Multiple sequence alignment - TraesCS1A01G392200

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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 TraesCS1A01G392200 chr1A 100.000 2681 0 0 1 2681 558706211 558703531 0.000000e+00 4951
1 TraesCS1A01G392200 chr1A 94.485 544 28 1 1 544 75803279 75803820 0.000000e+00 837
2 TraesCS1A01G392200 chr1A 92.265 543 41 1 1 543 492619580 492620121 0.000000e+00 769
3 TraesCS1A01G392200 chr1A 91.042 547 44 2 1 543 492429757 492430302 0.000000e+00 734
4 TraesCS1A01G392200 chr1A 85.819 409 40 2 133 541 328802246 328801856 4.130000e-113 418
5 TraesCS1A01G392200 chr1A 84.293 191 11 12 133 323 441843787 441843616 4.590000e-38 169
6 TraesCS1A01G392200 chr1B 90.834 2182 108 41 547 2681 643279797 643277661 0.000000e+00 2837
7 TraesCS1A01G392200 chr1D 93.667 1658 66 21 542 2174 466495154 466493511 0.000000e+00 2444
8 TraesCS1A01G392200 chr7D 90.976 543 43 5 1 542 193241227 193240690 0.000000e+00 726
9 TraesCS1A01G392200 chr4D 90.203 541 45 5 1 540 439747696 439747163 0.000000e+00 699
10 TraesCS1A01G392200 chr6B 89.194 546 48 8 1 541 14160929 14160390 0.000000e+00 671
11 TraesCS1A01G392200 chr6B 88.372 172 13 7 1 170 715015349 715015183 1.630000e-47 200
12 TraesCS1A01G392200 chr5D 85.424 542 57 7 1 541 410380727 410380207 6.530000e-151 544
13 TraesCS1A01G392200 chr7B 89.628 376 39 0 166 541 33626883 33626508 1.870000e-131 479
14 TraesCS1A01G392200 chr4B 90.947 243 14 7 1 241 602729948 602730184 1.200000e-83 320


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 TraesCS1A01G392200 chr1A 558703531 558706211 2680 True 4951 4951 100.000 1 2681 1 chr1A.!!$R3 2680
1 TraesCS1A01G392200 chr1A 75803279 75803820 541 False 837 837 94.485 1 544 1 chr1A.!!$F1 543
2 TraesCS1A01G392200 chr1A 492619580 492620121 541 False 769 769 92.265 1 543 1 chr1A.!!$F3 542
3 TraesCS1A01G392200 chr1A 492429757 492430302 545 False 734 734 91.042 1 543 1 chr1A.!!$F2 542
4 TraesCS1A01G392200 chr1B 643277661 643279797 2136 True 2837 2837 90.834 547 2681 1 chr1B.!!$R1 2134
5 TraesCS1A01G392200 chr1D 466493511 466495154 1643 True 2444 2444 93.667 542 2174 1 chr1D.!!$R1 1632
6 TraesCS1A01G392200 chr7D 193240690 193241227 537 True 726 726 90.976 1 542 1 chr7D.!!$R1 541
7 TraesCS1A01G392200 chr4D 439747163 439747696 533 True 699 699 90.203 1 540 1 chr4D.!!$R1 539
8 TraesCS1A01G392200 chr6B 14160390 14160929 539 True 671 671 89.194 1 541 1 chr6B.!!$R1 540
9 TraesCS1A01G392200 chr5D 410380207 410380727 520 True 544 544 85.424 1 541 1 chr5D.!!$R1 540

