Multiple sequence alignment - TraesCS4A01G419800

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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 TraesCS4A01G419800 chr4A 100.000 6347 0 0 1 6347 690624564 690618218 0.000000e+00 11721.0
1 TraesCS4A01G419800 chr4A 94.023 3463 132 25 2910 6347 690411342 690414754 0.000000e+00 5179.0
2 TraesCS4A01G419800 chr4A 91.230 878 38 21 979 1830 690409525 690410389 0.000000e+00 1158.0
3 TraesCS4A01G419800 chr4A 93.478 506 31 2 2308 2812 690410832 690411336 0.000000e+00 750.0
4 TraesCS4A01G419800 chr4A 91.469 422 18 6 1884 2305 690410389 690410792 1.190000e-156 564.0
5 TraesCS4A01G419800 chr4A 83.436 326 47 6 580 904 690409092 690409411 4.810000e-76 296.0
6 TraesCS4A01G419800 chr4A 93.782 193 12 0 2050 2242 690620230 690620038 2.240000e-74 291.0
7 TraesCS4A01G419800 chr4A 93.782 193 12 0 4335 4527 690622515 690622323 2.240000e-74 291.0
8 TraesCS4A01G419800 chr4A 91.795 195 16 0 4333 4527 690410535 690410729 8.110000e-69 272.0
9 TraesCS4A01G419800 chr4A 71.026 497 136 8 3094 3587 294120887 294121378 5.200000e-21 113.0
10 TraesCS4A01G419800 chr7D 94.949 2831 124 8 2910 5737 34373371 34376185 0.000000e+00 4418.0
11 TraesCS4A01G419800 chr7D 90.966 1915 116 14 4333 6198 34471550 34473456 0.000000e+00 2525.0
12 TraesCS4A01G419800 chr7D 83.376 2334 206 86 1 2238 34469493 34471740 0.000000e+00 1993.0
13 TraesCS4A01G419800 chr7D 95.539 1233 54 1 3001 4233 34756490 34755259 0.000000e+00 1971.0
14 TraesCS4A01G419800 chr7D 94.765 1108 56 2 4271 5376 34755262 34754155 0.000000e+00 1724.0
15 TraesCS4A01G419800 chr7D 90.000 870 40 17 993 1830 34758926 34758072 0.000000e+00 1081.0
16 TraesCS4A01G419800 chr7D 88.303 872 60 18 5374 6221 34754071 34753218 0.000000e+00 1007.0
17 TraesCS4A01G419800 chr7D 94.473 579 27 3 5739 6317 34376279 34376852 0.000000e+00 887.0
18 TraesCS4A01G419800 chr7D 88.997 718 34 20 1037 1725 34371609 34372310 0.000000e+00 846.0
19 TraesCS4A01G419800 chr7D 94.892 509 25 1 2308 2815 34372860 34373368 0.000000e+00 795.0
20 TraesCS4A01G419800 chr7D 91.555 521 27 7 1792 2305 34372310 34372820 0.000000e+00 702.0
21 TraesCS4A01G419800 chr7D 91.943 422 24 3 1884 2305 34758072 34757661 3.300000e-162 582.0
22 TraesCS4A01G419800 chr7D 95.938 320 13 0 2311 2630 34757618 34757299 2.620000e-143 520.0
23 TraesCS4A01G419800 chr7D 94.301 193 11 0 2050 2242 34374781 34374973 4.810000e-76 296.0
24 TraesCS4A01G419800 chr7D 93.814 194 11 1 2050 2242 34755198 34755005 2.240000e-74 291.0
25 TraesCS4A01G419800 chr7D 91.282 195 17 0 4333 4527 34757918 34757724 3.770000e-67 267.0
26 TraesCS4A01G419800 chr7D 96.154 130 4 1 2687 2815 34757097 34756968 1.790000e-50 211.0
27 TraesCS4A01G419800 chr7D 97.273 110 3 0 2910 3019 34756965 34756856 3.020000e-43 187.0
28 TraesCS4A01G419800 chr7D 90.845 142 5 5 6206 6347 34753129 34752996 3.910000e-42 183.0
