Multiple sequence alignment - TraesCS3A01G283300

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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 TraesCS3A01G283300 chr3A 100.000 2867 0 0 1 2867 511751438 511754304 0.000000e+00 5295.0
1 TraesCS3A01G283300 chr3A 90.566 53 3 2 226 277 24058701 24058650 5.130000e-08 69.4
2 TraesCS3A01G283300 chr3D 89.617 1801 87 48 1110 2867 391597249 391598992 0.000000e+00 2198.0
3 TraesCS3A01G283300 chr3D 89.750 800 50 10 313 1090 391596395 391597184 0.000000e+00 994.0
4 TraesCS3A01G283300 chr3D 94.074 270 13 3 1 269 391596124 391596391 9.560000e-110 407.0
5 TraesCS3A01G283300 chr3B 89.782 1468 80 29 1434 2867 508708018 508709449 0.000000e+00 1816.0
6 TraesCS3A01G283300 chr3B 92.308 897 44 9 533 1405 508707061 508707956 0.000000e+00 1251.0
7 TraesCS3A01G283300 chr3B 85.239 481 34 9 10 481 508706590 508707042 7.240000e-126 460.0
8 TraesCS3A01G283300 chr1D 77.405 447 90 11 2428 2867 431427273 431426831 3.670000e-64 255.0
9 TraesCS3A01G283300 chr1B 78.293 410 79 10 2465 2867 582545148 582544742 3.670000e-64 255.0
10 TraesCS3A01G283300 chr1B 96.970 33 1 0 420 452 627922252 627922284 3.990000e-04 56.5
11 TraesCS3A01G283300 chr1A 78.293 410 79 10 2465 2867 529665564 529665158 3.670000e-64 255.0
12 TraesCS3A01G283300 chr1A 93.023 43 2 1 458 500 436434180 436434139 8.580000e-06 62.1
13 TraesCS3A01G283300 chrUn 100.000 28 0 0 425 452 331949683 331949656 5.000000e-03 52.8
14 TraesCS3A01G283300 chr4B 96.774 31 1 0 422 452 44882135 44882165 5.000000e-03 52.8


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 TraesCS3A01G283300 chr3A 511751438 511754304 2866 False 5295.000000 5295 100.000000 1 2867 1 chr3A.!!$F1 2866
1 TraesCS3A01G283300 chr3D 391596124 391598992 2868 False 1199.666667 2198 91.147000 1 2867 3 chr3D.!!$F1 2866
2 TraesCS3A01G283300 chr3B 508706590 508709449 2859 False 1175.666667 1816 89.109667 10 2867 3 chr3B.!!$F1 2857

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
403 413 0.464554 GGCCTCATGTTCCTACCAGC 60.465 60.0 0.0 0.0 0.00 4.85 F
846 878 1.368268 AAGGGTTCCTTCCTTGCCCA 61.368 55.0 0.0 0.0 40.17 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 1468 0.036388 TACTGCTGGCTTACCACTGC 60.036 55.0 0.0 0.0 42.67 4.40 R
2264 2403 0.237235 ACGCCATGCAGTTTGTAACG 59.763 50.0 0.0 0.0 36.23 3.18 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
91 101 5.070685 GGAGTGTTCCTGTTCCACTTATTT 58.929 41.667 0.00 0.00 39.43 1.40
92 102 5.181433 GGAGTGTTCCTGTTCCACTTATTTC 59.819 44.000 0.00 0.00 39.43 2.17
102 112 8.585018 CCTGTTCCACTTATTTCTTTGGTATTT 58.415 33.333 0.00 0.00 0.00 1.40
174 184 7.334421 TCAAGATGTTAGTTTAGCAATCAGTCC 59.666 37.037 0.00 0.00 0.00 3.85
193 203 7.327214 TCAGTCCATTGCTTGTAAAAACTTTT 58.673 30.769 0.00 0.00 0.00 2.27
197 207 5.006165 CCATTGCTTGTAAAAACTTTTGCGA 59.994 36.000 0.00 0.00 35.84 5.10
258 268 5.521372 CCCTCCGTAAACTTTTATAAGACGG 59.479 44.000 14.50 14.50 44.43 4.79
271 281 9.643693 CTTTTATAAGACGGTTTAGGTCACTAA 57.356 33.333 0.00 0.00 36.87 2.24
