Multiple sequence alignment - TraesCS5D01G137500

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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 TraesCS5D01G137500 chr5D 100.000 2594 0 0 1 2594 218560239 218562832 0.000000e+00 4791.0
1 TraesCS5D01G137500 chr5D 90.952 210 18 1 1376 1584 218565066 218565275 5.470000e-72 281.0
2 TraesCS5D01G137500 chr5D 90.756 119 11 0 1003 1121 218564694 218564812 2.670000e-35 159.0
3 TraesCS5D01G137500 chr5D 94.340 53 2 1 352 403 218560512 218560564 2.140000e-11 80.5
4 TraesCS5D01G137500 chr5D 94.340 53 2 1 274 326 218560590 218560641 2.140000e-11 80.5
5 TraesCS5D01G137500 chr5B 91.273 1673 61 31 1 1609 241169056 241170707 0.000000e+00 2202.0
6 TraesCS5D01G137500 chr5B 87.601 863 66 21 1765 2594 241170764 241171618 0.000000e+00 963.0
7 TraesCS5D01G137500 chr5B 90.865 208 19 0 1376 1583 241188352 241188559 1.970000e-71 279.0
8 TraesCS5D01G137500 chr5B 90.756 119 11 0 1003 1121 241188014 241188132 2.670000e-35 159.0
9 TraesCS5D01G137500 chr5B 96.226 53 1 1 352 403 241169332 241169384 4.600000e-13 86.1
10 TraesCS5D01G137500 chr5B 94.340 53 2 1 274 326 241169410 241169461 2.140000e-11 80.5
11 TraesCS5D01G137500 chr5A 89.160 1679 76 42 1 1609 291595856 291597498 0.000000e+00 1995.0
12 TraesCS5D01G137500 chr5A 83.861 632 41 23 887 1509 556716975 556716396 1.760000e-151 545.0
13 TraesCS5D01G137500 chr5A 87.566 378 32 7 2045 2411 291598079 291598452 8.580000e-115 424.0
14 TraesCS5D01G137500 chr5A 92.222 270 16 2 1781 2047 291597583 291597850 6.780000e-101 377.0
15 TraesCS5D01G137500 chr5A 90.500 200 19 0 1376 1575 291600957 291601156 5.500000e-67 265.0
16 TraesCS5D01G137500 chr5A 92.929 99 6 1 2497 2594 664887310 664887212 2.690000e-30 143.0
17 TraesCS5D01G137500 chr5A 91.919 99 7 1 2497 2594 496333112 496333014 1.250000e-28 137.0
18 TraesCS5D01G137500 chr5A 94.366 71 4 0 1679 1749 291597515 291597585 2.730000e-20 110.0
19 TraesCS5D01G137500 chr2A 83.826 643 43 23 876 1509 703274106 703274696 2.920000e-154 555.0
20 TraesCS5D01G137500 chr7A 83.516 637 45 22 876 1504 450885569 450886153 8.170000e-150 540.0
21 TraesCS5D01G137500 chr7A 82.399 642 51 28 876 1508 660580574 660581162 1.070000e-138 503.0
22 TraesCS5D01G137500 chr7A 92.929 99 6 1 2497 2594 653010706 653010608 2.690000e-30 143.0
23 TraesCS5D01G137500 chr7A 87.879 99 10 2 2497 2594 37122529 37122626 5.870000e-22 115.0
24 TraesCS5D01G137500 chr3A 87.791 344 27 6 876 1212 211756019 211756354 3.130000e-104 388.0
25 TraesCS5D01G137500 chr3A 92.929 99 6 1 2497 2594 80080891 80080793 2.690000e-30 143.0
26 TraesCS5D01G137500 chr3A 91.919 99 7 1 2497 2594 17190053 17190151 1.250000e-28 137.0
27 TraesCS5D01G137500 chr1D 91.919 99 7 1 2497 2594 404284873 404284971 1.250000e-28 137.0
28 TraesCS5D01G137500 chr6B 88.889 99 10 1 2497 2594 703438835 703438737 1.260000e-23 121.0
29 TraesCS5D01G137500 chr2D 87.879 99 11 1 2497 2594 25006892 25006794 5.870000e-22 115.0
30 TraesCS5D01G137500 chr7B 93.023 43 2 1 2451 2493 546319946 546319905 7.750000e-06 62.1


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 TraesCS5D01G137500 chr5D 218560239 218562832 2593 False 1650.666667 4791 96.226667 1 2594 3 chr5D.!!$F1 2593
