Multiple sequence alignment - TraesCS6D01G140900

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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 TraesCS6D01G140900 chr6D 100.000 4008 0 0 1 4008 110445841 110441834 0.000000e+00 7402
1 TraesCS6D01G140900 chr6A 91.779 3114 141 52 1 3058 134950593 134947539 0.000000e+00 4226
2 TraesCS6D01G140900 chr6A 85.598 979 101 21 3056 4006 134947300 134946334 0.000000e+00 990
3 TraesCS6D01G140900 chr6B 91.051 2827 104 47 120 2876 198987292 198984545 0.000000e+00 3681
4 TraesCS6D01G140900 chr6B 82.595 948 117 28 3080 4006 198983547 198982627 0.000000e+00 793
5 TraesCS6D01G140900 chr6B 93.590 78 5 0 653 730 198978788 198978711 2.530000e-22 117
6 TraesCS6D01G140900 chr7D 80.519 308 37 17 1244 1544 594730818 594730527 8.720000e-52 215
7 TraesCS6D01G140900 chr7D 89.091 165 15 2 2242 2403 594729870 594729706 6.790000e-48 202
8 TraesCS6D01G140900 chr7A 89.091 165 15 2 2242 2403 686937954 686938118 6.790000e-48 202
9 TraesCS6D01G140900 chr2D 86.170 188 21 5 2229 2412 450235629 450235815 8.790000e-47 198
10 TraesCS6D01G140900 chr7B 88.485 165 16 2 2242 2403 667070583 667070419 3.160000e-46 196
11 TraesCS6D01G140900 chr2B 86.413 184 20 4 2229 2408 530307294 530307476 3.160000e-46 196
12 TraesCS6D01G140900 chr2A 91.489 141 11 1 2248 2387 594581072 594581212 4.090000e-45 193


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 TraesCS6D01G140900 chr6D 110441834 110445841 4007 True 7402.000000 7402 100.000000 1 4008 1 chr6D.!!$R1 4007
1 TraesCS6D01G140900 chr6A 134946334 134950593 4259 True 2608.000000 4226 88.688500 1 4006 2 chr6A.!!$R1 4005
2 TraesCS6D01G140900 chr6B 198978711 198987292 8581 True 1530.333333 3681 89.078667 120 4006 3 chr6B.!!$R1 3886
3 TraesCS6D01G140900 chr7D 594729706 594730818 1112 True 208.500000 215 84.805000 1244 2403 2 chr7D.!!$R1 1159

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
455 466 0.454196 GCGTTTACGGATTGCCCATT 59.546 50.0 4.29 0.0 40.23 3.16 F
1874 2039 0.391263 CGGTGGAAGTGTAAGCCCTC 60.391 60.0 0.00 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1898 2063 0.031314 CAGATGACGCGAGGCTATGT 59.969 55.0 15.93 0.0 42.42 2.29 R
3348 4674 0.173255 GTGCCGGAAATTCCATGGTG 59.827 55.0 12.58 0.0 35.91 4.17 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
35 36 0.796870 GCACGCGCCAAAGTTAATCC 60.797 55.000 5.73 0.00 0.00 3.01
38 39 1.813859 GCGCCAAAGTTAATCCCCC 59.186 57.895 0.00 0.00 0.00 5.40
43 44 3.021695 GCCAAAGTTAATCCCCCACTAC 58.978 50.000 0.00 0.00 0.00 2.73
