Multiple sequence alignment - TraesCS2D01G583800

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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 TraesCS2D01G583800 chr2D 100.000 2240 0 0 1 2240 643784588 643782349 0.000000e+00 4137
1 TraesCS2D01G583800 chr2B 94.839 1182 42 10 375 1545 793344848 793346021 0.000000e+00 1827
2 TraesCS2D01G583800 chr2B 80.518 657 66 24 1589 2202 793346027 793346664 4.390000e-122 448
3 TraesCS2D01G583800 chr2B 94.717 265 14 0 1 265 793344442 793344706 1.600000e-111 412


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 TraesCS2D01G583800 chr2D 643782349 643784588 2239 True 4137.000000 4137 100.000000 1 2240 1 chr2D.!!$R1 2239
1 TraesCS2D01G583800 chr2B 793344442 793346664 2222 False 895.666667 1827 90.024667 1 2202 3 chr2B.!!$F1 2201

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
202 203 0.036306 TCAAGAAAGCCTTCCGGGAC 59.964 55.0 0.0 0.0 37.23 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1772 0.179034 GAGTGCCTTGCTCCATAGGG 60.179 60.0 0.0 0.0 31.95 3.53 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
121 122 2.502492 CGCCGACCAGATGGAGGAT 61.502 63.158 17.83 0.00 38.24 3.24
172 173 1.901948 TGTCTGGGTCGACGCTTCT 60.902 57.895 29.62 0.00 36.71 2.85
202 203 0.036306 TCAAGAAAGCCTTCCGGGAC 59.964 55.000 0.00 0.00 37.23 4.46
226 227 1.737793 GCCACCAAGTCCTACAAATCG 59.262 52.381 0.00 0.00 0.00 3.34
247 248 2.251642 GGCTCGCACCGTCAACTTT 61.252 57.895 0.00 0.00 0.00 2.66
253 254 1.852067 GCACCGTCAACTTTGCCGAT 61.852 55.000 0.00 0.00 30.04 4.18
255 256 0.250124 ACCGTCAACTTTGCCGATGA 60.250 50.000 0.00 0.00 30.04 2.92
261 262 4.377943 CGTCAACTTTGCCGATGATGTAAA 60.378 41.667 0.00 0.00 30.04 2.01
265 266 4.526970 ACTTTGCCGATGATGTAAATCCT 58.473 39.130 0.00 0.00 0.00 3.24
266 267 5.680619 ACTTTGCCGATGATGTAAATCCTA 58.319 37.500 0.00 0.00 0.00 2.94
267 268 6.299141 ACTTTGCCGATGATGTAAATCCTAT 58.701 36.000 0.00 0.00 0.00 2.57
269 270 4.832248 TGCCGATGATGTAAATCCTATCC 58.168 43.478 0.00 0.00 0.00 2.59
270 271 4.532126 TGCCGATGATGTAAATCCTATCCT 59.468 41.667 0.00 0.00 0.00 3.24
271 272 5.013079 TGCCGATGATGTAAATCCTATCCTT 59.987 40.000 0.00 0.00 0.00 3.36
272 273 6.212589 TGCCGATGATGTAAATCCTATCCTTA 59.787 38.462 0.00 0.00 0.00 2.69
273 274 6.535508 GCCGATGATGTAAATCCTATCCTTAC 59.464 42.308 0.00 0.00 0.00 2.34
275 276 7.310423 CCGATGATGTAAATCCTATCCTTACCA 60.310 40.741 0.00 0.00 0.00 3.25
276 277 8.260818 CGATGATGTAAATCCTATCCTTACCAT 58.739 37.037 0.00 0.00 0.00 3.55
277 278 9.965902 GATGATGTAAATCCTATCCTTACCATT 57.034 33.333 0.00 0.00 0.00 3.16
289 319 5.098218 TCCTTACCATTTTGTTTCGTTCG 57.902 39.130 0.00 0.00 0.00 3.95
291 321 4.907582 CCTTACCATTTTGTTTCGTTCGTC 59.092 41.667 0.00 0.00 0.00 4.20
297 327 5.685511 CCATTTTGTTTCGTTCGTCAATTCT 59.314 36.000 0.00 0.00 0.00 2.40
302 332 7.416154 TTGTTTCGTTCGTCAATTCTATCTT 57.584 32.000 0.00 0.00 0.00 2.40
303 333 6.817396 TGTTTCGTTCGTCAATTCTATCTTG 58.183 36.000 0.00 0.00 0.00 3.02
305 335 6.389622 TTCGTTCGTCAATTCTATCTTGTG 57.610 37.500 0.00 0.00 0.00 3.33
306 336 5.466819 TCGTTCGTCAATTCTATCTTGTGT 58.533 37.500 0.00 0.00 0.00 3.72
307 337 5.344933 TCGTTCGTCAATTCTATCTTGTGTG 59.655 40.000 0.00 0.00 0.00 3.82
