Multiple sequence alignment - TraesCS2A01G243900

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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 TraesCS2A01G243900 chr2A 100.000 2291 0 0 1 2291 345463175 345460885 0.000000e+00 4231.0
1 TraesCS2A01G243900 chr2A 97.037 540 16 0 1 540 335745568 335745029 0.000000e+00 909.0
2 TraesCS2A01G243900 chr2A 96.667 540 18 0 1 540 335023472 335022933 0.000000e+00 898.0
3 TraesCS2A01G243900 chr2D 92.541 1086 69 6 538 1620 258813437 258814513 0.000000e+00 1546.0
4 TraesCS2A01G243900 chr2D 90.108 647 50 4 1659 2291 258814514 258815160 0.000000e+00 828.0
5 TraesCS2A01G243900 chr7A 96.673 541 16 2 1 540 253543904 253543365 0.000000e+00 898.0
6 TraesCS2A01G243900 chr7A 96.834 537 17 0 1 537 349127482 349126946 0.000000e+00 898.0
7 TraesCS2A01G243900 chr5A 96.667 540 18 0 1 540 254035693 254035154 0.000000e+00 898.0
8 TraesCS2A01G243900 chr5A 96.667 540 18 0 1 540 325675204 325675743 0.000000e+00 898.0
9 TraesCS2A01G243900 chr5A 81.146 785 139 7 538 1315 142844696 142845478 2.500000e-174 621.0
10 TraesCS2A01G243900 chr5A 80.570 772 131 11 553 1315 520448243 520447482 5.490000e-161 577.0
11 TraesCS2A01G243900 chr5A 78.591 738 149 7 541 1271 534623347 534622612 1.590000e-131 479.0
12 TraesCS2A01G243900 chr4A 96.667 540 18 0 1 540 314622393 314622932 0.000000e+00 898.0
13 TraesCS2A01G243900 chr4A 96.660 539 18 0 1 539 314142798 314142260 0.000000e+00 896.0
14 TraesCS2A01G243900 chr1A 96.673 541 16 2 1 540 227291302 227290763 0.000000e+00 898.0
15 TraesCS2A01G243900 chr1A 78.918 721 144 6 534 1248 521870939 521870221 1.230000e-132 483.0
16 TraesCS2A01G243900 chr3D 86.041 788 96 12 538 1315 213674872 213674089 0.000000e+00 833.0
17 TraesCS2A01G243900 chr6A 83.163 784 121 9 538 1314 432305788 432306567 0.000000e+00 706.0
18 TraesCS2A01G243900 chr7B 77.876 791 158 16 534 1316 676013115 676012334 2.060000e-130 475.0
19 TraesCS2A01G243900 chr6B 77.020 792 157 22 534 1314 32795537 32796314 4.520000e-117 431.0
20 TraesCS2A01G243900 chr1D 100.000 29 0 0 1894 1922 135465753 135465725 1.000000e-03 54.7


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 TraesCS2A01G243900 chr2A 345460885 345463175 2290 True 4231 4231 100.0000 1 2291 1 chr2A.!!$R3 2290
1 TraesCS2A01G243900 chr2A 335745029 335745568 539 True 909 909 97.0370 1 540 1 chr2A.!!$R2 539
2 TraesCS2A01G243900 chr2A 335022933 335023472 539 True 898 898 96.6670 1 540 1 chr2A.!!$R1 539