44 45 3.308904 GCCAAAGTTAATCCCCCACTACT 60.309 47.826 0.00 0.00 0.00 2.57
45 46 4.524053 CCAAAGTTAATCCCCCACTACTC 58.476 47.826 0.00 0.00 0.00 2.59
60 61 4.822896 CCACTACTCCAGTATCTACCACTC 59.177 50.000 0.00 0.00 34.98 3.51
79 80 2.878406 CTCCTTCCAGAAAGTTCGCAAA 59.122 45.455 0.00 0.00 32.69 3.68
81 82 2.287608 CCTTCCAGAAAGTTCGCAAACC 60.288 50.000 0.00 0.00 35.92 3.27
85 86 3.383185 TCCAGAAAGTTCGCAAACCAATT 59.617 39.130 0.00 0.00 35.92 2.32
91 92 7.329226 CAGAAAGTTCGCAAACCAATTAATCAT 59.671 33.333 0.00 0.00 35.92 2.45
137 142 4.133013 ACGTATGTATTTGGTCCACCTC 57.867 45.455 0.00 0.00 36.82 3.85
232 242 2.159382 GGGGCTTTTCTGACATTTCGA 58.841 47.619 0.00 0.00 0.00 3.71
235 245 2.226437 GGCTTTTCTGACATTTCGAGCA 59.774 45.455 0.00 0.00 0.00 4.26
236 246 3.486584 GCTTTTCTGACATTTCGAGCAG 58.513 45.455 0.00 0.00 0.00 4.24
424 435 1.177401 GCTTCCACCTTTGGGACATC 58.823 55.000 0.00 0.00 44.11 3.06
447 458 0.996462 CATGTGACGCGTTTACGGAT 59.004 50.000 15.53 3.99 40.23 4.18
454 465 1.711060 CGCGTTTACGGATTGCCCAT 61.711 55.000 0.00 0.00 40.23 4.00
455 466 0.454196 GCGTTTACGGATTGCCCATT 59.546 50.000 4.29 0.00 40.23 3.16
458 469 3.175929 CGTTTACGGATTGCCCATTTTC 58.824 45.455 0.00 0.00 35.37 2.29
459 470 3.175929 GTTTACGGATTGCCCATTTTCG 58.824 45.455 0.00 0.00 34.14 3.46
460 471 2.116827 TACGGATTGCCCATTTTCGT 57.883 45.000 0.00 0.00 34.14 3.85
461 472 0.525761 ACGGATTGCCCATTTTCGTG 59.474 50.000 0.00 0.00 34.14 4.35
462 473 0.808125 CGGATTGCCCATTTTCGTGA 59.192 50.000 0.00 0.00 34.14 4.35
463 474 1.467374 CGGATTGCCCATTTTCGTGAC 60.467 52.381 0.00 0.00 34.14 3.67
464 475 1.543802 GGATTGCCCATTTTCGTGACA 59.456 47.619 0.00 0.00 34.14 3.58
465 476 2.166254 GGATTGCCCATTTTCGTGACAT 59.834 45.455 0.00 0.00 34.14 3.06
466 477 3.438360 GATTGCCCATTTTCGTGACATC 58.562 45.455 0.00 0.00 0.00 3.06
469 480 3.006940 TGCCCATTTTCGTGACATCTAC 58.993 45.455 0.00 0.00 0.00 2.59
473 484 4.809426 CCCATTTTCGTGACATCTACCTAC 59.191 45.833 0.00 0.00 0.00 3.18
474 485 5.416083 CCATTTTCGTGACATCTACCTACA 58.584 41.667 0.00 0.00 0.00 2.74
529 543 7.617723 TGGGTTGCTTACTTAATAATTCCACAT 59.382 33.333 0.00 0.00 0.00 3.21
573 587 1.382522 GCACATGATGGTGGTAGTGG 58.617 55.000 0.00 0.00 39.19 4.00
575 589 2.358957 CACATGATGGTGGTAGTGGTG 58.641 52.381 0.00 0.00 35.13 4.17
766 795 2.466846 TCCTTTGATCATCCGTCCAGA 58.533 47.619 0.00 0.00 0.00 3.86
767 796 2.837591 TCCTTTGATCATCCGTCCAGAA 59.162 45.455 0.00 0.00 0.00 3.02
770 799 3.694043 TTGATCATCCGTCCAGAACAA 57.306 42.857 0.00 0.00 0.00 2.83
771 800 3.251479 TGATCATCCGTCCAGAACAAG 57.749 47.619 0.00 0.00 0.00 3.16