314 344 7.693951 CGTCAATTCTATCTTGTGTGGAATTTC 59.306 37.037 0.00 0.00 35.35 2.17
326 356 4.947388 GTGTGGAATTTCTGCATACCCTTA 59.053 41.667 0.00 0.00 32.28 2.69
334 364 5.912149 TTCTGCATACCCTTAGATCCATT 57.088 39.130 0.00 0.00 0.00 3.16
338 368 8.311395 TCTGCATACCCTTAGATCCATTATAG 57.689 38.462 0.00 0.00 0.00 1.31
340 370 9.201989 CTGCATACCCTTAGATCCATTATAGTA 57.798 37.037 0.00 0.00 0.00 1.82
341 371 9.729550 TGCATACCCTTAGATCCATTATAGTAT 57.270 33.333 0.00 0.00 0.00 2.12
402 448 2.224257 GGAGGAAGCAGTGGAGATCATC 60.224 54.545 0.00 0.00 0.00 2.92
426 472 1.106944 ACTGGGTGAAAAAGGCCACG 61.107 55.000 5.01 0.00 34.30 4.94
452 498 5.073144 ACAACCTCATCAACTCCCTCTTTTA 59.927 40.000 0.00 0.00 0.00 1.52
456 502 5.023533 TCATCAACTCCCTCTTTTATCCG 57.976 43.478 0.00 0.00 0.00 4.18
468 514 3.863424 TCTTTTATCCGAGCGACATCAAC 59.137 43.478 0.00 0.00 0.00 3.18
608 661 2.555757 AGGCAAAGTTCATGAGCAAGTC 59.444 45.455 12.41 2.67 0.00 3.01
634 687 5.190528 TCTCAATCCCAGTTTATCTCTTGCT 59.809 40.000 0.00 0.00 0.00 3.91
651 704 2.676748 TGCTTGGATGGTTTCAAGGTT 58.323 42.857 0.00 0.00 40.31 3.50
670 723 3.452627 GGTTCTCAAGCTTCCCTATCTGA 59.547 47.826 0.00 0.00 0.00 3.27
724 777 2.578178 CTCCTCTCAAGCGTCGCG 60.578 66.667 12.30 0.00 0.00 5.87
804 857 0.902531 TCCTCCCCGATGAACAACTC 59.097 55.000 0.00 0.00 0.00 3.01
881 934 1.191535 CTACCCAAGACGATGGTGGA 58.808 55.000 0.00 0.00 38.91 4.02
1115 1168 1.583451 CGATCATGCGCGGGTTTTG 60.583 57.895 8.83 0.00 0.00 2.44
1167 1220 3.351416 GTTGCCGACCACCCGTTC 61.351 66.667 0.00 0.00 0.00 3.95
1168 1221 3.862991 TTGCCGACCACCCGTTCA 61.863 61.111 0.00 0.00 0.00 3.18
1212 1265 0.721718 CTGGAGTGATCGTTTTCGCC 59.278 55.000 0.00 0.00 43.73 5.54
1245 1298 0.462789 ACCCTACCAAGTAATCGGCG 59.537 55.000 0.00 0.00 0.00 6.46
1250 1303 1.648504 ACCAAGTAATCGGCGTTAGC 58.351 50.000 6.85 0.00 44.18 3.09
1301 1354 2.037144 GGAGCTTGGCATGATGGAAAT 58.963 47.619 4.32 0.00 0.00 2.17
1317 1370 7.905265 TGATGGAAATATTTTGCTCCTTTCAA 58.095 30.769 1.43 0.00 0.00 2.69
1325 1378 2.128771 TGCTCCTTTCAATGCTACCC 57.871 50.000 0.00 0.00 0.00 3.69
1332 1386 6.174720 TCCTTTCAATGCTACCCTATAGTG 57.825 41.667 0.00 0.00 0.00 2.74
1338 1392 6.243148 TCAATGCTACCCTATAGTGTATCGA 58.757 40.000 0.00 0.00 0.00 3.59
1371 1425 6.380095 AGTATTACTACTGAGTACTGCAGC 57.620 41.667 15.27 0.00 37.91 5.25
1390 1444 6.276091 TGCAGCATTGAACTCTACTATGTAG 58.724 40.000 0.00 0.00 0.00 2.74
1392 1446 7.068226 TGCAGCATTGAACTCTACTATGTAGTA 59.932 37.037 0.00 0.42 37.73 1.82
1393 1447 7.921214 GCAGCATTGAACTCTACTATGTAGTAA 59.079 37.037 4.89 0.00 38.24 2.24
1394 1448 9.973450 CAGCATTGAACTCTACTATGTAGTAAT 57.027 33.333 4.89 0.00 38.24 1.89
1396 1450 9.413048 GCATTGAACTCTACTATGTAGTAATCC 57.587 37.037 4.89 0.00 38.24 3.01
1397 1451 9.915629 CATTGAACTCTACTATGTAGTAATCCC 57.084 37.037 4.89 0.00 38.24 3.85
1398 1452 7.741027 TGAACTCTACTATGTAGTAATCCCG 57.259 40.000 4.89 0.00 38.24 5.14
1424 1478 7.095187 GGAACATGTTTCAGTATCGTTTCTCTT 60.095 37.037 13.36 0.00 0.00 2.85
1494 1549 4.367386 AAAGCATCAAATAGCTGAGTGC 57.633 40.909 0.00 0.00 41.70 4.40
1498 1553 5.128205 AGCATCAAATAGCTGAGTGCATTA 58.872 37.500 0.00 0.00 45.94 1.90
1505 1560 7.756272 TCAAATAGCTGAGTGCATTACAATTTG 59.244 33.333 0.00 0.00 45.94 2.32
1506 1561 7.395190 AATAGCTGAGTGCATTACAATTTGA 57.605 32.000 2.79 0.00 45.94 2.69