29 TraesCS4A01G419800 chr7D 100.000 95 0 0 2816 2910 382008720 382008814 6.540000e-40 176.0
30 TraesCS4A01G419800 chr7D 78.333 120 20 6 401 517 605837860 605837976 8.830000e-09 73.1
31 TraesCS4A01G419800 chr7D 95.238 42 2 0 5742 5783 34376209 34376250 4.110000e-07 67.6
32 TraesCS4A01G419800 chr7A 91.592 2022 106 25 4315 6317 35001823 34999847 0.000000e+00 2734.0
33 TraesCS4A01G419800 chr7A 91.652 1114 67 10 4340 5427 34744480 34745593 0.000000e+00 1519.0
34 TraesCS4A01G419800 chr7A 90.312 898 56 13 5423 6317 34963791 34962922 0.000000e+00 1147.0
35 TraesCS4A01G419800 chr7A 89.241 883 57 10 5457 6317 34745589 34746455 0.000000e+00 1070.0
36 TraesCS4A01G419800 chr7A 87.436 780 46 23 977 1725 35003041 35002283 0.000000e+00 850.0
37 TraesCS4A01G419800 chr7A 84.884 860 85 15 932 1776 34743354 34744183 0.000000e+00 826.0
38 TraesCS4A01G419800 chr7A 86.687 323 26 7 1916 2238 34744358 34744663 6.090000e-90 342.0
39 TraesCS4A01G419800 chr7A 94.819 193 10 0 2050 2242 35001804 35001612 1.030000e-77 302.0
40 TraesCS4A01G419800 chr7A 85.098 255 24 6 1837 2081 35002065 35001815 1.370000e-61 248.0
41 TraesCS4A01G419800 chr7A 80.317 315 34 12 598 909 34742925 34743214 4.980000e-51 213.0
42 TraesCS4A01G419800 chr7A 69.084 1103 294 43 3094 4164 605159794 605160881 3.130000e-18 104.0
43 TraesCS4A01G419800 chr2B 95.511 401 17 1 4516 4916 704812733 704813132 1.930000e-179 640.0
44 TraesCS4A01G419800 chr2B 88.971 272 27 3 1287 1557 704812365 704812634 3.670000e-87 333.0
45 TraesCS4A01G419800 chr2B 71.608 398 96 15 3344 3728 502774839 502775232 6.780000e-15 93.5
46 TraesCS4A01G419800 chrUn 100.000 95 0 0 2816 2910 403918329 403918235 6.540000e-40 176.0
47 TraesCS4A01G419800 chrUn 89.831 59 5 1 2758 2815 132257939 132257881 2.450000e-09 75.0
48 TraesCS4A01G419800 chr5B 100.000 95 0 0 2816 2910 713040365 713040459 6.540000e-40 176.0
49 TraesCS4A01G419800 chr5A 100.000 95 0 0 2816 2910 16617820 16617914 6.540000e-40 176.0
50 TraesCS4A01G419800 chr5A 100.000 95 0 0 2816 2910 300054420 300054326 6.540000e-40 176.0
51 TraesCS4A01G419800 chr4D 100.000 95 0 0 2816 2910 123373232 123373138 6.540000e-40 176.0
52 TraesCS4A01G419800 chr4D 100.000 95 0 0 2816 2910 123584023 123583929 6.540000e-40 176.0
53 TraesCS4A01G419800 chr4D 96.078 102 4 0 2910 3011 74079405 74079506 3.940000e-37 167.0
54 TraesCS4A01G419800 chr2D 100.000 95 0 0 2816 2910 17961778 17961872 6.540000e-40 176.0
55 TraesCS4A01G419800 chr2D 100.000 95 0 0 2816 2910 635042702 635042608 6.540000e-40 176.0
56 TraesCS4A01G419800 chr1D 72.987 559 127 24 3093 3640 18932829 18933374 2.350000e-39 174.0
57 TraesCS4A01G419800 chr1D 96.040 101 4 0 2910 3010 95869103 95869003 1.420000e-36 165.0
58 TraesCS4A01G419800 chr6D 97.000 100 3 0 2910 3009 320698132 320698231 1.090000e-37 169.0
