Multiple sequence alignment - TraesCS7D01G215200

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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 TraesCS7D01G215200 chr7D 100.000 5094 0 0 1 5094 174802941 174797848 0.000000e+00 9407.0
1 TraesCS7D01G215200 chr7B 92.985 3849 169 44 1 3794 139726049 139722247 0.000000e+00 5518.0
2 TraesCS7D01G215200 chr7B 93.401 985 36 13 3794 4754 139721870 139720891 0.000000e+00 1432.0
3 TraesCS7D01G215200 chr7B 83.853 353 29 12 4755 5093 139720830 139720492 1.380000e-80 311.0
4 TraesCS7D01G215200 chr7A 92.545 3407 156 47 1639 4971 177007729 177004347 0.000000e+00 4795.0
5 TraesCS7D01G215200 chr7A 93.025 1061 32 13 438 1473 177008834 177007791 0.000000e+00 1511.0
6 TraesCS7D01G215200 chr7A 91.743 218 16 2 1 217 177009432 177009216 8.290000e-78 302.0
7 TraesCS7D01G215200 chr7A 86.294 197 27 0 1068 1264 587496625 587496821 1.110000e-51 215.0
8 TraesCS7D01G215200 chr7A 93.548 124 8 0 4971 5094 176993921 176993798 8.710000e-43 185.0
9 TraesCS7D01G215200 chr7A 95.745 47 2 0 1625 1671 543305647 543305601 5.470000e-10 76.8
10 TraesCS7D01G215200 chr7A 97.727 44 1 0 1625 1668 690714183 690714226 5.470000e-10 76.8
11 TraesCS7D01G215200 chr3D 91.519 1969 119 19 1843 3794 27900118 27898181 0.000000e+00 2667.0
12 TraesCS7D01G215200 chr3D 94.611 167 8 1 1629 1795 27900288 27900123 1.820000e-64 257.0
13 TraesCS7D01G215200 chr5A 87.512 1033 72 21 1365 2382 654922408 654923398 0.000000e+00 1140.0
14 TraesCS7D01G215200 chr5A 93.304 448 29 1 2378 2825 654933441 654933887 0.000000e+00 660.0
15 TraesCS7D01G215200 chr5A 88.055 293 35 0 1064 1356 219249658 219249950 1.050000e-91 348.0
16 TraesCS7D01G215200 chr4A 87.372 293 37 0 1064 1356 419985596 419985304 2.270000e-88 337.0
17 TraesCS7D01G215200 chr6B 78.035 519 90 21 3278 3776 565216461 565216975 6.410000e-79 305.0
18 TraesCS7D01G215200 chr6B 97.727 44 1 0 1625 1668 26549079 26549122 5.470000e-10 76.8
19 TraesCS7D01G215200 chr6A 78.035 519 90 21 3278 3776 520430506 520431020 6.410000e-79 305.0
20 TraesCS7D01G215200 chr6A 89.529 191 20 0 1064 1254 214806221 214806031 5.100000e-60 243.0
21 TraesCS7D01G215200 chr3A 90.576 191 18 0 1064 1254 573516288 573516098 2.350000e-63 254.0
22 TraesCS7D01G215200 chr6D 86.792 212 28 0 3278 3489 379006411 379006622 2.370000e-58 237.0
23 TraesCS7D01G215200 chr2D 95.745 47 2 0 1625 1671 152014173 152014127 5.470000e-10 76.8
24 TraesCS7D01G215200 chr1B 97.727 44 1 0 1625 1668 681772609 681772652 5.470000e-10 76.8


