Multiple sequence alignment - TraesCS6D01G104000

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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 TraesCS6D01G104000 chr6D 100.000 2870 0 0 1 2870 67568268 67571137 0.000000e+00 5301
1 TraesCS6D01G104000 chr6B 89.442 1326 83 27 587 1870 142612120 142613430 0.000000e+00 1620
2 TraesCS6D01G104000 chr6B 86.897 580 34 20 23 587 142611506 142612058 1.890000e-171 612
3 TraesCS6D01G104000 chr6B 86.689 293 24 3 2554 2846 142616259 142616536 7.720000e-81 311
4 TraesCS6D01G104000 chr6A 89.163 1338 73 30 748 2037 85261498 85262811 0.000000e+00 1602
5 TraesCS6D01G104000 chr6A 91.181 669 46 6 2206 2870 85264485 85265144 0.000000e+00 896
6 TraesCS6D01G104000 chr6A 83.452 562 38 23 52 587 85260524 85261056 3.350000e-129 472
7 TraesCS6D01G104000 chr6A 93.431 137 9 0 583 719 85261363 85261499 1.350000e-48 204
8 TraesCS6D01G104000 chr1B 84.071 678 91 13 2193 2869 375783990 375783329 3.120000e-179 638
9 TraesCS6D01G104000 chr1B 82.105 190 26 6 2429 2617 333785999 333786181 3.830000e-34 156
10 TraesCS6D01G104000 chr1D 83.236 686 97 12 2186 2869 276493554 276492885 5.260000e-172 614
11 TraesCS6D01G104000 chr7A 83.744 406 59 6 1001 1404 704387759 704388159 7.510000e-101 377
12 TraesCS6D01G104000 chr4B 82.299 435 71 4 1001 1435 640937 640509 3.490000e-99 372
13 TraesCS6D01G104000 chr7B 83.251 406 61 6 1001 1404 702535218 702535618 1.620000e-97 366
14 TraesCS6D01G104000 chr7B 82.426 404 68 2 1001 1404 702854453 702854053 1.640000e-92 350
15 TraesCS6D01G104000 chr7D 82.222 405 67 4 1001 1404 612977377 612977777 7.610000e-91 344
16 TraesCS6D01G104000 chr4A 84.967 306 43 2 1001 1306 603534972 603534670 9.990000e-80 307


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 TraesCS6D01G104000 chr6D 67568268 67571137 2869 False 5301.000000 5301 100.00000 1 2870 1 chr6D.!!$F1 2869
1 TraesCS6D01G104000 chr6B 142611506 142616536 5030 False 847.666667 1620 87.67600 23 2846 3 chr6B.!!$F1 2823
2 TraesCS6D01G104000 chr6A 85260524 85265144 4620 False 793.500000 1602 89.30675 52 2870 4 chr6A.!!$F1 2818
3 TraesCS6D01G104000 chr1B 375783329 375783990 661 True 638.000000 638 84.07100 2193 2869 1 chr1B.!!$R1 676
4 TraesCS6D01G104000 chr1D 276492885 276493554 669 True 614.000000 614 83.23600 2186 2869 1 chr1D.!!$R1 683