772 801 2.567169 TGATCATCCGTCCAGAACAAGT 59.433 45.455 0.00 0.00 0.00 3.16
778 808 5.411361 TCATCCGTCCAGAACAAGTTTAATG 59.589 40.000 0.00 0.00 0.00 1.90
787 817 7.776030 TCCAGAACAAGTTTAATGTAAGTCCAA 59.224 33.333 0.00 0.00 0.00 3.53
960 996 2.034066 TTTCGCTTGGCCCAGAGG 59.966 61.111 8.31 0.00 0.00 3.69
1050 1087 2.908796 GGATTCCCTCCCACGACC 59.091 66.667 0.00 0.00 38.19 4.79
1051 1088 2.499685 GATTCCCTCCCACGACCG 59.500 66.667 0.00 0.00 0.00 4.79
1052 1089 2.038329 ATTCCCTCCCACGACCGA 59.962 61.111 0.00 0.00 0.00 4.69
1056 1093 4.436998 CCTCCCACGACCGAGCAC 62.437 72.222 0.00 0.00 0.00 4.40
1057 1094 4.778415 CTCCCACGACCGAGCACG 62.778 72.222 0.00 0.00 39.43 5.34
1200 1239 1.829533 AAGTGTTGCTGCTGGTGGG 60.830 57.895 0.00 0.00 0.00 4.61
1201 1240 2.519302 GTGTTGCTGCTGGTGGGT 60.519 61.111 0.00 0.00 0.00 4.51
1202 1241 2.519063 TGTTGCTGCTGGTGGGTG 60.519 61.111 0.00 0.00 0.00 4.61
1203 1242 3.982241 GTTGCTGCTGGTGGGTGC 61.982 66.667 0.00 0.00 0.00 5.01
1549 1604 3.537874 CCCATCGGGTCCTCGTCC 61.538 72.222 0.00 0.00 38.25 4.79
1874 2039 0.391263 CGGTGGAAGTGTAAGCCCTC 60.391 60.000 0.00 0.00 0.00 4.30
1883 2048 1.541588 GTGTAAGCCCTCCTTGCTTTG 59.458 52.381 2.55 0.00 46.47 2.77
1898 2063 3.030291 TGCTTTGCTTTCCTCCAAGAAA 58.970 40.909 0.00 0.00 34.64 2.52
1900 2065 3.181476 GCTTTGCTTTCCTCCAAGAAACA 60.181 43.478 0.00 0.00 32.45 2.83
1903 2068 5.964958 TTGCTTTCCTCCAAGAAACATAG 57.035 39.130 0.00 0.00 32.45 2.23
1919 2084 0.747255 ATAGCCTCGCGTCATCTGTT 59.253 50.000 5.77 0.00 0.00 3.16
1923 2088 1.269309 GCCTCGCGTCATCTGTTCTAT 60.269 52.381 5.77 0.00 0.00 1.98
1924 2089 2.031069 GCCTCGCGTCATCTGTTCTATA 60.031 50.000 5.77 0.00 0.00 1.31
1925 2090 3.556513 CCTCGCGTCATCTGTTCTATAC 58.443 50.000 5.77 0.00 0.00 1.47
1929 2094 4.083961 TCGCGTCATCTGTTCTATACTAGC 60.084 45.833 5.77 0.00 0.00 3.42
1942 2107 0.108804 TACTAGCGCACCTTGCTGAC 60.109 55.000 11.47 0.00 43.85 3.51
1957 2122 1.401905 GCTGACCTTTATTGGCCTTCG 59.598 52.381 3.32 0.00 0.00 3.79
1981 2148 3.744719 CAGGGCTCGTCGTCGGAA 61.745 66.667 1.55 0.00 37.69 4.30
2118 2288 6.158023 TGTAAGTGCCTAACTAGATTAGCC 57.842 41.667 0.00 0.00 38.56 3.93
2123 2293 3.070159 TGCCTAACTAGATTAGCCAGCTG 59.930 47.826 6.78 6.78 39.29 4.24
2136 2314 3.960571 AGCCAGCTGACTGTTTTATCAT 58.039 40.909 17.39 0.00 42.81 2.45
2137 2315 4.338879 AGCCAGCTGACTGTTTTATCATT 58.661 39.130 17.39 0.00 42.81 2.57
2142 2320 6.312487 CAGCTGACTGTTTTATCATTGAGTG 58.688 40.000 8.42 0.00 39.22 3.51
2158 2336 5.565592 TTGAGTGCATGTAATTGATCACC 57.434 39.130 0.00 0.00 0.00 4.02