59 TraesCS4A01G419800 chr6A 96.040 101 4 0 2910 3010 538097732 538097832 1.420000e-36 165.0
60 TraesCS4A01G419800 chr3B 94.393 107 6 0 2910 3016 521797870 521797764 1.420000e-36 165.0
61 TraesCS4A01G419800 chr3B 100.000 28 0 0 535 562 6954671 6954698 1.100000e-02 52.8
62 TraesCS4A01G419800 chr1B 96.040 101 4 0 2910 3010 156850476 156850576 1.420000e-36 165.0
63 TraesCS4A01G419800 chr1B 69.459 1110 291 43 3109 4185 631864422 631863328 1.860000e-25 128.0
64 TraesCS4A01G419800 chr3A 68.962 1118 300 42 3094 4178 512265482 512266585 1.460000e-16 99.0
65 TraesCS4A01G419800 chr3A 71.393 402 96 17 3344 3731 165767011 165766615 3.150000e-13 87.9
66 TraesCS4A01G419800 chr7B 79.231 130 20 7 392 517 689919238 689919364 4.080000e-12 84.2
67 TraesCS4A01G419800 chr1A 94.286 35 2 0 2761 2795 540208359 540208393 3.000000e-03 54.7


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 TraesCS4A01G419800 chr4A 690618218 690624564 6346 True 11721.000000 11721 100.000000 1 6347 1 chr4A.!!$R1 6346
1 TraesCS4A01G419800 chr4A 690409092 690414754 5662 False 1369.833333 5179 90.905167 580 6347 6 chr4A.!!$F2 5767
2 TraesCS4A01G419800 chr4A 690620038 690622515 2477 True 291.000000 291 93.782000 2050 4527 2 chr4A.!!$R2 2477
3 TraesCS4A01G419800 chr7D 34469493 34473456 3963 False 2259.000000 2525 87.171000 1 6198 2 chr7D.!!$F4 6197
4 TraesCS4A01G419800 chr7D 34371609 34376852 5243 False 1144.514286 4418 93.486429 1037 6317 7 chr7D.!!$F3 5280
5 TraesCS4A01G419800 chr7D 34752996 34758926 5930 True 729.454545 1971 93.259636 993 6347 11 chr7D.!!$R1 5354
6 TraesCS4A01G419800 chr7A 34962922 34963791 869 True 1147.000000 1147 90.312000 5423 6317 1 chr7A.!!$R1 894
7 TraesCS4A01G419800 chr7A 34999847 35003041 3194 True 1033.500000 2734 89.736250 977 6317 4 chr7A.!!$R2 5340
8 TraesCS4A01G419800 chr7A 34742925 34746455 3530 False 794.000000 1519 86.556200 598 6317 5 chr7A.!!$F2 5719
9 TraesCS4A01G419800 chr2B 704812365 704813132 767 False 486.500000 640 92.241000 1287 4916 2 chr2B.!!$F2 3629

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
926 944 0.036388 TCTAGCTCCCCGCAAAGTTG 60.036 55.000 0.00 0.0 42.61 3.16 F
1395 1611 1.006102 CAAGACCGAGGTTCGTGCT 60.006 57.895 0.00 0.0 38.40 4.40 F
1628 1846 1.096386 CATGCAGCTTCTCCTCAGGC 61.096 60.000 0.00 0.0 0.00 4.85 F
2036 2577 1.494824 CGGTTCTCGTCGGACTTTTT 58.505 50.000 6.57 0.0 0.00 1.94 F
5148 6303 1.334160 TTCTTCGTGCCACTACCTCA 58.666 50.000 0.00 0.0 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2006 2547 1.508088 GAGAACCGCCTGGCATTTG 59.492 57.895 20.29 6.23 39.70 2.32 R
4721 5873 5.574443 GGCATTAAACGTTAGAACTCGTAGT 59.426 40.000 0.00 0.00 39.39 2.73 R
4761 5913 4.444306 GGCAGACTGGCATTGTAATAGGTA 60.444 45.833 23.18 0.00 43.14 3.08 R
5316 6471 0.875059 CCTCCGGCTTCACAAAGAAC 59.125 55.000 0.00 0.00 34.14 3.01 R
