Multiple sequence alignment - TraesCS3B01G084300

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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 TraesCS3B01G084300 chr3B 100.000 2402 0 0 1 2402 53200618 53198217 0.000000e+00 4436.0
1 TraesCS3B01G084300 chr3B 83.974 780 86 22 678 1440 50397720 50398477 0.000000e+00 712.0
2 TraesCS3B01G084300 chr3B 80.022 921 112 39 729 1622 50413570 50414445 1.220000e-172 616.0
3 TraesCS3B01G084300 chr3A 88.746 853 66 16 810 1644 42320471 42319631 0.000000e+00 1016.0
4 TraesCS3B01G084300 chr3A 86.185 637 64 12 1636 2270 42319586 42318972 0.000000e+00 667.0
5 TraesCS3B01G084300 chr3A 84.793 651 69 11 1001 1639 40173113 40173745 5.640000e-176 627.0
6 TraesCS3B01G084300 chr3A 81.297 802 83 31 35 817 42321247 42320494 2.660000e-164 588.0
7 TraesCS3B01G084300 chr3A 83.107 663 85 20 753 1396 40185417 40186071 1.600000e-161 579.0
8 TraesCS3B01G084300 chr3A 85.988 521 54 9 1134 1642 42389985 42389472 7.550000e-150 540.0
9 TraesCS3B01G084300 chr3A 80.855 491 82 9 1884 2369 495248076 495248559 2.250000e-100 375.0
10 TraesCS3B01G084300 chr3D 89.217 779 64 16 872 1644 30374831 30374067 0.000000e+00 955.0
11 TraesCS3B01G084300 chr3D 84.109 988 111 25 678 1642 29607673 29608637 0.000000e+00 913.0
12 TraesCS3B01G084300 chr3D 87.958 764 83 7 1636 2394 30374022 30373263 0.000000e+00 893.0
13 TraesCS3B01G084300 chr3D 87.398 492 43 13 343 822 30375337 30374853 4.510000e-152 547.0
14 TraesCS3B01G084300 chr3D 78.756 579 91 17 1076 1640 29410463 29411023 2.270000e-95 359.0
15 TraesCS3B01G084300 chr3D 84.182 373 38 16 729 1086 29615209 29615575 2.290000e-90 342.0
16 TraesCS3B01G084300 chr3D 85.030 167 20 5 935 1099 29623805 29623968 5.310000e-37 165.0
17 TraesCS3B01G084300 chr3D 80.583 206 34 4 2072 2273 588129315 588129518 1.150000e-33 154.0
18 TraesCS3B01G084300 chr5B 83.270 526 80 6 1883 2402 497008280 497008803 6.010000e-131 477.0
19 TraesCS3B01G084300 chr5D 82.868 537 62 21 1883 2402 412623221 412623744 2.810000e-124 455.0
20 TraesCS3B01G084300 chr2D 82.081 519 82 7 1883 2399 496446660 496447169 1.320000e-117 433.0
21 TraesCS3B01G084300 chr6D 82.066 513 76 13 1899 2402 60059952 60059447 7.940000e-115 424.0
22 TraesCS3B01G084300 chr5A 82.587 402 63 4 1984 2381 524735586 524735984 4.910000e-92 348.0
23 TraesCS3B01G084300 chr5A 80.797 276 50 3 2128 2402 32165052 32164779 1.870000e-51 213.0
24 TraesCS3B01G084300 chr5A 73.029 482 100 16 1908 2384 402159088 402158632 2.490000e-30 143.0
25 TraesCS3B01G084300 chr1A 79.087 526 89 14 1883 2402 30791745 30792255 2.290000e-90 342.0
