Multiple sequence alignment - TraesCS7D01G211000

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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 TraesCS7D01G211000 chr7D 100.000 5437 0 0 1 5437 169381591 169387027 0.000000e+00 10041.0
1 TraesCS7D01G211000 chr7D 87.494 2039 183 34 1751 3761 638149214 638151208 0.000000e+00 2287.0
2 TraesCS7D01G211000 chr7D 87.705 244 24 5 1924 2165 91688665 91688904 4.150000e-71 279.0
3 TraesCS7D01G211000 chr7B 92.355 4840 217 70 675 5437 134554237 134559000 0.000000e+00 6746.0
4 TraesCS7D01G211000 chr7B 87.705 244 24 5 1924 2165 43246671 43246432 4.150000e-71 279.0
5 TraesCS7D01G211000 chr7B 82.390 318 27 15 271 582 134553564 134553858 3.250000e-62 250.0
6 TraesCS7D01G211000 chr7A 92.885 1546 68 16 3920 5437 171383817 171385348 0.000000e+00 2207.0
7 TraesCS7D01G211000 chr7A 84.422 2388 163 84 1 2314 171380076 171382328 0.000000e+00 2156.0
8 TraesCS7D01G211000 chr7A 91.739 1501 109 11 2377 3871 171382322 171383813 0.000000e+00 2071.0
9 TraesCS7D01G211000 chr7A 86.853 251 20 8 1924 2164 93255372 93255619 8.980000e-68 268.0
10 TraesCS7D01G211000 chr3D 87.024 1942 188 35 1788 3709 570094450 570092553 0.000000e+00 2132.0
11 TraesCS7D01G211000 chr1A 88.462 78 6 3 46 122 551546528 551546453 2.090000e-14 91.6


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 TraesCS7D01G211000 chr7D 169381591 169387027 5436 False 10041.000000 10041 100.0000 1 5437 1 chr7D.!!$F2 5436
1 TraesCS7D01G211000 chr7D 638149214 638151208 1994 False 2287.000000 2287 87.4940 1751 3761 1 chr7D.!!$F3 2010
2 TraesCS7D01G211000 chr7B 134553564 134559000 5436 False 3498.000000 6746 87.3725 271 5437 2 chr7B.!!$F1 5166
3 TraesCS7D01G211000 chr7A 171380076 171385348 5272 False 2144.666667 2207 89.6820 1 5437 3 chr7A.!!$F2 5436
4 TraesCS7D01G211000 chr3D 570092553 570094450 1897 True 2132.000000 2132 87.0240 1788 3709 1 chr3D.!!$R1 1921

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
786 1099 0.033228 TTGCAAGCATCCAAAACCCG 59.967 50.000 0.00 0.00 0.00 5.28 F
1032 1376 0.041312 CGTTGCTGTCGGGAAAACAG 60.041 55.000 0.00 0.00 45.57 3.16 F
1034 1378 0.106918 TTGCTGTCGGGAAAACAGGT 60.107 50.000 5.51 0.00 43.50 4.00 F
1037 1381 0.107831 CTGTCGGGAAAACAGGTGGA 59.892 55.000 0.00 0.00 40.36 4.02 F
1511 1894 0.469144 TCTTGGCCTTGGGTTGGTTC 60.469 55.000 3.32 0.00 0.00 3.62 F
1566 1949 1.000145 GGAGTTTCTCGGTCGCATTC 59.000 55.000 0.00 0.00 0.00 2.67 F
2420 2842 1.002087 AGTCCACAACGTTCCTGATCC 59.998 52.381 0.00 0.00 0.00 3.36 F
4014 4444 1.265635 TCCCAAGAACGTTCGCAATTG 59.734 47.619 21.87 18.98 0.00 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2339 2761 0.179250 CCACAGAAATTGCGTCGTCG 60.179 55.000 0.00 0.00 40.37 5.12 R
2994 3421 0.251832 GGGAGACTCACTCTGGACCA 60.252 60.000 4.53 0.00 44.37 4.02 R
3095 3522 2.666190 CAGGGCATGCCGTATCCG 60.666 66.667 30.23 15.17 36.85 4.18 R
3153 3580 1.345741 TGCAGTTTGAGTCCTGAGAGG 59.654 52.381 0.00 0.00 36.46 3.69 R
3458 3887 1.366366 GTGCTGTACACGTCCCTGT 59.634 57.895 0.00 0.00 40.07 4.00 R
3489 3918 2.432510 CTCCTGACCTCCATAGTTCACC 59.567 54.545 0.00 0.00 0.00 4.02 R
4305 4735 0.180642 TACGCAACCAACTTCCCACA 59.819 50.000 0.00 0.00 0.00 4.17 R
5149 5612 0.112995 AATGGAGCTCCTGTTTGCCA 59.887 50.000 32.28 11.70 36.82 4.92 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
68 69 5.700832 ACATGTGTAGTGTTCGATGAAATGT 59.299 36.000 0.00 0.00 0.00 2.71
71 72 3.924073 TGTAGTGTTCGATGAAATGTCCG 59.076 43.478 0.00 0.00 0.00 4.79