1 TraesCS5D01G137500 chr5D 218564694 218565275 581 False 220.000000 281 90.854000 1003 1584 2 chr5D.!!$F2 581
2 TraesCS5D01G137500 chr5B 241169056 241171618 2562 False 832.900000 2202 92.360000 1 2594 4 chr5B.!!$F1 2593
3 TraesCS5D01G137500 chr5B 241188014 241188559 545 False 219.000000 279 90.810500 1003 1583 2 chr5B.!!$F2 580
4 TraesCS5D01G137500 chr5A 291595856 291601156 5300 False 634.200000 1995 90.762800 1 2411 5 chr5A.!!$F1 2410
5 TraesCS5D01G137500 chr5A 556716396 556716975 579 True 545.000000 545 83.861000 887 1509 1 chr5A.!!$R2 622
6 TraesCS5D01G137500 chr2A 703274106 703274696 590 False 555.000000 555 83.826000 876 1509 1 chr2A.!!$F1 633
7 TraesCS5D01G137500 chr7A 450885569 450886153 584 False 540.000000 540 83.516000 876 1504 1 chr7A.!!$F2 628
8 TraesCS5D01G137500 chr7A 660580574 660581162 588 False 503.000000 503 82.399000 876 1508 1 chr7A.!!$F3 632

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
533 565 1.834188 CCACCATGGTTAAGTGACCC 58.166 55.0 16.84 0.0 39.01 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1659 1807 0.119561 ACAGTGGGGTGGGGTGTATA 59.88 55.0 0.0 0.0 0.0 1.47 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
308 317 8.024865 TGACTGTTTTAATGCAGATGAATGAAG 58.975 33.333 12.06 0.00 36.62 3.02
507 539 3.883489 GCTTGGAAGTAGTGTCTGGTTTT 59.117 43.478 0.00 0.00 0.00 2.43
514 546 3.883489 AGTAGTGTCTGGTTTTTCCAAGC 59.117 43.478 0.00 0.00 46.59 4.01
533 565 1.834188 CCACCATGGTTAAGTGACCC 58.166 55.000 16.84 0.00 39.01 4.46
636 673 3.313526 CAGAATTCGGGATCACAACATCC 59.686 47.826 0.00 0.00 41.74 3.51
657 700 6.752285 TCCAACTCCAGAATGATGATGATA 57.248 37.500 0.00 0.00 39.69 2.15
700 743 2.513897 GGCCCTACACACCGATGC 60.514 66.667 0.00 0.00 0.00 3.91
808 851 4.714632 ACAACTACAAGTGTACTGCCAAT 58.285 39.130 0.00 0.00 0.00 3.16
855 898 5.545063 TTTACAGTGAGTGATTCCTGTCA 57.455 39.130 0.00 0.00 37.96 3.58
885 929 2.064581 GTGGCCCTCACCGGAGTAT 61.065 63.158 9.46 0.00 40.39 2.12
1121 1184 2.037511 TCAAATTCTTCGGGTGGTACGT 59.962 45.455 0.00 0.00 0.00 3.57
1124 1187 2.945447 TTCTTCGGGTGGTACGTATG 57.055 50.000 0.00 0.00 0.00 2.39
1125 1188 0.457035 TCTTCGGGTGGTACGTATGC 59.543 55.000 0.00 0.00 0.00 3.14
1128 1191 0.825410 TCGGGTGGTACGTATGCATT 59.175 50.000 3.54 0.00 0.00 3.56
1129 1192 1.207570 TCGGGTGGTACGTATGCATTT 59.792 47.619 3.54 0.00 0.00 2.32
1130 1193 1.329292 CGGGTGGTACGTATGCATTTG 59.671 52.381 3.54 0.00 0.00 2.32
1131 1194 1.064952 GGGTGGTACGTATGCATTTGC 59.935 52.381 3.54 0.00 42.50 3.68
1147 1210 4.865925 GCATTTGCATTGCTCTCATTTGTA 59.134 37.500 10.49 0.00 41.59 2.41
1217 1319 6.147864 ACTGTCTGCTGCATTTTTCTTTTA 57.852 33.333 1.31 0.00 0.00 1.52
1218 1320 6.572519 ACTGTCTGCTGCATTTTTCTTTTAA 58.427 32.000 1.31 0.00 0.00 1.52
1242 1344 4.386711 AGAACCTTAAAGTCTTTCACCGG 58.613 43.478 0.00 0.00 0.00 5.28
1259 1361 2.882137 ACCGGTGACCAAAACTATGTTG 59.118 45.455 6.12 0.00 0.00 3.33
1279 1381 7.094508 TGTTGAAGTTTAATTCAGCAACAGA 57.905 32.000 6.93 0.00 44.25 3.41
1280 1382 7.715657 TGTTGAAGTTTAATTCAGCAACAGAT 58.284 30.769 6.93 0.00 44.25 2.90
1281 1383 7.862372 TGTTGAAGTTTAATTCAGCAACAGATC 59.138 33.333 6.93 0.00 44.25 2.75
