Multiple sequence alignment - TraesCS6B01G192900

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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 TraesCS6B01G192900 chr6B 100.000 2200 0 0 380 2579 227268495 227270694 0.000000e+00 4063.0
1 TraesCS6B01G192900 chr6B 100.000 55 0 0 1 55 227268116 227268170 4.540000e-18 102.0
2 TraesCS6B01G192900 chr6B 93.103 58 3 1 2006 2063 90102797 90102853 1.640000e-12 84.2
3 TraesCS6B01G192900 chr6D 91.597 1666 65 37 381 2006 129150948 129152578 0.000000e+00 2231.0
4 TraesCS6B01G192900 chr6D 83.424 549 37 24 2060 2579 129152574 129153097 6.500000e-126 460.0
5 TraesCS6B01G192900 chr6D 100.000 52 0 0 4 55 129150875 129150926 2.110000e-16 97.1
6 TraesCS6B01G192900 chr6D 94.643 56 3 0 2014 2069 114156754 114156699 1.270000e-13 87.9
7 TraesCS6B01G192900 chr6A 91.441 1659 85 32 380 2006 166508193 166506560 0.000000e+00 2224.0
8 TraesCS6B01G192900 chr6A 86.618 553 36 10 2060 2579 166506564 166506017 6.190000e-161 577.0
9 TraesCS6B01G192900 chr6A 100.000 55 0 0 1 55 166508233 166508179 4.540000e-18 102.0
10 TraesCS6B01G192900 chr7D 79.330 537 77 20 1052 1580 512281824 512281314 1.900000e-91 346.0
11 TraesCS6B01G192900 chr7B 78.652 534 86 15 1052 1580 544139563 544139053 1.910000e-86 329.0
12 TraesCS6B01G192900 chr7A 78.358 536 84 19 1052 1580 585066490 585065980 4.140000e-83 318.0
13 TraesCS6B01G192900 chr2D 98.000 50 1 0 2014 2063 79419695 79419744 1.270000e-13 87.9
14 TraesCS6B01G192900 chr5D 94.643 56 2 1 2014 2068 214083958 214083903 4.570000e-13 86.1
15 TraesCS6B01G192900 chr5D 91.667 60 4 1 2006 2065 528145929 528145871 5.910000e-12 82.4
16 TraesCS6B01G192900 chrUn 89.394 66 5 2 2014 2078 158062275 158062211 5.910000e-12 82.4
17 TraesCS6B01G192900 chrUn 89.394 66 5 2 2014 2078 478545568 478545504 5.910000e-12 82.4
18 TraesCS6B01G192900 chr3B 89.394 66 5 2 2014 2078 825002692 825002628 5.910000e-12 82.4
19 TraesCS6B01G192900 chr3A 91.803 61 2 3 2006 2066 75151743 75151686 5.910000e-12 82.4


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 TraesCS6B01G192900 chr6B 227268116 227270694 2578 False 2082.500000 4063 100.000000 1 2579 2 chr6B.!!$F2 2578
1 TraesCS6B01G192900 chr6D 129150875 129153097 2222 False 929.366667 2231 91.673667 4 2579 3 chr6D.!!$F1 2575
2 TraesCS6B01G192900 chr6A 166506017 166508233 2216 True 967.666667 2224 92.686333 1 2579 3 chr6A.!!$R1 2578
3 TraesCS6B01G192900 chr7D 512281314 512281824 510 True 346.000000 346 79.330000 1052 1580 1 chr7D.!!$R1 528
4 TraesCS6B01G192900 chr7B 544139053 544139563 510 True 329.000000 329 78.652000 1052 1580 1 chr7B.!!$R1 528