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
305 332 0.034756 CCGTGTCTGTGGACCATGAA 59.965 55.0 0.0 0.0 41.47 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1884 2300 0.030297 ATCTCTCAGGAGGTGCCCAT 60.03 55.0 0.0 0.0 39.86 4.0 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
47 48 3.882888 TGAATTTATTCATCGGTCCCAGC 59.117 43.478 1.12 0.00 41.51 4.85
49 50 1.507140 TTATTCATCGGTCCCAGCCT 58.493 50.000 0.00 0.00 0.00 4.58
50 51 0.758734 TATTCATCGGTCCCAGCCTG 59.241 55.000 0.00 0.00 0.00 4.85
94 97 7.048629 TGTTTCTGCAATTCAAGGTCAATTA 57.951 32.000 0.00 0.00 0.00 1.40
97 100 6.500684 TCTGCAATTCAAGGTCAATTAGTC 57.499 37.500 0.00 0.00 0.00 2.59
107 110 3.200825 AGGTCAATTAGTCCACCCTGATG 59.799 47.826 0.00 0.00 0.00 3.07
121 131 2.769270 CCTGATGGATGCCGATACGGA 61.769 57.143 14.43 0.05 42.44 4.69
136 146 0.755327 ACGGAAAGCTGTGCCCTTTT 60.755 50.000 0.00 0.00 32.98 2.27
192 212 1.078285 AAACCGTGTGTTGGTCCGT 60.078 52.632 0.00 0.00 39.29 4.69
305 332 0.034756 CCGTGTCTGTGGACCATGAA 59.965 55.000 0.00 0.00 41.47 2.57
308 335 2.359900 GTGTCTGTGGACCATGAATCC 58.640 52.381 0.00 8.62 41.47 3.01
309 336 1.984424 TGTCTGTGGACCATGAATCCA 59.016 47.619 13.12 13.12 44.20 3.41
362 389 1.219522 CTGTCGTCGTTGGGTTCCAC 61.220 60.000 0.00 0.00 30.78 4.02
364 391 2.109387 CGTCGTTGGGTTCCACCA 59.891 61.111 0.00 0.00 41.02 4.17
422 452 0.918619 CACGCCGTTACCTATTCGTG 59.081 55.000 0.00 0.00 40.65 4.35
549 583 3.064207 TCCAGTTCTAAACGCATGTCAC 58.936 45.455 0.00 0.00 36.23 3.67
550 584 2.159841 CCAGTTCTAAACGCATGTCACG 60.160 50.000 0.00 0.00 36.23 4.35
635 982 4.840716 TTTACCGGCCTAAGTTTGGATA 57.159 40.909 7.60 0.00 0.00 2.59
660 1007 8.278729 AGGTTTTGAATGAATGCAAAGAAAAA 57.721 26.923 0.00 0.00 35.64 1.94
670 1017 8.899427 TGAATGCAAAGAAAAACCATTAATCA 57.101 26.923 0.00 0.00 0.00 2.57
694 1043 6.249035 TCATTTCCATTCCTTCGTAACAAC 57.751 37.500 0.00 0.00 0.00 3.32
739 1088 4.328440 CGTCTGGATGAGCAAAAGTAGAAG 59.672 45.833 0.00 0.00 0.00 2.85
745 1094 3.808728 TGAGCAAAAGTAGAAGCAGTGT 58.191 40.909 0.00 0.00 0.00 3.55
751 1100 6.017852 AGCAAAAGTAGAAGCAGTGTAGTTTC 60.018 38.462 0.00 0.00 29.55 2.78
855 1210 2.038295 AGAGACCTTCCAGAAACAGCAG 59.962 50.000 0.00 0.00 0.00 4.24
858 1213 1.707427 ACCTTCCAGAAACAGCAGGAT 59.293 47.619 0.00 0.00 0.00 3.24
888 1245 1.705256 CCGCGCGCTCCTATTTATAA 58.295 50.000 30.48 0.00 0.00 0.98