272 282 9.995003 TTTTATAAGACGGTTTAGGTCACTAAA 57.005 29.630 0.00 0.00 44.62 1.85
273 283 9.643693 TTTATAAGACGGTTTAGGTCACTAAAG 57.356 33.333 0.53 0.00 46.69 1.85
286 296 4.170292 TCACTAAAGCGTGACCTTAGAC 57.830 45.455 0.00 0.00 38.89 2.59
287 297 2.915463 CACTAAAGCGTGACCTTAGACG 59.085 50.000 0.00 0.00 37.06 4.18
288 298 2.555757 ACTAAAGCGTGACCTTAGACGT 59.444 45.455 0.00 0.00 37.89 4.34
289 299 2.061740 AAAGCGTGACCTTAGACGTC 57.938 50.000 7.70 7.70 37.89 4.34
290 300 1.245732 AAGCGTGACCTTAGACGTCT 58.754 50.000 23.66 23.66 37.89 4.18
291 301 1.245732 AGCGTGACCTTAGACGTCTT 58.754 50.000 25.44 5.05 37.89 3.01
292 302 2.430465 AGCGTGACCTTAGACGTCTTA 58.570 47.619 25.44 14.36 37.89 2.10
293 303 3.015327 AGCGTGACCTTAGACGTCTTAT 58.985 45.455 25.44 6.83 37.89 1.73
294 304 3.106672 GCGTGACCTTAGACGTCTTATG 58.893 50.000 25.44 14.23 37.89 1.90
295 305 3.181503 GCGTGACCTTAGACGTCTTATGA 60.182 47.826 25.44 1.74 37.89 2.15
296 306 4.673580 GCGTGACCTTAGACGTCTTATGAA 60.674 45.833 25.44 10.90 37.89 2.57
297 307 5.396484 CGTGACCTTAGACGTCTTATGAAA 58.604 41.667 25.44 10.50 0.00 2.69
305 315 9.199982 CCTTAGACGTCTTATGAAAGTTTACAA 57.800 33.333 25.44 5.44 34.13 2.41
308 318 8.084590 AGACGTCTTATGAAAGTTTACAAAGG 57.915 34.615 13.58 0.00 34.13 3.11
310 320 6.206048 ACGTCTTATGAAAGTTTACAAAGGGG 59.794 38.462 0.00 0.00 34.13 4.79
352 362 4.156922 CACAAGCACGGGGACATTTAAATA 59.843 41.667 0.00 0.00 0.00 1.40
380 390 7.537306 CCAAATGTTGTCGATTCGAGTATTTTT 59.463 33.333 9.42 4.95 36.23 1.94
396 406 1.347062 TTTTTGGGGCCTCATGTTCC 58.653 50.000 5.88 0.00 0.00 3.62
403 413 0.464554 GGCCTCATGTTCCTACCAGC 60.465 60.000 0.00 0.00 0.00 4.85
407 417 2.092753 CCTCATGTTCCTACCAGCATGT 60.093 50.000 0.00 0.00 39.54 3.21
416 426 3.281240 CCAGCATGTGTTCTGGCC 58.719 61.111 0.00 0.00 42.79 5.36
485 495 5.980715 ACTAAAACCGCAACACTTATTTTGG 59.019 36.000 0.00 0.00 0.00 3.28
500 510 4.553330 ATTTTGGAAGCGGAGAGAGTAA 57.447 40.909 0.00 0.00 0.00 2.24
576 608 5.739752 TTTGGTAGATTCATTGATCAGCG 57.260 39.130 0.00 0.00 0.00 5.18
586 618 2.124983 GATCAGCGCTTCCCTGCA 60.125 61.111 7.50 0.00 0.00 4.41
599 631 1.589716 CCCTGCACAACAAGCTAGGC 61.590 60.000 0.00 0.00 32.50 3.93
600 632 1.499056 CTGCACAACAAGCTAGGCG 59.501 57.895 0.00 0.00 0.00 5.52
637 669 3.258123 GCATGGAAAGCAGGGTTTCTTTA 59.742 43.478 19.61 9.90 36.76 1.85
676 708 6.259608 CACTGACTCTGAACTGAACTGAAAAT 59.740 38.462 0.00 0.00 0.00 1.82
710 742 1.486726 GCATGTCACCTAAGGTAGCCT 59.513 52.381 0.00 0.00 32.11 4.58
771 803 2.427245 AATCGCCTGAGACCCTCCG 61.427 63.158 0.00 0.00 0.00 4.63
846 878 1.368268 AAGGGTTCCTTCCTTGCCCA 61.368 55.000 0.00 0.00 40.17 5.36
979 1011 3.493767 AACCTCGGAGAAAGCTTTCTT 57.506 42.857 35.70 22.59 46.84 2.52
1073 1105 4.697352 AGCAGATCACACCTGTTTATTCAC 59.303 41.667 0.00 0.00 34.29 3.18
1116 1192 6.959639 TCCTTGTGAACAGCTCTAAAATTT 57.040 33.333 0.00 0.00 0.00 1.82
1119 1195 7.500892 TCCTTGTGAACAGCTCTAAAATTTGTA 59.499 33.333 0.00 0.00 0.00 2.41