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 TraesCS7D01G215200 chr7D 174797848 174802941 5093 True 9407.000000 9407 100.000000 1 5094 1 chr7D.!!$R1 5093
1 TraesCS7D01G215200 chr7B 139720492 139726049 5557 True 2420.333333 5518 90.079667 1 5093 3 chr7B.!!$R1 5092
2 TraesCS7D01G215200 chr7A 177004347 177009432 5085 True 2202.666667 4795 92.437667 1 4971 3 chr7A.!!$R3 4970
3 TraesCS7D01G215200 chr3D 27898181 27900288 2107 True 1462.000000 2667 93.065000 1629 3794 2 chr3D.!!$R1 2165
4 TraesCS7D01G215200 chr5A 654922408 654923398 990 False 1140.000000 1140 87.512000 1365 2382 1 chr5A.!!$F2 1017
5 TraesCS7D01G215200 chr6B 565216461 565216975 514 False 305.000000 305 78.035000 3278 3776 1 chr6B.!!$F2 498
6 TraesCS7D01G215200 chr6A 520430506 520431020 514 False 305.000000 305 78.035000 3278 3776 1 chr6A.!!$F1 498

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
185 219 0.038618 GCCGAGCCAAACCGAAAAAT 60.039 50.000 0.00 0.00 0.00 1.82 F
485 702 1.678123 GCAGAGGAGTGTGTGCATCAT 60.678 52.381 0.00 0.00 36.72 2.45 F
487 704 1.904537 AGAGGAGTGTGTGCATCATCA 59.095 47.619 2.20 0.00 0.00 3.07 F
1504 1769 0.235404 GCGCTGGTTTGCAAATTTGG 59.765 50.000 16.21 7.48 0.00 3.28 F
1562 1829 0.036164 TGCTGTTAGTGCGGGAATGT 59.964 50.000 0.00 0.00 0.00 2.71 F
3218 3510 1.971357 CACCTGTTGTAGAGTGGGTCT 59.029 52.381 0.00 0.00 39.59 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1486 1748 0.867086 CCCAAATTTGCAAACCAGCG 59.133 50.000 15.41 1.61 37.31 5.18 R
1504 1769 1.069906 CGCATCGCCAGCTAAATTACC 60.070 52.381 0.00 0.00 0.00 2.85 R
1541 1808 1.331756 CATTCCCGCACTAACAGCATC 59.668 52.381 0.00 0.00 0.00 3.91 R
3435 3731 1.501741 CATCCTGCGTTTTCCACCG 59.498 57.895 0.00 0.00 0.00 4.94 R
3496 3792 9.077885 AGTGTGATAAACAATTAAACATGTCCT 57.922 29.630 0.00 0.00 41.57 3.85 R
5059 5862 0.032813 AACTGGAAGCATGGGATGGG 60.033 55.000 0.00 0.00 37.60 4.00 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
114 131 6.042143 AGCAATACAAAACTCCAACAACAAG 58.958 36.000 0.00 0.00 0.00 3.16
115 132 5.234116 GCAATACAAAACTCCAACAACAAGG 59.766 40.000 0.00 0.00 0.00 3.61
116 133 6.568869 CAATACAAAACTCCAACAACAAGGA 58.431 36.000 0.00 0.00 0.00 3.36
121 138 0.954452 CTCCAACAACAAGGAGTGGC 59.046 55.000 0.00 0.00 45.08 5.01
122 139 0.257328 TCCAACAACAAGGAGTGGCA 59.743 50.000 0.00 0.00 0.00 4.92
123 140 1.110442 CCAACAACAAGGAGTGGCAA 58.890 50.000 0.00 0.00 0.00 4.52
124 141 1.480137 CCAACAACAAGGAGTGGCAAA 59.520 47.619 0.00 0.00 0.00 3.68
125 142 2.102925 CCAACAACAAGGAGTGGCAAAT 59.897 45.455 0.00 0.00 0.00 2.32
126 143 3.432046 CCAACAACAAGGAGTGGCAAATT 60.432 43.478 0.00 0.00 0.00 1.82