2629 2837 2.259618 CGTCGTGTTCCCTCTTGTATG 58.740 52.381 0.00 0.00 0.00 2.39
2697 2905 8.352201 AGTGTAGTATACTACTCTACTCGACAG 58.648 40.741 31.82 0.00 45.79 3.51
2698 2906 8.349245 GTGTAGTATACTACTCTACTCGACAGA 58.651 40.741 32.68 13.38 46.74 3.41
2965 3181 5.899120 TCAAGATACTAAGACTTGTCGCT 57.101 39.130 0.00 0.00 40.89 4.93
3000 3216 0.387367 AGTAGCAACGCACGTCTCAG 60.387 55.000 0.00 0.00 0.00 3.35
3115 4434 4.722194 ACATTATTGTCGTCATGTTGCAC 58.278 39.130 0.00 0.00 0.00 4.57
3223 4549 5.050634 TGCATTGTGTTTAGTACGTGAAGAC 60.051 40.000 0.00 0.00 0.00 3.01
3239 4565 3.689161 TGAAGACGCAATCCTACAATTGG 59.311 43.478 10.83 0.00 37.17 3.16
3258 4584 9.288576 ACAATTGGTATCAATATCATGGTGTAG 57.711 33.333 10.83 0.00 42.29 2.74
3263 4589 6.879458 GGTATCAATATCATGGTGTAGGGAAC 59.121 42.308 0.00 0.00 0.00 3.62
3278 4604 7.159372 GTGTAGGGAACTGAGAACTAAAATCA 58.841 38.462 0.00 0.00 43.88 2.57
3281 4607 5.998363 AGGGAACTGAGAACTAAAATCACAC 59.002 40.000 0.00 0.00 41.13 3.82
3315 4641 7.217200 TGATATATGAGTTTGCTAACCAGGTC 58.783 38.462 7.43 0.00 34.71 3.85
3320 4646 5.876357 TGAGTTTGCTAACCAGGTCTTATT 58.124 37.500 7.43 0.00 34.71 1.40
3348 4674 3.128349 CTGCAAATGGCCTTGATAATGC 58.872 45.455 3.32 4.90 43.89 3.56
3351 4677 3.460103 CAAATGGCCTTGATAATGCACC 58.540 45.455 3.32 0.00 0.00 5.01
3377 4703 1.295792 TTTCCGGCACTCGATTATGC 58.704 50.000 0.00 7.69 42.43 3.14
3378 4704 0.176910 TTCCGGCACTCGATTATGCA 59.823 50.000 15.71 0.00 43.93 3.96
3402 4728 1.787155 CAAATATTCCGACCTCTCGCG 59.213 52.381 0.00 0.00 38.70 5.87
3404 4730 0.311165 ATATTCCGACCTCTCGCGTG 59.689 55.000 5.77 3.13 38.70 5.34
3410 4736 0.456142 CGACCTCTCGCGTGAATGAA 60.456 55.000 12.41 0.00 31.91 2.57
3510 4837 4.141158 CCAGAAGGTATTTAGGGGCTTCAT 60.141 45.833 0.00 0.00 0.00 2.57
3513 4840 7.060421 CAGAAGGTATTTAGGGGCTTCATAAA 58.940 38.462 0.00 1.47 36.28 1.40
3525 4852 3.119637 GGCTTCATAAAGGCGCTGTTTTA 60.120 43.478 7.64 10.71 46.59 1.52
3526 4853 4.440112 GGCTTCATAAAGGCGCTGTTTTAT 60.440 41.667 7.64 12.49 46.59 1.40
3536 4863 3.342269 GCGCTGTTTTATACACACATCG 58.658 45.455 0.00 0.00 34.11 3.84
3546 4893 9.987901 GTTTTATACACACATCGAACATTTTTG 57.012 29.630 0.00 0.00 0.00 2.44
3551 4898 9.737427 ATACACACATCGAACATTTTTGTTTAA 57.263 25.926 0.00 0.00 31.35 1.52
3552 4899 8.641499 ACACACATCGAACATTTTTGTTTAAT 57.359 26.923 0.00 0.00 31.35 1.40
3581 4928 9.947433 ATCAATGTTTCCAAAATACATGTTGAT 57.053 25.926 2.30 0.00 33.10 2.57
3647 4994 5.630680 GGTGAACATTTTGAGCACACATTAG 59.369 40.000 0.00 0.00 30.76 1.73
3655 5002 8.767085 CATTTTGAGCACACATTAGACATTTTT 58.233 29.630 0.00 0.00 0.00 1.94