6234 7684 0.811616 GCCCTCACCGTTGCAGATAG 60.812 60.000 0.00 0.00 0.00 2.08 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 7.887996 TTTCTATGCACATTTGTCATTTTCC 57.112 32.000 0.00 0.00 0.00 3.13
69 70 7.440198 TCTATGCACATTTGTCATTTTCCAAA 58.560 30.769 0.00 0.00 35.25 3.28
70 71 8.095792 TCTATGCACATTTGTCATTTTCCAAAT 58.904 29.630 0.00 0.00 40.85 2.32
75 76 9.896263 GCACATTTGTCATTTTCCAAATATTTT 57.104 25.926 0.00 0.00 38.79 1.82
218 219 9.936759 AAAGAAAAACAAATAAACACTCAAGGA 57.063 25.926 0.00 0.00 0.00 3.36
226 227 0.180406 AACACTCAAGGACTGCGGTT 59.820 50.000 0.00 0.00 0.00 4.44
232 234 0.588252 CAAGGACTGCGGTTCTGTTG 59.412 55.000 7.42 0.00 30.42 3.33
237 239 1.227823 CTGCGGTTCTGTTGGTCCA 60.228 57.895 0.00 0.00 0.00 4.02
238 240 1.227823 TGCGGTTCTGTTGGTCCAG 60.228 57.895 0.00 0.00 0.00 3.86
247 249 0.038166 TGTTGGTCCAGGCCATTCTC 59.962 55.000 5.01 0.00 38.48 2.87
250 252 2.670148 GGTCCAGGCCATTCTCGGT 61.670 63.158 5.01 0.00 0.00 4.69
266 268 2.558313 GTGTTGCTTGAGGCGAGC 59.442 61.111 0.00 0.00 45.43 5.03
267 269 2.669569 TGTTGCTTGAGGCGAGCC 60.670 61.111 5.89 5.89 45.43 4.70
276 278 3.710722 AGGCGAGCCTCTTGTGGG 61.711 66.667 11.42 0.00 44.43 4.61
277 279 4.021925 GGCGAGCCTCTTGTGGGT 62.022 66.667 6.90 0.00 40.97 4.51
278 280 2.032681 GCGAGCCTCTTGTGGGTT 59.967 61.111 0.00 0.00 38.02 4.11
279 281 2.328099 GCGAGCCTCTTGTGGGTTG 61.328 63.158 0.00 4.35 40.86 3.77
281 283 1.230635 CGAGCCTCTTGTGGGTTGTG 61.231 60.000 0.00 0.00 38.02 3.33
282 284 0.890996 GAGCCTCTTGTGGGTTGTGG 60.891 60.000 0.00 0.00 38.02 4.17
283 285 1.150536 GCCTCTTGTGGGTTGTGGA 59.849 57.895 0.00 0.00 0.00 4.02
284 286 1.172812 GCCTCTTGTGGGTTGTGGAC 61.173 60.000 0.00 0.00 0.00 4.02
292 294 2.267961 GGTTGTGGACCGGCCTAG 59.732 66.667 14.76 0.00 39.00 3.02
293 295 2.590114 GGTTGTGGACCGGCCTAGT 61.590 63.158 14.76 0.00 39.00 2.57
294 296 1.259840 GGTTGTGGACCGGCCTAGTA 61.260 60.000 14.76 0.00 39.00 1.82
296 298 1.208776 GTTGTGGACCGGCCTAGTATT 59.791 52.381 14.76 0.00 37.63 1.89
297 299 1.575419 TGTGGACCGGCCTAGTATTT 58.425 50.000 14.76 0.00 37.63 1.40
299 301 1.208776 GTGGACCGGCCTAGTATTTGT 59.791 52.381 14.76 0.00 37.63 2.83
300 302 2.431782 GTGGACCGGCCTAGTATTTGTA 59.568 50.000 14.76 0.00 37.63 2.41
301 303 2.696707 TGGACCGGCCTAGTATTTGTAG 59.303 50.000 14.76 0.00 37.63 2.74
302 304 2.547430 GGACCGGCCTAGTATTTGTAGC 60.547 54.545 0.00 0.00 0.00 3.58
303 305 2.101917 GACCGGCCTAGTATTTGTAGCA 59.898 50.000 0.00 0.00 0.00 3.49
304 306 2.704065 ACCGGCCTAGTATTTGTAGCAT 59.296 45.455 0.00 0.00 0.00 3.79
309 318 5.368989 GGCCTAGTATTTGTAGCATGTCTT 58.631 41.667 0.00 0.00 0.00 3.01
333 342 5.713792 TTCTTCTTTGTTTGTTCCACACA 57.286 34.783 0.00 0.00 0.00 3.72
419 428 4.392047 TCATTTCTCTGCAACACATGTCT 58.608 39.130 0.00 0.00 0.00 3.41
488 498 9.866936 CATTTTGTTCCACTCATTTAACATTTG 57.133 29.630 0.00 0.00 32.31 2.32
675 685 9.632807 TTGGACTATGCAAACATGTTTTTATAC 57.367 29.630 21.10 10.82 37.04 1.47