93 94 3.008485 GGGAGAGAAAAGGCTTGAGAGAA 59.992 47.826 0.00 0.00 0.00 2.87
111 112 6.070938 TGAGAGAAGAGTGTTGATGATGACAT 60.071 38.462 0.00 0.00 39.67 3.06
120 121 0.106569 GATGATGACATGTGGGCCCA 60.107 55.000 24.45 24.45 36.82 5.36
179 180 4.856801 GCGGGCCACGGATGTCAT 62.857 66.667 4.39 0.00 44.51 3.06
180 181 2.818841 CGGGCCACGGATGTCATA 59.181 61.111 4.39 0.00 39.42 2.15
181 182 1.145156 CGGGCCACGGATGTCATAA 59.855 57.895 4.39 0.00 39.42 1.90
184 185 1.148310 GGCCACGGATGTCATAATCG 58.852 55.000 0.00 0.00 0.00 3.34
206 207 0.036388 ATCATTGTGAGCCGAACGGT 60.036 50.000 14.63 1.93 37.65 4.83
207 208 0.604073 TCATTGTGAGCCGAACGGTA 59.396 50.000 14.63 0.00 37.65 4.02
209 210 1.127951 CATTGTGAGCCGAACGGTAAC 59.872 52.381 14.63 10.61 37.65 2.50
210 211 0.390124 TTGTGAGCCGAACGGTAACT 59.610 50.000 14.63 3.53 37.65 2.24
211 212 1.246649 TGTGAGCCGAACGGTAACTA 58.753 50.000 14.63 0.00 37.65 2.24
212 213 1.200716 TGTGAGCCGAACGGTAACTAG 59.799 52.381 14.63 0.00 37.65 2.57
213 214 1.200948 GTGAGCCGAACGGTAACTAGT 59.799 52.381 14.63 0.00 37.65 2.57
228 230 4.558538 AACTAGTGTTTCTTTGCAGCAG 57.441 40.909 0.00 0.00 31.37 4.24
254 256 3.340814 ACTCAAGTTGGTAGGCATCAG 57.659 47.619 2.34 0.00 0.00 2.90
255 257 2.026822 ACTCAAGTTGGTAGGCATCAGG 60.027 50.000 2.34 0.00 0.00 3.86
256 258 1.985159 TCAAGTTGGTAGGCATCAGGT 59.015 47.619 2.34 0.00 0.00 4.00
257 259 2.375174 TCAAGTTGGTAGGCATCAGGTT 59.625 45.455 2.34 0.00 0.00 3.50
258 260 2.749621 CAAGTTGGTAGGCATCAGGTTC 59.250 50.000 0.00 0.00 0.00 3.62
259 261 2.269940 AGTTGGTAGGCATCAGGTTCT 58.730 47.619 0.00 0.00 0.00 3.01
260 262 2.237392 AGTTGGTAGGCATCAGGTTCTC 59.763 50.000 0.00 0.00 0.00 2.87
261 263 1.951209 TGGTAGGCATCAGGTTCTCA 58.049 50.000 0.00 0.00 0.00 3.27
262 264 2.265367 TGGTAGGCATCAGGTTCTCAA 58.735 47.619 0.00 0.00 0.00 3.02
263 265 2.642311 TGGTAGGCATCAGGTTCTCAAA 59.358 45.455 0.00 0.00 0.00 2.69
264 266 3.073798 TGGTAGGCATCAGGTTCTCAAAA 59.926 43.478 0.00 0.00 0.00 2.44
265 267 4.079253 GGTAGGCATCAGGTTCTCAAAAA 58.921 43.478 0.00 0.00 0.00 1.94
339 342 1.102978 ATGACCCAAATTGCGGTAGC 58.897 50.000 6.20 0.00 45.41 3.58
340 343 0.037590 TGACCCAAATTGCGGTAGCT 59.962 50.000 6.20 0.00 45.42 3.32
424 427 2.053627 CAAGAAAGCGTCACAAATGCC 58.946 47.619 0.00 0.00 41.10 4.40
426 429 0.598065 GAAAGCGTCACAAATGCCCT 59.402 50.000 0.00 0.00 41.10 5.19
427 430 0.314935 AAAGCGTCACAAATGCCCTG 59.685 50.000 0.00 0.00 41.10 4.45
432 435 1.610624 CGTCACAAATGCCCTGGTAGT 60.611 52.381 0.00 0.00 0.00 2.73
478 482 0.179059 TCGACACTTGCACCACACAT 60.179 50.000 0.00 0.00 0.00 3.21
595 626 2.686816 GGCCAACGACAATGACCGG 61.687 63.158 0.00 0.00 0.00 5.28
613 644 4.933064 CGGCCTCGATCGCCTCAC 62.933 72.222 18.51 0.00 44.73 3.51
614 645 3.532155 GGCCTCGATCGCCTCACT 61.532 66.667 11.09 0.00 43.48 3.41
615 646 2.279120 GCCTCGATCGCCTCACTG 60.279 66.667 11.09 0.00 0.00 3.66
616 647 2.415010 CCTCGATCGCCTCACTGG 59.585 66.667 11.09 0.00 39.35 4.00
640 671 2.807895 GCAACATGCAGCGCCTTG 60.808 61.111 2.29 0.00 44.26 3.61
641 672 2.807895 CAACATGCAGCGCCTTGC 60.808 61.111 14.21 14.21 46.98 4.01
684 990 7.415229 CAAACTTCACTTTACTACCTTCCAAC 58.585 38.462 0.00 0.00 0.00 3.77
700 1008 3.986116 AACTCCGCCCTCCTCCTCC 62.986 68.421 0.00 0.00 0.00 4.30
786 1099 0.033228 TTGCAAGCATCCAAAACCCG 59.967 50.000 0.00 0.00 0.00 5.28
834 1158 1.671901 AACCCAAACCAAGCACACGG 61.672 55.000 0.00 0.00 0.00 4.94
915 1240 2.726351 CGCTCCTTGTCCTCCTCCC 61.726 68.421 0.00 0.00 0.00 4.30
