Multiple sequence alignment - TraesCS5A01G383100

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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 TraesCS5A01G383100 chr5A 100.000 4715 0 0 1 4715 580943290 580948004 0.000000e+00 8708
1 TraesCS5A01G383100 chr5D 95.754 3792 101 12 942 4715 460755466 460759215 0.000000e+00 6056
2 TraesCS5A01G383100 chr5D 91.156 995 34 25 1 956 460754460 460755439 0.000000e+00 1301
3 TraesCS5A01G383100 chr5D 88.889 108 12 0 3993 4100 374635039 374635146 2.960000e-27 134
4 TraesCS5A01G383100 chr5B 94.666 3337 138 17 646 3949 566683704 566687033 0.000000e+00 5140
5 TraesCS5A01G383100 chr5B 97.414 580 12 3 4139 4715 566687044 566687623 0.000000e+00 985
6 TraesCS5A01G383100 chr5B 95.979 572 15 4 6 576 566682790 566683354 0.000000e+00 922
7 TraesCS5A01G383100 chr4D 87.063 286 35 2 40 325 35062204 35061921 5.890000e-84 322
8 TraesCS5A01G383100 chr4D 91.538 130 8 2 39 166 30136310 30136438 4.850000e-40 176
9 TraesCS5A01G383100 chr4D 88.571 140 13 2 34 171 38280698 38280560 2.920000e-37 167
10 TraesCS5A01G383100 chr4D 88.525 122 11 2 39 158 30018449 30018569 1.370000e-30 145
11 TraesCS5A01G383100 chr4A 89.286 140 11 3 34 171 564945601 564945464 6.270000e-39 172
12 TraesCS5A01G383100 chr4B 87.943 141 12 4 34 171 42010706 42010568 1.360000e-35 161
13 TraesCS5A01G383100 chr4B 87.218 133 14 2 34 164 42762403 42762272 1.060000e-31 148


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 TraesCS5A01G383100 chr5A 580943290 580948004 4714 False 8708.0 8708 100.000000 1 4715 1 chr5A.!!$F1 4714
1 TraesCS5A01G383100 chr5D 460754460 460759215 4755 False 3678.5 6056 93.455000 1 4715 2 chr5D.!!$F2 4714
2 TraesCS5A01G383100 chr5B 566682790 566687623 4833 False 2349.0 5140 96.019667 6 4715 3 chr5B.!!$F1 4709

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
629 641 0.035343 GAACGGGGAAGAGGGGAAAG 60.035 60.0 0.00 0.00 0.0 2.62 F
644 656 0.102300 GAAAGAGAGAGAGAGCGGGC 59.898 60.0 0.00 0.00 0.0 6.13 F
937 1255 0.249238 CCACATCGCTGCTCTAGTCC 60.249 60.0 0.00 0.00 0.0 3.85 F
2079 2445 0.179121 TACCAGTACGATTGCAGGCG 60.179 55.0 8.49 8.49 0.0 5.52 F
2082 2448 0.647410 CAGTACGATTGCAGGCGAAG 59.353 55.0 15.76 1.07 0.0 3.79 F
3593 3962 0.743097 GATTTCCATGAGCACCAGGC 59.257 55.0 0.00 0.00 45.3 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 2037 1.746516 GCAGCATCCTCCTTCTTCAGG 60.747 57.143 0.00 0.00 45.64 3.86 R
2010 2376 2.092753 TGCCTTCTTGATCTGCCTAAGG 60.093 50.000 0.00 0.00 37.21 2.69 R
