Multiple sequence alignment - TraesCS2A01G178300

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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 TraesCS2A01G178300 chr2A 100.000 2312 0 0 1 2312 137239328 137241639 0.000000e+00 4270
1 TraesCS2A01G178300 chr1A 96.561 727 25 0 1 727 576361082 576361808 0.000000e+00 1205
2 TraesCS2A01G178300 chr7B 96.016 728 25 2 1 727 117988440 117987716 0.000000e+00 1181
3 TraesCS2A01G178300 chr7B 95.748 729 26 3 1 727 63946758 63947483 0.000000e+00 1170
4 TraesCS2A01G178300 chr3A 96.016 728 25 2 1 727 735367934 735368658 0.000000e+00 1181
5 TraesCS2A01G178300 chr3A 95.736 727 30 1 1 727 743180875 743181600 0.000000e+00 1170
6 TraesCS2A01G178300 chr6A 95.873 727 30 0 1 727 589188113 589187387 0.000000e+00 1177
7 TraesCS2A01G178300 chr6A 95.598 727 30 2 1 727 533984416 533983692 0.000000e+00 1164
8 TraesCS2A01G178300 chr5A 95.759 731 26 3 1 729 687283542 687282815 0.000000e+00 1173
9 TraesCS2A01G178300 chr4A 95.598 727 30 1 1 727 601290363 601291087 0.000000e+00 1164
10 TraesCS2A01G178300 chr2D 89.093 816 47 15 726 1516 131147542 131148340 0.000000e+00 976
11 TraesCS2A01G178300 chr2D 90.202 347 32 2 1967 2312 131148653 131148998 3.500000e-123 451
12 TraesCS2A01G178300 chr2D 96.154 156 6 0 726 881 131134064 131134219 2.950000e-64 255
13 TraesCS2A01G178300 chr2B 88.622 791 46 15 726 1474 184654723 184655511 0.000000e+00 922
14 TraesCS2A01G178300 chr2B 86.765 340 33 3 1974 2312 184658146 184658474 3.630000e-98 368
15 TraesCS2A01G178300 chr2B 92.568 148 8 3 1669 1813 184657936 184658083 2.330000e-50 209
16 TraesCS2A01G178300 chr2B 90.361 83 6 1 1562 1644 184655694 184655774 8.730000e-20 108
17 TraesCS2A01G178300 chrUn 86.931 681 45 12 726 1368 17491697 17491023 0.000000e+00 725
18 TraesCS2A01G178300 chrUn 86.931 681 45 12 726 1368 339822524 339821850 0.000000e+00 725
19 TraesCS2A01G178300 chrUn 88.788 330 35 2 1968 2297 17482508 17482181 9.950000e-109 403
20 TraesCS2A01G178300 chrUn 88.788 330 35 2 1968 2297 373409566 373409893 9.950000e-109 403
21 TraesCS2A01G178300 chrUn 87.662 154 12 2 1660 1813 17482680 17482534 3.050000e-39 172
22 TraesCS2A01G178300 chrUn 87.662 154 12 2 1660 1813 373409394 373409540 3.050000e-39 172
23 TraesCS2A01G178300 chrUn 95.402 87 4 0 1433 1519 17482799 17482713 3.100000e-29 139
24 TraesCS2A01G178300 chrUn 96.429 84 3 0 1433 1516 373409275 373409358 3.100000e-29 139


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 TraesCS2A01G178300 chr2A 137239328 137241639 2311 False 4270.00 4270 100.000000 1 2312 1 chr2A.!!$F1 2311
1 TraesCS2A01G178300 chr1A 576361082 576361808 726 False 1205.00 1205 96.561000 1 727 1 chr1A.!!$F1 726
2 TraesCS2A01G178300 chr7B 117987716 117988440 724 True 1181.00 1181 96.016000 1 727 1 chr7B.!!$R1 726
3 TraesCS2A01G178300 chr7B 63946758 63947483 725 False 1170.00 1170 95.748000 1 727 1 chr7B.!!$F1 726
4 TraesCS2A01G178300 chr3A 735367934 735368658 724 False 1181.00 1181 96.016000 1 727 1 chr3A.!!$F1 726