26 TraesCS3B01G084300 chr1A 75.778 450 97 11 1938 2381 510613843 510614286 1.450000e-52 217.0
27 TraesCS3B01G084300 chr7A 84.507 71 10 1 1883 1953 628387798 628387867 4.280000e-08 69.4


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 TraesCS3B01G084300 chr3B 53198217 53200618 2401 True 4436.000000 4436 100.000000 1 2402 1 chr3B.!!$R1 2401
1 TraesCS3B01G084300 chr3B 50397720 50398477 757 False 712.000000 712 83.974000 678 1440 1 chr3B.!!$F1 762
2 TraesCS3B01G084300 chr3B 50413570 50414445 875 False 616.000000 616 80.022000 729 1622 1 chr3B.!!$F2 893
3 TraesCS3B01G084300 chr3A 42318972 42321247 2275 True 757.000000 1016 85.409333 35 2270 3 chr3A.!!$R2 2235
4 TraesCS3B01G084300 chr3A 40173113 40173745 632 False 627.000000 627 84.793000 1001 1639 1 chr3A.!!$F1 638
5 TraesCS3B01G084300 chr3A 40185417 40186071 654 False 579.000000 579 83.107000 753 1396 1 chr3A.!!$F2 643
6 TraesCS3B01G084300 chr3A 42389472 42389985 513 True 540.000000 540 85.988000 1134 1642 1 chr3A.!!$R1 508
7 TraesCS3B01G084300 chr3D 29607673 29608637 964 False 913.000000 913 84.109000 678 1642 1 chr3D.!!$F2 964
8 TraesCS3B01G084300 chr3D 30373263 30375337 2074 True 798.333333 955 88.191000 343 2394 3 chr3D.!!$R1 2051
9 TraesCS3B01G084300 chr3D 29410463 29411023 560 False 359.000000 359 78.756000 1076 1640 1 chr3D.!!$F1 564
10 TraesCS3B01G084300 chr5B 497008280 497008803 523 False 477.000000 477 83.270000 1883 2402 1 chr5B.!!$F1 519
11 TraesCS3B01G084300 chr5D 412623221 412623744 523 False 455.000000 455 82.868000 1883 2402 1 chr5D.!!$F1 519
12 TraesCS3B01G084300 chr2D 496446660 496447169 509 False 433.000000 433 82.081000 1883 2399 1 chr2D.!!$F1 516
13 TraesCS3B01G084300 chr6D 60059447 60059952 505 True 424.000000 424 82.066000 1899 2402 1 chr6D.!!$R1 503
14 TraesCS3B01G084300 chr1A 30791745 30792255 510 False 342.000000 342 79.087000 1883 2402 1 chr1A.!!$F1 519

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
889 959 0.179 ATAGCTAGGCAGGCACACAC 59.821 55.0 0.0 0.0 0.0 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 2138 1.841302 TTCAAGGACGGAGCATGGCT 61.841 55.0 0.0 0.0 43.88 4.75 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
27 28 9.715123 AAAAATGCTTTAAACTTCGAATTTTGG 57.285 25.926 20.12 12.37 0.00 3.28
28 29 8.432110 AAATGCTTTAAACTTCGAATTTTGGT 57.568 26.923 20.12 2.70 0.00 3.67
29 30 7.637709 ATGCTTTAAACTTCGAATTTTGGTC 57.362 32.000 20.12 9.39 0.00 4.02
30 31 6.565234 TGCTTTAAACTTCGAATTTTGGTCA 58.435 32.000 20.12 11.29 0.00 4.02
31 32 6.474102 TGCTTTAAACTTCGAATTTTGGTCAC 59.526 34.615 20.12 8.90 0.00 3.67
