Multiple sequence alignment - TraesCS1A01G115600

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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 TraesCS1A01G115600 chr1A 100.000 3075 0 0 1 3075 120013555 120010481 0.000000e+00 5679.0
1 TraesCS1A01G115600 chr1B 95.225 1110 45 3 1960 3069 172382089 172380988 0.000000e+00 1749.0
2 TraesCS1A01G115600 chr1B 93.732 1069 40 12 658 1709 172388407 172387349 0.000000e+00 1578.0
3 TraesCS1A01G115600 chr1B 97.333 150 4 0 1757 1906 172387338 172387189 3.930000e-64 255.0
4 TraesCS1A01G115600 chr1D 88.415 1502 107 27 1585 3075 112771205 112769760 0.000000e+00 1748.0
5 TraesCS1A01G115600 chr1D 88.799 1241 86 33 3 1205 112772779 112771554 0.000000e+00 1472.0
6 TraesCS1A01G115600 chr1D 96.552 145 5 0 1196 1340 112771398 112771254 1.100000e-59 241.0
7 TraesCS1A01G115600 chr1D 93.750 48 3 0 1708 1755 111059162 111059115 4.250000e-09 73.1
8 TraesCS1A01G115600 chrUn 79.918 244 40 8 155 392 462845002 462844762 1.470000e-38 171.0
9 TraesCS1A01G115600 chrUn 95.745 47 2 0 1709 1755 17053365 17053319 3.290000e-10 76.8
10 TraesCS1A01G115600 chr4D 77.949 195 36 7 19 209 459315441 459315250 6.970000e-22 115.0
11 TraesCS1A01G115600 chr3D 89.247 93 9 1 1046 1138 90369654 90369745 6.970000e-22 115.0
12 TraesCS1A01G115600 chr3D 97.727 44 1 0 1712 1755 591618642 591618685 3.290000e-10 76.8
13 TraesCS1A01G115600 chr6D 93.651 63 4 0 1076 1138 152263886 152263948 9.080000e-16 95.3
14 TraesCS1A01G115600 chr6B 93.651 63 4 0 1076 1138 276740052 276740114 9.080000e-16 95.3
15 TraesCS1A01G115600 chr6A 93.651 63 4 0 1076 1138 190599621 190599559 9.080000e-16 95.3
16 TraesCS1A01G115600 chr2D 97.872 47 1 0 1709 1755 621952188 621952142 7.070000e-12 82.4
17 TraesCS1A01G115600 chr2D 95.652 46 2 0 1710 1755 376700728 376700773 1.180000e-09 75.0
18 TraesCS1A01G115600 chr2D 97.059 34 1 0 219 252 527267987 527267954 1.190000e-04 58.4
19 TraesCS1A01G115600 chr4A 95.918 49 1 1 1707 1755 9380667 9380714 9.140000e-11 78.7
20 TraesCS1A01G115600 chr2A 95.833 48 2 0 1708 1755 317944901 317944854 9.140000e-11 78.7
21 TraesCS1A01G115600 chr3B 95.745 47 1 1 1713 1758 636452042 636452088 1.180000e-09 75.0
22 TraesCS1A01G115600 chr7B 89.091 55 4 1 1711 1765 56386868 56386816 1.980000e-07 67.6
23 TraesCS1A01G115600 chr2B 89.130 46 5 0 219 264 78821497 78821542 1.190000e-04 58.4


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 TraesCS1A01G115600 chr1A 120010481 120013555 3074 True 5679.000000 5679 100.000000 1 3075 1 chr1A.!!$R1 3074
1 TraesCS1A01G115600 chr1B 172380988 172382089 1101 True 1749.000000 1749 95.225000 1960 3069 1 chr1B.!!$R1 1109
2 TraesCS1A01G115600 chr1B 172387189 172388407 1218 True 916.500000 1578 95.532500 658 1906 2 chr1B.!!$R2 1248
3 TraesCS1A01G115600 chr1D 112769760 112772779 3019 True 1153.666667 1748 91.255333 3 3075 3 chr1D.!!$R2 3072

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