732 743 8.452989 AATTTCGTTTCAGATGCTTTAACATC 57.547 30.769 0.00 0.00 45.62 3.06
830 843 8.397575 TGTCACTTACATATTTTTGCAACCTA 57.602 30.769 0.00 0.00 31.43 3.08
864 878 9.554724 TTATTAAAAGTAGAGCGAGCATTTTTG 57.445 29.630 0.00 0.00 0.00 2.44
865 879 5.438761 AAAAGTAGAGCGAGCATTTTTGT 57.561 34.783 0.00 0.00 0.00 2.83
866 880 6.554334 AAAAGTAGAGCGAGCATTTTTGTA 57.446 33.333 0.00 0.00 0.00 2.41
872 886 4.032900 AGAGCGAGCATTTTTGTATACACG 59.967 41.667 4.68 4.53 0.00 4.49
917 935 5.471456 CACAATGAACATATTCTAGCTCCCC 59.529 44.000 0.00 0.00 35.69 4.81
926 944 0.036388 TCTAGCTCCCCGCAAAGTTG 60.036 55.000 0.00 0.00 42.61 3.16
1395 1611 1.006102 CAAGACCGAGGTTCGTGCT 60.006 57.895 0.00 0.00 38.40 4.40
1453 1670 1.154035 CCGGCCGTTGAATTTCAGC 60.154 57.895 26.12 3.37 0.00 4.26
1628 1846 1.096386 CATGCAGCTTCTCCTCAGGC 61.096 60.000 0.00 0.00 0.00 4.85
1692 1910 4.091424 GCTTCGTAATGCTGTCAATTGAC 58.909 43.478 28.10 28.10 44.97 3.18
1750 1968 5.220265 CGGATAAGTTGCATTTGTGAATTGC 60.220 40.000 0.00 0.00 0.00 3.56
1751 1969 5.638657 GGATAAGTTGCATTTGTGAATTGCA 59.361 36.000 0.00 0.00 31.83 4.08
1815 2033 4.008074 ACTGTGACTGTGGTGGATAAAG 57.992 45.455 0.00 0.00 0.00 1.85
1826 2044 7.937394 ACTGTGGTGGATAAAGTATAAATAGCC 59.063 37.037 0.00 0.00 0.00 3.93
1907 2440 5.786457 TCACTTTACTACATTCCCACCCTTA 59.214 40.000 0.00 0.00 0.00 2.69
1924 2457 5.404066 CACCCTTACCAAAAGCAAATAAACG 59.596 40.000 0.00 0.00 0.00 3.60
1958 2491 6.910433 TCGTGTTCAGCTCAAAATTTAAGTTC 59.090 34.615 0.00 0.00 0.00 3.01
2036 2577 1.494824 CGGTTCTCGTCGGACTTTTT 58.505 50.000 6.57 0.00 0.00 1.94
4621 5772 5.485353 AGAACCAGAATTCCTGATACTGTCA 59.515 40.000 0.65 0.00 45.78 3.58
4721 5873 3.127589 TCTTTTCTCGTTGCATTCGTCA 58.872 40.909 10.66 0.00 0.00 4.35
4761 5913 8.237267 CGTTTAATGCCTCAGAACTAATCTTTT 58.763 33.333 0.00 0.00 35.73 2.27
4766 5918 7.490657 TGCCTCAGAACTAATCTTTTACCTA 57.509 36.000 0.00 0.00 35.73 3.08
4958 6110 6.734502 TCCGTTGGTGTCCATATCTAAATA 57.265 37.500 0.00 0.00 31.53 1.40
5148 6303 1.334160 TTCTTCGTGCCACTACCTCA 58.666 50.000 0.00 0.00 0.00 3.86
5271 6426 4.332428 AGGTACGCAATCCTACCATAAC 57.668 45.455 1.08 0.00 35.71 1.89
5316 6471 2.213499 AGCCGGATTGCTTTTATCGAG 58.787 47.619 5.05 0.00 38.85 4.04
5405 6647 1.000060 CTTTGTTGGGCCTGTGTCATG 60.000 52.381 4.53 0.00 0.00 3.07
5471 6713 6.317857 GTGATGGCATTCTTTTTCTGTCTAC 58.682 40.000 0.00 0.00 0.00 2.59
5473 6715 6.716628 TGATGGCATTCTTTTTCTGTCTACTT 59.283 34.615 0.00 0.00 0.00 2.24
5689 6934 5.828299 TGAAAGGTGGAGTACAAAAACTG 57.172 39.130 0.00 0.00 0.00 3.16
5705 6950 5.365403 AAAACTGTTGACACGAACTGAAA 57.635 34.783 0.00 0.00 0.00 2.69
5737 6982 7.175641 CCCCAAATATGTGGATCATTTCTAGAC 59.824 40.741 14.07 0.00 41.65 2.59
5864 7210 3.944422 CAACTACATCGTATGTTGCCC 57.056 47.619 5.94 0.00 41.63 5.36
5878 7224 3.426615 TGTTGCCCGAAAATAATCCAGT 58.573 40.909 0.00 0.00 0.00 4.00