923 1248 1.000646 GTCCTCCTCCCTCGTGTCT 60.001 63.158 0.00 0.00 0.00 3.41
945 1270 2.041405 CCACCTCCTCCTCCTCCC 60.041 72.222 0.00 0.00 0.00 4.30
946 1271 2.641746 CCACCTCCTCCTCCTCCCT 61.642 68.421 0.00 0.00 0.00 4.20
960 1300 0.324285 CTCCCTCTCTTGCAACAGCT 59.676 55.000 0.00 0.00 0.00 4.24
961 1301 1.552337 CTCCCTCTCTTGCAACAGCTA 59.448 52.381 0.00 0.00 0.00 3.32
1028 1372 2.975799 GCCGTTGCTGTCGGGAAA 60.976 61.111 14.23 0.00 46.90 3.13
1029 1373 2.548295 GCCGTTGCTGTCGGGAAAA 61.548 57.895 14.23 0.00 46.90 2.29
1030 1374 1.281656 CCGTTGCTGTCGGGAAAAC 59.718 57.895 6.84 0.00 43.68 2.43
1031 1375 1.440938 CCGTTGCTGTCGGGAAAACA 61.441 55.000 6.84 0.00 43.68 2.83
1032 1376 0.041312 CGTTGCTGTCGGGAAAACAG 60.041 55.000 0.00 0.00 45.57 3.16
1033 1377 0.310854 GTTGCTGTCGGGAAAACAGG 59.689 55.000 5.51 0.00 43.50 4.00
1034 1378 0.106918 TTGCTGTCGGGAAAACAGGT 60.107 50.000 5.51 0.00 43.50 4.00
1037 1381 0.107831 CTGTCGGGAAAACAGGTGGA 59.892 55.000 0.00 0.00 40.36 4.02
1049 1393 0.972983 CAGGTGGAGGAGGACACGAT 60.973 60.000 0.00 0.00 38.46 3.73
1253 1606 2.066999 CCTTCTCCTTCTCCGGGGG 61.067 68.421 0.00 0.00 0.00 5.40
1505 1888 1.484653 GTTTGTTTCTTGGCCTTGGGT 59.515 47.619 3.32 0.00 0.00 4.51
1511 1894 0.469144 TCTTGGCCTTGGGTTGGTTC 60.469 55.000 3.32 0.00 0.00 3.62
1522 1905 1.611519 GGTTGGTTCGGTTGATTCCA 58.388 50.000 0.00 0.00 0.00 3.53
1525 1908 2.817258 GTTGGTTCGGTTGATTCCATGA 59.183 45.455 0.00 0.00 31.63 3.07
1557 1940 4.621991 TCTTGTCTTCTTGGAGTTTCTCG 58.378 43.478 0.00 0.00 0.00 4.04
1566 1949 1.000145 GGAGTTTCTCGGTCGCATTC 59.000 55.000 0.00 0.00 0.00 2.67
1601 1984 4.559153 GGTTGGATCACCATTTTTGTCAG 58.441 43.478 0.00 0.00 46.34 3.51
1784 2175 6.096705 ACATGAATGACCTGTCAAAAAGAACA 59.903 34.615 3.79 0.00 43.58 3.18
1865 2269 5.968582 CCAACAGGGATTTGTTCTTTGGAAC 60.969 44.000 2.38 2.38 44.75 3.62
1877 2281 5.489335 GTTCTTTGGAACGTTGCATTTTTC 58.511 37.500 23.52 10.50 41.70 2.29
1878 2282 5.004922 TCTTTGGAACGTTGCATTTTTCT 57.995 34.783 23.52 0.00 0.00 2.52
1888 2292 4.557296 CGTTGCATTTTTCTGTCCTGTCAT 60.557 41.667 0.00 0.00 0.00 3.06
1939 2345 9.793245 GACCGTCGACATATTAAAATAAGAATG 57.207 33.333 17.16 0.00 0.00 2.67
1994 2403 7.961283 GCTACTAGTATAAACCAACAAGCAAAC 59.039 37.037 2.33 0.00 0.00 2.93
2056 2465 3.614176 TCAGATCAATCTTTCTGTTCGCG 59.386 43.478 0.00 0.00 40.22 5.87
2170 2592 5.756195 TCTGATTGTTAATATGCAGGCAC 57.244 39.130 0.00 0.00 0.00 5.01
2336 2758 1.134560 GTGATAAGAACTCGGCCTCGT 59.865 52.381 0.00 0.00 37.69 4.18
2339 2761 2.262471 TAAGAACTCGGCCTCGTCGC 62.262 60.000 0.00 0.00 37.69 5.19
2391 2813 2.286872 CAGTGTTCCATCATGAGCCTC 58.713 52.381 0.09 0.00 0.00 4.70
2403 2825 4.012374 TCATGAGCCTCATTTCCAAAGTC 58.988 43.478 3.97 0.00 34.28 3.01
2408 2830 2.627699 GCCTCATTTCCAAAGTCCACAA 59.372 45.455 0.00 0.00 0.00 3.33
2420 2842 1.002087 AGTCCACAACGTTCCTGATCC 59.998 52.381 0.00 0.00 0.00 3.36
2423 2845 1.375523 ACAACGTTCCTGATCCGCC 60.376 57.895 0.00 0.00 0.00 6.13
2532 2957 2.672195 GCAAGGCAACCAAGATTACTGC 60.672 50.000 0.00 0.00 37.17 4.40
2781 3208 3.337358 TGTTAGGTGTGCACATGATCAG 58.663 45.455 24.69 0.00 0.00 2.90
2994 3421 2.978946 ATGGGTTCCCGTCCGCAAT 61.979 57.895 3.27 0.00 0.00 3.56
3084 3511 2.224426 TGAATATCATGGTACCCCGCAC 60.224 50.000 10.07 0.00 0.00 5.34
3149 3576 8.704849 TCTTCAAGAAATCTTAACCAATTCCA 57.295 30.769 0.00 0.00 34.28 3.53
3153 3580 7.176690 TCAAGAAATCTTAACCAATTCCAGTCC 59.823 37.037 0.00 0.00 34.28 3.85