896 1253 3.244422 CGCTCCTATTTATAACCTGCCCA 60.244 47.826 0.00 0.00 0.00 5.36
897 1254 4.072839 GCTCCTATTTATAACCTGCCCAC 58.927 47.826 0.00 0.00 0.00 4.61
898 1255 4.315803 CTCCTATTTATAACCTGCCCACG 58.684 47.826 0.00 0.00 0.00 4.94
899 1256 3.968649 TCCTATTTATAACCTGCCCACGA 59.031 43.478 0.00 0.00 0.00 4.35
900 1257 4.409574 TCCTATTTATAACCTGCCCACGAA 59.590 41.667 0.00 0.00 0.00 3.85
937 1294 1.267806 CATCACCCAACAGCACTCAAC 59.732 52.381 0.00 0.00 0.00 3.18
950 1307 3.857217 CTCAACCAGAGCAGAGCAT 57.143 52.632 0.00 0.00 37.59 3.79
951 1308 2.110901 CTCAACCAGAGCAGAGCATT 57.889 50.000 0.00 0.00 37.59 3.56
952 1309 2.008329 CTCAACCAGAGCAGAGCATTC 58.992 52.381 0.00 0.00 37.59 2.67
953 1310 0.725686 CAACCAGAGCAGAGCATTCG 59.274 55.000 0.00 0.00 0.00 3.34
954 1311 1.023513 AACCAGAGCAGAGCATTCGC 61.024 55.000 0.00 0.00 38.99 4.70
955 1312 2.178890 CCAGAGCAGAGCATTCGCC 61.179 63.158 0.00 0.00 39.83 5.54
957 1314 1.449246 AGAGCAGAGCATTCGCCAC 60.449 57.895 0.00 0.00 39.83 5.01
958 1315 1.449246 GAGCAGAGCATTCGCCACT 60.449 57.895 0.00 0.00 39.83 4.00
959 1316 1.703438 GAGCAGAGCATTCGCCACTG 61.703 60.000 0.00 0.00 42.33 3.66
961 1318 0.740868 GCAGAGCATTCGCCACTGTA 60.741 55.000 0.00 0.00 41.83 2.74
962 1319 1.284657 CAGAGCATTCGCCACTGTAG 58.715 55.000 0.00 0.00 39.83 2.74
963 1320 0.460987 AGAGCATTCGCCACTGTAGC 60.461 55.000 0.00 0.00 39.83 3.58
964 1321 0.460987 GAGCATTCGCCACTGTAGCT 60.461 55.000 0.00 0.00 39.83 3.32
965 1322 0.824109 AGCATTCGCCACTGTAGCTA 59.176 50.000 0.00 0.00 39.83 3.32
966 1323 1.202463 AGCATTCGCCACTGTAGCTAG 60.202 52.381 0.00 0.00 39.83 3.42
968 1325 0.824109 ATTCGCCACTGTAGCTAGCA 59.176 50.000 18.83 0.00 0.00 3.49
969 1326 0.108804 TTCGCCACTGTAGCTAGCAC 60.109 55.000 18.83 13.33 0.00 4.40
972 1334 0.526524 GCCACTGTAGCTAGCACTCG 60.527 60.000 18.83 10.51 0.00 4.18
1005 1367 4.760047 GACACGGCGAGCATGGGT 62.760 66.667 16.62 0.00 0.00 4.51
1524 1889 4.521292 TCGGGCGGGTACGGGTAT 62.521 66.667 0.00 0.00 41.36 2.73
1798 2211 1.853963 GAGCTACCTGGAGGACAAGA 58.146 55.000 0.00 0.00 38.94 3.02
1872 2288 2.789436 CGACGACGACGACTACTAGAGA 60.789 54.545 15.32 0.00 42.66 3.10
1879 2295 4.449068 ACGACGACTACTAGAGAAAACGAA 59.551 41.667 0.00 0.00 0.00 3.85
1880 2296 5.050091 ACGACGACTACTAGAGAAAACGAAA 60.050 40.000 0.00 0.00 0.00 3.46
