Multiple sequence alignment - TraesCS5D01G091800

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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 TraesCS5D01G091800 chr5D 100.000 2231 0 0 1 2231 99419757 99417527 0.000000e+00 4120.0
1 TraesCS5D01G091800 chr5D 95.556 45 2 0 1189 1233 99350859 99350815 3.070000e-09 73.1
2 TraesCS5D01G091800 chr5A 91.410 2177 117 34 84 2231 103568183 103570318 0.000000e+00 2920.0
3 TraesCS5D01G091800 chr5A 91.129 124 11 0 1065 1188 103901734 103901857 3.810000e-38 169.0
4 TraesCS5D01G091800 chr5A 75.789 380 62 15 1688 2053 57649315 57648952 4.930000e-37 165.0
5 TraesCS5D01G091800 chr5A 94.000 50 3 0 1184 1233 103902126 103902175 2.380000e-10 76.8
6 TraesCS5D01G091800 chr5B 92.537 1273 55 19 567 1838 108551815 108550582 0.000000e+00 1788.0
7 TraesCS5D01G091800 chr5B 90.328 548 35 15 37 568 108552467 108551922 0.000000e+00 702.0
8 TraesCS5D01G091800 chr5B 89.431 369 27 9 1870 2231 108550579 108550216 2.610000e-124 455.0
9 TraesCS5D01G091800 chr2A 84.790 309 42 3 1717 2022 367684671 367684977 2.780000e-79 305.0
10 TraesCS5D01G091800 chr2A 80.427 281 36 12 1747 2023 551494240 551493975 1.750000e-46 196.0
11 TraesCS5D01G091800 chr2B 81.034 290 49 4 1716 2002 680519473 680519759 2.230000e-55 226.0
12 TraesCS5D01G091800 chr1B 76.571 350 59 14 1689 2021 656054512 656054855 1.060000e-38 171.0
13 TraesCS5D01G091800 chr7B 83.333 180 27 3 1861 2039 470839779 470839956 1.770000e-36 163.0
14 TraesCS5D01G091800 chr7D 75.812 277 56 8 1791 2063 235394565 235394296 1.800000e-26 130.0
15 TraesCS5D01G091800 chr4B 86.301 73 10 0 1157 1229 445240823 445240895 1.840000e-11 80.5
16 TraesCS5D01G091800 chr3D 100.000 30 0 0 1015 1044 608512067 608512038 3.090000e-04 56.5
17 TraesCS5D01G091800 chr3B 100.000 30 0 0 1015 1044 818926808 818926779 3.090000e-04 56.5
18 TraesCS5D01G091800 chr3A 100.000 30 0 0 1015 1044 741625240 741625211 3.090000e-04 56.5


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 TraesCS5D01G091800 chr5D 99417527 99419757 2230 True 4120.000000 4120 100.000000 1 2231 1 chr5D.!!$R2 2230
1 TraesCS5D01G091800 chr5A 103568183 103570318 2135 False 2920.000000 2920 91.410000 84 2231 1 chr5A.!!$F1 2147
2 TraesCS5D01G091800 chr5B 108550216 108552467 2251 True 981.666667 1788 90.765333 37 2231 3 chr5B.!!$R1 2194

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
427 452 0.250513 AGTTTGACTCGATCTGGGGC 59.749 55.0 0.0 0.0 0.0 5.8 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 1523 0.03563 ATGGAAGTGACTGGAGCAGC 60.036 55.0 0.0 0.0 34.37 5.25 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
23 24 4.862641 AGGGTGCTGGATATAAAAGTGT 57.137 40.909 0.00 0.00 0.00 3.55
24 25 5.193099 AGGGTGCTGGATATAAAAGTGTT 57.807 39.130 0.00 0.00 0.00 3.32
25 26 4.949856 AGGGTGCTGGATATAAAAGTGTTG 59.050 41.667 0.00 0.00 0.00 3.33