5 TraesCS6B01G192900 chr7A 585065980 585066490 510 True 318.000000 318 78.358000 1052 1580 1 chr7A.!!$R1 528

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
784 826 0.17668 AGTGGCTCTGATTGGTAGCG 59.823 55.0 0.0 0.0 37.11 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1646 1689 0.040204 AAAGGGAGGTGCAAGGATGG 59.96 55.0 0.0 0.0 0.0 3.51 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
471 472 2.230660 GTGGGTTTTGTTCTCCAGGAG 58.769 52.381 10.70 10.70 0.00 3.69
484 485 1.303643 CAGGAGGGAGTTTGTGGGC 60.304 63.158 0.00 0.00 0.00 5.36
604 616 2.418669 TCCCCTTTCTGTTCCTTCTGT 58.581 47.619 0.00 0.00 0.00 3.41
606 618 1.882623 CCCTTTCTGTTCCTTCTGTGC 59.117 52.381 0.00 0.00 0.00 4.57
607 619 1.882623 CCTTTCTGTTCCTTCTGTGCC 59.117 52.381 0.00 0.00 0.00 5.01
630 642 5.236478 CCGTGCGGAAATGATTAGATTTACT 59.764 40.000 4.35 0.00 37.50 2.24
713 725 5.444613 CGTTGTGTTCGATTTACCATCTCTG 60.445 44.000 0.00 0.00 0.00 3.35
755 794 3.962481 CGAGATTTGAATTCGGCGAAATC 59.038 43.478 27.40 26.79 35.79 2.17
756 795 4.282873 GAGATTTGAATTCGGCGAAATCC 58.717 43.478 28.84 19.58 36.06 3.01
774 816 6.238211 CGAAATCCAAGTAATAAGTGGCTCTG 60.238 42.308 0.00 0.00 32.10 3.35
775 817 5.957771 ATCCAAGTAATAAGTGGCTCTGA 57.042 39.130 0.00 0.00 32.10 3.27
776 818 5.957771 TCCAAGTAATAAGTGGCTCTGAT 57.042 39.130 0.00 0.00 32.10 2.90
778 820 6.115446 TCCAAGTAATAAGTGGCTCTGATTG 58.885 40.000 9.03 0.00 30.43 2.67
780 822 5.700402 AGTAATAAGTGGCTCTGATTGGT 57.300 39.130 9.03 0.00 30.43 3.67
781 823 6.808321 AGTAATAAGTGGCTCTGATTGGTA 57.192 37.500 9.03 0.00 30.43 3.25
782 824 6.821388 AGTAATAAGTGGCTCTGATTGGTAG 58.179 40.000 9.03 0.00 30.43 3.18
783 825 2.409948 AAGTGGCTCTGATTGGTAGC 57.590 50.000 0.00 0.00 35.47 3.58
784 826 0.176680 AGTGGCTCTGATTGGTAGCG 59.823 55.000 0.00 0.00 37.11 4.26
785 827 0.811616 GTGGCTCTGATTGGTAGCGG 60.812 60.000 0.00 0.00 37.11 5.52
786 828 1.264749 TGGCTCTGATTGGTAGCGGT 61.265 55.000 0.00 0.00 37.11 5.68
787 829 0.811616 GGCTCTGATTGGTAGCGGTG 60.812 60.000 0.00 0.00 37.11 4.94
793 835 3.638592 ATTGGTAGCGGTGGGTGGC 62.639 63.158 0.00 0.00 0.00 5.01
795 837 3.078836 GGTAGCGGTGGGTGGCTA 61.079 66.667 0.00 0.00 40.58 3.93
800 842 3.782443 CGGTGGGTGGCTAGGGAC 61.782 72.222 0.00 0.00 0.00 4.46
828 870 4.383649 CGCTTTTGACATGTTGATTTCCTG 59.616 41.667 0.00 0.00 0.00 3.86
855 897 2.162408 CAGGATCTTGTTTCCGAAAGCC 59.838 50.000 0.00 0.00 38.36 4.35
860 902 2.065906 TTGTTTCCGAAAGCCGTGCC 62.066 55.000 0.00 0.00 36.31 5.01
895 937 0.951558 ACGATTGTTTGTGCCTGGAC 59.048 50.000 0.00 0.00 0.00 4.02
