Multiple sequence alignment - TraesCS4D01G013900

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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 TraesCS4D01G013900 chr4D 100.000 5159 0 0 1 5159 6491054 6496212 0.000000e+00 9527
1 TraesCS4D01G013900 chr4A 95.702 2443 78 10 2731 5159 596921571 596919142 0.000000e+00 3904
2 TraesCS4D01G013900 chr4A 85.656 739 73 16 1963 2694 596922518 596921806 0.000000e+00 747
3 TraesCS4D01G013900 chr4A 94.004 467 26 1 1127 1593 596923374 596922910 0.000000e+00 706
4 TraesCS4D01G013900 chr4A 92.800 375 16 8 772 1135 596924045 596923671 2.730000e-147 532
5 TraesCS4D01G013900 chr4A 90.520 327 23 3 1649 1967 596922894 596922568 4.770000e-115 425
6 TraesCS4D01G013900 chr4B 88.427 3275 224 45 689 3862 11671830 11675050 0.000000e+00 3805
7 TraesCS4D01G013900 chr4B 92.264 711 43 6 1 701 11668279 11668987 0.000000e+00 998
8 TraesCS4D01G013900 chr4B 86.790 810 72 13 3856 4658 11675306 11676087 0.000000e+00 870
9 TraesCS4D01G013900 chr4B 92.702 507 28 6 4657 5159 11676116 11676617 0.000000e+00 723
10 TraesCS4D01G013900 chr4B 79.412 238 24 5 632 862 646186341 646186122 1.500000e-30 145
11 TraesCS4D01G013900 chr5B 82.833 233 15 12 636 863 530653383 530653595 8.820000e-43 185
12 TraesCS4D01G013900 chr5B 80.258 233 24 6 634 862 15277902 15277688 6.920000e-34 156
13 TraesCS4D01G013900 chr5B 91.818 110 9 0 753 862 639784221 639784112 2.490000e-33 154
14 TraesCS4D01G013900 chr2B 82.328 232 17 5 637 864 49080656 49080445 4.100000e-41 180
15 TraesCS4D01G013900 chr5D 82.589 224 16 11 646 864 35562226 35562021 5.310000e-40 176
16 TraesCS4D01G013900 chr7D 81.624 234 19 9 635 864 91749070 91748857 6.870000e-39 172
17 TraesCS4D01G013900 chr7D 81.385 231 19 5 638 864 80797957 80797747 3.200000e-37 167
18 TraesCS4D01G013900 chr7D 81.333 225 19 9 636 856 91387164 91387369 1.490000e-35 161
19 TraesCS4D01G013900 chr7D 91.071 112 10 0 753 864 168292966 168293077 8.950000e-33 152
20 TraesCS4D01G013900 chr7D 90.909 110 10 0 753 862 500257504 500257613 1.160000e-31 148
21 TraesCS4D01G013900 chrUn 80.508 236 24 5 632 864 91866458 91866674 1.490000e-35 161
22 TraesCS4D01G013900 chrUn 80.258 233 24 6 634 862 344216357 344216143 6.920000e-34 156
23 TraesCS4D01G013900 chrUn 80.258 233 24 6 634 862 471140614 471140828 6.920000e-34 156
24 TraesCS4D01G013900 chr1B 90.909 110 10 0 753 862 394913498 394913607 1.160000e-31 148
25 TraesCS4D01G013900 chr3B 88.281 128 8 4 633 754 92662570 92662696 4.160000e-31 147


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 TraesCS4D01G013900 chr4D 6491054 6496212 5158 False 9527.0 9527 100.00000 1 5159 1 chr4D.!!$F1 5158
1 TraesCS4D01G013900 chr4A 596919142 596924045 4903 True 1262.8 3904 91.73640 772 5159 5 chr4A.!!$R1 4387
2 TraesCS4D01G013900 chr4B 11668279 11676617 8338 False 1599.0 3805 90.04575 1 5159 4 chr4B.!!$F1 5158

