Multiple sequence alignment - TraesCS1D01G442000

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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 TraesCS1D01G442000 chr1D 100.000 2558 0 0 1 2558 486761674 486759117 0.000000e+00 4724
1 TraesCS1D01G442000 chr1D 80.723 747 74 31 996 1724 486858668 486857974 3.770000e-143 518
2 TraesCS1D01G442000 chr1D 79.227 828 67 49 334 1107 396150301 396151077 1.780000e-131 479
3 TraesCS1D01G442000 chr1D 80.376 479 52 12 1149 1608 396166703 396167158 2.450000e-85 326
4 TraesCS1D01G442000 chr1D 82.234 394 36 13 2179 2558 396181147 396181520 2.470000e-80 309
5 TraesCS1D01G442000 chr1A 87.724 1841 130 31 1 1793 584358542 584356750 0.000000e+00 2060
6 TraesCS1D01G442000 chr1A 91.353 532 23 5 2031 2558 584356462 584355950 0.000000e+00 706
7 TraesCS1D01G442000 chr1A 91.667 192 14 1 1791 1982 584356664 584356475 5.430000e-67 265
8 TraesCS1D01G442000 chr1B 84.058 1311 128 36 525 1790 677909056 677907782 0.000000e+00 1188
9 TraesCS1D01G442000 chr1B 80.815 761 77 30 996 1730 677987982 677987265 1.350000e-147 532
10 TraesCS1D01G442000 chr1B 93.548 279 10 6 140 418 677909432 677909162 2.370000e-110 409
11 TraesCS1D01G442000 chr1B 96.341 82 2 1 444 524 677909168 677909087 1.600000e-27 134


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 TraesCS1D01G442000 chr1D 486759117 486761674 2557 True 4724.000000 4724 100.000000 1 2558 1 chr1D.!!$R1 2557
1 TraesCS1D01G442000 chr1D 486857974 486858668 694 True 518.000000 518 80.723000 996 1724 1 chr1D.!!$R2 728
2 TraesCS1D01G442000 chr1D 396150301 396151077 776 False 479.000000 479 79.227000 334 1107 1 chr1D.!!$F1 773
3 TraesCS1D01G442000 chr1A 584355950 584358542 2592 True 1010.333333 2060 90.248000 1 2558 3 chr1A.!!$R1 2557
4 TraesCS1D01G442000 chr1B 677907782 677909432 1650 True 577.000000 1188 91.315667 140 1790 3 chr1B.!!$R2 1650
5 TraesCS1D01G442000 chr1B 677987265 677987982 717 True 532.000000 532 80.815000 996 1730 1 chr1B.!!$R1 734

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
271 272 0.391263 GCCAGTGCCAGTACCAGTAC 60.391 60.0 0.0 0.0 36.35 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2131 2332 0.179119 GCTGAAGGGTTGATGCATGC 60.179 55.0 11.82 11.82 0.0 4.06 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
38 39 6.789262 ACATTCTTTATGCAAGTAGTGATGC 58.211 36.000 0.00 0.00 42.86 3.91
111 112 6.516527 GCAGTGATGTTCAAAGGGAATACAAA 60.517 38.462 0.00 0.00 37.93 2.83
121 122 8.117813 TCAAAGGGAATACAAAGGTACATTTC 57.882 34.615 1.81 0.00 30.94 2.17
136 137 6.091713 AGGTACATTTCGTCCAAAATCTAACG 59.908 38.462 0.00 0.00 36.50 3.18
137 138 5.934935 ACATTTCGTCCAAAATCTAACGT 57.065 34.783 0.00 0.00 36.55 3.99
138 139 5.685841 ACATTTCGTCCAAAATCTAACGTG 58.314 37.500 0.00 0.00 36.55 4.49
156 157 1.296715 GGTGGTGGCTGGACAGTAG 59.703 63.158 0.82 0.00 0.00 2.57