909 951 2.601763 GCCTGGACGTTACAATTCGTAG 59.398 50.000 0.00 0.00 40.39 3.51
912 954 5.585390 CCTGGACGTTACAATTCGTAGTAT 58.415 41.667 0.00 0.00 40.39 2.12
913 955 5.684626 CCTGGACGTTACAATTCGTAGTATC 59.315 44.000 0.00 0.00 40.39 2.24
914 956 6.193514 TGGACGTTACAATTCGTAGTATCA 57.806 37.500 0.00 0.00 40.39 2.15
915 957 6.798482 TGGACGTTACAATTCGTAGTATCAT 58.202 36.000 0.00 0.00 40.39 2.45
916 958 7.929159 TGGACGTTACAATTCGTAGTATCATA 58.071 34.615 0.00 0.00 40.39 2.15
917 959 8.570488 TGGACGTTACAATTCGTAGTATCATAT 58.430 33.333 0.00 0.00 40.39 1.78
952 994 1.577328 ATTCTTGTTGCGTGGCTCGG 61.577 55.000 11.21 0.00 40.26 4.63
959 1001 2.357760 GCGTGGCTCGGTTTGGTA 60.358 61.111 11.21 0.00 40.26 3.25
966 1008 1.923227 GCTCGGTTTGGTAGCTTGCC 61.923 60.000 0.00 0.00 33.40 4.52
981 1023 0.968405 TTGCCCTTGGAAGATTGCAC 59.032 50.000 0.00 0.00 0.00 4.57
1026 1068 3.810941 TGATGTTTACCGTTGTCTGTTCC 59.189 43.478 0.00 0.00 0.00 3.62
1039 1081 0.792640 CTGTTCCGTGTGCAGCTTAG 59.207 55.000 0.00 0.00 0.00 2.18
1266 1309 1.752694 ACCTGTTGTTGCGGCTGTT 60.753 52.632 0.00 0.00 0.00 3.16
1269 1312 2.340453 CTGTTGTTGCGGCTGTTGCT 62.340 55.000 0.00 0.00 39.59 3.91
1389 1432 2.286502 AAGAGGAAGGAGGGGCCC 60.287 66.667 17.12 17.12 37.37 5.80
1584 1627 3.511934 AGCTCGACAAGATTTAGGTGTCT 59.488 43.478 0.00 0.00 39.61 3.41
1611 1654 3.259123 GGGAAGAAATGGTTGCAATCTGT 59.741 43.478 11.73 0.00 0.00 3.41
1612 1655 4.240096 GGAAGAAATGGTTGCAATCTGTG 58.760 43.478 11.73 0.00 0.00 3.66
1642 1685 0.537143 ATCCGTCTTTGCTGTGCCAA 60.537 50.000 0.00 0.00 0.00 4.52
1643 1686 0.537143 TCCGTCTTTGCTGTGCCAAT 60.537 50.000 0.00 0.00 0.00 3.16
1644 1687 0.314935 CCGTCTTTGCTGTGCCAATT 59.685 50.000 0.00 0.00 0.00 2.32
1645 1688 1.411394 CGTCTTTGCTGTGCCAATTG 58.589 50.000 0.00 0.00 0.00 2.32
1646 1689 1.142474 GTCTTTGCTGTGCCAATTGC 58.858 50.000 0.00 0.00 41.77 3.56
1647 1690 0.033781 TCTTTGCTGTGCCAATTGCC 59.966 50.000 0.00 0.00 40.16 4.52
1648 1691 0.249953 CTTTGCTGTGCCAATTGCCA 60.250 50.000 0.00 0.00 40.16 4.92
1701 1744 4.102649 GCATTTCCTAAATTGTACGGCAC 58.897 43.478 0.00 0.00 0.00 5.01
1740 1783 0.887836 TGGCAGCTGCAAGAACTCAG 60.888 55.000 37.63 0.00 44.36 3.35
1743 1786 1.155042 CAGCTGCAAGAACTCAGTCC 58.845 55.000 0.00 0.00 34.07 3.85
1744 1787 1.055040 AGCTGCAAGAACTCAGTCCT 58.945 50.000 1.02 0.00 34.07 3.85
1862 1905 4.827692 TGTACTATTGTCCCATGTGTGTC 58.172 43.478 0.00 0.00 0.00 3.67
1913 1956 3.604582 TGGTTCATCATATTGCGTGTGA 58.395 40.909 0.00 0.00 32.16 3.58
1923 1966 7.371126 TCATATTGCGTGTGAGTTCATTTTA 57.629 32.000 0.00 0.00 0.00 1.52