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
606 612 0.030705 AGCTAGGGAATGAGCCTCCA 60.031 55.0 0.00 0.00 39.65 3.86 F
2105 5365 0.041400 TGTCGTGTGCTTTTCATGCG 60.041 50.0 0.00 0.00 0.00 4.73 F
2165 5425 0.247537 GGGTATAATAATGCGCGCGC 60.248 55.0 45.02 45.02 42.35 6.86 F
3494 6988 0.388659 TGTGTGGCATGAGTTTTGGC 59.611 50.0 0.00 0.00 39.89 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2390 5657 0.037590 AAATGGAACGCTGCCCAGTA 59.962 50.000 2.68 0.0 35.67 2.74 R
3061 6531 0.184451 ACATGCTGATCCCATCCACC 59.816 55.000 0.00 0.0 0.00 4.61 R
4123 7880 2.152016 GCTAGGTTTTCTCCGTGCTTT 58.848 47.619 0.00 0.0 0.00 3.51 R
4664 8485 0.805711 GCCACAGTTTGCAACACACC 60.806 55.000 0.00 0.0 0.00 4.16 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
66 67 3.680620 TTCGAGGGCATGGCTTCCG 62.681 63.158 23.14 19.84 0.00 4.30
164 165 0.035056 AGGACCCATGAAGGAAAGCG 60.035 55.000 0.00 0.00 41.22 4.68
167 168 0.035056 ACCCATGAAGGAAAGCGAGG 60.035 55.000 0.00 0.00 41.22 4.63
181 182 2.959484 CGAGGTGGGAGTGCATGGT 61.959 63.158 0.00 0.00 0.00 3.55
228 229 3.083349 TCCCGGAGCCTGTGGATG 61.083 66.667 0.73 0.00 0.00 3.51
249 250 0.249398 CCTACCCTTTCTGTCACCGG 59.751 60.000 0.00 0.00 0.00 5.28
253 254 1.371183 CCTTTCTGTCACCGGAGCA 59.629 57.895 9.46 1.69 0.00 4.26
255 256 0.671781 CTTTCTGTCACCGGAGCAGG 60.672 60.000 9.46 0.00 37.30 4.85
273 274 2.485426 CAGGCACACGATTGATTGTCTT 59.515 45.455 0.00 0.00 0.00 3.01
278 279 4.715896 CACACGATTGATTGTCTTTGAGG 58.284 43.478 0.00 0.00 0.00 3.86
314 315 2.104170 GAGAGGGAGATTCGTTGTCCT 58.896 52.381 4.77 0.00 37.90 3.85
316 317 0.905357 AGGGAGATTCGTTGTCCTGG 59.095 55.000 4.77 0.00 37.90 4.45
324 325 1.052124 TCGTTGTCCTGGGTCACCTT 61.052 55.000 0.00 0.00 37.76 3.50
374 375 1.608055 TCCAGGAATTGCACACACTG 58.392 50.000 0.00 0.00 0.00 3.66
379 380 2.158561 GAATTGCACACACTGGGGGC 62.159 60.000 0.00 0.00 0.00 5.80
401 407 0.106519 AGGGTGCAGTGAAGTGCTTT 60.107 50.000 11.22 0.00 44.32 3.51
409 415 5.639506 GTGCAGTGAAGTGCTTTAATCTCTA 59.360 40.000 11.22 0.00 44.32 2.43
447 453 1.871126 GCAGGTTTTGGCTCTGAGGC 61.871 60.000 22.95 22.95 41.77 4.70
456 462 0.179051 GGCTCTGAGGCAGATTGAGG 60.179 60.000 24.49 0.00 39.92 3.86
461 467 2.765135 TCTGAGGCAGATTGAGGAAGAG 59.235 50.000 0.00 0.00 35.39 2.85
464 470 0.254178 GGCAGATTGAGGAAGAGGCA 59.746 55.000 0.00 0.00 0.00 4.75
469 475 3.388676 CAGATTGAGGAAGAGGCAGAGAT 59.611 47.826 0.00 0.00 0.00 2.75
470 476 4.039339 AGATTGAGGAAGAGGCAGAGATT 58.961 43.478 0.00 0.00 0.00 2.40
558 564 5.072741 ACAGAACAGAAAGCCACACATAAT 58.927 37.500 0.00 0.00 0.00 1.28
560 566 4.460382 AGAACAGAAAGCCACACATAATGG 59.540 41.667 0.00 0.00 40.50 3.16
566 572 2.356135 AGCCACACATAATGGTCGAAC 58.644 47.619 0.00 0.00 39.63 3.95
567 573 1.062002 GCCACACATAATGGTCGAACG 59.938 52.381 0.00 0.00 39.63 3.95