3 TraesCS2A01G243900 chr2D 258813437 258815160 1723 False 1187 1546 91.3245 538 2291 2 chr2D.!!$F1 1753
4 TraesCS2A01G243900 chr7A 253543365 253543904 539 True 898 898 96.6730 1 540 1 chr7A.!!$R1 539
5 TraesCS2A01G243900 chr7A 349126946 349127482 536 True 898 898 96.8340 1 537 1 chr7A.!!$R2 536
6 TraesCS2A01G243900 chr5A 254035154 254035693 539 True 898 898 96.6670 1 540 1 chr5A.!!$R1 539
7 TraesCS2A01G243900 chr5A 325675204 325675743 539 False 898 898 96.6670 1 540 1 chr5A.!!$F2 539
8 TraesCS2A01G243900 chr5A 142844696 142845478 782 False 621 621 81.1460 538 1315 1 chr5A.!!$F1 777
9 TraesCS2A01G243900 chr5A 520447482 520448243 761 True 577 577 80.5700 553 1315 1 chr5A.!!$R2 762
10 TraesCS2A01G243900 chr5A 534622612 534623347 735 True 479 479 78.5910 541 1271 1 chr5A.!!$R3 730
11 TraesCS2A01G243900 chr4A 314622393 314622932 539 False 898 898 96.6670 1 540 1 chr4A.!!$F1 539
12 TraesCS2A01G243900 chr4A 314142260 314142798 538 True 896 896 96.6600 1 539 1 chr4A.!!$R1 538
13 TraesCS2A01G243900 chr1A 227290763 227291302 539 True 898 898 96.6730 1 540 1 chr1A.!!$R1 539
14 TraesCS2A01G243900 chr1A 521870221 521870939 718 True 483 483 78.9180 534 1248 1 chr1A.!!$R2 714
15 TraesCS2A01G243900 chr3D 213674089 213674872 783 True 833 833 86.0410 538 1315 1 chr3D.!!$R1 777
16 TraesCS2A01G243900 chr6A 432305788 432306567 779 False 706 706 83.1630 538 1314 1 chr6A.!!$F1 776
17 TraesCS2A01G243900 chr7B 676012334 676013115 781 True 475 475 77.8760 534 1316 1 chr7B.!!$R1 782
18 TraesCS2A01G243900 chr6B 32795537 32796314 777 False 431 431 77.0200 534 1314 1 chr6B.!!$F1 780

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
492 495 0.313043 TCGACTCCCACAGAAACGAC 59.687 55.0 0.0 0.0 0.0 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1798 1821 0.03213 ATCTATCGCGCATCACCGTT 59.968 50.0 8.75 0.0 0.0 4.44 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
72 73 5.927281 AGGCTGTTTTTAGAGTCCGTATA 57.073 39.130 0.00 0.00 0.00 1.47
211 212 7.981142 TGTTTAGATTAAAAGTTCGCCATAGG 58.019 34.615 0.00 0.00 0.00 2.57
293 294 7.068593 CCCACCTTGATCAATAAAGCTTTCATA 59.931 37.037 16.57 0.00 0.00 2.15
344 345 3.038710 CAGTTTCTTGCTTGTTCTTCGC 58.961 45.455 0.00 0.00 0.00 4.70
492 495 0.313043 TCGACTCCCACAGAAACGAC 59.687 55.000 0.00 0.00 0.00 4.34
902 916 8.459635 GGTTGTCCTTAAAGATGATAAAGGAAC 58.540 37.037 4.32 1.19 46.76 3.62
970 985 2.309613 TGACAGCAGAAGCATTGGTTT 58.690 42.857 2.14 0.00 45.49 3.27