157 158 1.481056 GGTGGTGGCTGGACAGTAGT 61.481 60.000 0.82 0.00 0.00 2.73
186 187 1.153549 GGTCACCAGCGGATGACTC 60.154 63.158 11.36 0.00 43.91 3.36
258 259 0.817634 TCGGTTTTCCAGTGCCAGTG 60.818 55.000 0.00 0.00 40.70 3.66
264 265 1.414866 TTCCAGTGCCAGTGCCAGTA 61.415 55.000 0.00 0.00 36.33 2.74
265 266 1.672356 CCAGTGCCAGTGCCAGTAC 60.672 63.158 0.00 0.00 36.33 2.73
266 267 1.672356 CAGTGCCAGTGCCAGTACC 60.672 63.158 0.00 0.00 36.33 3.34
267 268 2.146724 AGTGCCAGTGCCAGTACCA 61.147 57.895 0.00 0.00 36.33 3.25
268 269 1.672356 GTGCCAGTGCCAGTACCAG 60.672 63.158 0.00 0.00 36.33 4.00
271 272 0.391263 GCCAGTGCCAGTACCAGTAC 60.391 60.000 0.00 0.00 36.35 2.73
272 273 0.973632 CCAGTGCCAGTACCAGTACA 59.026 55.000 10.41 0.00 38.48 2.90
274 275 2.413837 CAGTGCCAGTACCAGTACAAC 58.586 52.381 10.41 3.61 38.48 3.32
275 276 2.043992 AGTGCCAGTACCAGTACAACA 58.956 47.619 10.41 2.78 38.48 3.33
276 277 2.436542 AGTGCCAGTACCAGTACAACAA 59.563 45.455 10.41 0.00 38.48 2.83
277 278 3.118186 AGTGCCAGTACCAGTACAACAAA 60.118 43.478 10.41 0.00 38.48 2.83
278 279 3.628487 GTGCCAGTACCAGTACAACAAAA 59.372 43.478 10.41 0.00 38.48 2.44
279 280 4.096682 GTGCCAGTACCAGTACAACAAAAA 59.903 41.667 10.41 0.00 38.48 1.94
280 281 4.336993 TGCCAGTACCAGTACAACAAAAAG 59.663 41.667 10.41 0.00 38.48 2.27
281 282 4.577283 GCCAGTACCAGTACAACAAAAAGA 59.423 41.667 10.41 0.00 38.48 2.52
435 443 4.075793 CTCCCTCCCTCCCGTCCA 62.076 72.222 0.00 0.00 0.00 4.02
445 457 2.358247 CCCGTCCACCAGTTTCCG 60.358 66.667 0.00 0.00 0.00 4.30
578 621 4.856801 AGCCCGTGCGCATTAGGG 62.857 66.667 31.59 31.59 46.44 3.53
663 711 3.697542 CTCATGCCAGAATGTTGGAATCA 59.302 43.478 0.04 0.00 40.87 2.57
664 712 3.444742 TCATGCCAGAATGTTGGAATCAC 59.555 43.478 0.04 0.00 40.87 3.06
665 713 3.159213 TGCCAGAATGTTGGAATCACT 57.841 42.857 0.04 0.00 40.87 3.41
666 714 2.821378 TGCCAGAATGTTGGAATCACTG 59.179 45.455 0.04 0.00 40.87 3.66
667 715 2.821969 GCCAGAATGTTGGAATCACTGT 59.178 45.455 0.04 0.00 40.87 3.55
668 716 4.009675 GCCAGAATGTTGGAATCACTGTA 58.990 43.478 0.04 0.00 40.87 2.74
669 717 4.641989 GCCAGAATGTTGGAATCACTGTAT 59.358 41.667 0.04 0.00 40.87 2.29
670 718 5.449588 GCCAGAATGTTGGAATCACTGTATG 60.450 44.000 0.04 0.00 40.87 2.39
671 719 5.649395 CCAGAATGTTGGAATCACTGTATGT 59.351 40.000 0.00 0.00 40.87 2.29
680 737 6.280643 TGGAATCACTGTATGTACTGTATGC 58.719 40.000 0.00 0.67 36.74 3.14
754 811 0.486879 ACATTTTGCCTCCTTCCCCA 59.513 50.000 0.00 0.00 0.00 4.96
768 825 5.865085 TCCTTCCCCATAATTGAGATTACG 58.135 41.667 0.00 0.00 30.87 3.18
770 827 6.100569 TCCTTCCCCATAATTGAGATTACGAA 59.899 38.462 0.00 0.00 30.87 3.85
771 828 6.942576 CCTTCCCCATAATTGAGATTACGAAT 59.057 38.462 0.00 0.00 30.87 3.34
772 829 7.448469 CCTTCCCCATAATTGAGATTACGAATT 59.552 37.037 0.00 0.00 30.87 2.17
773 830 8.760980 TTCCCCATAATTGAGATTACGAATTT 57.239 30.769 0.00 0.00 30.87 1.82
774 831 9.854668 TTCCCCATAATTGAGATTACGAATTTA 57.145 29.630 0.00 0.00 30.87 1.40