2790 3159 0.322975 TTGACTCTGCTGCCCTTCTC 59.677 55.000 0.00 0.00 0.00 2.87 R
3593 3962 0.105778 GCAGTAGCCAGGCCTAAGAG 59.894 60.000 3.98 0.00 33.58 2.85 R
3621 3990 1.134848 AGATTGAACGCAGCCTCTCTC 60.135 52.381 0.00 0.00 0.00 3.20 R
4690 5073 1.160137 CCCTATAATTCAGCTGCGGC 58.840 55.000 10.33 10.33 39.06 6.53 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
40 41 3.011517 AGTGGGCAGGTAGGCAGG 61.012 66.667 0.00 0.00 46.44 4.85
41 42 4.803908 GTGGGCAGGTAGGCAGGC 62.804 72.222 0.00 0.00 46.44 4.85
43 44 4.496336 GGGCAGGTAGGCAGGCAG 62.496 72.222 0.00 0.00 46.44 4.85
66 67 3.668447 CAGCTGTCAATTGAGGTAGTGT 58.332 45.455 8.80 0.00 0.00 3.55
618 630 0.898789 GGAGAGAGTGTGAACGGGGA 60.899 60.000 0.00 0.00 0.00 4.81
621 633 0.966920 GAGAGTGTGAACGGGGAAGA 59.033 55.000 0.00 0.00 0.00 2.87
624 636 1.003718 GTGTGAACGGGGAAGAGGG 60.004 63.158 0.00 0.00 0.00 4.30
625 637 2.221299 TGTGAACGGGGAAGAGGGG 61.221 63.158 0.00 0.00 0.00 4.79
627 639 1.151987 TGAACGGGGAAGAGGGGAA 60.152 57.895 0.00 0.00 0.00 3.97
628 640 0.768997 TGAACGGGGAAGAGGGGAAA 60.769 55.000 0.00 0.00 0.00 3.13
629 641 0.035343 GAACGGGGAAGAGGGGAAAG 60.035 60.000 0.00 0.00 0.00 2.62
640 652 2.031870 GAGGGGAAAGAGAGAGAGAGC 58.968 57.143 0.00 0.00 0.00 4.09
641 653 0.744281 GGGGAAAGAGAGAGAGAGCG 59.256 60.000 0.00 0.00 0.00 5.03
644 656 0.102300 GAAAGAGAGAGAGAGCGGGC 59.898 60.000 0.00 0.00 0.00 6.13
669 951 5.301045 GGGTGGGAATTGTATAAGTTAAGCC 59.699 44.000 0.00 0.00 0.00 4.35
706 988 0.539986 TGGACCGGGTTCTGATTAGC 59.460 55.000 6.32 0.00 0.00 3.09
911 1228 2.887152 CCACTCTCCTTCCAAGGTTTTG 59.113 50.000 5.24 0.04 46.54 2.44
927 1245 3.726004 TGGGTGATCCACATCGCT 58.274 55.556 0.00 0.00 41.46 4.93
937 1255 0.249238 CCACATCGCTGCTCTAGTCC 60.249 60.000 0.00 0.00 0.00 3.85
1277 1643 3.388841 GGACGAGCCCTCCAAGAA 58.611 61.111 0.00 0.00 0.00 2.52
1279 1645 1.448717 GACGAGCCCTCCAAGAAGC 60.449 63.158 0.00 0.00 0.00 3.86
1671 2037 1.522580 GAAGCTCATCGACCTGGCC 60.523 63.158 0.00 0.00 0.00 5.36
1764 2130 2.729378 GCTCAAGTTTGATTGCGCC 58.271 52.632 4.18 0.00 35.39 6.53
1782 2148 2.504367 GCCAACATATATCGCACCCTT 58.496 47.619 0.00 0.00 0.00 3.95
1821 2187 2.608090 CGCGGAGATATACGAGCAGATA 59.392 50.000 0.00 0.00 0.00 1.98
1851 2217 4.003788 CCCTCCAACACCGTCGCT 62.004 66.667 0.00 0.00 0.00 4.93
1856 2222 1.372004 CCAACACCGTCGCTCGTAA 60.372 57.895 0.00 0.00 37.94 3.18
1902 2268 3.941483 ACTCTGGTCAAATTGATAAGGCG 59.059 43.478 0.00 0.00 0.00 5.52
1950 2316 5.633830 ATGCTCAAACTTCAAACATCGAT 57.366 34.783 0.00 0.00 0.00 3.59