1507 1562 5.306532 AGCTGAGTGCATTACAATTTGAG 57.693 39.130 2.79 0.00 45.94 3.02
1513 1570 9.844790 CTGAGTGCATTACAATTTGAGAAAATA 57.155 29.630 2.79 0.00 0.00 1.40
1515 1572 9.294030 GAGTGCATTACAATTTGAGAAAATAGG 57.706 33.333 2.79 0.00 0.00 2.57
1522 1579 9.793259 TTACAATTTGAGAAAATAGGAGACACT 57.207 29.630 2.79 0.00 0.00 3.55
1526 1583 9.442047 AATTTGAGAAAATAGGAGACACTACAG 57.558 33.333 0.00 0.00 0.00 2.74
1546 1603 9.778741 ACTACAGTGAGTTAATCTTTGAAATGA 57.221 29.630 0.00 0.00 0.00 2.57
1625 1682 8.924511 TTACTTCATTTCCTCATGATAATCCC 57.075 34.615 0.00 0.00 33.07 3.85
1641 1698 8.726870 TGATAATCCCCTTTACTTTCTTTACG 57.273 34.615 0.00 0.00 0.00 3.18
1648 1705 8.210265 TCCCCTTTACTTTCTTTACGTTAAGAA 58.790 33.333 22.11 22.11 41.17 2.52
1658 1715 7.786305 TCTTTACGTTAAGAATGTAGTGACG 57.214 36.000 14.21 0.00 34.59 4.35
1663 1720 7.081526 ACGTTAAGAATGTAGTGACGTAGAT 57.918 36.000 0.00 0.00 40.02 1.98
1720 1782 7.588497 AAAATATCTTGAAACCCTATGGAGC 57.412 36.000 0.00 0.00 34.81 4.70
1740 1802 2.459934 CAAGGCACTCGTTTTGGTTTC 58.540 47.619 0.00 0.00 38.49 2.78
1741 1803 1.029681 AGGCACTCGTTTTGGTTTCC 58.970 50.000 0.00 0.00 0.00 3.13
1742 1804 0.031585 GGCACTCGTTTTGGTTTCCC 59.968 55.000 0.00 0.00 0.00 3.97
1746 1808 3.254903 GCACTCGTTTTGGTTTCCCTAAT 59.745 43.478 0.00 0.00 0.00 1.73
1775 1837 2.943690 CTGCATGCTATTGCTCTTGACT 59.056 45.455 20.33 0.00 43.18 3.41
1778 1840 5.857268 TGCATGCTATTGCTCTTGACTATA 58.143 37.500 20.33 0.00 43.18 1.31
1780 1842 6.938596 TGCATGCTATTGCTCTTGACTATATT 59.061 34.615 20.33 0.00 43.18 1.28
1782 1844 7.625817 GCATGCTATTGCTCTTGACTATATTGG 60.626 40.741 11.37 0.00 39.57 3.16
1783 1845 6.830912 TGCTATTGCTCTTGACTATATTGGT 58.169 36.000 0.00 0.00 40.48 3.67
1784 1846 7.282585 TGCTATTGCTCTTGACTATATTGGTT 58.717 34.615 0.00 0.00 40.48 3.67
1785 1847 7.442364 TGCTATTGCTCTTGACTATATTGGTTC 59.558 37.037 0.00 0.00 40.48 3.62
1786 1848 6.851222 ATTGCTCTTGACTATATTGGTTCG 57.149 37.500 0.00 0.00 0.00 3.95
1787 1849 5.339008 TGCTCTTGACTATATTGGTTCGT 57.661 39.130 0.00 0.00 0.00 3.85
1800 1862 4.377839 TTGGTTCGTCATTTTTCTGCAA 57.622 36.364 0.00 0.00 0.00 4.08
1805 1867 5.276348 GGTTCGTCATTTTTCTGCAACTTTG 60.276 40.000 0.00 0.00 0.00 2.77
1812 1874 8.690840 GTCATTTTTCTGCAACTTTGTACATAC 58.309 33.333 0.00 0.00 0.00 2.39
1866 1928 9.103048 GTTGAATTTTCTAGTTCGTTACATGTG 57.897 33.333 9.11 0.00 0.00 3.21
1867 1929 7.295201 TGAATTTTCTAGTTCGTTACATGTGC 58.705 34.615 9.11 0.03 0.00 4.57
1868 1930 6.795098 ATTTTCTAGTTCGTTACATGTGCA 57.205 33.333 9.11 0.00 0.00 4.57
1869 1931 6.606234 TTTTCTAGTTCGTTACATGTGCAA 57.394 33.333 9.11 0.00 0.00 4.08
1871 1933 6.795098 TTCTAGTTCGTTACATGTGCAAAT 57.205 33.333 9.11 0.00 0.00 2.32
1872 1934 6.164408 TCTAGTTCGTTACATGTGCAAATG 57.836 37.500 15.63 15.63 0.00 2.32
1889 1971 4.545610 CAAATGTTTGTCGTTATGCTGGT 58.454 39.130 0.00 0.00 33.59 4.00
1892 1974 4.217754 TGTTTGTCGTTATGCTGGTTTC 57.782 40.909 0.00 0.00 0.00 2.78
1894 1976 4.219033 GTTTGTCGTTATGCTGGTTTCTG 58.781 43.478 0.00 0.00 0.00 3.02
1907 1989 6.769512 TGCTGGTTTCTGTAGTTAGAAATCT 58.230 36.000 11.44 0.00 45.40 2.40
1909 1991 8.540388 TGCTGGTTTCTGTAGTTAGAAATCTAT 58.460 33.333 11.44 0.00 45.40 1.98