5 TraesCS2A01G178300 chr3A 743180875 743181600 725 False 1170.00 1170 95.736000 1 727 1 chr3A.!!$F2 726
6 TraesCS2A01G178300 chr6A 589187387 589188113 726 True 1177.00 1177 95.873000 1 727 1 chr6A.!!$R2 726
7 TraesCS2A01G178300 chr6A 533983692 533984416 724 True 1164.00 1164 95.598000 1 727 1 chr6A.!!$R1 726
8 TraesCS2A01G178300 chr5A 687282815 687283542 727 True 1173.00 1173 95.759000 1 729 1 chr5A.!!$R1 728
9 TraesCS2A01G178300 chr4A 601290363 601291087 724 False 1164.00 1164 95.598000 1 727 1 chr4A.!!$F1 726
10 TraesCS2A01G178300 chr2D 131147542 131148998 1456 False 713.50 976 89.647500 726 2312 2 chr2D.!!$F2 1586
11 TraesCS2A01G178300 chr2B 184654723 184658474 3751 False 401.75 922 89.579000 726 2312 4 chr2B.!!$F1 1586
12 TraesCS2A01G178300 chrUn 17491023 17491697 674 True 725.00 725 86.931000 726 1368 1 chrUn.!!$R1 642
13 TraesCS2A01G178300 chrUn 339821850 339822524 674 True 725.00 725 86.931000 726 1368 1 chrUn.!!$R2 642
14 TraesCS2A01G178300 chrUn 17482181 17482799 618 True 238.00 403 90.617333 1433 2297 3 chrUn.!!$R3 864
15 TraesCS2A01G178300 chrUn 373409275 373409893 618 False 238.00 403 90.959667 1433 2297 3 chrUn.!!$F1 864

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
349 350 0.871722 CCGTGATTTGGTCGCTTTGA 59.128 50.000 0.0 0.0 35.15 2.69 F
756 761 1.139853 CTACCTGCTCCCTTGGACATC 59.860 57.143 0.0 0.0 0.00 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1173 1224 0.178068 GGAGCTCGAACTTGGGCATA 59.822 55.0 7.83 0.0 0.00 3.14 R
1936 4317 0.257905 AAAGGAGGATTAACCCCGGC 59.742 55.0 0.00 0.0 40.05 6.13 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
106 107 7.595502 CGCGGAGTCATTCTTACTAAAGATAAT 59.404 37.037 0.00 0.00 41.36 1.28
218 219 3.307762 GGCCCATTCTATATGGTCAGTCC 60.308 52.174 0.00 0.00 37.48 3.85
274 275 8.961634 TGTAGTGTTGCTAATATATTTGGCAAA 58.038 29.630 25.83 16.01 43.04 3.68
349 350 0.871722 CCGTGATTTGGTCGCTTTGA 59.128 50.000 0.00 0.00 35.15 2.69
486 487 2.901839 ACCTGTTTACGGAGGTGTGTAT 59.098 45.455 0.00 0.00 41.27 2.29
524 525 3.434596 GGCGAGGGATACTTTTACCCAAT 60.435 47.826 0.00 0.00 45.43 3.16
546 547 1.496001 TGGGTGGCAGCATGATCTTAT 59.504 47.619 19.48 0.00 39.69 1.73
733 738 3.305131 GCCCCTTTTCGAAAAACTACTGG 60.305 47.826 22.67 18.06 0.00 4.00
756 761 1.139853 CTACCTGCTCCCTTGGACATC 59.860 57.143 0.00 0.00 0.00 3.06
890 913 4.154347 CAGGACTCCCGGCAGAGC 62.154 72.222 0.00 0.00 37.39 4.09
923 958 1.456544 ACAAATACCACGCAACGTACG 59.543 47.619 15.01 15.01 38.32 3.67
947 987 5.451937 GCCTGCTCAGTAAGTATCACACATA 60.452 44.000 0.00 0.00 0.00 2.29
950 990 7.255766 CCTGCTCAGTAAGTATCACACATATCT 60.256 40.741 0.00 0.00 0.00 1.98
952 992 8.787852 TGCTCAGTAAGTATCACACATATCTAG 58.212 37.037 0.00 0.00 0.00 2.43
961 1001 9.339850 AGTATCACACATATCTAGAGTTAACGT 57.660 33.333 0.00 0.00 0.00 3.99
998 1049 1.792949 CTGCACGTAACAGAAGTCCAC 59.207 52.381 11.36 0.00 37.32 4.02
1059 1110 4.406173 CTCCTGTCGTGCGTCGCT 62.406 66.667 19.50 0.00 39.67 4.93