775 832 9.280174 TCCCCATAATTGAGATTACGAATTTAC 57.720 33.333 0.00 0.00 30.87 2.01
802 862 3.383620 AGATCAGTATGCAGCAGTAGC 57.616 47.619 0.00 0.00 37.15 3.58
847 907 8.758829 TGTATCTGAACAGGTATAATGTTGAGT 58.241 33.333 14.19 7.84 41.08 3.41
906 966 8.623903 TCAGTACCATAGTTGTATTAACTACCG 58.376 37.037 1.98 0.00 35.77 4.02
930 990 7.015289 CGGTGTACAATCTTGTAATGTTGAAG 58.985 38.462 0.00 0.00 44.46 3.02
966 1027 2.328473 TCTTGATTGCGAAGACTGTCG 58.672 47.619 1.52 3.58 43.98 4.35
1115 1205 2.315925 ACAGGAATGTATGTCTGCCG 57.684 50.000 0.00 0.00 0.00 5.69
1124 1214 4.010667 TGTATGTCTGCCGGTTACTTTT 57.989 40.909 1.90 0.00 0.00 2.27
1213 1307 1.065551 CATACGATGTGGACTCTGCGA 59.934 52.381 0.00 0.00 0.00 5.10
1308 1402 3.689649 GCGGTTCTATGTTCCAGTTCATT 59.310 43.478 0.00 0.00 0.00 2.57
1311 1405 5.010282 GGTTCTATGTTCCAGTTCATTGGT 58.990 41.667 0.00 0.00 39.35 3.67
1335 1429 2.417516 CTGATCCGGCCGAACGAT 59.582 61.111 30.73 21.30 35.47 3.73
1364 1458 2.175202 TCTCTGTCCTTCTCCAGCTTC 58.825 52.381 0.00 0.00 0.00 3.86
1368 1462 2.038295 CTGTCCTTCTCCAGCTTCTGTT 59.962 50.000 0.00 0.00 0.00 3.16
1416 1510 4.135747 TGGAACAATGATGCTACATCGA 57.864 40.909 3.33 0.00 31.92 3.59
1417 1511 4.707105 TGGAACAATGATGCTACATCGAT 58.293 39.130 0.00 0.00 31.92 3.59
1418 1512 4.751600 TGGAACAATGATGCTACATCGATC 59.248 41.667 0.00 0.00 31.92 3.69
1419 1513 4.143242 GGAACAATGATGCTACATCGATCG 60.143 45.833 9.36 9.36 0.00 3.69
1506 1609 3.006967 TGAACCTTTACCAGCAGTCTCTC 59.993 47.826 0.00 0.00 0.00 3.20
1575 1678 2.821969 GTGATCCAAAGCTGTGAACCAT 59.178 45.455 5.12 0.00 0.00 3.55
1580 1686 2.095567 CCAAAGCTGTGAACCATTCTCG 60.096 50.000 5.12 0.00 0.00 4.04
1731 1844 7.979786 TCTTAGCATAGATTATTCCCCTAGG 57.020 40.000 0.06 0.06 0.00 3.02
1734 1847 5.854843 AGCATAGATTATTCCCCTAGGCTA 58.145 41.667 2.05 0.00 45.11 3.93
1738 1851 8.055790 GCATAGATTATTCCCCTAGGCTATTTT 58.944 37.037 2.05 0.00 37.26 1.82
1745 1858 5.663158 TCCCCTAGGCTATTTTTGCTATT 57.337 39.130 2.05 0.00 0.00 1.73
1755 1868 6.350110 GGCTATTTTTGCTATTCACAACTCCA 60.350 38.462 0.00 0.00 0.00 3.86
1772 1885 6.041523 ACAACTCCAGGAGCTCTTATTATCTC 59.958 42.308 17.31 0.00 32.04 2.75
1777 1890 3.837731 AGGAGCTCTTATTATCTCAGGGC 59.162 47.826 14.64 0.00 33.86 5.19
1783 1896 6.014669 AGCTCTTATTATCTCAGGGCTTACAG 60.015 42.308 0.00 0.00 41.93 2.74
1793 1906 4.357325 TCAGGGCTTACAGATCTCTTTCT 58.643 43.478 0.00 0.00 0.00 2.52
1794 1907 4.161189 TCAGGGCTTACAGATCTCTTTCTG 59.839 45.833 0.00 0.09 46.94 3.02
1798 1911 5.482908 GGCTTACAGATCTCTTTCTGAACA 58.517 41.667 8.36 0.00 44.88 3.18
1799 1912 5.934625 GGCTTACAGATCTCTTTCTGAACAA 59.065 40.000 8.36 0.00 44.88 2.83
1801 1914 7.201600 GGCTTACAGATCTCTTTCTGAACAATC 60.202 40.741 8.36 0.00 44.88 2.67
1809 2010 4.307432 TCTTTCTGAACAATCGGAGTGTC 58.693 43.478 11.85 6.36 41.88 3.67
1825 2026 4.407296 GGAGTGTCCTTCCTGTATGAGATT 59.593 45.833 0.00 0.00 32.53 2.40