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
373 386 0.806868 CACATCATGTCAGTGCCACC 59.193 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2362 2426 0.315886 TGGTGAAGCATTGCAAGCAG 59.684 50.0 18.74 7.58 0.0 4.24 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
358 371 1.691219 CTACAGTTGGGCCCCACAT 59.309 57.895 26.94 16.90 30.78 3.21
373 386 0.806868 CACATCATGTCAGTGCCACC 59.193 55.000 0.00 0.00 0.00 4.61
394 407 3.320826 CCTCATCCATATACGGTGACACA 59.679 47.826 8.08 0.00 0.00 3.72
609 625 0.984230 GTTCTCCCCTCCACACATCA 59.016 55.000 0.00 0.00 0.00 3.07
617 633 3.056607 CCCCTCCACACATCATTTGTTTC 60.057 47.826 0.00 0.00 36.00 2.78
624 640 6.479331 TCCACACATCATTTGTTTCACATTTG 59.521 34.615 0.00 0.00 36.00 2.32
625 641 6.258287 CCACACATCATTTGTTTCACATTTGT 59.742 34.615 0.00 0.00 36.00 2.83
627 643 8.176365 CACACATCATTTGTTTCACATTTGTTT 58.824 29.630 0.00 0.00 36.00 2.83
628 644 8.728833 ACACATCATTTGTTTCACATTTGTTTT 58.271 25.926 0.00 0.00 36.00 2.43
629 645 9.557338 CACATCATTTGTTTCACATTTGTTTTT 57.443 25.926 0.00 0.00 36.00 1.94
679 695 5.452777 GGTTAGGTACCGAACGACATATAC 58.547 45.833 25.68 10.24 37.12 1.47
680 696 5.239525 GGTTAGGTACCGAACGACATATACT 59.760 44.000 25.68 0.00 37.12 2.12
681 697 6.426937 GGTTAGGTACCGAACGACATATACTA 59.573 42.308 25.68 0.00 37.12 1.82
682 698 7.360438 GGTTAGGTACCGAACGACATATACTAG 60.360 44.444 25.68 0.00 37.12 2.57
684 700 4.997395 GGTACCGAACGACATATACTAGGA 59.003 45.833 0.00 0.00 0.00 2.94
685 701 5.106908 GGTACCGAACGACATATACTAGGAC 60.107 48.000 0.00 0.00 0.00 3.85
727 765 1.565390 CCCCTTGTCAGCCTCATCCA 61.565 60.000 0.00 0.00 0.00 3.41
890 928 4.821589 CAGCCGTCGCTTCCTCCC 62.822 72.222 0.00 0.00 45.55 4.30
909 947 2.046700 TTCAACGGCCCCGATCAC 60.047 61.111 14.44 0.00 42.83 3.06
1323 1366 3.465403 CTCCCGGACCTCCTGCTG 61.465 72.222 0.73 0.00 0.00 4.41
1689 1732 2.508663 GGCTCGTAACGTCCAGCC 60.509 66.667 10.27 10.27 44.63 4.85
1696 1739 0.179108 GTAACGTCCAGCCAGCTAGG 60.179 60.000 0.00 0.00 41.84 3.02
1704 1747 1.381872 AGCCAGCTAGGTCGGTCAT 60.382 57.895 10.70 0.00 40.61 3.06
1892 1935 4.077188 GCGTGCTGTTGACCGAGC 62.077 66.667 0.00 0.00 35.65 5.03
1960 2017 6.220726 ACTAAGAAAGTGCATGTTGGTTTT 57.779 33.333 0.00 0.00 36.93 2.43
1980 2037 0.317854 GTTGACAAGTCGGCCTTTGC 60.318 55.000 0.00 0.83 0.00 3.68
1981 2038 0.465460 TTGACAAGTCGGCCTTTGCT 60.465 50.000 0.00 0.00 37.74 3.91
1982 2039 0.465460 TGACAAGTCGGCCTTTGCTT 60.465 50.000 0.00 0.00 37.74 3.91