1980 2023 5.302360 TGGTTGTATAGTTGGTGTTCTCAC 58.698 41.667 0.00 0.00 43.19 3.51
1982 2025 5.638234 GGTTGTATAGTTGGTGTTCTCACTC 59.362 44.000 0.00 0.00 43.41 3.51
1992 2035 5.357257 TGGTGTTCTCACTCTTGTTAGTTC 58.643 41.667 0.00 0.00 43.41 3.01
2006 2049 9.199982 CTCTTGTTAGTTCGGAAAATTGTACTA 57.800 33.333 0.00 0.00 0.00 1.82
2007 2050 9.199982 TCTTGTTAGTTCGGAAAATTGTACTAG 57.800 33.333 0.00 0.00 0.00 2.57
2008 2051 9.199982 CTTGTTAGTTCGGAAAATTGTACTAGA 57.800 33.333 0.00 0.00 0.00 2.43
2009 2052 9.715121 TTGTTAGTTCGGAAAATTGTACTAGAT 57.285 29.630 0.00 0.00 0.00 1.98
2010 2053 9.362539 TGTTAGTTCGGAAAATTGTACTAGATC 57.637 33.333 0.00 0.00 0.00 2.75
2011 2054 9.362539 GTTAGTTCGGAAAATTGTACTAGATCA 57.637 33.333 0.00 0.00 0.00 2.92
2012 2055 7.829378 AGTTCGGAAAATTGTACTAGATCAC 57.171 36.000 0.00 0.00 0.00 3.06
2013 2056 6.817140 AGTTCGGAAAATTGTACTAGATCACC 59.183 38.462 0.00 0.00 0.00 4.02
2014 2057 6.288941 TCGGAAAATTGTACTAGATCACCA 57.711 37.500 0.00 0.00 0.00 4.17
2015 2058 6.103997 TCGGAAAATTGTACTAGATCACCAC 58.896 40.000 0.00 0.00 0.00 4.16
2016 2059 6.070995 TCGGAAAATTGTACTAGATCACCACT 60.071 38.462 0.00 0.00 0.00 4.00
2017 2060 7.123098 TCGGAAAATTGTACTAGATCACCACTA 59.877 37.037 0.00 0.00 0.00 2.74
2018 2061 7.222224 CGGAAAATTGTACTAGATCACCACTAC 59.778 40.741 0.00 0.00 0.00 2.73
2019 2062 8.258708 GGAAAATTGTACTAGATCACCACTACT 58.741 37.037 0.00 0.00 0.00 2.57
2020 2063 9.654663 GAAAATTGTACTAGATCACCACTACTT 57.345 33.333 0.00 0.00 0.00 2.24
2024 2067 8.874744 TTGTACTAGATCACCACTACTTTAGT 57.125 34.615 0.00 0.00 40.28 2.24
2057 2100 7.953752 ACTCTCTTATATTTCTTTACGGAGGG 58.046 38.462 0.00 0.00 0.00 4.30
2058 2101 7.783596 ACTCTCTTATATTTCTTTACGGAGGGA 59.216 37.037 0.00 0.00 0.00 4.20
2059 2102 8.179509 TCTCTTATATTTCTTTACGGAGGGAG 57.820 38.462 0.00 0.00 0.00 4.30
2060 2103 7.783596 TCTCTTATATTTCTTTACGGAGGGAGT 59.216 37.037 0.00 0.00 0.00 3.85
2061 2104 9.075678 CTCTTATATTTCTTTACGGAGGGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
2062 2105 8.854117 TCTTATATTTCTTTACGGAGGGAGTAC 58.146 37.037 0.00 0.00 0.00 2.73
2063 2106 8.773033 TTATATTTCTTTACGGAGGGAGTACT 57.227 34.615 0.00 0.00 0.00 2.73
2077 2122 2.233922 GGAGTACTTGGTTAGCTCTGCA 59.766 50.000 0.00 0.00 0.00 4.41
2096 2141 7.415541 GCTCTGCACTCAAATATACATCCAAAA 60.416 37.037 0.00 0.00 0.00 2.44
2097 2142 8.523915 TCTGCACTCAAATATACATCCAAAAT 57.476 30.769 0.00 0.00 0.00 1.82
2098 2143 9.625747 TCTGCACTCAAATATACATCCAAAATA 57.374 29.630 0.00 0.00 0.00 1.40
2117 2162 7.540055 CCAAAATAGAAGAGCAATGAGAAACAC 59.460 37.037 0.00 0.00 0.00 3.32
2134 2179 4.345859 AACACGGTTATGGTTCTTGAGA 57.654 40.909 0.00 0.00 0.00 3.27
