Multiple sequence alignment - TraesCS3B01G107500

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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 TraesCS3B01G107500 chr3B 100.000 6901 0 0 1 6901 72933358 72940258 0.000000e+00 12744.0
1 TraesCS3B01G107500 chr3D 94.089 4974 173 41 708 5626 46552714 46557621 0.000000e+00 7444.0
2 TraesCS3B01G107500 chr3D 95.511 1292 44 4 5623 6901 46557645 46558935 0.000000e+00 2052.0
3 TraesCS3B01G107500 chr3D 90.354 508 48 1 187 694 46539284 46539790 0.000000e+00 665.0
4 TraesCS3B01G107500 chr3D 87.255 306 33 3 3736 4037 332631111 332630808 1.840000e-90 344.0
5 TraesCS3B01G107500 chr3A 93.704 4876 161 44 2100 6901 57960481 57955678 0.000000e+00 7169.0
6 TraesCS3B01G107500 chr3A 90.828 1352 62 18 777 2113 57961805 57960501 0.000000e+00 1753.0
7 TraesCS3B01G107500 chr3A 90.518 791 60 10 6 785 57962780 57961994 0.000000e+00 1031.0
8 TraesCS3B01G107500 chr7B 89.542 306 28 4 3736 4037 13823711 13823406 1.090000e-102 385.0
9 TraesCS3B01G107500 chr7B 86.032 315 36 6 3737 4045 616539803 616540115 1.430000e-86 331.0
10 TraesCS3B01G107500 chr7B 85.065 308 36 10 3737 4037 405063176 405062872 8.700000e-79 305.0
11 TraesCS3B01G107500 chr7B 89.222 167 14 2 2245 2407 147586614 147586448 9.070000e-49 206.0
12 TraesCS3B01G107500 chr5A 89.811 265 21 4 3754 4013 476664745 476665008 1.110000e-87 335.0
13 TraesCS3B01G107500 chr7D 84.194 310 39 10 3737 4039 148145171 148145477 6.770000e-75 292.0
14 TraesCS3B01G107500 chr1D 85.664 286 31 9 3737 4016 63558874 63559155 6.770000e-75 292.0
15 TraesCS3B01G107500 chr2D 89.140 221 18 4 2245 2461 196365211 196365429 3.170000e-68 270.0
16 TraesCS3B01G107500 chr2D 86.207 174 22 2 5734 5907 196365735 196365906 3.290000e-43 187.0
17 TraesCS3B01G107500 chr6A 89.222 167 14 2 2245 2407 576945102 576944936 9.070000e-49 206.0
18 TraesCS3B01G107500 chrUn 88.024 167 16 2 2245 2407 50316819 50316653 1.960000e-45 195.0
19 TraesCS3B01G107500 chrUn 88.024 167 16 2 2245 2407 307457563 307457397 1.960000e-45 195.0
20 TraesCS3B01G107500 chr2B 88.462 52 6 0 454 505 795430851 795430902 5.780000e-06 63.9


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 TraesCS3B01G107500 chr3B 72933358 72940258 6900 False 12744.000000 12744 100.000000 1 6901 1 chr3B.!!$F1 6900
1 TraesCS3B01G107500 chr3D 46552714 46558935 6221 False 4748.000000 7444 94.800000 708 6901 2 chr3D.!!$F2 6193
2 TraesCS3B01G107500 chr3D 46539284 46539790 506 False 665.000000 665 90.354000 187 694 1 chr3D.!!$F1 507
3 TraesCS3B01G107500 chr3A 57955678 57962780 7102 True 3317.666667 7169 91.683333 6 6901 3 chr3A.!!$R1 6895