1983 2040 0.238553 GACAAGTCGGCCTTTGCTTC 59.761 55.000 0.00 0.00 37.74 3.86
1984 2041 0.179018 ACAAGTCGGCCTTTGCTTCT 60.179 50.000 0.00 0.00 37.74 2.85
2011 2068 3.444034 TCTTCTCTTCTCGTGGTATGGTG 59.556 47.826 0.00 0.00 0.00 4.17
2060 2117 3.303791 GCGGACGACTCAATGAAAACTTT 60.304 43.478 0.00 0.00 0.00 2.66
2064 2122 6.262601 GGACGACTCAATGAAAACTTTGAAA 58.737 36.000 0.00 0.00 0.00 2.69
2065 2123 6.750039 GGACGACTCAATGAAAACTTTGAAAA 59.250 34.615 0.00 0.00 0.00 2.29
2077 2135 9.195411 TGAAAACTTTGAAAACTCATATCATGC 57.805 29.630 0.00 0.00 0.00 4.06
2109 2167 6.313905 GGATCTATAACGTGGGCTATTGATTG 59.686 42.308 0.00 0.00 0.00 2.67
2111 2169 6.220930 TCTATAACGTGGGCTATTGATTGAC 58.779 40.000 0.00 0.00 0.00 3.18
2148 2206 1.204704 CACGTGGGCTACTGATTGAGA 59.795 52.381 7.95 0.00 0.00 3.27
2149 2207 1.899814 ACGTGGGCTACTGATTGAGAA 59.100 47.619 0.00 0.00 0.00 2.87
2153 2211 4.376146 GTGGGCTACTGATTGAGAATCTC 58.624 47.826 2.75 2.75 38.72 2.75
2154 2212 4.033009 TGGGCTACTGATTGAGAATCTCA 58.967 43.478 9.18 9.18 38.87 3.27
2155 2213 4.657504 TGGGCTACTGATTGAGAATCTCAT 59.342 41.667 14.31 4.46 40.39 2.90
2157 2215 5.454471 GGGCTACTGATTGAGAATCTCATGT 60.454 44.000 14.31 12.39 40.39 3.21
2170 2228 9.194972 TGAGAATCTCATGTTCTTACTGATACT 57.805 33.333 9.18 0.00 35.39 2.12
2171 2229 9.462174 GAGAATCTCATGTTCTTACTGATACTG 57.538 37.037 5.22 0.00 36.13 2.74
2172 2230 7.925483 AGAATCTCATGTTCTTACTGATACTGC 59.075 37.037 0.00 0.00 32.17 4.40
2173 2231 5.582550 TCTCATGTTCTTACTGATACTGCG 58.417 41.667 0.00 0.00 0.00 5.18
2174 2232 4.112634 TCATGTTCTTACTGATACTGCGC 58.887 43.478 0.00 0.00 0.00 6.09
2175 2233 2.888594 TGTTCTTACTGATACTGCGCC 58.111 47.619 4.18 0.00 0.00 6.53
2176 2234 2.202566 GTTCTTACTGATACTGCGCCC 58.797 52.381 4.18 0.00 0.00 6.13
2177 2235 0.384309 TCTTACTGATACTGCGCCCG 59.616 55.000 4.18 0.00 0.00 6.13
2178 2236 1.215655 CTTACTGATACTGCGCCCGC 61.216 60.000 4.18 5.60 42.35 6.13
2179 2237 2.638330 TTACTGATACTGCGCCCGCC 62.638 60.000 4.18 0.00 41.09 6.13
2180 2238 4.227134 CTGATACTGCGCCCGCCT 62.227 66.667 4.18 0.00 41.09 5.52
2181 2239 2.835895 TGATACTGCGCCCGCCTA 60.836 61.111 4.18 0.17 41.09 3.93
2182 2240 2.159819 CTGATACTGCGCCCGCCTAT 62.160 60.000 4.18 5.09 41.09 2.57
2183 2241 1.738099 GATACTGCGCCCGCCTATG 60.738 63.158 4.18 0.96 41.09 2.23
2184 2242 3.883744 ATACTGCGCCCGCCTATGC 62.884 63.158 4.18 0.00 41.09 3.14
2189 2247 2.591429 CGCCCGCCTATGCATGAA 60.591 61.111 10.16 0.00 37.32 2.57
2190 2248 2.186160 CGCCCGCCTATGCATGAAA 61.186 57.895 10.16 0.00 37.32 2.69