2010 2376 0.757935 ATGATGCCCATGGTGAAGCC 60.758 55.000 11.73 0.00 33.39 4.35
2079 2445 0.179121 TACCAGTACGATTGCAGGCG 60.179 55.000 8.49 8.49 0.00 5.52
2082 2448 0.647410 CAGTACGATTGCAGGCGAAG 59.353 55.000 15.76 1.07 0.00 3.79
2276 2642 2.618241 ACGTTGCTGTTCACAATGATGT 59.382 40.909 2.93 0.00 41.61 3.06
2350 2716 6.499000 AGGAAAAGCTATCCCTTACCTCTATC 59.501 42.308 13.46 0.00 37.71 2.08
2581 2950 4.346730 AGGCATGATGGAGAAATTTGTGA 58.653 39.130 0.00 0.00 0.00 3.58
2777 3146 2.378038 AGTGAAGGCAAACAGAGCAAA 58.622 42.857 0.00 0.00 0.00 3.68
2820 3189 4.260132 GCAGCAGAGTCAAATGAAGATACG 60.260 45.833 0.00 0.00 0.00 3.06
2838 3207 7.310072 AGATACGATAAGAGATGATACACGG 57.690 40.000 0.00 0.00 0.00 4.94
3039 3408 1.250840 GGTCCTTGGGCGCTGAAATT 61.251 55.000 7.64 0.00 0.00 1.82
3285 3654 2.483013 CGCTGTTCGGGATTATCTGGAA 60.483 50.000 0.00 0.00 33.78 3.53
3462 3831 2.263895 AGGAGGCCCTGTACAACATA 57.736 50.000 0.00 0.00 42.42 2.29
3486 3855 1.451387 GGCTTACCACCATGTCGGG 60.451 63.158 2.95 0.00 40.22 5.14
3503 3872 4.056125 GCTCAAAACCCTGGCGGC 62.056 66.667 0.00 0.00 33.26 6.53
3579 3948 2.875317 GCTTCCATTCGAGGAGGATTTC 59.125 50.000 6.97 0.00 39.25 2.17
3593 3962 0.743097 GATTTCCATGAGCACCAGGC 59.257 55.000 0.00 0.00 45.30 4.85
3615 3984 1.956629 TTAGGCCTGGCTACTGCGAC 61.957 60.000 17.99 0.00 40.82 5.19
3621 3990 4.208686 GGCTACTGCGACCTCCGG 62.209 72.222 0.00 0.00 40.82 5.14
3681 4050 1.078918 CGGAGCAACTGATCTGGCA 60.079 57.895 4.49 0.00 33.46 4.92
3684 4053 1.339438 GGAGCAACTGATCTGGCAAGA 60.339 52.381 0.00 0.00 36.69 3.02
3780 4149 0.392863 ATGTGGATGCTGCTACGCAA 60.393 50.000 0.00 0.00 44.06 4.85
3790 4159 2.789208 CTGCTACGCAACATTTCCATG 58.211 47.619 0.00 0.00 38.41 3.66
3805 4174 3.342377 TCCATGTAATCGTGAAGGCAA 57.658 42.857 0.00 0.00 32.78 4.52
3806 4175 3.884895 TCCATGTAATCGTGAAGGCAAT 58.115 40.909 0.00 0.00 32.78 3.56
3818 4187 4.858692 CGTGAAGGCAATCGATTTTTCATT 59.141 37.500 22.25 13.66 0.00 2.57
3855 4224 8.785329 AAGAGATTCTAGACTTTGAAATGGTC 57.215 34.615 0.00 0.00 0.00 4.02
3862 4231 3.913163 AGACTTTGAAATGGTCCTCCTCT 59.087 43.478 0.00 0.00 34.23 3.69
3877 4246 3.397482 CTCCTCTCAGGTTTTGTCACAG 58.603 50.000 0.00 0.00 36.53 3.66
3885 4254 3.192422 CAGGTTTTGTCACAGTGGTTTCA 59.808 43.478 0.00 0.00 0.00 2.69
3930 4299 7.874016 TCCTTCCAATTTGATCATGAAACAAAG 59.126 33.333 24.63 16.85 37.04 2.77
3995 4374 7.448777 TCAGAGCGATAAAATATACAGACCTCT 59.551 37.037 0.00 0.00 0.00 3.69
4004 4383 2.996249 TACAGACCTCTATCCGTCGT 57.004 50.000 0.00 0.00 34.10 4.34
4016 4395 2.894763 TCCGTCGTTCTTTTTCCAGA 57.105 45.000 0.00 0.00 0.00 3.86