1882 2298 6.183359 CGACGACTACTAGAGAAAACGAAAAC 60.183 42.308 0.00 0.00 0.00 2.43
1883 2299 5.622856 ACGACTACTAGAGAAAACGAAAACG 59.377 40.000 0.00 0.00 0.00 3.60
1884 2300 5.848036 CGACTACTAGAGAAAACGAAAACGA 59.152 40.000 0.00 0.00 0.00 3.85
1885 2301 6.522510 CGACTACTAGAGAAAACGAAAACGAT 59.477 38.462 0.00 0.00 0.00 3.73
1911 2327 4.499183 CACCTCCTGAGAGATTGTTGTAC 58.501 47.826 0.00 0.00 43.39 2.90
1912 2328 4.021104 CACCTCCTGAGAGATTGTTGTACA 60.021 45.833 0.00 0.00 43.39 2.90
1915 2334 2.668457 CCTGAGAGATTGTTGTACACGC 59.332 50.000 0.00 0.00 0.00 5.34
1919 2338 2.037251 AGAGATTGTTGTACACGCTGGT 59.963 45.455 0.00 0.00 0.00 4.00
1955 2377 6.882458 GCATCTTCTTTGCTTTTATTCTGG 57.118 37.500 0.00 0.00 37.14 3.86
1974 2396 4.709397 TCTGGCCGGATTTGTTGAATAAAT 59.291 37.500 11.27 0.00 0.00 1.40
1983 2405 7.510896 CGGATTTGTTGAATAAATACGCGAAAC 60.511 37.037 16.92 3.54 42.68 2.78
2005 2427 5.985781 ACAAATTAACAACGAGTGTAGCAG 58.014 37.500 0.00 0.00 40.60 4.24
2012 2434 3.179830 CAACGAGTGTAGCAGTACATCC 58.820 50.000 0.00 0.00 41.29 3.51
2032 4052 8.550710 ACATCCAATTGAAATGTTTTATGTGG 57.449 30.769 16.26 0.00 29.51 4.17
2054 4077 2.126467 CTTGGCACCGACAAATTGTTG 58.874 47.619 6.38 6.38 40.84 3.33
2091 4114 4.160736 CCTACACTGGCTTTGCTTTTAC 57.839 45.455 0.00 0.00 0.00 2.01
2092 4115 3.821033 CCTACACTGGCTTTGCTTTTACT 59.179 43.478 0.00 0.00 0.00 2.24
2093 4116 5.001232 CCTACACTGGCTTTGCTTTTACTA 58.999 41.667 0.00 0.00 0.00 1.82
2107 4130 9.509855 TTTGCTTTTACTATTGTGTTTGTACAG 57.490 29.630 0.00 0.00 34.24 2.74
2117 4140 4.188462 TGTGTTTGTACAGTCTTGACTGG 58.812 43.478 27.66 14.22 41.76 4.00
2147 4507 7.493645 TCTGCAGTCTTAACAATGACATAGATG 59.506 37.037 14.67 0.00 35.81 2.90
2159 4519 8.704668 ACAATGACATAGATGTATGGTGTCTAA 58.295 33.333 13.91 0.00 41.95 2.10
2166 4526 6.179906 AGATGTATGGTGTCTAATCCTTGG 57.820 41.667 0.00 0.00 0.00 3.61
2171 4531 1.473434 GGTGTCTAATCCTTGGCCTCG 60.473 57.143 3.32 0.00 0.00 4.63
2182 4542 2.899339 GGCCTCGCCTCTCAATGC 60.899 66.667 0.00 0.00 46.69 3.56
2190 4550 1.854227 GCCTCTCAATGCCGTACTAC 58.146 55.000 0.00 0.00 0.00 2.73
2191 4551 1.136305 GCCTCTCAATGCCGTACTACA 59.864 52.381 0.00 0.00 0.00 2.74
2204 4564 6.275335 TGCCGTACTACAATGGTAATTAGTC 58.725 40.000 0.00 0.00 0.00 2.59
2231 4592 5.164061 GGATTGAACGTTGCATTCATTCAAC 60.164 40.000 5.00 11.62 40.88 3.18