3658 5005 8.969121 TTGAGCACACATTAGACATTTTTATG 57.031 30.769 0.00 0.00 0.00 1.90
3671 5018 7.604549 AGACATTTTTATGAATGACATGCACA 58.395 30.769 0.00 0.00 38.93 4.57
3700 5047 7.231705 TCTTACATGTGCAAAACATTTGTTG 57.768 32.000 9.11 1.82 44.51 3.33
3705 5052 3.370366 TGTGCAAAACATTTGTTGAGTGC 59.630 39.130 14.99 14.99 39.51 4.40
3711 5058 6.421801 GCAAAACATTTGTTGAGTGCTAGAAT 59.578 34.615 14.75 0.00 37.75 2.40
3813 5160 8.325421 TGGAACATATTTCTGTAAAGCGTAAA 57.675 30.769 0.00 0.00 0.00 2.01
3814 5161 8.784994 TGGAACATATTTCTGTAAAGCGTAAAA 58.215 29.630 0.00 0.00 0.00 1.52
3815 5162 9.615295 GGAACATATTTCTGTAAAGCGTAAAAA 57.385 29.630 0.00 0.00 0.00 1.94
3841 5188 7.217447 AGTTTCTTAAATGTCACGAACGTTTTG 59.783 33.333 0.46 3.18 43.10 2.44
3937 5285 6.783892 AATGTATTTTCAAGCGTGCATTTT 57.216 29.167 0.00 0.00 0.00 1.82
3946 5294 4.515191 TCAAGCGTGCATTTTTCTAGAAGT 59.485 37.500 5.12 0.00 0.00 3.01
3960 5308 9.498307 TTTTTCTAGAAGTCACGAACAATTTTC 57.502 29.630 5.12 0.00 0.00 2.29
3962 5310 7.639162 TCTAGAAGTCACGAACAATTTTCTC 57.361 36.000 0.00 0.00 0.00 2.87
3965 5313 7.264373 AGAAGTCACGAACAATTTTCTCAAT 57.736 32.000 0.00 0.00 0.00 2.57
3967 5315 5.679906 AGTCACGAACAATTTTCTCAATCG 58.320 37.500 0.00 0.00 35.16 3.34
3972 5320 8.927721 TCACGAACAATTTTCTCAATCGTATAA 58.072 29.630 0.00 0.00 39.72 0.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 3.117246 TGGTAGATACTGGAGTAGTGGGG 60.117 52.174 0.00 0.00 40.65 4.96
38 39 4.822896 GGAGTGGTAGATACTGGAGTAGTG 59.177 50.000 0.00 0.00 40.65 2.74
43 44 3.892588 GGAAGGAGTGGTAGATACTGGAG 59.107 52.174 0.00 0.00 0.00 3.86
44 45 3.271225 TGGAAGGAGTGGTAGATACTGGA 59.729 47.826 0.00 0.00 0.00 3.86
45 46 3.639094 CTGGAAGGAGTGGTAGATACTGG 59.361 52.174 0.00 0.00 0.00 4.00
60 61 2.287608 GGTTTGCGAACTTTCTGGAAGG 60.288 50.000 16.37 0.00 39.79 3.46
79 80 4.199310 CGGAGTGGTCATGATTAATTGGT 58.801 43.478 0.00 0.00 0.00 3.67
137 142 0.391395 CACTCCCAGCTGAGCTCAAG 60.391 60.000 18.85 13.28 36.40 3.02
197 206 1.302192 CCCCTTCACCTTTCGCGAA 60.302 57.895 19.38 19.38 0.00 4.70
201 211 1.269723 GAAAAGCCCCTTCACCTTTCG 59.730 52.381 0.00 0.00 0.00 3.46
208 218 2.978156 ATGTCAGAAAAGCCCCTTCA 57.022 45.000 0.00 0.00 0.00 3.02
232 242 3.209410 CTTTCCCGCTTAATGATCTGCT 58.791 45.455 0.00 0.00 0.00 4.24
235 245 3.933861 ACCTTTCCCGCTTAATGATCT 57.066 42.857 0.00 0.00 0.00 2.75
236 246 4.065789 CCTACCTTTCCCGCTTAATGATC 58.934 47.826 0.00 0.00 0.00 2.92
424 435 2.384309 TAAACGCGTCACATGGCCG 61.384 57.895 14.44 0.00 0.00 6.13
447 458 2.513753 AGATGTCACGAAAATGGGCAA 58.486 42.857 0.00 0.00 0.00 4.52