1283 1385 7.939782 TGAAGTTTAATTCAGCAACAGATCAA 58.060 30.769 0.00 0.00 34.31 2.57
1287 1389 8.800332 AGTTTAATTCAGCAACAGATCAAGAAT 58.200 29.630 0.00 0.00 0.00 2.40
1303 1406 7.997223 AGATCAAGAATTCAAGATTAGGCATCA 59.003 33.333 8.44 0.00 33.75 3.07
1318 1421 1.129251 GCATCACCGTTCATCAGTGTG 59.871 52.381 0.00 0.00 33.21 3.82
1332 1435 7.946381 TCATCAGTGTGTCTATCTAGAGTTT 57.054 36.000 0.00 0.00 32.01 2.66
1333 1436 9.462606 TTCATCAGTGTGTCTATCTAGAGTTTA 57.537 33.333 0.00 0.00 32.01 2.01
1610 1758 0.923358 TGAATGATACACCCCACCCC 59.077 55.000 0.00 0.00 0.00 4.95
1611 1759 0.923358 GAATGATACACCCCACCCCA 59.077 55.000 0.00 0.00 0.00 4.96
1612 1760 0.926293 AATGATACACCCCACCCCAG 59.074 55.000 0.00 0.00 0.00 4.45
1614 1762 0.418245 TGATACACCCCACCCCAGTA 59.582 55.000 0.00 0.00 0.00 2.74
1616 1764 1.697982 GATACACCCCACCCCAGTATC 59.302 57.143 0.00 0.00 35.72 2.24
1617 1765 0.720232 TACACCCCACCCCAGTATCT 59.280 55.000 0.00 0.00 0.00 1.98
1618 1766 0.720232 ACACCCCACCCCAGTATCTA 59.280 55.000 0.00 0.00 0.00 1.98
1619 1767 1.297141 ACACCCCACCCCAGTATCTAT 59.703 52.381 0.00 0.00 0.00 1.98
1620 1768 1.978580 CACCCCACCCCAGTATCTATC 59.021 57.143 0.00 0.00 0.00 2.08
1621 1769 1.873732 ACCCCACCCCAGTATCTATCT 59.126 52.381 0.00 0.00 0.00 1.98
1622 1770 2.260822 CCCCACCCCAGTATCTATCTG 58.739 57.143 0.00 0.00 0.00 2.90
1623 1771 2.427889 CCCCACCCCAGTATCTATCTGT 60.428 54.545 0.00 0.00 0.00 3.41
1624 1772 3.318313 CCCACCCCAGTATCTATCTGTT 58.682 50.000 0.00 0.00 0.00 3.16
1625 1773 4.489737 CCCACCCCAGTATCTATCTGTTA 58.510 47.826 0.00 0.00 0.00 2.41
1626 1774 4.283722 CCCACCCCAGTATCTATCTGTTAC 59.716 50.000 0.00 0.00 0.00 2.50
1627 1775 5.148502 CCACCCCAGTATCTATCTGTTACT 58.851 45.833 0.00 0.00 32.94 2.24
1628 1776 6.312529 CCACCCCAGTATCTATCTGTTACTA 58.687 44.000 0.00 0.00 31.88 1.82
1629 1777 6.208994 CCACCCCAGTATCTATCTGTTACTAC 59.791 46.154 0.00 0.00 31.88 2.73
1630 1778 7.005296 CACCCCAGTATCTATCTGTTACTACT 58.995 42.308 0.00 0.00 31.88 2.57
1631 1779 7.506261 CACCCCAGTATCTATCTGTTACTACTT 59.494 40.741 0.00 0.00 31.88 2.24
1632 1780 7.724951 ACCCCAGTATCTATCTGTTACTACTTC 59.275 40.741 0.00 0.00 31.88 3.01
1633 1781 7.177041 CCCCAGTATCTATCTGTTACTACTTCC 59.823 44.444 0.00 0.00 31.88 3.46
1634 1782 7.945664 CCCAGTATCTATCTGTTACTACTTCCT 59.054 40.741 0.00 0.00 31.88 3.36
1635 1783 9.005777 CCAGTATCTATCTGTTACTACTTCCTC 57.994 40.741 0.00 0.00 31.88 3.71
1636 1784 9.005777 CAGTATCTATCTGTTACTACTTCCTCC 57.994 40.741 0.00 0.00 31.88 4.30
1637 1785 7.879160 AGTATCTATCTGTTACTACTTCCTCCG 59.121 40.741 0.00 0.00 31.47 4.63
1638 1786 5.999044 TCTATCTGTTACTACTTCCTCCGT 58.001 41.667 0.00 0.00 0.00 4.69
1639 1787 6.054295 TCTATCTGTTACTACTTCCTCCGTC 58.946 44.000 0.00 0.00 0.00 4.79
1640 1788 4.298103 TCTGTTACTACTTCCTCCGTCT 57.702 45.455 0.00 0.00 0.00 4.18
1641 1789 5.426689 TCTGTTACTACTTCCTCCGTCTA 57.573 43.478 0.00 0.00 0.00 2.59
1642 1790 5.809001 TCTGTTACTACTTCCTCCGTCTAA 58.191 41.667 0.00 0.00 0.00 2.10
1643 1791 6.240894 TCTGTTACTACTTCCTCCGTCTAAA 58.759 40.000 0.00 0.00 0.00 1.85
1644 1792 6.716628 TCTGTTACTACTTCCTCCGTCTAAAA 59.283 38.462 0.00 0.00 0.00 1.52