3242 3669 6.369059 ACTTCTTTCTGATATTTGCATCGG 57.631 37.500 0.00 0.00 33.32 4.18
3260 3687 3.071479 TCGGCTCCACAAATAAAGTGAC 58.929 45.455 0.00 0.00 39.30 3.67
3261 3688 3.074412 CGGCTCCACAAATAAAGTGACT 58.926 45.455 0.00 0.00 39.30 3.41
3340 3767 6.762702 TTATATCCATGCATTATGCTGTGG 57.237 37.500 25.23 25.23 45.31 4.17
3392 3821 1.532437 TGCGCTTCTTGTGATCTGTTG 59.468 47.619 9.73 0.00 0.00 3.33
3458 3887 4.261155 GCAGTTCTGCATTTTGTGTACTGA 60.261 41.667 18.26 0.00 34.41 3.41
3489 3918 3.189910 TGTACAGCACGGTAGTACAGAAG 59.810 47.826 7.48 1.03 42.08 2.85
3670 4099 4.290985 TGAAATGGGTTCAGTTCCATCCTA 59.709 41.667 4.51 0.00 44.53 2.94
3673 4103 4.069312 TGGGTTCAGTTCCATCCTACTA 57.931 45.455 0.00 0.00 0.00 1.82
3675 4105 4.031611 GGGTTCAGTTCCATCCTACTACT 58.968 47.826 0.00 0.00 0.00 2.57
3823 4253 6.961576 TGGAAATCTGTTGGTAGTTAAAACG 58.038 36.000 0.00 0.00 0.00 3.60
3898 4328 7.823745 TTCATTAGAAATAATCCTGCCCTTC 57.176 36.000 0.00 0.00 0.00 3.46
3899 4329 7.154191 TCATTAGAAATAATCCTGCCCTTCT 57.846 36.000 0.00 0.00 0.00 2.85
3900 4330 7.000472 TCATTAGAAATAATCCTGCCCTTCTG 59.000 38.462 0.00 0.00 0.00 3.02
3901 4331 4.870021 AGAAATAATCCTGCCCTTCTGT 57.130 40.909 0.00 0.00 0.00 3.41
3902 4332 4.786425 AGAAATAATCCTGCCCTTCTGTC 58.214 43.478 0.00 0.00 0.00 3.51
3959 4389 1.405105 GTGAAGCAACTGTTCAAGCCA 59.595 47.619 0.00 0.00 35.71 4.75
3981 4411 3.455990 TGCTTCTGCATTTCAGCAAAA 57.544 38.095 6.75 0.00 45.31 2.44
3987 4417 3.069872 TCTGCATTTCAGCAAAACATGGT 59.930 39.130 0.00 0.00 45.13 3.55
4014 4444 1.265635 TCCCAAGAACGTTCGCAATTG 59.734 47.619 21.87 18.98 0.00 2.32
4081 4511 3.128242 CCAGCAATCACTTCAACCTCATC 59.872 47.826 0.00 0.00 0.00 2.92
4305 4735 2.957402 TGTTGCAGATGTTTCCCTCT 57.043 45.000 0.00 0.00 0.00 3.69
4363 4793 1.406065 ATCGGATGGGCTCAGTCAGG 61.406 60.000 0.00 0.00 0.00 3.86
4369 4799 2.745492 GGCTCAGTCAGGCTGCAC 60.745 66.667 10.34 9.19 44.64 4.57
4746 5176 8.206325 AGTAGCAGTTATGTGATTTCTGATTG 57.794 34.615 0.00 0.00 0.00 2.67
4791 5230 7.175990 GTCCAATATACAGGAGTTTTTGGTTGA 59.824 37.037 0.00 0.00 33.85 3.18
4809 5248 1.960689 TGATGGAATATCGCGTGGAGA 59.039 47.619 5.77 0.00 0.00 3.71
4811 5250 1.107945 TGGAATATCGCGTGGAGACA 58.892 50.000 5.77 0.00 38.70 3.41
4865 5304 2.299582 TCATGTCCAAACAATGCCCAAG 59.700 45.455 0.00 0.00 39.30 3.61
4991 5430 5.095691 ACTCATGAGCAAACTAAAACACG 57.904 39.130 22.83 0.00 0.00 4.49
5021 5460 1.696336 CCATCATCAGGTAGGTCAGGG 59.304 57.143 0.00 0.00 0.00 4.45
5133 5585 7.678947 ACTTCAGAAATACAAGGATCAACAG 57.321 36.000 0.00 0.00 0.00 3.16
5146 5609 5.186198 AGGATCAACAGTGTTACCATTAGC 58.814 41.667 20.43 4.15 0.00 3.09
5149 5612 3.071479 CAACAGTGTTACCATTAGCGGT 58.929 45.455 8.49 0.00 43.46 5.68
5211 5677 1.597195 TCATTGCACACACACGAGTTC 59.403 47.619 0.00 0.00 0.00 3.01
5212 5678 1.330213 CATTGCACACACACGAGTTCA 59.670 47.619 0.00 0.00 0.00 3.18
5257 5723 8.696175 CGTCCAAAATTATTAAACAAACTGGAC 58.304 33.333 13.23 13.23 43.60 4.02
5261 5727 8.484008 CAAAATTATTAAACAAACTGGACCACG 58.516 33.333 0.00 0.00 0.00 4.94
5293 5759 1.435346 AAGGTTTCCAGGTGGAGGGG 61.435 60.000 0.00 0.00 46.36 4.79
5302 5768 4.748144 GTGGAGGGGCCTTGCAGG 62.748 72.222 10.86 0.00 38.80 4.85
5335 5801 1.604278 GTCAACTCTTCAGCCCAACAC 59.396 52.381 0.00 0.00 0.00 3.32
5357 5823 6.316140 ACACATCTGCATATTTTAGCGAGAAA 59.684 34.615 0.00 0.00 0.00 2.52
5367 5833 3.564027 GCGAGAAACCCGCCATCG 61.564 66.667 0.00 0.00 46.22 3.84
5371 5837 3.192922 GAAACCCGCCATCGTCCG 61.193 66.667 0.00 0.00 0.00 4.79