1882 2083 5.299148 TCTGCAATTTGGTCCTGAATTTTG 58.701 37.500 0.00 0.00 0.00 2.44
1900 2101 6.639632 ATTTTGTGAACAGAACAGCTACAT 57.360 33.333 0.00 0.00 0.00 2.29
1904 2105 4.684242 TGTGAACAGAACAGCTACATTACG 59.316 41.667 0.00 0.00 0.00 3.18
1914 2115 3.736252 CAGCTACATTACGCCACTACATC 59.264 47.826 0.00 0.00 0.00 3.06
1919 2120 5.333299 ACATTACGCCACTACATCACTTA 57.667 39.130 0.00 0.00 0.00 2.24
1958 2159 1.519455 GGCGAGTCAGGAACATCGG 60.519 63.158 0.00 0.00 35.76 4.18
1982 2183 4.648762 ACTGATGAGGAGAGGACTATTGTG 59.351 45.833 0.00 0.00 0.00 3.33
1983 2184 3.963374 TGATGAGGAGAGGACTATTGTGG 59.037 47.826 0.00 0.00 0.00 4.17
1984 2185 2.111384 TGAGGAGAGGACTATTGTGGC 58.889 52.381 0.00 0.00 0.00 5.01
1985 2186 1.414550 GAGGAGAGGACTATTGTGGCC 59.585 57.143 0.00 0.00 0.00 5.36
1986 2187 0.470341 GGAGAGGACTATTGTGGCCC 59.530 60.000 0.00 0.00 0.00 5.80
1987 2188 1.501582 GAGAGGACTATTGTGGCCCT 58.498 55.000 0.00 0.00 0.00 5.19
1988 2189 1.139853 GAGAGGACTATTGTGGCCCTG 59.860 57.143 0.00 0.00 0.00 4.45
1989 2190 0.464554 GAGGACTATTGTGGCCCTGC 60.465 60.000 0.00 0.00 0.00 4.85
1990 2191 1.819632 GGACTATTGTGGCCCTGCG 60.820 63.158 0.00 0.00 0.00 5.18
1991 2192 2.438434 ACTATTGTGGCCCTGCGC 60.438 61.111 0.00 0.00 0.00 6.09
1992 2193 2.124570 CTATTGTGGCCCTGCGCT 60.125 61.111 9.73 0.00 37.74 5.92
1993 2194 1.146041 CTATTGTGGCCCTGCGCTA 59.854 57.895 9.73 0.00 37.74 4.26
1994 2195 0.250467 CTATTGTGGCCCTGCGCTAT 60.250 55.000 9.73 0.00 37.74 2.97
1995 2196 0.534877 TATTGTGGCCCTGCGCTATG 60.535 55.000 9.73 0.00 37.74 2.23
1996 2197 3.861292 TATTGTGGCCCTGCGCTATGG 62.861 57.143 9.73 7.56 37.74 2.74
2015 2216 4.980805 GGCTTCACCGACACGCCA 62.981 66.667 0.00 0.00 40.41 5.69
2016 2217 3.712881 GCTTCACCGACACGCCAC 61.713 66.667 0.00 0.00 0.00 5.01
2017 2218 3.403057 CTTCACCGACACGCCACG 61.403 66.667 0.00 0.00 0.00 4.94
2038 2239 2.685380 AGTGCTCGAGGAAGGGGG 60.685 66.667 15.58 0.00 0.00 5.40
2048 2249 4.491409 GAAGGGGGAAGAGCGGGC 62.491 72.222 0.00 0.00 0.00 6.13
2170 2371 5.414454 TCAGCCGATTGCAACTAGTTTTATT 59.586 36.000 5.07 0.00 44.83 1.40
2174 2375 6.471198 GCCGATTGCAACTAGTTTTATTTACC 59.529 38.462 5.07 0.00 40.77 2.85
2177 2378 6.593268 TTGCAACTAGTTTTATTTACCCCC 57.407 37.500 5.07 0.00 0.00 5.40
2183 2384 6.127101 ACTAGTTTTATTTACCCCCATCAGC 58.873 40.000 0.00 0.00 0.00 4.26
2202 2403 4.097135 TCAGCAACTCTAGTCTGTAGATGC 59.903 45.833 9.26 9.26 32.59 3.91
2247 2448 9.952030 TGGAAAACATTACATATGAACAGTCTA 57.048 29.630 10.38 0.00 0.00 2.59
2279 2480 0.249120 CTGGTGACCGGCACTTCATA 59.751 55.000 22.54 4.81 46.86 2.15
2305 2506 2.867109 AGCAACCATACAGCTCAGTT 57.133 45.000 0.00 0.00 32.05 3.16
2309 2510 5.070001 AGCAACCATACAGCTCAGTTAAAA 58.930 37.500 0.00 0.00 32.05 1.52
2352 2553 5.660417 TCAGAGAAGGCAAGATAGAATCTGT 59.340 40.000 0.00 0.00 40.13 3.41
2355 2556 7.814107 CAGAGAAGGCAAGATAGAATCTGTATC 59.186 40.741 0.00 0.00 40.13 2.24