357 364 0.531200 AGTACGGTTGTGCCTCTAGC 59.469 55.0 0.0 0.0 44.14 3.42 F
1358 1567 0.463474 TGCCGCATGATTCCGATTGA 60.463 50.0 0.0 0.0 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2037 2258 1.079987 TCTTCTGCTGCCTCCTCCT 59.920 57.895 0.0 0.0 0.0 3.69 R
3018 3242 0.807496 GCACTGCCACATTTCCTCTC 59.193 55.000 0.0 0.0 0.0 3.20 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
48 51 7.553334 TCTTTTACGAGAGGCATAACTATGTT 58.447 34.615 0.00 0.00 36.11 2.71
51 54 5.599999 ACGAGAGGCATAACTATGTTTCT 57.400 39.130 0.00 2.73 36.11 2.52
60 63 5.050702 GCATAACTATGTTTCTCGAGGAAGC 60.051 44.000 13.56 8.34 36.11 3.86
64 67 5.491982 ACTATGTTTCTCGAGGAAGCAAAT 58.508 37.500 13.56 4.54 45.51 2.32
89 92 5.600908 GTGCGTCCACAAGAACTAAATAA 57.399 39.130 0.00 0.00 41.67 1.40
90 93 6.178239 GTGCGTCCACAAGAACTAAATAAT 57.822 37.500 0.00 0.00 41.67 1.28
91 94 6.021596 GTGCGTCCACAAGAACTAAATAATG 58.978 40.000 0.00 0.00 41.67 1.90
186 193 4.201930 CGTGCCTCTACGAGAAGTAAATCT 60.202 45.833 0.00 0.00 46.46 2.40
189 196 5.884232 TGCCTCTACGAGAAGTAAATCTGTA 59.116 40.000 0.00 0.00 34.45 2.74
192 199 6.543100 CCTCTACGAGAAGTAAATCTGTACCT 59.457 42.308 0.00 0.00 34.45 3.08
198 205 3.694535 AGTAAATCTGTACCTCTCGCG 57.305 47.619 0.00 0.00 0.00 5.87
212 219 4.153655 ACCTCTCGCGGAAAGAAAAATAAC 59.846 41.667 6.13 0.00 0.00 1.89
214 221 2.838452 CTCGCGGAAAGAAAAATAACGC 59.162 45.455 6.13 0.00 41.84 4.84
217 224 2.337352 GCGGAAAGAAAAATAACGCGTG 59.663 45.455 14.98 0.00 36.14 5.34
218 225 3.547601 CGGAAAGAAAAATAACGCGTGT 58.452 40.909 14.98 5.77 0.00 4.49
228 235 6.650239 AAAATAACGCGTGTTTTTCCTTTT 57.350 29.167 20.86 14.01 39.54 2.27
266 273 2.159476 GCATCTCGCAGAAGCAAATTCA 60.159 45.455 8.01 0.00 38.67 2.57
277 284 3.018423 AGCAAATTCATACCTCCACCC 57.982 47.619 0.00 0.00 0.00 4.61
283 290 1.946984 TCATACCTCCACCCGAAGTT 58.053 50.000 0.00 0.00 0.00 2.66
287 294 4.472108 TCATACCTCCACCCGAAGTTATTT 59.528 41.667 0.00 0.00 0.00 1.40
301 308 4.002906 AGTTATTTCGTGCCTCTTGTGA 57.997 40.909 0.00 0.00 0.00 3.58
304 311 3.904136 ATTTCGTGCCTCTTGTGAAAG 57.096 42.857 0.00 0.00 32.66 2.62
345 352 2.228138 TCTTTTGCGAACAGTACGGT 57.772 45.000 0.00 0.00 0.00 4.83
357 364 0.531200 AGTACGGTTGTGCCTCTAGC 59.469 55.000 0.00 0.00 44.14 3.42
370 377 2.208431 CCTCTAGCAGAAGCAAATCCG 58.792 52.381 0.00 0.00 45.49 4.18
392 399 6.071672 TCCGTGCCTTCATGAAAAATAAATCA 60.072 34.615 9.88 0.00 0.00 2.57
393 400 6.589523 CCGTGCCTTCATGAAAAATAAATCAA 59.410 34.615 9.88 0.00 0.00 2.57
396 403 8.392612 GTGCCTTCATGAAAAATAAATCAATGG 58.607 33.333 9.88 3.57 0.00 3.16
399 406 8.823818 CCTTCATGAAAAATAAATCAATGGCTC 58.176 33.333 9.88 0.00 0.00 4.70
409 416 2.995466 TCAATGGCTCTCGCAAAAAG 57.005 45.000 0.00 0.00 38.10 2.27
413 420 4.050553 CAATGGCTCTCGCAAAAAGAAAA 58.949 39.130 0.00 0.00 38.10 2.29
481 488 6.367374 AAAAGACCAGAGGAAAACCAAAAA 57.633 33.333 0.00 0.00 0.00 1.94
486 493 3.384467 CCAGAGGAAAACCAAAAAGCTGA 59.616 43.478 0.00 0.00 0.00 4.26
490 497 6.036408 CAGAGGAAAACCAAAAAGCTGAAAAG 59.964 38.462 0.00 0.00 0.00 2.27