127 144 4.202202 CCAACAACAAGGAGTGGCAAATTA 60.202 41.667 0.00 0.00 0.00 1.40
128 145 5.355596 CAACAACAAGGAGTGGCAAATTAA 58.644 37.500 0.00 0.00 0.00 1.40
144 161 3.737559 ATTAATCAGGTCCCTGCACAA 57.262 42.857 8.53 2.72 43.31 3.33
185 219 0.038618 GCCGAGCCAAACCGAAAAAT 60.039 50.000 0.00 0.00 0.00 1.82
485 702 1.678123 GCAGAGGAGTGTGTGCATCAT 60.678 52.381 0.00 0.00 36.72 2.45
486 703 2.277969 CAGAGGAGTGTGTGCATCATC 58.722 52.381 0.00 0.00 0.00 2.92
487 704 1.904537 AGAGGAGTGTGTGCATCATCA 59.095 47.619 2.20 0.00 0.00 3.07
728 954 4.107051 CCTGCTTTTGGCCGCTCG 62.107 66.667 0.00 0.00 40.92 5.03
729 955 4.766088 CTGCTTTTGGCCGCTCGC 62.766 66.667 0.00 0.00 40.92 5.03
1413 1669 2.442236 TCCATCCAAAATCTCCAGCC 57.558 50.000 0.00 0.00 0.00 4.85
1488 1750 2.727544 TTTTTCCTGTGCCTGCGC 59.272 55.556 0.00 0.00 0.00 6.09
1504 1769 0.235404 GCGCTGGTTTGCAAATTTGG 59.765 50.000 16.21 7.48 0.00 3.28
1541 1808 1.811965 TGCGGATTTCATTCTGTGGTG 59.188 47.619 0.00 0.00 0.00 4.17
1554 1821 1.466167 CTGTGGTGATGCTGTTAGTGC 59.534 52.381 0.00 0.00 0.00 4.40
1555 1822 0.443869 GTGGTGATGCTGTTAGTGCG 59.556 55.000 0.00 0.00 0.00 5.34
1562 1829 0.036164 TGCTGTTAGTGCGGGAATGT 59.964 50.000 0.00 0.00 0.00 2.71
1599 1866 4.377431 GCTGCATCGGAATCGGTAAATTAG 60.377 45.833 0.00 0.00 36.95 1.73
1696 1963 2.736826 GCCTAGGTGGGTCAGGAGC 61.737 68.421 11.31 0.00 36.00 4.70
1761 2031 6.546428 TGTTTTGGGTTCTTTCCATGTTAA 57.454 33.333 0.00 0.00 33.82 2.01
1799 2069 4.652822 GTTGGTTGAACCTGAATACTCCT 58.347 43.478 16.33 0.00 39.58 3.69
1800 2070 5.801380 GTTGGTTGAACCTGAATACTCCTA 58.199 41.667 16.33 0.00 39.58 2.94
1801 2071 5.416271 TGGTTGAACCTGAATACTCCTAC 57.584 43.478 16.33 0.00 39.58 3.18
1802 2072 5.091552 TGGTTGAACCTGAATACTCCTACT 58.908 41.667 16.33 0.00 39.58 2.57
1944 2217 3.242608 TGAAGCAACGTTTTGTGAGCTAC 60.243 43.478 8.73 0.00 40.62 3.58
1985 2258 3.499048 CGTAGCATTCACGTTCTGTAGT 58.501 45.455 0.00 0.00 34.74 2.73
1989 2262 4.987832 AGCATTCACGTTCTGTAGTCTAG 58.012 43.478 0.00 0.00 0.00 2.43
1998 2271 4.238514 GTTCTGTAGTCTAGCTGTTGGTG 58.761 47.826 0.00 0.00 0.00 4.17
2012 2285 4.275936 GCTGTTGGTGTGTTCAGTTAGATT 59.724 41.667 0.00 0.00 0.00 2.40
2099 2373 7.302524 TGGAAAGTTACATTTTTATGACTCGC 58.697 34.615 0.00 0.00 0.00 5.03
2104 2378 2.936498 ACATTTTTATGACTCGCGGGAG 59.064 45.455 26.24 26.24 46.13 4.30
2119 2393 2.906354 CGGGAGTGCTAAAGTATGCTT 58.094 47.619 0.00 0.00 36.30 3.91
2137 2413 4.935702 TGCTTGATTTTCCTGTTCACAAG 58.064 39.130 0.00 0.00 37.09 3.16
2170 2446 7.800380 GTGTACATCACTGCATTAATATTGCTC 59.200 37.037 0.00 0.00 43.13 4.26