26 27 4.705023 GGGTGCTGGATATAAAAGTGTTGT 59.295 41.667 0.00 0.00 0.00 3.32
27 28 5.185056 GGGTGCTGGATATAAAAGTGTTGTT 59.815 40.000 0.00 0.00 0.00 2.83
28 29 6.092748 GGTGCTGGATATAAAAGTGTTGTTG 58.907 40.000 0.00 0.00 0.00 3.33
29 30 6.294508 GGTGCTGGATATAAAAGTGTTGTTGT 60.295 38.462 0.00 0.00 0.00 3.32
30 31 6.582295 GTGCTGGATATAAAAGTGTTGTTGTG 59.418 38.462 0.00 0.00 0.00 3.33
31 32 5.572896 GCTGGATATAAAAGTGTTGTTGTGC 59.427 40.000 0.00 0.00 0.00 4.57
32 33 6.641169 TGGATATAAAAGTGTTGTTGTGCA 57.359 33.333 0.00 0.00 0.00 4.57
33 34 7.043961 TGGATATAAAAGTGTTGTTGTGCAA 57.956 32.000 0.00 0.00 34.16 4.08
34 35 7.144661 TGGATATAAAAGTGTTGTTGTGCAAG 58.855 34.615 0.00 0.00 37.83 4.01
35 36 6.089417 GGATATAAAAGTGTTGTTGTGCAAGC 59.911 38.462 0.00 0.00 37.83 4.01
51 52 3.436704 TGCAAGCTGAGAATTTAAGGTCG 59.563 43.478 0.00 0.00 0.00 4.79
55 56 5.153950 AGCTGAGAATTTAAGGTCGAACT 57.846 39.130 0.00 0.00 0.00 3.01
57 58 4.929808 GCTGAGAATTTAAGGTCGAACTGA 59.070 41.667 2.28 0.00 0.00 3.41
62 63 6.702329 AGAATTTAAGGTCGAACTGATCACT 58.298 36.000 2.28 0.00 0.00 3.41
66 67 2.520069 AGGTCGAACTGATCACTGTCT 58.480 47.619 0.00 0.00 0.00 3.41
68 69 2.029828 GGTCGAACTGATCACTGTCTGT 60.030 50.000 0.00 0.00 32.52 3.41
71 72 2.029918 CGAACTGATCACTGTCTGTGGA 60.030 50.000 9.69 0.00 46.20 4.02
72 73 3.321497 GAACTGATCACTGTCTGTGGAC 58.679 50.000 9.69 5.46 46.20 4.02
73 74 2.603021 ACTGATCACTGTCTGTGGACT 58.397 47.619 9.69 0.00 46.20 3.85
74 75 2.560542 ACTGATCACTGTCTGTGGACTC 59.439 50.000 9.69 5.80 46.20 3.36
76 77 0.891373 ATCACTGTCTGTGGACTCCG 59.109 55.000 9.69 0.00 46.20 4.63
77 78 0.467474 TCACTGTCTGTGGACTCCGT 60.467 55.000 9.69 0.00 46.20 4.69
78 79 0.319040 CACTGTCTGTGGACTCCGTG 60.319 60.000 2.02 0.00 42.68 4.94
81 82 0.387929 TGTCTGTGGACTCCGTGAAC 59.612 55.000 0.00 0.00 42.54 3.18
82 83 0.674534 GTCTGTGGACTCCGTGAACT 59.325 55.000 0.00 0.00 39.24 3.01
83 84 0.959553 TCTGTGGACTCCGTGAACTC 59.040 55.000 0.00 0.00 0.00 3.01
84 85 0.387367 CTGTGGACTCCGTGAACTCG 60.387 60.000 0.00 0.00 0.00 4.18
85 86 1.105167 TGTGGACTCCGTGAACTCGT 61.105 55.000 0.00 0.00 0.00 4.18
86 87 0.877071 GTGGACTCCGTGAACTCGTA 59.123 55.000 0.00 0.00 0.00 3.43
102 103 0.682852 CGTATAGGGGCCGGATTTGA 59.317 55.000 5.05 0.00 0.00 2.69
114 115 3.548014 GCCGGATTTGATAATCGTGGTTG 60.548 47.826 5.05 0.00 40.91 3.77
120 121 7.597369 CGGATTTGATAATCGTGGTTGTAGATA 59.403 37.037 0.00 0.00 40.91 1.98
122 123 8.603242 ATTTGATAATCGTGGTTGTAGATACC 57.397 34.615 0.00 0.00 36.17 2.73
127 128 9.871238 GATAATCGTGGTTGTAGATACCATTAT 57.129 33.333 0.00 0.00 46.63 1.28
129 130 8.974060 AATCGTGGTTGTAGATACCATTATTT 57.026 30.769 0.00 0.00 46.63 1.40
131 132 8.795842 TCGTGGTTGTAGATACCATTATTTTT 57.204 30.769 0.00 0.00 46.63 1.94
175 181 5.758784 GGTTAAGTGCTGGATACCTATCAAC 59.241 44.000 0.00 0.00 34.40 3.18
178 184 2.438021 GTGCTGGATACCTATCAACCCA 59.562 50.000 0.00 0.00 34.40 4.51