32 33 6.474102 GCTTTAAACTTCGAATTTTGGTCACA 59.526 34.615 20.12 0.28 0.00 3.58
33 34 7.009723 GCTTTAAACTTCGAATTTTGGTCACAA 59.990 33.333 20.12 5.83 34.07 3.33
37 38 6.056428 ACTTCGAATTTTGGTCACAACTAC 57.944 37.500 0.00 0.00 36.06 2.73
140 142 9.996554 ATTCAGTATTTCAAAAGTTTTTAGGGG 57.003 29.630 0.00 0.00 0.00 4.79
142 144 8.635328 TCAGTATTTCAAAAGTTTTTAGGGGAC 58.365 33.333 0.00 0.00 0.00 4.46
152 154 6.800072 AGTTTTTAGGGGACATTTGTTGAA 57.200 33.333 0.00 0.00 0.00 2.69
155 157 7.931407 AGTTTTTAGGGGACATTTGTTGAATTC 59.069 33.333 0.00 0.00 0.00 2.17
156 158 6.985653 TTTAGGGGACATTTGTTGAATTCA 57.014 33.333 3.38 3.38 0.00 2.57
170 172 8.854979 TTGTTGAATTCACATGAGTAGTTTTG 57.145 30.769 7.89 0.00 0.00 2.44
181 183 9.903682 CACATGAGTAGTTTTGAATTTTCATCT 57.096 29.630 0.00 0.00 37.00 2.90
306 308 9.938280 AATTGAATTCATGAACATTGTCTGAAT 57.062 25.926 11.07 12.70 37.98 2.57
308 310 9.844790 TTGAATTCATGAACATTGTCTGAATAC 57.155 29.630 11.07 0.00 35.96 1.89
309 311 9.012161 TGAATTCATGAACATTGTCTGAATACA 57.988 29.630 11.07 0.00 35.96 2.29
310 312 9.844790 GAATTCATGAACATTGTCTGAATACAA 57.155 29.630 11.07 0.00 43.16 2.41
311 313 9.850628 AATTCATGAACATTGTCTGAATACAAG 57.149 29.630 11.07 0.00 42.33 3.16
312 314 8.620116 TTCATGAACATTGTCTGAATACAAGA 57.380 30.769 3.38 0.00 42.33 3.02
313 315 8.620116 TCATGAACATTGTCTGAATACAAGAA 57.380 30.769 0.00 0.00 42.33 2.52
314 316 8.506437 TCATGAACATTGTCTGAATACAAGAAC 58.494 33.333 0.00 0.00 42.33 3.01
315 317 7.800155 TGAACATTGTCTGAATACAAGAACA 57.200 32.000 0.00 0.00 42.33 3.18
316 318 8.394971 TGAACATTGTCTGAATACAAGAACAT 57.605 30.769 0.00 0.00 42.33 2.71
317 319 8.849168 TGAACATTGTCTGAATACAAGAACATT 58.151 29.630 0.00 0.00 42.33 2.71
318 320 9.683069 GAACATTGTCTGAATACAAGAACATTT 57.317 29.630 0.00 0.00 42.33 2.32
324 326 9.299963 TGTCTGAATACAAGAACATTTTGTTTG 57.700 29.630 0.00 0.00 41.28 2.93
438 448 6.257849 GGGACCAAAGAAAAGAATTGACAAAC 59.742 38.462 0.00 0.00 0.00 2.93
439 449 6.816140 GGACCAAAGAAAAGAATTGACAAACA 59.184 34.615 0.00 0.00 0.00 2.83
443 453 9.890352 CCAAAGAAAAGAATTGACAAACAAAAA 57.110 25.926 0.00 0.00 42.03 1.94
451 463 8.130307 AGAATTGACAAACAAAAACATACTGC 57.870 30.769 0.00 0.00 42.03 4.40
524 536 0.609662 TCTGAGCATACACAGCAGCA 59.390 50.000 0.00 0.00 34.79 4.41
527 539 0.392193 GAGCATACACAGCAGCACCT 60.392 55.000 0.00 0.00 0.00 4.00
543 555 3.055094 AGCACCTGTATTCTGTGGGTTAG 60.055 47.826 0.00 0.00 0.00 2.34
584 596 8.242053 ACTGCAAGAAGTAATGATTCTCAAATG 58.758 33.333 0.00 0.00 35.98 2.32
606 618 4.155826 TGAAAATGTGCAAGGAGTAATCCG 59.844 41.667 3.06 0.00 34.28 4.18