1208 1294 3.553828 AAGAACGGTTGGTTTGAGAGA 57.446 42.857 0.00 0.00 39.50 3.10
1214 1300 5.880054 ACGGTTGGTTTGAGAGATATTTG 57.120 39.130 0.00 0.00 0.00 2.32
1241 1327 7.161404 ACACTGTGCTCTGAATTCTAACAATA 58.839 34.615 7.90 0.00 0.00 1.90
1382 1468 0.540454 TCTCATGCTGGAAGGCTCTG 59.460 55.000 0.00 0.00 0.00 3.35
1459 1582 3.103447 TCTCATATTTCGCTCTGCCTG 57.897 47.619 0.00 0.00 0.00 4.85
1468 1595 5.468540 TTTCGCTCTGCCTGTATATGTAT 57.531 39.130 0.00 0.00 0.00 2.29
1570 1697 1.267261 GCCTACATCTACGAGACGCAT 59.733 52.381 0.00 0.00 0.00 4.73
1594 1721 1.491505 GGCGCTACTTCAAGATCGGC 61.492 60.000 7.64 0.00 35.54 5.54
1741 1871 3.637273 GCCGTGGGTCCTCCTTGT 61.637 66.667 0.00 0.00 36.20 3.16
1759 1889 3.887621 TGTTCCCTACACTATCTGCAC 57.112 47.619 0.00 0.00 0.00 4.57
1785 1917 9.199982 CATATGCTCTTTTGTTTCTGAATGTTT 57.800 29.630 0.00 0.00 0.00 2.83
1786 1918 7.704789 ATGCTCTTTTGTTTCTGAATGTTTC 57.295 32.000 0.00 0.00 0.00 2.78
1792 1924 8.400947 TCTTTTGTTTCTGAATGTTTCTCTCTG 58.599 33.333 0.00 0.00 0.00 3.35
1793 1925 7.630242 TTTGTTTCTGAATGTTTCTCTCTGT 57.370 32.000 0.00 0.00 0.00 3.41
1794 1926 6.851222 TGTTTCTGAATGTTTCTCTCTGTC 57.149 37.500 0.00 0.00 0.00 3.51
1824 1957 1.086696 CGTTCCTGATGCGATGGTTT 58.913 50.000 0.00 0.00 0.00 3.27
1867 2001 0.467804 GGAAGCCAAGAGAGCCTAGG 59.532 60.000 3.67 3.67 0.00 3.02
1873 2007 3.135530 AGCCAAGAGAGCCTAGGTTTATG 59.864 47.826 11.31 2.64 0.00 1.90
1878 2012 4.810345 AGAGAGCCTAGGTTTATGTAGCT 58.190 43.478 11.31 0.00 0.00 3.32
1879 2013 4.830600 AGAGAGCCTAGGTTTATGTAGCTC 59.169 45.833 11.31 7.16 0.00 4.09
1934 2068 4.319177 AGAAGAGAAACGAGTGGAAATGG 58.681 43.478 0.00 0.00 0.00 3.16
1951 2085 2.268076 GGAAATGGCTGCCGTGTGT 61.268 57.895 15.33 2.75 0.00 3.72
1972 2106 4.201841 TGTTGTGATCAATATGCTTCAGCG 60.202 41.667 0.00 0.00 38.73 5.18
2073 2207 5.716094 TGATGAATGAAACATTCAAGGCTG 58.284 37.500 24.11 0.00 43.95 4.85
2074 2208 3.916761 TGAATGAAACATTCAAGGCTGC 58.083 40.909 20.07 0.00 43.95 5.25
2103 2242 4.155280 TGAAATGTGATGTGATGTGCTCAG 59.845 41.667 0.00 0.00 33.51 3.35
2117 2256 1.712081 CTCAGCACGAAATGGAGCG 59.288 57.895 0.00 0.00 0.00 5.03
2119 2258 2.358615 AGCACGAAATGGAGCGCA 60.359 55.556 11.47 0.00 0.00 6.09
2128 2267 1.805428 AATGGAGCGCAACCACAACC 61.805 55.000 24.31 8.69 40.36 3.77
2148 2287 6.718454 ACAACCAGTCTCTGAATGAATGAAAT 59.282 34.615 0.00 0.00 32.44 2.17
2149 2288 7.232127 ACAACCAGTCTCTGAATGAATGAAATT 59.768 33.333 0.00 0.00 33.95 1.82
2150 2289 7.154435 ACCAGTCTCTGAATGAATGAAATTG 57.846 36.000 0.00 0.00 31.99 2.32
2152 2291 7.449395 ACCAGTCTCTGAATGAATGAAATTGAA 59.551 33.333 0.00 0.00 31.99 2.69
2154 2293 9.687210 CAGTCTCTGAATGAATGAAATTGAAAA 57.313 29.630 0.00 0.00 31.99 2.29
2155 2294 9.688592 AGTCTCTGAATGAATGAAATTGAAAAC 57.311 29.630 0.00 0.00 36.07 2.43
2156 2295 8.919661 GTCTCTGAATGAATGAAATTGAAAACC 58.080 33.333 0.00 0.00 36.07 3.27
2157 2296 8.090214 TCTCTGAATGAATGAAATTGAAAACCC 58.910 33.333 0.00 0.00 36.07 4.11
2161 2300 9.001542 TGAATGAATGAAATTGAAAACCCATTC 57.998 29.630 0.00 0.00 36.07 2.67