459 470 6.034683 GTGAAATTCGTGTAGGTAGATGTCAC 59.965 42.308 0.00 0.00 0.00 3.67
460 471 6.097356 GTGAAATTCGTGTAGGTAGATGTCA 58.903 40.000 0.00 0.00 0.00 3.58
461 472 6.097356 TGTGAAATTCGTGTAGGTAGATGTC 58.903 40.000 0.00 0.00 0.00 3.06
462 473 6.032956 TGTGAAATTCGTGTAGGTAGATGT 57.967 37.500 0.00 0.00 0.00 3.06
463 474 7.539712 AATGTGAAATTCGTGTAGGTAGATG 57.460 36.000 0.00 0.00 0.00 2.90
464 475 8.561738 AAAATGTGAAATTCGTGTAGGTAGAT 57.438 30.769 0.00 0.00 0.00 1.98
465 476 7.972832 AAAATGTGAAATTCGTGTAGGTAGA 57.027 32.000 0.00 0.00 0.00 2.59
529 543 1.627864 TGACGATGTTCCCAGACAGA 58.372 50.000 0.00 0.00 32.19 3.41
602 616 2.037136 GTTGCAGCGCTCCATGAGT 61.037 57.895 7.13 0.00 31.39 3.41
695 713 6.764308 AGTCGGTTAGTGCTAATTAGTACA 57.236 37.500 28.34 15.63 40.73 2.90
699 717 8.350722 TCTATCAAGTCGGTTAGTGCTAATTAG 58.649 37.037 8.20 8.20 0.00 1.73
766 795 6.238814 CGGGTTGGACTTACATTAAACTTGTT 60.239 38.462 0.00 0.00 0.00 2.83
767 796 5.239963 CGGGTTGGACTTACATTAAACTTGT 59.760 40.000 0.00 0.00 0.00 3.16
770 799 4.758165 CACGGGTTGGACTTACATTAAACT 59.242 41.667 0.00 0.00 0.00 2.66
771 800 4.756135 TCACGGGTTGGACTTACATTAAAC 59.244 41.667 0.00 0.00 0.00 2.01
772 801 4.756135 GTCACGGGTTGGACTTACATTAAA 59.244 41.667 0.00 0.00 0.00 1.52
778 808 2.467566 ATGTCACGGGTTGGACTTAC 57.532 50.000 0.00 0.00 35.11 2.34
787 817 3.625764 CCGATCATTTTTATGTCACGGGT 59.374 43.478 0.00 0.00 35.24 5.28
868 904 1.811266 CGATTCTGGCCCACGTGAG 60.811 63.158 19.30 4.39 0.00 3.51
909 945 0.107214 TGATCTCGTGGATTTGGGGC 60.107 55.000 0.00 0.00 34.33 5.80
1107 1145 0.040067 CAAAAGTGAGTGGAAGCCGC 60.040 55.000 0.00 0.00 0.00 6.53
1175 1214 1.370900 GCAGCAACACTTGGAAGCG 60.371 57.895 0.00 0.00 0.00 4.68
1200 1239 2.546494 GCACCTCACACCACAGCAC 61.546 63.158 0.00 0.00 0.00 4.40
1201 1240 2.203195 GCACCTCACACCACAGCA 60.203 61.111 0.00 0.00 0.00 4.41
1202 1241 3.349006 CGCACCTCACACCACAGC 61.349 66.667 0.00 0.00 0.00 4.40
1203 1242 1.004560 ATCGCACCTCACACCACAG 60.005 57.895 0.00 0.00 0.00 3.66
1476 1531 3.171828 TTGGCGTGGTGGATGTCGT 62.172 57.895 0.00 0.00 0.00 4.34
1874 2039 1.331214 TGGAGGAAAGCAAAGCAAGG 58.669 50.000 0.00 0.00 0.00 3.61
1883 2048 3.129462 GGCTATGTTTCTTGGAGGAAAGC 59.871 47.826 0.00 0.00 36.12 3.51
1898 2063 0.031314 CAGATGACGCGAGGCTATGT 59.969 55.000 15.93 0.00 42.42 2.29
1900 2065 0.747255 AACAGATGACGCGAGGCTAT 59.253 50.000 15.93 0.00 42.42 2.97
1903 2068 0.100682 TAGAACAGATGACGCGAGGC 59.899 55.000 15.93 1.62 42.12 4.70
1919 2084 2.795175 GCAAGGTGCGCTAGTATAGA 57.205 50.000 9.73 0.00 35.23 1.98