2336 2612 3.181476 TGCGAGCTGCTGTAAGATATTGA 60.181 43.478 7.01 0.00 46.63 2.57
2400 2676 6.663093 TGGCAACCATTGACTCTTAATATTGT 59.337 34.615 0.00 0.00 40.19 2.71
2563 2843 7.728847 ATTAGTTTCATTTGCCTGTTTTTCC 57.271 32.000 0.00 0.00 0.00 3.13
2568 2850 4.227197 TCATTTGCCTGTTTTTCCCCTTA 58.773 39.130 0.00 0.00 0.00 2.69
2586 2868 5.370679 CCCTTAAACTATTAGCGGGCTTTA 58.629 41.667 0.00 0.00 31.13 1.85
2589 2871 3.918294 AACTATTAGCGGGCTTTACCA 57.082 42.857 0.00 0.00 42.05 3.25
2872 3160 6.509418 TTAAATTTGACCCAGATTCTTCCG 57.491 37.500 0.00 0.00 0.00 4.30
2875 3163 3.502123 TTGACCCAGATTCTTCCGTTT 57.498 42.857 0.00 0.00 0.00 3.60
2992 3280 9.134734 CGAGTAAATTATGCCTCTCTAAGATTC 57.865 37.037 0.00 0.00 0.00 2.52
3218 3510 1.971357 CACCTGTTGTAGAGTGGGTCT 59.029 52.381 0.00 0.00 39.59 3.85
3274 3570 3.254166 AGCTGTCAAACTATTGTTGGCTG 59.746 43.478 0.00 0.00 37.79 4.85
3390 3686 4.515361 CTCTTGTTCTCAGAGCATTGGAT 58.485 43.478 0.00 0.00 0.00 3.41
3435 3731 2.543777 TCGCAGCTGGGGAAATATAC 57.456 50.000 28.30 0.79 35.23 1.47
3686 4002 3.181445 TGCACTGGACTACATGGTTTCTT 60.181 43.478 0.00 0.00 0.00 2.52
3836 4533 5.972935 TCCGATGTGTTACTTACATGTCAT 58.027 37.500 0.00 0.00 38.78 3.06
3898 4595 6.308041 TCTTGTTAGATCGAAAACTCATCGTG 59.692 38.462 9.26 0.00 40.99 4.35
3907 4604 0.456221 AACTCATCGTGGACCTAGCG 59.544 55.000 0.00 0.00 0.00 4.26
3928 4625 2.553086 GACCAGTACAACAACGGTTCA 58.447 47.619 0.00 0.00 34.21 3.18
4099 4796 3.727726 CCTACGCACATCATGATAACCA 58.272 45.455 8.15 0.00 0.00 3.67
4121 4818 2.099405 CGCCACCCCTGTCAATATTTT 58.901 47.619 0.00 0.00 0.00 1.82
4200 4897 5.675970 TCGTCGTTATTTTGCTTGAAGAAG 58.324 37.500 0.00 0.00 0.00 2.85
4213 4910 0.325272 GAAGAAGCCGAAAGAGGGGT 59.675 55.000 0.00 0.00 36.70 4.95
4219 4916 2.592993 CCGAAAGAGGGGTGGCTCA 61.593 63.158 0.00 0.00 0.00 4.26
4221 4918 1.831652 CGAAAGAGGGGTGGCTCAGT 61.832 60.000 0.00 0.00 0.00 3.41
4259 4956 2.962825 AAACTTGGGGAGGGGGTGGA 62.963 60.000 0.00 0.00 0.00 4.02
4341 5041 1.622607 ATGGAGGGCGGATTCGTTCA 61.623 55.000 0.00 0.00 38.89 3.18
4365 5066 5.414789 TCCACGAAAATAATGAGGAGTCA 57.585 39.130 0.00 0.00 37.02 3.41
4452 5157 0.689080 TGAGTGAGGGAGAGATGGCC 60.689 60.000 0.00 0.00 0.00 5.36
4486 5191 1.620819 TGTCTCTGGCTGGTCTTCTTC 59.379 52.381 0.00 0.00 0.00 2.87
4504 5212 8.068380 GTCTTCTTCTGGTTGTGTAAAACATAC 58.932 37.037 0.00 0.00 38.99 2.39
4505 5213 7.990886 TCTTCTTCTGGTTGTGTAAAACATACT 59.009 33.333 0.00 0.00 38.99 2.12
4508 5216 7.386848 TCTTCTGGTTGTGTAAAACATACTAGC 59.613 37.037 0.00 0.00 38.99 3.42
4509 5217 6.526526 TCTGGTTGTGTAAAACATACTAGCA 58.473 36.000 0.00 0.00 38.99 3.49
