Multiple sequence alignment - TraesCS7D01G411700

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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 TraesCS7D01G411700 chr7D 100.000 2341 0 0 1 2341 530355369 530353029 0.000000e+00 4324.0
1 TraesCS7D01G411700 chr7D 93.548 62 4 0 1859 1920 617233135 617233074 2.480000e-15 93.5
2 TraesCS7D01G411700 chr7D 91.803 61 5 0 1838 1898 495853771 495853711 4.140000e-13 86.1
3 TraesCS7D01G411700 chr7B 91.822 2091 122 19 1 2049 568802299 568800216 0.000000e+00 2868.0
4 TraesCS7D01G411700 chr7B 92.459 305 20 3 2039 2341 568799074 568798771 1.280000e-117 433.0
5 TraesCS7D01G411700 chr7A 90.756 476 38 3 957 1427 610499258 610498784 4.250000e-177 630.0
6 TraesCS7D01G411700 chr7A 85.093 483 59 6 414 883 610499777 610499295 4.520000e-132 481.0
7 TraesCS7D01G411700 chr7A 82.000 250 26 9 1974 2204 52661962 52661713 6.600000e-46 195.0
8 TraesCS7D01G411700 chr7A 86.486 74 10 0 1846 1919 732577407 732577480 5.360000e-12 82.4
9 TraesCS7D01G411700 chr3A 83.200 250 23 9 1974 2204 227371222 227370973 6.550000e-51 211.0
10 TraesCS7D01G411700 chr3A 84.337 83 13 0 1838 1920 23322950 23322868 5.360000e-12 82.4
11 TraesCS7D01G411700 chr6B 80.062 321 30 16 1918 2204 610081950 610081630 8.480000e-50 207.0
12 TraesCS7D01G411700 chr6B 83.750 80 12 1 1845 1923 515065476 515065555 8.970000e-10 75.0
13 TraesCS7D01G411700 chr6B 84.848 66 9 1 2276 2341 459803707 459803643 5.400000e-07 65.8
14 TraesCS7D01G411700 chr1D 82.661 248 24 10 1974 2202 411519665 411519418 3.940000e-48 202.0
15 TraesCS7D01G411700 chr1D 97.619 84 2 0 2121 2204 268031447 268031530 6.740000e-31 145.0
16 TraesCS7D01G411700 chr5A 82.400 250 25 9 1974 2204 496034289 496034538 1.420000e-47 200.0
17 TraesCS7D01G411700 chr5A 79.795 292 39 15 1561 1837 573584079 573584365 6.600000e-46 195.0
18 TraesCS7D01G411700 chr5A 97.143 35 1 0 1918 1952 699365684 699365718 2.510000e-05 60.2
19 TraesCS7D01G411700 chr3B 82.400 250 25 10 1974 2204 473179711 473179462 1.420000e-47 200.0
20 TraesCS7D01G411700 chr4A 79.439 321 32 17 1918 2204 742707741 742707421 1.840000e-46 196.0
21 TraesCS7D01G411700 chr3D 80.114 176 24 9 1570 1738 439807707 439807536 1.140000e-23 121.0
22 TraesCS7D01G411700 chr3D 87.838 74 9 0 1845 1918 585995879 585995952 1.150000e-13 87.9