1942 2107 4.338118 TGCTAAATCGAAGGCCAATAAAGG 59.662 41.667 5.01 0.00 0.00 3.11
1957 2122 0.179108 ACGACGAGCCCTGCTAAATC 60.179 55.000 0.00 0.00 39.88 2.17
2123 2293 6.615088 ACATGCACTCAATGATAAAACAGTC 58.385 36.000 0.00 0.00 0.00 3.51
2136 2314 4.094739 CGGTGATCAATTACATGCACTCAA 59.905 41.667 0.00 0.00 0.00 3.02
2137 2315 3.622612 CGGTGATCAATTACATGCACTCA 59.377 43.478 0.00 0.00 0.00 3.41
2142 2320 3.206150 AGACCGGTGATCAATTACATGC 58.794 45.455 14.63 0.00 0.00 4.06
2158 2336 4.315803 AGACCTGTTTAATCACAAGACCG 58.684 43.478 0.00 0.00 0.00 4.79
2607 2815 0.249322 ACAAGAGGGAACACGACGTG 60.249 55.000 25.72 25.72 39.75 4.49
2608 2816 1.321474 TACAAGAGGGAACACGACGT 58.679 50.000 0.00 0.00 0.00 4.34
2609 2817 2.094906 TCATACAAGAGGGAACACGACG 60.095 50.000 0.00 0.00 0.00 5.12
2610 2818 3.587797 TCATACAAGAGGGAACACGAC 57.412 47.619 0.00 0.00 0.00 4.34
2611 2819 4.503910 CAATCATACAAGAGGGAACACGA 58.496 43.478 0.00 0.00 0.00 4.35
2612 2820 3.063997 GCAATCATACAAGAGGGAACACG 59.936 47.826 0.00 0.00 0.00 4.49
2613 2821 4.009675 TGCAATCATACAAGAGGGAACAC 58.990 43.478 0.00 0.00 0.00 3.32
2629 2837 4.966366 GCTCGAGAAACATTACATGCAATC 59.034 41.667 18.75 0.00 0.00 2.67
2853 3067 4.158764 GGAGATAAGTATCCTGTGGATCCG 59.841 50.000 7.39 0.00 42.11 4.18
2965 3181 6.453092 GTTGCTACTGGTACAACTTAGAGAA 58.547 40.000 0.00 0.00 40.36 2.87
3000 3216 2.033801 CCGATCTCATTTGACCAATGCC 59.966 50.000 0.00 0.00 42.06 4.40
3058 3523 8.574196 AAAAAGATGTGTTTCCATTTAACTCG 57.426 30.769 0.00 0.00 0.00 4.18
3223 4549 5.749596 TTGATACCAATTGTAGGATTGCG 57.250 39.130 4.43 0.00 36.04 4.85
3239 4565 7.604164 CAGTTCCCTACACCATGATATTGATAC 59.396 40.741 0.00 0.00 0.00 2.24
3258 4584 5.998363 AGTGTGATTTTAGTTCTCAGTTCCC 59.002 40.000 0.00 0.00 0.00 3.97
3291 4617 7.445945 AGACCTGGTTAGCAAACTCATATATC 58.554 38.462 0.00 0.00 35.81 1.63
3295 4621 5.499004 AAGACCTGGTTAGCAAACTCATA 57.501 39.130 0.00 0.00 35.81 2.15
3315 4641 4.869861 GGCCATTTGCAGGTTTACAATAAG 59.130 41.667 0.00 0.00 43.89 1.73
3320 4646 2.008242 AGGCCATTTGCAGGTTTACA 57.992 45.000 5.01 0.00 43.89 2.41
3348 4674 0.173255 GTGCCGGAAATTCCATGGTG 59.827 55.000 12.58 0.00 35.91 4.17
3351 4677 0.378257 CGAGTGCCGGAAATTCCATG 59.622 55.000 13.04 3.56 35.91 3.66
3377 4703 3.535561 AGAGGTCGGAATATTTGCAGTG 58.464 45.455 0.00 0.00 0.00 3.66
3378 4704 3.738281 CGAGAGGTCGGAATATTTGCAGT 60.738 47.826 0.00 0.00 42.87 4.40
3402 4728 8.746922 TGTTCTTCATTTTAGCATTCATTCAC 57.253 30.769 0.00 0.00 0.00 3.18
3487 4814 3.202151 TGAAGCCCCTAAATACCTTCTGG 59.798 47.826 0.00 0.00 34.51 3.86
3510 4837 4.755629 TGTGTGTATAAAACAGCGCCTTTA 59.244 37.500 2.29 6.59 39.29 1.85