4 TraesCS3B01G107500 chr2D 196365211 196365906 695 False 228.500000 270 87.673500 2245 5907 2 chr2D.!!$F1 3662

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
154 155 0.752009 AGCTCCCATCTGCAGCAATG 60.752 55.000 9.47 8.68 35.46 2.82 F
1517 1741 0.456628 GCGTCTCTAACTGACCCCTC 59.543 60.000 0.00 0.00 0.00 4.30 F
3273 3548 0.197661 TTTAGGGGAAGGTGAGGGGT 59.802 55.000 0.00 0.00 0.00 4.95 F
3463 3750 0.250901 AGCTGCCATTGTTTCCGAGT 60.251 50.000 0.00 0.00 0.00 4.18 F
5063 5378 1.201880 GTTCGGAGTACCACCTCTGTC 59.798 57.143 5.39 0.00 38.69 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 1900 0.041833 TGGAAGAGGAGGAGAGGTGG 59.958 60.0 0.00 0.0 0.00 4.61 R
3514 3801 0.620556 CCACAAGCCTAGTCATGGGT 59.379 55.0 0.00 0.0 36.81 4.51 R
5251 5566 0.165944 CGTTACTTTGCTTCTGCCCG 59.834 55.0 0.00 0.0 38.71 6.13 R
5301 5616 0.176680 CAAGGAGTCCATGTCCTCGG 59.823 60.0 12.86 0.0 44.17 4.63 R
6787 7225 0.941542 TGCGCTCTTTTGCTTACGTT 59.058 45.0 9.73 0.0 0.00 3.99 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
27 28 6.407475 AAATGCATAAAAGGAAATTCGTGC 57.593 33.333 0.00 0.00 0.00 5.34
37 38 8.831715 AAAAGGAAATTCGTGCTTAATTTGAT 57.168 26.923 8.35 0.00 36.82 2.57
43 44 7.624360 AATTCGTGCTTAATTTGATAGTGGA 57.376 32.000 0.00 0.00 0.00 4.02
49 50 7.205297 GTGCTTAATTTGATAGTGGATGCATT 58.795 34.615 0.00 0.00 0.00 3.56
64 65 6.016024 GTGGATGCATTCTTATGGAGCATTTA 60.016 38.462 6.53 0.00 45.08 1.40
65 66 6.550481 TGGATGCATTCTTATGGAGCATTTAA 59.450 34.615 6.53 0.00 45.08 1.52
100 101 1.961793 TTATGCATTCAGGGCCGTAC 58.038 50.000 3.54 0.00 0.00 3.67
146 147 1.863267 CGAAGCTAAGCTCCCATCTG 58.137 55.000 0.00 0.00 38.25 2.90
154 155 0.752009 AGCTCCCATCTGCAGCAATG 60.752 55.000 9.47 8.68 35.46 2.82
167 168 2.555757 GCAGCAATGGAAAGTTCTCTGT 59.444 45.455 0.00 0.00 0.00 3.41
173 174 3.093717 TGGAAAGTTCTCTGTGACGAC 57.906 47.619 0.00 0.00 0.00 4.34
185 186 2.355837 GACGACGCTCAGGCAACA 60.356 61.111 0.00 0.00 38.60 3.33
225 226 1.300620 CTCCTGGACAAACGTCGCA 60.301 57.895 0.00 0.00 33.96 5.10
234 235 2.277084 ACAAACGTCGCAGAGAACTTT 58.723 42.857 0.00 0.00 36.95 2.66
235 236 3.450578 ACAAACGTCGCAGAGAACTTTA 58.549 40.909 0.00 0.00 36.95 1.85
237 238 3.366440 AACGTCGCAGAGAACTTTAGT 57.634 42.857 0.00 0.00 36.95 2.24
276 277 1.673033 CGTGAAGGCCGAGAAGTTGAT 60.673 52.381 0.00 0.00 0.00 2.57
322 323 4.497291 TCCTGTGGTGTTCTTGTACTTT 57.503 40.909 0.00 0.00 0.00 2.66
328 329 2.691011 GGTGTTCTTGTACTTTTGGGCA 59.309 45.455 0.00 0.00 0.00 5.36
410 411 7.036425 TCCTATCTTTTAATTAGTTGGGGTGGT 60.036 37.037 0.00 0.00 0.00 4.16