5882 7228 3.442273 TGCCCGAAAATAATCCAGTGTTC 59.558 43.478 0.00 0.00 0.00 3.18
5887 7233 5.220529 CCGAAAATAATCCAGTGTTCGTACC 60.221 44.000 8.41 0.00 36.91 3.34
5888 7234 5.349270 CGAAAATAATCCAGTGTTCGTACCA 59.651 40.000 2.59 0.00 34.64 3.25
5940 7286 2.882777 CGTAGCCTCGCACTGCTG 60.883 66.667 0.00 0.00 38.52 4.41
6028 7374 3.026694 GTTCAATTGCTAGCCATTCCCT 58.973 45.455 13.29 0.00 0.00 4.20
6202 7548 7.229306 ACATGTGGATTGGCTATACATTAACTG 59.771 37.037 0.00 0.00 30.15 3.16
6234 7684 4.319177 TGCCAGCTAAGAGAAGTTCTTTC 58.681 43.478 6.88 0.00 43.68 2.62
6336 7786 9.298250 AGTACAGTCAGTCAAGATCTTAACTTA 57.702 33.333 8.66 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 9.896263 AAAATATTTGGAAAATGACAAATGTGC 57.104 25.926 11.60 0.00 44.44 4.57
135 136 7.164230 TCTTTTACTTTTGCTTTGTCTTCCA 57.836 32.000 0.00 0.00 0.00 3.53
143 144 8.546597 TTGCTTTCTTCTTTTACTTTTGCTTT 57.453 26.923 0.00 0.00 0.00 3.51
196 197 7.277760 GCAGTCCTTGAGTGTTTATTTGTTTTT 59.722 33.333 1.30 0.00 35.61 1.94
197 198 6.756542 GCAGTCCTTGAGTGTTTATTTGTTTT 59.243 34.615 1.30 0.00 35.61 2.43
198 199 6.273071 GCAGTCCTTGAGTGTTTATTTGTTT 58.727 36.000 1.30 0.00 35.61 2.83
201 202 4.466828 CGCAGTCCTTGAGTGTTTATTTG 58.533 43.478 1.30 0.00 35.61 2.32
205 206 1.414919 ACCGCAGTCCTTGAGTGTTTA 59.585 47.619 1.30 0.00 35.61 2.01
218 219 1.227853 GGACCAACAGAACCGCAGT 60.228 57.895 0.00 0.00 0.00 4.40
226 227 0.038166 GAATGGCCTGGACCAACAGA 59.962 55.000 3.32 0.00 44.65 3.41
232 234 2.190578 CCGAGAATGGCCTGGACC 59.809 66.667 3.32 0.00 0.00 4.46
237 239 1.675641 GCAACACCGAGAATGGCCT 60.676 57.895 3.32 0.00 0.00 5.19
238 240 1.244019 AAGCAACACCGAGAATGGCC 61.244 55.000 0.00 0.00 0.00 5.36
247 249 2.664851 TCGCCTCAAGCAACACCG 60.665 61.111 0.00 0.00 44.04 4.94
250 252 2.669569 GGCTCGCCTCAAGCAACA 60.670 61.111 0.00 0.00 44.04 3.33
266 268 0.537371 GGTCCACAACCCACAAGAGG 60.537 60.000 0.00 0.00 42.85 3.69
267 269 0.884704 CGGTCCACAACCCACAAGAG 60.885 60.000 0.00 0.00 46.27 2.85
269 271 1.896660 CCGGTCCACAACCCACAAG 60.897 63.158 0.00 0.00 46.27 3.16
270 272 2.193517 CCGGTCCACAACCCACAA 59.806 61.111 0.00 0.00 46.27 3.33
271 273 4.572571 GCCGGTCCACAACCCACA 62.573 66.667 1.90 0.00 46.27 4.17
274 276 3.324108 TAGGCCGGTCCACAACCC 61.324 66.667 15.92 0.13 46.27 4.11
275 277 1.259840 TACTAGGCCGGTCCACAACC 61.260 60.000 15.92 0.87 45.45 3.77
276 278 0.828677 ATACTAGGCCGGTCCACAAC 59.171 55.000 15.92 0.00 37.29 3.32
277 279 1.575419 AATACTAGGCCGGTCCACAA 58.425 50.000 15.92 0.00 37.29 3.33
278 280 1.208535 CAAATACTAGGCCGGTCCACA 59.791 52.381 15.92 3.97 37.29 4.17
279 281 1.208776 ACAAATACTAGGCCGGTCCAC 59.791 52.381 15.92 0.00 37.29 4.02
281 283 2.547430 GCTACAAATACTAGGCCGGTCC 60.547 54.545 0.08 4.26 0.00 4.46
282 284 2.101917 TGCTACAAATACTAGGCCGGTC 59.898 50.000 0.00 0.00 0.00 4.79
283 285 2.112998 TGCTACAAATACTAGGCCGGT 58.887 47.619 1.90 9.24 0.00 5.28