231 237 2.096417 GCGTTGTCAGTGTCCATTGTAC 60.096 50.000 0.00 0.00 0.00 2.90
232 238 3.390135 CGTTGTCAGTGTCCATTGTACT 58.610 45.455 0.00 0.00 0.00 2.73
233 239 3.428870 CGTTGTCAGTGTCCATTGTACTC 59.571 47.826 0.00 0.00 0.00 2.59
234 240 3.678056 TGTCAGTGTCCATTGTACTCC 57.322 47.619 0.00 0.00 0.00 3.85
235 241 3.239449 TGTCAGTGTCCATTGTACTCCT 58.761 45.455 0.00 0.00 0.00 3.69
236 242 4.412843 TGTCAGTGTCCATTGTACTCCTA 58.587 43.478 0.00 0.00 0.00 2.94
237 243 5.023452 TGTCAGTGTCCATTGTACTCCTAT 58.977 41.667 0.00 0.00 0.00 2.57
238 244 6.192044 TGTCAGTGTCCATTGTACTCCTATA 58.808 40.000 0.00 0.00 0.00 1.31
354 379 1.059838 CTACGTCGCGTCGTGATCA 59.940 57.895 34.85 18.16 43.93 2.92
427 452 0.250513 AGTTTGACTCGATCTGGGGC 59.749 55.000 0.00 0.00 0.00 5.80
470 495 3.743396 GGCGATTCAAGATGATACAGTCC 59.257 47.826 0.00 0.00 0.00 3.85
537 562 5.220416 CGCCTACAAAGTTTACTGCTACATC 60.220 44.000 0.00 0.00 0.00 3.06
754 887 6.733334 ACACCCCCATAAATTATTTGGAAAGT 59.267 34.615 0.00 0.00 31.94 2.66
774 907 0.370273 GATGCGCTACCAAACAGACG 59.630 55.000 9.73 0.00 0.00 4.18
822 955 8.862085 AGCTACTTACTTAATCAACCTCTATCC 58.138 37.037 0.00 0.00 0.00 2.59
846 979 4.444591 CCTCTCCTCTCCAATCAAATCCAG 60.445 50.000 0.00 0.00 0.00 3.86
945 1078 1.069906 CCTCAACGACCAAAAGCGAAG 60.070 52.381 0.00 0.00 0.00 3.79
950 1083 0.512952 CGACCAAAAGCGAAGACAGG 59.487 55.000 0.00 0.00 0.00 4.00
1382 1518 3.989817 CCAAACAGCTTCCATTAGTTTGC 59.010 43.478 14.76 0.00 44.51 3.68
1383 1519 4.262164 CCAAACAGCTTCCATTAGTTTGCT 60.262 41.667 14.76 0.00 44.51 3.91
1384 1520 4.773323 AACAGCTTCCATTAGTTTGCTC 57.227 40.909 0.00 0.00 0.00 4.26
1385 1521 4.026356 ACAGCTTCCATTAGTTTGCTCT 57.974 40.909 0.00 0.00 0.00 4.09
1386 1522 4.006319 ACAGCTTCCATTAGTTTGCTCTC 58.994 43.478 0.00 0.00 0.00 3.20
1387 1523 3.063180 CAGCTTCCATTAGTTTGCTCTCG 59.937 47.826 0.00 0.00 0.00 4.04
1474 1610 1.996191 GCTAGTCCTCTTCGTTGCAAG 59.004 52.381 0.00 0.00 0.00 4.01
1481 1618 2.031683 CCTCTTCGTTGCAAGTTTTCGT 59.968 45.455 0.00 0.00 0.00 3.85
1486 1623 4.809455 TCGTTGCAAGTTTTCGTTTTTC 57.191 36.364 0.00 0.00 0.00 2.29
1488 1625 4.918583 TCGTTGCAAGTTTTCGTTTTTCTT 59.081 33.333 0.00 0.00 0.00 2.52
1489 1626 5.402867 TCGTTGCAAGTTTTCGTTTTTCTTT 59.597 32.000 0.00 0.00 0.00 2.52
1490 1627 6.068300 CGTTGCAAGTTTTCGTTTTTCTTTT 58.932 32.000 0.00 0.00 0.00 2.27
1534 1671 6.483687 ACTAGTGTGTTCAAATTCGTGAAAC 58.516 36.000 0.00 0.00 39.18 2.78
1536 1673 5.890334 AGTGTGTTCAAATTCGTGAAACAT 58.110 33.333 0.00 0.00 39.18 2.71
1537 1674 5.743398 AGTGTGTTCAAATTCGTGAAACATG 59.257 36.000 0.00 0.00 39.18 3.21
1542 1679 6.983307 TGTTCAAATTCGTGAAACATGGAAAT 59.017 30.769 0.00 0.00 39.18 2.17
1543 1680 7.042858 TGTTCAAATTCGTGAAACATGGAAATG 60.043 33.333 0.00 0.00 39.18 2.32
1545 1682 6.640499 TCAAATTCGTGAAACATGGAAATGTC 59.360 34.615 0.00 0.00 35.74 3.06
1546 1683 3.804518 TCGTGAAACATGGAAATGTCG 57.195 42.857 0.00 0.00 35.74 4.35