994 1011 5.886960 AAGACTTGGCTTATTACTTGCAG 57.113 39.130 0.00 0.00 0.00 4.41
1138 1156 4.155826 TGGCGTGTGATTTTCCTCTTATTG 59.844 41.667 0.00 0.00 0.00 1.90
1261 1283 9.679661 TGAATGATACTGTGCCTTTTCTTATTA 57.320 29.630 0.00 0.00 0.00 0.98
1264 1286 8.856153 TGATACTGTGCCTTTTCTTATTAACA 57.144 30.769 0.00 0.00 0.00 2.41
1337 1359 4.082523 CACCCCATCCGTGTCGCT 62.083 66.667 0.00 0.00 0.00 4.93
1369 1391 4.639334 ACTTTTCGTCCTCTTCTTAACCC 58.361 43.478 0.00 0.00 0.00 4.11
1374 1396 2.427812 CGTCCTCTTCTTAACCCTCCTC 59.572 54.545 0.00 0.00 0.00 3.71
1517 1539 7.417612 ACACATCGACTGGAAATTATATTTGC 58.582 34.615 0.00 0.00 0.00 3.68
1526 1548 9.657419 ACTGGAAATTATATTTGCTCCAAAAAG 57.343 29.630 5.47 0.00 36.90 2.27
1539 1561 5.048504 TGCTCCAAAAAGACTAAGCATGAAG 60.049 40.000 0.00 0.00 35.02 3.02
1596 1618 2.545322 GGCGGGATCTACCTAAACGAAG 60.545 54.545 0.00 0.00 38.98 3.79
1614 1636 1.577468 AGTTTGCGTTGTCATGTCGA 58.423 45.000 0.00 0.00 0.00 4.20
1620 1642 2.287970 TGCGTTGTCATGTCGAACTACT 60.288 45.455 0.00 0.00 0.00 2.57
1621 1643 2.090658 GCGTTGTCATGTCGAACTACTG 59.909 50.000 0.00 0.00 0.00 2.74
1622 1644 3.305964 CGTTGTCATGTCGAACTACTGT 58.694 45.455 0.00 0.00 0.00 3.55
1623 1645 4.469552 CGTTGTCATGTCGAACTACTGTA 58.530 43.478 0.00 0.00 0.00 2.74
1624 1646 4.320164 CGTTGTCATGTCGAACTACTGTAC 59.680 45.833 0.00 0.00 0.00 2.90
1625 1647 4.430137 TGTCATGTCGAACTACTGTACC 57.570 45.455 0.00 0.00 0.00 3.34
1626 1648 4.077108 TGTCATGTCGAACTACTGTACCT 58.923 43.478 0.00 0.00 0.00 3.08
1627 1649 4.082949 TGTCATGTCGAACTACTGTACCTG 60.083 45.833 0.00 0.00 0.00 4.00
1628 1650 4.155462 GTCATGTCGAACTACTGTACCTGA 59.845 45.833 0.00 0.00 0.00 3.86
1629 1651 4.155462 TCATGTCGAACTACTGTACCTGAC 59.845 45.833 0.00 0.00 0.00 3.51
1630 1652 2.816087 TGTCGAACTACTGTACCTGACC 59.184 50.000 0.00 0.00 0.00 4.02
1631 1653 2.079158 TCGAACTACTGTACCTGACCG 58.921 52.381 0.00 0.00 0.00 4.79
1632 1654 2.079158 CGAACTACTGTACCTGACCGA 58.921 52.381 0.00 0.00 0.00 4.69
1633 1655 2.681848 CGAACTACTGTACCTGACCGAT 59.318 50.000 0.00 0.00 0.00 4.18
1634 1656 3.128242 CGAACTACTGTACCTGACCGATT 59.872 47.826 0.00 0.00 0.00 3.34
1635 1657 4.421948 GAACTACTGTACCTGACCGATTG 58.578 47.826 0.00 0.00 0.00 2.67
1636 1658 3.428532 ACTACTGTACCTGACCGATTGT 58.571 45.455 0.00 0.00 0.00 2.71
1637 1659 3.442977 ACTACTGTACCTGACCGATTGTC 59.557 47.826 0.00 0.00 44.72 3.18
1638 1660 2.526432 ACTGTACCTGACCGATTGTCT 58.474 47.619 0.00 0.00 44.75 3.41
1639 1661 2.231478 ACTGTACCTGACCGATTGTCTG 59.769 50.000 0.00 0.00 44.75 3.51