2170 2309 6.590234 ATTGAAAACCCATTCTAACTGTCC 57.410 37.500 0.00 0.00 0.00 4.02
2171 2310 5.055265 TGAAAACCCATTCTAACTGTCCA 57.945 39.130 0.00 0.00 0.00 4.02
2172 2311 5.450453 TGAAAACCCATTCTAACTGTCCAA 58.550 37.500 0.00 0.00 0.00 3.53
2173 2312 5.300792 TGAAAACCCATTCTAACTGTCCAAC 59.699 40.000 0.00 0.00 0.00 3.77
2174 2313 4.724279 AACCCATTCTAACTGTCCAACT 57.276 40.909 0.00 0.00 0.00 3.16
2175 2314 5.836024 AACCCATTCTAACTGTCCAACTA 57.164 39.130 0.00 0.00 0.00 2.24
2176 2315 5.836024 ACCCATTCTAACTGTCCAACTAA 57.164 39.130 0.00 0.00 0.00 2.24
2177 2316 6.388619 ACCCATTCTAACTGTCCAACTAAT 57.611 37.500 0.00 0.00 0.00 1.73
2178 2317 6.180472 ACCCATTCTAACTGTCCAACTAATG 58.820 40.000 0.00 0.00 0.00 1.90
2179 2318 6.012858 ACCCATTCTAACTGTCCAACTAATGA 60.013 38.462 0.00 0.00 0.00 2.57
2180 2319 6.884295 CCCATTCTAACTGTCCAACTAATGAA 59.116 38.462 0.00 0.00 0.00 2.57
2181 2320 7.148239 CCCATTCTAACTGTCCAACTAATGAAC 60.148 40.741 0.00 0.00 0.00 3.18
2182 2321 7.148239 CCATTCTAACTGTCCAACTAATGAACC 60.148 40.741 0.00 0.00 0.00 3.62
2183 2322 6.428083 TCTAACTGTCCAACTAATGAACCA 57.572 37.500 0.00 0.00 0.00 3.67
2184 2323 6.833041 TCTAACTGTCCAACTAATGAACCAA 58.167 36.000 0.00 0.00 0.00 3.67
2185 2324 7.284074 TCTAACTGTCCAACTAATGAACCAAA 58.716 34.615 0.00 0.00 0.00 3.28
2186 2325 6.976934 AACTGTCCAACTAATGAACCAAAT 57.023 33.333 0.00 0.00 0.00 2.32
2187 2326 9.226606 CTAACTGTCCAACTAATGAACCAAATA 57.773 33.333 0.00 0.00 0.00 1.40
2188 2327 8.472007 AACTGTCCAACTAATGAACCAAATAA 57.528 30.769 0.00 0.00 0.00 1.40
2189 2328 8.650143 ACTGTCCAACTAATGAACCAAATAAT 57.350 30.769 0.00 0.00 0.00 1.28
2190 2329 9.088987 ACTGTCCAACTAATGAACCAAATAATT 57.911 29.630 0.00 0.00 0.00 1.40
2202 2341 8.408043 TGAACCAAATAATTCTGAACACATCT 57.592 30.769 0.00 0.00 0.00 2.90
2204 2343 7.396540 ACCAAATAATTCTGAACACATCTCC 57.603 36.000 0.00 0.00 0.00 3.71
2205 2344 6.947733 ACCAAATAATTCTGAACACATCTCCA 59.052 34.615 0.00 0.00 0.00 3.86
2233 2372 4.349636 TCCACTGAACACCTTAATCCTTGA 59.650 41.667 0.00 0.00 0.00 3.02
2245 2384 8.186821 CACCTTAATCCTTGAGATGAATGAAAC 58.813 37.037 0.00 0.00 34.56 2.78
2264 2403 8.706322 ATGAAACCCAATTATTGTCTATACCC 57.294 34.615 4.15 0.00 0.00 3.69
2306 2445 6.290026 CGTCGTATTCATCGCAAAATGAAAAG 60.290 38.462 9.42 5.56 45.91 2.27
2308 2447 6.960992 TCGTATTCATCGCAAAATGAAAAGAG 59.039 34.615 9.42 4.03 45.91 2.85
2324 2467 7.672983 TGAAAAGAGAAACAGGCTAATGTAG 57.327 36.000 0.00 0.00 31.70 2.74
2336 2491 5.096954 GGCTAATGTAGGCGAAAAGAATC 57.903 43.478 0.00 0.00 41.69 2.52
2356 2522 4.329638 TCAATCCTTTTCCATGCCCTTA 57.670 40.909 0.00 0.00 0.00 2.69
2384 2550 3.751518 ACAGGAAATGGGACTTGTACAC 58.248 45.455 0.00 0.00 0.00 2.90
2385 2551 3.394606 ACAGGAAATGGGACTTGTACACT 59.605 43.478 0.00 0.00 0.00 3.55
2403 2569 1.825474 ACTTCTGTACTGGATGGACCG 59.175 52.381 0.00 0.00 42.61 4.79
2406 2572 0.103208 CTGTACTGGATGGACCGCTC 59.897 60.000 0.00 0.00 42.61 5.03
2407 2573 0.613572 TGTACTGGATGGACCGCTCA 60.614 55.000 0.00 0.00 42.61 4.26