23 TraesCS7D01G411700 chr3D 86.301 73 10 0 1848 1920 604633169 604633241 1.930000e-11 80.5
24 TraesCS7D01G411700 chr5D 78.488 172 31 5 1571 1738 426474895 426474726 8.850000e-20 108.0
25 TraesCS7D01G411700 chr2A 78.613 173 19 14 1570 1738 720553538 720553380 5.320000e-17 99.0
26 TraesCS7D01G411700 chr4D 82.051 117 17 4 1627 1739 339082111 339082227 1.910000e-16 97.1
27 TraesCS7D01G411700 chr6D 86.747 83 11 0 1838 1920 157676799 157676881 2.480000e-15 93.5
28 TraesCS7D01G411700 chr1B 78.832 137 24 4 1607 1739 478047159 478047024 1.150000e-13 87.9
29 TraesCS7D01G411700 chr1A 74.641 209 34 14 1912 2103 222752743 222752949 8.970000e-10 75.0
30 TraesCS7D01G411700 chr6A 97.297 37 1 0 1917 1953 158468163 158468199 1.940000e-06 63.9


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 TraesCS7D01G411700 chr7D 530353029 530355369 2340 True 4324.0 4324 100.0000 1 2341 1 chr7D.!!$R2 2340
1 TraesCS7D01G411700 chr7B 568798771 568802299 3528 True 1650.5 2868 92.1405 1 2341 2 chr7B.!!$R1 2340
2 TraesCS7D01G411700 chr7A 610498784 610499777 993 True 555.5 630 87.9245 414 1427 2 chr7A.!!$R2 1013

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
387 394 0.18135 GGACTATGGGGAAGCACCAG 59.819 60.0 0.0 0.0 42.15 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2024 0.597377 CCGGCTTGTCTGGTTTTTGC 60.597 55.0 0.0 0.0 36.43 3.68 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
32 34 1.227853 GGGTGGTTGAGTTGTCGCT 60.228 57.895 0.00 0.00 0.00 4.93
84 86 0.669318 CGTCGCCTCAAACCTGCTAA 60.669 55.000 0.00 0.00 0.00 3.09
143 145 1.872237 GCAACTTGCAGACGACAGGTA 60.872 52.381 8.97 0.00 44.26 3.08
146 148 1.000163 ACTTGCAGACGACAGGTACAG 60.000 52.381 0.00 0.00 0.00 2.74
154 156 1.630244 CGACAGGTACAGCTTGCAGC 61.630 60.000 0.00 0.47 42.84 5.25
184 186 4.633565 GGCCTCTTCAGTTGATAAAGTGAG 59.366 45.833 0.00 0.00 34.01 3.51
207 209 8.865090 TGAGAAAAGTTAAGTGAGAGAGAGAAT 58.135 33.333 0.00 0.00 0.00 2.40
229 231 3.010584 TGGGGAAGGAAAGGAGAGAAATG 59.989 47.826 0.00 0.00 0.00 2.32
243 245 1.203100 AGAAATGGGACCTTGCTGCTT 60.203 47.619 0.00 0.00 0.00 3.91
265 267 4.930696 TGTGTCTACCATCCACTTCTCTA 58.069 43.478 0.00 0.00 0.00 2.43
282 284 1.137086 TCTACGCTTCATGGAGCTTCC 59.863 52.381 23.56 0.00 40.52 3.46
285 287 1.221840 GCTTCATGGAGCTTCCCGA 59.778 57.895 19.38 0.00 39.57 5.14