1640 1662 2.231478 CTGTACCTGACCGATTGTCTGT 59.769 50.000 0.00 0.00 44.75 3.41
1641 1663 2.631062 TGTACCTGACCGATTGTCTGTT 59.369 45.455 0.00 0.00 44.75 3.16
1642 1664 2.169832 ACCTGACCGATTGTCTGTTG 57.830 50.000 0.00 0.00 44.75 3.33
1643 1665 0.798776 CCTGACCGATTGTCTGTTGC 59.201 55.000 0.00 0.00 44.75 4.17
1644 1666 1.511850 CTGACCGATTGTCTGTTGCA 58.488 50.000 0.00 0.00 44.75 4.08
1645 1667 1.195448 CTGACCGATTGTCTGTTGCAC 59.805 52.381 0.00 0.00 44.75 4.57
1646 1668 0.517316 GACCGATTGTCTGTTGCACC 59.483 55.000 0.00 0.00 41.03 5.01
1647 1669 0.889186 ACCGATTGTCTGTTGCACCC 60.889 55.000 0.00 0.00 0.00 4.61
1648 1670 0.888736 CCGATTGTCTGTTGCACCCA 60.889 55.000 0.00 0.00 0.00 4.51
1649 1671 0.518636 CGATTGTCTGTTGCACCCAG 59.481 55.000 6.28 6.28 0.00 4.45
1650 1672 0.883833 GATTGTCTGTTGCACCCAGG 59.116 55.000 11.57 0.00 0.00 4.45
1651 1673 0.540365 ATTGTCTGTTGCACCCAGGG 60.540 55.000 2.85 2.85 0.00 4.45
1652 1674 1.932156 TTGTCTGTTGCACCCAGGGT 61.932 55.000 4.76 4.76 35.62 4.34
1653 1675 1.057275 TGTCTGTTGCACCCAGGGTA 61.057 55.000 12.21 0.00 32.11 3.69
1654 1676 0.321653 GTCTGTTGCACCCAGGGTAG 60.322 60.000 12.21 4.69 32.11 3.18
1655 1677 0.766674 TCTGTTGCACCCAGGGTAGT 60.767 55.000 12.21 0.00 32.11 2.73
1656 1678 0.110486 CTGTTGCACCCAGGGTAGTT 59.890 55.000 12.21 0.00 32.11 2.24
1657 1679 0.179004 TGTTGCACCCAGGGTAGTTG 60.179 55.000 12.21 0.00 32.11 3.16
1675 1697 1.228276 GGAGGCCCCCGATTGATTC 60.228 63.158 0.00 0.00 0.00 2.52
1697 1720 6.541111 TCATATGCTCGTGTGTAGTAGTAG 57.459 41.667 0.00 0.00 0.00 2.57
1720 1743 0.959553 GAGGCCCTCGTCGATCAATA 59.040 55.000 0.00 0.00 0.00 1.90
1728 1751 3.611549 CCTCGTCGATCAATAGATGCATG 59.388 47.826 2.46 0.00 33.72 4.06
1779 1802 6.018737 GATCGATCGATGCAAATATCTCAC 57.981 41.667 33.86 11.61 34.60 3.51
1792 1815 6.695429 CAAATATCTCACTATAGCCTCTGCA 58.305 40.000 0.00 0.00 41.13 4.41
1798 1821 4.729868 TCACTATAGCCTCTGCATACTCA 58.270 43.478 0.00 0.00 41.13 3.41
1803 1826 0.108138 GCCTCTGCATACTCAACGGT 60.108 55.000 0.00 0.00 37.47 4.83
1814 1837 0.869880 CTCAACGGTGATGCGCGATA 60.870 55.000 12.10 0.00 31.85 2.92
1816 1839 0.869880 CAACGGTGATGCGCGATAGA 60.870 55.000 12.10 0.00 39.76 1.98
1819 1842 0.436150 CGGTGATGCGCGATAGATTG 59.564 55.000 12.10 0.00 39.76 2.67
1835 1858 3.878778 AGATTGGAGAAGGTGTATGCAC 58.121 45.455 5.22 5.22 44.53 4.57
1863 1897 1.094785 CCCCCTGTTGCGAAATGTAG 58.905 55.000 0.00 0.00 0.00 2.74
1867 1901 1.398390 CCTGTTGCGAAATGTAGGAGC 59.602 52.381 0.00 0.00 0.00 4.70