2171 2221 1.273048 GTGAGCAATGGCAAACATGGA 59.727 47.619 0.00 0.00 44.61 3.41
2243 2320 0.478072 AGGCCTTGTGGTTGATCACA 59.522 50.000 0.00 0.00 44.81 3.58
2254 2331 6.638610 TGTGGTTGATCACAAGTTGAAAAAT 58.361 32.000 10.54 0.00 43.70 1.82
2263 2340 7.712264 TCACAAGTTGAAAAATTATGCCTTG 57.288 32.000 10.54 0.00 29.22 3.61
2265 2342 5.997129 ACAAGTTGAAAAATTATGCCTTGGG 59.003 36.000 10.54 0.00 29.22 4.12
2278 2355 1.270826 GCCTTGGGAAAGCTGAAGTTC 59.729 52.381 0.00 0.00 0.00 3.01
2291 2368 5.568392 AGCTGAAGTTCAAATCAGGATTCT 58.432 37.500 7.06 0.00 42.62 2.40
2292 2369 6.008960 AGCTGAAGTTCAAATCAGGATTCTT 58.991 36.000 7.06 0.00 42.62 2.52
2301 2378 7.953158 TCAAATCAGGATTCTTCGTATGATC 57.047 36.000 0.00 0.00 0.00 2.92
2302 2379 7.500141 TCAAATCAGGATTCTTCGTATGATCA 58.500 34.615 0.00 0.00 0.00 2.92
2309 2386 5.641209 GGATTCTTCGTATGATCAGGAATGG 59.359 44.000 0.09 0.00 0.00 3.16
2317 2394 2.216881 TGATCAGGAATGGGGATTGGT 58.783 47.619 0.00 0.00 0.00 3.67
2366 2443 0.035152 TGCGCATTCTGATCCAAGGT 60.035 50.000 5.66 0.00 0.00 3.50
2369 2446 2.569059 CGCATTCTGATCCAAGGTGAT 58.431 47.619 0.00 0.00 0.00 3.06
2383 2460 4.681025 CCAAGGTGATCAATTTTCAACACG 59.319 41.667 0.00 0.00 33.09 4.49
2524 2603 1.071385 CCCCTCTAGACATGATGTGCC 59.929 57.143 1.23 0.00 0.00 5.01
2552 2631 1.136110 CAACTCTTTTGCCGGGTGTTT 59.864 47.619 2.18 0.00 0.00 2.83
2558 2637 1.175983 TTTGCCGGGTGTTTAGCAGG 61.176 55.000 2.18 0.00 41.74 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
471 472 4.660938 AGCCGCCCACAAACTCCC 62.661 66.667 0.00 0.00 0.00 4.30
515 526 2.691522 CGCGAGCATCACAGAACG 59.308 61.111 0.00 0.00 33.17 3.95
604 616 1.013596 CTAATCATTTCCGCACGGCA 58.986 50.000 3.66 0.00 34.68 5.69
606 618 4.552166 AAATCTAATCATTTCCGCACGG 57.448 40.909 1.73 1.73 0.00 4.94
607 619 6.287107 AGTAAATCTAATCATTTCCGCACG 57.713 37.500 0.00 0.00 0.00 5.34
639 651 0.322636 TCCGGGCGGCTTTAATTTGA 60.323 50.000 9.56 0.00 34.68 2.69
653 665 1.808945 GCATGATTCAGCTAATCCGGG 59.191 52.381 0.00 0.00 42.97 5.73
713 725 5.240844 TCTCGAAAACTGAAAATTTCTCCCC 59.759 40.000 7.29 0.00 34.22 4.81
755 794 5.297776 CCAATCAGAGCCACTTATTACTTGG 59.702 44.000 0.00 0.00 0.00 3.61
756 795 5.882557 ACCAATCAGAGCCACTTATTACTTG 59.117 40.000 0.00 0.00 0.00 3.16
774 816 1.451387 CCACCCACCGCTACCAATC 60.451 63.158 0.00 0.00 0.00 2.67
775 817 2.674754 CCACCCACCGCTACCAAT 59.325 61.111 0.00 0.00 0.00 3.16
776 818 4.338710 GCCACCCACCGCTACCAA 62.339 66.667 0.00 0.00 0.00 3.67
778 820 3.078836 TAGCCACCCACCGCTACC 61.079 66.667 0.00 0.00 36.53 3.18
780 822 2.762459 CCTAGCCACCCACCGCTA 60.762 66.667 0.00 0.00 36.53 4.26