444 445 1.102154 TGCTGTTTGTGGGTGTTGAG 58.898 50.000 0.00 0.00 0.00 3.02
488 489 4.038642 GCTTCATTAATAAAATGGGGCGGA 59.961 41.667 0.00 0.00 0.00 5.54
489 490 5.452636 GCTTCATTAATAAAATGGGGCGGAA 60.453 40.000 0.00 0.00 0.00 4.30
512 513 6.514012 AGGAAACCCCTTTCATTCAATTTT 57.486 33.333 0.00 0.00 44.85 1.82
513 514 6.910191 AGGAAACCCCTTTCATTCAATTTTT 58.090 32.000 0.00 0.00 44.85 1.94
892 1101 5.172687 TCAGCCCATGTGTTTATTACTCA 57.827 39.130 0.00 0.00 34.98 3.41
955 1165 3.741476 CAAGGCAAGGACGCTGGC 61.741 66.667 0.00 0.00 39.56 4.85
1102 1313 1.608154 GCCAGGTTCCCCTTCCTAC 59.392 63.158 0.00 0.00 39.89 3.18
1160 1371 3.188100 TTGCGGCTGCTCGAATCG 61.188 61.111 20.27 0.00 43.34 3.34
1161 1372 3.641159 TTGCGGCTGCTCGAATCGA 62.641 57.895 20.27 4.91 43.34 3.59
1162 1373 2.885644 GCGGCTGCTCGAATCGAA 60.886 61.111 11.21 0.00 38.39 3.71
1163 1374 2.240500 GCGGCTGCTCGAATCGAAT 61.241 57.895 11.21 0.00 38.39 3.34
1164 1375 1.849306 CGGCTGCTCGAATCGAATC 59.151 57.895 6.84 2.23 34.74 2.52
1223 1434 6.849811 CGTTGATGAGTGATAGAATCATTTGC 59.150 38.462 0.00 0.00 42.04 3.68
1246 1457 1.823610 GAGAACGGGCTGGTAGTTAGT 59.176 52.381 0.00 0.00 0.00 2.24
1247 1458 3.019564 GAGAACGGGCTGGTAGTTAGTA 58.980 50.000 0.00 0.00 0.00 1.82
1248 1459 2.757314 AGAACGGGCTGGTAGTTAGTAC 59.243 50.000 0.00 0.00 0.00 2.73
1457 1681 6.200808 TGATGCATTGTCACAATAATTAGCG 58.799 36.000 1.72 0.00 0.00 4.26
1500 1724 6.641314 CACATAGGGTTAGTTATGTTAGAGCG 59.359 42.308 0.00 0.00 38.18 5.03
1517 1741 0.456628 GCGTCTCTAACTGACCCCTC 59.543 60.000 0.00 0.00 0.00 4.30
1529 1753 3.641906 ACTGACCCCTCATAATCGGTTAG 59.358 47.826 0.00 0.00 37.84 2.34
1542 1766 9.543231 TCATAATCGGTTAGGAGGAGTATAAAT 57.457 33.333 0.00 0.00 0.00 1.40
1564 1788 8.897872 AAATTCACGTTTTCTCCTCTAAAGTA 57.102 30.769 0.00 0.00 0.00 2.24
1571 1795 7.028361 CGTTTTCTCCTCTAAAGTACACCTAG 58.972 42.308 0.00 0.00 0.00 3.02
1641 1865 3.255725 CCGCGACCTTTAAACATACTCA 58.744 45.455 8.23 0.00 0.00 3.41
1643 1867 3.306166 CGCGACCTTTAAACATACTCAGG 59.694 47.826 0.00 0.00 0.00 3.86
1652 1876 2.365635 ATACTCAGGCGCCCACCT 60.366 61.111 26.15 0.00 42.30 4.00
1675 1899 3.418047 CGGAGTAAAAATTCCCCACACT 58.582 45.455 0.00 0.00 0.00 3.55
1676 1900 3.439129 CGGAGTAAAAATTCCCCACACTC 59.561 47.826 0.00 0.00 0.00 3.51
1679 1903 4.149598 AGTAAAAATTCCCCACACTCCAC 58.850 43.478 0.00 0.00 0.00 4.02
1700 1924 2.628021 CCTCTCCTCCTCTTCCATTCCA 60.628 54.545 0.00 0.00 0.00 3.53
1802 2033 6.333416 GGCCATTTTAAGTGAAGAAATCTCC 58.667 40.000 0.00 0.00 0.00 3.71
1822 2053 6.002704 TCTCCGAGTTTTAAGTGAGTCTAGT 58.997 40.000 0.00 0.00 0.00 2.57