2408 2574 0.753262 GTACTGGATGGACCGCTCAT 59.247 55.000 0.00 0.00 42.61 2.90
2409 2575 0.752658 TACTGGATGGACCGCTCATG 59.247 55.000 0.00 0.00 42.61 3.07
2410 2576 1.227764 CTGGATGGACCGCTCATGG 60.228 63.158 0.00 0.00 42.61 3.66
2411 2577 1.688884 TGGATGGACCGCTCATGGA 60.689 57.895 0.00 0.00 42.61 3.41
2412 2578 1.056125 TGGATGGACCGCTCATGGAT 61.056 55.000 0.00 0.00 42.61 3.41
2427 2606 2.826674 TGGATTGGGATCAAAGGGAC 57.173 50.000 0.00 0.00 36.36 4.46
2671 2850 2.819595 CGTTGGCCAGGATGTCGG 60.820 66.667 5.11 0.00 0.00 4.79
2739 2918 0.458543 CGTTCATCTGGTCCACGAGG 60.459 60.000 0.00 0.00 32.51 4.63
2774 2953 0.543277 TTGAAGATCTGGATGGCGCT 59.457 50.000 7.64 0.00 0.00 5.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
91 101 5.575157 TGCCTACCATTCAAATACCAAAGA 58.425 37.500 0.00 0.00 0.00 2.52
92 102 5.913137 TGCCTACCATTCAAATACCAAAG 57.087 39.130 0.00 0.00 0.00 2.77
102 112 3.430453 CTTCCCTTTTGCCTACCATTCA 58.570 45.455 0.00 0.00 0.00 2.57
107 117 1.177401 CAGCTTCCCTTTTGCCTACC 58.823 55.000 0.00 0.00 0.00 3.18
110 120 1.425448 ACTACAGCTTCCCTTTTGCCT 59.575 47.619 0.00 0.00 0.00 4.75
174 184 6.030379 TCGCAAAAGTTTTTACAAGCAATG 57.970 33.333 0.00 0.00 0.00 2.82
193 203 8.986261 GAAAATATTCTTGCACATTTGCTCGCA 61.986 37.037 5.29 0.00 39.85 5.10
197 207 6.704310 AGGAAAATATTCTTGCACATTTGCT 58.296 32.000 5.29 0.00 41.33 3.91
219 229 4.727677 ACGGAGGGAGTACTATTCTAAGG 58.272 47.826 0.00 0.00 0.00 2.69
271 281 1.245732 AGACGTCTAAGGTCACGCTT 58.754 50.000 18.46 0.00 39.73 4.68
272 282 1.245732 AAGACGTCTAAGGTCACGCT 58.754 50.000 20.39 0.00 39.73 5.07
273 283 2.907910 TAAGACGTCTAAGGTCACGC 57.092 50.000 20.39 0.00 39.73 5.34
274 284 4.611310 TCATAAGACGTCTAAGGTCACG 57.389 45.455 20.39 2.15 41.90 4.35
275 285 6.388278 ACTTTCATAAGACGTCTAAGGTCAC 58.612 40.000 20.39 0.00 35.60 3.67
276 286 6.585695 ACTTTCATAAGACGTCTAAGGTCA 57.414 37.500 20.39 1.34 35.60 4.02
277 287 7.886405 AAACTTTCATAAGACGTCTAAGGTC 57.114 36.000 20.39 0.00 35.30 3.85
278 288 8.362639 TGTAAACTTTCATAAGACGTCTAAGGT 58.637 33.333 20.39 14.03 35.30 3.50
279 289 8.752766 TGTAAACTTTCATAAGACGTCTAAGG 57.247 34.615 20.39 12.13 35.30 2.69
282 292 9.199982 CCTTTGTAAACTTTCATAAGACGTCTA 57.800 33.333 20.39 7.83 35.30 2.59
283 293 7.172703 CCCTTTGTAAACTTTCATAAGACGTCT 59.827 37.037 13.58 13.58 35.30 4.18
284 294 7.295930 CCCTTTGTAAACTTTCATAAGACGTC 58.704 38.462 7.70 7.70 35.30 4.34
285 295 6.206048 CCCCTTTGTAAACTTTCATAAGACGT 59.794 38.462 0.00 0.00 35.30 4.34
286 296 6.349033 CCCCCTTTGTAAACTTTCATAAGACG 60.349 42.308 0.00 0.00 35.30 4.18
287 297 6.492429 ACCCCCTTTGTAAACTTTCATAAGAC 59.508 38.462 0.00 0.00 35.30 3.01
288 298 6.616577 ACCCCCTTTGTAAACTTTCATAAGA 58.383 36.000 0.00 0.00 35.30 2.10
289 299 6.911250 ACCCCCTTTGTAAACTTTCATAAG 57.089 37.500 0.00 0.00 37.40 1.73
290 300 7.296098 TGTACCCCCTTTGTAAACTTTCATAA 58.704 34.615 0.00 0.00 0.00 1.90
291 301 6.850234 TGTACCCCCTTTGTAAACTTTCATA 58.150 36.000 0.00 0.00 0.00 2.15
292 302 5.707495 TGTACCCCCTTTGTAAACTTTCAT 58.293 37.500 0.00 0.00 0.00 2.57