569 575 1.663643 CACACATAATGGTCGAACGGG 59.336 52.381 0.00 0.00 0.00 5.28
606 612 0.030705 AGCTAGGGAATGAGCCTCCA 60.031 55.000 0.00 0.00 39.65 3.86
613 619 2.295885 GGAATGAGCCTCCACATTGAG 58.704 52.381 0.00 0.00 36.94 3.02
619 625 0.251354 GCCTCCACATTGAGCTCTCA 59.749 55.000 16.19 1.52 37.91 3.27
624 630 1.728971 CCACATTGAGCTCTCACGAAC 59.271 52.381 16.19 0.00 39.66 3.95
625 631 1.388093 CACATTGAGCTCTCACGAACG 59.612 52.381 16.19 0.00 39.66 3.95
635 641 0.600255 CTCACGAACGGGCAGAGTTT 60.600 55.000 0.00 0.00 31.14 2.66
703 3569 7.397192 ACAATTACAAGCTGATTTGGACCTAAT 59.603 33.333 0.35 0.35 32.32 1.73
707 3573 6.064717 ACAAGCTGATTTGGACCTAATATCC 58.935 40.000 0.82 0.00 36.70 2.59
804 3670 5.583061 ACACATTCTTCGCGGTATCAATTTA 59.417 36.000 6.13 0.00 0.00 1.40
895 3776 1.123861 TGAGCTCAGAGGGTGCACTT 61.124 55.000 13.74 5.37 38.46 3.16
974 3856 0.609131 CAGATCACCCGGCAAAACCT 60.609 55.000 0.00 0.00 35.61 3.50
1064 3951 2.197324 CTCCCCCTCCTCTCTCGG 59.803 72.222 0.00 0.00 0.00 4.63
1136 4328 0.257616 CTCCTCCTCCTCCTCGTCTT 59.742 60.000 0.00 0.00 0.00 3.01
1147 4339 0.452585 CCTCGTCTTCCTCTTCCGTC 59.547 60.000 0.00 0.00 0.00 4.79
1359 4553 0.474854 TGAGTGTGCCCCTTCCCTAA 60.475 55.000 0.00 0.00 0.00 2.69
1390 4584 1.430992 TTCTCCCTCGGTTCTTGGTT 58.569 50.000 0.00 0.00 0.00 3.67
1405 4599 2.639286 GTTTGGTCTGCGGTGCTG 59.361 61.111 0.00 0.00 0.00 4.41
1408 4602 0.323302 TTTGGTCTGCGGTGCTGATA 59.677 50.000 1.73 0.00 38.63 2.15
1414 4608 1.482182 TCTGCGGTGCTGATAGATTGT 59.518 47.619 0.00 0.00 31.90 2.71
1420 4614 4.825422 CGGTGCTGATAGATTGTATGGAT 58.175 43.478 0.00 0.00 0.00 3.41
1424 4618 5.704515 GTGCTGATAGATTGTATGGATGCTT 59.295 40.000 0.00 0.00 0.00 3.91
1462 4656 2.758327 ATGGTCTCCTACGCGGCA 60.758 61.111 12.47 0.00 0.00 5.69
1531 4725 1.758906 GAGAAGAGGTAGCCCGCCT 60.759 63.158 0.00 0.00 39.42 5.52
1624 4818 2.627945 CATTTTAGTGAGCCAGCGGTA 58.372 47.619 0.00 0.00 0.00 4.02
1654 4848 6.648725 ATGTACTACAGATTTCGTTTGCTC 57.351 37.500 0.00 0.00 0.00 4.26
1690 4884 0.319405 AACATTTTGCAGAGCCTGGC 59.681 50.000 11.65 11.65 31.21 4.85
1729 4923 1.879380 TGCGTGCAGAGCTACAATTTT 59.121 42.857 14.22 0.00 35.28 1.82
1738 4932 6.151648 TGCAGAGCTACAATTTTATGAGCTTT 59.848 34.615 0.00 0.00 43.39 3.51
1816 5010 5.862846 TCAGAATGAGAAGGATTCGGCAAAT 60.863 40.000 0.00 0.00 42.56 2.32
1849 5043 4.350368 TGACCATGCAACTTCACTCTTA 57.650 40.909 0.00 0.00 0.00 2.10
1885 5079 2.360165 CTGAAACTGGAGCTGCAACTTT 59.640 45.455 9.92 9.67 0.00 2.66
1904 5105 9.394767 GCAACTTTTAAATTGGGAATATGGAAT 57.605 29.630 4.22 0.00 0.00 3.01
1921 5122 4.081406 TGGAATGTTATGCAACTTGCTCT 58.919 39.130 14.78 5.19 45.31 4.09
1927 5128 1.882912 ATGCAACTTGCTCTTGTCGA 58.117 45.000 14.78 0.00 45.31 4.20
1942 5143 1.000607 TGTCGAGGTCAGCTGTGTAAC 60.001 52.381 14.67 3.98 37.35 2.50
1944 5145 1.269723 TCGAGGTCAGCTGTGTAACTG 59.730 52.381 14.67 0.00 38.04 3.16