4557 5267 3.399181 CCCGTCAGGCAGGGCTTA 61.399 66.667 0.00 0.00 41.34 3.09
4703 5418 0.543749 ACCCTTACATGGAGCTGCTC 59.456 55.000 21.17 21.17 0.00 4.26
4704 5419 0.531532 CCCTTACATGGAGCTGCTCG 60.532 60.000 22.25 11.94 0.00 5.03
4759 5505 3.576550 TGCGCCCTCATGTAGTATTCATA 59.423 43.478 4.18 0.00 0.00 2.15
4814 5599 7.120579 AGCGGATTTTTCATGTTCATTGTAGTA 59.879 33.333 0.00 0.00 0.00 1.82
4836 5621 7.945134 AGTACTGAAATGTTTCTTCAATTGCT 58.055 30.769 0.00 0.00 38.02 3.91
4840 5625 7.330208 ACTGAAATGTTTCTTCAATTGCTATGC 59.670 33.333 0.00 0.00 38.02 3.14
4848 5633 8.715088 GTTTCTTCAATTGCTATGCTGATTTTT 58.285 29.630 0.00 0.00 0.00 1.94
4905 5707 5.824429 TCTTGTTTGCTGTTTCTGAGATTG 58.176 37.500 0.00 0.00 0.00 2.67
4906 5708 4.572985 TGTTTGCTGTTTCTGAGATTGG 57.427 40.909 0.00 0.00 0.00 3.16
4911 5713 2.363683 CTGTTTCTGAGATTGGGAGGC 58.636 52.381 0.00 0.00 0.00 4.70
4916 5719 3.814504 TCTGAGATTGGGAGGCTTTTT 57.185 42.857 0.00 0.00 0.00 1.94
4917 5720 3.424703 TCTGAGATTGGGAGGCTTTTTG 58.575 45.455 0.00 0.00 0.00 2.44
4934 5737 4.335400 TTTTGCCATTTTCCTTGTCTCC 57.665 40.909 0.00 0.00 0.00 3.71
4971 5774 2.758089 GGCAGCTGCGGACTGAATG 61.758 63.158 31.19 0.00 43.26 2.67
4972 5775 1.742880 GCAGCTGCGGACTGAATGA 60.743 57.895 25.23 0.00 37.32 2.57
4983 5786 3.551890 CGGACTGAATGACTGATTAACCG 59.448 47.826 0.00 0.00 0.00 4.44
5012 5815 0.916358 ATCAGCAGCCCAGTTACCCT 60.916 55.000 0.00 0.00 0.00 4.34
5015 5818 0.842467 AGCAGCCCAGTTACCCTCTT 60.842 55.000 0.00 0.00 0.00 2.85
5053 5856 0.396974 TTGGCTGGCTCACTTGGTTT 60.397 50.000 2.00 0.00 0.00 3.27
5058 5861 2.301346 CTGGCTCACTTGGTTTTGTCT 58.699 47.619 0.00 0.00 0.00 3.41
5059 5862 2.291741 CTGGCTCACTTGGTTTTGTCTC 59.708 50.000 0.00 0.00 0.00 3.36
5060 5863 1.609072 GGCTCACTTGGTTTTGTCTCC 59.391 52.381 0.00 0.00 0.00 3.71
5061 5864 1.609072 GCTCACTTGGTTTTGTCTCCC 59.391 52.381 0.00 0.00 0.00 4.30
5062 5865 2.930950 CTCACTTGGTTTTGTCTCCCA 58.069 47.619 0.00 0.00 0.00 4.37
5086 5889 3.094572 CCATGCTTCCAGTTCCAGAAAT 58.905 45.455 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 4.846779 TGTTGGAGTTTTGTATTGCTCC 57.153 40.909 0.00 0.00 45.64 4.70
114 131 3.381590 GGACCTGATTAATTTGCCACTCC 59.618 47.826 0.00 0.00 0.00 3.85
115 132 3.381590 GGGACCTGATTAATTTGCCACTC 59.618 47.826 0.00 0.00 0.00 3.51
116 133 3.011708 AGGGACCTGATTAATTTGCCACT 59.988 43.478 0.00 0.00 0.00 4.00
117 134 3.131046 CAGGGACCTGATTAATTTGCCAC 59.869 47.826 13.06 0.00 46.30 5.01
118 135 3.364549 CAGGGACCTGATTAATTTGCCA 58.635 45.455 13.06 0.00 46.30 4.92
119 136 2.101415 GCAGGGACCTGATTAATTTGCC 59.899 50.000 22.03 0.00 46.30 4.52