2382 2583 9.880157 TGGAGTTATATCTAACAAACCTTGTAC 57.120 33.333 4.07 0.00 44.59 2.90
2430 2631 1.542492 CAGCTGCAGGTGAGGAAAAT 58.458 50.000 36.58 0.00 45.66 1.82
2431 2632 2.715046 CAGCTGCAGGTGAGGAAAATA 58.285 47.619 36.58 0.00 45.66 1.40
2435 2636 4.164988 AGCTGCAGGTGAGGAAAATAGTAT 59.835 41.667 19.45 0.00 0.00 2.12
2436 2637 4.274459 GCTGCAGGTGAGGAAAATAGTATG 59.726 45.833 17.12 0.00 0.00 2.39
2437 2638 4.780815 TGCAGGTGAGGAAAATAGTATGG 58.219 43.478 0.00 0.00 0.00 2.74
2438 2639 4.227300 TGCAGGTGAGGAAAATAGTATGGT 59.773 41.667 0.00 0.00 0.00 3.55
2439 2640 4.576463 GCAGGTGAGGAAAATAGTATGGTG 59.424 45.833 0.00 0.00 0.00 4.17
2441 2642 5.036916 AGGTGAGGAAAATAGTATGGTGGA 58.963 41.667 0.00 0.00 0.00 4.02
2449 2653 6.093633 GGAAAATAGTATGGTGGACACAGTTC 59.906 42.308 4.69 0.00 0.00 3.01
2463 2667 6.979817 TGGACACAGTTCAAAATTCTGAATTG 59.020 34.615 15.80 13.68 44.36 2.32
2509 2713 7.410120 AAAGTTCAGGTCAGTTCAAAATTCT 57.590 32.000 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 9.624697 GAACATCACTGCTTGAATAAATTAACA 57.375 29.630 0.00 0.00 37.92 2.41
72 73 9.624697 TGAACATCACTGCTTGAATAAATTAAC 57.375 29.630 0.00 0.00 37.92 2.01
81 82 3.318839 CCCTTTGAACATCACTGCTTGAA 59.681 43.478 0.00 0.00 37.92 2.69
87 88 6.573664 TTGTATTCCCTTTGAACATCACTG 57.426 37.500 0.00 0.00 35.31 3.66
111 112 6.091713 CGTTAGATTTTGGACGAAATGTACCT 59.908 38.462 2.37 0.00 37.69 3.08
121 122 2.158841 CCACCACGTTAGATTTTGGACG 59.841 50.000 0.00 0.00 41.00 4.79
136 137 1.764571 TACTGTCCAGCCACCACCAC 61.765 60.000 0.00 0.00 0.00 4.16
137 138 1.460497 TACTGTCCAGCCACCACCA 60.460 57.895 0.00 0.00 0.00 4.17
138 139 1.296715 CTACTGTCCAGCCACCACC 59.703 63.158 0.00 0.00 0.00 4.61
156 157 1.445582 GGTGACCGACCGATCACAC 60.446 63.158 17.47 4.79 45.83 3.82
157 158 2.967397 GGTGACCGACCGATCACA 59.033 61.111 17.47 0.00 45.83 3.58
258 259 4.577283 TCTTTTTGTTGTACTGGTACTGGC 59.423 41.667 11.44 3.71 37.00 4.85
289 290 3.087031 GAGCACCTGTACTGGTACTGTA 58.913 50.000 24.87 0.00 41.74 2.74
291 292 1.204941 GGAGCACCTGTACTGGTACTG 59.795 57.143 24.87 14.45 38.45 2.74
432 440 1.812686 CGAGGACGGAAACTGGTGGA 61.813 60.000 0.00 0.00 35.72 4.02
435 443 1.366366 CACGAGGACGGAAACTGGT 59.634 57.895 0.00 0.00 44.46 4.00
467 479 1.208870 CCAATGCGCGCAAACAGTA 59.791 52.632 39.68 13.62 0.00 2.74
578 621 2.796593 ACAGAAACCGCTAACAACGTAC 59.203 45.455 0.00 0.00 0.00 3.67
663 711 5.289595 CCATTCGCATACAGTACATACAGT 58.710 41.667 0.00 0.00 0.00 3.55
664 712 4.686091 CCCATTCGCATACAGTACATACAG 59.314 45.833 0.00 0.00 0.00 2.74
665 713 4.342665 TCCCATTCGCATACAGTACATACA 59.657 41.667 0.00 0.00 0.00 2.29
666 714 4.878439 TCCCATTCGCATACAGTACATAC 58.122 43.478 0.00 0.00 0.00 2.39
667 715 5.738619 ATCCCATTCGCATACAGTACATA 57.261 39.130 0.00 0.00 0.00 2.29
668 716 4.623932 ATCCCATTCGCATACAGTACAT 57.376 40.909 0.00 0.00 0.00 2.29
669 717 4.126437 CAATCCCATTCGCATACAGTACA 58.874 43.478 0.00 0.00 0.00 2.90
