAAGAC 59.672 47.826 0.00 0.00 0.00 3.01
2516 2665 3.307339 CCAGAGGTGAAAGAAGGAAGGAG 60.307 52.174 0.00 0.00 0.00 3.69
2541 2698 5.010933 AGAAGAAGTGATTCCGTAGAGTCA 58.989 41.667 0.00 0.00 36.48 3.41
2795 3780 1.406341 GCAAAGGCGTGGACCTATGTA 60.406 52.381 0.00 0.00 39.93 2.29
2844 3829 1.076632 TTGGGGCTTCACAACGGTT 60.077 52.632 0.00 0.00 0.00 4.44


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

AutoCloner maintained by Alex Coulton.