5409 5875 0.326264 CCTCCACAGGGTCCTTGAAG 59.674 60.000 8.21 2.37 35.89 3.02
5433 5899 0.455410 CCTTCTCACTCAGCTCCTCG 59.545 60.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.047655 CCGTAGGCAACAAGGCGA 60.048 61.111 0.00 0.00 46.14 5.54
35 36 3.390135 ACACTACACATGTTGTCCTTCG 58.610 45.455 0.00 0.00 39.91 3.79
37 38 3.807622 CGAACACTACACATGTTGTCCTT 59.192 43.478 0.00 0.00 40.36 3.36
51 52 3.517602 CCGGACATTTCATCGAACACTA 58.482 45.455 0.00 0.00 0.00 2.74
68 69 0.324943 CAAGCCTTTTCTCTCCCGGA 59.675 55.000 0.73 0.00 0.00 5.14
71 72 2.569404 TCTCTCAAGCCTTTTCTCTCCC 59.431 50.000 0.00 0.00 0.00 4.30
93 94 4.259356 CCACATGTCATCATCAACACTCT 58.741 43.478 0.00 0.00 31.15 3.24
111 112 2.017668 AAGTTGGACATGGGCCCACA 62.018 55.000 31.51 18.84 31.11 4.17
120 121 4.647611 TGATTGACCGTTAAGTTGGACAT 58.352 39.130 0.00 0.00 30.35 3.06
176 177 4.751600 GGCTCACAATGATGTCGATTATGA 59.248 41.667 0.00 0.00 37.82 2.15
177 178 4.376717 CGGCTCACAATGATGTCGATTATG 60.377 45.833 0.00 0.00 37.82 1.90
178 179 3.742882 CGGCTCACAATGATGTCGATTAT 59.257 43.478 0.00 0.00 37.82 1.28
179 180 3.123050 CGGCTCACAATGATGTCGATTA 58.877 45.455 0.00 0.00 37.82 1.75
180 181 1.935873 CGGCTCACAATGATGTCGATT 59.064 47.619 0.00 0.00 37.82 3.34
181 182 1.136891 TCGGCTCACAATGATGTCGAT 59.863 47.619 0.00 0.00 37.82 3.59
184 185 1.061131 CGTTCGGCTCACAATGATGTC 59.939 52.381 0.00 0.00 37.82 3.06
187 188 0.036388 ACCGTTCGGCTCACAATGAT 60.036 50.000 11.32 0.00 0.00 2.45
191 192 0.390124 AGTTACCGTTCGGCTCACAA 59.610 50.000 11.32 0.00 0.00 3.33
206 207 5.364778 TCTGCTGCAAAGAAACACTAGTTA 58.635 37.500 3.02 0.00 36.84 2.24
207 208 4.199310 TCTGCTGCAAAGAAACACTAGTT 58.801 39.130 3.02 0.00 40.40 2.24
209 210 5.368256 AATCTGCTGCAAAGAAACACTAG 57.632 39.130 3.02 0.00 0.00 2.57
210 211 7.824289 AGTATAATCTGCTGCAAAGAAACACTA 59.176 33.333 3.02 0.00 0.00 2.74
211 212 5.972107 ATAATCTGCTGCAAAGAAACACT 57.028 34.783 3.02 0.00 0.00 3.55
212 213 6.846350 AGTATAATCTGCTGCAAAGAAACAC 58.154 36.000 3.02 0.00 0.00 3.32
213 214 6.654582 TGAGTATAATCTGCTGCAAAGAAACA 59.345 34.615 3.02 0.00 0.00 2.83
228 230 7.217200 TGATGCCTACCAACTTGAGTATAATC 58.783 38.462 0.00 0.00 0.00 1.75
263 265 5.600696 CTGATGCCTACCAACTTTGTTTTT 58.399 37.500 0.00 0.00 0.00 1.94
264 266 4.501400 GCTGATGCCTACCAACTTTGTTTT 60.501 41.667 0.00 0.00 0.00 2.43
265 267 3.005791 GCTGATGCCTACCAACTTTGTTT 59.994 43.478 0.00 0.00 0.00 2.83
266 268 2.558359 GCTGATGCCTACCAACTTTGTT 59.442 45.455 0.00 0.00 0.00 2.83
267 269 2.162681 GCTGATGCCTACCAACTTTGT 58.837 47.619 0.00 0.00 0.00 2.83
268 270 2.927553 GCTGATGCCTACCAACTTTG 57.072 50.000 0.00 0.00 0.00 2.77
387 390 9.237846 CGCTTTCTTGTAATCTTTTTCTTTTCT 57.762 29.630 0.00 0.00 0.00 2.52
388 391 9.020813 ACGCTTTCTTGTAATCTTTTTCTTTTC 57.979 29.630 0.00 0.00 0.00 2.29
389 392 8.926715 ACGCTTTCTTGTAATCTTTTTCTTTT 57.073 26.923 0.00 0.00 0.00 2.27
390 393 8.188139 TGACGCTTTCTTGTAATCTTTTTCTTT 58.812 29.630 0.00 0.00 0.00 2.52
391 394 7.644157 GTGACGCTTTCTTGTAATCTTTTTCTT 59.356 33.333 0.00 0.00 0.00 2.52
392 395 7.132863 GTGACGCTTTCTTGTAATCTTTTTCT 58.867 34.615 0.00 0.00 0.00 2.52
393 396 6.910433 TGTGACGCTTTCTTGTAATCTTTTTC 59.090 34.615 0.00 0.00 0.00 2.29
394 397 6.791303 TGTGACGCTTTCTTGTAATCTTTTT 58.209 32.000 0.00 0.00 0.00 1.94
395 398 6.371809 TGTGACGCTTTCTTGTAATCTTTT 57.628 33.333 0.00 0.00 0.00 2.27
396 399 6.371809 TTGTGACGCTTTCTTGTAATCTTT 57.628 33.333 0.00 0.00 0.00 2.52