1911 1993 9.319143 CTGGTTTCTGTAGTTAGAAATCTATGG 57.681 37.037 11.44 0.00 45.40 2.74
1912 1994 8.265055 TGGTTTCTGTAGTTAGAAATCTATGGG 58.735 37.037 11.44 0.00 45.40 4.00
1920 2002 6.435164 AGTTAGAAATCTATGGGGTTGCAAT 58.565 36.000 0.59 0.00 0.00 3.56
1922 2004 5.603170 AGAAATCTATGGGGTTGCAATTG 57.397 39.130 0.59 0.00 0.00 2.32
1968 2051 9.496873 TTGATCTCCGAAACAATTTAAACTAGA 57.503 29.630 0.00 0.00 0.00 2.43
1969 2052 9.667107 TGATCTCCGAAACAATTTAAACTAGAT 57.333 29.630 0.00 0.00 0.00 1.98
1972 2055 9.595823 TCTCCGAAACAATTTAAACTAGATAGG 57.404 33.333 0.00 0.00 0.00 2.57
1973 2056 8.205131 TCCGAAACAATTTAAACTAGATAGGC 57.795 34.615 0.00 0.00 0.00 3.93
1974 2057 7.825270 TCCGAAACAATTTAAACTAGATAGGCA 59.175 33.333 0.00 0.00 0.00 4.75
1975 2058 7.908601 CCGAAACAATTTAAACTAGATAGGCAC 59.091 37.037 0.00 0.00 0.00 5.01
1976 2059 8.447833 CGAAACAATTTAAACTAGATAGGCACA 58.552 33.333 0.00 0.00 0.00 4.57
1991 2074 6.611642 AGATAGGCACAATAGTTCTGGTAGAA 59.388 38.462 0.00 0.00 0.00 2.10
2004 2087 8.409358 AGTTCTGGTAGAAAAATATTGTGCTT 57.591 30.769 0.00 0.00 35.75 3.91
2027 2110 3.435186 GCTGCAAGAGGCCGTTCC 61.435 66.667 0.00 0.00 43.89 3.62
2038 2121 3.434940 AGGCCGTTCCTTCTGTATTTT 57.565 42.857 0.00 0.00 44.75 1.82
2080 2164 1.152383 GCCGCGATAGAAGTGGGAAC 61.152 60.000 8.23 0.00 39.52 3.62
2093 2177 5.767168 AGAAGTGGGAACAAAGATTGAGAAG 59.233 40.000 0.00 0.00 46.06 2.85
2096 2180 4.827284 GTGGGAACAAAGATTGAGAAGGAA 59.173 41.667 0.00 0.00 46.06 3.36
2101 2185 7.777440 GGGAACAAAGATTGAGAAGGAAGATAT 59.223 37.037 0.00 0.00 0.00 1.63
2105 2189 9.829507 ACAAAGATTGAGAAGGAAGATATGTAG 57.170 33.333 0.00 0.00 0.00 2.74
2114 2198 5.212532 AGGAAGATATGTAGAAGCTGCTG 57.787 43.478 3.74 0.00 0.00 4.41
2118 2202 2.315925 TATGTAGAAGCTGCTGTGGC 57.684 50.000 3.74 0.00 39.26 5.01
2177 2277 4.631773 GCTGGAGCTTGCTGATCA 57.368 55.556 0.00 0.00 38.21 2.92
2180 2280 0.252479 CTGGAGCTTGCTGATCAGGT 59.748 55.000 23.89 4.39 31.67 4.00
2192 2292 1.680207 TGATCAGGTCGAGCTCATCAG 59.320 52.381 24.70 9.60 0.00 2.90
2202 2302 2.850439 GCTCATCAGCAGTGCAAGA 58.150 52.632 19.20 15.11 46.06 3.02
2203 2303 1.162698 GCTCATCAGCAGTGCAAGAA 58.837 50.000 19.20 0.00 46.06 2.52
2204 2304 1.743958 GCTCATCAGCAGTGCAAGAAT 59.256 47.619 19.20 1.75 46.06 2.40
2205 2305 2.223294 GCTCATCAGCAGTGCAAGAATC 60.223 50.000 19.20 2.66 46.06 2.52
2206 2306 2.355132 CTCATCAGCAGTGCAAGAATCC 59.645 50.000 19.20 0.00 0.00 3.01
2207 2307 2.089201 CATCAGCAGTGCAAGAATCCA 58.911 47.619 19.20 0.00 0.00 3.41
2208 2308 2.275134 TCAGCAGTGCAAGAATCCAA 57.725 45.000 19.20 0.00 0.00 3.53
2209 2309 2.799017 TCAGCAGTGCAAGAATCCAAT 58.201 42.857 19.20 0.00 0.00 3.16
2210 2310 3.159472 TCAGCAGTGCAAGAATCCAATT 58.841 40.909 19.20 0.00 0.00 2.32
2211 2311 3.057104 TCAGCAGTGCAAGAATCCAATTG 60.057 43.478 19.20 0.00 0.00 2.32
2212 2312 3.057104 CAGCAGTGCAAGAATCCAATTGA 60.057 43.478 19.20 0.00 0.00 2.57
2213 2313 3.057033 AGCAGTGCAAGAATCCAATTGAC 60.057 43.478 19.20 0.00 0.00 3.18
2214 2314 3.495193 CAGTGCAAGAATCCAATTGACG 58.505 45.455 7.12 0.00 0.00 4.35
2215 2315 3.058016 CAGTGCAAGAATCCAATTGACGT 60.058 43.478 7.12 0.00 0.00 4.34
2216 2316 4.154015 CAGTGCAAGAATCCAATTGACGTA 59.846 41.667 7.12 0.00 0.00 3.57
2217 2317 4.943705 AGTGCAAGAATCCAATTGACGTAT 59.056 37.500 7.12 0.00 0.00 3.06