783 825 3.782443 GTCCCTAGCCACCCACCG 61.782 72.222 0.00 0.00 0.00 4.94
784 826 2.198304 CTTGTCCCTAGCCACCCACC 62.198 65.000 0.00 0.00 0.00 4.61
785 827 1.299976 CTTGTCCCTAGCCACCCAC 59.700 63.158 0.00 0.00 0.00 4.61
786 828 1.151899 ACTTGTCCCTAGCCACCCA 60.152 57.895 0.00 0.00 0.00 4.51
787 829 1.602771 GACTTGTCCCTAGCCACCC 59.397 63.158 0.00 0.00 0.00 4.61
793 835 2.737252 GTCAAAAGCGACTTGTCCCTAG 59.263 50.000 0.00 0.00 32.92 3.02
795 837 1.134220 TGTCAAAAGCGACTTGTCCCT 60.134 47.619 0.00 0.00 36.82 4.20
800 842 3.951306 TCAACATGTCAAAAGCGACTTG 58.049 40.909 0.00 0.00 43.27 3.16
828 870 4.261801 TCGGAAACAAGATCCTGATTTCC 58.738 43.478 18.74 18.74 43.20 3.13
860 902 4.452733 GTCGTTGCGGGGAGGAGG 62.453 72.222 0.00 0.00 0.00 4.30
916 958 9.798994 CAACAAGAATCCTAAACGTAGTAGTAT 57.201 33.333 0.00 0.00 45.00 2.12
917 959 7.756722 GCAACAAGAATCCTAAACGTAGTAGTA 59.243 37.037 0.00 0.00 45.00 1.82
918 960 6.589139 GCAACAAGAATCCTAAACGTAGTAGT 59.411 38.462 0.00 0.00 45.00 2.73
919 961 6.237490 CGCAACAAGAATCCTAAACGTAGTAG 60.237 42.308 0.00 0.00 45.00 2.57
922 964 4.387862 ACGCAACAAGAATCCTAAACGTAG 59.612 41.667 0.00 0.00 0.00 3.51
952 994 0.603065 CCAAGGGCAAGCTACCAAAC 59.397 55.000 7.92 0.00 0.00 2.93
959 1001 1.553706 CAATCTTCCAAGGGCAAGCT 58.446 50.000 0.00 0.00 0.00 3.74
966 1008 4.038402 AGAAACAAGTGCAATCTTCCAAGG 59.962 41.667 0.00 0.00 0.00 3.61
981 1023 4.453819 AGCATCGAAAGAGGAAGAAACAAG 59.546 41.667 0.00 0.00 46.52 3.16
1026 1068 3.926527 TGAATAACTCTAAGCTGCACACG 59.073 43.478 1.02 0.00 0.00 4.49
1039 1081 6.655003 TCCTTGTGTTCCATCTTGAATAACTC 59.345 38.462 0.00 0.00 0.00 3.01
1389 1432 0.592637 TGCAAGTTGAGCACCGATTG 59.407 50.000 7.16 0.00 37.02 2.67
1584 1627 3.838565 TGCAACCATTTCTTCCCTGTAA 58.161 40.909 0.00 0.00 0.00 2.41
1611 1654 3.981071 AAGACGGATGATGAACCTTCA 57.019 42.857 0.00 0.00 42.14 3.02
1612 1655 3.181506 GCAAAGACGGATGATGAACCTTC 60.182 47.826 0.00 0.00 0.00 3.46
1645 1688 2.440980 GGGAGGTGCAAGGATGGC 60.441 66.667 0.00 0.00 33.57 4.40
1646 1689 0.040204 AAAGGGAGGTGCAAGGATGG 59.960 55.000 0.00 0.00 0.00 3.51
1647 1690 1.005215 AGAAAGGGAGGTGCAAGGATG 59.995 52.381 0.00 0.00 0.00 3.51
1648 1691 1.376649 AGAAAGGGAGGTGCAAGGAT 58.623 50.000 0.00 0.00 0.00 3.24
1740 1783 3.452474 CATTCGGAATGACTGAGAGGAC 58.548 50.000 23.11 0.00 41.46 3.85
1743 1786 3.533606 ACCATTCGGAATGACTGAGAG 57.466 47.619 27.77 13.86 41.46 3.20
1744 1787 3.981071 AACCATTCGGAATGACTGAGA 57.019 42.857 27.77 0.00 41.46 3.27
1862 1905 8.893219 TGGCTACTATTACTGATCAGAATTTG 57.107 34.615 29.27 18.45 0.00 2.32