4140 4521 8.637986 AGTACATGAAAAACTGCCTAAATCAAA 58.362 29.630 0.00 0.00 0.00 2.69
4141 4522 7.951530 ACATGAAAAACTGCCTAAATCAAAG 57.048 32.000 0.00 0.00 0.00 2.77
4142 4523 7.500141 ACATGAAAAACTGCCTAAATCAAAGT 58.500 30.769 0.00 0.00 0.00 2.66
4143 4524 8.637986 ACATGAAAAACTGCCTAAATCAAAGTA 58.362 29.630 0.00 0.00 0.00 2.24
4144 4525 8.915654 CATGAAAAACTGCCTAAATCAAAGTAC 58.084 33.333 0.00 0.00 0.00 2.73
4145 4526 8.001881 TGAAAAACTGCCTAAATCAAAGTACA 57.998 30.769 0.00 0.00 0.00 2.90
4146 4527 8.637986 TGAAAAACTGCCTAAATCAAAGTACAT 58.362 29.630 0.00 0.00 0.00 2.29
4147 4528 8.816640 AAAAACTGCCTAAATCAAAGTACATG 57.183 30.769 0.00 0.00 0.00 3.21
4148 4529 7.759489 AAACTGCCTAAATCAAAGTACATGA 57.241 32.000 0.00 4.14 0.00 3.07
4149 4530 7.759489 AACTGCCTAAATCAAAGTACATGAA 57.241 32.000 0.00 0.00 0.00 2.57
4150 4531 7.759489 ACTGCCTAAATCAAAGTACATGAAA 57.241 32.000 0.00 0.00 0.00 2.69
4151 4532 8.177119 ACTGCCTAAATCAAAGTACATGAAAA 57.823 30.769 0.00 0.00 0.00 2.29
4152 4533 8.637986 ACTGCCTAAATCAAAGTACATGAAAAA 58.362 29.630 0.00 0.00 0.00 1.94
4153 4534 8.810652 TGCCTAAATCAAAGTACATGAAAAAC 57.189 30.769 0.00 0.00 0.00 2.43
4154 4535 8.637986 TGCCTAAATCAAAGTACATGAAAAACT 58.362 29.630 0.00 0.00 0.00 2.66
4155 4536 8.915654 GCCTAAATCAAAGTACATGAAAAACTG 58.084 33.333 0.00 0.00 0.00 3.16
4156 4537 8.915654 CCTAAATCAAAGTACATGAAAAACTGC 58.084 33.333 0.00 0.00 0.00 4.40
4157 4538 7.713764 AAATCAAAGTACATGAAAAACTGCC 57.286 32.000 0.00 0.00 0.00 4.85
4158 4539 6.655078 ATCAAAGTACATGAAAAACTGCCT 57.345 33.333 0.00 0.00 0.00 4.75
4159 4540 7.759489 ATCAAAGTACATGAAAAACTGCCTA 57.241 32.000 0.00 0.00 0.00 3.93
4160 4541 7.575414 TCAAAGTACATGAAAAACTGCCTAA 57.425 32.000 0.00 0.00 0.00 2.69
4161 4542 8.001881 TCAAAGTACATGAAAAACTGCCTAAA 57.998 30.769 0.00 0.00 0.00 1.85
4162 4543 8.470805 TCAAAGTACATGAAAAACTGCCTAAAA 58.529 29.630 0.00 0.00 0.00 1.52
4163 4544 8.539674 CAAAGTACATGAAAAACTGCCTAAAAC 58.460 33.333 0.00 0.00 0.00 2.43
4164 4545 7.341445 AGTACATGAAAAACTGCCTAAAACA 57.659 32.000 0.00 0.00 0.00 2.83
4165 4546 7.777095 AGTACATGAAAAACTGCCTAAAACAA 58.223 30.769 0.00 0.00 0.00 2.83
4461 4844 3.364964 GCAGTTTACAACAAGGGTCATCG 60.365 47.826 0.00 0.00 0.00 3.84
4690 5073 7.606858 AAATGTAGTGTCAAGATGATGAGTG 57.393 36.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.811431 TGCTAATTTTGCTACAGTGCGT 59.189 40.909 4.54 0.00 35.36 5.24
26 27 4.496336 CTGCCTGCCTACCTGCCC 62.496 72.222 0.00 0.00 0.00 5.36
33 34 4.105553 CAGCTGCCTGCCTGCCTA 62.106 66.667 0.00 0.00 44.23 3.93