288 290 2.852495 TTCATGGAGCTTCCCGACGC 62.852 60.000 0.00 0.00 35.03 5.19
290 292 1.756950 ATGGAGCTTCCCGACGCTA 60.757 57.895 0.00 0.00 36.45 4.26
301 304 1.299926 CGACGCTATGTAGGCCCAC 60.300 63.158 0.00 0.00 0.00 4.61
387 394 0.181350 GGACTATGGGGAAGCACCAG 59.819 60.000 0.00 0.00 42.15 4.00
389 396 0.912486 ACTATGGGGAAGCACCAGAC 59.088 55.000 0.00 0.00 42.15 3.51
394 401 0.890996 GGGGAAGCACCAGACTGTTG 60.891 60.000 0.93 0.00 41.20 3.33
423 430 1.236628 CTCATGCCCTTATGAGCTGC 58.763 55.000 0.00 0.00 45.21 5.25
424 431 0.547553 TCATGCCCTTATGAGCTGCA 59.452 50.000 1.02 0.00 34.85 4.41
428 435 1.213678 TGCCCTTATGAGCTGCAAGAT 59.786 47.619 1.02 0.00 34.07 2.40
437 445 0.247460 AGCTGCAAGATACACGAGCA 59.753 50.000 1.02 0.00 34.07 4.26
441 449 1.270571 TGCAAGATACACGAGCACCAA 60.271 47.619 0.00 0.00 0.00 3.67
557 565 1.226603 GACGTCGGTCATCTTCCCG 60.227 63.158 0.00 0.00 45.55 5.14
649 657 4.642488 TGGTGGGCGAGTGGGGTA 62.642 66.667 0.00 0.00 0.00 3.69
662 670 2.165998 GTGGGGTAGTACTGTCGTCTT 58.834 52.381 5.39 0.00 0.00 3.01
756 774 5.523369 TCATATCATGTCTCGTAGCAACAG 58.477 41.667 0.00 0.00 0.00 3.16
835 855 4.712122 TTCAGCGTATGACACATCACTA 57.288 40.909 0.00 0.00 37.77 2.74
907 927 9.362151 TCTTCTGGTTTATTGTAAGGTTTCATT 57.638 29.630 0.00 0.00 0.00 2.57
912 932 8.973182 TGGTTTATTGTAAGGTTTCATTATCCC 58.027 33.333 0.00 0.00 0.00 3.85
937 957 9.019656 CCTATATCTATAAGAAGGGATCGATGG 57.980 40.741 0.54 0.00 0.00 3.51
951 971 4.202121 GGATCGATGGCACTACTAACTTCA 60.202 45.833 0.54 0.00 0.00 3.02
998 1018 5.512942 TCTTGGGTGTTCATTCTTGGATA 57.487 39.130 0.00 0.00 0.00 2.59
1057 1077 1.112315 GGTGTTGTTCATGGTGGCCA 61.112 55.000 0.00 0.00 38.19 5.36
1068 1088 2.649129 GGTGGCCATGTTGCTTCCC 61.649 63.158 9.72 0.00 0.00 3.97
1097 1117 5.705905 AGCCTTGCCCGAAATAATTATCTAC 59.294 40.000 0.00 0.00 0.00 2.59
1101 1121 7.095187 CCTTGCCCGAAATAATTATCTACAGAC 60.095 40.741 0.00 0.00 0.00 3.51
1145 1166 5.995282 TCTATGTTCTGTGTTGTTACCCAAG 59.005 40.000 0.00 0.00 32.51 3.61
1160 1181 4.380843 ACCCAAGTGTTGTCCATATTCA 57.619 40.909 0.00 0.00 0.00 2.57
1226 1247 3.814842 CCTACACTGTTTCTGAATGCACA 59.185 43.478 0.00 0.00 0.00 4.57
1256 1277 1.520120 CGTCGAGCACTGCCATGAT 60.520 57.895 0.00 0.00 0.00 2.45
1334 1355 4.212004 CGATTCTGTCTCTGCAAGAAACAA 59.788 41.667 2.08 0.00 46.34 2.83
1460 1485 1.074405 ACATGACAGGTGGTTGCATCT 59.926 47.619 0.00 0.00 0.00 2.90