1864 2095 2.234908 ACTGGACAGTGGTCTGCTAATC 59.765 50.000 3.82 0.00 44.77 1.75
1876 2107 5.993441 TGGTCTGCTAATCATATGATGTGTG 59.007 40.000 18.85 10.19 34.49 3.82
1887 2119 7.920160 TCATATGATGTGTGCTTTAAGTTCA 57.080 32.000 0.00 0.00 0.00 3.18
1892 2124 6.671190 TGATGTGTGCTTTAAGTTCAAGATG 58.329 36.000 0.85 0.00 0.00 2.90
1932 2165 5.291971 GGTGATCTTTTGACTGTGCAAATT 58.708 37.500 0.00 0.00 37.57 1.82
1934 2167 5.978919 GTGATCTTTTGACTGTGCAAATTCA 59.021 36.000 0.00 0.00 37.57 2.57
1944 2178 7.884257 TGACTGTGCAAATTCATCATTCTTAA 58.116 30.769 0.00 0.00 0.00 1.85
1947 2181 9.715121 ACTGTGCAAATTCATCATTCTTAAATT 57.285 25.926 0.00 0.00 0.00 1.82
2016 2250 6.037610 ACTCACTTCATTCTTCAACAGTGAAC 59.962 38.462 0.00 0.00 39.99 3.18
2037 2271 4.679373 CCAGTAGGTGCAGAATACTGAT 57.321 45.455 24.30 0.00 46.01 2.90
2104 2338 6.927416 TGTAGCGACCTAACTTATTCTTTGA 58.073 36.000 0.00 0.00 0.00 2.69
2110 2344 8.662141 GCGACCTAACTTATTCTTTGAATACAA 58.338 33.333 0.11 0.00 0.00 2.41
2333 2600 7.667635 TCAGTACTACATCTATGAGAATGGAGG 59.332 40.741 0.00 0.00 29.45 4.30
2384 2655 6.867662 ACTTACAAGTTCATCTGGTTCAAG 57.132 37.500 0.00 0.00 35.21 3.02
2400 2671 7.388776 TCTGGTTCAAGTTTCTCAATGTATCAG 59.611 37.037 0.00 0.00 0.00 2.90
2428 2699 4.207891 GTGTGATCTTACACCCATGTCT 57.792 45.455 5.24 0.00 43.94 3.41
2680 2952 8.880878 ACAGTGTTGTAGTTTTGTTTTTCTTT 57.119 26.923 0.00 0.00 35.25 2.52
2759 3031 8.192110 GTCTTTGTAACAGTTGGTATTGGAAAA 58.808 33.333 0.00 0.00 0.00 2.29
3214 3489 6.925610 TGCTACATTACAGCAAATAGAAGG 57.074 37.500 0.00 0.00 45.71 3.46
3272 3547 0.919710 CTTTAGGGGAAGGTGAGGGG 59.080 60.000 0.00 0.00 0.00 4.79
3273 3548 0.197661 TTTAGGGGAAGGTGAGGGGT 59.802 55.000 0.00 0.00 0.00 4.95
3274 3549 1.103811 TTAGGGGAAGGTGAGGGGTA 58.896 55.000 0.00 0.00 0.00 3.69
3315 3602 1.232621 TGCTGAGCACTGACACATGC 61.233 55.000 1.40 0.00 42.39 4.06
3463 3750 0.250901 AGCTGCCATTGTTTCCGAGT 60.251 50.000 0.00 0.00 0.00 4.18
3514 3801 3.882888 CAGAACCTGTTAGCAAAGGTCAA 59.117 43.478 0.00 0.00 46.29 3.18
3537 3824 1.278985 CATGACTAGGCTTGTGGGACA 59.721 52.381 6.27 0.00 0.00 4.02
3718 4005 5.008118 GCTCTTTTGATACCAAGGCATAGAC 59.992 44.000 0.00 0.00 33.23 2.59
3802 4089 3.967987 ACAGATTATGGGGTGGAGTAGAC 59.032 47.826 0.00 0.00 0.00 2.59
4008 4298 6.686630 TGTGGACAAATTTCGAATGCTAAAT 58.313 32.000 0.00 0.00 0.00 1.40
4031 4321 3.194968 GTCCACTTATTTGAGGACGGAGA 59.805 47.826 0.00 0.00 40.89 3.71
4296 4593 3.877508 ACTCTTCGAACCCAACAAAAGAG 59.122 43.478 0.00 8.06 43.29 2.85
4392 4689 6.647229 TGATGTTGCTCATGAATCTTCTACT 58.353 36.000 0.00 0.00 36.83 2.57