2191 2249 1.723608 CGCCCGCCTATGCATGAAAA 61.724 55.000 10.16 0.00 37.32 2.29
2205 2263 4.989797 TGCATGAAAATTGCACTTAACCAG 59.010 37.500 0.00 0.00 44.73 4.00
2207 2265 4.662468 TGAAAATTGCACTTAACCAGCA 57.338 36.364 0.00 0.00 36.32 4.41
2216 2274 4.399618 TGCACTTAACCAGCAGTAAAAACA 59.600 37.500 0.00 0.00 33.75 2.83
2220 2278 7.671827 CACTTAACCAGCAGTAAAAACAAAAC 58.328 34.615 0.00 0.00 0.00 2.43
2222 2280 7.873505 ACTTAACCAGCAGTAAAAACAAAACAA 59.126 29.630 0.00 0.00 0.00 2.83
2252 2316 7.069569 CAGAAAAGATGCAATTGAAAAAGCTG 58.930 34.615 10.34 2.82 32.91 4.24
2255 2319 5.204409 AGATGCAATTGAAAAAGCTGTCA 57.796 34.783 10.34 0.00 32.91 3.58
2266 2330 5.596361 TGAAAAAGCTGTCACCATTTTAGGA 59.404 36.000 0.00 0.00 0.00 2.94
2267 2331 6.267471 TGAAAAAGCTGTCACCATTTTAGGAT 59.733 34.615 0.00 0.00 0.00 3.24
2268 2332 6.670695 AAAAGCTGTCACCATTTTAGGATT 57.329 33.333 0.00 0.00 0.00 3.01
2269 2333 6.670695 AAAGCTGTCACCATTTTAGGATTT 57.329 33.333 0.00 0.00 0.00 2.17
2308 2372 1.999051 GCACTCGCCAATAGACACG 59.001 57.895 0.00 0.00 0.00 4.49
2321 2385 6.670233 CCAATAGACACGAGATCTAGTAACC 58.330 44.000 8.26 1.44 32.27 2.85
2325 2389 2.613133 ACACGAGATCTAGTAACCGCTC 59.387 50.000 8.26 0.00 0.00 5.03
2341 2405 4.385825 ACCGCTCAAGAAACAATAGTTGA 58.614 39.130 0.00 0.00 38.17 3.18
2357 2421 0.684535 TTGAAGCATCACCTCACGGA 59.315 50.000 0.00 0.00 34.61 4.69
2362 2426 1.448540 CATCACCTCACGGAGCACC 60.449 63.158 0.00 0.00 0.00 5.01
2379 2443 0.316204 ACCTGCTTGCAATGCTTCAC 59.684 50.000 17.72 0.00 37.94 3.18
2385 2449 0.527113 TTGCAATGCTTCACCATCGG 59.473 50.000 6.82 0.00 0.00 4.18
2397 2461 2.885644 CATCGGTCCAAGTCGCCG 60.886 66.667 0.00 0.00 46.12 6.46
2417 2481 2.033448 CCAACAGCCCGCCAACTA 59.967 61.111 0.00 0.00 0.00 2.24
2468 2532 4.032310 AGATCTGAAGAGAGCCAACAGAT 58.968 43.478 0.00 0.00 46.42 2.90
2472 2536 0.107945 AAGAGAGCCAACAGATCCGC 60.108 55.000 0.00 0.00 0.00 5.54
2488 2552 2.985847 GCCAACACCTGCCCTCAC 60.986 66.667 0.00 0.00 0.00 3.51
2492 2556 0.538057 CAACACCTGCCCTCACATGT 60.538 55.000 0.00 0.00 0.00 3.21
2504 2568 0.107643 TCACATGTCCTTTGTCGGCA 59.892 50.000 0.00 0.00 0.00 5.69
2505 2569 1.167851 CACATGTCCTTTGTCGGCAT 58.832 50.000 0.00 0.00 0.00 4.40
2529 2593 4.081642 TGGATCAAGTGTTGTAGAGGTAGC 60.082 45.833 0.00 0.00 0.00 3.58
2532 2596 3.570975 TCAAGTGTTGTAGAGGTAGCGAA 59.429 43.478 0.00 0.00 0.00 4.70
2564 2628 0.391661 TCTTCCAACAGCTCATCGCC 60.392 55.000 0.00 0.00 40.39 5.54
2574 2642 0.661552 GCTCATCGCCGTCACTAGTA 59.338 55.000 0.00 0.00 0.00 1.82
