Multiple sequence alignment - TraesCS3B01G122500

Loading Multiple Alignment...

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 TraesCS3B01G122500 chr3B 100.000 2868 0 0 1 2868 92595992 92593125 0.000000e+00 5297.0
1 TraesCS3B01G122500 chr3B 88.800 125 13 1 2166 2290 172450832 172450709 4.950000e-33 152.0
2 TraesCS3B01G122500 chr3D 86.364 1958 183 45 38 1945 58400420 58398497 0.000000e+00 2060.0
3 TraesCS3B01G122500 chr3D 87.234 470 32 7 1942 2405 58398368 58397921 7.090000e-141 510.0
4 TraesCS3B01G122500 chr3D 85.801 493 45 12 2399 2868 58397535 58397045 1.530000e-137 499.0
5 TraesCS3B01G122500 chr3D 89.256 121 12 1 2166 2285 120315101 120314981 1.780000e-32 150.0
6 TraesCS3B01G122500 chr3D 83.740 123 14 3 1800 1920 120315802 120315684 8.400000e-21 111.0
7 TraesCS3B01G122500 chr3A 83.994 1968 178 64 38 1945 67361537 67359647 0.000000e+00 1762.0
8 TraesCS3B01G122500 chr3A 89.785 558 54 3 1942 2498 67359512 67358957 0.000000e+00 712.0
9 TraesCS3B01G122500 chr3A 84.083 289 34 5 2562 2840 67357621 67357335 4.710000e-68 268.0
10 TraesCS3B01G122500 chr3A 87.069 116 9 3 1807 1920 127274749 127274638 3.000000e-25 126.0
11 TraesCS3B01G122500 chr7A 87.255 102 11 2 2451 2551 682003823 682003923 6.490000e-22 115.0
12 TraesCS3B01G122500 chr1D 100.000 30 0 0 402 431 85922193 85922222 3.990000e-04 56.5


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 TraesCS3B01G122500 chr3B 92593125 92595992 2867 True 5297 5297 100.000000 1 2868 1 chr3B.!!$R1 2867
1 TraesCS3B01G122500 chr3D 58397045 58400420 3375 True 1023 2060 86.466333 38 2868 3 chr3D.!!$R1 2830
2 TraesCS3B01G122500 chr3A 67357335 67361537 4202 True 914 1762 85.954000 38 2840 3 chr3A.!!$R2 2802

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
759 796 0.606604 AAGTCGCGAAGGCTTTCCTA 59.393 50.0 12.06 0.0 43.28 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 2339 0.027586 GCTTTCGTGACGTGCTGTTT 59.972 50.0 4.4 0.0 0.0 2.83 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
87 88 9.520515 AGTGAACATATTTTGTATTCCTGAACT 57.479 29.630 0.00 0.00 37.68 3.01
88 89 9.559958 GTGAACATATTTTGTATTCCTGAACTG 57.440 33.333 0.00 0.00 37.68 3.16
98 100 9.883142 TTTGTATTCCTGAACTGTTTGAAAATT 57.117 25.926 0.00 0.00 0.00 1.82
100 102 9.959749 TGTATTCCTGAACTGTTTGAAAATTAC 57.040 29.630 0.00 0.74 0.00 1.89
101 103 9.113876 GTATTCCTGAACTGTTTGAAAATTACG 57.886 33.333 0.00 0.00 0.00 3.18
113 115 9.746711 TGTTTGAAAATTACGAACACATTTTTG 57.253 25.926 11.77 0.00 36.92 2.44
123 125 7.734538 ACGAACACATTTTTGTAGTTTTCAG 57.265 32.000 0.00 0.00 0.00 3.02
164 166 6.751425 GCGACCATTGTTTGAATTCATGATTA 59.249 34.615 9.40 0.00 0.00 1.75
165 167 7.436080 GCGACCATTGTTTGAATTCATGATTAT 59.564 33.333 9.40 0.00 0.00 1.28
197 200 7.200778 ACATTTTTGGAATGCATAAACAACC 57.799 32.000 0.00 0.00 0.00 3.77
312 327 9.956720 AAGTTATTGAACATTTTCTGAAGTCAG 57.043 29.630 1.65 1.65 40.47 3.51