1547 1684 3.394719 TCGTGAAACATGGAAATGTCGA 58.605 40.909 0.00 0.00 35.74 4.20
1548 1685 3.185594 TCGTGAAACATGGAAATGTCGAC 59.814 43.478 9.11 9.11 35.74 4.20
1549 1686 3.059257 CGTGAAACATGGAAATGTCGACA 60.059 43.478 22.48 22.48 35.74 4.35
1550 1687 4.219033 GTGAAACATGGAAATGTCGACAC 58.781 43.478 22.71 8.79 36.32 3.67
1551 1688 4.024048 GTGAAACATGGAAATGTCGACACT 60.024 41.667 22.71 7.18 36.32 3.55
1552 1689 4.578516 TGAAACATGGAAATGTCGACACTT 59.421 37.500 22.71 17.67 32.87 3.16
1553 1690 5.067153 TGAAACATGGAAATGTCGACACTTT 59.933 36.000 22.71 20.47 32.87 2.66
1554 1691 5.514274 AACATGGAAATGTCGACACTTTT 57.486 34.783 22.71 18.33 33.64 2.27
1555 1692 6.627395 AACATGGAAATGTCGACACTTTTA 57.373 33.333 22.71 9.78 31.66 1.52
1556 1693 6.817765 ACATGGAAATGTCGACACTTTTAT 57.182 33.333 22.71 11.69 31.66 1.40
1557 1694 7.214467 ACATGGAAATGTCGACACTTTTATT 57.786 32.000 22.71 7.25 31.66 1.40
1558 1695 7.657336 ACATGGAAATGTCGACACTTTTATTT 58.343 30.769 22.71 16.02 31.66 1.40
1559 1696 8.141268 ACATGGAAATGTCGACACTTTTATTTT 58.859 29.630 22.71 15.27 31.66 1.82
1560 1697 8.977505 CATGGAAATGTCGACACTTTTATTTTT 58.022 29.630 22.71 14.50 31.66 1.94
1562 1699 9.672086 TGGAAATGTCGACACTTTTATTTTTAG 57.328 29.630 22.71 0.00 31.66 1.85
1563 1700 9.887406 GGAAATGTCGACACTTTTATTTTTAGA 57.113 29.630 22.71 0.00 31.66 2.10
1566 1703 9.673454 AATGTCGACACTTTTATTTTTAGAACC 57.327 29.630 22.71 0.00 0.00 3.62
1567 1704 7.346695 TGTCGACACTTTTATTTTTAGAACCG 58.653 34.615 15.76 0.00 0.00 4.44
1597 1734 5.038033 CGACAAAATTCGGGTTCAGAAAAA 58.962 37.500 0.00 0.00 35.26 1.94
1638 1775 4.500035 GGTTTAGAAAACGGTTTGCATCCA 60.500 41.667 13.86 0.00 0.00 3.41
1668 1805 9.528018 ACTGAAAATTGTTCGTTGTTCAATTAT 57.472 25.926 0.00 0.00 39.72 1.28
1730 1872 1.671328 TGACATTTTTGTCGGTCGCAA 59.329 42.857 2.05 0.00 41.43 4.85
1785 1927 7.687445 TCGTACCAAGTTTTAGAAGTTGAAAC 58.313 34.615 13.68 10.17 45.11 2.78
1834 1976 0.655733 ATTATTTTGTCGGCCGCTCG 59.344 50.000 23.51 0.00 0.00 5.03
1838 1980 4.764336 TTGTCGGCCGCTCGTACG 62.764 66.667 23.51 9.53 0.00 3.67
1840 1982 4.766088 GTCGGCCGCTCGTACGTT 62.766 66.667 23.51 0.00 0.00 3.99
1841 1983 4.465512 TCGGCCGCTCGTACGTTC 62.466 66.667 23.51 7.27 0.00 3.95
1843 1985 4.424566 GGCCGCTCGTACGTTCCA 62.425 66.667 16.05 0.00 0.00 3.53
1844 1986 2.431260 GCCGCTCGTACGTTCCAA 60.431 61.111 16.05 0.00 0.00 3.53
1845 1987 2.023223 GCCGCTCGTACGTTCCAAA 61.023 57.895 16.05 0.00 0.00 3.28
1846 1988 1.559149 GCCGCTCGTACGTTCCAAAA 61.559 55.000 16.05 0.00 0.00 2.44
1847 1989 0.437295 CCGCTCGTACGTTCCAAAAG 59.563 55.000 16.05 4.29 0.00 2.27
1848 1990 1.134226 CGCTCGTACGTTCCAAAAGT 58.866 50.000 16.05 0.00 0.00 2.66
1849 1991 1.523934 CGCTCGTACGTTCCAAAAGTT 59.476 47.619 16.05 0.00 0.00 2.66
1850 1992 2.658224 CGCTCGTACGTTCCAAAAGTTG 60.658 50.000 16.05 0.00 0.00 3.16
1851 1993 2.540931 GCTCGTACGTTCCAAAAGTTGA 59.459 45.455 16.05 0.00 0.00 3.18