1507 1532 0.378257 CAGATGCCCGCATGTTGTAC 59.622 55.000 6.96 0.00 36.70 2.90
1526 1551 2.423577 ACTTCCGGCAATACAAGTCAC 58.576 47.619 0.00 0.00 0.00 3.67
1530 1555 2.550606 TCCGGCAATACAAGTCACAAAC 59.449 45.455 0.00 0.00 0.00 2.93
1532 1557 3.749088 CCGGCAATACAAGTCACAAACTA 59.251 43.478 0.00 0.00 37.17 2.24
1535 1560 5.095490 GGCAATACAAGTCACAAACTATGC 58.905 41.667 0.00 0.00 37.17 3.14
1536 1561 5.335583 GGCAATACAAGTCACAAACTATGCA 60.336 40.000 0.00 0.00 37.17 3.96
1537 1562 5.569059 GCAATACAAGTCACAAACTATGCAC 59.431 40.000 0.00 0.00 37.17 4.57
1545 1570 4.023279 GTCACAAACTATGCACATTGACCA 60.023 41.667 8.93 0.00 28.70 4.02
1581 1606 1.066645 GGCCCTCTTTTGATTTGCAGG 60.067 52.381 0.00 0.00 0.00 4.85
1595 1620 8.899427 TTGATTTGCAGGATTTTCAAAACATA 57.101 26.923 0.00 0.00 34.24 2.29
1599 1624 6.271488 TGCAGGATTTTCAAAACATAGGAG 57.729 37.500 0.00 0.00 0.00 3.69
1600 1625 5.105063 GCAGGATTTTCAAAACATAGGAGC 58.895 41.667 0.00 0.00 0.00 4.70
1604 1629 5.418840 GGATTTTCAAAACATAGGAGCAGGA 59.581 40.000 0.00 0.00 0.00 3.86
1605 1630 6.071391 GGATTTTCAAAACATAGGAGCAGGAA 60.071 38.462 0.00 0.00 0.00 3.36
1648 1673 4.757149 GGCATGTCCACTTCAATCCTATAC 59.243 45.833 0.00 0.00 34.01 1.47
1747 1773 7.865706 ATGAAATGGAGTACACTTATTCCAC 57.134 36.000 1.66 0.00 44.54 4.02
1758 1784 6.976934 ACACTTATTCCACAGGAAACAATT 57.023 33.333 2.16 0.00 45.41 2.32
1759 1785 6.981722 ACACTTATTCCACAGGAAACAATTC 58.018 36.000 2.16 0.00 45.41 2.17
1767 1793 8.561738 TTCCACAGGAAACAATTCTATAGAAC 57.438 34.615 17.35 3.87 38.93 3.01
1776 1802 8.594881 AAACAATTCTATAGAACGAGCATAGG 57.405 34.615 17.35 2.85 36.80 2.57
1819 1845 7.998964 TCTAACCCTCCAAAATCCTATGAAATC 59.001 37.037 0.00 0.00 0.00 2.17
1822 1848 5.400653 CCCTCCAAAATCCTATGAAATCCCT 60.401 44.000 0.00 0.00 0.00 4.20
1824 1850 6.612863 CCTCCAAAATCCTATGAAATCCCTTT 59.387 38.462 0.00 0.00 0.00 3.11
1825 1851 7.784550 CCTCCAAAATCCTATGAAATCCCTTTA 59.215 37.037 0.00 0.00 0.00 1.85
1842 1872 7.817910 TCCCTTTAAATCAAGGACCTAAGTA 57.182 36.000 0.00 0.00 45.79 2.24
1867 1897 3.684305 ACACGTGTGACATGAACATATGG 59.316 43.478 22.71 1.39 32.32 2.74
1870 1900 3.126686 CGTGTGACATGAACATATGGCAA 59.873 43.478 7.80 0.00 46.98 4.52
1878 1908 3.884895 TGAACATATGGCAACTCCGAAT 58.115 40.909 7.80 0.00 37.80 3.34
1879 1909 3.627123 TGAACATATGGCAACTCCGAATG 59.373 43.478 7.80 0.00 37.80 2.67