323 338 9.918630 CATTTTCTGAAGTCAGGAACATTATTT 57.081 29.630 8.42 0.00 40.95 1.40
353 368 9.781633 TTCATGATTCCATTTCTGAACATTTTT 57.218 25.926 0.00 0.00 0.00 1.94
381 396 9.995379 GAATTCTCGAAGAAGTTTTAAATTTGC 57.005 29.630 0.00 0.00 37.69 3.68
400 415 8.776376 AATTTGCGAACATTTATCAAAATCCT 57.224 26.923 0.00 0.00 32.87 3.24
540 574 6.481313 TGCGTCCATTTTTCAAATTCATGAAA 59.519 30.769 13.09 1.91 45.07 2.69
577 611 6.702972 TGCAAACATTATTCAAAATCGTGG 57.297 33.333 0.00 0.00 0.00 4.94
587 621 8.879342 TTATTCAAAATCGTGGACATGTTTTT 57.121 26.923 0.00 0.00 32.48 1.94
592 626 8.973378 TCAAAATCGTGGACATGTTTTTATTTC 58.027 29.630 0.00 0.00 31.63 2.17
594 628 6.834168 ATCGTGGACATGTTTTTATTTCCT 57.166 33.333 0.00 0.00 30.05 3.36
597 631 6.432783 TCGTGGACATGTTTTTATTTCCTGAT 59.567 34.615 0.00 0.00 30.05 2.90
599 633 7.362056 CGTGGACATGTTTTTATTTCCTGATCT 60.362 37.037 0.00 0.00 30.05 2.75
630 664 7.851822 ACATGTGTGAACGTTTTATGAATTC 57.148 32.000 0.46 0.00 0.00 2.17
631 665 6.577055 ACATGTGTGAACGTTTTATGAATTCG 59.423 34.615 0.46 0.00 0.00 3.34
751 788 3.268013 ACATTTTCAAAGTCGCGAAGG 57.732 42.857 12.06 0.01 0.00 3.46
752 789 1.978782 CATTTTCAAAGTCGCGAAGGC 59.021 47.619 12.06 0.00 0.00 4.35
757 794 3.967715 AAGTCGCGAAGGCTTTCC 58.032 55.556 12.06 0.00 43.28 3.13
759 796 0.606604 AAGTCGCGAAGGCTTTCCTA 59.393 50.000 12.06 0.00 43.28 2.94
769 806 5.726963 GCGAAGGCTTTCCTAAAATCGTTAG 60.727 44.000 0.00 0.00 43.40 2.34
773 810 6.354130 AGGCTTTCCTAAAATCGTTAGCATA 58.646 36.000 0.00 0.00 42.06 3.14
785 822 9.561069 AAAATCGTTAGCATATTCTACATCCTT 57.439 29.630 0.00 0.00 0.00 3.36
868 907 3.082165 TTTTTGAAGCGACCGGTCA 57.918 47.368 32.80 12.28 0.00 4.02
875 914 1.827399 AAGCGACCGGTCAGACCAAT 61.827 55.000 32.80 6.34 38.47 3.16
931 971 1.039856 CCCTTTGGGTGTTGTTCCTG 58.960 55.000 0.00 0.00 38.25 3.86
953 993 9.559732 TCCTGTGTTCCATAAAATATCTACATG 57.440 33.333 0.00 0.00 0.00 3.21
990 1035 4.513442 ACTATGTGCCTCGCAAAGAATAA 58.487 39.130 0.00 0.00 41.47 1.40
991 1036 4.572389 ACTATGTGCCTCGCAAAGAATAAG 59.428 41.667 0.00 0.00 41.47 1.73
1032 1077 3.567585 TGTAGCAAGCTAAACAATGTGCA 59.432 39.130 2.92 0.00 34.44 4.57
1033 1078 3.017265 AGCAAGCTAAACAATGTGCAC 57.983 42.857 10.75 10.75 34.44 4.57
1034 1079 2.061028 GCAAGCTAAACAATGTGCACC 58.939 47.619 15.69 0.00 32.29 5.01
1035 1080 2.545532 GCAAGCTAAACAATGTGCACCA 60.546 45.455 15.69 2.61 32.29 4.17
1038 1083 3.221771 AGCTAAACAATGTGCACCAAGA 58.778 40.909 15.69 0.00 0.00 3.02
1039 1084 3.254166 AGCTAAACAATGTGCACCAAGAG 59.746 43.478 15.69 3.75 0.00 2.85
1041 1086 4.261572 GCTAAACAATGTGCACCAAGAGAA 60.262 41.667 15.69 0.00 0.00 2.87
1084 1140 1.474879 CTCAAAGTCGTCTCCCTCTCC 59.525 57.143 0.00 0.00 0.00 3.71
1106 1162 0.400213 ACATGAAGGCGACAAGGGAA 59.600 50.000 0.00 0.00 0.00 3.97
1124 1180 4.414999 GGAACGTTTCCTTAGCGAAAAT 57.585 40.909 0.46 0.00 46.57 1.82
1125 1181 5.535043 GGAACGTTTCCTTAGCGAAAATA 57.465 39.130 0.46 0.00 46.57 1.40
1127 1183 5.106987 GGAACGTTTCCTTAGCGAAAATACA 60.107 40.000 0.46 0.00 46.57 2.29