1147 1198 4.293648 CACACCTGACCGTGCCGA 62.294 66.667 0.00 0.00 37.25 5.54
1162 1213 2.351244 CCGAGGCTGCCAGACTACA 61.351 63.158 22.65 0.00 30.20 2.74
1173 1224 2.266055 GACTACAAGCTGCCGCCT 59.734 61.111 0.00 0.00 36.60 5.52
1185 1236 2.481471 GCCGCCTATGCCCAAGTTC 61.481 63.158 0.00 0.00 0.00 3.01
1327 1378 2.738846 CCATGAGGACTTCTTCGTTGTG 59.261 50.000 0.00 0.00 36.89 3.33
1344 1397 1.415374 GTGTCGTGCACGTATGAAGT 58.585 50.000 35.74 0.00 38.45 3.01
1369 1422 3.685272 TGTTCGTGTGCTTGTTTAGTTGA 59.315 39.130 0.00 0.00 0.00 3.18
1395 1448 4.004348 ACGAGAGTGTGCCGATCT 57.996 55.556 0.00 0.00 46.97 2.75
1417 1473 1.876714 CGGCCGACGTTATCCTGTG 60.877 63.158 24.07 0.00 37.93 3.66
1446 1502 1.069432 GCGACTCGTGACTTGTGAGTA 60.069 52.381 0.00 0.00 42.71 2.59
1509 1706 8.700973 ACGGGATGTACATGTGCATTATATATA 58.299 33.333 27.08 0.00 36.05 0.86
1556 1753 6.961359 ATATATACACACACACACACACAC 57.039 37.500 0.00 0.00 0.00 3.82
1557 1754 2.457366 TACACACACACACACACACA 57.543 45.000 0.00 0.00 0.00 3.72
1558 1755 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1559 1756 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
1560 1757 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
1603 1800 1.489560 GCTCTACAAGGGTGGGGTGT 61.490 60.000 0.00 0.00 0.00 4.16
1615 1816 1.134946 GTGGGGTGTGCTGATAAATGC 59.865 52.381 0.00 0.00 0.00 3.56
1665 2715 7.815383 TCCTATTATCCTTGATGACCAAATGT 58.185 34.615 0.00 0.00 33.76 2.71
1768 4148 7.712204 AAAGCCTTCCGGAATAGAATAAAAA 57.288 32.000 19.21 0.00 0.00 1.94
1879 4260 3.657015 CTCTGAGTGAGCTTGTTCTGA 57.343 47.619 0.00 0.00 35.84 3.27
1880 4261 3.987547 CTCTGAGTGAGCTTGTTCTGAA 58.012 45.455 0.00 0.00 35.84 3.02
1881 4262 4.567971 CTCTGAGTGAGCTTGTTCTGAAT 58.432 43.478 0.00 0.00 35.84 2.57
1882 4263 4.564041 TCTGAGTGAGCTTGTTCTGAATC 58.436 43.478 0.00 0.00 0.00 2.52
1883 4264 4.282957 TCTGAGTGAGCTTGTTCTGAATCT 59.717 41.667 0.00 0.00 0.00 2.40
1884 4265 4.965814 TGAGTGAGCTTGTTCTGAATCTT 58.034 39.130 0.00 0.00 0.00 2.40
1885 4266 6.015095 TCTGAGTGAGCTTGTTCTGAATCTTA 60.015 38.462 0.00 0.00 0.00 2.10
1886 4267 6.162079 TGAGTGAGCTTGTTCTGAATCTTAG 58.838 40.000 0.00 0.00 0.00 2.18
1887 4268 6.015095 TGAGTGAGCTTGTTCTGAATCTTAGA 60.015 38.462 0.00 0.00 0.00 2.10
1888 4269 6.162777 AGTGAGCTTGTTCTGAATCTTAGAC 58.837 40.000 0.00 0.00 0.00 2.59
1889 4270 6.014669 AGTGAGCTTGTTCTGAATCTTAGACT 60.015 38.462 0.00 0.00 0.00 3.24
1890 4271 6.648725 GTGAGCTTGTTCTGAATCTTAGACTT 59.351 38.462 0.00 0.00 0.00 3.01
1891 4272 7.172361 GTGAGCTTGTTCTGAATCTTAGACTTT 59.828 37.037 0.00 0.00 0.00 2.66
1892 4273 7.716998 TGAGCTTGTTCTGAATCTTAGACTTTT 59.283 33.333 0.00 0.00 0.00 2.27
1893 4274 7.869800 AGCTTGTTCTGAATCTTAGACTTTTG 58.130 34.615 0.00 0.00 0.00 2.44
1894 4275 7.040823 AGCTTGTTCTGAATCTTAGACTTTTGG 60.041 37.037 0.00 0.00 0.00 3.28
1895 4276 7.041098 GCTTGTTCTGAATCTTAGACTTTTGGA 60.041 37.037 0.00 0.00 0.00 3.53
1896 4277 8.924511 TTGTTCTGAATCTTAGACTTTTGGAT 57.075 30.769 0.00 0.00 0.00 3.41