1916 1956 4.537135 TTACTGAGGTGAGGATGACAAC 57.463 45.455 0.00 0.00 0.00 3.32
1917 1957 2.614259 ACTGAGGTGAGGATGACAACT 58.386 47.619 0.00 0.00 38.05 3.16
1918 1958 2.975489 ACTGAGGTGAGGATGACAACTT 59.025 45.455 0.00 0.00 35.31 2.66
1954 1994 5.779529 CCATCATGGCTAACTTTATTGCT 57.220 39.130 0.00 0.00 0.00 3.91
1960 2015 8.574251 TCATGGCTAACTTTATTGCTCTTAAA 57.426 30.769 0.00 0.00 0.00 1.52
1962 2017 7.753309 TGGCTAACTTTATTGCTCTTAAACA 57.247 32.000 0.00 0.00 0.00 2.83
1969 2024 9.696917 AACTTTATTGCTCTTAAACAGGAATTG 57.303 29.630 6.25 2.37 34.17 2.32
1970 2025 7.814587 ACTTTATTGCTCTTAAACAGGAATTGC 59.185 33.333 6.25 0.00 34.17 3.56
1972 2027 5.528043 TTGCTCTTAAACAGGAATTGCAA 57.472 34.783 0.00 0.00 35.88 4.08
1987 2042 0.102120 TGCAAAAACCAGACAAGCCG 59.898 50.000 0.00 0.00 0.00 5.52
1989 2044 1.028905 CAAAAACCAGACAAGCCGGA 58.971 50.000 5.05 0.00 0.00 5.14
1990 2045 1.407258 CAAAAACCAGACAAGCCGGAA 59.593 47.619 5.05 0.00 0.00 4.30
2029 2084 7.817641 AGAGCTACAAACCTTATTACAAAAGC 58.182 34.615 0.00 0.00 0.00 3.51
2031 2086 7.947282 AGCTACAAACCTTATTACAAAAGCAA 58.053 30.769 0.00 0.00 0.00 3.91
2050 3257 3.058639 GCAATAACTAGCTAGCACATGCC 60.059 47.826 20.91 7.89 43.38 4.40
2147 3354 0.179029 CCCACCATACCGATTGTCCC 60.179 60.000 0.00 0.00 0.00 4.46
2161 3368 3.627395 TTGTCCCGAGCAATAGTCAAT 57.373 42.857 0.00 0.00 0.00 2.57
2203 3410 1.077716 CCTCCACCCGGTTGAATCC 60.078 63.158 0.00 0.00 0.00 3.01
2219 3427 2.516227 ATCCCTTCTCACTCTGACGA 57.484 50.000 0.00 0.00 0.00 4.20
2234 3442 1.066858 TGACGAGAGGATGGCAACTTC 60.067 52.381 0.00 0.00 39.93 3.01
2236 3444 1.556911 ACGAGAGGATGGCAACTTCAT 59.443 47.619 9.45 0.00 42.34 2.57
2244 3452 6.096001 AGAGGATGGCAACTTCATTTATGAAC 59.904 38.462 9.45 0.00 41.51 3.18
2249 3457 5.479724 TGGCAACTTCATTTATGAACCATCA 59.520 36.000 7.89 0.00 41.51 3.07
2292 3501 8.560374 CAAGTTTCAGTTTTGTTTTTGGGTTTA 58.440 29.630 0.00 0.00 0.00 2.01
2303 3512 2.841442 TTGGGTTTATTTTTGGCGGG 57.159 45.000 0.00 0.00 0.00 6.13
2305 3514 2.885616 TGGGTTTATTTTTGGCGGGTA 58.114 42.857 0.00 0.00 0.00 3.69
2306 3515 2.561858 TGGGTTTATTTTTGGCGGGTAC 59.438 45.455 0.00 0.00 0.00 3.34
2313 3522 0.321830 TTTTGGCGGGTACTAGGCAC 60.322 55.000 14.58 0.00 40.24 5.01
2319 3528 1.746517 GGGTACTAGGCACCATCCG 59.253 63.158 15.44 0.00 37.84 4.18