397 400 6.371809 TTTGTGACGCTTTCTTGTAATCTT 57.628 33.333 0.00 0.00 0.00 2.40
398 401 6.373779 CATTTGTGACGCTTTCTTGTAATCT 58.626 36.000 0.00 0.00 0.00 2.40
399 402 5.059710 GCATTTGTGACGCTTTCTTGTAATC 59.940 40.000 0.00 0.00 0.00 1.75
412 415 1.086696 CTACCAGGGCATTTGTGACG 58.913 55.000 0.00 0.00 0.00 4.35
424 427 2.236395 CCACCTTTCACCTACTACCAGG 59.764 54.545 0.00 0.00 41.87 4.45
426 429 3.263369 TCCACCTTTCACCTACTACCA 57.737 47.619 0.00 0.00 0.00 3.25
427 430 4.838904 ATTCCACCTTTCACCTACTACC 57.161 45.455 0.00 0.00 0.00 3.18
469 473 1.577328 GACCGCTGGAATGTGTGGTG 61.577 60.000 2.81 0.00 45.76 4.17
478 482 2.668632 GGTGGATGACCGCTGGAA 59.331 61.111 1.50 0.00 45.13 3.53
608 639 3.855503 TTGCTGCCTGCCAGTGAGG 62.856 63.158 0.00 0.00 43.71 3.86
609 640 2.281970 TTGCTGCCTGCCAGTGAG 60.282 61.111 0.00 0.00 43.71 3.51
610 641 2.595463 GTTGCTGCCTGCCAGTGA 60.595 61.111 0.00 0.00 43.71 3.41
611 642 2.273179 ATGTTGCTGCCTGCCAGTG 61.273 57.895 0.00 0.00 43.71 3.66
612 643 2.116772 ATGTTGCTGCCTGCCAGT 59.883 55.556 0.00 0.00 43.71 4.00
613 644 2.571757 CATGTTGCTGCCTGCCAG 59.428 61.111 0.00 0.00 44.67 4.85
614 645 3.687102 GCATGTTGCTGCCTGCCA 61.687 61.111 0.00 0.00 40.96 4.92
615 646 3.642778 CTGCATGTTGCTGCCTGCC 62.643 63.158 0.00 0.00 45.31 4.85
616 647 2.126071 CTGCATGTTGCTGCCTGC 60.126 61.111 0.00 1.96 45.31 4.85
623 654 2.807895 CAAGGCGCTGCATGTTGC 60.808 61.111 7.64 0.00 45.29 4.17
635 666 4.421479 CAGCAGCAGCAGCAAGGC 62.421 66.667 12.92 4.03 45.49 4.35
684 990 4.150454 AGGAGGAGGAGGGCGGAG 62.150 72.222 0.00 0.00 0.00 4.63
834 1158 0.819582 ATGCTGGTTGCTGGTTATGC 59.180 50.000 0.00 0.00 43.37 3.14
837 1161 1.305219 GCGATGCTGGTTGCTGGTTA 61.305 55.000 0.00 0.00 43.37 2.85
838 1162 2.629656 GCGATGCTGGTTGCTGGTT 61.630 57.895 0.00 0.00 43.37 3.67
843 1167 1.226491 GTGATGCGATGCTGGTTGC 60.226 57.895 0.00 0.00 43.25 4.17
895 1220 3.708220 GAGGAGGACAAGGAGCGCG 62.708 68.421 0.00 0.00 0.00 6.86
896 1221 2.185608 GAGGAGGACAAGGAGCGC 59.814 66.667 0.00 0.00 0.00 5.92
897 1222 2.726351 GGGAGGAGGACAAGGAGCG 61.726 68.421 0.00 0.00 0.00 5.03
898 1223 1.306568 AGGGAGGAGGACAAGGAGC 60.307 63.158 0.00 0.00 0.00 4.70
899 1224 1.040339 CGAGGGAGGAGGACAAGGAG 61.040 65.000 0.00 0.00 0.00 3.69
900 1225 1.000486 CGAGGGAGGAGGACAAGGA 60.000 63.158 0.00 0.00 0.00 3.36
901 1226 1.305381 ACGAGGGAGGAGGACAAGG 60.305 63.158 0.00 0.00 0.00 3.61
902 1227 0.900647 ACACGAGGGAGGAGGACAAG 60.901 60.000 0.00 0.00 0.00 3.16
903 1228 0.898789 GACACGAGGGAGGAGGACAA 60.899 60.000 0.00 0.00 0.00 3.18
904 1229 1.304217 GACACGAGGGAGGAGGACA 60.304 63.158 0.00 0.00 0.00 4.02
905 1230 0.255318 TAGACACGAGGGAGGAGGAC 59.745 60.000 0.00 0.00 0.00 3.85
906 1231 0.255318 GTAGACACGAGGGAGGAGGA 59.745 60.000 0.00 0.00 0.00 3.71
907 1232 2.796500 GTAGACACGAGGGAGGAGG 58.204 63.158 0.00 0.00 0.00 4.30
923 1248 1.212934 AGGAGGAGGAGGTGGTCGTA 61.213 60.000 0.00 0.00 0.00 3.43
931 1256 0.998945 AGAGAGGGAGGAGGAGGAGG 60.999 65.000 0.00 0.00 0.00 4.30
945 1270 3.124976 GCTTTCTAGCTGTTGCAAGAGAG 59.875 47.826 26.47 15.60 44.27 3.20
946 1271 3.070018 GCTTTCTAGCTGTTGCAAGAGA 58.930 45.455 26.47 6.31 44.27 3.10
960 1300 6.282568 AGAGGGATAGTTCTAGGCTTTCTA 57.717 41.667 0.00 0.00 0.00 2.10
961 1301 5.150944 AGAGGGATAGTTCTAGGCTTTCT 57.849 43.478 0.00 0.00 0.00 2.52
972 1312 2.753507 CGAGGCCTGTAGAGGGATAGTT 60.754 54.545 12.00 0.00 40.19 2.24
1023 1367 0.038310 CCTCCTCCACCTGTTTTCCC 59.962 60.000 0.00 0.00 0.00 3.97
1024 1368 1.064825 TCCTCCTCCACCTGTTTTCC 58.935 55.000 0.00 0.00 0.00 3.13