670 718 3.498397 CCAATCCCATTCGCATACAGTAC 59.502 47.826 0.00 0.00 0.00 2.73
671 719 3.389656 TCCAATCCCATTCGCATACAGTA 59.610 43.478 0.00 0.00 0.00 2.74
680 737 3.181473 ACATGCAATTCCAATCCCATTCG 60.181 43.478 0.00 0.00 0.00 3.34
768 825 8.777413 TGCATACTGATCTAGCATTGTAAATTC 58.223 33.333 0.00 0.00 0.00 2.17
770 827 7.094890 GCTGCATACTGATCTAGCATTGTAAAT 60.095 37.037 0.00 0.00 34.35 1.40
771 828 6.203530 GCTGCATACTGATCTAGCATTGTAAA 59.796 38.462 0.00 0.00 34.35 2.01
772 829 5.698089 GCTGCATACTGATCTAGCATTGTAA 59.302 40.000 0.00 0.00 34.35 2.41
773 830 5.221501 TGCTGCATACTGATCTAGCATTGTA 60.222 40.000 0.00 0.00 36.37 2.41
774 831 4.063689 GCTGCATACTGATCTAGCATTGT 58.936 43.478 0.00 0.00 34.35 2.71
775 832 4.062991 TGCTGCATACTGATCTAGCATTG 58.937 43.478 0.00 0.00 36.37 2.82
847 907 6.070481 TGACTGTATCAACATTTACCCTGCTA 60.070 38.462 0.00 0.00 34.37 3.49
885 945 6.155049 ACACCGGTAGTTAATACAACTATGGT 59.845 38.462 6.87 13.76 41.17 3.55
906 966 6.801862 GCTTCAACATTACAAGATTGTACACC 59.198 38.462 4.94 0.00 42.84 4.16
930 990 6.963805 GCAATCAAGAAAAGTACTGATACTGC 59.036 38.462 0.00 0.00 41.00 4.40
966 1027 0.247460 GGGAACAGGCAAAATGAGGC 59.753 55.000 0.00 0.00 0.00 4.70
1213 1307 1.945394 GCCATCTCGAATGACAGCAAT 59.055 47.619 8.56 0.00 0.00 3.56
1267 1361 1.361668 CTGCGGAAACTGATGTCCCG 61.362 60.000 0.00 0.00 42.74 5.14
1308 1402 2.060383 CCGGATCAGGAGCTCACCA 61.060 63.158 17.19 0.00 0.00 4.17
1311 1405 3.157252 GGCCGGATCAGGAGCTCA 61.157 66.667 16.86 0.00 0.00 4.26
1335 1429 4.158025 GGAGAAGGACAGAGAATTACGTCA 59.842 45.833 0.00 0.00 0.00 4.35
1393 1487 4.332543 TCGATGTAGCATCATTGTTCCAAC 59.667 41.667 9.40 0.00 32.68 3.77
1416 1510 2.550978 CCCGTAAGCAACAGATTCGAT 58.449 47.619 0.00 0.00 0.00 3.59
1417 1511 2.004583 CCCGTAAGCAACAGATTCGA 57.995 50.000 0.00 0.00 0.00 3.71
1418 1512 0.373716 GCCCGTAAGCAACAGATTCG 59.626 55.000 0.00 0.00 0.00 3.34
1419 1513 1.448985 TGCCCGTAAGCAACAGATTC 58.551 50.000 0.00 0.00 40.56 2.52
1506 1609 1.596203 ATGCTGCCGTCGGATGATG 60.596 57.895 17.49 0.21 0.00 3.07
1551 1654 1.133253 CACAGCTTTGGATCACGCG 59.867 57.895 3.53 3.53 0.00 6.01
1575 1678 0.318441 CTGAACTGAGGCCACGAGAA 59.682 55.000 5.01 0.00 0.00 2.87
1580 1686 0.398318 AGGAACTGAACTGAGGCCAC 59.602 55.000 5.01 0.00 37.18 5.01
1710 1823 5.854843 AGCCTAGGGGAATAATCTATGCTA 58.145 41.667 11.72 0.00 34.72 3.49
1715 1828 7.888546 GCAAAAATAGCCTAGGGGAATAATCTA 59.111 37.037 11.72 0.81 33.58 1.98
1731 1844 6.620678 TGGAGTTGTGAATAGCAAAAATAGC 58.379 36.000 0.00 0.00 0.00 2.97
1734 1847 5.774690 TCCTGGAGTTGTGAATAGCAAAAAT 59.225 36.000 0.00 0.00 0.00 1.82
1738 1851 3.869912 GCTCCTGGAGTTGTGAATAGCAA 60.870 47.826 23.92 0.00 31.39 3.91
1745 1858 1.722034 AAGAGCTCCTGGAGTTGTGA 58.278 50.000 23.92 0.00 31.39 3.58
1755 1868 3.837731 GCCCTGAGATAATAAGAGCTCCT 59.162 47.826 10.93 0.00 0.00 3.69
1772 1885 4.161189 TCAGAAAGAGATCTGTAAGCCCTG 59.839 45.833 0.00 0.64 45.65 4.45