527 534 4.037446 AGTCATCTAAAAGCCAAAAACGCA 59.963 37.500 0.00 0.00 0.00 5.24
566 573 8.502161 AAATAGAAACAAATCCGAAGAAAACG 57.498 30.769 0.00 0.00 0.00 3.60
567 574 5.494632 AGAAACAAATCCGAAGAAAACGT 57.505 34.783 0.00 0.00 0.00 3.99
577 584 3.242155 CCGAAGAAAACGTATAATGCGCA 60.242 43.478 14.96 14.96 0.00 6.09
581 588 5.229921 AGAAAACGTATAATGCGCAACAT 57.770 34.783 17.11 13.47 42.30 2.71
585 592 2.933260 ACGTATAATGCGCAACATGTGA 59.067 40.909 17.11 0.00 39.60 3.58
586 593 3.559655 ACGTATAATGCGCAACATGTGAT 59.440 39.130 17.11 0.00 39.60 3.06
647 682 3.452474 GAGGAGTACTCGCTCGTTAGTA 58.548 50.000 16.56 0.00 36.29 1.82
683 718 8.747538 ATTTTGGTACAGAGGTGGTATATTTC 57.252 34.615 0.00 0.00 42.39 2.17
687 722 6.901300 TGGTACAGAGGTGGTATATTTCTCTT 59.099 38.462 0.00 0.00 33.09 2.85
732 767 9.820725 TCCGATAAAATTAGGAAATTAGAACGA 57.179 29.630 0.00 0.00 34.12 3.85
853 888 1.334239 CGTCTTCTCATCCGATCGTCC 60.334 57.143 15.09 0.00 0.00 4.79
872 907 4.503123 CGTCCCAGACAGCCATTAATATCA 60.503 45.833 0.00 0.00 32.09 2.15
922 957 4.003788 CCACGAGCCACGAACCCT 62.004 66.667 7.86 0.00 45.77 4.34
944 979 2.576053 GCGCACGATCGAGACGAA 60.576 61.111 24.34 0.00 39.99 3.85
1163 1201 1.823828 ATATCTGTTCACGCGTCGAC 58.176 50.000 9.86 11.96 0.00 4.20
1352 1561 4.929198 CGATTGCCGCATGATTCC 57.071 55.556 0.00 0.00 0.00 3.01
1358 1567 0.463474 TGCCGCATGATTCCGATTGA 60.463 50.000 0.00 0.00 0.00 2.57
1403 1614 3.545703 ACTTTGAGGATTGAATAGGCCG 58.454 45.455 0.00 0.00 0.00 6.13
1404 1615 1.967319 TTGAGGATTGAATAGGCCGC 58.033 50.000 0.00 0.00 0.00 6.53
1416 1630 2.462456 TAGGCCGCATGATTCTGATC 57.538 50.000 0.00 0.00 0.00 2.92
1420 1634 1.143305 CCGCATGATTCTGATCGACC 58.857 55.000 0.00 0.00 34.91 4.79
1459 1674 7.104290 AGTAAGCCACTACTTTAAGGATTGAC 58.896 38.462 0.00 0.00 34.98 3.18
1493 1708 1.729149 GCAACTGCGGCTTCACATTAC 60.729 52.381 0.00 0.00 0.00 1.89
1711 1931 6.460781 CCTCGCCCAACATTATACACTTATA 58.539 40.000 0.00 0.00 0.00 0.98
1712 1932 7.103641 CCTCGCCCAACATTATACACTTATAT 58.896 38.462 0.00 0.00 0.00 0.86
1713 1933 7.064609 CCTCGCCCAACATTATACACTTATATG 59.935 40.741 0.00 0.00 0.00 1.78
1714 1934 6.876789 TCGCCCAACATTATACACTTATATGG 59.123 38.462 0.00 0.00 0.00 2.74
1715 1935 6.653320 CGCCCAACATTATACACTTATATGGT 59.347 38.462 0.00 0.00 0.00 3.55
1716 1936 7.820386 CGCCCAACATTATACACTTATATGGTA 59.180 37.037 0.00 0.00 0.00 3.25
1724 1944 8.890410 TTATACACTTATATGGTACTCCCTCC 57.110 38.462 0.00 0.00 0.00 4.30
1725 1945 4.150359 ACACTTATATGGTACTCCCTCCG 58.850 47.826 0.00 0.00 0.00 4.63
1726 1946 4.150359 CACTTATATGGTACTCCCTCCGT 58.850 47.826 0.00 0.00 0.00 4.69
1727 1947 5.163055 ACACTTATATGGTACTCCCTCCGTA 60.163 44.000 0.00 0.00 0.00 4.02
1728 1948 5.771666 CACTTATATGGTACTCCCTCCGTAA 59.228 44.000 0.00 0.00 0.00 3.18
1730 1950 6.492772 ACTTATATGGTACTCCCTCCGTAAAG 59.507 42.308 0.00 0.00 0.00 1.85
1732 1952 3.173953 TGGTACTCCCTCCGTAAAGAA 57.826 47.619 0.00 0.00 0.00 2.52