1645 1793 7.231317 TCTGTTACTACTTCCTCCGTCTAAAAA 59.769 37.037 0.00 0.00 0.00 1.94
1668 1816 8.409358 AAAAGCTTGAATGATATATACACCCC 57.591 34.615 0.00 0.00 0.00 4.95
1669 1817 6.702449 AGCTTGAATGATATATACACCCCA 57.298 37.500 0.00 0.00 0.00 4.96
1670 1818 6.476378 AGCTTGAATGATATATACACCCCAC 58.524 40.000 0.00 0.00 0.00 4.61
1671 1819 5.648092 GCTTGAATGATATATACACCCCACC 59.352 44.000 0.00 0.00 0.00 4.61
1672 1820 5.772393 TGAATGATATATACACCCCACCC 57.228 43.478 0.00 0.00 0.00 4.61
1675 1823 3.253220 TGATATATACACCCCACCCCAC 58.747 50.000 0.00 0.00 0.00 4.61
1677 1825 1.518367 ATATACACCCCACCCCACTG 58.482 55.000 0.00 0.00 0.00 3.66
1681 1829 1.537889 CACCCCACCCCACTGTCTA 60.538 63.158 0.00 0.00 0.00 2.59
1724 1872 1.227645 GCATCTACCATCGCCAGCA 60.228 57.895 0.00 0.00 0.00 4.41
1763 1911 5.755849 CCTTTTCAGGTAATACCACCATCT 58.244 41.667 12.54 0.00 41.95 2.90
1832 1980 0.606401 TGCTTGCTTGTCCTGCTACC 60.606 55.000 0.00 0.00 0.00 3.18
1838 1986 2.449031 CTTGTCCTGCTACCACGGCA 62.449 60.000 0.00 0.00 38.10 5.69
1841 1989 0.177141 GTCCTGCTACCACGGCATTA 59.823 55.000 0.00 0.00 39.07 1.90
1898 2046 2.622064 ACTCTATTCCGTGCATTCCC 57.378 50.000 0.00 0.00 0.00 3.97
1900 2048 2.505819 ACTCTATTCCGTGCATTCCCTT 59.494 45.455 0.00 0.00 0.00 3.95
1901 2049 3.134458 CTCTATTCCGTGCATTCCCTTC 58.866 50.000 0.00 0.00 0.00 3.46
1902 2050 1.867233 CTATTCCGTGCATTCCCTTCG 59.133 52.381 0.00 0.00 0.00 3.79
1938 2089 6.238648 GGTTATCACCCTTGAATAAACATCGG 60.239 42.308 0.00 0.00 37.03 4.18
1957 2108 5.074584 TCGGTGGTTTTGCTTTACTTTTT 57.925 34.783 0.00 0.00 0.00 1.94
1974 2125 9.912634 TTTACTTTTTGGTCTTCATGATGAATC 57.087 29.630 8.50 8.94 35.59 2.52
1983 2139 7.046652 GGTCTTCATGATGAATCGATGGATAT 58.953 38.462 8.50 0.00 35.59 1.63
1984 2140 7.224362 GGTCTTCATGATGAATCGATGGATATC 59.776 40.741 8.50 1.82 35.59 1.63
1985 2141 7.224362 GTCTTCATGATGAATCGATGGATATCC 59.776 40.741 15.39 15.39 35.59 2.59
1986 2142 6.949715 TTCATGATGAATCGATGGATATCCA 58.050 36.000 26.49 26.49 40.01 3.41
1987 2143 7.396418 TTCATGATGAATCGATGGATATCCAA 58.604 34.615 27.89 12.73 39.50 3.53
2011 2167 0.894835 TAATGGCTCACTCGTGCTGA 59.105 50.000 0.00 0.00 0.00 4.26
2029 2185 3.181520 GCTGACCACTATTGCGTAAACAG 60.182 47.826 0.00 0.00 0.00 3.16
2039 2195 7.265495 CACTATTGCGTAAACAGTTAAAACTCG 59.735 37.037 1.89 0.00 37.08 4.18
2047 2203 2.030274 ACAGTTAAAACTCGGGCAATGC 60.030 45.455 0.00 0.00 37.08 3.56
2079 2466 3.057104 TGTTGAAGCTGAAGGCATTGATG 60.057 43.478 0.00 0.00 44.79 3.07
2111 2498 6.154445 ACATGTCAGAATTTTCATGTGAAGC 58.846 36.000 8.50 0.00 45.64 3.86
2122 2509 9.941325 AATTTTCATGTGAAGCCATTTACATTA 57.059 25.926 0.00 0.00 41.43 1.90
2124 2511 6.135290 TCATGTGAAGCCATTTACATTAGC 57.865 37.500 0.00 0.00 41.43 3.09
2224 2616 4.101790 GCCCGATGCACACAACCG 62.102 66.667 0.00 0.00 40.77 4.44
2247 2648 7.274250 ACCGTGTATCTTGTTAATAGTCGAAAC 59.726 37.037 0.00 0.00 0.00 2.78
2250 2651 8.100306 GTGTATCTTGTTAATAGTCGAAACGTG 58.900 37.037 0.00 0.00 0.00 4.49
2266 2668 1.618837 ACGTGTGGAGTTACTGCAGAT 59.381 47.619 23.35 7.41 31.31 2.90
2293 2695 7.302350 TGTCAAATGGTAATACTGTCGAATG 57.698 36.000 0.00 0.00 0.00 2.67
2311 2713 2.649531 TGGAAAGAAGAGGCCGAAAA 57.350 45.000 0.00 0.00 0.00 2.29