2292 4653 2.923605 TAAAAGGGGCGTAAAATGCG 57.076 45.000 0.00 0.00 0.00 4.73
2323 4684 4.405680 TCCAGAACATAGGACATACTGTGG 59.594 45.833 0.00 0.00 34.33 4.17
2331 6255 2.578021 AGGACATACTGTGGCTGGATTT 59.422 45.455 0.00 0.00 35.58 2.17
2376 6301 4.837896 GCTTGGAAGCCAATTAGTATCC 57.162 45.455 0.00 0.00 46.20 2.59
2420 6345 3.602390 CGAAAAGCTCGGAGAACAAAA 57.398 42.857 9.69 0.00 44.20 2.44
2476 6401 2.158813 AGAGGCTCACTTGACCGAAAAA 60.159 45.455 18.26 0.00 0.00 1.94
2483 6408 5.123979 GCTCACTTGACCGAAAAATCCTAAT 59.876 40.000 0.00 0.00 0.00 1.73
2505 6430 2.161211 GCTCTGCTTTGAAGGCTACTTG 59.839 50.000 0.00 0.00 36.97 3.16
2515 6440 6.869206 TTGAAGGCTACTTGTCCTACTAAT 57.131 37.500 0.00 0.00 36.97 1.73
2520 6445 7.439108 AGGCTACTTGTCCTACTAATTTCAT 57.561 36.000 0.00 0.00 0.00 2.57
2568 6526 9.007901 CAAGAAAGAAGGACATCTCTAACATTT 57.992 33.333 0.00 0.00 0.00 2.32
2600 6558 2.094734 CACGTAGGGTTACCGAAATTGC 59.905 50.000 0.00 0.00 43.47 3.56
2815 6774 8.542132 CCTTGTTAACATGACAAAACAAAGATG 58.458 33.333 20.00 0.00 40.28 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.597672 ACAAAGGGAGGAAAAATTGTTCAAAC 59.402 34.615 10.53 1.31 0.00 2.93
1 2 6.597280 CACAAAGGGAGGAAAAATTGTTCAAA 59.403 34.615 10.53 0.00 0.00 2.69
2 3 6.070538 TCACAAAGGGAGGAAAAATTGTTCAA 60.071 34.615 10.53 0.00 0.00 2.69
3 4 5.423610 TCACAAAGGGAGGAAAAATTGTTCA 59.576 36.000 10.53 0.00 0.00 3.18
4 5 5.912892 TCACAAAGGGAGGAAAAATTGTTC 58.087 37.500 0.00 0.00 0.00 3.18
5 6 5.948742 TCACAAAGGGAGGAAAAATTGTT 57.051 34.783 0.00 0.00 0.00 2.83
6 7 5.948742 TTCACAAAGGGAGGAAAAATTGT 57.051 34.783 0.00 0.00 0.00 2.71
7 8 7.806409 AAATTCACAAAGGGAGGAAAAATTG 57.194 32.000 0.00 0.00 0.00 2.32
9 10 9.725019 GAATAAATTCACAAAGGGAGGAAAAAT 57.275 29.630 0.00 0.00 36.80 1.82
10 11 8.709308 TGAATAAATTCACAAAGGGAGGAAAAA 58.291 29.630 1.23 0.00 41.51 1.94
11 12 8.256356 TGAATAAATTCACAAAGGGAGGAAAA 57.744 30.769 1.23 0.00 41.51 2.29
12 13 7.847711 TGAATAAATTCACAAAGGGAGGAAA 57.152 32.000 1.23 0.00 41.51 3.13
44 45 3.441572 CCAAGAATAAACTGTCCAGGCTG 59.558 47.826 7.75 7.75 0.00 4.85
47 48 2.755103 GCCCAAGAATAAACTGTCCAGG 59.245 50.000 0.00 0.00 0.00 4.45
49 50 3.806949 AGCCCAAGAATAAACTGTCCA 57.193 42.857 0.00 0.00 0.00 4.02
50 51 3.826729 ACAAGCCCAAGAATAAACTGTCC 59.173 43.478 0.00 0.00 0.00 4.02
97 100 2.060567 ATCGGCATCCATCAGGGTGG 62.061 60.000 0.00 0.00 46.69 4.61