1025 1369 1.420138 TGTCCTCCTCCACCTGTTTTC 59.580 52.381 0.00 0.00 0.00 2.29
1026 1370 1.143073 GTGTCCTCCTCCACCTGTTTT 59.857 52.381 0.00 0.00 0.00 2.43
1027 1371 0.765510 GTGTCCTCCTCCACCTGTTT 59.234 55.000 0.00 0.00 0.00 2.83
1028 1372 1.472662 CGTGTCCTCCTCCACCTGTT 61.473 60.000 0.00 0.00 0.00 3.16
1029 1373 1.908793 CGTGTCCTCCTCCACCTGT 60.909 63.158 0.00 0.00 0.00 4.00
1030 1374 0.972983 ATCGTGTCCTCCTCCACCTG 60.973 60.000 0.00 0.00 0.00 4.00
1031 1375 0.972983 CATCGTGTCCTCCTCCACCT 60.973 60.000 0.00 0.00 0.00 4.00
1032 1376 1.517832 CATCGTGTCCTCCTCCACC 59.482 63.158 0.00 0.00 0.00 4.61
1033 1377 1.153549 GCATCGTGTCCTCCTCCAC 60.154 63.158 0.00 0.00 0.00 4.02
1034 1378 2.359169 GGCATCGTGTCCTCCTCCA 61.359 63.158 0.00 0.00 0.00 3.86
1037 1381 4.148825 GCGGCATCGTGTCCTCCT 62.149 66.667 0.00 0.00 38.89 3.69
1141 1494 2.989639 CCTCCATGCCCGTCTCAA 59.010 61.111 0.00 0.00 0.00 3.02
1253 1606 0.756815 GCCCCATTTCCAGTCATCCC 60.757 60.000 0.00 0.00 0.00 3.85
1257 1610 1.299648 CTCGCCCCATTTCCAGTCA 59.700 57.895 0.00 0.00 0.00 3.41
1505 1888 3.081061 CTCATGGAATCAACCGAACCAA 58.919 45.455 0.00 0.00 36.01 3.67
1511 1894 3.441163 CAAATGCTCATGGAATCAACCG 58.559 45.455 0.00 0.00 0.00 4.44
1522 1905 5.075493 AGAAGACAAGAACCAAATGCTCAT 58.925 37.500 0.00 0.00 0.00 2.90
1525 1908 4.038402 CCAAGAAGACAAGAACCAAATGCT 59.962 41.667 0.00 0.00 0.00 3.79
1557 1940 1.153349 GTCCCTGGAGAATGCGACC 60.153 63.158 0.00 0.00 0.00 4.79
1566 1949 1.192146 TCCAACCGAAGTCCCTGGAG 61.192 60.000 0.00 0.00 32.42 3.86
1689 2073 2.096811 GTGTCCAATTTGCAAACATGCG 60.097 45.455 15.41 10.53 37.69 4.73
1784 2175 3.117888 AGGGTTCAACTCACTCATGTGTT 60.118 43.478 0.00 0.00 44.14 3.32
1865 2269 3.243035 TGACAGGACAGAAAAATGCAACG 60.243 43.478 0.00 0.00 0.00 4.10
1877 2281 1.025113 CAGCAGGCATGACAGGACAG 61.025 60.000 0.62 0.00 0.00 3.51
1878 2282 1.002990 CAGCAGGCATGACAGGACA 60.003 57.895 0.62 0.00 0.00 4.02
1888 2292 1.077501 GCTTATGACCCAGCAGGCA 60.078 57.895 0.00 0.00 40.58 4.75
1939 2345 8.877779 CATGCCTATATCTAAATACAGACTTGC 58.122 37.037 0.00 0.00 0.00 4.01
1944 2350 7.258441 GCGACATGCCTATATCTAAATACAGA 58.742 38.462 0.00 0.00 37.76 3.41
1994 2403 2.022129 GAGGTCGACGGTGCAAGTG 61.022 63.158 9.92 0.00 0.00 3.16
1999 2408 1.006571 TTTGAGAGGTCGACGGTGC 60.007 57.895 9.92 0.00 0.00 5.01
2056 2465 7.875971 ACAGGACTTTGTCAAAGATTAATCAC 58.124 34.615 28.07 7.37 41.02 3.06
2170 2592 6.150976 TGCCAATGTTTATGGAAGTGAAGTAG 59.849 38.462 0.00 0.00 40.56 2.57
2339 2761 0.179250 CCACAGAAATTGCGTCGTCG 60.179 55.000 0.00 0.00 40.37 5.12
2340 2762 1.144969 TCCACAGAAATTGCGTCGTC 58.855 50.000 0.00 0.00 0.00 4.20
2341 2763 1.808411 ATCCACAGAAATTGCGTCGT 58.192 45.000 0.00 0.00 0.00 4.34
2391 2813 3.708563 ACGTTGTGGACTTTGGAAATG 57.291 42.857 0.00 0.00 0.00 2.32
2403 2825 1.635663 GCGGATCAGGAACGTTGTGG 61.636 60.000 5.00 0.00 0.00 4.17
2408 2830 1.258445 AAGAGGCGGATCAGGAACGT 61.258 55.000 0.00 0.00 0.00 3.99
2420 2842 3.132289 TCCCTGTAACAAGATAAGAGGCG 59.868 47.826 0.00 0.00 0.00 5.52
2423 2845 5.422331 TGAGGTCCCTGTAACAAGATAAGAG 59.578 44.000 0.00 0.00 0.00 2.85
2524 2949 3.226347 GTTTGCAAGTGTCGCAGTAATC 58.774 45.455 0.00 0.00 41.18 1.75
2641 3066 4.290155 CCGAAGACAAAGTCCATGTTTTG 58.710 43.478 11.02 11.02 39.55 2.44
2781 3208 1.809547 GAGTCCAGAAGCTTTCCTTGC 59.190 52.381 0.00 0.00 32.78 4.01
2994 3421 0.251832 GGGAGACTCACTCTGGACCA 60.252 60.000 4.53 0.00 44.37 4.02