1733 1953 3.509442 TGGTACTCCCTCCGTAAAGAAA 58.491 45.455 0.00 0.00 0.00 2.52
1734 1954 4.098894 TGGTACTCCCTCCGTAAAGAAAT 58.901 43.478 0.00 0.00 0.00 2.17
1736 1956 5.901276 TGGTACTCCCTCCGTAAAGAAATAT 59.099 40.000 0.00 0.00 0.00 1.28
1738 1958 7.564660 TGGTACTCCCTCCGTAAAGAAATATAA 59.435 37.037 0.00 0.00 0.00 0.98
1739 1959 8.087136 GGTACTCCCTCCGTAAAGAAATATAAG 58.913 40.741 0.00 0.00 0.00 1.73
1740 1960 7.063934 ACTCCCTCCGTAAAGAAATATAAGG 57.936 40.000 0.00 0.00 0.00 2.69
1741 1961 6.042897 ACTCCCTCCGTAAAGAAATATAAGGG 59.957 42.308 0.00 0.00 41.93 3.95
1742 1962 5.001874 CCCTCCGTAAAGAAATATAAGGGC 58.998 45.833 0.00 0.00 34.93 5.19
1743 1963 4.689345 CCTCCGTAAAGAAATATAAGGGCG 59.311 45.833 0.00 0.00 0.00 6.13
1747 1967 7.271511 TCCGTAAAGAAATATAAGGGCGTTTA 58.728 34.615 0.00 0.00 0.00 2.01
1748 1968 7.439056 TCCGTAAAGAAATATAAGGGCGTTTAG 59.561 37.037 0.00 0.00 0.00 1.85
1749 1969 7.439056 CCGTAAAGAAATATAAGGGCGTTTAGA 59.561 37.037 0.00 0.00 0.00 2.10
1750 1970 8.985805 CGTAAAGAAATATAAGGGCGTTTAGAT 58.014 33.333 0.00 0.00 0.00 1.98
1752 1972 8.974060 AAAGAAATATAAGGGCGTTTAGATCA 57.026 30.769 0.00 0.00 0.00 2.92
1753 1973 7.964604 AGAAATATAAGGGCGTTTAGATCAC 57.035 36.000 0.00 0.00 0.00 3.06
1755 1975 8.211629 AGAAATATAAGGGCGTTTAGATCACTT 58.788 33.333 0.00 0.00 0.00 3.16
1804 2025 2.481441 TGTGCAGGGATTAGGACATCT 58.519 47.619 0.00 0.00 30.92 2.90
1872 2093 6.064717 AGGCCAAGGTCAGAATAATTCATAC 58.935 40.000 5.01 0.00 0.00 2.39
1940 2161 9.100197 AGATATTGTTCTTTTTACCCCAACATT 57.900 29.630 0.00 0.00 0.00 2.71
1941 2162 9.366216 GATATTGTTCTTTTTACCCCAACATTC 57.634 33.333 0.00 0.00 0.00 2.67
1942 2163 6.800072 TTGTTCTTTTTACCCCAACATTCT 57.200 33.333 0.00 0.00 0.00 2.40
1943 2164 6.800072 TGTTCTTTTTACCCCAACATTCTT 57.200 33.333 0.00 0.00 0.00 2.52
1944 2165 6.811954 TGTTCTTTTTACCCCAACATTCTTC 58.188 36.000 0.00 0.00 0.00 2.87
1945 2166 6.183360 TGTTCTTTTTACCCCAACATTCTTCC 60.183 38.462 0.00 0.00 0.00 3.46
1946 2167 4.836175 TCTTTTTACCCCAACATTCTTCCC 59.164 41.667 0.00 0.00 0.00 3.97
1947 2168 2.911552 TTACCCCAACATTCTTCCCC 57.088 50.000 0.00 0.00 0.00 4.81
1948 2169 0.621609 TACCCCAACATTCTTCCCCG 59.378 55.000 0.00 0.00 0.00 5.73
1949 2170 1.379843 CCCCAACATTCTTCCCCGG 60.380 63.158 0.00 0.00 0.00 5.73
1950 2171 1.379843 CCCAACATTCTTCCCCGGG 60.380 63.158 15.80 15.80 0.00 5.73
1951 2172 1.379843 CCAACATTCTTCCCCGGGG 60.380 63.158 35.80 35.80 0.00 5.73
1952 2173 1.688811 CAACATTCTTCCCCGGGGA 59.311 57.895 39.67 39.67 43.52 4.81
1967 2188 4.139038 CCCGGGGAATATTTACGTTGAAT 58.861 43.478 14.71 0.00 0.00 2.57
1968 2189 4.023536 CCCGGGGAATATTTACGTTGAATG 60.024 45.833 14.71 0.00 0.00 2.67
2005 2226 1.667154 TAGTGCTGCGGAAGAGCGAT 61.667 55.000 0.00 0.00 40.67 4.58
2029 2250 2.557924 GTTTGATGAGTTGATGGCCACA 59.442 45.455 8.16 5.62 0.00 4.17
2037 2258 4.783621 GATGGCCACAGCTGCGGA 62.784 66.667 25.00 4.67 39.73 5.54
2087 2308 3.799420 GCAGACCTAGAAATTGCTAGTCG 59.201 47.826 17.70 7.32 36.88 4.18