1128 1184 6.402875 GGAACGTTTCCTTAGCGAAAATACAT 60.403 38.462 0.46 0.00 46.57 2.29
1129 1185 6.103222 ACGTTTCCTTAGCGAAAATACATC 57.897 37.500 0.00 0.00 33.68 3.06
1130 1186 5.188194 CGTTTCCTTAGCGAAAATACATCG 58.812 41.667 0.00 0.00 42.99 3.84
1152 1208 3.065575 CGACCTTTCGGGATTCCTG 57.934 57.895 5.04 5.04 41.89 3.86
1207 1263 2.019984 CACTCTTTTGCATAGCTCCCC 58.980 52.381 0.00 0.00 0.00 4.81
1266 1324 3.190849 CTGATCACGCGCCACCAG 61.191 66.667 5.73 5.32 0.00 4.00
1267 1325 3.939837 CTGATCACGCGCCACCAGT 62.940 63.158 5.73 0.00 0.00 4.00
1268 1326 3.188786 GATCACGCGCCACCAGTC 61.189 66.667 5.73 0.00 0.00 3.51
1269 1327 4.760047 ATCACGCGCCACCAGTCC 62.760 66.667 5.73 0.00 0.00 3.85
1724 1788 3.181462 CGAGGACAATGAGAATGGGATCA 60.181 47.826 0.00 0.00 0.00 2.92
1768 1839 1.778026 CGTCGCTTCTGATCGATCAAG 59.222 52.381 27.09 22.56 36.18 3.02
1798 1869 3.251729 GCCCATTGTGCTGTGATATACTG 59.748 47.826 0.00 0.00 0.00 2.74
1799 1870 4.454678 CCCATTGTGCTGTGATATACTGT 58.545 43.478 0.00 0.00 0.00 3.55
1805 1876 6.635030 TGTGCTGTGATATACTGTACTAGG 57.365 41.667 0.00 0.00 41.87 3.02
1820 1892 6.429385 ACTGTACTAGGTCTGTACTTGTGTAC 59.571 42.308 0.00 0.00 46.74 2.90
1835 1907 3.806380 TGTGTACGCTTTTGGGAGTTTA 58.194 40.909 8.10 0.00 36.14 2.01
1836 1908 3.560896 TGTGTACGCTTTTGGGAGTTTAC 59.439 43.478 8.10 0.00 36.14 2.01
1861 1944 7.393515 ACCGCTCTGTACATAGTATATTGATGA 59.606 37.037 9.72 0.00 0.00 2.92
1862 1945 8.244113 CCGCTCTGTACATAGTATATTGATGAA 58.756 37.037 9.72 0.00 0.00 2.57
1863 1946 9.794685 CGCTCTGTACATAGTATATTGATGAAT 57.205 33.333 9.72 0.00 0.00 2.57
1939 2022 6.001449 TCCCCCTGTTGTTTAGAATAGATG 57.999 41.667 0.00 0.00 0.00 2.90
1995 2218 5.891551 TCCACTAGTTCCTTTTGCTTTTCTT 59.108 36.000 0.00 0.00 0.00 2.52
2001 2224 6.333416 AGTTCCTTTTGCTTTTCTTCTTCAC 58.667 36.000 0.00 0.00 0.00 3.18
2005 2228 5.394553 CCTTTTGCTTTTCTTCTTCACCACT 60.395 40.000 0.00 0.00 0.00 4.00
2011 2234 0.679505 TCTTCTTCACCACTCACCGG 59.320 55.000 0.00 0.00 0.00 5.28
2031 2272 3.548014 CGGTCGCTTGATCAAACAACTTT 60.548 43.478 9.88 0.00 0.00 2.66
2032 2273 3.730715 GGTCGCTTGATCAAACAACTTTG 59.269 43.478 9.88 0.00 38.56 2.77
2033 2274 4.351192 GTCGCTTGATCAAACAACTTTGT 58.649 39.130 9.88 0.00 44.72 2.83
2034 2275 4.437820 GTCGCTTGATCAAACAACTTTGTC 59.562 41.667 9.88 0.00 41.31 3.18
2035 2276 3.418619 CGCTTGATCAAACAACTTTGTCG 59.581 43.478 9.88 0.67 41.31 4.35
2036 2277 3.180387 GCTTGATCAAACAACTTTGTCGC 59.820 43.478 9.88 1.00 41.31 5.19
2037 2278 4.601019 CTTGATCAAACAACTTTGTCGCT 58.399 39.130 9.88 0.00 41.31 4.93
2038 2279 4.209452 TGATCAAACAACTTTGTCGCTC 57.791 40.909 0.00 0.00 41.31 5.03
2039 2280 3.876914 TGATCAAACAACTTTGTCGCTCT 59.123 39.130 0.00 0.00 41.31 4.09
2040 2281 3.944422 TCAAACAACTTTGTCGCTCTC 57.056 42.857 0.00 0.00 41.31 3.20
2041 2282 3.531538 TCAAACAACTTTGTCGCTCTCT 58.468 40.909 0.00 0.00 41.31 3.10
2042 2283 3.938963 TCAAACAACTTTGTCGCTCTCTT 59.061 39.130 0.00 0.00 41.31 2.85