1923 1966 7.566760 TTGAACTGAACATACTCAAACATGT 57.433 32.000 0.00 0.00 36.96 3.21
1980 2023 8.084590 AGTACAATTTTCCGAACTAACAAGAG 57.915 34.615 0.00 0.00 0.00 2.85
1982 2025 9.199982 TCTAGTACAATTTTCCGAACTAACAAG 57.800 33.333 0.00 0.00 0.00 3.16
1992 2035 6.106673 AGTGGTGATCTAGTACAATTTTCCG 58.893 40.000 0.00 0.00 0.00 4.30
2031 2074 9.075678 CCCTCCGTAAAGAAATATAAGAGAGTA 57.924 37.037 0.00 0.00 0.00 2.59
2032 2075 7.783596 TCCCTCCGTAAAGAAATATAAGAGAGT 59.216 37.037 0.00 0.00 0.00 3.24
2033 2076 8.179509 TCCCTCCGTAAAGAAATATAAGAGAG 57.820 38.462 0.00 0.00 0.00 3.20
2034 2077 7.783596 ACTCCCTCCGTAAAGAAATATAAGAGA 59.216 37.037 0.00 0.00 0.00 3.10
2035 2078 7.953752 ACTCCCTCCGTAAAGAAATATAAGAG 58.046 38.462 0.00 0.00 0.00 2.85
2036 2079 7.909485 ACTCCCTCCGTAAAGAAATATAAGA 57.091 36.000 0.00 0.00 0.00 2.10
2037 2080 8.858094 AGTACTCCCTCCGTAAAGAAATATAAG 58.142 37.037 0.00 0.00 0.00 1.73
2038 2081 8.773033 AGTACTCCCTCCGTAAAGAAATATAA 57.227 34.615 0.00 0.00 0.00 0.98
2039 2082 8.636213 CAAGTACTCCCTCCGTAAAGAAATATA 58.364 37.037 0.00 0.00 0.00 0.86
2040 2083 7.418712 CCAAGTACTCCCTCCGTAAAGAAATAT 60.419 40.741 0.00 0.00 0.00 1.28
2041 2084 6.127253 CCAAGTACTCCCTCCGTAAAGAAATA 60.127 42.308 0.00 0.00 0.00 1.40
2042 2085 5.338137 CCAAGTACTCCCTCCGTAAAGAAAT 60.338 44.000 0.00 0.00 0.00 2.17
2043 2086 4.020839 CCAAGTACTCCCTCCGTAAAGAAA 60.021 45.833 0.00 0.00 0.00 2.52
2044 2087 3.512724 CCAAGTACTCCCTCCGTAAAGAA 59.487 47.826 0.00 0.00 0.00 2.52
2045 2088 3.094572 CCAAGTACTCCCTCCGTAAAGA 58.905 50.000 0.00 0.00 0.00 2.52
2046 2089 2.830321 ACCAAGTACTCCCTCCGTAAAG 59.170 50.000 0.00 0.00 0.00 1.85
2047 2090 2.893424 ACCAAGTACTCCCTCCGTAAA 58.107 47.619 0.00 0.00 0.00 2.01
2048 2091 2.610438 ACCAAGTACTCCCTCCGTAA 57.390 50.000 0.00 0.00 0.00 3.18
2049 2092 2.610438 AACCAAGTACTCCCTCCGTA 57.390 50.000 0.00 0.00 0.00 4.02
2050 2093 2.454538 CTAACCAAGTACTCCCTCCGT 58.545 52.381 0.00 0.00 0.00 4.69
2051 2094 1.136500 GCTAACCAAGTACTCCCTCCG 59.864 57.143 0.00 0.00 0.00 4.63
2052 2095 2.431419 GAGCTAACCAAGTACTCCCTCC 59.569 54.545 0.00 0.00 0.00 4.30
2053 2096 3.131400 CAGAGCTAACCAAGTACTCCCTC 59.869 52.174 0.00 0.00 0.00 4.30
2054 2097 3.100671 CAGAGCTAACCAAGTACTCCCT 58.899 50.000 0.00 0.00 0.00 4.20
2055 2098 2.418884 GCAGAGCTAACCAAGTACTCCC 60.419 54.545 0.00 0.00 0.00 4.30
2056 2099 2.233922 TGCAGAGCTAACCAAGTACTCC 59.766 50.000 0.00 0.00 0.00 3.85
2057 2100 3.056465 AGTGCAGAGCTAACCAAGTACTC 60.056 47.826 0.00 0.00 0.00 2.59
2058 2101 2.900546 AGTGCAGAGCTAACCAAGTACT 59.099 45.455 0.00 0.00 0.00 2.73
2059 2102 3.254892 GAGTGCAGAGCTAACCAAGTAC 58.745 50.000 0.00 0.00 0.00 2.73