2218 2318 5.030295 GTGCAAGAATCCAATTGACGTATG 58.970 41.667 7.12 0.22 0.00 2.39
2219 2319 4.037690 GCAAGAATCCAATTGACGTATGC 58.962 43.478 7.12 6.66 0.00 3.14
2220 2320 4.201950 GCAAGAATCCAATTGACGTATGCT 60.202 41.667 7.12 0.00 0.00 3.79
2221 2321 5.677091 GCAAGAATCCAATTGACGTATGCTT 60.677 40.000 7.12 2.66 0.00 3.91
2222 2322 5.490139 AGAATCCAATTGACGTATGCTTG 57.510 39.130 7.12 0.00 0.00 4.01
2223 2323 4.943705 AGAATCCAATTGACGTATGCTTGT 59.056 37.500 7.12 0.00 0.00 3.16
2224 2324 6.112734 AGAATCCAATTGACGTATGCTTGTA 58.887 36.000 7.12 0.00 0.00 2.41
2225 2325 6.597672 AGAATCCAATTGACGTATGCTTGTAA 59.402 34.615 7.12 0.00 0.00 2.41
2226 2326 6.942532 ATCCAATTGACGTATGCTTGTAAT 57.057 33.333 7.12 0.00 0.00 1.89
2227 2327 6.117911 TCCAATTGACGTATGCTTGTAATG 57.882 37.500 7.12 0.00 0.00 1.90
2228 2328 4.734854 CCAATTGACGTATGCTTGTAATGC 59.265 41.667 7.12 0.00 37.54 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 95 4.720902 TGGTCGGCGAGGACGGTA 62.721 66.667 11.20 0.00 37.82 4.02
172 173 4.634703 TTCTTGAGCCCGCCGCAA 62.635 61.111 0.00 0.00 41.38 4.85
193 194 3.047877 GTGGCAACGTCCCGGAAG 61.048 66.667 0.73 0.00 42.51 3.46
202 203 0.250124 TGTAGGACTTGGTGGCAACG 60.250 55.000 0.00 0.00 42.51 4.10
247 248 4.532126 AGGATAGGATTTACATCATCGGCA 59.468 41.667 0.00 0.00 0.00 5.69
255 256 9.936329 ACAAAATGGTAAGGATAGGATTTACAT 57.064 29.630 0.00 0.00 0.00 2.29
261 262 7.116736 ACGAAACAAAATGGTAAGGATAGGAT 58.883 34.615 0.00 0.00 0.00 3.24
265 266 6.427547 ACGAACGAAACAAAATGGTAAGGATA 59.572 34.615 0.14 0.00 0.00 2.59
266 267 5.239963 ACGAACGAAACAAAATGGTAAGGAT 59.760 36.000 0.14 0.00 0.00 3.24
267 268 4.575645 ACGAACGAAACAAAATGGTAAGGA 59.424 37.500 0.14 0.00 0.00 3.36
269 270 5.503498 TGACGAACGAAACAAAATGGTAAG 58.497 37.500 0.14 0.00 0.00 2.34
270 271 5.481200 TGACGAACGAAACAAAATGGTAA 57.519 34.783 0.14 0.00 0.00 2.85
271 272 5.481200 TTGACGAACGAAACAAAATGGTA 57.519 34.783 0.14 0.00 0.00 3.25
272 273 4.358494 TTGACGAACGAAACAAAATGGT 57.642 36.364 0.14 0.00 0.00 3.55
273 274 5.685511 AGAATTGACGAACGAAACAAAATGG 59.314 36.000 0.14 0.00 0.00 3.16
275 276 8.504005 AGATAGAATTGACGAACGAAACAAAAT 58.496 29.630 0.14 0.00 0.00 1.82
276 277 7.857569 AGATAGAATTGACGAACGAAACAAAA 58.142 30.769 0.14 0.00 0.00 2.44
277 278 7.416154 AGATAGAATTGACGAACGAAACAAA 57.584 32.000 0.14 0.00 0.00 2.83
279 280 6.422701 ACAAGATAGAATTGACGAACGAAACA 59.577 34.615 0.14 0.00 0.00 2.83
280 281 6.732392 CACAAGATAGAATTGACGAACGAAAC 59.268 38.462 0.14 0.00 0.00 2.78
284 314 5.444613 CCACACAAGATAGAATTGACGAACG 60.445 44.000 0.00 0.00 0.00 3.95
289 319 8.734386 AGAAATTCCACACAAGATAGAATTGAC 58.266 33.333 0.00 0.00 37.27 3.18
291 321 7.487189 GCAGAAATTCCACACAAGATAGAATTG 59.513 37.037 0.00 0.00 37.27 2.32
297 327 6.318648 GGTATGCAGAAATTCCACACAAGATA 59.681 38.462 0.00 0.00 0.00 1.98
302 332 3.088532 GGGTATGCAGAAATTCCACACA 58.911 45.455 0.00 0.00 0.00 3.72
303 333 3.356290 AGGGTATGCAGAAATTCCACAC 58.644 45.455 0.00 0.00 0.00 3.82
305 335 5.437060 TCTAAGGGTATGCAGAAATTCCAC 58.563 41.667 0.00 0.00 0.00 4.02
306 336 5.708736 TCTAAGGGTATGCAGAAATTCCA 57.291 39.130 0.00 0.00 0.00 3.53
307 337 5.707764 GGATCTAAGGGTATGCAGAAATTCC 59.292 44.000 0.00 0.00 0.00 3.01