2043 2284 4.034048 TCAAACAACTTTGTCGCTCTCTTC 59.966 41.667 0.00 0.00 41.31 2.87
2044 2285 2.484889 ACAACTTTGTCGCTCTCTTCC 58.515 47.619 0.00 0.00 36.50 3.46
2045 2286 2.103263 ACAACTTTGTCGCTCTCTTCCT 59.897 45.455 0.00 0.00 36.50 3.36
2046 2287 2.447244 ACTTTGTCGCTCTCTTCCTG 57.553 50.000 0.00 0.00 0.00 3.86
2047 2288 1.074752 CTTTGTCGCTCTCTTCCTGC 58.925 55.000 0.00 0.00 0.00 4.85
2048 2289 0.681733 TTTGTCGCTCTCTTCCTGCT 59.318 50.000 0.00 0.00 0.00 4.24
2049 2290 1.545841 TTGTCGCTCTCTTCCTGCTA 58.454 50.000 0.00 0.00 0.00 3.49
2050 2291 1.545841 TGTCGCTCTCTTCCTGCTAA 58.454 50.000 0.00 0.00 0.00 3.09
2051 2292 1.474478 TGTCGCTCTCTTCCTGCTAAG 59.526 52.381 0.00 0.00 0.00 2.18
2052 2293 1.474879 GTCGCTCTCTTCCTGCTAAGT 59.525 52.381 0.00 0.00 0.00 2.24
2053 2294 2.683867 GTCGCTCTCTTCCTGCTAAGTA 59.316 50.000 0.00 0.00 0.00 2.24
2073 2314 9.260002 CTAAGTAAATGAAAAACCAGCAATTGT 57.740 29.630 7.40 0.00 0.00 2.71
2123 2365 0.603569 ACGTCACGAAAGCAGGAGAT 59.396 50.000 2.91 0.00 0.00 2.75
2133 2375 2.758736 AGCAGGAGATCACTCACAAC 57.241 50.000 0.00 0.00 44.22 3.32
2143 2385 6.428159 GGAGATCACTCACAACACAGTTTATT 59.572 38.462 0.00 0.00 44.22 1.40
2193 2441 3.056322 GCAAGGAAAGATGGCAATGAACT 60.056 43.478 0.00 0.00 0.00 3.01
2208 2456 7.498900 TGGCAATGAACTACAGTTGGAATATAG 59.501 37.037 0.00 0.00 38.56 1.31
2229 2477 3.119101 AGGACTACTTAACCAGATGTGCG 60.119 47.826 0.00 0.00 0.00 5.34
2316 2564 6.377327 TCTCAGTGTTTGATTGAAGGTTTC 57.623 37.500 0.00 0.00 34.68 2.78
2346 2594 2.299013 GTTGTGGGGGAAAAGGAATGTC 59.701 50.000 0.00 0.00 0.00 3.06
2371 2619 1.059098 TGACATTCTCAGGGTGCTGT 58.941 50.000 0.00 0.00 0.00 4.40
2375 2623 4.263462 TGACATTCTCAGGGTGCTGTATTT 60.263 41.667 0.00 0.00 0.00 1.40
2397 2645 5.107109 TCATTTTGTCACTGTTTGATCGG 57.893 39.130 0.00 0.00 36.32 4.18
2405 2653 4.753107 GTCACTGTTTGATCGGAGGTTTTA 59.247 41.667 0.00 0.00 36.32 1.52
2406 2654 5.411669 GTCACTGTTTGATCGGAGGTTTTAT 59.588 40.000 0.00 0.00 36.32 1.40
2407 2655 5.642063 TCACTGTTTGATCGGAGGTTTTATC 59.358 40.000 0.00 0.00 0.00 1.75
2413 2661 6.494893 TTGATCGGAGGTTTTATCAAACTG 57.505 37.500 2.71 0.00 41.92 3.16
2415 2663 6.414732 TGATCGGAGGTTTTATCAAACTGAT 58.585 36.000 2.71 0.00 41.92 2.90
2416 2664 6.316140 TGATCGGAGGTTTTATCAAACTGATG 59.684 38.462 2.71 0.00 41.92 3.07
2417 2665 4.941263 TCGGAGGTTTTATCAAACTGATGG 59.059 41.667 2.71 0.00 41.92 3.51
2449 3089 6.472686 AATCCTTAGTCAGACTGTATGGTC 57.527 41.667 13.84 0.00 36.56 4.02
2493 3133 6.547510 AGCCTGAACTACAAACTTCAAAAGAT 59.452 34.615 0.00 0.00 0.00 2.40
2532 4471 7.342769 ACGAAATATACTGGAGATGTGTGTA 57.657 36.000 0.00 0.00 0.00 2.90
2534 4473 7.147966 ACGAAATATACTGGAGATGTGTGTACA 60.148 37.037 0.00 0.00 41.89 2.90
2535 4474 7.167635 CGAAATATACTGGAGATGTGTGTACAC 59.832 40.741 19.36 19.36 46.59 2.90
2576 4515 8.987890 ACATTTACATAACAATTTGTTCAAGCC 58.012 29.630 17.64 0.00 40.22 4.35
2665 4617 2.099756 AGCACTTTCACAAGAAGGCAAC 59.900 45.455 0.00 0.00 34.44 4.17