3095 3522 2.666190 CAGGGCATGCCGTATCCG 60.666 66.667 30.23 15.17 36.85 4.18
3153 3580 1.345741 TGCAGTTTGAGTCCTGAGAGG 59.654 52.381 0.00 0.00 36.46 3.69
3238 3665 3.689649 GTCACTTTATTTGTGGAGCCGAT 59.310 43.478 0.00 0.00 36.21 4.18
3242 3669 3.440522 GGGAGTCACTTTATTTGTGGAGC 59.559 47.826 0.00 0.00 36.21 4.70
3340 3767 4.009675 TGTATGGTGAAGGAAATCTGTGC 58.990 43.478 0.00 0.00 0.00 4.57
3354 3782 5.101628 AGCGCAATGTTTTTATGTATGGTG 58.898 37.500 11.47 0.00 0.00 4.17
3392 3821 8.871686 AACCTCAACAAAGTGAATTTTCATAC 57.128 30.769 0.00 0.00 39.73 2.39
3458 3887 1.366366 GTGCTGTACACGTCCCTGT 59.634 57.895 0.00 0.00 40.07 4.00
3489 3918 2.432510 CTCCTGACCTCCATAGTTCACC 59.567 54.545 0.00 0.00 0.00 4.02
3717 4147 2.037136 CGTGCAAAGCCTGGAGAGG 61.037 63.158 0.00 0.00 43.19 3.69
3732 4162 3.601356 GTTTGATCTGATTCATCGCGTG 58.399 45.455 5.77 3.96 0.00 5.34
3823 4253 3.423571 CGATGATCAAGAAGCAAACAGC 58.576 45.455 0.00 0.00 46.19 4.40
3888 4318 1.704628 TCATTTGACAGAAGGGCAGGA 59.295 47.619 0.00 0.00 0.00 3.86
3899 4329 8.156280 CTGAAAAATGCTCAGTGTCATTTGACA 61.156 37.037 19.21 9.27 44.78 3.58
3900 4330 5.978919 TGAAAAATGCTCAGTGTCATTTGAC 59.021 36.000 19.21 16.64 40.73 3.18
3901 4331 6.146601 TGAAAAATGCTCAGTGTCATTTGA 57.853 33.333 19.21 9.52 40.73 2.69
3902 4332 5.404366 CCTGAAAAATGCTCAGTGTCATTTG 59.596 40.000 19.21 11.17 40.73 2.32
3981 4411 3.524095 TCTTGGGATCACAAACCATGT 57.476 42.857 12.36 0.00 45.34 3.21
3987 4417 2.546368 CGAACGTTCTTGGGATCACAAA 59.454 45.455 24.80 0.18 0.00 2.83
4014 4444 2.427453 TGATCAAGTAGTTCTCGGGAGC 59.573 50.000 0.00 0.00 0.00 4.70
4305 4735 0.180642 TACGCAACCAACTTCCCACA 59.819 50.000 0.00 0.00 0.00 4.17
4363 4793 4.648626 TCTGTGGCCTGGTGCAGC 62.649 66.667 9.47 9.47 43.89 5.25
4369 4799 1.962144 CTTGCTTTCTGTGGCCTGG 59.038 57.895 3.32 0.00 0.00 4.45
4791 5230 1.686587 TGTCTCCACGCGATATTCCAT 59.313 47.619 15.93 0.00 0.00 3.41
4865 5304 1.269726 CCATGTGTTGGTGAGGTTTGC 60.270 52.381 0.00 0.00 40.99 3.68
4991 5430 1.072965 CCTGATGATGGGAAGGTAGCC 59.927 57.143 0.00 0.00 0.00 3.93
5021 5460 6.674694 ATAATGTGTGCAAGAGAGATGTTC 57.325 37.500 0.00 0.00 0.00 3.18
5071 5510 6.173339 ACATGTTACTCTTGGATAGTTGGTG 58.827 40.000 0.00 0.00 0.00 4.17
5111 5563 6.998074 ACACTGTTGATCCTTGTATTTCTGAA 59.002 34.615 0.00 0.00 0.00 3.02
5113 5565 6.808008 ACACTGTTGATCCTTGTATTTCTG 57.192 37.500 0.00 0.00 0.00 3.02
5133 5585 1.946747 TGCCACCGCTAATGGTAACAC 60.947 52.381 0.00 0.00 43.65 3.32
5146 5609 2.281761 AGCTCCTGTTTGCCACCG 60.282 61.111 0.00 0.00 0.00 4.94
5149 5612 0.112995 AATGGAGCTCCTGTTTGCCA 59.887 50.000 32.28 11.70 36.82 4.92
5187 5651 1.866601 TCGTGTGTGTGCAATGAGAAG 59.133 47.619 0.00 0.00 0.00 2.85
5190 5654 1.220529 ACTCGTGTGTGTGCAATGAG 58.779 50.000 3.51 3.51 32.62 2.90
5211 5677 7.145323 TGGACGATGACATGTGTATAATACTG 58.855 38.462 1.15 0.00 0.00 2.74
5212 5678 7.284919 TGGACGATGACATGTGTATAATACT 57.715 36.000 1.15 0.00 0.00 2.12
5257 5723 1.867233 CCTTGTCACTCACTTTCGTGG 59.133 52.381 0.00 0.00 41.53 4.94
5261 5727 3.945285 TGGAAACCTTGTCACTCACTTTC 59.055 43.478 0.00 0.00 0.00 2.62
5272 5738 0.478507 CCTCCACCTGGAAACCTTGT 59.521 55.000 0.00 0.00 44.91 3.16
5302 5768 2.159366 AGAGTTGACATCGACGATGACC 60.159 50.000 37.26 27.60 42.09 4.02
5335 5801 6.138761 GGTTTCTCGCTAAAATATGCAGATG 58.861 40.000 0.00 0.00 0.00 2.90
5409 5875 2.418060 GGAGCTGAGTGAGAAGGCTAAC 60.418 54.545 0.00 0.00 33.13 2.34


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

AutoCloner maintained by Alex Coulton.