293 303 5.126699 TGTACCCCCTTTGTAAACTTTCA 57.873 39.130 0.00 0.00 0.00 2.69
294 304 6.151648 GGTATGTACCCCCTTTGTAAACTTTC 59.848 42.308 0.00 0.00 40.53 2.62
295 305 6.012113 GGTATGTACCCCCTTTGTAAACTTT 58.988 40.000 0.00 0.00 40.53 2.66
296 306 5.074790 TGGTATGTACCCCCTTTGTAAACTT 59.925 40.000 6.74 0.00 45.87 2.66
297 307 4.602732 TGGTATGTACCCCCTTTGTAAACT 59.397 41.667 6.74 0.00 45.87 2.66
305 315 0.850784 GCCATGGTATGTACCCCCTT 59.149 55.000 14.67 0.00 45.87 3.95
308 318 0.548989 TGTGCCATGGTATGTACCCC 59.451 55.000 14.67 0.00 45.87 4.95
310 320 2.878406 GTGATGTGCCATGGTATGTACC 59.122 50.000 14.67 2.18 46.62 3.34
326 336 0.677731 ATGTCCCCGTGCTTGTGATG 60.678 55.000 0.00 0.00 0.00 3.07
352 362 2.416547 CTCGAATCGACAACATTTGGCT 59.583 45.455 0.00 0.00 36.19 4.75
380 390 0.623723 GTAGGAACATGAGGCCCCAA 59.376 55.000 0.00 0.00 0.00 4.12
390 400 3.009473 AGAACACATGCTGGTAGGAACAT 59.991 43.478 0.00 0.00 0.00 2.71
403 413 1.818674 GTTAAGGGGCCAGAACACATG 59.181 52.381 4.39 0.00 0.00 3.21
407 417 0.847373 TGTGTTAAGGGGCCAGAACA 59.153 50.000 4.39 9.47 0.00 3.18
416 426 3.197116 ACGGAAGGAGTATGTGTTAAGGG 59.803 47.826 0.00 0.00 0.00 3.95
485 495 5.699097 ACTGATATTACTCTCTCCGCTTC 57.301 43.478 0.00 0.00 0.00 3.86
526 538 4.174762 GCTTTACTTTCTGGACCGTAGAG 58.825 47.826 0.00 0.00 0.00 2.43
530 542 1.418637 TGGCTTTACTTTCTGGACCGT 59.581 47.619 0.00 0.00 0.00 4.83
576 608 1.006922 GCTTGTTGTGCAGGGAAGC 60.007 57.895 0.00 0.00 32.87 3.86
586 618 0.679505 TGTCTCGCCTAGCTTGTTGT 59.320 50.000 0.00 0.00 0.00 3.32
599 631 3.470567 GCGCCTGTCGTTGTCTCG 61.471 66.667 0.00 0.00 41.07 4.04
600 632 1.738099 ATGCGCCTGTCGTTGTCTC 60.738 57.895 4.18 0.00 41.07 3.36
637 669 4.643387 AGTGGGCGCGGCTTTCTT 62.643 61.111 32.30 10.96 0.00 2.52
686 718 2.315925 ACCTTAGGTGACATGCATCG 57.684 50.000 1.74 0.00 32.98 3.84
710 742 2.701587 CAAGGTTGCACGACCAGAA 58.298 52.632 10.18 0.00 42.35 3.02
771 803 3.457234 CCAAGGAAAGCAAGAACAAACC 58.543 45.455 0.00 0.00 0.00 3.27
952 984 1.807142 CTTTCTCCGAGGTTTCTTGCC 59.193 52.381 0.00 0.00 0.00 4.52
953 985 1.197949 GCTTTCTCCGAGGTTTCTTGC 59.802 52.381 0.00 0.00 0.00 4.01
998 1030 0.539438 GGCACCAAGAACACCCATGA 60.539 55.000 0.00 0.00 0.00 3.07
1073 1105 3.060339 GGAAATGAACAAAAGCAGCAACG 60.060 43.478 0.00 0.00 0.00 4.10
1116 1192 5.045942 TGGAGTGCAACATAGGAGAAATACA 60.046 40.000 0.00 0.00 41.43 2.29
1119 1195 4.263462 TGTGGAGTGCAACATAGGAGAAAT 60.263 41.667 0.00 0.00 41.43 2.17
1190 1269 6.148811 TCAAATATCTCTCAAACCAACCGTTC 59.851 38.462 0.00 0.00 31.78 3.95
1208 1294 7.392673 AGAATTCAGAGCACAGTGTTCAAATAT 59.607 33.333 18.61 8.14 29.40 1.28
1214 1300 5.466728 TGTTAGAATTCAGAGCACAGTGTTC 59.533 40.000 9.32 9.32 0.00 3.18
1247 1333 6.183360 ACGCATATCTAATCGTGCAAGAAAAA 60.183 34.615 6.39 0.00 37.44 1.94
1283 1369 0.833949 GGGAAGAAGGGCTCTCGATT 59.166 55.000 0.00 0.00 31.02 3.34
1382 1468 0.036388 TACTGCTGGCTTACCACTGC 60.036 55.000 0.00 0.00 42.67 4.40
1444 1566 5.468540 ACATATACAGGCAGAGCGAAATA 57.531 39.130 0.00 0.00 0.00 1.40