1898 4279 9.436957 TGTTCTGAATCTTAGACTTTTGGATAC 57.563 33.333 0.00 0.00 0.00 2.24
1899 4280 9.660180 GTTCTGAATCTTAGACTTTTGGATACT 57.340 33.333 0.00 0.00 37.61 2.12
1903 4284 8.730680 TGAATCTTAGACTTTTGGATACTTTGC 58.269 33.333 0.00 0.00 37.61 3.68
1904 4285 8.870075 AATCTTAGACTTTTGGATACTTTGCT 57.130 30.769 0.00 0.00 37.61 3.91
1905 4286 8.870075 ATCTTAGACTTTTGGATACTTTGCTT 57.130 30.769 0.00 0.00 37.61 3.91
1906 4287 9.959721 ATCTTAGACTTTTGGATACTTTGCTTA 57.040 29.630 0.00 0.00 37.61 3.09
1907 4288 9.787435 TCTTAGACTTTTGGATACTTTGCTTAA 57.213 29.630 0.00 0.00 37.61 1.85
1920 4301 9.692749 GATACTTTGCTTAATAAATAAAGGGGC 57.307 33.333 11.02 0.00 33.77 5.80
1921 4302 7.733773 ACTTTGCTTAATAAATAAAGGGGCT 57.266 32.000 11.02 0.00 33.77 5.19
1922 4303 7.555965 ACTTTGCTTAATAAATAAAGGGGCTG 58.444 34.615 11.02 0.00 33.77 4.85
1923 4304 5.529581 TGCTTAATAAATAAAGGGGCTGC 57.470 39.130 0.00 0.00 0.00 5.25
1924 4305 4.959210 TGCTTAATAAATAAAGGGGCTGCA 59.041 37.500 0.50 0.00 0.00 4.41
1925 4306 5.163457 TGCTTAATAAATAAAGGGGCTGCAC 60.163 40.000 0.50 0.00 0.00 4.57
1926 4307 5.508200 TTAATAAATAAAGGGGCTGCACG 57.492 39.130 0.50 0.00 0.00 5.34
1927 4308 1.099689 TAAATAAAGGGGCTGCACGC 58.900 50.000 0.50 0.00 38.13 5.34
1928 4309 0.897863 AAATAAAGGGGCTGCACGCA 60.898 50.000 0.50 0.00 41.67 5.24
1929 4310 0.684153 AATAAAGGGGCTGCACGCAT 60.684 50.000 0.50 0.00 41.67 4.73
1930 4311 1.103398 ATAAAGGGGCTGCACGCATC 61.103 55.000 0.50 0.00 41.67 3.91
1931 4312 2.476852 TAAAGGGGCTGCACGCATCA 62.477 55.000 0.50 0.00 41.67 3.07
1932 4313 3.650298 AAGGGGCTGCACGCATCAT 62.650 57.895 0.50 0.00 41.67 2.45
1933 4314 3.142838 GGGGCTGCACGCATCATT 61.143 61.111 0.50 0.00 41.67 2.57
1934 4315 2.410469 GGGCTGCACGCATCATTC 59.590 61.111 0.50 0.00 41.67 2.67
1935 4316 2.117156 GGGCTGCACGCATCATTCT 61.117 57.895 0.50 0.00 41.67 2.40
1936 4317 1.063649 GGCTGCACGCATCATTCTG 59.936 57.895 0.50 0.00 41.67 3.02
1937 4318 1.585521 GCTGCACGCATCATTCTGC 60.586 57.895 0.00 0.00 38.92 4.26
1938 4319 1.063649 CTGCACGCATCATTCTGCC 59.936 57.895 0.00 0.00 39.00 4.85
1939 4320 2.023741 GCACGCATCATTCTGCCG 59.976 61.111 0.00 0.00 39.00 5.69
1940 4321 2.711311 CACGCATCATTCTGCCGG 59.289 61.111 0.00 0.00 39.00 6.13
1941 4322 2.514592 ACGCATCATTCTGCCGGG 60.515 61.111 2.18 0.00 39.00 5.73
1942 4323 3.282157 CGCATCATTCTGCCGGGG 61.282 66.667 2.18 0.00 39.00 5.73
1943 4324 2.124151 GCATCATTCTGCCGGGGT 60.124 61.111 2.18 0.00 36.10 4.95
1944 4325 1.754234 GCATCATTCTGCCGGGGTT 60.754 57.895 2.18 0.00 36.10 4.11
1945 4326 0.465460 GCATCATTCTGCCGGGGTTA 60.465 55.000 2.18 0.00 36.10 2.85
1946 4327 2.021723 GCATCATTCTGCCGGGGTTAA 61.022 52.381 2.18 0.00 36.10 2.01
1947 4328 2.586425 CATCATTCTGCCGGGGTTAAT 58.414 47.619 2.18 0.00 0.00 1.40
1948 4329 2.341846 TCATTCTGCCGGGGTTAATC 57.658 50.000 2.18 0.00 0.00 1.75
1949 4330 1.133915 TCATTCTGCCGGGGTTAATCC 60.134 52.381 2.18 0.00 0.00 3.01
1950 4331 1.133792 CATTCTGCCGGGGTTAATCCT 60.134 52.381 2.18 0.00 36.25 3.24