2687 4639 4.335315 ACCGGTTGCACTAATCACATATTG 59.665 41.667 0.00 0.00 0.00 1.90
2757 4713 5.163794 CCACGGGACATAAAACATCTACAAC 60.164 44.000 0.00 0.00 0.00 3.32
2772 4728 5.664294 TCTACAACCGGACTTAGCAAATA 57.336 39.130 9.46 0.00 0.00 1.40
2775 4731 4.585879 ACAACCGGACTTAGCAAATATGT 58.414 39.130 9.46 0.00 0.00 2.29
2816 4772 2.797278 GCCCGATCAGTGTCCGGAT 61.797 63.158 21.45 0.00 45.58 4.18
2817 4773 1.461091 GCCCGATCAGTGTCCGGATA 61.461 60.000 21.45 0.10 45.58 2.59
2835 4791 2.452600 TATGTCCATTTTGAGCCCCC 57.547 50.000 0.00 0.00 0.00 5.40
2841 4802 1.629861 CCATTTTGAGCCCCCATTTGT 59.370 47.619 0.00 0.00 0.00 2.83
2855 4816 4.037923 CCCCATTTGTATGTAACCATGCTC 59.962 45.833 0.00 0.00 35.02 4.26
2858 4819 5.360714 CCATTTGTATGTAACCATGCTCCTT 59.639 40.000 0.00 0.00 35.02 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 62 9.520515 AGTTCAGGAATACAAAATATGTTCACT 57.479 29.630 0.00 0.00 43.63 3.41
86 87 9.965748 AAAAATGTGTTCGTAATTTTCAAACAG 57.034 25.926 0.00 0.00 33.51 3.16
87 88 9.746711 CAAAAATGTGTTCGTAATTTTCAAACA 57.253 25.926 0.00 0.00 33.51 2.83
88 89 9.748100 ACAAAAATGTGTTCGTAATTTTCAAAC 57.252 25.926 0.00 0.00 33.51 2.93
98 100 8.666573 TCTGAAAACTACAAAAATGTGTTCGTA 58.333 29.630 0.00 0.00 32.30 3.43
100 102 7.483375 TGTCTGAAAACTACAAAAATGTGTTCG 59.517 33.333 0.00 0.00 32.30 3.95
101 103 8.682128 TGTCTGAAAACTACAAAAATGTGTTC 57.318 30.769 0.00 0.00 32.75 3.18
113 115 8.221766 CGACCTTAGAAAATGTCTGAAAACTAC 58.778 37.037 0.00 0.00 37.12 2.73
116 118 5.851703 GCGACCTTAGAAAATGTCTGAAAAC 59.148 40.000 0.00 0.00 37.12 2.43
123 125 3.636404 GTCGCGACCTTAGAAAATGTC 57.364 47.619 28.61 0.00 0.00 3.06
171 174 8.134261 GGTTGTTTATGCATTCCAAAAATGTTT 58.866 29.630 3.54 0.00 0.00 2.83
292 307 6.376864 TGTTCCTGACTTCAGAAAATGTTCAA 59.623 34.615 7.87 0.00 46.59 2.69
312 327 9.820725 TGGAATCATGAATTCAAATAATGTTCC 57.179 29.630 13.09 17.86 44.81 3.62
323 338 8.124808 TGTTCAGAAATGGAATCATGAATTCA 57.875 30.769 11.26 11.26 44.81 2.57
357 372 8.073768 TCGCAAATTTAAAACTTCTTCGAGAAT 58.926 29.630 0.00 0.00 33.13 2.40
477 510 9.308318 TGATGAATCGAAAATATTCACGAACTA 57.692 29.630 16.61 9.13 43.96 2.24
519 553 9.796180 AAGGATTTCATGAATTTGAAAAATGGA 57.204 25.926 9.40 0.00 45.77 3.41
556 590 7.865875 TGTCCACGATTTTGAATAATGTTTG 57.134 32.000 0.00 0.00 0.00 2.93
571 605 6.432783 TCAGGAAATAAAAACATGTCCACGAT 59.567 34.615 0.00 0.00 35.05 3.73
574 608 7.830739 AGATCAGGAAATAAAAACATGTCCAC 58.169 34.615 0.00 0.00 35.05 4.02
607 641 6.577055 ACGAATTCATAAAACGTTCACACATG 59.423 34.615 0.00 1.50 33.48 3.21
641 675 8.344098 GCTGGAAAAATGTTCATGATTTCAAAA 58.656 29.630 16.57 5.15 32.91 2.44
644 678 6.424509 GTGCTGGAAAAATGTTCATGATTTCA 59.575 34.615 16.57 8.88 32.91 2.69
686 722 6.517034 CGTGCATTCAAAAGTATTTGCAATTG 59.483 34.615 0.00 0.00 44.52 2.32
698 734 8.005662 TCAAAATATGTTCGTGCATTCAAAAG 57.994 30.769 0.00 0.00 0.00 2.27
751 788 8.560374 AGAATATGCTAACGATTTTAGGAAAGC 58.440 33.333 0.00 0.00 0.00 3.51