2318 2720 3.539604 AGAAGAGGCCGAAAATGATCAG 58.460 45.455 0.09 0.00 0.00 2.90
2322 2724 0.106719 GGCCGAAAATGATCAGGGGA 60.107 55.000 0.09 0.00 0.00 4.81
2485 4220 8.788325 TTCTAACTGATCCCTTAAAAGTTAGC 57.212 34.615 16.44 0.00 45.05 3.09
2487 4222 4.514401 ACTGATCCCTTAAAAGTTAGCGG 58.486 43.478 0.00 0.00 0.00 5.52
2488 4223 4.224370 ACTGATCCCTTAAAAGTTAGCGGA 59.776 41.667 0.00 0.00 0.00 5.54
2489 4224 4.766375 TGATCCCTTAAAAGTTAGCGGAG 58.234 43.478 0.00 0.00 0.00 4.63
2490 4225 4.224370 TGATCCCTTAAAAGTTAGCGGAGT 59.776 41.667 0.00 0.00 0.00 3.85
2492 4227 5.945144 TCCCTTAAAAGTTAGCGGAGTAT 57.055 39.130 0.00 0.00 0.00 2.12
2494 4229 7.422465 TCCCTTAAAAGTTAGCGGAGTATAA 57.578 36.000 0.00 0.00 0.00 0.98
2496 4231 6.481313 CCCTTAAAAGTTAGCGGAGTATAACC 59.519 42.308 0.00 0.00 34.10 2.85
2497 4232 7.270779 CCTTAAAAGTTAGCGGAGTATAACCT 58.729 38.462 0.00 0.00 34.10 3.50
2498 4233 8.416329 CCTTAAAAGTTAGCGGAGTATAACCTA 58.584 37.037 0.00 0.00 34.10 3.08
2504 4239 9.676861 AAGTTAGCGGAGTATAACCTAAAATTT 57.323 29.630 0.00 0.00 34.10 1.82
2520 4432 0.322322 ATTTCGCCACACCTAACCGA 59.678 50.000 0.00 0.00 0.00 4.69
2524 4436 1.153229 GCCACACCTAACCGATCCC 60.153 63.158 0.00 0.00 0.00 3.85
2535 4447 5.668991 ACCTAACCGATCCCCTAAAATTAGT 59.331 40.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
308 317 4.095483 CCATCCTGTTTGTTAGCTCATCAC 59.905 45.833 0.00 0.00 0.00 3.06
507 539 2.158385 ACTTAACCATGGTGGCTTGGAA 60.158 45.455 20.60 3.65 42.67 3.53
514 546 1.074727 TGGGTCACTTAACCATGGTGG 59.925 52.381 20.60 14.19 45.02 4.61
533 565 1.868498 CAAACCAGCCAATTGCAGTTG 59.132 47.619 14.58 14.58 44.83 3.16
636 673 7.498239 ACAAGTATCATCATCATTCTGGAGTTG 59.502 37.037 0.00 0.00 0.00 3.16
855 898 4.204028 GGCCACCACCACACCACT 62.204 66.667 0.00 0.00 0.00 4.00
885 929 2.971901 TATGGACGGGATGAGAGCTA 57.028 50.000 0.00 0.00 0.00 3.32
959 1003 0.322366 AGCCAAGCTTTCTCCTCTGC 60.322 55.000 0.00 0.00 33.89 4.26
1124 1187 3.682858 ACAAATGAGAGCAATGCAAATGC 59.317 39.130 17.46 17.46 44.15 3.56
1125 1188 7.064134 ACAATACAAATGAGAGCAATGCAAATG 59.936 33.333 8.35 0.00 0.00 2.32
1128 1191 6.028146 ACAATACAAATGAGAGCAATGCAA 57.972 33.333 8.35 0.00 0.00 4.08
1129 1192 5.648178 ACAATACAAATGAGAGCAATGCA 57.352 34.783 8.35 0.00 0.00 3.96
1130 1193 5.517770 GGAACAATACAAATGAGAGCAATGC 59.482 40.000 0.00 0.00 0.00 3.56
1131 1194 5.740569 CGGAACAATACAAATGAGAGCAATG 59.259 40.000 0.00 0.00 0.00 2.82
1132 1195 5.647658 TCGGAACAATACAAATGAGAGCAAT 59.352 36.000 0.00 0.00 0.00 3.56
1133 1196 5.000591 TCGGAACAATACAAATGAGAGCAA 58.999 37.500 0.00 0.00 0.00 3.91
1134 1197 4.574892 TCGGAACAATACAAATGAGAGCA 58.425 39.130 0.00 0.00 0.00 4.26
1135 1198 5.545658 TTCGGAACAATACAAATGAGAGC 57.454 39.130 0.00 0.00 0.00 4.09
1136 1199 7.538678 CCTTTTTCGGAACAATACAAATGAGAG 59.461 37.037 0.00 0.00 0.00 3.20
1147 1210 4.156477 TGGAATCCCTTTTTCGGAACAAT 58.844 39.130 0.00 0.00 31.75 2.71
1217 1319 6.183360 CCGGTGAAAGACTTTAAGGTTCTTTT 60.183 38.462 10.51 6.24 31.71 2.27
1218 1320 5.298527 CCGGTGAAAGACTTTAAGGTTCTTT 59.701 40.000 9.39 9.39 33.89 2.52
1226 1328 3.118334 TGGTCACCGGTGAAAGACTTTAA 60.118 43.478 37.75 10.20 41.85 1.52