314 344 8.083828 ACTATAATGGATCTAAGGGTATGCAG 57.916 38.462 0.00 0.00 0.00 4.41
355 401 7.040892 CGGCTGCAGATATATATATTGGCAAAT 60.041 37.037 20.43 2.12 34.21 2.32
362 408 6.077993 TCCTCCGGCTGCAGATATATATATT 58.922 40.000 20.43 0.00 0.00 1.28
363 409 5.645201 TCCTCCGGCTGCAGATATATATAT 58.355 41.667 20.43 4.86 0.00 0.86
364 410 5.061721 TCCTCCGGCTGCAGATATATATA 57.938 43.478 20.43 0.00 0.00 0.86
365 411 3.916035 TCCTCCGGCTGCAGATATATAT 58.084 45.455 20.43 0.00 0.00 0.86
366 412 3.382083 TCCTCCGGCTGCAGATATATA 57.618 47.619 20.43 0.00 0.00 0.86
367 413 2.238084 TCCTCCGGCTGCAGATATAT 57.762 50.000 20.43 0.00 0.00 0.86
368 414 1.895798 CTTCCTCCGGCTGCAGATATA 59.104 52.381 20.43 0.00 0.00 0.86
369 415 0.683973 CTTCCTCCGGCTGCAGATAT 59.316 55.000 20.43 0.00 0.00 1.63
370 416 2.032860 GCTTCCTCCGGCTGCAGATA 62.033 60.000 20.43 0.00 0.00 1.98
371 417 2.906458 CTTCCTCCGGCTGCAGAT 59.094 61.111 20.43 0.00 0.00 2.90
372 418 4.087892 GCTTCCTCCGGCTGCAGA 62.088 66.667 20.43 0.00 0.00 4.26
373 419 4.399395 TGCTTCCTCCGGCTGCAG 62.399 66.667 10.11 10.11 0.00 4.41
402 448 1.269051 GCCTTTTTCACCCAGTCGTTG 60.269 52.381 0.00 0.00 0.00 4.10
426 472 3.008485 AGAGGGAGTTGATGAGGTTGTTC 59.992 47.826 0.00 0.00 0.00 3.18
452 498 4.402192 CGTTGATGTCGCTCGGAT 57.598 55.556 0.00 0.00 0.00 4.18
494 540 1.359459 GCCTTTGAAGTAGACCGCGG 61.359 60.000 26.86 26.86 0.00 6.46
547 593 2.357034 GTGAAACTGGCGAGGCGA 60.357 61.111 0.00 0.00 0.00 5.54
608 661 6.038050 GCAAGAGATAAACTGGGATTGAGAAG 59.962 42.308 0.00 0.00 0.00 2.85
634 687 4.177537 TGAGAACCTTGAAACCATCCAA 57.822 40.909 0.00 0.00 0.00 3.53
651 704 2.697751 GCTCAGATAGGGAAGCTTGAGA 59.302 50.000 2.10 0.00 0.00 3.27
804 857 3.195002 ACCATGTTCGCGATGCCG 61.195 61.111 10.88 0.00 39.16 5.69
881 934 1.676014 GCAGCGTAACCTGGACATTCT 60.676 52.381 0.00 0.00 33.44 2.40
1212 1265 1.622607 TAGGGTCAAGGACATGGCCG 61.623 60.000 13.29 0.00 46.33 6.13
1245 1298 8.178313 GGTAGTTTCTGAAATCTTGATGCTAAC 58.822 37.037 6.06 0.04 0.00 2.34
1250 1303 6.373774 AGCTGGTAGTTTCTGAAATCTTGATG 59.626 38.462 6.06 0.00 0.00 3.07
1301 1354 5.127031 GGGTAGCATTGAAAGGAGCAAAATA 59.873 40.000 0.00 0.00 0.00 1.40
1317 1370 7.396339 TCAATTCGATACACTATAGGGTAGCAT 59.604 37.037 25.69 12.81 0.00 3.79
1360 1414 3.594134 AGAGTTCAATGCTGCAGTACTC 58.406 45.455 19.73 19.73 0.00 2.59
1362 1416 4.499183 AGTAGAGTTCAATGCTGCAGTAC 58.501 43.478 16.64 5.68 0.00 2.73
1371 1425 9.915629 GGGATTACTACATAGTAGAGTTCAATG 57.084 37.037 10.87 0.00 39.69 2.82
1390 1444 4.007659 ACTGAAACATGTTCCGGGATTAC 58.992 43.478 12.39 0.00 0.00 1.89
1392 1446 3.154827 ACTGAAACATGTTCCGGGATT 57.845 42.857 12.39 0.00 0.00 3.01
1393 1447 2.879103 ACTGAAACATGTTCCGGGAT 57.121 45.000 12.39 0.00 0.00 3.85
1394 1448 3.677700 CGATACTGAAACATGTTCCGGGA 60.678 47.826 12.39 0.00 0.00 5.14
1395 1449 2.607635 CGATACTGAAACATGTTCCGGG 59.392 50.000 12.39 5.52 0.00 5.73
1396 1450 3.259064 ACGATACTGAAACATGTTCCGG 58.741 45.455 12.39 6.86 0.00 5.14
1397 1451 4.921470 AACGATACTGAAACATGTTCCG 57.079 40.909 12.39 5.91 0.00 4.30
1398 1452 6.369065 AGAGAAACGATACTGAAACATGTTCC 59.631 38.462 12.39 0.00 0.00 3.62
1475 1529 2.995283 TGCACTCAGCTATTTGATGCT 58.005 42.857 0.00 0.00 45.94 3.79
1498 1553 9.220767 GTAGTGTCTCCTATTTTCTCAAATTGT 57.779 33.333 0.00 0.00 34.29 2.71