40 41 0.170561 CTCAATTGACAGCTGCCTGC 59.829 55.000 15.27 1.27 43.02 4.85
41 42 0.809385 CCTCAATTGACAGCTGCCTG 59.191 55.000 15.27 4.22 44.80 4.85
42 43 0.403271 ACCTCAATTGACAGCTGCCT 59.597 50.000 15.27 0.00 0.00 4.75
43 44 2.012673 CTACCTCAATTGACAGCTGCC 58.987 52.381 15.27 2.30 0.00 4.85
66 67 0.320050 TCAGGTATGCTGCACGACAA 59.680 50.000 3.57 0.00 0.00 3.18
618 630 3.881713 GCTCTCTCTCTCTTTCCCCTCTT 60.882 52.174 0.00 0.00 0.00 2.85
621 633 1.684869 CGCTCTCTCTCTCTTTCCCCT 60.685 57.143 0.00 0.00 0.00 4.79
624 636 0.744281 CCCGCTCTCTCTCTCTTTCC 59.256 60.000 0.00 0.00 0.00 3.13
625 637 0.102300 GCCCGCTCTCTCTCTCTTTC 59.898 60.000 0.00 0.00 0.00 2.62
627 639 2.118404 CGCCCGCTCTCTCTCTCTT 61.118 63.158 0.00 0.00 0.00 2.85
628 640 2.515991 CGCCCGCTCTCTCTCTCT 60.516 66.667 0.00 0.00 0.00 3.10
629 641 3.591835 CCGCCCGCTCTCTCTCTC 61.592 72.222 0.00 0.00 0.00 3.20
640 652 2.618368 ATACAATTCCCACCCGCCCG 62.618 60.000 0.00 0.00 0.00 6.13
641 653 0.475044 TATACAATTCCCACCCGCCC 59.525 55.000 0.00 0.00 0.00 6.13
644 656 5.008316 GCTTAACTTATACAATTCCCACCCG 59.992 44.000 0.00 0.00 0.00 5.28
669 951 5.928839 CGGTCCAAATCTCAGTATTAGGATG 59.071 44.000 0.00 0.00 0.00 3.51
677 959 1.946984 ACCCGGTCCAAATCTCAGTA 58.053 50.000 0.00 0.00 0.00 2.74
678 960 1.003233 GAACCCGGTCCAAATCTCAGT 59.997 52.381 0.00 0.00 0.00 3.41
706 988 3.955650 TTTTACCCCTCGAGACAGAAG 57.044 47.619 15.71 0.00 0.00 2.85
762 1045 1.373497 CGCACCAGCTTCGTCTTCT 60.373 57.895 0.00 0.00 39.10 2.85
911 1228 2.182842 GCAGCGATGTGGATCACCC 61.183 63.158 1.22 0.00 32.73 4.61
925 1243 4.228567 GCCGGGGACTAGAGCAGC 62.229 72.222 2.18 0.00 0.00 5.25
926 1244 2.443016 AGCCGGGGACTAGAGCAG 60.443 66.667 2.18 0.00 0.00 4.24
927 1245 2.442272 GAGCCGGGGACTAGAGCA 60.442 66.667 2.18 0.00 0.00 4.26
1046 1403 4.208686 CCTCCTGCTCGTACGCCC 62.209 72.222 11.24 4.15 0.00 6.13
1194 1557 4.821589 GCCAGGGCCTCGAAGTCG 62.822 72.222 0.95 0.00 36.47 4.18
1596 1962 2.279741 GCCAGCATCACGAAGTTGATA 58.720 47.619 0.00 0.00 41.61 2.15
1671 2037 1.746516 GCAGCATCCTCCTTCTTCAGG 60.747 57.143 0.00 0.00 45.64 3.86
1764 2130 3.476552 ACCAAGGGTGCGATATATGTTG 58.523 45.455 0.00 0.00 32.98 3.33
1902 2268 9.874205 TTGATAAAATCCTCCAACAAATCAATC 57.126 29.630 0.00 0.00 0.00 2.67
1950 2316 5.576563 TCAGTAAATCAAGAAGACCCCAA 57.423 39.130 0.00 0.00 0.00 4.12
2010 2376 2.092753 TGCCTTCTTGATCTGCCTAAGG 60.093 50.000 0.00 0.00 37.21 2.69
2276 2642 5.102953 AGCAGCTTCCACATATGAACTAA 57.897 39.130 10.38 0.00 0.00 2.24
2350 2716 3.200825 TCCTCCATCCCTTCTAAAGCTTG 59.799 47.826 0.00 0.00 0.00 4.01