4464 4761 5.774690 TGATTCCTCTTGTTGCCATTTACTT 59.225 36.000 0.00 0.00 0.00 2.24
4525 4822 3.753797 GAGAGTCAAACCCATTTGGAGAC 59.246 47.826 0.00 1.46 44.61 3.36
4546 4843 6.426587 AGACCTATGTGCCAATTATTGTCTT 58.573 36.000 4.15 0.00 0.00 3.01
4590 4887 8.973835 TTAAGTTGGTTTTGACAGTGTTTAAG 57.026 30.769 0.00 0.00 0.00 1.85
4685 4982 3.564644 GGAGATCATGTGATTGGAAGCAG 59.435 47.826 0.00 0.00 34.37 4.24
4728 5025 3.802948 TCTTAAAGGCTAGAGGAAGCG 57.197 47.619 0.00 0.00 43.74 4.68
4925 5222 1.555075 TGTAGCCTGATTCTGGGTGTC 59.445 52.381 20.68 14.62 35.06 3.67
5063 5378 1.201880 GTTCGGAGTACCACCTCTGTC 59.798 57.143 5.39 0.00 38.69 3.51
5091 5406 6.509418 TGTTTCCTTATACAGCCACATTTC 57.491 37.500 0.00 0.00 0.00 2.17
5301 5616 6.541641 AGTTCTGATGAATATGAAGAGGCAAC 59.458 38.462 0.00 0.00 34.40 4.17
5566 5882 4.247267 TGTAAACACTACTTCCCTCGTG 57.753 45.455 0.00 0.00 0.00 4.35
5603 5919 4.469227 GGACATCAGGGCAGACATATCTAT 59.531 45.833 0.00 0.00 32.25 1.98
5655 6002 5.694910 ACCAACGGTGATAAGCGATTATTAG 59.305 40.000 9.06 2.69 32.98 1.73
5702 6108 8.441312 AAGCATGTTTTTCATTGATCAGTTTT 57.559 26.923 0.00 0.00 34.09 2.43
5768 6174 8.842358 TTCTTACACCAAATATTCGACTTTCT 57.158 30.769 0.00 0.00 0.00 2.52
6191 6601 0.896923 TTGGCATGGTTGATTGAGGC 59.103 50.000 0.00 0.00 0.00 4.70
6213 6623 4.811557 GCGTAACTTCTTCTATGCAGGATT 59.188 41.667 0.00 0.00 31.58 3.01
6299 6709 3.562557 GCAGTAAAGGTTCTGTTTCCGAA 59.437 43.478 0.00 0.00 34.57 4.30
6301 6711 5.410439 GCAGTAAAGGTTCTGTTTCCGAATA 59.590 40.000 0.00 0.00 34.57 1.75
6346 6757 6.477253 TGCATGTAGGAAACCTATTGTGTAA 58.523 36.000 0.00 0.00 38.48 2.41
6471 6883 3.222603 ACGACCTGGAATTGCTCTTTTT 58.777 40.909 0.00 0.00 0.00 1.94
6537 6949 8.421249 TTTAAACCTGTGGATCTTTGATCATT 57.579 30.769 0.00 0.00 0.00 2.57
6538 6950 6.923199 AAACCTGTGGATCTTTGATCATTT 57.077 33.333 0.00 0.00 0.00 2.32
6694 7124 2.224426 TGGCATTTGACCGACAACTACT 60.224 45.455 0.00 0.00 38.29 2.57
6736 7174 4.469586 TGGATTGATGTAGAACAGTAGCCA 59.530 41.667 0.00 0.00 0.00 4.75
6787 7225 2.725637 TGGACGTGCCACTATACTACA 58.274 47.619 4.04 0.00 43.33 2.74
6795 7233 4.501921 GTGCCACTATACTACAACGTAAGC 59.498 45.833 0.00 0.00 45.62 3.09
6796 7234 4.158209 TGCCACTATACTACAACGTAAGCA 59.842 41.667 0.00 0.00 45.62 3.91
6804 7242 2.663279 ACAACGTAAGCAAAAGAGCG 57.337 45.000 0.00 0.00 45.62 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.543868 CACGAATTTCCTTTTATGCATTTACCA 59.456 33.333 3.54 0.00 0.00 3.25
1 2 7.464045 GCACGAATTTCCTTTTATGCATTTACC 60.464 37.037 3.54 0.00 0.00 2.85
2 3 7.275560 AGCACGAATTTCCTTTTATGCATTTAC 59.724 33.333 3.54 0.00 34.27 2.01