136 146 1.597854 CACGCCACCAGAAAGCTGA 60.598 57.895 0.00 0.00 45.17 4.26
192 212 2.281484 GCGTTCCACAGGAGGCAA 60.281 61.111 6.37 0.00 34.55 4.52
269 296 2.272471 GCAACAGGGGCCTCTACC 59.728 66.667 3.71 0.00 0.00 3.18
305 332 1.278413 CTCTCCCGATGCATCATGGAT 59.722 52.381 26.67 0.00 30.06 3.41
308 335 1.793258 GTCTCTCCCGATGCATCATG 58.207 55.000 25.70 15.63 0.00 3.07
309 336 0.316522 CGTCTCTCCCGATGCATCAT 59.683 55.000 25.70 0.00 0.00 2.45
310 337 1.037579 ACGTCTCTCCCGATGCATCA 61.038 55.000 25.70 6.28 0.00 3.07
311 338 0.596083 CACGTCTCTCCCGATGCATC 60.596 60.000 17.10 17.10 0.00 3.91
312 339 1.439228 CACGTCTCTCCCGATGCAT 59.561 57.895 0.00 0.00 0.00 3.96
313 340 2.885113 CACGTCTCTCCCGATGCA 59.115 61.111 0.00 0.00 0.00 3.96
362 389 3.414700 GGCGCAGACAACGACTGG 61.415 66.667 10.83 0.00 35.06 4.00
422 452 8.562892 TGCTTGATGCTTCTAGAAAATATAAGC 58.437 33.333 23.11 23.11 43.37 3.09
549 583 4.207019 GGCAAGTTTCTTGATTTGTTCACG 59.793 41.667 12.77 0.00 32.84 4.35
550 584 4.207019 CGGCAAGTTTCTTGATTTGTTCAC 59.793 41.667 12.77 0.00 32.84 3.18
551 585 4.142271 ACGGCAAGTTTCTTGATTTGTTCA 60.142 37.500 12.77 0.00 0.00 3.18
635 982 7.862512 TTTTCTTTGCATTCATTCAAAACCT 57.137 28.000 0.00 0.00 32.55 3.50
660 1007 8.557304 AAGGAATGGAAATGATGATTAATGGT 57.443 30.769 0.00 0.00 0.00 3.55
670 1017 6.852664 GTTGTTACGAAGGAATGGAAATGAT 58.147 36.000 0.00 0.00 0.00 2.45
694 1043 4.102649 GTCAGGTTCACTTTTGGTTTTCG 58.897 43.478 0.00 0.00 0.00 3.46
739 1088 1.798813 CCTTCACCGAAACTACACTGC 59.201 52.381 0.00 0.00 0.00 4.40
745 1094 8.801882 ATTATCATTTTCCTTCACCGAAACTA 57.198 30.769 0.00 0.00 0.00 2.24
751 1100 8.466798 AGGTTTTATTATCATTTTCCTTCACCG 58.533 33.333 0.00 0.00 0.00 4.94
774 1123 6.894339 AAAATGTATTCGGTTTCTTCAGGT 57.106 33.333 0.00 0.00 0.00 4.00
786 1135 4.259930 GGACGAACGGGTAAAATGTATTCG 60.260 45.833 0.00 0.00 42.26 3.34
833 1188 3.239449 TGCTGTTTCTGGAAGGTCTCTA 58.761 45.455 0.00 0.00 0.00 2.43
888 1245 2.129555 AATGAGCTTCGTGGGCAGGT 62.130 55.000 0.00 0.00 0.00 4.00
898 1255 1.224965 GATGGAGGCGAATGAGCTTC 58.775 55.000 0.00 0.00 41.73 3.86
899 1256 0.543277 TGATGGAGGCGAATGAGCTT 59.457 50.000 0.00 0.00 37.29 3.74
900 1257 0.763652 ATGATGGAGGCGAATGAGCT 59.236 50.000 0.00 0.00 37.29 4.09
937 1294 2.178890 GGCGAATGCTCTGCTCTGG 61.179 63.158 0.00 0.00 42.25 3.86