1951 4332 0.544697 TTCTGCCGGGGTTAATCCTC 59.455 55.000 2.18 0.00 36.25 3.71
1952 4333 1.148498 CTGCCGGGGTTAATCCTCC 59.852 63.158 2.18 0.00 36.25 4.30
1953 4334 1.307517 TGCCGGGGTTAATCCTCCT 60.308 57.895 2.18 0.00 36.25 3.69
1954 4335 0.917333 TGCCGGGGTTAATCCTCCTT 60.917 55.000 2.18 0.00 36.25 3.36
1955 4336 0.257905 GCCGGGGTTAATCCTCCTTT 59.742 55.000 2.18 0.00 36.25 3.11
1956 4337 1.341679 GCCGGGGTTAATCCTCCTTTT 60.342 52.381 2.18 0.00 36.25 2.27
1957 4338 2.651455 CCGGGGTTAATCCTCCTTTTC 58.349 52.381 4.37 0.00 36.25 2.29
1958 4339 2.241430 CCGGGGTTAATCCTCCTTTTCT 59.759 50.000 4.37 0.00 36.25 2.52
1959 4340 3.457012 CCGGGGTTAATCCTCCTTTTCTA 59.543 47.826 4.37 0.00 36.25 2.10
1960 4341 4.080186 CCGGGGTTAATCCTCCTTTTCTAA 60.080 45.833 4.37 0.00 36.25 2.10
1961 4342 5.503002 CGGGGTTAATCCTCCTTTTCTAAA 58.497 41.667 4.37 0.00 36.25 1.85
1962 4343 5.947566 CGGGGTTAATCCTCCTTTTCTAAAA 59.052 40.000 4.37 0.00 36.25 1.52
1963 4344 6.434965 CGGGGTTAATCCTCCTTTTCTAAAAA 59.565 38.462 4.37 0.00 36.25 1.94
2017 4430 7.504911 AGTTTTATTCAGCCTCTGCATCATATT 59.495 33.333 0.00 0.00 41.13 1.28
2102 4515 5.537300 AGCACGATGATAAGTAGGTGAAT 57.463 39.130 0.00 0.00 0.00 2.57
2115 4528 4.588951 AGTAGGTGAATATTCGAGCCATCA 59.411 41.667 19.16 7.08 0.00 3.07
2183 4596 5.008613 CCATTGAAACCGAACGGATCATATT 59.991 40.000 20.14 8.65 38.96 1.28
2191 4604 4.093408 CCGAACGGATCATATTTGGCTATG 59.907 45.833 7.53 0.00 37.50 2.23
2199 4612 5.581350 TCATATTTGGCTATGTCCCATCA 57.419 39.130 0.00 0.00 32.13 3.07
2244 4657 3.165875 CACCCAGACCTCTACAAGAAGA 58.834 50.000 0.00 0.00 0.00 2.87
2297 4710 3.125316 GGTAGCTCTCAAAATGAACCACG 59.875 47.826 0.00 0.00 0.00 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
106 107 6.910191 TCCATGCCAATTCCTCTTAATAAGA 58.090 36.000 2.44 2.44 35.87 2.10
199 200 4.840680 TGGAGGACTGACCATATAGAATGG 59.159 45.833 2.46 2.46 44.54 3.16
201 202 7.639062 ATTTGGAGGACTGACCATATAGAAT 57.361 36.000 0.00 0.00 42.04 2.40
274 275 5.128033 TGTGATCAATCCCATGTAACCAT 57.872 39.130 0.00 0.00 0.00 3.55
420 421 1.549170 AGGACCATAAACGAAGCGTCT 59.451 47.619 0.00 0.00 39.99 4.18
459 460 1.542915 CCTCCGTAAACAGGTCTCGAA 59.457 52.381 0.00 0.00 0.00 3.71
486 487 1.737816 GCCGTAGCCTCCAATCGTA 59.262 57.895 0.00 0.00 0.00 3.43
524 525 1.142936 AGATCATGCTGCCACCCATA 58.857 50.000 0.00 0.00 0.00 2.74
546 547 4.402528 CCGTCGGTGGCCCAATCA 62.403 66.667 2.08 0.00 0.00 2.57
635 640 3.949754 CACACAGCCAATAATGTCCTCAT 59.050 43.478 0.00 0.00 35.59 2.90
676 681 7.835682 ACTTAAAAGGTTTAAGTAACACCCAGT 59.164 33.333 19.54 0.00 41.77 4.00
678 683 9.692325 TTACTTAAAAGGTTTAAGTAACACCCA 57.308 29.630 26.88 14.27 45.23 4.51
709 714 4.022329 CAGTAGTTTTTCGAAAAGGGGCAT 60.022 41.667 21.53 9.21 0.00 4.40
733 738 0.617820 TCCAAGGGAGCAGGTAGGAC 60.618 60.000 0.00 0.00 0.00 3.85
890 913 4.939439 GTGGTATTTGTAGGGTTGTAGTGG 59.061 45.833 0.00 0.00 0.00 4.00
923 958 3.190874 GTGTGATACTTACTGAGCAGGC 58.809 50.000 2.20 0.00 0.00 4.85
998 1049 1.450312 GTGTTCCTCGAGGCCATGG 60.450 63.158 27.39 7.63 34.44 3.66