2028 5285 5.304101 ACTCTTCAGAGAACTTGATCACTGT 59.696 40.000 10.93 0.00 44.74 3.55
2038 5295 4.392047 ACTTGATCACTGTTGCAGATTCA 58.608 39.130 0.00 0.87 35.18 2.57
2105 5365 0.041400 TGTCGTGTGCTTTTCATGCG 60.041 50.000 0.00 0.00 0.00 4.73
2164 5424 1.355971 AGGGTATAATAATGCGCGCG 58.644 50.000 28.44 28.44 36.07 6.86
2165 5425 0.247537 GGGTATAATAATGCGCGCGC 60.248 55.000 45.02 45.02 42.35 6.86
2195 5455 9.933723 CAAAGTAAGAAGGAAATGATGGAAAAT 57.066 29.630 0.00 0.00 0.00 1.82
2220 5481 0.968405 TTTGCTGCTGGGGTGATTTC 59.032 50.000 0.00 0.00 0.00 2.17
2241 5502 4.397420 TCCTGCATTGAAAGTTGAAGCTA 58.603 39.130 0.00 0.00 0.00 3.32
2243 5504 4.164294 CTGCATTGAAAGTTGAAGCTAGC 58.836 43.478 6.62 6.62 0.00 3.42
2247 5508 5.629097 CATTGAAAGTTGAAGCTAGCAGAG 58.371 41.667 18.83 0.00 0.00 3.35
2249 5510 5.157940 TGAAAGTTGAAGCTAGCAGAGAT 57.842 39.130 18.83 0.00 0.00 2.75
2250 5511 5.555017 TGAAAGTTGAAGCTAGCAGAGATT 58.445 37.500 18.83 0.95 36.16 2.40
2251 5512 5.410746 TGAAAGTTGAAGCTAGCAGAGATTG 59.589 40.000 18.83 0.00 32.64 2.67
2252 5513 3.871485 AGTTGAAGCTAGCAGAGATTGG 58.129 45.455 18.83 0.00 32.64 3.16
2253 5514 3.517100 AGTTGAAGCTAGCAGAGATTGGA 59.483 43.478 18.83 0.00 32.64 3.53
2254 5515 3.533606 TGAAGCTAGCAGAGATTGGAC 57.466 47.619 18.83 0.00 32.64 4.02
2255 5516 2.169352 TGAAGCTAGCAGAGATTGGACC 59.831 50.000 18.83 0.00 32.64 4.46
2256 5517 2.173126 AGCTAGCAGAGATTGGACCT 57.827 50.000 18.83 0.00 0.00 3.85
2288 5550 8.100791 TGAAGATACCTAAAAAGTGTGCATACT 58.899 33.333 10.73 10.73 0.00 2.12
2289 5551 7.849804 AGATACCTAAAAAGTGTGCATACTG 57.150 36.000 17.51 5.87 0.00 2.74
2305 5567 5.123820 TGCATACTGTAAAAGCTTGCCTTAG 59.876 40.000 0.00 0.00 36.64 2.18
2332 5594 1.798223 TCTTGACGTGCAATTCCTTCG 59.202 47.619 0.00 0.00 35.59 3.79
2349 5616 3.939592 CCTTCGAAGGTTCAGGGATAAAC 59.060 47.826 32.16 0.00 41.41 2.01
2360 5627 7.775561 AGGTTCAGGGATAAACTATAAAAGCAG 59.224 37.037 0.00 0.00 0.00 4.24
2366 5633 9.780186 AGGGATAAACTATAAAAGCAGTATCAC 57.220 33.333 0.00 0.00 0.00 3.06
2390 5657 2.578021 ACACATCACCCTTATCTGGCTT 59.422 45.455 0.00 0.00 0.00 4.35
2446 5713 2.494059 CTTTTTCTCCTGCTTGGACGA 58.506 47.619 0.00 0.00 40.56 4.20
2479 5746 3.133003 CCTCCACTTTGTCTCGACCATAT 59.867 47.826 0.00 0.00 0.00 1.78
2480 5747 4.115516 CTCCACTTTGTCTCGACCATATG 58.884 47.826 0.00 0.00 0.00 1.78
2515 5782 7.841956 TGGTTATGTTTTGTTTATACATGGGG 58.158 34.615 0.00 0.00 34.55 4.96
2518 5785 9.930693 GTTATGTTTTGTTTATACATGGGGAAA 57.069 29.630 0.00 0.00 34.55 3.13
2594 5862 4.106029 TGAACGGAGATCGACCTAAAAG 57.894 45.455 9.57 0.00 42.43 2.27
2659 5927 3.241995 GCTACGCGAAACAGTAGGAATTG 60.242 47.826 15.93 0.00 40.32 2.32
2698 6150 9.502091 TTTCATGCTAGTAAGTTACTGATTTGT 57.498 29.630 23.14 4.26 39.81 2.83
2758 6225 5.583061 TGTTAACTGTGGTGTAGACACTTTG 59.417 40.000 12.32 4.08 45.73 2.77
2870 6337 8.296713 AGAATTTCGCAGAAGTTTGCTTAATTA 58.703 29.630 7.94 0.00 45.90 1.40