759 796 9.561069 AAGGATGTAGAATATGCTAACGATTTT 57.439 29.630 0.00 0.00 0.00 1.82
773 810 9.739276 TTCACAAACTATTCAAGGATGTAGAAT 57.261 29.630 0.00 0.00 36.14 2.40
828 866 3.701532 TGTTCGCGGACTTTCAAAAAT 57.298 38.095 20.15 0.00 0.00 1.82
863 902 0.248289 ACGGGTTATTGGTCTGACCG 59.752 55.000 21.15 9.64 42.58 4.79
868 907 0.615544 TCCCGACGGGTTATTGGTCT 60.616 55.000 31.54 0.00 44.74 3.85
875 914 3.136123 CGCTCTCCCGACGGGTTA 61.136 66.667 31.54 19.46 44.74 2.85
919 958 1.757682 TGGAACACAGGAACAACACC 58.242 50.000 0.00 0.00 0.00 4.16
953 993 6.432783 AGGCACATAGTATGAGTCTATGAGAC 59.567 42.308 17.13 12.04 44.13 3.36
990 1035 1.165270 GGTTTTATGGTGTCGCTGCT 58.835 50.000 0.00 0.00 0.00 4.24
991 1036 1.135689 CAGGTTTTATGGTGTCGCTGC 60.136 52.381 0.00 0.00 0.00 5.25
1032 1077 3.379452 CCAGGAGGTAGATTCTCTTGGT 58.621 50.000 12.29 0.00 46.81 3.67
1084 1140 2.009774 CCCTTGTCGCCTTCATGTTAG 58.990 52.381 0.00 0.00 0.00 2.34
1106 1162 5.220340 CGATGTATTTTCGCTAAGGAAACGT 60.220 40.000 0.00 0.00 35.75 3.99
1143 1199 6.015350 TCGATGTATTTAGAGTCAGGAATCCC 60.015 42.308 0.00 0.00 0.00 3.85
1144 1200 6.982852 TCGATGTATTTAGAGTCAGGAATCC 58.017 40.000 0.00 0.00 0.00 3.01
1145 1201 8.873215 TTTCGATGTATTTAGAGTCAGGAATC 57.127 34.615 0.00 0.00 0.00 2.52
1148 1204 9.314321 GAATTTTCGATGTATTTAGAGTCAGGA 57.686 33.333 0.00 0.00 0.00 3.86
1151 1207 9.443323 TTGGAATTTTCGATGTATTTAGAGTCA 57.557 29.630 0.00 0.00 0.00 3.41
1152 1208 9.704098 GTTGGAATTTTCGATGTATTTAGAGTC 57.296 33.333 0.00 0.00 0.00 3.36
1207 1263 0.890996 GGAAGGGAATATGCTGGGCG 60.891 60.000 0.00 0.00 0.00 6.13
1215 1271 1.843851 TGGAAGCGTGGAAGGGAATAT 59.156 47.619 0.00 0.00 0.00 1.28
1266 1324 0.314935 CATGGGTGTTGCTTGTGGAC 59.685 55.000 0.00 0.00 0.00 4.02
1267 1325 0.827089 CCATGGGTGTTGCTTGTGGA 60.827 55.000 2.85 0.00 0.00 4.02
1268 1326 1.667151 CCATGGGTGTTGCTTGTGG 59.333 57.895 2.85 0.00 0.00 4.17
1269 1327 1.005867 GCCATGGGTGTTGCTTGTG 60.006 57.895 15.13 0.00 0.00 3.33
1270 1328 2.563798 CGCCATGGGTGTTGCTTGT 61.564 57.895 15.13 0.00 0.00 3.16
1271 1329 2.259204 CGCCATGGGTGTTGCTTG 59.741 61.111 15.13 0.00 0.00 4.01
1272 1330 3.683937 GCGCCATGGGTGTTGCTT 61.684 61.111 15.13 0.00 35.34 3.91
1301 1359 1.188219 AGCACGAAGAGGGAAGCAGA 61.188 55.000 0.00 0.00 0.00 4.26
1303 1361 1.293498 GAGCACGAAGAGGGAAGCA 59.707 57.895 0.00 0.00 0.00 3.91
1307 1365 1.303398 AGACGAGCACGAAGAGGGA 60.303 57.895 11.40 0.00 42.66 4.20
1431 1489 3.289834 CAGCCGCCAACTGCTTGT 61.290 61.111 0.00 0.00 33.60 3.16
1600 1664 1.630244 CCTCGCTCTTCAACGCTTGG 61.630 60.000 0.00 0.00 0.00 3.61
1602 1666 0.946221 CACCTCGCTCTTCAACGCTT 60.946 55.000 0.00 0.00 0.00 4.68
1724 1788 2.671070 CCTCCAGAACCACGCCAT 59.329 61.111 0.00 0.00 0.00 4.40
1768 1839 4.440127 CACAATGGGCGGCCAAGC 62.440 66.667 36.08 5.22 0.00 4.01
1820 1892 0.109919 GCGGTAAACTCCCAAAAGCG 60.110 55.000 0.00 0.00 0.00 4.68
1835 1907 7.393515 TCATCAATATACTATGTACAGAGCGGT 59.606 37.037 17.28 6.30 0.00 5.68