1459 1582 7.549488 GGGAGCCTGAAACATACATACATATAC 59.451 40.741 0.00 0.00 0.00 1.47
1468 1595 2.237143 CAGAGGGAGCCTGAAACATACA 59.763 50.000 0.00 0.00 31.76 2.29
1570 1697 1.080093 CTTGAAGTAGCGCCGGACA 60.080 57.895 5.05 0.00 0.00 4.02
1594 1721 4.143333 CCGGGGCTCACGTACTGG 62.143 72.222 0.00 0.00 0.00 4.00
1730 1857 1.278413 GTGTAGGGAACAAGGAGGACC 59.722 57.143 0.00 0.00 40.63 4.46
1734 1861 4.442192 GCAGATAGTGTAGGGAACAAGGAG 60.442 50.000 0.00 0.00 40.63 3.69
1741 1871 6.101650 CATATGTGCAGATAGTGTAGGGAA 57.898 41.667 9.65 0.00 0.00 3.97
1759 1889 8.752766 AACATTCAGAAACAAAAGAGCATATG 57.247 30.769 0.00 0.00 0.00 1.78
1806 1938 2.083774 TCAAACCATCGCATCAGGAAC 58.916 47.619 0.00 0.00 0.00 3.62
1824 1957 1.228337 AGCCTGCATGCACAAGTCA 60.228 52.632 18.46 0.00 0.00 3.41
1867 2001 3.187700 CCTCACCACGAGCTACATAAAC 58.812 50.000 0.00 0.00 40.78 2.01
1873 2007 0.601558 TTCACCTCACCACGAGCTAC 59.398 55.000 0.00 0.00 40.78 3.58
1878 2012 1.070786 GCCTTTCACCTCACCACGA 59.929 57.895 0.00 0.00 0.00 4.35
1879 2013 0.606401 ATGCCTTTCACCTCACCACG 60.606 55.000 0.00 0.00 0.00 4.94
1934 2068 0.664166 CAACACACGGCAGCCATTTC 60.664 55.000 13.30 0.00 0.00 2.17
1951 2085 3.313249 CCGCTGAAGCATATTGATCACAA 59.687 43.478 0.00 0.00 42.21 3.33
1972 2106 0.676782 ACGGCACAAGGATAACAGCC 60.677 55.000 0.00 0.00 38.73 4.85
2067 2201 1.965643 ACATTTCACATGTGCAGCCTT 59.034 42.857 21.38 0.57 0.00 4.35
2073 2207 4.163458 TCACATCACATTTCACATGTGC 57.837 40.909 21.38 0.00 46.49 4.57
2103 2242 1.797537 GTTGCGCTCCATTTCGTGC 60.798 57.895 9.73 0.00 37.18 5.34
2117 2256 0.947244 CAGAGACTGGTTGTGGTTGC 59.053 55.000 0.00 0.00 0.00 4.17
2119 2258 3.136443 TCATTCAGAGACTGGTTGTGGTT 59.864 43.478 0.00 0.00 31.51 3.67
2128 2267 9.687210 TTTTCAATTTCATTCATTCAGAGACTG 57.313 29.630 0.00 0.00 0.00 3.51
2148 2287 5.450453 TGGACAGTTAGAATGGGTTTTCAA 58.550 37.500 0.00 0.00 0.00 2.69
2149 2288 5.055265 TGGACAGTTAGAATGGGTTTTCA 57.945 39.130 0.00 0.00 0.00 2.69
2150 2289 5.535030 AGTTGGACAGTTAGAATGGGTTTTC 59.465 40.000 0.00 0.00 0.00 2.29
2152 2291 5.061721 AGTTGGACAGTTAGAATGGGTTT 57.938 39.130 0.00 0.00 0.00 3.27
2154 2293 5.836024 TTAGTTGGACAGTTAGAATGGGT 57.164 39.130 0.00 0.00 0.00 4.51
2155 2294 6.414732 TCATTAGTTGGACAGTTAGAATGGG 58.585 40.000 0.00 0.00 0.00 4.00
2156 2295 7.148239 GGTTCATTAGTTGGACAGTTAGAATGG 60.148 40.741 0.00 0.00 35.27 3.16
2157 2296 7.390440 TGGTTCATTAGTTGGACAGTTAGAATG 59.610 37.037 0.00 0.00 35.27 2.67
2161 2300 7.504924 TTTGGTTCATTAGTTGGACAGTTAG 57.495 36.000 0.00 0.00 35.27 2.34
2175 2314 9.643693 GATGTGTTCAGAATTATTTGGTTCATT 57.356 29.630 0.00 0.00 0.00 2.57
2176 2315 9.028284 AGATGTGTTCAGAATTATTTGGTTCAT 57.972 29.630 0.00 0.00 0.00 2.57
2177 2316 8.408043 AGATGTGTTCAGAATTATTTGGTTCA 57.592 30.769 0.00 0.00 0.00 3.18
2178 2317 7.970614 GGAGATGTGTTCAGAATTATTTGGTTC 59.029 37.037 0.00 0.00 0.00 3.62
2179 2318 7.451255 TGGAGATGTGTTCAGAATTATTTGGTT 59.549 33.333 0.00 0.00 0.00 3.67
2180 2319 6.947733 TGGAGATGTGTTCAGAATTATTTGGT 59.052 34.615 0.00 0.00 0.00 3.67