2948 6415 6.797454 ACAACAATTTTGTGTTACGGTATGT 58.203 32.000 0.00 0.00 41.31 2.29
2991 6460 5.633830 ATGTAATGCTTGTTCAGGTCTTG 57.366 39.130 0.00 0.00 0.00 3.02
3026 6496 9.793259 ACCTTTCTAATTAGACATTTTCTGTGA 57.207 29.630 14.85 0.00 38.54 3.58
3259 6730 7.976826 TCAAACGTGTTTTACTAGTTTGTGAT 58.023 30.769 15.78 0.00 46.65 3.06
3284 6755 4.951715 TCAAATATCTTTGGCTCAGTGCAT 59.048 37.500 3.97 0.00 45.15 3.96
3370 6841 3.343617 TGCCTTTACCTATTCAGTGTGC 58.656 45.455 0.00 0.00 0.00 4.57
3494 6988 0.388659 TGTGTGGCATGAGTTTTGGC 59.611 50.000 0.00 0.00 39.89 4.52
3503 6997 1.705256 TGAGTTTTGGCGCTACTACG 58.295 50.000 7.64 0.00 0.00 3.51
3663 7157 8.188139 ACTAATTTACCCATTCGTATTTTGCAG 58.812 33.333 0.00 0.00 0.00 4.41
4088 7845 0.889186 CGGTTCAAACTGGTCCTGGG 60.889 60.000 0.33 0.00 0.00 4.45
4094 7851 2.024846 TCAAACTGGTCCTGGGTTGAAA 60.025 45.455 11.61 0.00 0.00 2.69
4095 7852 2.763448 CAAACTGGTCCTGGGTTGAAAA 59.237 45.455 7.21 0.00 0.00 2.29
4123 7880 4.469657 AGGATTGGCAGTTGAAACTACAA 58.530 39.130 12.18 12.18 38.53 2.41
4237 8008 5.841957 ATATCCTCAAATGTTTCACTGGC 57.158 39.130 0.00 0.00 0.00 4.85
4238 8009 2.238521 TCCTCAAATGTTTCACTGGCC 58.761 47.619 0.00 0.00 0.00 5.36
4239 8010 1.962807 CCTCAAATGTTTCACTGGCCA 59.037 47.619 4.71 4.71 0.00 5.36
4240 8011 2.564062 CCTCAAATGTTTCACTGGCCAT 59.436 45.455 5.51 0.00 0.00 4.40
4241 8012 3.007182 CCTCAAATGTTTCACTGGCCATT 59.993 43.478 5.51 0.00 0.00 3.16
4242 8013 4.220382 CCTCAAATGTTTCACTGGCCATTA 59.780 41.667 5.51 0.00 0.00 1.90
4243 8014 5.132897 TCAAATGTTTCACTGGCCATTAC 57.867 39.130 5.51 0.00 0.00 1.89
4277 8055 3.593096 ACCTATATGCTGATGATGCACG 58.407 45.455 0.00 0.00 43.59 5.34
4598 8388 4.245845 TCCTAACAATTTTGAAACCGGC 57.754 40.909 0.00 0.00 0.00 6.13
4865 8689 2.708051 TCTTGGCAAGAGAATGAGCTG 58.292 47.619 25.38 0.00 32.71 4.24
4881 8705 1.808945 AGCTGCCAGATTCAAAGTTCG 59.191 47.619 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
164 165 1.377725 CACCATGCACTCCCACCTC 60.378 63.158 0.00 0.00 0.00 3.85
167 168 2.361610 CCCACCATGCACTCCCAC 60.362 66.667 0.00 0.00 0.00 4.61
181 182 1.523154 GCTTGTTGAACGCATCCCCA 61.523 55.000 0.00 0.00 0.00 4.96
228 229 0.035343 GGTGACAGAAAGGGTAGGGC 60.035 60.000 0.00 0.00 0.00 5.19
249 250 1.089920 AATCAATCGTGTGCCTGCTC 58.910 50.000 0.00 0.00 0.00 4.26
253 254 2.479566 AGACAATCAATCGTGTGCCT 57.520 45.000 0.00 0.00 0.00 4.75
255 256 4.145876 TCAAAGACAATCAATCGTGTGC 57.854 40.909 0.00 0.00 0.00 4.57
273 274 1.131638 ATCGGGCTAAGCATCCTCAA 58.868 50.000 0.00 0.00 0.00 3.02
278 279 2.165437 CCTCTCTATCGGGCTAAGCATC 59.835 54.545 0.00 0.00 0.00 3.91
314 315 2.030027 ATCACTCTGAAGGTGACCCA 57.970 50.000 0.00 0.00 44.82 4.51
316 317 2.355209 GGGAATCACTCTGAAGGTGACC 60.355 54.545 0.00 0.00 44.82 4.02
324 325 0.620556 GGGCTTGGGAATCACTCTGA 59.379 55.000 0.00 0.00 0.00 3.27