1836 1908 7.762382 TCATCAATATACTATGTACAGAGCGG 58.238 38.462 17.28 0.00 0.00 5.52
1861 1944 8.677148 ACACTCGATTGCCATTTATTAGTATT 57.323 30.769 2.19 0.00 0.00 1.89
1862 1945 8.559536 CAACACTCGATTGCCATTTATTAGTAT 58.440 33.333 2.19 0.00 0.00 2.12
1863 1946 7.551262 ACAACACTCGATTGCCATTTATTAGTA 59.449 33.333 2.19 0.00 0.00 1.82
1864 1947 6.374333 ACAACACTCGATTGCCATTTATTAGT 59.626 34.615 2.19 0.00 0.00 2.24
1865 1948 6.785191 ACAACACTCGATTGCCATTTATTAG 58.215 36.000 2.19 0.00 0.00 1.73
1866 1949 6.751514 ACAACACTCGATTGCCATTTATTA 57.248 33.333 2.19 0.00 0.00 0.98
1951 2173 6.668718 AGTGGAGTATCATGCTGATATCTCAT 59.331 38.462 20.62 4.92 40.97 2.90
1995 2218 1.802337 CGACCGGTGAGTGGTGAAGA 61.802 60.000 14.63 0.00 40.63 2.87
2001 2224 2.507110 ATCAAGCGACCGGTGAGTGG 62.507 60.000 14.63 0.00 0.00 4.00
2005 2228 0.034198 TTTGATCAAGCGACCGGTGA 59.966 50.000 14.63 1.96 0.00 4.02
2011 2234 4.351192 ACAAAGTTGTTTGATCAAGCGAC 58.649 39.130 26.80 26.80 45.22 5.19
2031 2272 1.474478 CTTAGCAGGAAGAGAGCGACA 59.526 52.381 0.00 0.00 0.00 4.35
2032 2273 1.474879 ACTTAGCAGGAAGAGAGCGAC 59.525 52.381 0.00 0.00 0.00 5.19
2033 2274 1.840737 ACTTAGCAGGAAGAGAGCGA 58.159 50.000 0.00 0.00 0.00 4.93
2034 2275 3.784701 TTACTTAGCAGGAAGAGAGCG 57.215 47.619 0.58 0.00 0.00 5.03
2035 2276 5.665459 TCATTTACTTAGCAGGAAGAGAGC 58.335 41.667 0.58 0.00 0.00 4.09
2036 2277 8.553459 TTTTCATTTACTTAGCAGGAAGAGAG 57.447 34.615 0.58 0.00 0.00 3.20
2037 2278 8.784043 GTTTTTCATTTACTTAGCAGGAAGAGA 58.216 33.333 0.58 0.00 0.00 3.10
2038 2279 8.023706 GGTTTTTCATTTACTTAGCAGGAAGAG 58.976 37.037 0.58 0.00 0.00 2.85
2039 2280 7.504238 TGGTTTTTCATTTACTTAGCAGGAAGA 59.496 33.333 0.58 0.00 0.00 2.87
2040 2281 7.657336 TGGTTTTTCATTTACTTAGCAGGAAG 58.343 34.615 0.00 0.00 0.00 3.46
2041 2282 7.589958 TGGTTTTTCATTTACTTAGCAGGAA 57.410 32.000 0.00 0.00 0.00 3.36
2042 2283 6.294508 GCTGGTTTTTCATTTACTTAGCAGGA 60.295 38.462 0.00 0.00 32.11 3.86
2043 2284 5.863935 GCTGGTTTTTCATTTACTTAGCAGG 59.136 40.000 0.00 0.00 32.11 4.85
2044 2285 6.446318 TGCTGGTTTTTCATTTACTTAGCAG 58.554 36.000 0.00 0.00 33.10 4.24
2045 2286 6.398234 TGCTGGTTTTTCATTTACTTAGCA 57.602 33.333 0.00 0.00 35.36 3.49
2046 2287 7.889589 ATTGCTGGTTTTTCATTTACTTAGC 57.110 32.000 0.00 0.00 0.00 3.09
2047 2288 9.260002 ACAATTGCTGGTTTTTCATTTACTTAG 57.740 29.630 5.05 0.00 0.00 2.18
2048 2289 9.606631 AACAATTGCTGGTTTTTCATTTACTTA 57.393 25.926 5.05 0.00 0.00 2.24
2049 2290 8.397148 CAACAATTGCTGGTTTTTCATTTACTT 58.603 29.630 5.05 0.00 0.00 2.24
2050 2291 7.012232 CCAACAATTGCTGGTTTTTCATTTACT 59.988 33.333 18.10 0.00 0.00 2.24
2051 2292 7.131565 CCAACAATTGCTGGTTTTTCATTTAC 58.868 34.615 18.10 0.00 0.00 2.01
2052 2293 6.238593 GCCAACAATTGCTGGTTTTTCATTTA 60.239 34.615 24.98 0.00 33.92 1.40
2053 2294 5.450274 GCCAACAATTGCTGGTTTTTCATTT 60.450 36.000 24.98 0.00 33.92 2.32
2095 2337 2.780993 CTTTCGTGACGTGCTGTTTTT 58.219 42.857 4.40 0.00 0.00 1.94