743 771 8.641498 AATCACAATCAGTAAGTTCTTCCATT 57.359 30.769 0.00 0.00 0.00 3.16
888 958 1.788229 TATAGCTAGGCAGGCACACA 58.212 50.000 0.00 0.00 0.00 3.72
889 959 0.179000 ATAGCTAGGCAGGCACACAC 59.821 55.000 0.00 0.00 0.00 3.82
899 969 2.415893 GCAGGCACACACCAATGTATTC 60.416 50.000 0.00 0.00 36.72 1.75
902 972 2.414029 GGCACACACCAATGTATTCACG 60.414 50.000 0.00 0.00 36.72 4.35
966 1041 4.143452 GGAAAAGAAGAACTGTACGTACGC 60.143 45.833 20.18 9.85 0.00 4.42
967 1042 3.631145 AAGAAGAACTGTACGTACGCA 57.369 42.857 20.18 5.21 0.00 5.24
1081 1161 0.901580 CATGGCTGCCACCCTTCTTT 60.902 55.000 25.99 1.71 35.80 2.52
1099 1179 3.699955 TTCTCCTCATGCGACGCCG 62.700 63.158 18.69 8.79 39.16 6.46
1151 1233 8.454894 TCTATTTAATTTGCAATGTCGCTGTTA 58.545 29.630 0.00 0.00 0.00 2.41
1172 1262 6.256539 TGTTAAGATCAGACGATGAAGCAATC 59.743 38.462 0.00 0.00 42.53 2.67
1312 1406 1.300620 CCAAACTGCACCGACGAGA 60.301 57.895 0.00 0.00 0.00 4.04
1314 1408 1.664965 AAACTGCACCGACGAGAGC 60.665 57.895 0.00 0.00 0.00 4.09
1322 1416 1.515952 CCGACGAGAGCTGCAAGAG 60.516 63.158 1.02 0.00 34.07 2.85
1353 1447 4.101790 GGCAACATGTCGCCGGTG 62.102 66.667 13.01 9.28 38.82 4.94
1375 1469 1.159285 CGAGGCTTTCTGCAATGACA 58.841 50.000 0.00 0.00 45.15 3.58
1469 1573 9.393512 GATGCCAATAATATAAGCAAGAGATCT 57.606 33.333 0.00 0.00 36.95 2.75
1531 1647 7.430441 AGTAACAATTTTACCATTGTGTGTCC 58.570 34.615 0.00 0.00 44.95 4.02
1545 1661 1.314730 GTGTCCCATTGGTTCGTGTT 58.685 50.000 1.20 0.00 0.00 3.32
1547 1663 1.142060 TGTCCCATTGGTTCGTGTTCT 59.858 47.619 1.20 0.00 0.00 3.01
1608 1732 8.726988 TGAACAAAAATAGTAGTTGATACCTGC 58.273 33.333 0.00 0.00 34.67 4.85
1631 1755 4.494690 CCGTGTTGATAGCATAAGCACAAG 60.495 45.833 0.00 0.00 45.49 3.16
1666 1842 5.324409 TCTTCACCCAAATGCAAGTCTATT 58.676 37.500 0.00 0.00 0.00 1.73
1676 1852 7.309133 CCAAATGCAAGTCTATTTACACTTCCA 60.309 37.037 0.00 0.00 30.06 3.53
1682 1858 8.391106 GCAAGTCTATTTACACTTCCAATACAG 58.609 37.037 0.00 0.00 30.06 2.74
1773 1949 1.720781 GGGAGCGGGGGTATAAGTTA 58.279 55.000 0.00 0.00 0.00 2.24
1783 1959 7.879677 AGCGGGGGTATAAGTTACATAAATAAC 59.120 37.037 0.00 0.00 35.62 1.89
2026 2204 5.597182 TGCCTACTCTACAACGATTATTCCT 59.403 40.000 0.00 0.00 0.00 3.36
2033 2211 7.050970 TCTACAACGATTATTCCTAGTGCAT 57.949 36.000 0.00 0.00 0.00 3.96
2071 2253 2.030805 GTCAAGCTTTTTCGGTGATGCT 60.031 45.455 0.00 0.00 0.00 3.79
2125 2307 1.550976 CAAGAGGGAGTGGTGGAGTAC 59.449 57.143 0.00 0.00 0.00 2.73
2135 2319 5.069516 GGAGTGGTGGAGTACGGATTATTTA 59.930 44.000 0.00 0.00 0.00 1.40
2170 2354 2.359975 CCACGGAAGGGTTGGCTC 60.360 66.667 0.00 0.00 0.00 4.70