379 380 1.669115 CACTTCACTGCACCCTCGG 60.669 63.158 0.00 0.00 0.00 4.63
401 407 3.118884 GGGCGAACAACACCTAGAGATTA 60.119 47.826 0.00 0.00 0.00 1.75
409 415 1.677552 CCTAGGGCGAACAACACCT 59.322 57.895 0.00 0.00 37.13 4.00
423 429 0.329596 AGAGCCAAAACCTGCCCTAG 59.670 55.000 0.00 0.00 0.00 3.02
435 441 0.986527 TCAATCTGCCTCAGAGCCAA 59.013 50.000 2.85 0.00 44.08 4.52
441 447 2.158928 CCTCTTCCTCAATCTGCCTCAG 60.159 54.545 0.00 0.00 0.00 3.35
447 453 2.765135 TCTCTGCCTCTTCCTCAATCTG 59.235 50.000 0.00 0.00 0.00 2.90
511 517 7.014808 TGTCCGACATAACTGTATCCATATGAA 59.985 37.037 3.65 0.00 35.14 2.57
513 519 6.687604 TGTCCGACATAACTGTATCCATATG 58.312 40.000 0.00 0.00 35.14 1.78
517 523 4.274978 TCTGTCCGACATAACTGTATCCA 58.725 43.478 0.62 0.00 35.14 3.41
525 531 4.143094 GCTTTCTGTTCTGTCCGACATAAC 60.143 45.833 18.31 18.31 36.22 1.89
535 541 2.418368 TGTGTGGCTTTCTGTTCTGT 57.582 45.000 0.00 0.00 0.00 3.41
558 564 0.251033 TCTTCTCTCCCGTTCGACCA 60.251 55.000 0.00 0.00 0.00 4.02
560 566 0.452585 CCTCTTCTCTCCCGTTCGAC 59.547 60.000 0.00 0.00 0.00 4.20
566 572 0.758685 AGGCATCCTCTTCTCTCCCG 60.759 60.000 0.00 0.00 0.00 5.14
567 573 1.506025 AAGGCATCCTCTTCTCTCCC 58.494 55.000 0.00 0.00 30.89 4.30
569 575 2.965147 AGCTAAGGCATCCTCTTCTCTC 59.035 50.000 0.00 0.00 41.70 3.20
606 612 1.670087 CCGTTCGTGAGAGCTCAATGT 60.670 52.381 17.77 0.00 41.85 2.71
613 619 2.811317 CTGCCCGTTCGTGAGAGC 60.811 66.667 0.00 0.00 43.69 4.09
619 625 3.089788 AAAAACTCTGCCCGTTCGT 57.910 47.368 0.00 0.00 0.00 3.85
686 693 5.912149 TGGATATTAGGTCCAAATCAGCT 57.088 39.130 0.00 0.00 42.56 4.24
822 3688 4.214758 GCAGCCTCTTTACCGAAGTTTTTA 59.785 41.667 0.00 0.00 36.70 1.52
974 3856 0.559205 TAGCGAGGGGATAAGGTGGA 59.441 55.000 0.00 0.00 0.00 4.02
1136 4328 3.379445 GGGTGCGACGGAAGAGGA 61.379 66.667 0.00 0.00 0.00 3.71
1359 4553 1.909986 GAGGGAGAAAGCTGGGTTAGT 59.090 52.381 0.00 0.00 0.00 2.24
1390 4584 0.108186 CTATCAGCACCGCAGACCAA 60.108 55.000 0.00 0.00 0.00 3.67
1531 4725 5.605534 GGATTACAGCAGCAGAGATTAAGA 58.394 41.667 0.00 0.00 0.00 2.10
1624 4818 8.547967 AACGAAATCTGTAGTACATTGATGTT 57.452 30.769 2.82 2.97 41.97 2.71
1654 4848 8.490355 GCAAAATGTTCAAAATTTAGGACAGAG 58.510 33.333 0.00 0.00 0.00 3.35
1816 5010 4.769345 TGCATGGTCATAGTCATTACCA 57.231 40.909 0.00 0.00 41.55 3.25
1849 5043 8.635765 TCCAGTTTCAGTAAGATTAGCATTTT 57.364 30.769 0.00 0.00 0.00 1.82
1885 5079 9.995003 GCATAACATTCCATATTCCCAATTTAA 57.005 29.630 0.00 0.00 0.00 1.52
1921 5122 1.324383 TACACAGCTGACCTCGACAA 58.676 50.000 23.35 0.00 0.00 3.18
1927 5128 3.206150 CAAACAGTTACACAGCTGACCT 58.794 45.455 23.35 5.16 36.56 3.85
1957 5158 7.789539 GTAATACATACAAGTTTTGCCCAAGCA 60.790 37.037 0.00 0.00 39.88 3.91
1958 5159 3.385193 ACATACAAGTTTTGCCCAAGC 57.615 42.857 0.00 0.00 40.48 4.01
1959 5160 7.033185 GGTAATACATACAAGTTTTGCCCAAG 58.967 38.462 0.00 0.00 36.14 3.61