2583 2651 3.003378 CGCCGTCACTAGTAGATCAATGA 59.997 47.826 3.59 0.00 0.00 2.57
2592 2660 7.230309 TCACTAGTAGATCAATGATGTCAGGAG 59.770 40.741 0.00 0.00 0.00 3.69
2650 2718 5.718146 TCTTCATTATTTTGCCATTGCGAA 58.282 33.333 0.00 0.00 41.78 4.70
2669 2738 4.792704 GCGAAAAACTTGCATTGGAAGAGA 60.793 41.667 22.76 0.00 34.14 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
173 185 1.068588 TGCGCTAGCCACTATACCAAG 59.931 52.381 9.73 0.00 44.33 3.61
358 371 0.986527 ATGAGGTGGCACTGACATGA 59.013 50.000 18.45 0.00 0.00 3.07
373 386 4.584327 TGTGTCACCGTATATGGATGAG 57.416 45.455 18.22 4.83 0.00 2.90
394 407 6.239217 TCTGTAGACATAAAGTGCATCCAT 57.761 37.500 0.00 0.00 0.00 3.41
438 451 5.049267 GGTTCTAAAACTTGGCATGAACGTA 60.049 40.000 7.45 0.00 35.61 3.57
487 500 7.701539 TGTCATGGATGTTTATTTTAGTGCT 57.298 32.000 0.00 0.00 0.00 4.40
498 511 4.341806 TGCTTGAACTTGTCATGGATGTTT 59.658 37.500 0.00 0.00 35.70 2.83
617 633 6.197981 GGTTGCCATGTTAAAAACAAATGTG 58.802 36.000 0.00 0.00 45.86 3.21
624 640 2.219903 GTGCGGTTGCCATGTTAAAAAC 59.780 45.455 0.00 0.00 41.78 2.43
625 641 2.159099 TGTGCGGTTGCCATGTTAAAAA 60.159 40.909 0.00 0.00 41.78 1.94
627 643 1.032794 TGTGCGGTTGCCATGTTAAA 58.967 45.000 0.00 0.00 41.78 1.52
628 644 1.067985 CATGTGCGGTTGCCATGTTAA 60.068 47.619 9.24 0.00 41.19 2.01
629 645 0.525311 CATGTGCGGTTGCCATGTTA 59.475 50.000 9.24 0.00 41.19 2.41
632 648 0.526739 CATCATGTGCGGTTGCCATG 60.527 55.000 10.50 10.50 44.39 3.66
633 649 1.811195 CATCATGTGCGGTTGCCAT 59.189 52.632 0.00 0.00 41.78 4.40
656 672 2.947448 ATGTCGTTCGGTACCTAACC 57.053 50.000 20.36 10.22 45.77 2.85
666 682 4.852104 GCATGTCCTAGTATATGTCGTTCG 59.148 45.833 0.00 0.00 0.00 3.95
684 700 2.669569 GTGCCAGTGGACGCATGT 60.670 61.111 15.20 0.00 37.33 3.21
685 701 3.792047 CGTGCCAGTGGACGCATG 61.792 66.667 15.20 5.46 37.33 4.06
712 750 1.300963 GGCTGGATGAGGCTGACAA 59.699 57.895 0.00 0.00 44.09 3.18
890 928 3.192922 GATCGGGGCCGTTGAACG 61.193 66.667 11.30 11.30 42.11 3.95
892 930 2.046700 GTGATCGGGGCCGTTGAA 60.047 61.111 0.00 0.00 40.74 2.69
909 947 0.536460 ACTTATAAATGGCGGCGGGG 60.536 55.000 9.78 0.00 0.00 5.73
911 949 1.802365 GGTACTTATAAATGGCGGCGG 59.198 52.381 9.78 0.00 0.00 6.13
947 985 0.035458 GGTGGTACAGTGAGCTTGCT 59.965 55.000 0.00 0.00 41.80 3.91
976 1019 2.302157 TCCGGTTCTCTCCCTTTTCTTC 59.698 50.000 0.00 0.00 0.00 2.87
977 1020 2.038689 GTCCGGTTCTCTCCCTTTTCTT 59.961 50.000 0.00 0.00 0.00 2.52
1608 1651 4.241555 ATCTCCATGTCCGCCGCC 62.242 66.667 0.00 0.00 0.00 6.13