120 137 2.760092 TGCAGGGACCTGATTAATTTGC 59.240 45.455 22.03 4.63 46.30 3.68
121 138 3.763360 TGTGCAGGGACCTGATTAATTTG 59.237 43.478 22.03 0.00 46.30 2.32
122 139 4.046286 TGTGCAGGGACCTGATTAATTT 57.954 40.909 22.03 0.00 46.30 1.82
123 140 3.737559 TGTGCAGGGACCTGATTAATT 57.262 42.857 22.03 0.00 46.30 1.40
124 141 3.245229 TGTTGTGCAGGGACCTGATTAAT 60.245 43.478 22.03 0.00 46.30 1.40
125 142 2.107378 TGTTGTGCAGGGACCTGATTAA 59.893 45.455 22.03 9.50 46.30 1.40
126 143 1.702401 TGTTGTGCAGGGACCTGATTA 59.298 47.619 22.03 4.58 46.30 1.75
127 144 0.478072 TGTTGTGCAGGGACCTGATT 59.522 50.000 22.03 0.00 46.30 2.57
128 145 0.250901 GTGTTGTGCAGGGACCTGAT 60.251 55.000 22.03 0.00 46.30 2.90
185 219 7.494625 ACTCGATCCGCTTCTCATTTTTATTTA 59.505 33.333 0.00 0.00 0.00 1.40
195 229 1.025113 ACGACTCGATCCGCTTCTCA 61.025 55.000 5.20 0.00 0.00 3.27
556 773 2.018086 AGGGAGGGAGAGAGAGGGG 61.018 68.421 0.00 0.00 0.00 4.79
558 775 0.998945 AGGAGGGAGGGAGAGAGAGG 60.999 65.000 0.00 0.00 0.00 3.69
817 1049 2.805353 CTGCGACGTTCACTCGGG 60.805 66.667 0.00 0.00 34.94 5.14
821 1053 4.647615 AGCGCTGCGACGTTCACT 62.648 61.111 28.07 8.33 34.88 3.41
1413 1669 5.933617 TCATCCCAGGTTGATGAAATCTAG 58.066 41.667 6.04 0.00 45.81 2.43
1486 1748 0.867086 CCCAAATTTGCAAACCAGCG 59.133 50.000 15.41 1.61 37.31 5.18
1488 1750 6.631971 AAATTACCCAAATTTGCAAACCAG 57.368 33.333 15.41 6.81 44.36 4.00
1504 1769 1.069906 CGCATCGCCAGCTAAATTACC 60.070 52.381 0.00 0.00 0.00 2.85
1541 1808 1.331756 CATTCCCGCACTAACAGCATC 59.668 52.381 0.00 0.00 0.00 3.91
1599 1866 5.989777 TGTCCAGCTTACTAAACAAGAGAAC 59.010 40.000 0.00 0.00 0.00 3.01
1696 1963 3.125316 GCAAACGACCAGAATAGTGAAGG 59.875 47.826 0.00 0.00 0.00 3.46
1761 2031 6.126409 TCAACCAACCTAAAAAGTGTGATCT 58.874 36.000 0.00 0.00 0.00 2.75
1797 2067 7.201732 CCACCAGTAAAAGCATATTCAAGTAGG 60.202 40.741 0.00 0.00 0.00 3.18
1798 2068 7.679638 GCCACCAGTAAAAGCATATTCAAGTAG 60.680 40.741 0.00 0.00 0.00 2.57
1799 2069 6.094881 GCCACCAGTAAAAGCATATTCAAGTA 59.905 38.462 0.00 0.00 0.00 2.24
1800 2070 5.105756 GCCACCAGTAAAAGCATATTCAAGT 60.106 40.000 0.00 0.00 0.00 3.16
1801 2071 5.105797 TGCCACCAGTAAAAGCATATTCAAG 60.106 40.000 0.00 0.00 0.00 3.02
1802 2072 4.769488 TGCCACCAGTAAAAGCATATTCAA 59.231 37.500 0.00 0.00 0.00 2.69
1944 2217 3.004315 ACGCACAAAAGTTCCAATACAGG 59.996 43.478 0.00 0.00 0.00 4.00
1985 2258 2.434336 ACTGAACACACCAACAGCTAGA 59.566 45.455 0.00 0.00 34.25 2.43
1989 2262 3.202906 TCTAACTGAACACACCAACAGC 58.797 45.455 0.00 0.00 34.25 4.40
1998 2271 2.412847 GCGCCACAATCTAACTGAACAC 60.413 50.000 0.00 0.00 0.00 3.32