1231 1333 1.670791 TTTGGTCACCGGTGAAAGAC 58.329 50.000 37.75 25.18 41.85 3.01
1236 1338 2.105134 ACATAGTTTTGGTCACCGGTGA 59.895 45.455 33.23 33.23 37.24 4.02
1242 1344 9.744468 ATTAAACTTCAACATAGTTTTGGTCAC 57.256 29.630 6.33 0.00 41.69 3.67
1259 1361 8.292448 TCTTGATCTGTTGCTGAATTAAACTTC 58.708 33.333 0.00 0.00 0.00 3.01
1278 1380 8.074972 GTGATGCCTAATCTTGAATTCTTGATC 58.925 37.037 7.05 0.00 36.15 2.92
1279 1381 7.014038 GGTGATGCCTAATCTTGAATTCTTGAT 59.986 37.037 7.05 7.37 36.15 2.57
1280 1382 6.319658 GGTGATGCCTAATCTTGAATTCTTGA 59.680 38.462 7.05 5.31 36.15 3.02
1281 1383 6.501781 GGTGATGCCTAATCTTGAATTCTTG 58.498 40.000 7.05 0.00 36.15 3.02
1283 1385 4.818546 CGGTGATGCCTAATCTTGAATTCT 59.181 41.667 7.05 0.00 36.15 2.40
1287 1389 3.627395 ACGGTGATGCCTAATCTTGAA 57.373 42.857 0.00 0.00 36.15 2.69
1303 1406 3.764434 AGATAGACACACTGATGAACGGT 59.236 43.478 0.00 0.00 38.85 4.83
1590 1738 1.286553 GGGGTGGGGTGTATCATTCAA 59.713 52.381 0.00 0.00 0.00 2.69
1610 1758 9.005777 GGAGGAAGTAGTAACAGATAGATACTG 57.994 40.741 0.00 0.00 36.60 2.74
1611 1759 7.879160 CGGAGGAAGTAGTAACAGATAGATACT 59.121 40.741 0.00 0.00 39.02 2.12
1612 1760 7.661027 ACGGAGGAAGTAGTAACAGATAGATAC 59.339 40.741 0.00 0.00 0.00 2.24
1614 1762 6.603224 ACGGAGGAAGTAGTAACAGATAGAT 58.397 40.000 0.00 0.00 0.00 1.98
1616 1764 6.056884 AGACGGAGGAAGTAGTAACAGATAG 58.943 44.000 0.00 0.00 0.00 2.08
1617 1765 5.999044 AGACGGAGGAAGTAGTAACAGATA 58.001 41.667 0.00 0.00 0.00 1.98
1618 1766 4.857679 AGACGGAGGAAGTAGTAACAGAT 58.142 43.478 0.00 0.00 0.00 2.90
1619 1767 4.298103 AGACGGAGGAAGTAGTAACAGA 57.702 45.455 0.00 0.00 0.00 3.41
1620 1768 6.506500 TTTAGACGGAGGAAGTAGTAACAG 57.493 41.667 0.00 0.00 0.00 3.16
1621 1769 6.899393 TTTTAGACGGAGGAAGTAGTAACA 57.101 37.500 0.00 0.00 0.00 2.41
1642 1790 8.860088 GGGGTGTATATATCATTCAAGCTTTTT 58.140 33.333 0.00 0.00 0.00 1.94
1643 1791 8.004215 TGGGGTGTATATATCATTCAAGCTTTT 58.996 33.333 0.00 0.00 0.00 2.27
1644 1792 7.448469 GTGGGGTGTATATATCATTCAAGCTTT 59.552 37.037 0.00 0.00 0.00 3.51
1645 1793 6.942576 GTGGGGTGTATATATCATTCAAGCTT 59.057 38.462 0.00 0.00 0.00 3.74
1646 1794 6.476378 GTGGGGTGTATATATCATTCAAGCT 58.524 40.000 0.00 0.00 0.00 3.74
1647 1795 5.648092 GGTGGGGTGTATATATCATTCAAGC 59.352 44.000 0.00 0.00 0.00 4.01
1648 1796 6.180472 GGGTGGGGTGTATATATCATTCAAG 58.820 44.000 0.00 0.00 0.00 3.02
1649 1797 5.014755 GGGGTGGGGTGTATATATCATTCAA 59.985 44.000 0.00 0.00 0.00 2.69
1650 1798 4.538490 GGGGTGGGGTGTATATATCATTCA 59.462 45.833 0.00 0.00 0.00 2.57
1651 1799 4.538490 TGGGGTGGGGTGTATATATCATTC 59.462 45.833 0.00 0.00 0.00 2.67
1652 1800 4.291249 GTGGGGTGGGGTGTATATATCATT 59.709 45.833 0.00 0.00 0.00 2.57
1653 1801 3.850173 GTGGGGTGGGGTGTATATATCAT 59.150 47.826 0.00 0.00 0.00 2.45
1654 1802 3.116120 AGTGGGGTGGGGTGTATATATCA 60.116 47.826 0.00 0.00 0.00 2.15
1655 1803 3.263425 CAGTGGGGTGGGGTGTATATATC 59.737 52.174 0.00 0.00 0.00 1.63
1656 1804 3.256704 CAGTGGGGTGGGGTGTATATAT 58.743 50.000 0.00 0.00 0.00 0.86
1657 1805 2.021837 ACAGTGGGGTGGGGTGTATATA 60.022 50.000 0.00 0.00 0.00 0.86
1658 1806 1.274767 ACAGTGGGGTGGGGTGTATAT 60.275 52.381 0.00 0.00 0.00 0.86
1659 1807 0.119561 ACAGTGGGGTGGGGTGTATA 59.880 55.000 0.00 0.00 0.00 1.47