2181 2365 1.141858 GGGTTGGCTCCTCCTCTTATG 59.858 57.143 0.00 0.00 35.26 1.90
2208 2392 1.202463 GCACTGCGACTATCCAGATGT 60.202 52.381 0.00 0.00 33.40 3.06
2249 2433 5.104817 TGGTGATCTTCTTGATGAGTATGCA 60.105 40.000 0.00 0.00 35.14 3.96
2293 2490 6.767902 TGCCTTCAATCATTGTATAGGTTCTC 59.232 38.462 13.73 3.08 31.90 2.87
2319 2517 7.818930 CCAAAGTTATGATTGTTATGTTTGGCT 59.181 33.333 0.00 0.00 36.15 4.75
2327 2525 4.481368 TGTTATGTTTGGCTCGGAGTAT 57.519 40.909 6.90 0.00 0.00 2.12
2384 2583 4.024556 GTGTTGGCGATCAATGAATCTAGG 60.025 45.833 0.00 0.00 37.73 3.02
2385 2584 4.130118 GTTGGCGATCAATGAATCTAGGT 58.870 43.478 0.00 0.00 37.73 3.08
2386 2585 4.422073 TGGCGATCAATGAATCTAGGTT 57.578 40.909 0.00 0.00 0.00 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.715123 CCAAAATTCGAAGTTTAAAGCATTTTT 57.285 25.926 21.66 7.44 40.09 1.94
2 3 8.888716 ACCAAAATTCGAAGTTTAAAGCATTTT 58.111 25.926 21.66 7.91 40.09 1.82
4 5 7.708752 TGACCAAAATTCGAAGTTTAAAGCATT 59.291 29.630 21.66 3.29 0.00 3.56
5 6 7.169140 GTGACCAAAATTCGAAGTTTAAAGCAT 59.831 33.333 21.66 5.65 0.00 3.79
6 7 6.474102 GTGACCAAAATTCGAAGTTTAAAGCA 59.526 34.615 21.66 14.57 0.00 3.91
7 8 6.474102 TGTGACCAAAATTCGAAGTTTAAAGC 59.526 34.615 21.66 12.52 0.00 3.51
8 9 7.979115 TGTGACCAAAATTCGAAGTTTAAAG 57.021 32.000 21.66 15.67 0.00 1.85
9 10 8.030106 AGTTGTGACCAAAATTCGAAGTTTAAA 58.970 29.630 21.66 6.66 30.94 1.52
10 11 7.540299 AGTTGTGACCAAAATTCGAAGTTTAA 58.460 30.769 21.66 9.88 30.94 1.52
11 12 7.090953 AGTTGTGACCAAAATTCGAAGTTTA 57.909 32.000 21.66 5.31 30.94 2.01
12 13 5.961272 AGTTGTGACCAAAATTCGAAGTTT 58.039 33.333 17.16 17.16 30.94 2.66
13 14 5.576447 AGTTGTGACCAAAATTCGAAGTT 57.424 34.783 4.77 4.77 30.94 2.66
14 15 5.587043 TGTAGTTGTGACCAAAATTCGAAGT 59.413 36.000 3.35 0.00 30.94 3.01
15 16 6.055231 TGTAGTTGTGACCAAAATTCGAAG 57.945 37.500 3.35 0.00 30.94 3.79
16 17 6.438259 TTGTAGTTGTGACCAAAATTCGAA 57.562 33.333 0.00 0.00 30.94 3.71
17 18 6.438259 TTTGTAGTTGTGACCAAAATTCGA 57.562 33.333 0.00 0.00 30.94 3.71
18 19 7.513190 TTTTTGTAGTTGTGACCAAAATTCG 57.487 32.000 0.00 0.00 36.85 3.34
46 47 9.323985 TCTGAAATTTCGAACAATTTTGGAAAT 57.676 25.926 13.34 12.80 36.64 2.17
49 50 8.709386 TTTCTGAAATTTCGAACAATTTTGGA 57.291 26.923 18.55 7.67 36.64 3.53
114 115 9.996554 CCCCTAAAAACTTTTGAAATACTGAAT 57.003 29.630 0.00 0.00 0.00 2.57
115 116 9.203163 TCCCCTAAAAACTTTTGAAATACTGAA 57.797 29.630 0.00 0.00 0.00 3.02
130 132 7.713073 TGAATTCAACAAATGTCCCCTAAAAAC 59.287 33.333 5.45 0.00 0.00 2.43
133 135 6.325028 TGTGAATTCAACAAATGTCCCCTAAA 59.675 34.615 10.35 0.00 0.00 1.85