945 1302 0.460987 AGCTACAGTGGCGAATGCTC 60.461 55.000 2.82 0.00 42.25 4.26
950 1307 0.108804 GTGCTAGCTACAGTGGCGAA 60.109 55.000 17.23 0.00 34.52 4.70
951 1308 0.965866 AGTGCTAGCTACAGTGGCGA 60.966 55.000 17.23 0.00 34.52 5.54
952 1309 0.526524 GAGTGCTAGCTACAGTGGCG 60.527 60.000 17.23 0.00 34.52 5.69
953 1310 0.526524 CGAGTGCTAGCTACAGTGGC 60.527 60.000 17.23 0.00 0.00 5.01
954 1311 0.526524 GCGAGTGCTAGCTACAGTGG 60.527 60.000 17.23 1.15 38.39 4.00
955 1312 0.863538 CGCGAGTGCTAGCTACAGTG 60.864 60.000 17.23 12.36 39.65 3.66
957 1314 1.298713 CCGCGAGTGCTAGCTACAG 60.299 63.158 17.23 11.17 39.65 2.74
958 1315 2.798689 CCGCGAGTGCTAGCTACA 59.201 61.111 17.23 0.00 39.65 2.74
959 1316 2.655685 GCCGCGAGTGCTAGCTAC 60.656 66.667 17.23 12.27 39.65 3.58
1158 1520 1.251527 TGAGCTTCTCGTCCCAGACC 61.252 60.000 0.00 0.00 32.35 3.85
1160 1522 1.251527 GGTGAGCTTCTCGTCCCAGA 61.252 60.000 0.00 0.00 32.35 3.86
1161 1523 1.216710 GGTGAGCTTCTCGTCCCAG 59.783 63.158 0.00 0.00 32.35 4.45
1226 1588 3.238241 CGTGGACGACGTCGATGC 61.238 66.667 41.52 28.90 43.50 3.91
1872 2288 1.269361 GGTGCCCATCGTTTTCGTTTT 60.269 47.619 0.00 0.00 44.46 2.43
1879 2295 1.002134 CAGGAGGTGCCCATCGTTT 60.002 57.895 0.00 0.00 37.37 3.60
1880 2296 1.903877 CTCAGGAGGTGCCCATCGTT 61.904 60.000 0.00 0.00 37.37 3.85
1882 2298 2.025767 CTCTCAGGAGGTGCCCATCG 62.026 65.000 0.00 0.00 37.37 3.84
1883 2299 0.689080 TCTCTCAGGAGGTGCCCATC 60.689 60.000 0.00 0.00 39.86 3.51
1884 2300 0.030297 ATCTCTCAGGAGGTGCCCAT 60.030 55.000 0.00 0.00 39.86 4.00
1885 2301 0.252881 AATCTCTCAGGAGGTGCCCA 60.253 55.000 0.00 0.00 39.86 5.36
1932 2354 5.290400 GCCAGAATAAAAGCAAAGAAGATGC 59.710 40.000 0.00 0.00 44.15 3.91
1933 2355 5.809051 GGCCAGAATAAAAGCAAAGAAGATG 59.191 40.000 0.00 0.00 0.00 2.90
1955 2377 4.439776 GCGTATTTATTCAACAAATCCGGC 59.560 41.667 0.00 0.00 28.85 6.13
1974 2396 5.075670 TCGTTGTTAATTTGTTTCGCGTA 57.924 34.783 5.77 0.00 0.00 4.42
1983 2405 5.985781 ACTGCTACACTCGTTGTTAATTTG 58.014 37.500 0.00 0.00 39.91 2.32
2012 2434 7.299586 CAAGGCCACATAAAACATTTCAATTG 58.700 34.615 5.01 0.00 0.00 2.32
2030 4050 2.992817 ATTTGTCGGTGCCAAGGCCA 62.993 55.000 5.01 0.00 41.09 5.36
2032 4052 0.667184 CAATTTGTCGGTGCCAAGGC 60.667 55.000 3.61 3.61 42.35 4.35
2074 4097 5.630680 CACAATAGTAAAAGCAAAGCCAGTG 59.369 40.000 0.00 0.00 0.00 3.66
2091 4114 7.715265 AGTCAAGACTGTACAAACACAATAG 57.285 36.000 1.20 0.00 40.75 1.73