1871 1905 1.526225 GCGAAATGTAGGAGCCCCC 60.526 63.158 0.00 0.00 0.00 5.40
1892 1926 2.351447 CCATACGCGGTACTGATCGATT 60.351 50.000 12.47 0.00 0.00 3.34
1893 1927 2.394545 TACGCGGTACTGATCGATTG 57.605 50.000 12.47 0.00 0.00 2.67
1922 1956 5.234466 AGACTTTGCATTACAGAGAACCT 57.766 39.130 0.00 0.00 34.59 3.50
1976 2010 2.518112 TTGCTTGCTTGGTGGCGA 60.518 55.556 0.00 0.00 34.52 5.54
1981 2015 1.453155 CTTGCTTGGTGGCGATAAGT 58.547 50.000 0.00 0.00 34.52 2.24
2012 2046 2.497675 GAGTAGAGACCCTGTTGCATCA 59.502 50.000 0.00 0.00 0.00 3.07
2014 2048 2.414994 AGAGACCCTGTTGCATCATG 57.585 50.000 0.00 0.00 0.00 3.07
2015 2049 0.737219 GAGACCCTGTTGCATCATGC 59.263 55.000 1.35 1.35 45.29 4.06
2033 2068 2.044946 GCAGTAGTTGGGGCCCTG 60.045 66.667 25.93 13.75 0.00 4.45
2034 2069 2.044946 CAGTAGTTGGGGCCCTGC 60.045 66.667 25.93 16.30 0.00 4.85
2047 2082 1.324740 GCCCTGCTTGAATCCATGCA 61.325 55.000 0.00 0.00 46.81 3.96
2055 2090 1.477553 TGAATCCATGCAAGAAGCCC 58.522 50.000 0.00 0.00 44.83 5.19
2056 2091 0.749049 GAATCCATGCAAGAAGCCCC 59.251 55.000 0.00 0.00 44.83 5.80
2057 2092 0.041535 AATCCATGCAAGAAGCCCCA 59.958 50.000 0.00 0.00 44.83 4.96
2079 2114 0.606401 CGTTGAAGAGCACCCATGGT 60.606 55.000 11.73 0.00 39.96 3.55
2145 2181 0.543277 TTGCAAGGAGCCATCTCGAT 59.457 50.000 0.00 0.00 44.83 3.59
2154 2190 2.099921 GAGCCATCTCGATGTGTACACT 59.900 50.000 25.60 12.04 37.11 3.55
2158 2194 3.243434 CCATCTCGATGTGTACACTACCC 60.243 52.174 25.60 11.38 37.11 3.69
2172 2208 2.747446 CACTACCCAGTTATTGGCACAC 59.253 50.000 0.00 0.00 46.32 3.82
2173 2209 2.006888 CTACCCAGTTATTGGCACACG 58.993 52.381 0.00 0.00 46.32 4.49
2195 2231 1.457455 CCTGCACCCCAGTTGGTTT 60.457 57.895 0.00 0.00 40.06 3.27
2204 2240 1.279271 CCCAGTTGGTTTCCTCTCGAT 59.721 52.381 0.00 0.00 0.00 3.59
2208 2244 3.927142 CAGTTGGTTTCCTCTCGATGTAC 59.073 47.826 0.00 0.00 0.00 2.90
2210 2246 4.039973 AGTTGGTTTCCTCTCGATGTACAA 59.960 41.667 0.00 0.00 0.00 2.41
2231 2267 2.901840 CCTATTGGTGCCGCGCAT 60.902 61.111 8.75 0.00 41.91 4.73
2247 2283 1.691976 CGCATGATACTCCCACCCTAA 59.308 52.381 0.00 0.00 0.00 2.69
2279 2315 2.613977 CGCAATGCCCAAAACCCAATTA 60.614 45.455 0.00 0.00 0.00 1.40
2285 2321 2.769095 GCCCAAAACCCAATTATGGCTA 59.231 45.455 0.00 0.00 46.09 3.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 3.245264 CCCTAACTCTTGTTTCCCCACAT 60.245 47.826 0.00 0.00 37.59 3.21
108 109 3.636231 CGTGGCCCTTGGTGGAGA 61.636 66.667 0.00 0.00 38.35 3.71