3 4 7.319646 AGCACGAATTTCCTTTTATGCATTTA 58.680 30.769 3.54 0.00 34.27 1.40
4 5 6.165577 AGCACGAATTTCCTTTTATGCATTT 58.834 32.000 3.54 0.00 34.27 2.32
21 22 6.458206 GCATCCACTATCAAATTAAGCACGAA 60.458 38.462 0.00 0.00 0.00 3.85
22 23 5.007626 GCATCCACTATCAAATTAAGCACGA 59.992 40.000 0.00 0.00 0.00 4.35
37 38 4.102996 TGCTCCATAAGAATGCATCCACTA 59.897 41.667 0.00 0.00 0.00 2.74
43 44 9.841295 ATTTTTAAATGCTCCATAAGAATGCAT 57.159 25.926 0.00 0.00 44.86 3.96
92 93 1.988406 ACTTCTCCAGGTACGGCCC 60.988 63.158 0.00 0.00 38.26 5.80
100 101 3.480470 ACACATTTGACACTTCTCCAGG 58.520 45.455 0.00 0.00 0.00 4.45
146 147 2.555757 ACAGAGAACTTTCCATTGCTGC 59.444 45.455 0.00 0.00 0.00 5.25
154 155 2.052157 CGTCGTCACAGAGAACTTTCC 58.948 52.381 0.00 0.00 0.00 3.13
167 168 2.355837 GTTGCCTGAGCGTCGTCA 60.356 61.111 0.00 0.00 44.31 4.35
173 174 0.936297 GCAAAAGTGTTGCCTGAGCG 60.936 55.000 6.78 0.00 44.31 5.03
225 226 3.100671 AGGCGATCCACTAAAGTTCTCT 58.899 45.455 0.00 0.00 33.74 3.10
234 235 1.133482 TCATCTCCAGGCGATCCACTA 60.133 52.381 0.00 0.00 33.74 2.74
235 236 0.397675 TCATCTCCAGGCGATCCACT 60.398 55.000 0.00 0.00 33.74 4.00
237 238 0.972134 GATCATCTCCAGGCGATCCA 59.028 55.000 0.00 0.00 33.74 3.41
322 323 8.760980 AGCTAGTTATTTTATTACATGCCCAA 57.239 30.769 0.00 0.00 0.00 4.12
342 343 8.470805 TCTCTCAAACCAAAGTATTAGAGCTAG 58.529 37.037 0.00 0.00 30.60 3.42
371 372 2.513753 AGATAGGATCCAGAGAGCACG 58.486 52.381 15.82 0.00 0.00 5.34
419 420 1.455587 CCCACAAACAGCACCCACT 60.456 57.895 0.00 0.00 0.00 4.00
420 421 1.756561 ACCCACAAACAGCACCCAC 60.757 57.895 0.00 0.00 0.00 4.61
444 445 3.814945 CGAAATCAGAAACCAGAGTTGC 58.185 45.455 0.00 0.00 35.97 4.17
604 607 5.627367 CAGTCTTTCTACAGAAGTCTTGTCG 59.373 44.000 0.00 0.00 35.21 4.35
892 1101 9.326413 CGAATAAAATGGTACTGAAGGATAGTT 57.674 33.333 0.00 0.00 0.00 2.24
1223 1434 1.313812 ACTACCAGCCCGTTCTCGAG 61.314 60.000 5.93 5.93 39.71 4.04
1246 1457 6.409234 CCCTGATGTCCCTAAATTTGCTAGTA 60.409 42.308 0.00 0.00 0.00 1.82
1247 1458 5.440610 CCTGATGTCCCTAAATTTGCTAGT 58.559 41.667 0.00 0.00 0.00 2.57
1248 1459 4.823989 CCCTGATGTCCCTAAATTTGCTAG 59.176 45.833 0.00 0.00 0.00 3.42
1457 1681 5.845391 ATGTGCTCTCTTAGACTCTTACC 57.155 43.478 0.00 0.00 0.00 2.85
1500 1724 5.278561 CGATTATGAGGGGTCAGTTAGAGAC 60.279 48.000 0.00 0.00 35.29 3.36
1509 1733 2.969950 CCTAACCGATTATGAGGGGTCA 59.030 50.000 0.00 0.00 30.99 4.02
1512 1736 2.567615 CCTCCTAACCGATTATGAGGGG 59.432 54.545 12.00 0.00 43.98 4.79
1529 1753 7.011202 GGAGAAAACGTGAATTTATACTCCTCC 59.989 40.741 0.00 0.00 35.71 4.30
1542 1766 6.698766 GTGTACTTTAGAGGAGAAAACGTGAA 59.301 38.462 0.00 0.00 0.00 3.18