1777 1890 7.009999 CCGATTGTTCAGAAAGAGATCTGTAAG 59.990 40.741 0.00 0.00 45.65 2.34
1778 1891 6.813649 CCGATTGTTCAGAAAGAGATCTGTAA 59.186 38.462 0.00 0.00 45.65 2.41
1783 1896 5.290643 CACTCCGATTGTTCAGAAAGAGATC 59.709 44.000 0.00 0.00 0.00 2.75
1793 1906 2.289444 GGAAGGACACTCCGATTGTTCA 60.289 50.000 0.38 0.00 42.75 3.18
1794 1907 2.028020 AGGAAGGACACTCCGATTGTTC 60.028 50.000 0.00 0.00 42.75 3.18
1798 1911 1.645710 ACAGGAAGGACACTCCGATT 58.354 50.000 0.00 0.00 42.75 3.34
1799 1912 2.526888 TACAGGAAGGACACTCCGAT 57.473 50.000 0.00 0.00 42.75 4.18
1801 1914 2.099921 CTCATACAGGAAGGACACTCCG 59.900 54.545 0.00 0.00 42.75 4.63
1809 2010 6.553100 AGAGAAGGTAATCTCATACAGGAAGG 59.447 42.308 7.04 0.00 46.73 3.46
1825 2026 8.740123 TGTCACAAAATGTAAAAGAGAAGGTA 57.260 30.769 0.00 0.00 0.00 3.08
1882 2083 4.434330 GCGTAATGTAGCTGTTCTGTTCAC 60.434 45.833 0.00 0.00 0.00 3.18
1925 2126 0.179121 TCGCCAACGCACGATAGATT 60.179 50.000 0.00 0.00 39.84 2.40
1926 2127 0.595053 CTCGCCAACGCACGATAGAT 60.595 55.000 0.00 0.00 37.72 1.98
1928 2129 1.472276 GACTCGCCAACGCACGATAG 61.472 60.000 0.00 0.00 37.72 2.08
1931 2132 4.273257 TGACTCGCCAACGCACGA 62.273 61.111 0.00 0.00 39.84 4.35
1932 2133 3.767230 CTGACTCGCCAACGCACG 61.767 66.667 0.00 0.00 39.84 5.34
1935 2136 2.357034 TTCCTGACTCGCCAACGC 60.357 61.111 0.00 0.00 39.84 4.84
1936 2137 0.670546 ATGTTCCTGACTCGCCAACG 60.671 55.000 0.00 0.00 42.01 4.10
1937 2138 1.079503 GATGTTCCTGACTCGCCAAC 58.920 55.000 0.00 0.00 0.00 3.77
1958 2159 4.892934 ACAATAGTCCTCTCCTCATCAGTC 59.107 45.833 0.00 0.00 0.00 3.51
1999 2200 3.712881 GTGGCGTGTCGGTGAAGC 61.713 66.667 0.00 0.00 0.00 3.86
2000 2201 3.403057 CGTGGCGTGTCGGTGAAG 61.403 66.667 0.00 0.00 0.00 3.02
2001 2202 4.953868 CCGTGGCGTGTCGGTGAA 62.954 66.667 6.23 0.00 41.58 3.18
2016 2217 3.997064 CTTCCTCGAGCACTGGCCG 62.997 68.421 6.99 0.00 42.56 6.13
2017 2218 2.125350 CTTCCTCGAGCACTGGCC 60.125 66.667 6.99 0.00 42.56 5.36
2018 2219 2.125350 CCTTCCTCGAGCACTGGC 60.125 66.667 6.99 0.00 41.61 4.85
2019 2220 2.581354 CCCTTCCTCGAGCACTGG 59.419 66.667 6.99 5.99 0.00 4.00
2020 2221 2.581354 CCCCTTCCTCGAGCACTG 59.419 66.667 6.99 0.00 0.00 3.66
2021 2222 2.685380 CCCCCTTCCTCGAGCACT 60.685 66.667 6.99 0.00 0.00 4.40
2022 2223 2.245438 CTTCCCCCTTCCTCGAGCAC 62.245 65.000 6.99 0.00 0.00 4.40
2023 2224 1.990060 CTTCCCCCTTCCTCGAGCA 60.990 63.158 6.99 0.00 0.00 4.26
2024 2225 1.681486 CTCTTCCCCCTTCCTCGAGC 61.681 65.000 6.99 0.00 0.00 5.03
2025 2226 1.681486 GCTCTTCCCCCTTCCTCGAG 61.681 65.000 5.13 5.13 0.00 4.04
2026 2227 1.686110 GCTCTTCCCCCTTCCTCGA 60.686 63.158 0.00 0.00 0.00 4.04
2027 2228 2.904131 GCTCTTCCCCCTTCCTCG 59.096 66.667 0.00 0.00 0.00 4.63
2028 2229 2.736826 CCGCTCTTCCCCCTTCCTC 61.737 68.421 0.00 0.00 0.00 3.71
2029 2230 2.689034 CCGCTCTTCCCCCTTCCT 60.689 66.667 0.00 0.00 0.00 3.36