1660 1808 1.151677 ACAGTGGGGTGGGGTGTAT 60.152 57.895 0.00 0.00 0.00 2.29
1661 1809 1.844289 GACAGTGGGGTGGGGTGTA 60.844 63.158 0.00 0.00 0.00 2.90
1662 1810 2.335134 TAGACAGTGGGGTGGGGTGT 62.335 60.000 0.00 0.00 0.00 4.16
1663 1811 0.914417 ATAGACAGTGGGGTGGGGTG 60.914 60.000 0.00 0.00 0.00 4.61
1664 1812 0.620700 GATAGACAGTGGGGTGGGGT 60.621 60.000 0.00 0.00 0.00 4.95
1665 1813 0.326618 AGATAGACAGTGGGGTGGGG 60.327 60.000 0.00 0.00 0.00 4.96
1666 1814 0.833287 CAGATAGACAGTGGGGTGGG 59.167 60.000 0.00 0.00 0.00 4.61
1667 1815 1.573108 ACAGATAGACAGTGGGGTGG 58.427 55.000 0.00 0.00 0.00 4.61
1668 1816 3.769844 AGTAACAGATAGACAGTGGGGTG 59.230 47.826 0.00 0.00 0.00 4.61
1669 1817 4.062490 AGTAACAGATAGACAGTGGGGT 57.938 45.455 0.00 0.00 0.00 4.95
1670 1818 5.202004 AGTAGTAACAGATAGACAGTGGGG 58.798 45.833 0.00 0.00 0.00 4.96
1671 1819 7.468906 GCTTAGTAGTAACAGATAGACAGTGGG 60.469 44.444 0.00 0.00 0.00 4.61
1672 1820 7.067129 TGCTTAGTAGTAACAGATAGACAGTGG 59.933 40.741 0.00 0.00 0.00 4.00
1675 1823 8.679100 ACTTGCTTAGTAGTAACAGATAGACAG 58.321 37.037 0.00 0.00 34.56 3.51
1681 1829 9.968870 GCTTATACTTGCTTAGTAGTAACAGAT 57.031 33.333 5.68 0.00 42.44 2.90
1742 1890 8.331931 AGATAGATGGTGGTATTACCTGAAAA 57.668 34.615 13.90 0.00 41.43 2.29
1746 1894 8.690884 CAGATAGATAGATGGTGGTATTACCTG 58.309 40.741 13.90 0.00 41.43 4.00
1747 1895 8.624670 TCAGATAGATAGATGGTGGTATTACCT 58.375 37.037 13.90 0.00 41.43 3.08
1748 1896 8.824756 TCAGATAGATAGATGGTGGTATTACC 57.175 38.462 5.87 5.87 41.24 2.85
1750 1898 9.480861 CCTTCAGATAGATAGATGGTGGTATTA 57.519 37.037 0.00 0.00 0.00 0.98
1751 1899 7.093112 GCCTTCAGATAGATAGATGGTGGTATT 60.093 40.741 0.00 0.00 0.00 1.89
1752 1900 6.382570 GCCTTCAGATAGATAGATGGTGGTAT 59.617 42.308 0.00 0.00 0.00 2.73
1753 1901 5.717178 GCCTTCAGATAGATAGATGGTGGTA 59.283 44.000 0.00 0.00 0.00 3.25
1754 1902 4.530161 GCCTTCAGATAGATAGATGGTGGT 59.470 45.833 0.00 0.00 0.00 4.16
1755 1903 4.776837 AGCCTTCAGATAGATAGATGGTGG 59.223 45.833 0.00 0.00 0.00 4.61
1756 1904 5.722263 CAGCCTTCAGATAGATAGATGGTG 58.278 45.833 0.00 0.00 0.00 4.17
1757 1905 4.222588 GCAGCCTTCAGATAGATAGATGGT 59.777 45.833 0.00 0.00 0.00 3.55
1758 1906 4.222366 TGCAGCCTTCAGATAGATAGATGG 59.778 45.833 0.00 0.00 0.00 3.51
1759 1907 5.402997 TGCAGCCTTCAGATAGATAGATG 57.597 43.478 0.00 0.00 0.00 2.90
1760 1908 4.081531 GCTGCAGCCTTCAGATAGATAGAT 60.082 45.833 28.76 0.00 33.54 1.98
1761 1909 3.257873 GCTGCAGCCTTCAGATAGATAGA 59.742 47.826 28.76 0.00 33.54 1.98
1762 1910 3.258872 AGCTGCAGCCTTCAGATAGATAG 59.741 47.826 34.39 0.00 43.38 2.08
1763 1911 3.006644 CAGCTGCAGCCTTCAGATAGATA 59.993 47.826 34.39 0.00 43.38 1.98
1838 1986 1.444672 GGCTAGACGGCCGGTTAAT 59.555 57.895 31.76 7.71 42.82 1.40
1898 2046 5.147162 GTGATAACCAAGCAACTTTCGAAG 58.853 41.667 0.00 0.00 0.00 3.79
1900 2048 3.500680 GGTGATAACCAAGCAACTTTCGA 59.499 43.478 0.00 0.00 0.00 3.71
1901 2049 3.365969 GGGTGATAACCAAGCAACTTTCG 60.366 47.826 0.36 0.00 0.00 3.46
1902 2050 3.826729 AGGGTGATAACCAAGCAACTTTC 59.173 43.478 0.36 0.00 0.00 2.62
1938 2089 5.872617 AGACCAAAAAGTAAAGCAAAACCAC 59.127 36.000 0.00 0.00 0.00 4.16