1505 1560 7.094118 ACTCACTGTAGTGTCTCCTATTTTCTC 60.094 40.741 11.44 0.00 45.76 2.87
1506 1561 6.722129 ACTCACTGTAGTGTCTCCTATTTTCT 59.278 38.462 11.44 0.00 45.76 2.52
1507 1562 6.926313 ACTCACTGTAGTGTCTCCTATTTTC 58.074 40.000 11.44 0.00 45.76 2.29
1513 1570 6.249951 AGATTAACTCACTGTAGTGTCTCCT 58.750 40.000 11.44 0.37 45.76 3.69
1515 1572 8.082852 TCAAAGATTAACTCACTGTAGTGTCTC 58.917 37.037 11.44 2.43 45.76 3.36
1601 1658 7.295672 AGGGGATTATCATGAGGAAATGAAGTA 59.704 37.037 0.09 0.00 39.90 2.24
1603 1660 6.550163 AGGGGATTATCATGAGGAAATGAAG 58.450 40.000 0.09 0.00 39.90 3.02
1621 1678 8.377799 TCTTAACGTAAAGAAAGTAAAGGGGAT 58.622 33.333 0.00 0.00 32.59 3.85
1622 1679 7.734942 TCTTAACGTAAAGAAAGTAAAGGGGA 58.265 34.615 0.00 0.00 32.59 4.81
1624 1681 9.821662 CATTCTTAACGTAAAGAAAGTAAAGGG 57.178 33.333 3.40 0.00 45.83 3.95
1641 1698 7.478322 TGGATCTACGTCACTACATTCTTAAC 58.522 38.462 0.00 0.00 0.00 2.01
1648 1705 6.222038 ACATTTGGATCTACGTCACTACAT 57.778 37.500 0.00 0.00 0.00 2.29
1655 1712 5.523916 AGTGCATTACATTTGGATCTACGTC 59.476 40.000 0.00 0.00 0.00 4.34
1658 1715 9.712305 ATACTAGTGCATTACATTTGGATCTAC 57.288 33.333 5.39 0.00 0.00 2.59
1663 1720 8.364894 ACGATATACTAGTGCATTACATTTGGA 58.635 33.333 5.39 0.00 0.00 3.53
1687 1749 9.379791 AGGGTTTCAAGATATTTTTCTACTACG 57.620 33.333 0.00 0.00 0.00 3.51
1710 1772 0.179034 GAGTGCCTTGCTCCATAGGG 60.179 60.000 0.00 0.00 31.95 3.53
1715 1777 0.465460 AAAACGAGTGCCTTGCTCCA 60.465 50.000 0.00 0.00 0.00 3.86
1720 1782 2.459934 GAAACCAAAACGAGTGCCTTG 58.540 47.619 0.00 0.00 0.00 3.61
1740 1802 4.170292 GCATGCAGCTGAATTATTAGGG 57.830 45.455 20.43 0.00 41.15 3.53
1775 1837 7.384439 TGCAGAAAAATGACGAACCAATATA 57.616 32.000 0.00 0.00 0.00 0.86
1778 1840 4.582701 TGCAGAAAAATGACGAACCAAT 57.417 36.364 0.00 0.00 0.00 3.16
1780 1842 3.380004 AGTTGCAGAAAAATGACGAACCA 59.620 39.130 0.00 0.00 0.00 3.67
1782 1844 5.288472 ACAAAGTTGCAGAAAAATGACGAAC 59.712 36.000 0.00 0.00 0.00 3.95
1783 1845 5.406649 ACAAAGTTGCAGAAAAATGACGAA 58.593 33.333 0.00 0.00 0.00 3.85
1784 1846 4.992688 ACAAAGTTGCAGAAAAATGACGA 58.007 34.783 0.00 0.00 0.00 4.20
1785 1847 5.741510 TGTACAAAGTTGCAGAAAAATGACG 59.258 36.000 0.00 0.00 0.00 4.35
1786 1848 7.698836 ATGTACAAAGTTGCAGAAAAATGAC 57.301 32.000 0.00 0.00 0.00 3.06
1787 1849 8.629158 AGTATGTACAAAGTTGCAGAAAAATGA 58.371 29.630 0.00 0.00 0.00 2.57
1844 1906 7.197071 TGCACATGTAACGAACTAGAAAATT 57.803 32.000 0.00 0.00 0.00 1.82
1850 1912 5.927030 ACATTTGCACATGTAACGAACTAG 58.073 37.500 16.70 0.00 35.51 2.57
1866 1928 3.364621 CCAGCATAACGACAAACATTTGC 59.635 43.478 4.25 0.00 41.79 3.68
1867 1929 4.545610 ACCAGCATAACGACAAACATTTG 58.454 39.130 2.77 2.77 43.62 2.32
1868 1930 4.846779 ACCAGCATAACGACAAACATTT 57.153 36.364 0.00 0.00 0.00 2.32
1869 1931 4.846779 AACCAGCATAACGACAAACATT 57.153 36.364 0.00 0.00 0.00 2.71
1871 1933 3.880490 AGAAACCAGCATAACGACAAACA 59.120 39.130 0.00 0.00 0.00 2.83
1872 1934 4.219033 CAGAAACCAGCATAACGACAAAC 58.781 43.478 0.00 0.00 0.00 2.93
1889 1971 8.388656 ACCCCATAGATTTCTAACTACAGAAA 57.611 34.615 1.14 1.14 45.86 2.52
1892 1974 6.483640 GCAACCCCATAGATTTCTAACTACAG 59.516 42.308 0.00 0.00 31.39 2.74
1894 1976 6.354130 TGCAACCCCATAGATTTCTAACTAC 58.646 40.000 0.00 0.00 31.39 2.73