2012 2285 4.578898 ACACGTCGAAGCGCCACA 62.579 61.111 2.29 0.00 34.88 4.17
2099 2373 2.604046 AGCATACTTTAGCACTCCCG 57.396 50.000 0.00 0.00 0.00 5.14
2104 2378 6.749118 CAGGAAAATCAAGCATACTTTAGCAC 59.251 38.462 0.00 0.00 32.29 4.40
2119 2393 6.353323 TGAGTACTTGTGAACAGGAAAATCA 58.647 36.000 0.00 0.33 0.00 2.57
2170 2446 6.073276 TGCAATGCTGTACTACTAACAAACAG 60.073 38.462 6.82 0.00 40.38 3.16
2363 2639 5.186603 TCAATGGTTGCCAAGCACATTATTA 59.813 36.000 12.08 0.00 42.32 0.98
2365 2641 3.514706 TCAATGGTTGCCAAGCACATTAT 59.485 39.130 12.08 0.00 42.32 1.28
2501 2781 1.905637 ACCTCGGGTCATTCCAAAAC 58.094 50.000 0.00 0.00 38.11 2.43
2562 2842 2.105993 AGCCCGCTAATAGTTTAAGGGG 59.894 50.000 0.00 0.00 36.53 4.79
2563 2843 3.487120 AGCCCGCTAATAGTTTAAGGG 57.513 47.619 0.00 0.00 37.92 3.95
2568 2850 4.224991 TGGTAAAGCCCGCTAATAGTTT 57.775 40.909 0.00 0.00 36.04 2.66
2586 2868 4.641989 GCAGAATGGATCAACACTAATGGT 59.358 41.667 0.00 0.00 35.86 3.55
2787 3071 5.297776 GCCTTAGCATAATGTGACATGAAGT 59.702 40.000 0.00 0.00 39.53 3.01
2872 3160 5.912955 CAGAACCTTGTGTTTCCGAATAAAC 59.087 40.000 0.00 0.00 37.29 2.01
2875 3163 3.500680 GCAGAACCTTGTGTTTCCGAATA 59.499 43.478 0.00 0.00 37.29 1.75
2992 3280 2.009774 AGATCTTCAATTTCGGCGGTG 58.990 47.619 7.21 0.41 0.00 4.94
3177 3465 6.603599 AGGTGTTGCCCTAAGAAGAATTAATC 59.396 38.462 0.00 0.00 38.26 1.75
3178 3466 6.378280 CAGGTGTTGCCCTAAGAAGAATTAAT 59.622 38.462 0.00 0.00 38.26 1.40
3274 3570 4.056050 CACCACGGATAAGCATACCTAAC 58.944 47.826 0.00 0.00 0.00 2.34
3435 3731 1.501741 CATCCTGCGTTTTCCACCG 59.498 57.895 0.00 0.00 0.00 4.94
3496 3792 9.077885 AGTGTGATAAACAATTAAACATGTCCT 57.922 29.630 0.00 0.00 41.57 3.85
3592 3908 1.346068 AGTGTCTCTTTCCTCACCTGC 59.654 52.381 0.00 0.00 0.00 4.85
3798 4494 7.303634 ACACATCGGATAAATACACAACTTC 57.696 36.000 0.00 0.00 0.00 3.01
3898 4595 0.682209 TGTACTGGTCCGCTAGGTCC 60.682 60.000 0.00 0.00 44.58 4.46
3907 4604 1.869132 GAACCGTTGTTGTACTGGTCC 59.131 52.381 0.00 0.00 33.97 4.46
3928 4625 2.437281 AGAGAACTCATCCCATCGCAAT 59.563 45.455 4.64 0.00 0.00 3.56
4099 4796 1.279025 ATATTGACAGGGGTGGCGGT 61.279 55.000 0.00 0.00 0.00 5.68
4121 4818 7.558444 GTGAAAATAATGGTATAAGGTGGGTGA 59.442 37.037 0.00 0.00 0.00 4.02
4140 4837 0.239347 GCTGCTGCGTCTGTGAAAAT 59.761 50.000 0.00 0.00 0.00 1.82
4173 4870 3.058777 TCAAGCAAAATAACGACGAACCC 60.059 43.478 0.00 0.00 0.00 4.11
4200 4897 3.978571 GAGCCACCCCTCTTTCGGC 62.979 68.421 0.00 0.00 43.31 5.54
4219 4916 0.107456 CATCCCAGCTATGGCGAACT 59.893 55.000 0.00 0.00 46.19 3.01