136 138 4.222336 TGTGAATTCAACAAATGTCCCCT 58.778 39.130 10.35 0.00 0.00 4.79
137 139 4.599047 TGTGAATTCAACAAATGTCCCC 57.401 40.909 10.35 0.00 0.00 4.81
138 140 5.782047 TCATGTGAATTCAACAAATGTCCC 58.218 37.500 10.35 0.00 35.30 4.46
140 142 8.292448 ACTACTCATGTGAATTCAACAAATGTC 58.708 33.333 10.35 0.00 35.30 3.06
142 144 9.467258 AAACTACTCATGTGAATTCAACAAATG 57.533 29.630 10.35 11.59 35.14 2.32
155 157 9.903682 AGATGAAAATTCAAAACTACTCATGTG 57.096 29.630 0.00 0.00 41.13 3.21
298 300 9.299963 CAAACAAAATGTTCTTGTATTCAGACA 57.700 29.630 0.00 0.00 40.14 3.41
299 301 9.515020 TCAAACAAAATGTTCTTGTATTCAGAC 57.485 29.630 0.00 0.00 40.14 3.51
307 309 9.434420 TTCTGAATTCAAACAAAATGTTCTTGT 57.566 25.926 9.88 0.00 40.14 3.16
397 406 9.189156 TCTTTGGTCCCTCTGATTTATAATTTG 57.811 33.333 0.00 0.00 0.00 2.32
438 448 3.568538 GAGCCAGTGCAGTATGTTTTTG 58.431 45.455 0.00 0.00 41.13 2.44
439 449 2.226437 CGAGCCAGTGCAGTATGTTTTT 59.774 45.455 0.00 0.00 41.13 1.94
443 453 1.448540 GCGAGCCAGTGCAGTATGT 60.449 57.895 0.00 0.00 41.13 2.29
444 454 1.153489 AGCGAGCCAGTGCAGTATG 60.153 57.895 0.00 0.00 41.13 2.39
445 455 1.153489 CAGCGAGCCAGTGCAGTAT 60.153 57.895 0.00 0.00 41.13 2.12
446 456 2.262603 CAGCGAGCCAGTGCAGTA 59.737 61.111 0.00 0.00 41.13 2.74
451 463 3.947132 CTGTCCCAGCGAGCCAGTG 62.947 68.421 0.00 0.00 0.00 3.66
484 496 4.112341 AGTGGTACCGCTCGCGTC 62.112 66.667 22.56 0.00 37.81 5.19
485 497 4.112341 GAGTGGTACCGCTCGCGT 62.112 66.667 33.60 11.62 42.55 6.01
499 511 1.133982 CTGTGTATGCTCAGAGCGAGT 59.866 52.381 17.81 8.75 46.26 4.18
524 536 2.238898 GGCTAACCCACAGAATACAGGT 59.761 50.000 0.00 0.00 0.00 4.00
584 596 4.156008 ACGGATTACTCCTTGCACATTTTC 59.844 41.667 0.00 0.00 39.65 2.29
589 601 2.829720 AGTACGGATTACTCCTTGCACA 59.170 45.455 0.00 0.00 36.09 4.57
606 618 9.477484 TTTTAGCTGCTAAATATGCTAGAGTAC 57.523 33.333 29.31 0.00 38.90 2.73
727 754 6.115446 TGGATGCTAATGGAAGAACTTACTG 58.885 40.000 0.00 0.00 0.00 2.74
888 958 6.681729 ATATAGACCCGTGAATACATTGGT 57.318 37.500 0.00 0.00 36.14 3.67
889 959 8.932791 GTTTATATAGACCCGTGAATACATTGG 58.067 37.037 0.00 0.00 0.00 3.16
899 969 5.412640 TGTGTGTGTTTATATAGACCCGTG 58.587 41.667 1.24 0.00 0.00 4.94
902 972 8.395633 GTGATTTGTGTGTGTTTATATAGACCC 58.604 37.037 1.24 0.00 0.00 4.46
932 1007 5.125578 AGTTCTTCTTTTCCCTGTGTTGTTC 59.874 40.000 0.00 0.00 0.00 3.18
966 1041 3.515901 AGGAGGAGGCTAACTACACTTTG 59.484 47.826 3.99 0.00 29.75 2.77
967 1042 3.515901 CAGGAGGAGGCTAACTACACTTT 59.484 47.826 3.99 0.00 29.75 2.66
1081 1161 2.184322 GGCGTCGCATGAGGAGAA 59.816 61.111 20.50 0.00 31.63 2.87
1151 1233 5.021033 AGATTGCTTCATCGTCTGATCTT 57.979 39.130 0.00 0.00 32.72 2.40