1957 2108 4.101430 TCCATCGATTCATCATGAAGACCA 59.899 41.667 6.19 0.00 40.05 4.02
1974 2125 5.295292 GCCATTACAGATTGGATATCCATCG 59.705 44.000 25.07 18.80 46.97 3.84
1983 2139 3.430790 CGAGTGAGCCATTACAGATTGGA 60.431 47.826 0.00 0.00 34.81 3.53
1984 2140 2.868583 CGAGTGAGCCATTACAGATTGG 59.131 50.000 0.00 0.00 36.03 3.16
1985 2141 3.308053 CACGAGTGAGCCATTACAGATTG 59.692 47.826 0.00 0.00 0.00 2.67
1986 2142 3.525537 CACGAGTGAGCCATTACAGATT 58.474 45.455 0.00 0.00 0.00 2.40
1987 2143 2.739932 GCACGAGTGAGCCATTACAGAT 60.740 50.000 7.50 0.00 0.00 2.90
2011 2167 6.864360 TTTAACTGTTTACGCAATAGTGGT 57.136 33.333 0.00 0.00 36.95 4.16
2029 2185 2.715737 TGCATTGCCCGAGTTTTAAC 57.284 45.000 6.12 0.00 0.00 2.01
2039 2195 2.769893 ACAATGAAACTTGCATTGCCC 58.230 42.857 18.97 0.00 40.29 5.36
2047 2203 5.461078 CCTTCAGCTTCAACAATGAAACTTG 59.539 40.000 0.00 0.00 44.64 3.16
2058 2445 3.192001 TCATCAATGCCTTCAGCTTCAAC 59.808 43.478 0.00 0.00 44.23 3.18
2059 2446 3.423749 TCATCAATGCCTTCAGCTTCAA 58.576 40.909 0.00 0.00 44.23 2.69
2079 2466 9.121517 CATGAAAATTCTGACATGTTACTGTTC 57.878 33.333 0.00 0.00 36.42 3.18
2111 2498 7.010738 CAGCAATTGAAAGGCTAATGTAAATGG 59.989 37.037 10.34 0.00 35.82 3.16
2122 2509 1.547472 GGGGCAGCAATTGAAAGGCT 61.547 55.000 10.34 0.00 38.70 4.58
2124 2511 0.248289 CAGGGGCAGCAATTGAAAGG 59.752 55.000 10.34 0.00 0.00 3.11
2224 2616 8.100306 CACGTTTCGACTATTAACAAGATACAC 58.900 37.037 0.00 0.00 0.00 2.90
2247 2648 2.370281 ATCTGCAGTAACTCCACACG 57.630 50.000 14.67 0.00 0.00 4.49
2250 2651 4.515191 TGACAAAATCTGCAGTAACTCCAC 59.485 41.667 14.67 1.80 0.00 4.02
2266 2668 7.731882 TCGACAGTATTACCATTTGACAAAA 57.268 32.000 4.41 0.00 0.00 2.44
2293 2695 3.081804 TCATTTTCGGCCTCTTCTTTCC 58.918 45.455 0.00 0.00 0.00 3.13
2311 2713 4.586884 CATTTCATCGATCCCCTGATCAT 58.413 43.478 0.00 0.00 46.50 2.45
2318 2720 3.409026 ACTAGCATTTCATCGATCCCC 57.591 47.619 0.00 0.00 0.00 4.81
2322 2724 7.253422 CAAGGAAAAACTAGCATTTCATCGAT 58.747 34.615 17.67 0.00 37.29 3.59
2467 4202 4.224370 ACTCCGCTAACTTTTAAGGGATCA 59.776 41.667 0.00 0.00 0.00 2.92
2485 4220 5.524646 TGGCGAAATTTTAGGTTATACTCCG 59.475 40.000 0.00 0.00 0.00 4.63
2487 4222 7.184779 GTGTGGCGAAATTTTAGGTTATACTC 58.815 38.462 0.00 0.00 0.00 2.59
2488 4223 6.094464 GGTGTGGCGAAATTTTAGGTTATACT 59.906 38.462 0.00 0.00 0.00 2.12
2489 4224 6.094464 AGGTGTGGCGAAATTTTAGGTTATAC 59.906 38.462 0.00 0.00 0.00 1.47
2490 4225 6.181908 AGGTGTGGCGAAATTTTAGGTTATA 58.818 36.000 0.00 0.00 0.00 0.98
2492 4227 4.400120 AGGTGTGGCGAAATTTTAGGTTA 58.600 39.130 0.00 0.00 0.00 2.85
2494 4229 2.871453 AGGTGTGGCGAAATTTTAGGT 58.129 42.857 0.00 0.00 0.00 3.08
2496 4231 4.670735 CGGTTAGGTGTGGCGAAATTTTAG 60.671 45.833 0.00 0.00 0.00 1.85
2497 4232 3.188873 CGGTTAGGTGTGGCGAAATTTTA 59.811 43.478 0.00 0.00 0.00 1.52
2498 4233 2.030628 CGGTTAGGTGTGGCGAAATTTT 60.031 45.455 0.00 0.00 0.00 1.82
2500 4235 1.161843 CGGTTAGGTGTGGCGAAATT 58.838 50.000 0.00 0.00 0.00 1.82
2504 4239 1.514087 GATCGGTTAGGTGTGGCGA 59.486 57.895 0.00 0.00 0.00 5.54
2568 4480 7.437793 AAATGCATCATTTTCGGTTCAAATT 57.562 28.000 0.00 0.00 40.60 1.82


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

AutoCloner maintained by Alex Coulton.