2096 2338 1.531058 GCTTTCGTGACGTGCTGTTTT 60.531 47.619 4.40 0.00 0.00 2.43
2097 2339 0.027586 GCTTTCGTGACGTGCTGTTT 59.972 50.000 4.40 0.00 0.00 2.83
2098 2340 1.087202 TGCTTTCGTGACGTGCTGTT 61.087 50.000 4.40 0.00 0.00 3.16
2099 2341 1.490693 CTGCTTTCGTGACGTGCTGT 61.491 55.000 4.40 0.00 0.00 4.40
2110 2352 2.266554 GTGAGTGATCTCCTGCTTTCG 58.733 52.381 0.00 0.00 39.75 3.46
2123 2365 6.751514 ACAAATAAACTGTGTTGTGAGTGA 57.248 33.333 0.00 0.00 33.09 3.41
2133 2375 9.117145 CAGCATAGTGTAAACAAATAAACTGTG 57.883 33.333 0.00 0.00 36.09 3.66
2143 2385 3.058293 GCAGTGCAGCATAGTGTAAACAA 60.058 43.478 11.09 0.00 0.00 2.83
2208 2456 3.187700 CGCACATCTGGTTAAGTAGTCC 58.812 50.000 0.00 0.00 0.00 3.85
2316 2564 4.301072 TTTCCCCCACAACTCTTCTATG 57.699 45.455 0.00 0.00 0.00 2.23
2346 2594 4.343526 AGCACCCTGAGAATGTCACTATAG 59.656 45.833 0.00 0.00 0.00 1.31
2371 2619 7.807433 CCGATCAAACAGTGACAAAATGAAATA 59.193 33.333 0.00 0.00 39.72 1.40
2375 2623 4.819088 TCCGATCAAACAGTGACAAAATGA 59.181 37.500 0.00 0.00 39.72 2.57
2397 2645 5.447818 CGCTCCATCAGTTTGATAAAACCTC 60.448 44.000 1.74 0.00 34.28 3.85
2405 2653 1.339438 ACAGCGCTCCATCAGTTTGAT 60.339 47.619 7.13 0.00 37.65 2.57
2406 2654 0.035317 ACAGCGCTCCATCAGTTTGA 59.965 50.000 7.13 0.00 0.00 2.69
2407 2655 1.725641 TACAGCGCTCCATCAGTTTG 58.274 50.000 7.13 0.00 0.00 2.93
2411 2659 1.069823 AGGATTACAGCGCTCCATCAG 59.930 52.381 7.13 0.00 0.00 2.90
2412 2660 1.123077 AGGATTACAGCGCTCCATCA 58.877 50.000 7.13 0.00 0.00 3.07
2413 2661 2.246719 AAGGATTACAGCGCTCCATC 57.753 50.000 7.13 9.27 0.00 3.51
2415 2663 2.100916 GACTAAGGATTACAGCGCTCCA 59.899 50.000 7.13 0.00 0.00 3.86
2416 2664 2.100916 TGACTAAGGATTACAGCGCTCC 59.899 50.000 7.13 5.54 0.00 4.70
2417 2665 3.066900 TCTGACTAAGGATTACAGCGCTC 59.933 47.826 7.13 0.00 0.00 5.03
2449 3089 5.117592 CAGGCTTTGTTTTGAAATAGCTTCG 59.882 40.000 0.00 0.00 36.78 3.79
2493 3133 3.579335 TTTCGTATCATCACACCGTCA 57.421 42.857 0.00 0.00 0.00 4.35
2576 4515 4.823989 AGAACAAGTTTCACTCTTCCCATG 59.176 41.667 0.00 0.00 0.00 3.66
2607 4550 4.634004 TGGGACAATTGTACTTTCGCTATG 59.366 41.667 20.14 0.00 31.92 2.23
2665 4617 4.335315 ACAATATGTGATTAGTGCAACCGG 59.665 41.667 0.00 0.00 37.80 5.28
2702 4654 4.103153 GTGATTGGTGGATATGAAGAGGGA 59.897 45.833 0.00 0.00 0.00 4.20
2757 4713 5.760253 AGATTGACATATTTGCTAAGTCCGG 59.240 40.000 0.00 0.00 28.93 5.14
2772 4728 2.872245 CCGCGGACATTTAGATTGACAT 59.128 45.455 24.07 0.00 0.00 3.06
2775 4731 2.546778 GTCCGCGGACATTTAGATTGA 58.453 47.619 44.88 12.02 44.02 2.57
2816 4772 1.643286 TGGGGGCTCAAAATGGACATA 59.357 47.619 0.00 0.00 0.00 2.29
2817 4773 0.413037 TGGGGGCTCAAAATGGACAT 59.587 50.000 0.00 0.00 0.00 3.06
2835 4791 6.455360 AAGGAGCATGGTTACATACAAATG 57.545 37.500 0.00 0.00 34.99 2.32
2841 4802 8.494433 AGAGAAAATAAGGAGCATGGTTACATA 58.506 33.333 0.00 0.00 34.99 2.29


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

AutoCloner maintained by Alex Coulton.