2581 2950 7.572814 TCAAGAATGGGAAGAAAAATGGTTTT 58.427 30.769 0.00 0.00 39.70 2.43
2604 2973 4.216472 GCATACTCGATATCCAGTGTCTCA 59.784 45.833 12.69 0.00 0.00 3.27
2685 3054 2.335712 CGCTTCCCCCAGCACTTTC 61.336 63.158 0.00 0.00 40.09 2.62
2745 3114 2.104792 TGCCTTCACTAACTCTGCAGTT 59.895 45.455 14.67 4.99 45.39 3.16
2777 3146 3.521126 TGCCCTTCTCTCTAGCAATTTCT 59.479 43.478 0.00 0.00 0.00 2.52
2790 3159 0.322975 TTGACTCTGCTGCCCTTCTC 59.677 55.000 0.00 0.00 0.00 2.87
2792 3161 1.471684 CATTTGACTCTGCTGCCCTTC 59.528 52.381 0.00 0.00 0.00 3.46
2820 3189 5.182190 TGCTCTCCGTGTATCATCTCTTATC 59.818 44.000 0.00 0.00 0.00 1.75
2838 3207 1.809547 GGAGGTTTCTGCTTTGCTCTC 59.190 52.381 0.00 0.00 0.00 3.20
3039 3408 1.690893 GGATCTGGAGCTCTGTATGCA 59.309 52.381 14.64 0.47 0.00 3.96
3285 3654 1.213013 CGAGTCCAGCTTGTACGCT 59.787 57.895 0.00 0.00 41.90 5.07
3301 3670 6.208402 CAGAGATTGATTAGAGGATTCTCCGA 59.792 42.308 0.00 0.00 42.75 4.55
3471 3840 1.195442 TGAGCCCGACATGGTGGTAA 61.195 55.000 0.00 0.00 35.15 2.85
3486 3855 4.056125 GCCGCCAGGGTTTTGAGC 62.056 66.667 0.00 0.00 38.44 4.26
3503 3872 5.978322 GCTAAAACCTTCTCGTAGTAGATGG 59.022 44.000 0.00 0.00 43.29 3.51
3593 3962 0.105778 GCAGTAGCCAGGCCTAAGAG 59.894 60.000 3.98 0.00 33.58 2.85
3595 3964 1.227380 CGCAGTAGCCAGGCCTAAG 60.227 63.158 3.98 0.00 37.52 2.18
3597 3966 2.043349 TCGCAGTAGCCAGGCCTA 60.043 61.111 3.98 0.00 37.52 3.93
3621 3990 1.134848 AGATTGAACGCAGCCTCTCTC 60.135 52.381 0.00 0.00 0.00 3.20
3681 4050 4.714308 CAGTAGGTCTTGAGGATCCTTCTT 59.286 45.833 17.42 4.04 31.40 2.52
3684 4053 4.067944 ACAGTAGGTCTTGAGGATCCTT 57.932 45.455 17.42 0.00 31.40 3.36
3753 4122 3.570540 AGCAGCATCCACATAGACTAGA 58.429 45.455 0.00 0.00 0.00 2.43
3755 4124 3.253432 CGTAGCAGCATCCACATAGACTA 59.747 47.826 0.00 0.00 0.00 2.59
3756 4125 2.035193 CGTAGCAGCATCCACATAGACT 59.965 50.000 0.00 0.00 0.00 3.24
3780 4149 4.096382 GCCTTCACGATTACATGGAAATGT 59.904 41.667 0.00 0.00 38.49 2.71
3805 4174 5.009631 TGGACTCCACAATGAAAAATCGAT 58.990 37.500 0.00 0.00 0.00 3.59
3806 4175 4.393834 TGGACTCCACAATGAAAAATCGA 58.606 39.130 0.00 0.00 0.00 3.59
3818 4187 4.982241 AGAATCTCTTTTGGACTCCACA 57.018 40.909 0.00 0.00 30.78 4.17
3855 4224 2.104792 TGTGACAAAACCTGAGAGGAGG 59.895 50.000 0.00 0.00 37.67 4.30
3862 4231 2.799126 ACCACTGTGACAAAACCTGA 57.201 45.000 9.86 0.00 0.00 3.86
3877 4246 9.113838 ACAGACATATTATCATTCTGAAACCAC 57.886 33.333 3.99 0.00 37.67 4.16
3885 4254 8.717717 TGGAAGGAACAGACATATTATCATTCT 58.282 33.333 0.00 0.00 30.76 2.40