1059 1110 4.931188 CTCGCCGCGCTGCTCATA 62.931 66.667 21.59 3.81 0.00 2.15
1147 1198 1.197430 AGCTTGTAGTCTGGCAGCCT 61.197 55.000 14.15 6.43 0.00 4.58
1162 1213 4.883354 GGGCATAGGCGGCAGCTT 62.883 66.667 13.08 3.16 44.37 3.74
1173 1224 0.178068 GGAGCTCGAACTTGGGCATA 59.822 55.000 7.83 0.00 0.00 3.14
1327 1378 1.415374 ACACTTCATACGTGCACGAC 58.585 50.000 42.94 4.12 43.02 4.34
1344 1397 2.999507 AAACAAGCACACGAACAACA 57.000 40.000 0.00 0.00 0.00 3.33
1369 1422 2.353803 GGCACACTCTCGTTTGATACCT 60.354 50.000 0.00 0.00 0.00 3.08
1417 1473 1.444553 CACGAGTCGCAGGAACTCC 60.445 63.158 13.59 0.00 34.60 3.85
1446 1502 3.902150 CGTAGACGTAGATCATGGCATT 58.098 45.455 0.00 0.00 34.11 3.56
1469 1525 1.299926 CCCGTCTAGGCACATACGC 60.300 63.158 0.00 0.00 39.21 4.42
1530 1727 9.738832 GTGTGTGTGTGTGTGTGTATATATATA 57.261 33.333 0.00 0.00 0.00 0.86
1531 1728 8.254508 TGTGTGTGTGTGTGTGTGTATATATAT 58.745 33.333 0.00 0.00 0.00 0.86
1532 1729 7.542824 GTGTGTGTGTGTGTGTGTGTATATATA 59.457 37.037 0.00 0.00 0.00 0.86
1533 1730 6.367695 GTGTGTGTGTGTGTGTGTGTATATAT 59.632 38.462 0.00 0.00 0.00 0.86
1534 1731 5.692654 GTGTGTGTGTGTGTGTGTGTATATA 59.307 40.000 0.00 0.00 0.00 0.86
1535 1732 4.509970 GTGTGTGTGTGTGTGTGTGTATAT 59.490 41.667 0.00 0.00 0.00 0.86
1536 1733 3.866327 GTGTGTGTGTGTGTGTGTGTATA 59.134 43.478 0.00 0.00 0.00 1.47
1537 1734 2.675844 GTGTGTGTGTGTGTGTGTGTAT 59.324 45.455 0.00 0.00 0.00 2.29
1538 1735 2.070028 GTGTGTGTGTGTGTGTGTGTA 58.930 47.619 0.00 0.00 0.00 2.90
1539 1736 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1540 1737 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1541 1738 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1542 1739 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1543 1740 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
1544 1741 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
1545 1742 1.737236 GATGTGTGTGTGTGTGTGTGT 59.263 47.619 0.00 0.00 0.00 3.72
1546 1743 1.736681 TGATGTGTGTGTGTGTGTGTG 59.263 47.619 0.00 0.00 0.00 3.82
1547 1744 2.009051 CTGATGTGTGTGTGTGTGTGT 58.991 47.619 0.00 0.00 0.00 3.72
1548 1745 2.009051 ACTGATGTGTGTGTGTGTGTG 58.991 47.619 0.00 0.00 0.00 3.82
1549 1746 2.401583 ACTGATGTGTGTGTGTGTGT 57.598 45.000 0.00 0.00 0.00 3.72
1550 1747 3.871006 ACTTACTGATGTGTGTGTGTGTG 59.129 43.478 0.00 0.00 0.00 3.82
1551 1748 4.137116 ACTTACTGATGTGTGTGTGTGT 57.863 40.909 0.00 0.00 0.00 3.72
1552 1749 5.696270 ACATACTTACTGATGTGTGTGTGTG 59.304 40.000 0.00 0.00 37.19 3.82
1553 1750 5.853936 ACATACTTACTGATGTGTGTGTGT 58.146 37.500 0.00 0.00 37.19 3.72
1554 1751 6.785488 AACATACTTACTGATGTGTGTGTG 57.215 37.500 0.00 0.00 38.26 3.82
1582 1779 0.416231 ACCCCACCCTTGTAGAGCTA 59.584 55.000 0.00 0.00 0.00 3.32
1583 1780 1.161113 ACCCCACCCTTGTAGAGCT 59.839 57.895 0.00 0.00 0.00 4.09
1587 1784 1.303317 GCACACCCCACCCTTGTAG 60.303 63.158 0.00 0.00 0.00 2.74
1603 1800 3.333804 TCTGTCAACGCATTTATCAGCA 58.666 40.909 0.00 0.00 0.00 4.41