211 212 1.856597 ACGAAGTACACGAAGTTGCAC 59.143 47.619 16.81 0.00 37.84 4.57
302 303 6.363065 ACTGAGATTGCAATCTGGATATTGT 58.637 36.000 39.54 23.72 45.39 2.71
344 345 0.514691 GTCTGTTTCCTGCGAGCAAG 59.485 55.000 0.00 0.00 0.00 4.01
492 495 1.667724 GTTTCGATGAGATGGTGGCTG 59.332 52.381 0.00 0.00 0.00 4.85
665 672 3.338249 CAACTTACATCTGTCCCACCAG 58.662 50.000 0.00 0.00 0.00 4.00
712 719 1.343142 GCCCCATCGAAGTTTGGTTTT 59.657 47.619 2.27 0.00 31.76 2.43
902 916 2.346099 ATTTCCGCCAACAATGAACG 57.654 45.000 0.00 0.00 0.00 3.95
970 985 7.165485 TCTGCAAGTAATAAGCCAAGTCTTAA 58.835 34.615 0.00 0.00 31.72 1.85
1038 1055 7.094248 CCATTCTCCATTGTGTCAATCACTTTA 60.094 37.037 0.00 0.00 46.27 1.85
1088 1106 8.964476 AACATAACAATCATCGAATAGGACTT 57.036 30.769 0.00 0.00 0.00 3.01
1244 1266 9.906660 TTACATTGTTAATAAGAAAAGGCACAG 57.093 29.630 0.00 0.00 0.00 3.66
1315 1337 2.829914 CACGGATGGGGTGCCATG 60.830 66.667 0.00 0.00 0.00 3.66
1328 1350 1.852895 GTAGAATAAGCAGCGACACGG 59.147 52.381 0.00 0.00 0.00 4.94
1337 1359 6.282199 AGAGGACGAAAAGTAGAATAAGCA 57.718 37.500 0.00 0.00 0.00 3.91
1339 1361 8.989653 AAGAAGAGGACGAAAAGTAGAATAAG 57.010 34.615 0.00 0.00 0.00 1.73
1369 1391 7.425577 TCATTCAATAACATAATGCGAGGAG 57.574 36.000 0.00 0.00 31.98 3.69
1374 1396 7.416817 TGAGGTTCATTCAATAACATAATGCG 58.583 34.615 0.00 0.00 31.98 4.73
1513 1535 5.301551 TCATGCTTAGTCTTTTTGGAGCAAA 59.698 36.000 0.00 0.00 42.58 3.68
1517 1539 6.808008 TCTTCATGCTTAGTCTTTTTGGAG 57.192 37.500 0.00 0.00 0.00 3.86
1570 1592 3.317455 TTAGGTAGATCCCGCCACTTA 57.683 47.619 0.00 0.00 36.75 2.24
1571 1593 2.169978 GTTTAGGTAGATCCCGCCACTT 59.830 50.000 0.00 0.00 36.75 3.16
1572 1594 1.761198 GTTTAGGTAGATCCCGCCACT 59.239 52.381 0.00 0.00 36.75 4.00
1596 1618 2.034076 GTTCGACATGACAACGCAAAC 58.966 47.619 0.00 0.00 0.00 2.93
1603 1625 4.521639 AGGTACAGTAGTTCGACATGACAA 59.478 41.667 0.00 0.00 0.00 3.18
1608 1630 3.442977 GGTCAGGTACAGTAGTTCGACAT 59.557 47.826 0.00 0.00 0.00 3.06
1614 1636 3.830755 ACAATCGGTCAGGTACAGTAGTT 59.169 43.478 0.00 0.00 0.00 2.24
1628 1650 0.889186 GGGTGCAACAGACAATCGGT 60.889 55.000 3.06 0.00 39.98 4.69
1629 1651 0.888736 TGGGTGCAACAGACAATCGG 60.889 55.000 3.06 0.00 39.98 4.18
1630 1652 0.518636 CTGGGTGCAACAGACAATCG 59.481 55.000 12.98 0.00 39.98 3.34
1631 1653 0.883833 CCTGGGTGCAACAGACAATC 59.116 55.000 18.42 0.00 39.98 2.67
1632 1654 0.540365 CCCTGGGTGCAACAGACAAT 60.540 55.000 18.42 0.00 39.98 2.71
1633 1655 1.152777 CCCTGGGTGCAACAGACAA 60.153 57.895 18.42 0.00 39.98 3.18