3905 4274 7.658575 ACTTTGTTTCATGATCAAATTGGAAGG 59.341 33.333 19.58 12.38 32.04 3.46
3930 4299 4.956075 AGGGTGTAAATGATTTCCATCCAC 59.044 41.667 14.15 6.00 33.53 4.02
3995 4374 4.240096 GTCTGGAAAAAGAACGACGGATA 58.760 43.478 0.00 0.00 0.00 2.59
4016 4395 1.512156 GGCCACAACGTGATTTCCGT 61.512 55.000 0.00 0.00 40.92 4.69
4027 4406 3.282831 GTGTATTTCACAGGCCACAAC 57.717 47.619 5.01 0.00 45.51 3.32
4136 4517 7.575414 TTAGGCAGTTTTTCATGTACTTTGA 57.425 32.000 0.00 0.00 0.00 2.69
4140 4521 7.341445 TGTTTTAGGCAGTTTTTCATGTACT 57.659 32.000 0.00 0.00 0.00 2.73
4141 4522 7.995463 TTGTTTTAGGCAGTTTTTCATGTAC 57.005 32.000 0.00 0.00 0.00 2.90
4142 4523 9.436957 TTTTTGTTTTAGGCAGTTTTTCATGTA 57.563 25.926 0.00 0.00 0.00 2.29
4143 4524 7.913674 TTTTGTTTTAGGCAGTTTTTCATGT 57.086 28.000 0.00 0.00 0.00 3.21
4144 4525 8.233190 TGTTTTTGTTTTAGGCAGTTTTTCATG 58.767 29.630 0.00 0.00 0.00 3.07
4145 4526 8.233868 GTGTTTTTGTTTTAGGCAGTTTTTCAT 58.766 29.630 0.00 0.00 0.00 2.57
4146 4527 7.442666 AGTGTTTTTGTTTTAGGCAGTTTTTCA 59.557 29.630 0.00 0.00 0.00 2.69
4147 4528 7.802738 AGTGTTTTTGTTTTAGGCAGTTTTTC 58.197 30.769 0.00 0.00 0.00 2.29
4148 4529 7.737972 AGTGTTTTTGTTTTAGGCAGTTTTT 57.262 28.000 0.00 0.00 0.00 1.94
4149 4530 7.064134 GCTAGTGTTTTTGTTTTAGGCAGTTTT 59.936 33.333 0.00 0.00 0.00 2.43
4150 4531 6.533723 GCTAGTGTTTTTGTTTTAGGCAGTTT 59.466 34.615 0.00 0.00 0.00 2.66
4151 4532 6.040247 GCTAGTGTTTTTGTTTTAGGCAGTT 58.960 36.000 0.00 0.00 0.00 3.16
4152 4533 5.359860 AGCTAGTGTTTTTGTTTTAGGCAGT 59.640 36.000 0.00 0.00 0.00 4.40
4153 4534 5.687285 CAGCTAGTGTTTTTGTTTTAGGCAG 59.313 40.000 0.00 0.00 0.00 4.85
4154 4535 5.587289 CAGCTAGTGTTTTTGTTTTAGGCA 58.413 37.500 0.00 0.00 0.00 4.75
4155 4536 4.444388 GCAGCTAGTGTTTTTGTTTTAGGC 59.556 41.667 0.00 0.00 0.00 3.93
4156 4537 5.587289 TGCAGCTAGTGTTTTTGTTTTAGG 58.413 37.500 0.00 0.00 0.00 2.69
4157 4538 6.291796 GCTTGCAGCTAGTGTTTTTGTTTTAG 60.292 38.462 5.72 0.00 38.45 1.85
4158 4539 5.518487 GCTTGCAGCTAGTGTTTTTGTTTTA 59.482 36.000 5.72 0.00 38.45 1.52
4159 4540 4.329801 GCTTGCAGCTAGTGTTTTTGTTTT 59.670 37.500 5.72 0.00 38.45 2.43
4160 4541 3.865164 GCTTGCAGCTAGTGTTTTTGTTT 59.135 39.130 5.72 0.00 38.45 2.83
4161 4542 3.447742 GCTTGCAGCTAGTGTTTTTGTT 58.552 40.909 5.72 0.00 38.45 2.83
4162 4543 3.084070 GCTTGCAGCTAGTGTTTTTGT 57.916 42.857 5.72 0.00 38.45 2.83
4690 5073 1.160137 CCCTATAATTCAGCTGCGGC 58.840 55.000 10.33 10.33 39.06 6.53


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

AutoCloner maintained by Alex Coulton.