1960 5161 6.722129 AGGTAATACATACAAGTTTTGCCCAA 59.278 34.615 0.00 0.00 36.42 4.12
2085 5345 1.398595 GCATGAAAAGCACACGACAC 58.601 50.000 0.00 0.00 0.00 3.67
2164 5424 6.072112 TCATTTCCTTCTTACTTTGTGTGC 57.928 37.500 0.00 0.00 0.00 4.57
2165 5425 7.040478 TCCATCATTTCCTTCTTACTTTGTGTG 60.040 37.037 0.00 0.00 0.00 3.82
2173 5433 9.927668 TGAAATTTTCCATCATTTCCTTCTTAC 57.072 29.630 6.68 0.00 38.23 2.34
2195 5455 1.070445 CACCCCAGCAGCAAATTGAAA 59.930 47.619 0.00 0.00 0.00 2.69
2220 5481 3.655276 AGCTTCAACTTTCAATGCAGG 57.345 42.857 0.00 0.00 0.00 4.85
2241 5502 1.277557 GTCACAGGTCCAATCTCTGCT 59.722 52.381 0.00 0.00 32.19 4.24
2243 5504 2.564504 TCAGTCACAGGTCCAATCTCTG 59.435 50.000 0.00 0.00 34.91 3.35
2247 5508 3.685139 TCTTCAGTCACAGGTCCAATC 57.315 47.619 0.00 0.00 0.00 2.67
2249 5510 3.260884 GGTATCTTCAGTCACAGGTCCAA 59.739 47.826 0.00 0.00 0.00 3.53
2250 5511 2.832129 GGTATCTTCAGTCACAGGTCCA 59.168 50.000 0.00 0.00 0.00 4.02
2251 5512 3.100671 AGGTATCTTCAGTCACAGGTCC 58.899 50.000 0.00 0.00 0.00 4.46
2252 5513 5.916661 TTAGGTATCTTCAGTCACAGGTC 57.083 43.478 0.00 0.00 0.00 3.85
2253 5514 6.681729 TTTTAGGTATCTTCAGTCACAGGT 57.318 37.500 0.00 0.00 0.00 4.00
2254 5515 7.118390 CACTTTTTAGGTATCTTCAGTCACAGG 59.882 40.741 0.00 0.00 0.00 4.00
2255 5516 7.657761 ACACTTTTTAGGTATCTTCAGTCACAG 59.342 37.037 0.00 0.00 0.00 3.66
2256 5517 7.441157 CACACTTTTTAGGTATCTTCAGTCACA 59.559 37.037 0.00 0.00 0.00 3.58
2288 5550 4.968259 TCAGACTAAGGCAAGCTTTTACA 58.032 39.130 0.00 0.00 0.00 2.41
2289 5551 5.941948 TTCAGACTAAGGCAAGCTTTTAC 57.058 39.130 0.00 0.00 0.00 2.01
2305 5567 4.398247 GAATTGCACGTCAAGATTCAGAC 58.602 43.478 0.00 0.00 38.22 3.51
2332 5594 8.622157 GCTTTTATAGTTTATCCCTGAACCTTC 58.378 37.037 0.00 0.00 0.00 3.46
2349 5616 9.197694 GATGTGTAGGTGATACTGCTTTTATAG 57.802 37.037 0.00 0.00 35.24 1.31
2360 5627 4.755266 AAGGGTGATGTGTAGGTGATAC 57.245 45.455 0.00 0.00 34.72 2.24
2366 5633 3.495100 GCCAGATAAGGGTGATGTGTAGG 60.495 52.174 0.00 0.00 0.00 3.18
2370 5637 3.287867 AAGCCAGATAAGGGTGATGTG 57.712 47.619 0.00 0.00 39.80 3.21
2371 5638 4.040755 AGTAAGCCAGATAAGGGTGATGT 58.959 43.478 0.00 0.00 39.80 3.06
2390 5657 0.037590 AAATGGAACGCTGCCCAGTA 59.962 50.000 2.68 0.00 35.67 2.74
2413 5680 3.763897 GGAGAAAAAGGCTTGGCATCTTA 59.236 43.478 0.00 0.00 0.00 2.10
2414 5681 2.564504 GGAGAAAAAGGCTTGGCATCTT 59.435 45.455 0.00 0.00 0.00 2.40
2415 5682 2.174360 GGAGAAAAAGGCTTGGCATCT 58.826 47.619 0.00 2.20 0.00 2.90
2416 5683 2.094338 CAGGAGAAAAAGGCTTGGCATC 60.094 50.000 0.00 0.00 0.00 3.91
2446 5713 6.779860 AGACAAAGTGGAGGTTACATATTGT 58.220 36.000 0.00 0.00 34.43 2.71
2515 5782 5.423015 TCCATGCTAAGACTGAGACATTTC 58.577 41.667 0.00 0.00 0.00 2.17
2518 5785 4.652881 TCATCCATGCTAAGACTGAGACAT 59.347 41.667 0.00 0.00 0.00 3.06
2561 5829 9.931210 GTCGATCTCCGTTCAAAATATTAAATT 57.069 29.630 0.00 0.00 39.75 1.82