1564 1788 1.875488 ATAAGGGTTCGGCTAGGTGT 58.125 50.000 0.00 0.00 0.00 4.16
1571 1795 2.028420 AACGGTTATAAGGGTTCGGC 57.972 50.000 0.00 0.00 0.00 5.54
1675 1899 0.336737 GGAAGAGGAGGAGAGGTGGA 59.663 60.000 0.00 0.00 0.00 4.02
1676 1900 0.041833 TGGAAGAGGAGGAGAGGTGG 59.958 60.000 0.00 0.00 0.00 4.61
1679 1903 2.046292 GGAATGGAAGAGGAGGAGAGG 58.954 57.143 0.00 0.00 0.00 3.69
1802 2033 6.696148 ACACAACTAGACTCACTTAAAACTCG 59.304 38.462 0.00 0.00 0.00 4.18
1822 2053 5.287274 CAGTGTTTACGCAAAATCAACACAA 59.713 36.000 14.14 0.00 46.37 3.33
1864 2095 8.453320 TCTTGAACTTAAAGCACACATCATATG 58.547 33.333 0.00 0.00 0.00 1.78
1886 2118 4.453478 CCGGGTGATTATCATGACATCTTG 59.547 45.833 14.84 5.35 0.00 3.02
1887 2119 4.505566 CCCGGGTGATTATCATGACATCTT 60.506 45.833 14.18 0.00 0.00 2.40
1892 2124 2.930826 ACCCGGGTGATTATCATGAC 57.069 50.000 29.69 0.00 0.00 3.06
1914 2146 6.146601 TGATGAATTTGCACAGTCAAAAGA 57.853 33.333 7.12 0.00 39.13 2.52
1947 2181 8.349245 CCAAACTCTGTATAACACAATCAACAA 58.651 33.333 0.00 0.00 36.48 2.83
1952 2186 8.492673 TCATCCAAACTCTGTATAACACAATC 57.507 34.615 0.00 0.00 36.48 2.67
1990 2224 6.816136 TCACTGTTGAAGAATGAAGTGAGTA 58.184 36.000 0.00 0.00 39.17 2.59
2016 2250 4.100035 TGATCAGTATTCTGCACCTACTGG 59.900 45.833 18.47 6.98 41.61 4.00
2084 2318 8.193250 TGTATTCAAAGAATAAGTTAGGTCGC 57.807 34.615 1.35 0.00 0.00 5.19
2333 2600 5.220416 GCATCTGAAGTCCATAACACGTAAC 60.220 44.000 0.00 0.00 0.00 2.50
2384 2655 7.041780 ACACAAGACACTGATACATTGAGAAAC 60.042 37.037 0.00 0.00 0.00 2.78
2400 2671 4.742440 TGGGTGTAAGATCACACAAGACAC 60.742 45.833 15.82 8.65 46.72 3.67
2428 2699 4.953579 GGTTCCTTGCCCTGTTTGAATATA 59.046 41.667 0.00 0.00 0.00 0.86
2651 2923 8.736751 AAAAACAAAACTACAACACTGTACTG 57.263 30.769 0.00 0.00 36.96 2.74
2680 2952 5.727630 AGATAGCCTGGACCCTTTCTATAA 58.272 41.667 0.00 0.00 0.00 0.98
3214 3489 6.855914 TGTGAAGTTCTCGATTTGCATTTTAC 59.144 34.615 4.17 0.00 0.00 2.01
3315 3602 5.129485 AGACAACACACCAGATAATCCCTAG 59.871 44.000 0.00 0.00 0.00 3.02
3463 3750 1.144708 TGCCAGTCCCAAAGATCAACA 59.855 47.619 0.00 0.00 0.00 3.33
3514 3801 0.620556 CCACAAGCCTAGTCATGGGT 59.379 55.000 0.00 0.00 36.81 4.51
3718 4005 6.042897 AGGGAGTATATTAGGAAGGAAAACCG 59.957 42.308 0.00 0.00 0.00 4.44
3802 4089 0.609151 TGCACCTTCCCAATGCATTG 59.391 50.000 28.91 28.91 44.17 2.82
3959 4249 3.450457 AGAGTGTGCTTCTATCTTCCCAG 59.550 47.826 0.00 0.00 0.00 4.45
4031 4321 8.732746 TTCAGCAAAAGAAACTTACTTACTCT 57.267 30.769 0.00 0.00 0.00 3.24
4128 4425 8.823818 CAAAGAACAGCAGAAATTTTTCTTCAT 58.176 29.630 11.70 0.00 44.70 2.57