3513 4840 2.773487 TGTGTGTATAAAACAGCGCCT 58.227 42.857 2.29 0.00 39.29 5.52
3525 4852 9.737427 TTAAACAAAAATGTTCGATGTGTGTAT 57.263 25.926 0.00 0.00 0.00 2.29
3526 4853 9.737427 ATTAAACAAAAATGTTCGATGTGTGTA 57.263 25.926 0.00 0.00 0.00 2.90
3586 4933 9.635520 AAAAATGTTCATTTTGCATTTCACAAA 57.364 22.222 19.62 0.00 40.58 2.83
3619 4966 2.020720 TGCTCAAAATGTTCACCGTGT 58.979 42.857 0.00 0.00 0.00 4.49
3624 4971 6.360681 GTCTAATGTGTGCTCAAAATGTTCAC 59.639 38.462 0.00 0.00 0.00 3.18
3635 4982 9.793252 ATTCATAAAAATGTCTAATGTGTGCTC 57.207 29.630 0.00 0.00 0.00 4.26
3647 4994 7.815398 TGTGCATGTCATTCATAAAAATGTC 57.185 32.000 0.00 0.00 37.77 3.06
3655 5002 9.571810 GTAAGAAAAATGTGCATGTCATTCATA 57.428 29.630 14.95 0.00 34.92 2.15
3658 5005 7.872163 TGTAAGAAAAATGTGCATGTCATTC 57.128 32.000 14.95 7.37 34.92 2.67
3671 5018 9.719279 CAAATGTTTTGCACATGTAAGAAAAAT 57.281 25.926 0.00 0.00 46.23 1.82
3806 5153 7.375017 CGTGACATTTAAGAAACTTTTTACGCT 59.625 33.333 0.00 0.00 0.00 5.07
3813 5160 6.778108 ACGTTCGTGACATTTAAGAAACTTT 58.222 32.000 0.00 0.00 0.00 2.66
3814 5161 6.354039 ACGTTCGTGACATTTAAGAAACTT 57.646 33.333 0.00 0.00 0.00 2.66
3815 5162 5.978934 ACGTTCGTGACATTTAAGAAACT 57.021 34.783 0.00 0.00 0.00 2.66
3816 5163 7.317177 CAAAACGTTCGTGACATTTAAGAAAC 58.683 34.615 0.00 0.00 0.00 2.78
3828 5175 1.735386 TCCAACCAAAACGTTCGTGA 58.265 45.000 0.00 0.00 0.00 4.35
3908 5255 8.304202 TGCACGCTTGAAAATACATTTTAATT 57.696 26.923 0.00 0.00 39.86 1.40
3910 5257 7.881643 ATGCACGCTTGAAAATACATTTTAA 57.118 28.000 0.00 0.00 39.86 1.52
3917 5265 6.452244 AGAAAAATGCACGCTTGAAAATAC 57.548 33.333 0.00 0.00 0.00 1.89
3919 5267 6.446318 TCTAGAAAAATGCACGCTTGAAAAT 58.554 32.000 0.00 0.00 0.00 1.82
3922 5270 5.008613 ACTTCTAGAAAAATGCACGCTTGAA 59.991 36.000 6.63 0.00 0.00 2.69
3923 5271 4.515191 ACTTCTAGAAAAATGCACGCTTGA 59.485 37.500 6.63 0.00 0.00 3.02
3924 5272 4.787598 ACTTCTAGAAAAATGCACGCTTG 58.212 39.130 6.63 0.00 0.00 4.01
3925 5273 4.515191 TGACTTCTAGAAAAATGCACGCTT 59.485 37.500 6.63 0.00 0.00 4.68
3926 5274 4.065088 TGACTTCTAGAAAAATGCACGCT 58.935 39.130 6.63 0.00 0.00 5.07
3930 5278 5.525745 TGTTCGTGACTTCTAGAAAAATGCA 59.474 36.000 6.63 0.00 0.00 3.96
3931 5279 5.985781 TGTTCGTGACTTCTAGAAAAATGC 58.014 37.500 6.63 0.00 0.00 3.56
3937 5285 7.709182 TGAGAAAATTGTTCGTGACTTCTAGAA 59.291 33.333 4.81 4.81 0.00 2.10
3946 5294 5.666969 ACGATTGAGAAAATTGTTCGTGA 57.333 34.783 0.00 0.00 37.02 4.35


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

AutoCloner maintained by Alex Coulton.