1212 1304 6.534793 GCATATGGGTGTAAAGAAACAAATGG 59.465 38.462 4.56 0.00 0.00 3.16
1214 1307 7.178274 TCTGCATATGGGTGTAAAGAAACAAAT 59.822 33.333 4.56 0.00 0.00 2.32
1312 1406 0.250640 CCACAGAACCTCTTGCAGCT 60.251 55.000 0.00 0.00 0.00 4.24
1314 1408 0.535780 TGCCACAGAACCTCTTGCAG 60.536 55.000 0.00 0.00 0.00 4.41
1426 1530 2.565841 CATCTCCATTTCTTCCCGGAC 58.434 52.381 0.73 0.00 0.00 4.79
1430 1534 2.442236 TGGCATCTCCATTTCTTCCC 57.558 50.000 0.00 0.00 40.72 3.97
1531 1647 2.226330 TCCAAGAACACGAACCAATGG 58.774 47.619 0.00 0.00 0.00 3.16
1545 1661 8.567948 GTCATTACTTTTGATTTGTCTCCAAGA 58.432 33.333 0.00 0.00 0.00 3.02
1547 1663 8.463930 AGTCATTACTTTTGATTTGTCTCCAA 57.536 30.769 0.00 0.00 29.00 3.53
1608 1732 2.935849 TGTGCTTATGCTATCAACACGG 59.064 45.455 1.96 0.00 40.48 4.94
1631 1755 4.320608 TGGGTGAAGATGAAAAACTTGC 57.679 40.909 0.00 0.00 0.00 4.01
1707 1883 4.895297 TCCTTGATGAAATTAATGAGGGGC 59.105 41.667 0.00 0.00 0.00 5.80
1792 1968 9.630098 ACATGTGACATTTCTATTTTTGATGTC 57.370 29.630 0.00 7.60 44.14 3.06
1793 1969 9.985730 AACATGTGACATTTCTATTTTTGATGT 57.014 25.926 0.00 0.00 33.93 3.06
1897 2073 3.699538 TGCTCATTGACGACCATAGTAGT 59.300 43.478 0.00 0.00 34.17 2.73
1960 2138 1.841302 TTCAAGGACGGAGCATGGCT 61.841 55.000 0.00 0.00 43.88 4.75
1972 2150 6.270927 CCACTCTCCCTATTATGATTCAAGGA 59.729 42.308 4.04 0.00 0.00 3.36
2026 2204 2.543037 TAGAGTGGGGACATGCACTA 57.457 50.000 3.99 0.00 46.14 2.74
2033 2211 4.141711 GCTTGACATTATAGAGTGGGGACA 60.142 45.833 0.00 0.00 38.70 4.02
2071 2253 4.406456 ACACATGTCTAGCCATCCAAAAA 58.594 39.130 0.00 0.00 0.00 1.94
2125 2307 7.651808 ACCATTCTTGCATCTTAAATAATCCG 58.348 34.615 0.00 0.00 0.00 4.18
2170 2354 4.815308 CAGTGCATTTCTCATAAGAGGAGG 59.185 45.833 0.00 0.00 42.34 4.30
2181 2365 2.541762 GGATAGTCGCAGTGCATTTCTC 59.458 50.000 16.83 5.73 0.00 2.87
2208 2392 2.752354 CACCAGGAATTCCGTATGCAAA 59.248 45.455 18.82 0.00 42.08 3.68
2249 2433 2.421107 GCATGTGGACTCACTCATCCAT 60.421 50.000 0.00 0.00 46.55 3.41
2293 2490 7.818930 AGCCAAACATAACAATCATAACTTTGG 59.181 33.333 0.00 0.00 38.66 3.28
2319 2517 5.477607 TTTGGTTCTCTCAAATACTCCGA 57.522 39.130 0.00 0.00 0.00 4.55
2327 2525 4.644234 TCTGCAACATTTGGTTCTCTCAAA 59.356 37.500 0.00 0.00 37.72 2.69
2358 2556 1.902938 TCATTGATCGCCAACACCAA 58.097 45.000 0.00 0.00 37.63 3.67
2359 2558 1.902938 TTCATTGATCGCCAACACCA 58.097 45.000 0.00 0.00 37.63 4.17
2361 2560 4.024556 CCTAGATTCATTGATCGCCAACAC 60.025 45.833 0.00 0.00 37.63 3.32


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

AutoCloner maintained by Alex Coulton.