284 286 2.902705 TGCTACAAATACTAGGCCGG 57.097 50.000 0.00 0.00 0.00 6.13
285 287 3.728845 ACATGCTACAAATACTAGGCCG 58.271 45.455 0.00 0.00 0.00 6.13
286 288 4.962155 AGACATGCTACAAATACTAGGCC 58.038 43.478 0.00 0.00 0.00 5.19
288 290 9.167311 AGAAAAAGACATGCTACAAATACTAGG 57.833 33.333 0.00 0.00 0.00 3.02
291 293 9.289782 AGAAGAAAAAGACATGCTACAAATACT 57.710 29.630 0.00 0.00 0.00 2.12
292 294 9.899226 AAGAAGAAAAAGACATGCTACAAATAC 57.101 29.630 0.00 0.00 0.00 1.89
294 296 9.252962 CAAAGAAGAAAAAGACATGCTACAAAT 57.747 29.630 0.00 0.00 0.00 2.32
296 298 7.771183 ACAAAGAAGAAAAAGACATGCTACAA 58.229 30.769 0.00 0.00 0.00 2.41
297 299 7.333528 ACAAAGAAGAAAAAGACATGCTACA 57.666 32.000 0.00 0.00 0.00 2.74
299 301 8.250332 ACAAACAAAGAAGAAAAAGACATGCTA 58.750 29.630 0.00 0.00 0.00 3.49
300 302 7.099120 ACAAACAAAGAAGAAAAAGACATGCT 58.901 30.769 0.00 0.00 0.00 3.79
301 303 7.294676 ACAAACAAAGAAGAAAAAGACATGC 57.705 32.000 0.00 0.00 0.00 4.06
302 304 8.382875 GGAACAAACAAAGAAGAAAAAGACATG 58.617 33.333 0.00 0.00 0.00 3.21
303 305 8.093927 TGGAACAAACAAAGAAGAAAAAGACAT 58.906 29.630 0.00 0.00 31.92 3.06
304 306 7.383843 GTGGAACAAACAAAGAAGAAAAAGACA 59.616 33.333 0.00 0.00 44.16 3.41
388 397 6.416161 GTGTTGCAGAGAAATGAAGAAAGAAC 59.584 38.462 0.00 0.00 0.00 3.01
391 400 5.824429 TGTGTTGCAGAGAAATGAAGAAAG 58.176 37.500 0.00 0.00 0.00 2.62
392 401 5.833406 TGTGTTGCAGAGAAATGAAGAAA 57.167 34.783 0.00 0.00 0.00 2.52
398 407 4.473199 CAGACATGTGTTGCAGAGAAATG 58.527 43.478 1.15 0.00 0.00 2.32
445 455 8.458573 AACAAAATGTTCCTGTTGTATACAGA 57.541 30.769 5.56 0.00 46.12 3.41
471 481 8.531622 TGTATTTGCAAATGTTAAATGAGTGG 57.468 30.769 30.43 0.00 0.00 4.00
691 702 9.180678 GAAACGAAATTTCTGTGACATATGTTT 57.819 29.630 15.92 13.04 43.06 2.83
694 705 8.229811 TCTGAAACGAAATTTCTGTGACATATG 58.770 33.333 15.92 0.00 46.05 1.78
696 707 7.722795 TCTGAAACGAAATTTCTGTGACATA 57.277 32.000 15.92 9.02 46.05 2.29
785 797 7.605691 AGTGACATCTTCTGAAAAGGTTATCTG 59.394 37.037 0.00 0.00 0.00 2.90
786 798 7.684529 AGTGACATCTTCTGAAAAGGTTATCT 58.315 34.615 0.00 0.00 0.00 1.98
787 799 7.913674 AGTGACATCTTCTGAAAAGGTTATC 57.086 36.000 0.00 0.00 0.00 1.75
856 869 5.723678 GCAAATGCCGTGTATACAAAAATGC 60.724 40.000 7.25 8.47 34.31 3.56
894 911 5.625150 GGGGAGCTAGAATATGTTCATTGT 58.375 41.667 4.92 0.00 36.79 2.71
926 944 5.279456 CCCATAAGCATTTACCTTTATGGGC 60.279 44.000 21.61 0.00 44.13 5.36
930 948 6.719829 GCCTACCCATAAGCATTTACCTTTAT 59.280 38.462 0.00 0.00 0.00 1.40
934 1073 3.181433 GGCCTACCCATAAGCATTTACCT 60.181 47.826 0.00 0.00 0.00 3.08
967 1106 4.108570 TCAGGCCTTGGATACTAAAAGGA 58.891 43.478 0.00 0.00 42.65 3.36
1081 1238 3.209812 CGAGCTCATCCCCGTCGA 61.210 66.667 15.40 0.00 32.32 4.20
1245 1432 3.842923 CCAGCGTGCGGAGGAGAT 61.843 66.667 0.00 0.00 0.00 2.75
1628 1846 3.472283 AGTAGGCAGAGAAGATGCATG 57.528 47.619 2.46 0.00 45.68 4.06