1852 1994 3.001533 GCTCGTACGTTCCAAAAGTTGAA 59.998 43.478 16.05 0.00 0.00 2.69
1853 1995 4.494526 GCTCGTACGTTCCAAAAGTTGAAA 60.495 41.667 16.05 0.00 0.00 2.69
1854 1996 4.896080 TCGTACGTTCCAAAAGTTGAAAC 58.104 39.130 16.05 0.00 0.00 2.78
1855 1997 4.391216 TCGTACGTTCCAAAAGTTGAAACA 59.609 37.500 16.05 0.00 0.00 2.83
1856 1998 5.064962 TCGTACGTTCCAAAAGTTGAAACAT 59.935 36.000 16.05 0.00 0.00 2.71
1857 1999 6.257411 TCGTACGTTCCAAAAGTTGAAACATA 59.743 34.615 16.05 0.00 0.00 2.29
1858 2000 6.906143 CGTACGTTCCAAAAGTTGAAACATAA 59.094 34.615 7.22 0.00 0.00 1.90
1859 2001 7.097329 CGTACGTTCCAAAAGTTGAAACATAAC 60.097 37.037 7.22 0.00 0.00 1.89
1860 2002 5.740099 ACGTTCCAAAAGTTGAAACATAACG 59.260 36.000 0.00 0.00 41.08 3.18
1861 2003 5.966503 CGTTCCAAAAGTTGAAACATAACGA 59.033 36.000 0.00 0.00 38.49 3.85
1862 2004 6.469595 CGTTCCAAAAGTTGAAACATAACGAA 59.530 34.615 0.00 0.00 38.49 3.85
1863 2005 7.008447 CGTTCCAAAAGTTGAAACATAACGAAA 59.992 33.333 0.00 0.00 38.49 3.46
1864 2006 8.648968 GTTCCAAAAGTTGAAACATAACGAAAA 58.351 29.630 0.00 0.00 33.39 2.29
1865 2007 8.934507 TCCAAAAGTTGAAACATAACGAAAAT 57.065 26.923 0.00 0.00 33.39 1.82
1866 2008 9.372369 TCCAAAAGTTGAAACATAACGAAAATT 57.628 25.926 0.00 0.00 33.39 1.82
1867 2009 9.980780 CCAAAAGTTGAAACATAACGAAAATTT 57.019 25.926 0.00 0.00 33.39 1.82
1920 2095 4.643784 GTCTCATTTGAAAGCCCTCATCAT 59.356 41.667 0.00 0.00 0.00 2.45
1936 2111 7.154656 CCCTCATCATCAGAAACACGAATATA 58.845 38.462 0.00 0.00 0.00 0.86
2002 2177 6.866010 AGATTGAAAAATCCAAAGCCAAAC 57.134 33.333 0.00 0.00 0.00 2.93
2060 2235 2.717639 AATCCTCTTCCATGGGAACG 57.282 50.000 13.02 0.00 36.71 3.95
2078 2254 1.283613 ACGGTGGGGAATTTGCATCTA 59.716 47.619 0.00 0.00 0.00 1.98
2105 2286 2.143876 AGTCCCCACATTACCATTGC 57.856 50.000 0.00 0.00 0.00 3.56
2186 2367 1.866601 GCCACAAAAACATGCCTTGAC 59.133 47.619 8.53 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.515512 ACACTTTTATATCCAGCACCCTAT 57.484 37.500 0.00 0.00 0.00 2.57
1 2 5.968676 ACACTTTTATATCCAGCACCCTA 57.031 39.130 0.00 0.00 0.00 3.53
2 3 4.862641 ACACTTTTATATCCAGCACCCT 57.137 40.909 0.00 0.00 0.00 4.34
3 4 4.705023 ACAACACTTTTATATCCAGCACCC 59.295 41.667 0.00 0.00 0.00 4.61
4 5 5.897377 ACAACACTTTTATATCCAGCACC 57.103 39.130 0.00 0.00 0.00 5.01
5 6 6.582295 CACAACAACACTTTTATATCCAGCAC 59.418 38.462 0.00 0.00 0.00 4.40
6 7 6.676950 CACAACAACACTTTTATATCCAGCA 58.323 36.000 0.00 0.00 0.00 4.41
7 8 5.572896 GCACAACAACACTTTTATATCCAGC 59.427 40.000 0.00 0.00 0.00 4.85
8 9 6.676950 TGCACAACAACACTTTTATATCCAG 58.323 36.000 0.00 0.00 0.00 3.86
9 10 6.641169 TGCACAACAACACTTTTATATCCA 57.359 33.333 0.00 0.00 0.00 3.41
10 11 6.089417 GCTTGCACAACAACACTTTTATATCC 59.911 38.462 0.00 0.00 33.68 2.59
11 12 6.863126 AGCTTGCACAACAACACTTTTATATC 59.137 34.615 0.00 0.00 33.68 1.63
12 13 6.642131 CAGCTTGCACAACAACACTTTTATAT 59.358 34.615 0.00 0.00 33.68 0.86
13 14 5.976534 CAGCTTGCACAACAACACTTTTATA 59.023 36.000 0.00 0.00 33.68 0.98