1644 1845 6.434302 TCCACATTTGGTCATCAAGGATAAT 58.566 36.000 0.00 0.00 44.35 1.28
1645 1846 5.825532 TCCACATTTGGTCATCAAGGATAA 58.174 37.500 0.00 0.00 44.35 1.75
1646 1847 5.439721 CTCCACATTTGGTCATCAAGGATA 58.560 41.667 0.00 0.00 44.35 2.59
1648 1849 3.689347 CTCCACATTTGGTCATCAAGGA 58.311 45.455 0.00 0.00 44.35 3.36
1649 1850 2.165030 GCTCCACATTTGGTCATCAAGG 59.835 50.000 0.00 0.00 44.35 3.61
1652 1853 1.003003 TCGCTCCACATTTGGTCATCA 59.997 47.619 0.00 0.00 44.35 3.07
1653 1854 1.398390 GTCGCTCCACATTTGGTCATC 59.602 52.381 0.00 0.00 44.35 2.92
1657 2707 0.396435 TCAGTCGCTCCACATTTGGT 59.604 50.000 0.00 0.00 44.35 3.67
1658 2708 1.399440 CATCAGTCGCTCCACATTTGG 59.601 52.381 0.00 0.00 45.56 3.28
1665 2715 1.514553 CTGCTCATCAGTCGCTCCA 59.485 57.895 0.00 0.00 38.02 3.86
1772 4152 9.319143 GCTCTTGTATGAACTATGTACAATTCT 57.681 33.333 0.00 0.00 37.60 2.40
1773 4153 9.319143 AGCTCTTGTATGAACTATGTACAATTC 57.681 33.333 0.00 5.33 37.60 2.17
1778 4159 8.756864 GCTAAAGCTCTTGTATGAACTATGTAC 58.243 37.037 0.00 0.00 38.21 2.90
1860 4241 4.282957 AGATTCAGAACAAGCTCACTCAGA 59.717 41.667 0.00 0.00 0.00 3.27
1861 4242 4.567971 AGATTCAGAACAAGCTCACTCAG 58.432 43.478 0.00 0.00 0.00 3.35
1862 4243 4.613925 AGATTCAGAACAAGCTCACTCA 57.386 40.909 0.00 0.00 0.00 3.41
1863 4244 6.310224 GTCTAAGATTCAGAACAAGCTCACTC 59.690 42.308 0.00 0.00 0.00 3.51
1864 4245 6.014669 AGTCTAAGATTCAGAACAAGCTCACT 60.015 38.462 0.00 0.00 0.00 3.41
1865 4246 6.162777 AGTCTAAGATTCAGAACAAGCTCAC 58.837 40.000 0.00 0.00 0.00 3.51
1866 4247 6.352016 AGTCTAAGATTCAGAACAAGCTCA 57.648 37.500 0.00 0.00 0.00 4.26
1867 4248 7.665561 AAAGTCTAAGATTCAGAACAAGCTC 57.334 36.000 0.00 0.00 0.00 4.09
1868 4249 7.040823 CCAAAAGTCTAAGATTCAGAACAAGCT 60.041 37.037 0.00 0.00 0.00 3.74
1869 4250 7.041098 TCCAAAAGTCTAAGATTCAGAACAAGC 60.041 37.037 0.00 0.00 0.00 4.01
1870 4251 8.383318 TCCAAAAGTCTAAGATTCAGAACAAG 57.617 34.615 0.00 0.00 0.00 3.16
1871 4252 8.924511 ATCCAAAAGTCTAAGATTCAGAACAA 57.075 30.769 0.00 0.00 0.00 2.83
1872 4253 9.436957 GTATCCAAAAGTCTAAGATTCAGAACA 57.563 33.333 0.00 0.00 0.00 3.18
1873 4254 9.660180 AGTATCCAAAAGTCTAAGATTCAGAAC 57.340 33.333 0.00 0.00 0.00 3.01
1877 4258 8.730680 GCAAAGTATCCAAAAGTCTAAGATTCA 58.269 33.333 0.00 0.00 0.00 2.57
1878 4259 8.951243 AGCAAAGTATCCAAAAGTCTAAGATTC 58.049 33.333 0.00 0.00 0.00 2.52
1879 4260 8.870075 AGCAAAGTATCCAAAAGTCTAAGATT 57.130 30.769 0.00 0.00 0.00 2.40
1880 4261 8.870075 AAGCAAAGTATCCAAAAGTCTAAGAT 57.130 30.769 0.00 0.00 0.00 2.40
1881 4262 9.787435 TTAAGCAAAGTATCCAAAAGTCTAAGA 57.213 29.630 0.00 0.00 0.00 2.10
1894 4275 9.692749 GCCCCTTTATTTATTAAGCAAAGTATC 57.307 33.333 0.00 0.00 0.00 2.24
1895 4276 9.434275 AGCCCCTTTATTTATTAAGCAAAGTAT 57.566 29.630 0.00 0.00 0.00 2.12
1896 4277 8.691797 CAGCCCCTTTATTTATTAAGCAAAGTA 58.308 33.333 0.00 0.00 0.00 2.24
1897 4278 7.555965 CAGCCCCTTTATTTATTAAGCAAAGT 58.444 34.615 0.00 0.00 0.00 2.66
1898 4279 6.479990 GCAGCCCCTTTATTTATTAAGCAAAG 59.520 38.462 0.00 5.48 0.00 2.77