2105 2326 2.253610 TCGTGTAGACAGGATGGGTTT 58.746 47.619 1.04 0.00 43.62 3.27
2168 2389 3.243839 GGTGAGAGAGAGGATGAAGATGC 60.244 52.174 0.00 0.00 0.00 3.91
2169 2390 2.964464 TGAGAGAGAGGATGAAGATGCC 59.036 50.000 0.00 0.00 0.00 4.40
2311 2532 5.391416 GCAAGAGCTGAGAATTTAAGTGTCC 60.391 44.000 0.00 0.00 37.91 4.02
2394 2616 4.162131 AGTTGGCACCAAAATCAAAAGTCT 59.838 37.500 3.10 0.00 37.70 3.24
2402 2624 7.328493 GCACCAAAATCAAAAGTCTATAACACC 59.672 37.037 0.00 0.00 0.00 4.16
2480 2702 7.067008 CCGGAGTTAATTTCACTGGTTTCATAT 59.933 37.037 0.00 0.00 0.00 1.78
2481 2703 9.104965 CGGAGTTAATTTCACTGGTTTCATATA 57.895 33.333 0.00 0.00 0.00 0.86
2499 2721 7.133133 TCATATACCCCCTAACAAAGACTTC 57.867 40.000 0.00 0.00 0.00 3.01
2500 2722 4.857130 ATACCCCCTAACAAAGACTTCC 57.143 45.455 0.00 0.00 0.00 3.46
2501 2723 2.714808 ACCCCCTAACAAAGACTTCCT 58.285 47.619 0.00 0.00 0.00 3.36
2502 2724 3.878086 ACCCCCTAACAAAGACTTCCTA 58.122 45.455 0.00 0.00 0.00 2.94
2588 2810 1.276421 GTCAGGGCAAGCTGAGACTAA 59.724 52.381 0.00 0.00 0.00 2.24
2694 2918 2.126463 TCGCGAAACCGAGCTCTG 60.126 61.111 6.20 8.03 32.74 3.35
2712 2936 2.317900 TCTGGTATCTTGGGAGGAAGGA 59.682 50.000 0.00 0.00 0.00 3.36
2758 2982 7.767198 CCATCATAGGATCAGCAAACAAAATTT 59.233 33.333 0.00 0.00 0.00 1.82
2788 3012 1.024579 CCCTTTATGACGCCGCTGTT 61.025 55.000 0.00 0.00 0.00 3.16
2791 3015 1.463056 CTTTATGACGCCGCTGTTGAA 59.537 47.619 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 34 5.833082 TCGAGAAACATAGTTATGCCTCTC 58.167 41.667 14.90 14.90 39.23 3.20
39 42 5.654603 TGCTTCCTCGAGAAACATAGTTA 57.345 39.130 15.71 0.00 32.88 2.24
40 43 4.537135 TGCTTCCTCGAGAAACATAGTT 57.463 40.909 15.71 0.00 32.88 2.24
41 44 4.537135 TTGCTTCCTCGAGAAACATAGT 57.463 40.909 15.71 0.00 30.83 2.12
48 51 3.329386 CACAGATTTGCTTCCTCGAGAA 58.671 45.455 15.71 5.59 0.00 2.87
51 54 1.442769 GCACAGATTTGCTTCCTCGA 58.557 50.000 0.00 0.00 39.59 4.04
60 63 1.872952 TCTTGTGGACGCACAGATTTG 59.127 47.619 0.00 0.00 36.35 2.32
64 67 0.464036 AGTTCTTGTGGACGCACAGA 59.536 50.000 0.00 0.00 36.35 3.41
89 92 1.573108 TTTCCTTCCGAGAGAGGCAT 58.427 50.000 0.00 0.00 0.00 4.40
90 93 1.348064 TTTTCCTTCCGAGAGAGGCA 58.652 50.000 0.00 0.00 0.00 4.75
91 94 2.474410 TTTTTCCTTCCGAGAGAGGC 57.526 50.000 0.00 0.00 0.00 4.70
123 130 4.503741 GCACAGTAATGCCTCTTTGAAA 57.496 40.909 0.00 0.00 39.86 2.69
149 156 2.227865 GAGGCACGGATTTACTTTTGCA 59.772 45.455 0.00 0.00 0.00 4.08
150 157 2.488153 AGAGGCACGGATTTACTTTTGC 59.512 45.455 0.00 0.00 0.00 3.68
152 159 3.930848 CGTAGAGGCACGGATTTACTTTT 59.069 43.478 0.00 0.00 38.26 2.27
186 193 1.250328 TTCTTTCCGCGAGAGGTACA 58.750 50.000 8.23 0.00 0.00 2.90
189 196 2.249844 TTTTTCTTTCCGCGAGAGGT 57.750 45.000 8.23 0.00 0.00 3.85
192 199 3.423907 GCGTTATTTTTCTTTCCGCGAGA 60.424 43.478 8.23 0.00 0.00 4.04
196 203 2.337352 CACGCGTTATTTTTCTTTCCGC 59.663 45.455 10.22 0.00 36.57 5.54
198 205 5.876576 AAACACGCGTTATTTTTCTTTCC 57.123 34.783 10.22 0.00 33.99 3.13