14 15 4.805192 CAGCTTGCACAACAACACTTTTAT 59.195 37.500 0.00 0.00 33.68 1.40
15 16 4.082517 TCAGCTTGCACAACAACACTTTTA 60.083 37.500 0.00 0.00 33.68 1.52
16 17 2.995258 CAGCTTGCACAACAACACTTTT 59.005 40.909 0.00 0.00 33.68 2.27
17 18 2.230992 TCAGCTTGCACAACAACACTTT 59.769 40.909 0.00 0.00 33.68 2.66
18 19 1.818060 TCAGCTTGCACAACAACACTT 59.182 42.857 0.00 0.00 33.68 3.16
19 20 1.402968 CTCAGCTTGCACAACAACACT 59.597 47.619 0.00 0.00 33.68 3.55
20 21 1.401552 TCTCAGCTTGCACAACAACAC 59.598 47.619 0.00 0.00 33.68 3.32
21 22 1.748950 TCTCAGCTTGCACAACAACA 58.251 45.000 0.00 0.00 33.68 3.33
22 23 2.849880 TTCTCAGCTTGCACAACAAC 57.150 45.000 0.00 0.00 33.68 3.32
23 24 4.389890 AAATTCTCAGCTTGCACAACAA 57.610 36.364 0.00 0.00 36.62 2.83
24 25 5.507817 CCTTAAATTCTCAGCTTGCACAACA 60.508 40.000 0.00 0.00 0.00 3.33
25 26 4.919754 CCTTAAATTCTCAGCTTGCACAAC 59.080 41.667 0.00 0.00 0.00 3.32
26 27 4.584325 ACCTTAAATTCTCAGCTTGCACAA 59.416 37.500 0.00 0.00 0.00 3.33
27 28 4.144297 ACCTTAAATTCTCAGCTTGCACA 58.856 39.130 0.00 0.00 0.00 4.57
28 29 4.670221 CGACCTTAAATTCTCAGCTTGCAC 60.670 45.833 0.00 0.00 0.00 4.57
29 30 3.436704 CGACCTTAAATTCTCAGCTTGCA 59.563 43.478 0.00 0.00 0.00 4.08
30 31 3.684788 TCGACCTTAAATTCTCAGCTTGC 59.315 43.478 0.00 0.00 0.00 4.01
31 32 5.409826 AGTTCGACCTTAAATTCTCAGCTTG 59.590 40.000 0.00 0.00 0.00 4.01
32 33 5.409826 CAGTTCGACCTTAAATTCTCAGCTT 59.590 40.000 0.00 0.00 0.00 3.74
33 34 4.932200 CAGTTCGACCTTAAATTCTCAGCT 59.068 41.667 0.00 0.00 0.00 4.24
34 35 4.929808 TCAGTTCGACCTTAAATTCTCAGC 59.070 41.667 0.00 0.00 0.00 4.26
35 36 6.813649 TGATCAGTTCGACCTTAAATTCTCAG 59.186 38.462 0.00 0.00 0.00 3.35
57 58 1.823648 ACGGAGTCCACAGACAGTGAT 60.824 52.381 10.49 0.00 46.11 3.06
62 63 0.387929 GTTCACGGAGTCCACAGACA 59.612 55.000 10.49 0.00 46.15 3.41
66 67 1.105167 ACGAGTTCACGGAGTCCACA 61.105 55.000 10.49 0.00 41.61 4.17
68 69 1.830279 ATACGAGTTCACGGAGTCCA 58.170 50.000 10.49 0.00 41.61 4.02
69 70 2.290093 CCTATACGAGTTCACGGAGTCC 59.710 54.545 0.00 0.00 41.61 3.85
72 73 1.607628 CCCCTATACGAGTTCACGGAG 59.392 57.143 0.00 0.00 37.61 4.63
73 74 1.683943 CCCCTATACGAGTTCACGGA 58.316 55.000 0.00 0.00 37.61 4.69
74 75 0.031721 GCCCCTATACGAGTTCACGG 59.968 60.000 0.00 0.00 37.61 4.94
76 77 0.031721 CGGCCCCTATACGAGTTCAC 59.968 60.000 0.00 0.00 0.00 3.18
77 78 1.111116 CCGGCCCCTATACGAGTTCA 61.111 60.000 0.00 0.00 0.00 3.18
78 79 0.825010 TCCGGCCCCTATACGAGTTC 60.825 60.000 0.00 0.00 0.00 3.01
81 82 0.974383 AAATCCGGCCCCTATACGAG 59.026 55.000 0.00 0.00 0.00 4.18
82 83 0.682852 CAAATCCGGCCCCTATACGA 59.317 55.000 0.00 0.00 0.00 3.43
83 84 0.682852 TCAAATCCGGCCCCTATACG 59.317 55.000 0.00 0.00 0.00 3.06
84 85 4.563140 TTATCAAATCCGGCCCCTATAC 57.437 45.455 0.00 0.00 0.00 1.47
85 86 4.141801 CGATTATCAAATCCGGCCCCTATA 60.142 45.833 0.00 0.00 38.66 1.31