1899 4280 6.070538 TGCAGCCCCTTTATTTATTAAGCAAA 60.071 34.615 0.00 0.00 0.00 3.68
1900 4281 5.423610 TGCAGCCCCTTTATTTATTAAGCAA 59.576 36.000 0.00 0.00 0.00 3.91
1901 4282 4.959210 TGCAGCCCCTTTATTTATTAAGCA 59.041 37.500 0.00 0.00 0.00 3.91
1902 4283 5.289595 GTGCAGCCCCTTTATTTATTAAGC 58.710 41.667 0.00 0.00 0.00 3.09
1903 4284 5.519722 CGTGCAGCCCCTTTATTTATTAAG 58.480 41.667 0.00 0.00 0.00 1.85
1904 4285 4.202070 GCGTGCAGCCCCTTTATTTATTAA 60.202 41.667 0.00 0.00 40.81 1.40
1905 4286 3.316868 GCGTGCAGCCCCTTTATTTATTA 59.683 43.478 0.00 0.00 40.81 0.98
1906 4287 2.100749 GCGTGCAGCCCCTTTATTTATT 59.899 45.455 0.00 0.00 40.81 1.40
1907 4288 1.681264 GCGTGCAGCCCCTTTATTTAT 59.319 47.619 0.00 0.00 40.81 1.40
1908 4289 1.099689 GCGTGCAGCCCCTTTATTTA 58.900 50.000 0.00 0.00 40.81 1.40
1909 4290 1.890174 GCGTGCAGCCCCTTTATTT 59.110 52.632 0.00 0.00 40.81 1.40
1910 4291 3.603365 GCGTGCAGCCCCTTTATT 58.397 55.556 0.00 0.00 40.81 1.40
1917 4298 2.332362 CAGAATGATGCGTGCAGCCC 62.332 60.000 7.72 0.00 42.64 5.19
1918 4299 1.063649 CAGAATGATGCGTGCAGCC 59.936 57.895 7.72 0.00 42.64 4.85
1919 4300 1.585521 GCAGAATGATGCGTGCAGC 60.586 57.895 2.62 2.62 43.45 5.25
1920 4301 4.684265 GCAGAATGATGCGTGCAG 57.316 55.556 0.00 0.00 39.69 4.41
1926 4307 0.465460 TAACCCCGGCAGAATGATGC 60.465 55.000 0.00 0.00 45.74 3.91
1927 4308 2.051334 TTAACCCCGGCAGAATGATG 57.949 50.000 0.00 0.00 39.69 3.07
1928 4309 2.489073 GGATTAACCCCGGCAGAATGAT 60.489 50.000 0.00 0.00 39.69 2.45
1929 4310 1.133915 GGATTAACCCCGGCAGAATGA 60.134 52.381 0.00 0.00 39.69 2.57
1930 4311 1.133792 AGGATTAACCCCGGCAGAATG 60.134 52.381 0.00 0.00 40.05 2.67
1931 4312 1.143073 GAGGATTAACCCCGGCAGAAT 59.857 52.381 0.00 0.00 40.05 2.40
1932 4313 0.544697 GAGGATTAACCCCGGCAGAA 59.455 55.000 0.00 0.00 40.05 3.02
1933 4314 1.342672 GGAGGATTAACCCCGGCAGA 61.343 60.000 0.00 0.00 40.05 4.26
1934 4315 1.148498 GGAGGATTAACCCCGGCAG 59.852 63.158 0.00 0.00 40.05 4.85
1935 4316 0.917333 AAGGAGGATTAACCCCGGCA 60.917 55.000 0.00 0.00 40.05 5.69
1936 4317 0.257905 AAAGGAGGATTAACCCCGGC 59.742 55.000 0.00 0.00 40.05 6.13
1937 4318 2.241430 AGAAAAGGAGGATTAACCCCGG 59.759 50.000 0.00 0.00 40.05 5.73
1938 4319 3.646736 AGAAAAGGAGGATTAACCCCG 57.353 47.619 0.00 0.00 40.05 5.73
1939 4320 7.786046 TTTTTAGAAAAGGAGGATTAACCCC 57.214 36.000 0.00 0.00 40.05 4.95
1997 4378 4.760715 GTCAATATGATGCAGAGGCTGAAT 59.239 41.667 0.00 0.00 41.91 2.57
2017 4430 6.622833 AATAATCATGATTGTGCATCGTCA 57.377 33.333 27.59 6.90 34.08 4.35
2102 4515 8.066612 TGTATAATCTCATGATGGCTCGAATA 57.933 34.615 0.00 0.00 32.44 1.75
2163 4576 4.334203 CCAAATATGATCCGTTCGGTTTCA 59.666 41.667 16.59 16.59 0.00 2.69
2191 4604 1.327303 TTTGGTGCAACTGATGGGAC 58.673 50.000 2.04 0.00 36.74 4.46
2214 4627 2.834549 AGAGGTCTGGGTGTTCATGTAG 59.165 50.000 0.00 0.00 0.00 2.74
2227 4640 4.090090 TCCCTTCTTCTTGTAGAGGTCTG 58.910 47.826 0.00 0.00 0.00 3.51
2244 4657 2.154567 TACACGCTACATCCTCCCTT 57.845 50.000 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.