2181 2320 7.395190 TGGAGATGTGTTCAGAATTATTTGG 57.605 36.000 0.00 0.00 0.00 3.28
2182 2321 8.900781 AGATGGAGATGTGTTCAGAATTATTTG 58.099 33.333 0.00 0.00 0.00 2.32
2183 2322 9.118300 GAGATGGAGATGTGTTCAGAATTATTT 57.882 33.333 0.00 0.00 0.00 1.40
2184 2323 8.492782 AGAGATGGAGATGTGTTCAGAATTATT 58.507 33.333 0.00 0.00 0.00 1.40
2185 2324 8.032045 AGAGATGGAGATGTGTTCAGAATTAT 57.968 34.615 0.00 0.00 0.00 1.28
2186 2325 7.418368 GGAGAGATGGAGATGTGTTCAGAATTA 60.418 40.741 0.00 0.00 0.00 1.40
2187 2326 6.310764 AGAGATGGAGATGTGTTCAGAATT 57.689 37.500 0.00 0.00 0.00 2.17
2188 2327 5.163322 GGAGAGATGGAGATGTGTTCAGAAT 60.163 44.000 0.00 0.00 0.00 2.40
2189 2328 4.161189 GGAGAGATGGAGATGTGTTCAGAA 59.839 45.833 0.00 0.00 0.00 3.02
2190 2329 3.703556 GGAGAGATGGAGATGTGTTCAGA 59.296 47.826 0.00 0.00 0.00 3.27
2202 2341 1.902508 GGTGTTCAGTGGAGAGATGGA 59.097 52.381 0.00 0.00 0.00 3.41
2204 2343 3.692257 AAGGTGTTCAGTGGAGAGATG 57.308 47.619 0.00 0.00 0.00 2.90
2205 2344 5.104735 GGATTAAGGTGTTCAGTGGAGAGAT 60.105 44.000 0.00 0.00 0.00 2.75
2233 2372 8.599624 AGACAATAATTGGGTTTCATTCATCT 57.400 30.769 0.00 0.00 34.12 2.90
2245 2384 7.218614 TGTAACGGGTATAGACAATAATTGGG 58.781 38.462 0.00 0.00 34.12 4.12
2264 2403 0.237235 ACGCCATGCAGTTTGTAACG 59.763 50.000 0.00 0.00 36.23 3.18
2306 2445 2.866762 CGCCTACATTAGCCTGTTTCTC 59.133 50.000 0.00 0.00 0.00 2.87
2308 2447 2.901249 TCGCCTACATTAGCCTGTTTC 58.099 47.619 0.00 0.00 0.00 2.78
2336 2491 5.362263 CAATAAGGGCATGGAAAAGGATTG 58.638 41.667 0.00 0.00 0.00 2.67
2356 2522 0.331278 TCCCATTTCCTGTCGCCAAT 59.669 50.000 0.00 0.00 0.00 3.16
2364 2530 4.021102 AGTGTACAAGTCCCATTTCCTG 57.979 45.455 0.00 0.00 0.00 3.86
2384 2550 1.471676 GCGGTCCATCCAGTACAGAAG 60.472 57.143 0.00 0.00 35.57 2.85
2385 2551 0.535335 GCGGTCCATCCAGTACAGAA 59.465 55.000 0.00 0.00 35.57 3.02
2398 2564 1.526917 CCCAATCCATGAGCGGTCC 60.527 63.158 12.85 0.00 0.00 4.46
2403 2569 2.626743 CCTTTGATCCCAATCCATGAGC 59.373 50.000 0.00 0.00 31.46 4.26
2406 2572 2.961062 GTCCCTTTGATCCCAATCCATG 59.039 50.000 0.00 0.00 31.46 3.66
2407 2573 2.423373 CGTCCCTTTGATCCCAATCCAT 60.423 50.000 0.00 0.00 31.46 3.41
2408 2574 1.064758 CGTCCCTTTGATCCCAATCCA 60.065 52.381 0.00 0.00 31.46 3.41
2409 2575 1.680338 CGTCCCTTTGATCCCAATCC 58.320 55.000 0.00 0.00 31.46 3.01
2410 2576 1.025041 GCGTCCCTTTGATCCCAATC 58.975 55.000 0.00 0.00 31.46 2.67
2411 2577 0.748005 CGCGTCCCTTTGATCCCAAT 60.748 55.000 0.00 0.00 31.46 3.16
2412 2578 1.376683 CGCGTCCCTTTGATCCCAA 60.377 57.895 0.00 0.00 0.00 4.12
2427 2606 3.906649 GACATCAGCACGCTCGCG 61.907 66.667 10.06 10.06 46.03 5.87
2486 2665 4.891727 ACATCATCGTCGGCCGGC 62.892 66.667 27.83 25.32 37.11 6.13
2671 2850 1.076332 AACGCCTACAACATCTTCGC 58.924 50.000 0.00 0.00 0.00 4.70
2672 2851 2.333926 TCAACGCCTACAACATCTTCG 58.666 47.619 0.00 0.00 0.00 3.79
2720 2899 0.458543 CCTCGTGGACCAGATGAACG 60.459 60.000 0.00 0.00 34.57 3.95


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

AutoCloner maintained by Alex Coulton.