86 87 3.370527 CGATTATCAAATCCGGCCCCTAT 60.371 47.826 0.00 0.00 38.66 2.57
129 130 4.022416 CCAACCTCATCCATCGTTGAAAAA 60.022 41.667 0.00 0.00 38.25 1.94
131 132 3.081061 CCAACCTCATCCATCGTTGAAA 58.919 45.455 0.00 0.00 38.25 2.69
134 135 2.113860 ACCAACCTCATCCATCGTTG 57.886 50.000 0.00 0.00 36.26 4.10
175 181 2.639286 GCGTGCACAAACTCTGGG 59.361 61.111 18.64 0.00 0.00 4.45
178 184 1.065551 GAAAAGGCGTGCACAAACTCT 59.934 47.619 18.64 3.22 0.00 3.24
231 237 3.426963 GCGCACTAGCTAGCTTATAGGAG 60.427 52.174 24.88 15.32 39.10 3.69
232 238 2.488545 GCGCACTAGCTAGCTTATAGGA 59.511 50.000 24.88 1.94 39.10 2.94
233 239 2.729467 CGCGCACTAGCTAGCTTATAGG 60.729 54.545 24.88 11.17 39.10 2.57
234 240 2.510874 CGCGCACTAGCTAGCTTATAG 58.489 52.381 24.88 16.88 39.10 1.31
235 241 1.199327 CCGCGCACTAGCTAGCTTATA 59.801 52.381 24.88 3.66 39.10 0.98
236 242 0.039074 CCGCGCACTAGCTAGCTTAT 60.039 55.000 24.88 8.71 39.10 1.73
237 243 1.359117 CCGCGCACTAGCTAGCTTA 59.641 57.895 24.88 8.09 39.10 3.09
238 244 2.105128 CCGCGCACTAGCTAGCTT 59.895 61.111 24.88 1.98 39.10 3.74
354 379 0.391597 AAGTCACCGTCCGTGTGATT 59.608 50.000 12.00 7.16 43.98 2.57
470 495 1.441729 ACGGATCCACGTAGCATGG 59.558 57.895 13.41 0.00 46.58 3.66
537 562 0.593128 CGGCTCTGTTTGTTGGGAAG 59.407 55.000 0.00 0.00 0.00 3.46
732 865 7.430760 TCACTTTCCAAATAATTTATGGGGG 57.569 36.000 7.26 2.73 34.89 5.40
733 866 7.442062 GCATCACTTTCCAAATAATTTATGGGG 59.558 37.037 7.26 4.64 34.89 4.96
754 887 1.438651 GTCTGTTTGGTAGCGCATCA 58.561 50.000 11.47 0.94 0.00 3.07
774 907 7.807680 AGCTTAACTAAGACTATTGTTTGTGC 58.192 34.615 0.54 0.00 35.33 4.57
822 955 3.181446 GGATTTGATTGGAGAGGAGAGGG 60.181 52.174 0.00 0.00 0.00 4.30
846 979 2.276740 CAAGGTGGATGAGGGGGC 59.723 66.667 0.00 0.00 0.00 5.80
945 1078 1.261480 TGTGCTCTCTTCTCCCTGTC 58.739 55.000 0.00 0.00 0.00 3.51
950 1083 2.105006 TGCAATGTGCTCTCTTCTCC 57.895 50.000 1.43 0.00 45.31 3.71
1232 1368 3.119173 AGCAGAGAAGAGATCAAACCGAG 60.119 47.826 0.00 0.00 0.00 4.63
1382 1518 1.153862 GTGACTGGAGCAGCGAGAG 60.154 63.158 0.00 0.00 34.37 3.20
1383 1519 1.181741 AAGTGACTGGAGCAGCGAGA 61.182 55.000 0.00 0.00 34.37 4.04
1384 1520 0.735632 GAAGTGACTGGAGCAGCGAG 60.736 60.000 0.00 0.00 34.37 5.03
1385 1521 1.290324 GAAGTGACTGGAGCAGCGA 59.710 57.895 0.00 0.00 34.37 4.93
1386 1522 1.739562 GGAAGTGACTGGAGCAGCG 60.740 63.158 0.00 0.00 34.37 5.18
1387 1523 0.035630 ATGGAAGTGACTGGAGCAGC 60.036 55.000 0.00 0.00 34.37 5.25
1500 1637 8.905103 ATTTGAACACACTAGTTAACAAACAC 57.095 30.769 8.61 0.00 31.97 3.32
1509 1646 6.671614 TTCACGAATTTGAACACACTAGTT 57.328 33.333 0.00 0.00 30.29 2.24
1534 1671 8.519492 AAAATAAAAGTGTCGACATTTCCATG 57.481 30.769 24.20 0.00 36.34 3.66
1536 1673 9.672086 CTAAAAATAAAAGTGTCGACATTTCCA 57.328 29.630 24.20 15.89 0.00 3.53
1537 1674 9.887406 TCTAAAAATAAAAGTGTCGACATTTCC 57.113 29.630 24.20 10.95 0.00 3.13
1542 1679 7.224362 TCGGTTCTAAAAATAAAAGTGTCGACA 59.776 33.333 15.76 15.76 0.00 4.35