212 219 2.034076 CTCGAAAAGGAAAAACACGCG 58.966 47.619 3.53 3.53 0.00 6.01
214 221 3.848554 GCCTCTCGAAAAGGAAAAACACG 60.849 47.826 15.90 0.00 35.83 4.49
217 224 3.629058 GTGCCTCTCGAAAAGGAAAAAC 58.371 45.455 15.90 5.80 35.83 2.43
218 225 2.289547 CGTGCCTCTCGAAAAGGAAAAA 59.710 45.455 15.90 0.00 35.83 1.94
228 235 4.056125 CACAGCCGTGCCTCTCGA 62.056 66.667 0.00 0.00 36.06 4.04
252 259 3.696051 TGGAGGTATGAATTTGCTTCTGC 59.304 43.478 0.00 0.00 40.20 4.26
266 273 5.032327 GAAATAACTTCGGGTGGAGGTAT 57.968 43.478 0.00 0.00 33.18 2.73
283 290 3.751175 CCTTTCACAAGAGGCACGAAATA 59.249 43.478 0.00 0.00 30.57 1.40
287 294 0.756294 TCCTTTCACAAGAGGCACGA 59.244 50.000 0.00 0.00 32.93 4.35
336 343 1.544691 CTAGAGGCACAACCGTACTGT 59.455 52.381 0.00 0.00 46.52 3.55
338 345 0.531200 GCTAGAGGCACAACCGTACT 59.469 55.000 0.00 0.00 46.52 2.73
345 352 3.540211 GCTTCTGCTAGAGGCACAA 57.460 52.632 12.94 0.00 45.45 3.33
357 364 0.883833 AAGGCACGGATTTGCTTCTG 59.116 50.000 0.00 0.00 42.56 3.02
370 377 8.392612 CCATTGATTTATTTTTCATGAAGGCAC 58.607 33.333 8.41 0.00 0.00 5.01
466 473 5.675684 TTTCAGCTTTTTGGTTTTCCTCT 57.324 34.783 0.00 0.00 41.38 3.69
467 474 6.106003 TCTTTTCAGCTTTTTGGTTTTCCTC 58.894 36.000 0.00 0.00 41.38 3.71
479 486 5.675684 TTTCAGGGTTTCTTTTCAGCTTT 57.324 34.783 0.00 0.00 0.00 3.51
481 488 5.675684 TTTTTCAGGGTTTCTTTTCAGCT 57.324 34.783 0.00 0.00 0.00 4.24
504 511 4.037446 TGCGTTTTTGGCTTTTAGATGACT 59.963 37.500 0.00 0.00 0.00 3.41
550 557 6.138546 CGCATTATACGTTTTCTTCGGATTTG 59.861 38.462 0.00 0.00 33.68 2.32
556 563 3.918635 TGCGCATTATACGTTTTCTTCG 58.081 40.909 5.66 0.00 0.00 3.79
557 564 5.083389 TGTTGCGCATTATACGTTTTCTTC 58.917 37.500 12.75 0.00 0.00 2.87
566 573 4.221342 CCATCACATGTTGCGCATTATAC 58.779 43.478 12.75 7.03 35.19 1.47
567 574 3.304592 GCCATCACATGTTGCGCATTATA 60.305 43.478 12.75 0.00 35.19 0.98
577 584 1.747709 GCTCTCAGCCATCACATGTT 58.252 50.000 0.00 0.00 34.48 2.71
581 588 2.125391 GCGCTCTCAGCCATCACA 60.125 61.111 0.00 0.00 38.18 3.58
600 610 2.179018 CCCGCAAGCGTCATTTGG 59.821 61.111 13.80 2.31 37.81 3.28
623 658 1.521010 CGAGCGAGTACTCCTCCGA 60.521 63.158 24.11 0.00 36.82 4.55
629 664 4.566360 AGAACTACTAACGAGCGAGTACTC 59.434 45.833 13.18 13.18 0.00 2.59
641 676 6.401394 ACCAAAATACGGGAGAACTACTAAC 58.599 40.000 0.00 0.00 0.00 2.34
647 682 4.529377 TCTGTACCAAAATACGGGAGAACT 59.471 41.667 0.00 0.00 33.01 3.01
853 888 4.516698 GTGGTGATATTAATGGCTGTCTGG 59.483 45.833 0.00 0.00 0.00 3.86
872 907 4.658786 AGGAAGAGGGGGCGTGGT 62.659 66.667 0.00 0.00 0.00 4.16
922 957 4.847516 CTCGATCGTGCGCGGGAA 62.848 66.667 21.04 0.00 38.89 3.97
1220 1423 2.730672 CGCGACGCAAGGGAAAGAG 61.731 63.158 21.35 0.00 46.39 2.85
1403 1614 4.889832 AAAAGGTCGATCAGAATCATGC 57.110 40.909 0.00 0.00 31.76 4.06
1404 1615 9.793252 AATTTAAAAAGGTCGATCAGAATCATG 57.207 29.630 0.00 0.00 31.76 3.07
1416 1630 8.508875 TGGCTTACTAGAAATTTAAAAAGGTCG 58.491 33.333 0.00 0.00 0.00 4.79
1435 1650 7.104290 AGTCAATCCTTAAAGTAGTGGCTTAC 58.896 38.462 0.00 0.00 0.00 2.34