4221 4918 1.419381 TACATCCCAGCTATGGCGAA 58.581 50.000 0.00 0.00 46.19 4.70
4259 4956 2.546778 CAAGATATACAACACCCGCGT 58.453 47.619 4.92 0.00 0.00 6.01
4341 5041 6.414732 TGACTCCTCATTATTTTCGTGGAAT 58.585 36.000 0.00 0.00 0.00 3.01
4452 5157 0.108615 GAGACAGACATGTGGGTCCG 60.109 60.000 18.18 0.00 40.68 4.79
4486 5191 6.426937 ACTGCTAGTATGTTTTACACAACCAG 59.573 38.462 0.00 0.00 39.50 4.00
4504 5212 1.204941 AGGCTACGGAACAACTGCTAG 59.795 52.381 0.00 0.00 0.00 3.42
4505 5213 1.203994 GAGGCTACGGAACAACTGCTA 59.796 52.381 0.00 0.00 0.00 3.49
4508 5216 0.391263 GGGAGGCTACGGAACAACTG 60.391 60.000 0.00 0.00 0.00 3.16
4509 5217 1.551019 GGGGAGGCTACGGAACAACT 61.551 60.000 0.00 0.00 0.00 3.16
4668 5383 2.175811 GTTCGATGCACCAACGGC 59.824 61.111 0.00 0.00 30.83 5.68
4708 5423 2.026542 AGCTCACATCACATGGTCACAT 60.027 45.455 0.00 0.00 37.99 3.21
4759 5505 6.192773 AGTCCTGAACCAATGATCATCAAAT 58.807 36.000 9.06 0.00 0.00 2.32
4768 5514 2.493675 CTCTCGAGTCCTGAACCAATGA 59.506 50.000 13.13 0.00 0.00 2.57
4814 5599 7.330208 GCATAGCAATTGAAGAAACATTTCAGT 59.670 33.333 10.34 0.00 39.61 3.41
4911 5713 4.751600 GGAGACAAGGAAAATGGCAAAAAG 59.248 41.667 0.00 0.00 0.00 2.27
4916 5719 2.892852 CAAGGAGACAAGGAAAATGGCA 59.107 45.455 0.00 0.00 0.00 4.92
4917 5720 2.232208 CCAAGGAGACAAGGAAAATGGC 59.768 50.000 0.00 0.00 0.00 4.40
4919 5722 3.160269 AGCCAAGGAGACAAGGAAAATG 58.840 45.455 0.00 0.00 0.00 2.32
4920 5723 3.075134 AGAGCCAAGGAGACAAGGAAAAT 59.925 43.478 0.00 0.00 0.00 1.82
4956 5759 0.390866 CAGTCATTCAGTCCGCAGCT 60.391 55.000 0.00 0.00 0.00 4.24
4971 5774 6.315393 TGATAAAAGCCTTCGGTTAATCAGTC 59.685 38.462 0.00 0.00 31.88 3.51
4972 5775 6.177610 TGATAAAAGCCTTCGGTTAATCAGT 58.822 36.000 0.00 0.00 31.88 3.41
4999 5802 0.984995 GACAAGAGGGTAACTGGGCT 59.015 55.000 0.00 0.00 0.00 5.19
5000 5803 0.690762 TGACAAGAGGGTAACTGGGC 59.309 55.000 0.00 0.00 0.00 5.36
5012 5815 1.286501 GCACGTGACAACTGACAAGA 58.713 50.000 22.23 0.00 0.00 3.02
5015 5818 0.108377 ACTGCACGTGACAACTGACA 60.108 50.000 22.23 3.74 0.00 3.58
5053 5856 1.002069 AAGCATGGGATGGGAGACAA 58.998 50.000 0.00 0.00 0.00 3.18
5058 5861 0.920763 ACTGGAAGCATGGGATGGGA 60.921 55.000 0.00 0.00 37.60 4.37
5059 5862 0.032813 AACTGGAAGCATGGGATGGG 60.033 55.000 0.00 0.00 37.60 4.00
5060 5863 1.396653 GAACTGGAAGCATGGGATGG 58.603 55.000 0.00 0.00 37.60 3.51
5061 5864 1.341285 TGGAACTGGAAGCATGGGATG 60.341 52.381 0.00 0.00 37.60 3.51
5062 5865 1.002069 TGGAACTGGAAGCATGGGAT 58.998 50.000 0.00 0.00 37.60 3.85


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

AutoCloner maintained by Alex Coulton.