1543 1680 7.566709 TCGGTTCTAAAAATAAAAGTGTCGAC 58.433 34.615 9.11 9.11 0.00 4.20
1545 1682 8.770850 TTTCGGTTCTAAAAATAAAAGTGTCG 57.229 30.769 0.00 0.00 0.00 4.35
1549 1686 9.389570 CGACATTTCGGTTCTAAAAATAAAAGT 57.610 29.630 0.00 0.00 41.89 2.66
1550 1687 9.601971 TCGACATTTCGGTTCTAAAAATAAAAG 57.398 29.630 0.73 0.00 45.90 2.27
1551 1688 9.384682 GTCGACATTTCGGTTCTAAAAATAAAA 57.615 29.630 11.55 0.00 45.90 1.52
1552 1689 8.557864 TGTCGACATTTCGGTTCTAAAAATAAA 58.442 29.630 15.76 0.00 45.90 1.40
1553 1690 8.085720 TGTCGACATTTCGGTTCTAAAAATAA 57.914 30.769 15.76 0.00 45.90 1.40
1554 1691 7.655236 TGTCGACATTTCGGTTCTAAAAATA 57.345 32.000 15.76 0.00 45.90 1.40
1555 1692 6.548441 TGTCGACATTTCGGTTCTAAAAAT 57.452 33.333 15.76 0.00 45.90 1.82
1556 1693 5.987777 TGTCGACATTTCGGTTCTAAAAA 57.012 34.783 15.76 0.00 45.90 1.94
1557 1694 5.987777 TTGTCGACATTTCGGTTCTAAAA 57.012 34.783 20.80 0.00 45.90 1.52
1558 1695 5.987777 TTTGTCGACATTTCGGTTCTAAA 57.012 34.783 20.80 2.76 45.90 1.85
1559 1696 5.987777 TTTTGTCGACATTTCGGTTCTAA 57.012 34.783 20.80 3.33 45.90 2.10
1560 1697 6.548441 AATTTTGTCGACATTTCGGTTCTA 57.452 33.333 20.80 0.00 45.90 2.10
1561 1698 5.432885 AATTTTGTCGACATTTCGGTTCT 57.567 34.783 20.80 0.00 45.90 3.01
1562 1699 4.317291 CGAATTTTGTCGACATTTCGGTTC 59.683 41.667 30.79 22.10 45.90 3.62
1563 1700 4.215965 CGAATTTTGTCGACATTTCGGTT 58.784 39.130 30.79 18.16 45.90 4.44
1564 1701 3.364565 CCGAATTTTGTCGACATTTCGGT 60.365 43.478 37.80 20.49 45.90 4.69
1565 1702 3.160545 CCGAATTTTGTCGACATTTCGG 58.839 45.455 36.35 36.35 45.90 4.30
1567 1704 4.155310 ACCCGAATTTTGTCGACATTTC 57.845 40.909 20.80 19.59 43.86 2.17
1597 1734 7.506114 TCTAAACCAGAGTAACATGTTCAGTT 58.494 34.615 15.85 6.51 0.00 3.16
1668 1805 3.825908 AAGGTGCTCCCAAAATCCTAA 57.174 42.857 0.00 0.00 34.66 2.69
1669 1806 3.825908 AAAGGTGCTCCCAAAATCCTA 57.174 42.857 0.00 0.00 34.66 2.94
1670 1807 2.702270 AAAGGTGCTCCCAAAATCCT 57.298 45.000 0.00 0.00 34.66 3.24
1711 1853 2.286772 ACTTGCGACCGACAAAAATGTC 60.287 45.455 0.00 0.00 35.59 3.06
1745 1887 3.118542 GGTACGAGCGACCGATAAAATT 58.881 45.455 3.95 0.00 0.00 1.82
1785 1927 3.438087 AGATCCTGCGTCTGACAAAAATG 59.562 43.478 8.73 0.00 0.00 2.32
1839 1981 8.758633 TTTTCGTTATGTTTCAACTTTTGGAA 57.241 26.923 0.00 0.00 0.00 3.53
1840 1982 8.934507 ATTTTCGTTATGTTTCAACTTTTGGA 57.065 26.923 0.00 0.00 0.00 3.53
1841 1983 9.980780 AAATTTTCGTTATGTTTCAACTTTTGG 57.019 25.926 0.00 0.00 0.00 3.28
2002 2177 0.872021 GCACGCATCCCTCTCTTACG 60.872 60.000 0.00 0.00 0.00 3.18
2029 2204 4.202357 TGGAAGAGGATTTATAGCACGCAT 60.202 41.667 0.00 0.00 0.00 4.73
2060 2235 3.096092 TGTTAGATGCAAATTCCCCACC 58.904 45.455 0.00 0.00 0.00 4.61
2078 2254 3.371595 GGTAATGTGGGGACTAGCATGTT 60.372 47.826 0.00 0.00 0.00 2.71
2105 2286 2.393271 AGACAATCTCCCTTCGCTTG 57.607 50.000 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.