2327 3536 1.227853 GGCACCATCCGGATGTACC 60.228 63.158 36.09 29.52 37.11 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 16 1.227853 AGCGACAACTCAACCACCC 60.228 57.895 0.00 0.00 0.00 4.61
32 34 2.953648 CCCTAAATGCATCACATCAGCA 59.046 45.455 0.00 0.00 38.34 4.41
84 86 4.388499 CCTAGTTGGCGCGTGGGT 62.388 66.667 8.43 0.00 0.00 4.51
126 128 1.000163 CTGTACCTGTCGTCTGCAAGT 60.000 52.381 0.00 0.00 33.76 3.16
154 156 1.878656 AACTGAAGAGGCCGTCTCCG 61.879 60.000 0.00 0.00 43.44 4.63
184 186 7.333174 CCCATTCTCTCTCTCACTTAACTTTTC 59.667 40.741 0.00 0.00 0.00 2.29
207 209 2.433444 TTCTCTCCTTTCCTTCCCCA 57.567 50.000 0.00 0.00 0.00 4.96
229 231 1.518903 GACACAAGCAGCAAGGTCCC 61.519 60.000 0.00 0.00 0.00 4.46
243 245 3.779444 AGAGAAGTGGATGGTAGACACA 58.221 45.455 0.00 0.00 37.58 3.72
282 284 2.338984 GGGCCTACATAGCGTCGG 59.661 66.667 0.84 0.00 33.49 4.79
285 287 1.686325 CTGGTGGGCCTACATAGCGT 61.686 60.000 21.99 0.00 35.27 5.07
288 290 1.349026 CCATCTGGTGGGCCTACATAG 59.651 57.143 21.99 17.56 44.79 2.23
290 292 2.234586 CCATCTGGTGGGCCTACAT 58.765 57.895 21.99 2.91 44.79 2.29
301 304 1.679680 CCAATGCAAGCTACCATCTGG 59.320 52.381 0.00 0.00 42.17 3.86
341 344 7.893833 ACCTAGGCATAAAAATCTAAAACCACT 59.106 33.333 9.30 0.00 0.00 4.00
389 396 4.149473 GCATGAGCTATGGTGGCAACAG 62.149 54.545 12.39 0.00 42.12 3.16
394 401 1.900498 GGGCATGAGCTATGGTGGC 60.900 63.158 0.00 0.00 41.70 5.01
423 430 4.481930 TTTTTGGTGCTCGTGTATCTTG 57.518 40.909 0.00 0.00 0.00 3.02
468 476 0.817634 CGTCTTGGCCCACAACTCAA 60.818 55.000 0.00 0.00 34.76 3.02
557 565 5.619220 AGCAACTTTCCTGATCTATGGATC 58.381 41.667 11.92 11.92 46.20 3.36
639 647 0.731417 CGACAGTACTACCCCACTCG 59.269 60.000 0.00 0.00 0.00 4.18
649 657 4.002316 GTGAGGTAGAAGACGACAGTACT 58.998 47.826 0.00 0.00 0.00 2.73
662 670 1.557099 ATCCAGCAACGTGAGGTAGA 58.443 50.000 0.00 0.00 0.00 2.59
756 774 0.871722 TTGTTGGATAGTGTGTGCGC 59.128 50.000 0.00 0.00 0.00 6.09
912 932 8.519526 GCCATCGATCCCTTCTTATAGATATAG 58.480 40.741 0.00 0.00 0.00 1.31
937 957 6.327934 TCGAAATAGGTGAAGTTAGTAGTGC 58.672 40.000 0.00 0.00 0.00 4.40
951 971 5.663556 AGAGAAGGAAGGAATCGAAATAGGT 59.336 40.000 0.00 0.00 0.00 3.08
998 1018 1.774254 TCACCTTGTGGACCTTCATGT 59.226 47.619 0.00 0.00 37.04 3.21
1097 1117 9.926158 AGAACATCAGCAATCTATTATAGTCTG 57.074 33.333 0.00 3.96 0.00 3.51