1635 1678 0.797249 CGTACTTGAGCCCGAACTCG 60.797 60.000 0.00 0.00 39.68 4.18
1689 1732 1.335415 CGATGATGACCGACCTAGCTG 60.335 57.143 0.00 0.00 0.00 4.24
1696 1739 3.330853 GCGCCGATGATGACCGAC 61.331 66.667 0.00 0.00 0.00 4.79
1892 1935 6.955963 GTGTCTCTGCATTTTATTACTTGTCG 59.044 38.462 0.00 0.00 0.00 4.35
1960 2017 1.021202 CAAAGGCCGACTTGTCAACA 58.979 50.000 0.00 0.00 39.96 3.33
1980 2037 5.391950 CCACGAGAAGAGAAGAGAAGAGAAG 60.392 48.000 0.00 0.00 0.00 2.85
1981 2038 4.457603 CCACGAGAAGAGAAGAGAAGAGAA 59.542 45.833 0.00 0.00 0.00 2.87
1982 2039 4.006989 CCACGAGAAGAGAAGAGAAGAGA 58.993 47.826 0.00 0.00 0.00 3.10
1983 2040 3.756434 ACCACGAGAAGAGAAGAGAAGAG 59.244 47.826 0.00 0.00 0.00 2.85
1984 2041 3.757270 ACCACGAGAAGAGAAGAGAAGA 58.243 45.455 0.00 0.00 0.00 2.87
2029 2086 1.270094 TGAGTCGTCCGCTTTCATGTT 60.270 47.619 0.00 0.00 0.00 2.71
2032 2089 2.002586 CATTGAGTCGTCCGCTTTCAT 58.997 47.619 0.00 0.00 0.00 2.57
2060 2117 4.260985 ACGGTGCATGATATGAGTTTTCA 58.739 39.130 0.00 0.00 37.81 2.69
2064 2122 2.473816 CGACGGTGCATGATATGAGTT 58.526 47.619 0.00 0.00 0.00 3.01
2065 2123 1.269778 CCGACGGTGCATGATATGAGT 60.270 52.381 5.48 0.00 0.00 3.41
2077 2135 2.603892 CCACGTTATAGATCCGACGGTG 60.604 54.545 14.79 0.04 39.63 4.94
2109 2167 4.047822 CGTGAAATCCTAGCATGAGAGTC 58.952 47.826 0.00 0.00 0.00 3.36
2111 2169 3.801050 CACGTGAAATCCTAGCATGAGAG 59.199 47.826 10.90 0.00 0.00 3.20
2148 2206 6.699204 CGCAGTATCAGTAAGAACATGAGATT 59.301 38.462 0.00 0.00 0.00 2.40
2149 2207 6.212235 CGCAGTATCAGTAAGAACATGAGAT 58.788 40.000 0.00 0.00 0.00 2.75
2153 2211 3.246226 GGCGCAGTATCAGTAAGAACATG 59.754 47.826 10.83 0.00 0.00 3.21
2154 2212 3.458189 GGCGCAGTATCAGTAAGAACAT 58.542 45.455 10.83 0.00 0.00 2.71
2155 2213 2.418197 GGGCGCAGTATCAGTAAGAACA 60.418 50.000 10.83 0.00 0.00 3.18
2157 2215 1.202371 CGGGCGCAGTATCAGTAAGAA 60.202 52.381 10.83 0.00 0.00 2.52
2172 2230 1.723608 TTTTCATGCATAGGCGGGCG 61.724 55.000 0.00 0.00 45.35 6.13
2173 2231 0.675633 ATTTTCATGCATAGGCGGGC 59.324 50.000 0.00 0.00 45.35 6.13
2174 2232 2.746269 CAATTTTCATGCATAGGCGGG 58.254 47.619 0.00 0.00 45.35 6.13
2175 2233 2.129607 GCAATTTTCATGCATAGGCGG 58.870 47.619 0.00 0.00 45.35 6.13
2183 2241 4.143052 GCTGGTTAAGTGCAATTTTCATGC 60.143 41.667 4.05 1.50 44.08 4.06
2184 2242 4.989797 TGCTGGTTAAGTGCAATTTTCATG 59.010 37.500 4.05 0.00 33.48 3.07
2185 2243 5.212532 TGCTGGTTAAGTGCAATTTTCAT 57.787 34.783 4.05 0.00 33.48 2.57
2186 2244 4.099266 ACTGCTGGTTAAGTGCAATTTTCA 59.901 37.500 4.05 0.66 36.22 2.69