2578 5846 4.392138 CCAACAACTTTTAGGTCGATCTCC 59.608 45.833 0.00 0.00 0.00 3.71
2659 5927 9.787532 TTACTAGCATGAAATAAGCAATTTGTC 57.212 29.630 0.00 0.00 37.93 3.18
2695 6147 5.626142 TGAAGCCTAACTGGTATTGAACAA 58.374 37.500 0.00 0.00 38.35 2.83
2778 6245 5.721960 AGCTCCTCCAAAATACTCTGTTCTA 59.278 40.000 0.00 0.00 0.00 2.10
2784 6251 5.013599 ACAGAAAGCTCCTCCAAAATACTCT 59.986 40.000 0.00 0.00 0.00 3.24
2793 6260 2.972713 ACTTGTACAGAAAGCTCCTCCA 59.027 45.455 0.00 0.00 0.00 3.86
2870 6337 9.688592 CTTCTGCTTCTGAATTACAAGAAAAAT 57.311 29.630 0.00 0.00 0.00 1.82
3025 6495 2.124695 GTCCCGGGCCAATCTGTC 60.125 66.667 18.49 0.00 0.00 3.51
3026 6496 2.308722 ATGTCCCGGGCCAATCTGT 61.309 57.895 18.49 0.00 0.00 3.41
3061 6531 0.184451 ACATGCTGATCCCATCCACC 59.816 55.000 0.00 0.00 0.00 4.61
3259 6730 6.121590 TGCACTGAGCCAAAGATATTTGATA 58.878 36.000 14.30 0.00 44.83 2.15
3296 6767 5.680619 TCACTCACTTCTGGTATTTGTGTT 58.319 37.500 0.00 0.00 0.00 3.32
3370 6841 5.181748 CAAAATTGAGAGACCCTACTCCAG 58.818 45.833 0.00 0.00 37.60 3.86
3494 6988 6.910972 TCAGATATTTCAAGAACGTAGTAGCG 59.089 38.462 0.00 0.00 45.00 4.26
3503 6997 6.803807 GGCAACAGTTCAGATATTTCAAGAAC 59.196 38.462 11.08 11.08 38.45 3.01
3663 7157 4.274950 TGCAACTTAGTAAGCAAACCAGAC 59.725 41.667 9.92 0.00 33.48 3.51
3711 7205 6.397272 GTTCATCCTGCCAATGAAAATGTTA 58.603 36.000 6.97 0.00 42.92 2.41
3845 7339 6.491403 GCCAAAACCATAGATATGAAGGACAT 59.509 38.462 1.32 0.00 42.39 3.06
4123 7880 2.152016 GCTAGGTTTTCTCCGTGCTTT 58.848 47.619 0.00 0.00 0.00 3.51
4237 8008 2.271800 GTCGTGCTTCTGGAGTAATGG 58.728 52.381 0.00 0.00 0.00 3.16
4238 8009 2.093973 AGGTCGTGCTTCTGGAGTAATG 60.094 50.000 0.00 0.00 0.00 1.90
4239 8010 2.180276 AGGTCGTGCTTCTGGAGTAAT 58.820 47.619 0.00 0.00 0.00 1.89
4240 8011 1.629043 AGGTCGTGCTTCTGGAGTAA 58.371 50.000 0.00 0.00 0.00 2.24
4241 8012 2.502142 TAGGTCGTGCTTCTGGAGTA 57.498 50.000 0.00 0.00 0.00 2.59
4242 8013 1.853963 ATAGGTCGTGCTTCTGGAGT 58.146 50.000 0.00 0.00 0.00 3.85
4243 8014 3.858877 GCATATAGGTCGTGCTTCTGGAG 60.859 52.174 0.00 0.00 36.02 3.86
4277 8055 0.514691 CTCAGTTGCTTTCGGTGAGC 59.485 55.000 0.00 0.00 40.53 4.26
4573 8361 6.277605 CCGGTTTCAAAATTGTTAGGAAACT 58.722 36.000 13.26 0.00 44.03 2.66
4595 8385 1.026182 TGCTAGTTTGCATCCTGCCG 61.026 55.000 0.00 0.00 44.23 5.69
4598 8388 2.229543 TGCTTTGCTAGTTTGCATCCTG 59.770 45.455 0.00 0.00 42.96 3.86
4664 8485 0.805711 GCCACAGTTTGCAACACACC 60.806 55.000 0.00 0.00 0.00 4.16
4782 8606 4.034163 CAGATGCAGTGAAGCTTCATGTAG 59.966 45.833 30.65 20.39 40.13 2.74
4865 8689 2.699954 TCCTCGAACTTTGAATCTGGC 58.300 47.619 0.00 0.00 0.00 4.85
4881 8705 5.128499 TCCTTCAAGATCTCTCACATTCCTC 59.872 44.000 0.00 0.00 0.00 3.71
5130 8954 5.297547 TCGCAATGATATTCTCTGTAACCC 58.702 41.667 0.00 0.00 0.00 4.11
5131 8955 5.986135 ACTCGCAATGATATTCTCTGTAACC 59.014 40.000 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.