1117 1137 6.430000 GGGTAACAACACAGAACATAGAACAT 59.570 38.462 0.00 0.00 39.74 2.71
1145 1166 5.104374 CCTGCAATTGAATATGGACAACAC 58.896 41.667 10.34 0.00 0.00 3.32
1160 1181 2.519771 TGCCTTCAGATCCTGCAATT 57.480 45.000 0.00 0.00 0.00 2.32
1256 1277 1.374947 CCCTTCAGCGAAACCCTCA 59.625 57.895 0.00 0.00 0.00 3.86
1334 1355 5.650703 TGACATCTTGAAGCATCATCAACAT 59.349 36.000 0.00 0.00 34.96 2.71
1385 1410 8.721478 CGGAATATTTTGGGATGTTACAGATAG 58.279 37.037 0.00 0.00 0.00 2.08
1387 1412 7.287061 TCGGAATATTTTGGGATGTTACAGAT 58.713 34.615 0.00 0.00 0.00 2.90
1448 1473 1.818674 CCCTTACAAGATGCAACCACC 59.181 52.381 0.00 0.00 0.00 4.61
1460 1485 1.344065 TTGAGCCGAGTCCCTTACAA 58.656 50.000 0.00 0.00 0.00 2.41
1507 1532 2.422597 TGTGACTTGTATTGCCGGAAG 58.577 47.619 5.05 0.09 0.00 3.46
1526 1551 6.157904 TCAAATGGTCAATGTGCATAGTTTG 58.842 36.000 0.00 0.00 0.00 2.93
1530 1555 6.198650 TCTTCAAATGGTCAATGTGCATAG 57.801 37.500 0.00 0.00 0.00 2.23
1532 1557 5.221481 TGTTCTTCAAATGGTCAATGTGCAT 60.221 36.000 0.00 0.00 0.00 3.96
1535 1560 7.718272 AAATGTTCTTCAAATGGTCAATGTG 57.282 32.000 0.00 0.00 0.00 3.21
1536 1561 8.090214 CCTAAATGTTCTTCAAATGGTCAATGT 58.910 33.333 0.00 0.00 0.00 2.71
1537 1562 7.063780 GCCTAAATGTTCTTCAAATGGTCAATG 59.936 37.037 0.00 0.00 0.00 2.82
1545 1570 5.583932 AGAGGGCCTAAATGTTCTTCAAAT 58.416 37.500 5.73 0.00 0.00 2.32
1581 1606 6.515272 TCCTGCTCCTATGTTTTGAAAATC 57.485 37.500 0.00 0.00 0.00 2.17
1648 1673 5.991606 TGGCATCAAAACTCTATCCTAATCG 59.008 40.000 0.00 0.00 0.00 3.34
1697 1722 8.806429 TGAAATCTAGCATTCATTCAAACCTA 57.194 30.769 6.07 0.00 30.94 3.08
1747 1773 6.535150 TGCTCGTTCTATAGAATTGTTTCCTG 59.465 38.462 17.95 3.76 36.33 3.86
1783 1809 6.963117 TTTGGAGGGTTAGAATCCTTAAGA 57.037 37.500 3.36 0.00 40.40 2.10
1784 1810 7.285629 GGATTTTGGAGGGTTAGAATCCTTAAG 59.714 40.741 0.00 0.00 40.40 1.85
1819 1845 8.272173 TGATACTTAGGTCCTTGATTTAAAGGG 58.728 37.037 0.00 0.00 45.85 3.95
1822 1848 9.444600 GTGTGATACTTAGGTCCTTGATTTAAA 57.555 33.333 0.00 0.00 0.00 1.52
1824 1850 7.093640 ACGTGTGATACTTAGGTCCTTGATTTA 60.094 37.037 0.00 0.00 0.00 1.40
1825 1851 6.106673 CGTGTGATACTTAGGTCCTTGATTT 58.893 40.000 0.00 0.00 0.00 2.17
1885 1925 4.323485 CCTCACCTCAGTAAACTTGCCATA 60.323 45.833 0.00 0.00 0.00 2.74
1918 1958 3.261390 CCATGATGGCCTTTCCTCAAAAA 59.739 43.478 3.32 0.00 35.26 1.94