1911 1993 7.094677 AAGATTTTCTTAATGCAATTGCAACCC 60.095 33.333 34.84 15.01 44.21 4.11
1912 1994 7.809665 AAGATTTTCTTAATGCAATTGCAACC 58.190 30.769 34.84 8.98 44.21 3.77
1959 2042 9.817809 CAGAACTATTGTGCCTATCTAGTTTAA 57.182 33.333 0.00 0.00 33.88 1.52
1960 2043 8.421784 CCAGAACTATTGTGCCTATCTAGTTTA 58.578 37.037 0.00 0.00 33.88 2.01
1961 2044 7.092846 ACCAGAACTATTGTGCCTATCTAGTTT 60.093 37.037 0.00 0.00 33.88 2.66
1962 2045 6.384305 ACCAGAACTATTGTGCCTATCTAGTT 59.616 38.462 0.00 0.00 35.82 2.24
1963 2046 5.900123 ACCAGAACTATTGTGCCTATCTAGT 59.100 40.000 0.00 0.00 0.00 2.57
1964 2047 6.412362 ACCAGAACTATTGTGCCTATCTAG 57.588 41.667 0.00 0.00 0.00 2.43
1965 2048 7.295340 TCTACCAGAACTATTGTGCCTATCTA 58.705 38.462 0.00 0.00 0.00 1.98
1966 2049 6.136857 TCTACCAGAACTATTGTGCCTATCT 58.863 40.000 0.00 0.00 0.00 1.98
1967 2050 6.406692 TCTACCAGAACTATTGTGCCTATC 57.593 41.667 0.00 0.00 0.00 2.08
1968 2051 6.808321 TTCTACCAGAACTATTGTGCCTAT 57.192 37.500 0.00 0.00 0.00 2.57
1969 2052 6.614694 TTTCTACCAGAACTATTGTGCCTA 57.385 37.500 0.00 0.00 33.26 3.93
1970 2053 5.499004 TTTCTACCAGAACTATTGTGCCT 57.501 39.130 0.00 0.00 33.26 4.75
1971 2054 6.569179 TTTTTCTACCAGAACTATTGTGCC 57.431 37.500 0.00 0.00 33.26 5.01
1977 2060 9.686683 AGCACAATATTTTTCTACCAGAACTAT 57.313 29.630 0.00 0.00 33.26 2.12
1978 2061 9.515226 AAGCACAATATTTTTCTACCAGAACTA 57.485 29.630 0.00 0.00 33.26 2.24
1979 2062 8.299570 CAAGCACAATATTTTTCTACCAGAACT 58.700 33.333 0.00 0.00 33.26 3.01
1980 2063 8.082242 ACAAGCACAATATTTTTCTACCAGAAC 58.918 33.333 0.00 0.00 33.26 3.01
1991 2074 2.029110 AGCGCCACAAGCACAATATTTT 60.029 40.909 2.29 0.00 44.04 1.82
2002 2085 2.559840 CTCTTGCAGCGCCACAAG 59.440 61.111 26.07 26.07 43.73 3.16
2038 2121 4.463050 AACCTCAAGAACATACCCCAAA 57.537 40.909 0.00 0.00 0.00 3.28
2041 2124 2.492088 GCAAACCTCAAGAACATACCCC 59.508 50.000 0.00 0.00 0.00 4.95
2043 2126 2.161609 CGGCAAACCTCAAGAACATACC 59.838 50.000 0.00 0.00 0.00 2.73
2044 2127 2.414161 GCGGCAAACCTCAAGAACATAC 60.414 50.000 0.00 0.00 0.00 2.39
2093 2177 4.749099 CACAGCAGCTTCTACATATCTTCC 59.251 45.833 0.00 0.00 0.00 3.46
2096 2180 3.494048 GCCACAGCAGCTTCTACATATCT 60.494 47.826 0.00 0.00 39.53 1.98
2101 2185 1.374631 CGCCACAGCAGCTTCTACA 60.375 57.895 0.00 0.00 39.83 2.74
2105 2189 4.395583 GCACGCCACAGCAGCTTC 62.396 66.667 0.00 0.00 39.83 3.86
2173 2273 1.602668 GCTGATGAGCTCGACCTGATC 60.603 57.143 9.64 5.90 42.52 2.92
2177 2277 0.969917 ACTGCTGATGAGCTCGACCT 60.970 55.000 9.64 0.00 46.39 3.85
2180 2280 1.153686 GCACTGCTGATGAGCTCGA 60.154 57.895 9.64 0.00 46.39 4.04
2192 2292 3.248266 GTCAATTGGATTCTTGCACTGC 58.752 45.455 5.42 0.00 0.00 4.40
2202 2302 6.751514 TTACAAGCATACGTCAATTGGATT 57.248 33.333 5.42 0.00 0.00 3.01
2203 2303 6.728200 CATTACAAGCATACGTCAATTGGAT 58.272 36.000 5.42 0.00 0.00 3.41
2204 2304 5.448496 GCATTACAAGCATACGTCAATTGGA 60.448 40.000 5.42 0.00 0.00 3.53
2205 2305 4.734854 GCATTACAAGCATACGTCAATTGG 59.265 41.667 5.42 0.00 0.00 3.16
2206 2306 5.331098 TGCATTACAAGCATACGTCAATTG 58.669 37.500 0.00 0.00 37.02 2.32
2207 2307 5.559427 TGCATTACAAGCATACGTCAATT 57.441 34.783 0.00 0.00 37.02 2.32


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

AutoCloner maintained by Alex Coulton.