1634 1656 1.057275 TACCCTGGGTGCAACAGACA 61.057 55.000 28.64 1.34 39.98 3.41
1635 1657 0.321653 CTACCCTGGGTGCAACAGAC 60.322 60.000 28.64 0.00 39.98 3.51
1636 1658 0.766674 ACTACCCTGGGTGCAACAGA 60.767 55.000 28.64 5.29 39.98 3.41
1637 1659 0.110486 AACTACCCTGGGTGCAACAG 59.890 55.000 28.64 18.83 39.98 3.16
1638 1660 0.179004 CAACTACCCTGGGTGCAACA 60.179 55.000 28.64 6.89 39.98 3.33
1639 1661 0.893727 CCAACTACCCTGGGTGCAAC 60.894 60.000 28.64 0.00 36.19 4.17
1640 1662 1.063070 TCCAACTACCCTGGGTGCAA 61.063 55.000 28.64 7.71 36.19 4.08
1641 1663 1.462432 TCCAACTACCCTGGGTGCA 60.462 57.895 28.64 8.52 36.19 4.57
1642 1664 1.299976 CTCCAACTACCCTGGGTGC 59.700 63.158 28.64 0.00 36.19 5.01
1643 1665 1.991230 CCTCCAACTACCCTGGGTG 59.009 63.158 28.64 19.24 36.19 4.61
1644 1666 1.923909 GCCTCCAACTACCCTGGGT 60.924 63.158 24.15 24.15 40.16 4.51
1645 1667 2.680370 GGCCTCCAACTACCCTGGG 61.680 68.421 12.28 12.28 34.46 4.45
1646 1668 2.680370 GGGCCTCCAACTACCCTGG 61.680 68.421 0.84 0.00 39.42 4.45
1647 1669 2.680370 GGGGCCTCCAACTACCCTG 61.680 68.421 0.84 0.00 42.40 4.45
1648 1670 2.286197 GGGGCCTCCAACTACCCT 60.286 66.667 0.84 0.00 42.40 4.34
1649 1671 3.417779 GGGGGCCTCCAACTACCC 61.418 72.222 20.04 4.97 42.01 3.69
1650 1672 3.793888 CGGGGGCCTCCAACTACC 61.794 72.222 25.09 1.36 37.22 3.18
1651 1673 1.632965 AATCGGGGGCCTCCAACTAC 61.633 60.000 25.09 0.00 37.22 2.73
1652 1674 1.307517 AATCGGGGGCCTCCAACTA 60.308 57.895 25.09 3.54 37.22 2.24
1653 1675 2.614013 AATCGGGGGCCTCCAACT 60.614 61.111 25.09 1.16 37.22 3.16
1654 1676 2.284515 ATCAATCGGGGGCCTCCAAC 62.285 60.000 25.09 0.00 37.22 3.77
1655 1677 1.580066 AATCAATCGGGGGCCTCCAA 61.580 55.000 25.09 1.94 37.22 3.53
1656 1678 1.994885 GAATCAATCGGGGGCCTCCA 61.995 60.000 25.09 9.68 37.22 3.86
1657 1679 1.228276 GAATCAATCGGGGGCCTCC 60.228 63.158 13.54 13.54 0.00 4.30
1675 1697 6.301687 ACTACTACTACACACGAGCATATG 57.698 41.667 0.00 0.00 0.00 1.78
1697 1720 2.630592 GATCGACGAGGGCCTCCAAC 62.631 65.000 27.36 16.79 34.83 3.77
1720 1743 3.570638 GCGCACGAGCATGCATCT 61.571 61.111 21.98 0.00 46.47 2.90
1736 1759 4.840005 GCCTCCACCTGCTACCGC 62.840 72.222 0.00 0.00 0.00 5.68
1779 1802 4.480541 CGTTGAGTATGCAGAGGCTATAG 58.519 47.826 0.00 0.00 41.91 1.31
1792 1815 1.145759 CGCGCATCACCGTTGAGTAT 61.146 55.000 8.75 0.00 34.35 2.12
1798 1821 0.032130 ATCTATCGCGCATCACCGTT 59.968 50.000 8.75 0.00 0.00 4.44
1803 1826 1.613437 TCTCCAATCTATCGCGCATCA 59.387 47.619 8.75 0.00 0.00 3.07