1936 1976 8.243426 TGTTTAAGAGCAATAAAGTTAGCCATG 58.757 33.333 0.00 0.00 0.00 3.66
1938 1978 7.094377 CCTGTTTAAGAGCAATAAAGTTAGCCA 60.094 37.037 0.00 0.00 0.00 4.75
1944 1984 7.814587 GCAATTCCTGTTTAAGAGCAATAAAGT 59.185 33.333 0.00 0.00 0.00 2.66
1945 1985 7.814107 TGCAATTCCTGTTTAAGAGCAATAAAG 59.186 33.333 0.00 0.00 0.00 1.85
1953 1993 6.760770 TGGTTTTTGCAATTCCTGTTTAAGAG 59.239 34.615 0.00 0.00 0.00 2.85
1954 1994 6.644347 TGGTTTTTGCAATTCCTGTTTAAGA 58.356 32.000 0.00 0.00 0.00 2.10
1960 2015 3.450457 TGTCTGGTTTTTGCAATTCCTGT 59.550 39.130 0.00 0.00 0.00 4.00
1962 2017 4.696455 CTTGTCTGGTTTTTGCAATTCCT 58.304 39.130 0.00 0.00 0.00 3.36
1967 2022 1.470632 CGGCTTGTCTGGTTTTTGCAA 60.471 47.619 0.00 0.00 0.00 4.08
1969 2024 0.597377 CCGGCTTGTCTGGTTTTTGC 60.597 55.000 0.00 0.00 36.43 3.68
1970 2025 1.028905 TCCGGCTTGTCTGGTTTTTG 58.971 50.000 0.00 0.00 42.13 2.44
1972 2027 1.318576 CTTCCGGCTTGTCTGGTTTT 58.681 50.000 0.00 0.00 42.13 2.43
1987 2042 2.882324 CTCTTGGACTAACGAGCTTCC 58.118 52.381 0.00 0.00 0.00 3.46
1989 2044 2.371910 GCTCTTGGACTAACGAGCTT 57.628 50.000 12.49 0.00 44.04 3.74
1997 2052 6.869206 ATAAGGTTTGTAGCTCTTGGACTA 57.131 37.500 0.00 0.00 0.00 2.59
2029 2084 3.499918 GGGCATGTGCTAGCTAGTTATTG 59.500 47.826 21.62 14.82 41.70 1.90
2031 2086 2.975489 AGGGCATGTGCTAGCTAGTTAT 59.025 45.455 21.62 10.87 41.70 1.89
2050 3257 2.337583 TCGTTCTTCGAATCAAGCAGG 58.662 47.619 0.00 0.00 45.98 4.85
2086 3293 8.487028 TGTGTTTTTGTTAATTGGGAAGGTTAT 58.513 29.630 0.00 0.00 0.00 1.89
2107 3314 1.079197 TCGGCTGCATCGATGTGTT 60.079 52.632 25.47 0.00 0.00 3.32
2161 3368 6.183360 GGCGGAATCAGATTCTTCAATTGTTA 60.183 38.462 20.41 0.00 39.24 2.41
2203 3410 1.742831 CCTCTCGTCAGAGTGAGAAGG 59.257 57.143 4.31 4.61 44.49 3.46
2219 3427 5.759059 TCATAAATGAAGTTGCCATCCTCT 58.241 37.500 0.00 0.00 33.08 3.69
2260 3469 6.421377 AAACAAAACTGAAACTTGCCATTC 57.579 33.333 0.00 0.00 0.00 2.67
2292 3501 1.004979 TGCCTAGTACCCGCCAAAAAT 59.995 47.619 0.00 0.00 0.00 1.82
2303 3512 1.000955 CATCCGGATGGTGCCTAGTAC 59.999 57.143 32.99 0.00 35.24 2.73
2305 3514 0.691078 ACATCCGGATGGTGCCTAGT 60.691 55.000 40.04 19.69 42.91 2.57
2306 3515 1.000955 GTACATCCGGATGGTGCCTAG 59.999 57.143 40.04 19.01 42.91 3.02


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

AutoCloner maintained by Alex Coulton.