2116 2317 4.787286 TGCATACCAACCGGCGGG 62.787 66.667 31.78 15.34 40.11 6.13
2117 2318 2.515991 ATGCATACCAACCGGCGG 60.516 61.111 27.06 27.06 34.57 6.13
2118 2319 2.715005 CATGCATACCAACCGGCG 59.285 61.111 0.00 0.00 34.57 6.46
2119 2320 1.737355 ATGCATGCATACCAACCGGC 61.737 55.000 31.35 0.00 34.49 6.13
2120 2321 0.311790 GATGCATGCATACCAACCGG 59.688 55.000 32.27 0.00 36.70 5.28
2121 2322 1.023502 TGATGCATGCATACCAACCG 58.976 50.000 32.27 0.00 36.70 4.44
2122 2323 2.481795 GGTTGATGCATGCATACCAACC 60.482 50.000 40.23 40.23 35.93 3.77
2123 2324 2.481795 GGGTTGATGCATGCATACCAAC 60.482 50.000 36.39 35.71 36.99 3.77
2124 2325 1.755959 GGGTTGATGCATGCATACCAA 59.244 47.619 36.39 30.47 36.99 3.67
2125 2326 1.063792 AGGGTTGATGCATGCATACCA 60.064 47.619 36.39 27.61 36.99 3.25
2126 2327 1.696063 AGGGTTGATGCATGCATACC 58.304 50.000 31.86 31.86 36.70 2.73
2127 2328 2.689471 TGAAGGGTTGATGCATGCATAC 59.311 45.455 32.27 25.80 36.70 2.39
2128 2329 2.953648 CTGAAGGGTTGATGCATGCATA 59.046 45.455 32.27 16.12 36.70 3.14
2129 2330 1.754803 CTGAAGGGTTGATGCATGCAT 59.245 47.619 32.66 32.66 39.69 3.96
2130 2331 1.179152 CTGAAGGGTTGATGCATGCA 58.821 50.000 25.04 25.04 0.00 3.96
2131 2332 0.179119 GCTGAAGGGTTGATGCATGC 60.179 55.000 11.82 11.82 0.00 4.06
2132 2333 0.458669 GGCTGAAGGGTTGATGCATG 59.541 55.000 2.46 0.00 0.00 4.06
2170 2371 1.668826 AGAGTTGCTGATGGGGGTAA 58.331 50.000 0.00 0.00 0.00 2.85
2174 2375 2.114616 AGACTAGAGTTGCTGATGGGG 58.885 52.381 0.00 0.00 0.00 4.96
2177 2378 5.826601 TCTACAGACTAGAGTTGCTGATG 57.173 43.478 0.00 0.00 32.86 3.07
2183 2384 5.347342 CAAGGCATCTACAGACTAGAGTTG 58.653 45.833 0.00 0.00 0.00 3.16
2267 2468 1.860950 CTTCGTCATATGAAGTGCCGG 59.139 52.381 16.71 0.00 36.68 6.13
2279 2480 2.009774 GCTGTATGGTTGCTTCGTCAT 58.990 47.619 0.00 0.00 0.00 3.06
2309 2510 7.675062 TCTCTGAGAAGCTTAATTCAGAAACT 58.325 34.615 25.54 7.66 43.75 2.66
2364 2565 6.594788 AGACCGTACAAGGTTTGTTAGATA 57.405 37.500 0.00 0.00 46.09 1.98
2382 2583 6.128418 ACAAAACAAAACCAAATCAAAGACCG 60.128 34.615 0.00 0.00 0.00 4.79
2430 2631 5.554437 TTTGAACTGTGTCCACCATACTA 57.446 39.130 0.00 0.00 0.00 1.82
2431 2632 4.431416 TTTGAACTGTGTCCACCATACT 57.569 40.909 0.00 0.00 0.00 2.12
2435 2636 4.097741 CAGAATTTTGAACTGTGTCCACCA 59.902 41.667 0.00 0.00 0.00 4.17
2436 2637 4.338118 TCAGAATTTTGAACTGTGTCCACC 59.662 41.667 0.00 0.00 33.93 4.61
2437 2638 5.499139 TCAGAATTTTGAACTGTGTCCAC 57.501 39.130 0.00 0.00 33.93 4.02
2438 2639 6.713762 ATTCAGAATTTTGAACTGTGTCCA 57.286 33.333 13.15 0.00 39.68 4.02
2439 2640 6.980397 ACAATTCAGAATTTTGAACTGTGTCC 59.020 34.615 20.80 0.00 43.46 4.02
2449 2653 8.007716 GTCAATGAAGCACAATTCAGAATTTTG 58.992 33.333 15.18 15.18 42.20 2.44
2482 2686 9.185192 GAATTTTGAACTGACCTGAACTTTATG 57.815 33.333 0.00 0.00 0.00 1.90
2483 2687 9.136323 AGAATTTTGAACTGACCTGAACTTTAT 57.864 29.630 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.