1814 1837 3.679917 CGTGCATACACCTTCTCCAATCT 60.680 47.826 0.00 0.00 44.40 2.40
1816 1839 2.236146 TCGTGCATACACCTTCTCCAAT 59.764 45.455 0.00 0.00 44.40 3.16
1819 1842 1.927895 CTCGTGCATACACCTTCTCC 58.072 55.000 0.00 0.00 44.40 3.71
1835 1858 3.710722 AACAGGGGGCTCTGCTCG 61.711 66.667 7.98 0.00 38.26 5.03
1844 1867 1.094785 CTACATTTCGCAACAGGGGG 58.905 55.000 0.00 0.00 0.00 5.40
1848 1871 1.398390 GGCTCCTACATTTCGCAACAG 59.602 52.381 0.00 0.00 0.00 3.16
1871 1905 0.589708 TCGATCAGTACCGCGTATGG 59.410 55.000 4.92 0.00 0.00 2.74
1872 1906 2.613730 ATCGATCAGTACCGCGTATG 57.386 50.000 4.92 0.00 0.00 2.39
1873 1907 2.551032 TCAATCGATCAGTACCGCGTAT 59.449 45.455 4.92 0.00 0.00 3.06
1892 1926 4.713553 TGTAATGCAAAGTCTCCAACTCA 58.286 39.130 0.00 0.00 37.17 3.41
1893 1927 4.997395 TCTGTAATGCAAAGTCTCCAACTC 59.003 41.667 0.00 0.00 37.17 3.01
1922 1956 0.944386 TCGCATCGATCGATCAGTCA 59.056 50.000 27.20 7.55 31.62 3.41
1976 2010 3.190079 TCTACTCGCGTGTACGACTTAT 58.810 45.455 16.41 0.00 43.02 1.73
1981 2015 0.994995 GTCTCTACTCGCGTGTACGA 59.005 55.000 16.41 15.50 43.02 3.43
2012 2046 2.438434 GCCCCAACTACTGCGCAT 60.438 61.111 12.24 3.79 0.00 4.73
2015 2049 3.717294 AGGGCCCCAACTACTGCG 61.717 66.667 21.43 0.00 0.00 5.18
2021 2055 2.097978 ATTCAAGCAGGGCCCCAACT 62.098 55.000 21.43 11.09 0.00 3.16
2033 2068 2.537401 GCTTCTTGCATGGATTCAAGC 58.463 47.619 8.78 8.78 42.31 4.01
2034 2069 2.159142 GGGCTTCTTGCATGGATTCAAG 60.159 50.000 0.00 0.00 45.15 3.02
2047 2082 2.304761 TCTTCAACGTATGGGGCTTCTT 59.695 45.455 0.00 0.00 0.00 2.52
2055 2090 1.338674 TGGGTGCTCTTCAACGTATGG 60.339 52.381 0.00 0.00 31.58 2.74
2056 2091 2.093306 TGGGTGCTCTTCAACGTATG 57.907 50.000 0.00 0.00 31.58 2.39
2057 2092 2.632377 CATGGGTGCTCTTCAACGTAT 58.368 47.619 0.00 0.00 31.58 3.06
2145 2181 4.563993 GCCAATAACTGGGTAGTGTACACA 60.564 45.833 27.06 10.99 46.54 3.72
2154 2190 1.339247 CCGTGTGCCAATAACTGGGTA 60.339 52.381 0.00 0.00 46.54 3.69
2158 2194 1.735571 GGTACCGTGTGCCAATAACTG 59.264 52.381 0.00 0.00 38.20 3.16
2172 2208 2.890766 AACTGGGGTGCAGGTACCG 61.891 63.158 6.18 2.66 41.79 4.02
2173 2209 1.303317 CAACTGGGGTGCAGGTACC 60.303 63.158 2.73 2.73 40.10 3.34
2195 2231 4.180377 AGGGTATTGTACATCGAGAGGA 57.820 45.455 0.00 0.00 0.00 3.71
2228 2264 3.617531 CGATTAGGGTGGGAGTATCATGC 60.618 52.174 0.00 0.00 36.25 4.06
2231 2267 2.090943 ACCGATTAGGGTGGGAGTATCA 60.091 50.000 0.00 0.00 46.96 2.15


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

AutoCloner maintained by Alex Coulton.