4143 4440 4.734398 AATTGTCAACCAAAGAACAGCA 57.266 36.364 0.00 0.00 36.44 4.41
4296 4593 2.808906 ATAGGTCAGGAAAAGCCCAC 57.191 50.000 0.00 0.00 37.37 4.61
4392 4689 0.178992 CAGCTGAAACACCTTCCCCA 60.179 55.000 8.42 0.00 32.53 4.96
4525 4822 5.163530 TGCAAGACAATAATTGGCACATAGG 60.164 40.000 0.00 0.00 42.71 2.57
4590 4887 9.065871 CACTAATAAGCTGAAAATAGCACAAAC 57.934 33.333 0.00 0.00 46.07 2.93
4728 5025 4.997395 TCACTAGACAAAGGAAGCATTGAC 59.003 41.667 0.00 0.00 0.00 3.18
4780 5077 6.372103 TCAAACCTCTTGAGTTTAACGTTTGA 59.628 34.615 5.91 17.88 43.12 2.69
4782 5079 6.746745 TCAAACCTCTTGAGTTTAACGTTT 57.253 33.333 5.91 0.00 35.71 3.60
4834 5131 3.183574 GGAAAGCGTTGTTGGCATAAAAC 59.816 43.478 0.00 0.00 0.00 2.43
4849 5146 9.450807 AATAAAATTCTAATTCGATGGAAAGCG 57.549 29.630 0.00 0.00 35.40 4.68
4925 5222 9.800433 TTCAACCATGCATATACATTGTTTAAG 57.200 29.630 0.00 0.00 34.64 1.85
5063 5378 5.123186 TGTGGCTGTATAAGGAAACAATTCG 59.877 40.000 0.00 0.00 36.36 3.34
5251 5566 0.165944 CGTTACTTTGCTTCTGCCCG 59.834 55.000 0.00 0.00 38.71 6.13
5301 5616 0.176680 CAAGGAGTCCATGTCCTCGG 59.823 60.000 12.86 0.00 44.17 4.63
5356 5671 2.172505 TCTCTTGGCAGACTTCAAACCA 59.827 45.455 0.00 0.00 0.00 3.67
5603 5919 9.146984 CAGAAACGTAGGAAATATGTTACTTCA 57.853 33.333 0.00 0.00 41.75 3.02
5779 6185 9.981114 CTCCCTAAACAAGTTTGACAATAAAAT 57.019 29.630 8.37 0.00 34.23 1.82
5978 6384 9.679661 TTTGGTGCATTCTCACTATCTTATTAA 57.320 29.630 0.00 0.00 37.16 1.40
6027 6433 2.292103 AAGATGCGTGAGAGAAGCTC 57.708 50.000 0.00 0.00 44.21 4.09
6191 6601 5.235186 CCAATCCTGCATAGAAGAAGTTACG 59.765 44.000 0.00 0.00 0.00 3.18
6213 6623 4.632327 TGACCATGAATCTGTTACACCA 57.368 40.909 0.00 0.00 0.00 4.17
6299 6709 9.019656 TGCAGTACAGGACAAATTAAACATTAT 57.980 29.630 0.00 0.00 0.00 1.28
6301 6711 7.283625 TGCAGTACAGGACAAATTAAACATT 57.716 32.000 0.00 0.00 0.00 2.71
6579 6998 1.303309 TCCTAGCGCCTCGTAAGTAC 58.697 55.000 2.29 0.00 39.48 2.73
6675 7102 3.496884 TGAAGTAGTTGTCGGTCAAATGC 59.503 43.478 0.00 0.00 37.81 3.56
6736 7174 5.066505 CCGCTCTAGCATTTTTATGAACCTT 59.933 40.000 2.44 0.00 42.21 3.50
6787 7225 0.941542 TGCGCTCTTTTGCTTACGTT 59.058 45.000 9.73 0.00 0.00 3.99
6795 7233 1.137404 CCCCGAATGCGCTCTTTTG 59.863 57.895 9.73 3.80 35.83 2.44
6796 7234 1.303317 ACCCCGAATGCGCTCTTTT 60.303 52.632 9.73 0.00 35.83 2.27
6804 7242 3.983044 ATCCTATTAGACCCCGAATGC 57.017 47.619 0.00 0.00 0.00 3.56
6856 7294 4.562082 TGTCCAAGGTACTAATTCACACG 58.438 43.478 0.00 0.00 38.49 4.49


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

AutoCloner maintained by Alex Coulton.