1449 1664 7.347222 TGCTTCTTATTCCCTAGTCAATCCTTA 59.653 37.037 0.00 0.00 0.00 2.69
1459 1674 3.557595 CGCAGTTGCTTCTTATTCCCTAG 59.442 47.826 2.29 0.00 39.32 3.02
1711 1931 3.393426 TCTTTACGGAGGGAGTACCAT 57.607 47.619 0.00 0.00 43.89 3.55
1712 1932 2.905415 TCTTTACGGAGGGAGTACCA 57.095 50.000 0.00 0.00 43.89 3.25
1713 1933 4.750021 ATTTCTTTACGGAGGGAGTACC 57.250 45.455 0.00 0.00 40.67 3.34
1714 1934 8.087136 CCTTATATTTCTTTACGGAGGGAGTAC 58.913 40.741 0.00 0.00 0.00 2.73
1715 1935 7.234166 CCCTTATATTTCTTTACGGAGGGAGTA 59.766 40.741 0.00 0.00 43.15 2.59
1716 1936 6.042897 CCCTTATATTTCTTTACGGAGGGAGT 59.957 42.308 0.00 0.00 43.15 3.85
1718 1938 5.221783 GCCCTTATATTTCTTTACGGAGGGA 60.222 44.000 8.71 0.00 43.15 4.20
1719 1939 5.001874 GCCCTTATATTTCTTTACGGAGGG 58.998 45.833 0.00 0.00 43.30 4.30
1720 1940 4.689345 CGCCCTTATATTTCTTTACGGAGG 59.311 45.833 0.00 0.00 0.00 4.30
1721 1941 5.295152 ACGCCCTTATATTTCTTTACGGAG 58.705 41.667 0.00 0.00 0.00 4.63
1723 1943 5.996669 AACGCCCTTATATTTCTTTACGG 57.003 39.130 0.00 0.00 0.00 4.02
1724 1944 8.356533 TCTAAACGCCCTTATATTTCTTTACG 57.643 34.615 0.00 0.00 0.00 3.18
1727 1947 8.837389 GTGATCTAAACGCCCTTATATTTCTTT 58.163 33.333 0.00 0.00 0.00 2.52
1728 1948 8.211629 AGTGATCTAAACGCCCTTATATTTCTT 58.788 33.333 0.00 0.00 0.00 2.52
1730 1950 7.964604 AGTGATCTAAACGCCCTTATATTTC 57.035 36.000 0.00 0.00 0.00 2.17
1732 1952 9.269453 GTAAAGTGATCTAAACGCCCTTATATT 57.731 33.333 0.00 0.00 0.00 1.28
1733 1953 8.426489 TGTAAAGTGATCTAAACGCCCTTATAT 58.574 33.333 0.00 0.00 0.00 0.86
1734 1954 7.784037 TGTAAAGTGATCTAAACGCCCTTATA 58.216 34.615 0.00 0.00 0.00 0.98
1736 1956 6.040209 TGTAAAGTGATCTAAACGCCCTTA 57.960 37.500 0.00 0.00 0.00 2.69
1738 1958 4.546829 TGTAAAGTGATCTAAACGCCCT 57.453 40.909 0.00 0.00 0.00 5.19
1739 1959 5.180680 AGTTTGTAAAGTGATCTAAACGCCC 59.819 40.000 0.00 0.00 34.29 6.13
1740 1960 6.237313 AGTTTGTAAAGTGATCTAAACGCC 57.763 37.500 0.00 0.00 34.29 5.68
1741 1961 8.068380 AGAAAGTTTGTAAAGTGATCTAAACGC 58.932 33.333 0.00 0.00 34.29 4.84
1742 1962 9.582223 GAGAAAGTTTGTAAAGTGATCTAAACG 57.418 33.333 0.00 0.00 34.29 3.60
1747 1967 9.274206 GGTTAGAGAAAGTTTGTAAAGTGATCT 57.726 33.333 0.00 0.00 0.00 2.75
1748 1968 9.052759 TGGTTAGAGAAAGTTTGTAAAGTGATC 57.947 33.333 0.00 0.00 0.00 2.92
1749 1969 8.974060 TGGTTAGAGAAAGTTTGTAAAGTGAT 57.026 30.769 0.00 0.00 0.00 3.06
1750 1970 8.795842 TTGGTTAGAGAAAGTTTGTAAAGTGA 57.204 30.769 0.00 0.00 0.00 3.41
1751 1971 8.889717 TCTTGGTTAGAGAAAGTTTGTAAAGTG 58.110 33.333 0.00 0.00 0.00 3.16
1752 1972 9.457436 TTCTTGGTTAGAGAAAGTTTGTAAAGT 57.543 29.630 0.00 0.00 33.51 2.66
1753 1973 9.717892 GTTCTTGGTTAGAGAAAGTTTGTAAAG 57.282 33.333 0.00 0.00 35.11 1.85
1755 1975 8.795842 TGTTCTTGGTTAGAGAAAGTTTGTAA 57.204 30.769 0.00 0.00 35.11 2.41
1804 2025 6.156775 TCATCTCATCCTTGATTTCCACAGTA 59.843 38.462 0.00 0.00 0.00 2.74
1872 2093 9.850628 AAAAACAACATTCTGATGATATGACAG 57.149 29.630 0.00 0.00 36.73 3.51