2187 2245 4.620982 ACTGCTGGTTAAGTGCAATTTTC 58.379 39.130 4.05 0.00 36.22 2.29
2188 2246 4.670896 ACTGCTGGTTAAGTGCAATTTT 57.329 36.364 4.05 0.00 36.22 1.82
2189 2247 5.782893 TTACTGCTGGTTAAGTGCAATTT 57.217 34.783 4.05 0.00 36.22 1.82
2190 2248 5.782893 TTTACTGCTGGTTAAGTGCAATT 57.217 34.783 4.23 4.23 36.22 2.32
2191 2249 5.782893 TTTTACTGCTGGTTAAGTGCAAT 57.217 34.783 0.00 0.00 36.22 3.56
2227 2285 7.069569 CAGCTTTTTCAATTGCATCTTTTCTG 58.930 34.615 0.00 0.00 0.00 3.02
2236 2300 3.118847 TGGTGACAGCTTTTTCAATTGCA 60.119 39.130 6.17 0.00 35.01 4.08
2237 2301 3.456280 TGGTGACAGCTTTTTCAATTGC 58.544 40.909 6.17 0.00 35.01 3.56
2300 2364 4.451774 GCGGTTACTAGATCTCGTGTCTAT 59.548 45.833 10.04 0.00 0.00 1.98
2308 2372 5.502153 TTCTTGAGCGGTTACTAGATCTC 57.498 43.478 0.00 0.00 0.00 2.75
2321 2385 4.848299 GCTTCAACTATTGTTTCTTGAGCG 59.152 41.667 0.00 0.00 33.52 5.03
2325 2389 6.583806 GGTGATGCTTCAACTATTGTTTCTTG 59.416 38.462 10.27 0.00 36.59 3.02
2362 2426 0.315886 TGGTGAAGCATTGCAAGCAG 59.684 50.000 18.74 7.58 0.00 4.24
2373 2437 0.321653 ACTTGGACCGATGGTGAAGC 60.322 55.000 0.00 0.00 35.25 3.86
2379 2443 2.511600 GGCGACTTGGACCGATGG 60.512 66.667 0.00 0.00 0.00 3.51
2385 2449 4.980805 TGGTGCGGCGACTTGGAC 62.981 66.667 12.98 0.00 0.00 4.02
2413 2477 9.826574 TTAGTGTGTTAATCAAGTGAAGTAGTT 57.173 29.630 0.00 0.00 0.00 2.24
2444 2508 5.019470 TCTGTTGGCTCTCTTCAGATCTTA 58.981 41.667 0.00 0.00 31.51 2.10
2460 2524 1.586154 GGTGTTGGCGGATCTGTTGG 61.586 60.000 2.89 0.00 0.00 3.77
2472 2536 1.075482 ATGTGAGGGCAGGTGTTGG 59.925 57.895 0.00 0.00 0.00 3.77
2488 2552 1.135315 CCAATGCCGACAAAGGACATG 60.135 52.381 0.00 0.00 31.67 3.21
2492 2556 1.004161 TGATCCAATGCCGACAAAGGA 59.996 47.619 0.00 0.00 37.26 3.36
2504 2568 5.505181 ACCTCTACAACACTTGATCCAAT 57.495 39.130 0.00 0.00 0.00 3.16
2505 2569 4.974645 ACCTCTACAACACTTGATCCAA 57.025 40.909 0.00 0.00 0.00 3.53
2529 2593 6.316140 TGTTGGAAGATATCATCAGGTTTTCG 59.684 38.462 9.96 0.00 0.00 3.46
2532 2596 5.591877 GCTGTTGGAAGATATCATCAGGTTT 59.408 40.000 9.96 0.00 33.62 3.27
2564 2628 6.729187 TGACATCATTGATCTACTAGTGACG 58.271 40.000 5.39 0.00 0.00 4.35
2574 2642 4.035814 TGGTCTCCTGACATCATTGATCT 58.964 43.478 0.00 0.00 44.61 2.75
2583 2651 4.392940 CTCAAGTTTTGGTCTCCTGACAT 58.607 43.478 0.00 0.00 44.61 3.06
2592 2660 4.729227 TTGTTTCCCTCAAGTTTTGGTC 57.271 40.909 0.00 0.00 0.00 4.02
2650 2718 4.895297 TCCTTCTCTTCCAATGCAAGTTTT 59.105 37.500 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.