2060 2103 2.897326 TGAGTGCAGAGCTAACCAAGTA 59.103 45.455 0.00 0.00 0.00 2.24
2061 2104 1.694150 TGAGTGCAGAGCTAACCAAGT 59.306 47.619 0.00 0.00 0.00 3.16
2062 2105 2.462456 TGAGTGCAGAGCTAACCAAG 57.538 50.000 0.00 0.00 0.00 3.61
2063 2106 2.928801 TTGAGTGCAGAGCTAACCAA 57.071 45.000 0.00 0.00 0.00 3.67
2096 2141 4.872691 CCGTGTTTCTCATTGCTCTTCTAT 59.127 41.667 0.00 0.00 0.00 1.98
2097 2142 4.245660 CCGTGTTTCTCATTGCTCTTCTA 58.754 43.478 0.00 0.00 0.00 2.10
2098 2143 3.070018 CCGTGTTTCTCATTGCTCTTCT 58.930 45.455 0.00 0.00 0.00 2.85
2117 2162 7.549488 AGAACTAAATCTCAAGAACCATAACCG 59.451 37.037 0.00 0.00 0.00 4.44
2130 2175 8.721478 GCTCACATGTTTTAGAACTAAATCTCA 58.279 33.333 0.00 8.14 35.27 3.27
2131 2176 8.721478 TGCTCACATGTTTTAGAACTAAATCTC 58.279 33.333 0.00 3.90 35.27 2.75
2134 2179 9.630098 CATTGCTCACATGTTTTAGAACTAAAT 57.370 29.630 0.00 0.00 35.27 1.40
2152 2202 1.630223 TCCATGTTTGCCATTGCTCA 58.370 45.000 0.00 0.00 38.71 4.26
2182 2232 8.774890 ATCATCAGATTAGAGCAATGACATAC 57.225 34.615 0.00 0.00 0.00 2.39
2243 2320 6.432403 TCCCAAGGCATAATTTTTCAACTT 57.568 33.333 0.00 0.00 0.00 2.66
2254 2331 2.897271 TCAGCTTTCCCAAGGCATAA 57.103 45.000 0.00 0.00 0.00 1.90
2263 2340 4.321527 CCTGATTTGAACTTCAGCTTTCCC 60.322 45.833 0.00 0.00 38.41 3.97
2265 2342 5.695851 TCCTGATTTGAACTTCAGCTTTC 57.304 39.130 0.00 0.00 38.41 2.62
2278 2355 7.095313 CCTGATCATACGAAGAATCCTGATTTG 60.095 40.741 0.00 0.00 0.00 2.32
2291 2368 3.313791 TCCCCATTCCTGATCATACGAA 58.686 45.455 0.00 0.00 0.00 3.85
2292 2369 2.970987 TCCCCATTCCTGATCATACGA 58.029 47.619 0.00 0.00 0.00 3.43
2301 2378 1.849039 AGAGACCAATCCCCATTCCTG 59.151 52.381 0.00 0.00 0.00 3.86
2302 2379 1.849039 CAGAGACCAATCCCCATTCCT 59.151 52.381 0.00 0.00 0.00 3.36
2309 2386 0.329596 ACAAGGCAGAGACCAATCCC 59.670 55.000 0.00 0.00 0.00 3.85
2317 2394 3.244526 TGAATACAGCAACAAGGCAGAGA 60.245 43.478 0.00 0.00 35.83 3.10
2366 2443 3.634448 ACCCACGTGTTGAAAATTGATCA 59.366 39.130 15.65 0.00 0.00 2.92
2369 2446 3.775202 CAACCCACGTGTTGAAAATTGA 58.225 40.909 15.65 0.00 46.77 2.57
2383 2460 4.095483 CAGCTCATACAGATTTCAACCCAC 59.905 45.833 0.00 0.00 0.00 4.61
2453 2530 6.619329 ATTCTATCTCCTGGAAAGGATAGC 57.381 41.667 19.33 0.00 38.16 2.97
2476 2553 6.652481 TGACCACAAATCAAGCAAAAGAAAAA 59.348 30.769 0.00 0.00 0.00 1.94
2524 2603 3.504863 CGGCAAAAGAGTTGATCAATGG 58.495 45.455 12.12 0.00 0.00 3.16
2552 2631 5.336372 GCATTTGTTTAACACATCCCTGCTA 60.336 40.000 0.00 0.00 34.43 3.49


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

AutoCloner maintained by Alex Coulton.