1943 2164 1.805180 ACGTAAATATTCCCCGGGGA 58.195 50.000 39.67 39.67 43.52 4.81
1944 2165 2.158784 TCAACGTAAATATTCCCCGGGG 60.159 50.000 35.80 35.80 0.00 5.73
1945 2166 3.196939 TCAACGTAAATATTCCCCGGG 57.803 47.619 15.80 15.80 0.00 5.73
1946 2167 4.577283 ACATTCAACGTAAATATTCCCCGG 59.423 41.667 0.00 0.00 0.00 5.73
1947 2168 5.744666 ACATTCAACGTAAATATTCCCCG 57.255 39.130 0.00 0.00 0.00 5.73
1948 2169 7.201487 GCAAAACATTCAACGTAAATATTCCCC 60.201 37.037 0.00 0.00 0.00 4.81
1949 2170 7.462200 CGCAAAACATTCAACGTAAATATTCCC 60.462 37.037 0.00 0.00 0.00 3.97
1950 2171 7.380320 CGCAAAACATTCAACGTAAATATTCC 58.620 34.615 0.00 0.00 0.00 3.01
1951 2172 6.887247 GCGCAAAACATTCAACGTAAATATTC 59.113 34.615 0.30 0.00 0.00 1.75
1952 2173 6.363626 TGCGCAAAACATTCAACGTAAATATT 59.636 30.769 8.16 0.00 0.00 1.28
1953 2174 5.859114 TGCGCAAAACATTCAACGTAAATAT 59.141 32.000 8.16 0.00 0.00 1.28
1954 2175 5.212934 TGCGCAAAACATTCAACGTAAATA 58.787 33.333 8.16 0.00 0.00 1.40
1955 2176 4.045104 TGCGCAAAACATTCAACGTAAAT 58.955 34.783 8.16 0.00 0.00 1.40
1956 2177 3.435566 TGCGCAAAACATTCAACGTAAA 58.564 36.364 8.16 0.00 0.00 2.01
1967 2188 4.002982 ACTATCTCAATCTGCGCAAAACA 58.997 39.130 13.05 0.00 0.00 2.83
1968 2189 4.337763 CACTATCTCAATCTGCGCAAAAC 58.662 43.478 13.05 0.00 0.00 2.43
2005 2226 4.458989 GTGGCCATCAACTCATCAAACTTA 59.541 41.667 9.72 0.00 0.00 2.24
2037 2258 1.079987 TCTTCTGCTGCCTCCTCCT 59.920 57.895 0.00 0.00 0.00 3.69
2087 2308 3.751518 ACAAAACCCATCCTGTCTACAC 58.248 45.455 0.00 0.00 0.00 2.90
2144 2365 2.038659 CTTCATCCTCTCTCTCACCCC 58.961 57.143 0.00 0.00 0.00 4.95
2148 2369 2.964464 GGCATCTTCATCCTCTCTCTCA 59.036 50.000 0.00 0.00 0.00 3.27
2168 2389 6.376978 GTTCACATTGATCAAGAACTGAAGG 58.623 40.000 22.42 9.86 37.67 3.46
2169 2390 6.206243 AGGTTCACATTGATCAAGAACTGAAG 59.794 38.462 25.82 13.96 37.67 3.02
2311 2532 1.819288 TCGTAGCAAGTCTTCCAGAGG 59.181 52.381 0.00 0.00 0.00 3.69
2379 2601 9.357652 CATGGTGTTATAGACTTTTGATTTTGG 57.642 33.333 0.00 0.00 0.00 3.28
2430 2652 8.183536 CGGAGACATCAAATTTTACATGATTGA 58.816 33.333 0.00 0.86 31.65 2.57
2433 2655 6.828273 TCCGGAGACATCAAATTTTACATGAT 59.172 34.615 0.00 0.00 34.22 2.45
2480 2702 3.878086 AGGAAGTCTTTGTTAGGGGGTA 58.122 45.455 0.00 0.00 0.00 3.69
2481 2703 2.714808 AGGAAGTCTTTGTTAGGGGGT 58.285 47.619 0.00 0.00 0.00 4.95
2588 2810 8.225603 TGCTACAAGATTTCAAACTCTTTCTT 57.774 30.769 0.00 0.00 29.34 2.52
2691 2915 2.317900 TCCTTCCTCCCAAGATACCAGA 59.682 50.000 0.00 0.00 0.00 3.86
2694 2918 1.769465 GGTCCTTCCTCCCAAGATACC 59.231 57.143 0.00 0.00 0.00 2.73
2736 2960 8.598075 GCTTAAATTTTGTTTGCTGATCCTATG 58.402 33.333 0.00 0.00 0.00 2.23
2758 2982 3.133362 CGTCATAAAGGGGTAGTGGCTTA 59.867 47.826 0.00 0.00 0.00 3.09
2807 3031 7.632462 GCAAGAAGATACTGATTGAGGAAGAGA 60.632 40.741 0.00 0.00 0.00 3.10
3018 3242 0.807496 GCACTGCCACATTTCCTCTC 59.193 55.000 0.00 0.00 0.00 3.20


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

AutoCloner maintained by Alex Coulton.