1692 1910 7.041635 TGCAAATGTCTAATGGGTTATGATG 57.958 36.000 0.00 0.00 0.00 3.07
1696 1914 8.514594 CGATTATGCAAATGTCTAATGGGTTAT 58.485 33.333 0.00 0.00 0.00 1.89
1882 2415 4.225267 AGGGTGGGAATGTAGTAAAGTGAG 59.775 45.833 0.00 0.00 0.00 3.51
1907 2440 5.006261 GCTTGAACGTTTATTTGCTTTTGGT 59.994 36.000 0.46 0.00 0.00 3.67
1924 2457 2.024176 GCTGAACACGAAGCTTGAAC 57.976 50.000 2.10 0.00 36.47 3.18
1958 2491 7.504403 ACTAAGTTACATCCATCTCCAGAATG 58.496 38.462 0.00 0.00 0.00 2.67
2006 2547 1.508088 GAGAACCGCCTGGCATTTG 59.492 57.895 20.29 6.23 39.70 2.32
2009 2550 3.665675 GACGAGAACCGCCTGGCAT 62.666 63.158 20.29 2.59 43.32 4.40
2047 2588 8.883731 GCACTGAATCAATGTATACACTTAAGT 58.116 33.333 7.96 1.12 0.00 2.24
2048 2589 9.102757 AGCACTGAATCAATGTATACACTTAAG 57.897 33.333 7.96 0.00 0.00 1.85
4721 5873 5.574443 GGCATTAAACGTTAGAACTCGTAGT 59.426 40.000 0.00 0.00 39.39 2.73
4761 5913 4.444306 GGCAGACTGGCATTGTAATAGGTA 60.444 45.833 23.18 0.00 43.14 3.08
4958 6110 8.034313 TCTATCTGCCAAATGGATTAAGTAGT 57.966 34.615 2.98 0.00 37.39 2.73
4981 6133 7.015292 TCGGTATTTGCATAGTAGGAGAATTCT 59.985 37.037 7.95 7.95 0.00 2.40
5148 6303 4.385825 TCAAGACGCTACTTGGAACATTT 58.614 39.130 15.90 0.00 44.84 2.32
5271 6426 1.075482 TTGAGCCCCTCCAGCAAAG 59.925 57.895 0.00 0.00 0.00 2.77
5316 6471 0.875059 CCTCCGGCTTCACAAAGAAC 59.125 55.000 0.00 0.00 34.14 3.01
5345 6500 6.058183 ACATGCTAGGGATCATTTGTACTTC 58.942 40.000 0.00 0.00 0.00 3.01
5349 6504 7.517320 ACAATACATGCTAGGGATCATTTGTA 58.483 34.615 0.00 0.00 0.00 2.41
5385 6627 1.000060 CATGACACAGGCCCAACAAAG 60.000 52.381 0.00 0.00 0.00 2.77
5405 6647 7.100409 ACTGAAGAAAAAGCTAGACCTCATAC 58.900 38.462 0.00 0.00 0.00 2.39
5480 6722 8.269317 ACAGAGCTGAGACTAGTAGTTTACTAT 58.731 37.037 3.85 0.00 40.25 2.12
5482 6724 6.373216 CACAGAGCTGAGACTAGTAGTTTACT 59.627 42.308 3.85 0.00 42.68 2.24
5551 6793 1.004745 AGGACGATGGCATGGACTTTT 59.995 47.619 16.77 0.00 0.00 2.27
5657 6900 7.970102 TGTACTCCACCTTTCAACTATTACTT 58.030 34.615 0.00 0.00 0.00 2.24
5669 6912 5.712917 TCAACAGTTTTTGTACTCCACCTTT 59.287 36.000 0.00 0.00 39.73 3.11
5689 6934 3.968724 GCTCAATTTCAGTTCGTGTCAAC 59.031 43.478 0.00 0.00 0.00 3.18
5705 6950 3.686227 TCCACATATTTGGGGCTCAAT 57.314 42.857 0.00 0.00 46.95 2.57
5864 7210 5.349270 TGGTACGAACACTGGATTATTTTCG 59.651 40.000 0.00 0.00 41.17 3.46
5878 7224 3.068448 TCAACTAGCTTGTGGTACGAACA 59.932 43.478 0.36 0.00 0.00 3.18
5914 7260 1.792301 CGAGGCTACGACGAGACAA 59.208 57.895 0.00 0.00 35.09 3.18
5940 7286 1.931635 TTAATTGGGGGCCTGTTGAC 58.068 50.000 0.84 0.00 0.00 3.18
6028 7374 1.475280 GACCGTACACATGCCTCACTA 59.525 52.381 0.00 0.00 0.00 2.74
6202 7548 2.169352 TCTTAGCTGGCATTCCTCTCAC 59.831 50.000 0.00 0.00 0.00 3.51
6234 7684 0.811616 GCCCTCACCGTTGCAGATAG 60.812 60.000 0.00 0.00 0.00 2.08


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

AutoCloner maintained by Alex Coulton.