2117 4140 5.335113 TGTCATTGTTAAGACTGCAGAATGC 60.335 40.000 23.35 13.25 46.92 3.56
2126 4149 9.770097 CCATACATCTATGTCATTGTTAAGACT 57.230 33.333 0.00 0.00 41.97 3.24
2127 4150 9.547753 ACCATACATCTATGTCATTGTTAAGAC 57.452 33.333 0.00 0.00 41.97 3.01
2128 4151 9.546428 CACCATACATCTATGTCATTGTTAAGA 57.454 33.333 0.00 0.00 41.97 2.10
2129 4152 9.330063 ACACCATACATCTATGTCATTGTTAAG 57.670 33.333 0.00 0.00 41.97 1.85
2130 4153 9.325198 GACACCATACATCTATGTCATTGTTAA 57.675 33.333 0.00 0.00 41.97 2.01
2147 4507 3.136626 AGGCCAAGGATTAGACACCATAC 59.863 47.826 5.01 0.00 0.00 2.39
2166 4526 2.899339 GGCATTGAGAGGCGAGGC 60.899 66.667 0.00 0.00 36.96 4.70
2171 4531 1.136305 TGTAGTACGGCATTGAGAGGC 59.864 52.381 0.00 0.00 0.00 4.70
2182 4542 7.437267 CCTTGACTAATTACCATTGTAGTACGG 59.563 40.741 0.00 0.00 0.00 4.02
2190 4550 7.910162 CGTTCAATCCTTGACTAATTACCATTG 59.090 37.037 0.00 0.00 39.87 2.82
2191 4551 7.610305 ACGTTCAATCCTTGACTAATTACCATT 59.390 33.333 0.00 0.00 39.87 3.16
2204 4564 3.899734 TGAATGCAACGTTCAATCCTTG 58.100 40.909 0.00 0.00 32.98 3.61
2231 4592 7.530010 ACTCATTTCATTTGTTATCGTCCTTG 58.470 34.615 0.00 0.00 0.00 3.61
2277 4638 0.538118 TACTCGCATTTTACGCCCCT 59.462 50.000 0.00 0.00 0.00 4.79
2318 4679 2.165167 ACATCACAAATCCAGCCACAG 58.835 47.619 0.00 0.00 0.00 3.66
2323 4684 5.291971 ACTTGAAAACATCACAAATCCAGC 58.708 37.500 0.00 0.00 37.92 4.85
2371 6295 5.069251 AGGTATGCACAAGACAGTAGGATAC 59.931 44.000 0.00 0.00 43.47 2.24
2376 6301 5.986135 GGAATAGGTATGCACAAGACAGTAG 59.014 44.000 0.00 0.00 0.00 2.57
2428 6353 2.425143 TTCATGCTTGAGCCCTAAGG 57.575 50.000 2.23 0.00 41.18 2.69
2476 6401 4.205587 CCTTCAAAGCAGAGCATTAGGAT 58.794 43.478 0.00 0.00 0.00 3.24
2483 6408 1.349026 AGTAGCCTTCAAAGCAGAGCA 59.651 47.619 0.00 0.00 0.00 4.26
2542 6470 8.558973 AATGTTAGAGATGTCCTTCTTTCTTG 57.441 34.615 0.00 0.00 0.00 3.02
2543 6471 9.579932 AAAATGTTAGAGATGTCCTTCTTTCTT 57.420 29.630 0.00 0.00 0.00 2.52
2568 6526 7.121463 TCGGTAACCCTACGTGTTACTTAATAA 59.879 37.037 20.33 4.69 44.68 1.40
2700 6658 6.623979 AAGGATAATCCATCTCTCTCATGG 57.376 41.667 0.00 0.00 39.61 3.66
2736 6694 7.617041 ACTGAGGTGAGCTAATGTAATTTTC 57.383 36.000 0.00 0.00 37.87 2.29
2815 6774 5.919141 ACTTACTCTCATGTCGTTTGTGTAC 59.081 40.000 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.