Multiple sequence alignment - TraesCS3A01G093300

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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 TraesCS3A01G093300 chr3A 100.000 4379 0 0 1 4379 59805641 59810019 0.000000e+00 8087.0
1 TraesCS3A01G093300 chr3A 94.611 668 35 1 1 667 87796536 87797203 0.000000e+00 1033.0
2 TraesCS3A01G093300 chr3D 93.799 2161 75 16 2238 4379 47655134 47657254 0.000000e+00 3193.0
3 TraesCS3A01G093300 chr3D 93.721 1529 79 11 671 2192 47653625 47655143 0.000000e+00 2276.0
4 TraesCS3A01G093300 chr3D 94.578 664 35 1 2 665 583558669 583559331 0.000000e+00 1026.0
5 TraesCS3A01G093300 chr3B 93.745 1375 62 9 2238 3607 74890385 74889030 0.000000e+00 2041.0
6 TraesCS3A01G093300 chr3B 92.636 774 45 7 670 1437 74891965 74891198 0.000000e+00 1103.0
7 TraesCS3A01G093300 chr3B 92.978 769 30 10 1442 2192 74891138 74890376 0.000000e+00 1099.0
8 TraesCS3A01G093300 chr3B 94.153 667 36 3 3 667 26690650 26691315 0.000000e+00 1013.0
9 TraesCS3A01G093300 chr3B 90.365 301 19 4 3607 3900 74889003 74888706 1.910000e-103 387.0
10 TraesCS3A01G093300 chr5D 95.060 668 32 1 1 667 477880102 477880769 0.000000e+00 1050.0
11 TraesCS3A01G093300 chr5D 94.925 670 31 3 1 667 15727227 15727896 0.000000e+00 1046.0
12 TraesCS3A01G093300 chr2D 95.060 668 32 1 1 667 643682883 643682216 0.000000e+00 1050.0
13 TraesCS3A01G093300 chr1B 94.012 668 39 1 1 667 526382616 526381949 0.000000e+00 1011.0
14 TraesCS3A01G093300 chr4A 93.713 668 40 2 1 667 684923940 684923274 0.000000e+00 1000.0
15 TraesCS3A01G093300 chr4A 93.563 668 43 0 1 668 583816193 583815526 0.000000e+00 996.0
16 TraesCS3A01G093300 chr6B 100.000 28 0 0 4040 4067 39057298 39057325 8.000000e-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 TraesCS3A01G093300 chr3A 59805641 59810019 4378 False 8087.0 8087 100.000 1 4379 1 chr3A.!!$F1 4378
1 TraesCS3A01G093300 chr3A 87796536 87797203 667 False 1033.0 1033 94.611 1 667 1 chr3A.!!$F2 666
2 TraesCS3A01G093300 chr3D 47653625 47657254 3629 False 2734.5 3193 93.760 671 4379 2 chr3D.!!$F2 3708
3 TraesCS3A01G093300 chr3D 583558669 583559331 662 False 1026.0 1026 94.578 2 665 1 chr3D.!!$F1 663
4 TraesCS3A01G093300 chr3B 74888706 74891965 3259 True 1157.5 2041 92.431 670 3900 4 chr3B.!!$R1 3230
5 TraesCS3A01G093300 chr3B 26690650 26691315 665 False 1013.0 1013 94.153 3 667 1 chr3B.!!$F1 664
6 TraesCS3A01G093300 chr5D 477880102 477880769 667 False 1050.0 1050 95.060 1 667 1 chr5D.!!$F2 666
7 TraesCS3A01G093300 chr5D 15727227 15727896 669 False 1046.0 1046 94.925 1 667 1 chr5D.!!$F1 666
8 TraesCS3A01G093300 chr2D 643682216 643682883 667 True 1050.0 1050 95.060 1 667 1 chr2D.!!$R1 666
9 TraesCS3A01G093300 chr1B 526381949 526382616 667 True 1011.0 1011 94.012 1 667 1 chr1B.!!$R1 666
10 TraesCS3A01G093300 chr4A 684923274 684923940 666 True 1000.0 1000 93.713 1 667 1 chr4A.!!$R2 666
11 TraesCS3A01G093300 chr4A 583815526 583816193 667 True 996.0 996 93.563 1 668 1 chr4A.!!$R1 667

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
601 605 0.035317 AACCTGCATGTTGAGCGAGA 59.965 50.0 6.57 0.00 33.85 4.04 F
1996 2078 0.539051 ATGTAGAGTGGCCACAGAGC 59.461 55.0 36.39 22.81 0.00 4.09 F
2231 2315 0.178953 ATTTTGTCCTGGCACCTGCT 60.179 50.0 0.00 0.00 41.70 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2212 2296 0.178953 AGCAGGTGCCAGGACAAAAT 60.179 50.000 0.00 0.0 43.38 1.82 R
3303 3390 0.038526 AAGTAAGACCACGAGCACGG 60.039 55.000 8.74 0.0 44.46 4.94 R
3795 3923 1.000385 CCAGCACGGCTTTCATTCAAA 60.000 47.619 0.00 0.0 36.40 2.69 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
81 82 8.414778 GGAACTTCTAAGATAGATCGAAAAGGA 58.585 37.037 0.00 0.00 34.22 3.36
139 141 9.921637 AACAACATGATAATACAACGGAAAAAT 57.078 25.926 0.00 0.00 0.00 1.82
169 171 2.108566 CAGAGCTCGGATGGGCTG 59.891 66.667 8.31 0.00 39.05 4.85
226 228 2.365635 GTGGAGCCTGGGGAGCTA 60.366 66.667 0.00 0.00 41.75 3.32
345 347 4.574674 AGGACTATGAAAGGCAATGTCA 57.425 40.909 0.00 0.00 33.25 3.58
384 387 1.102978 TCATCGAGACGGATTGCAGA 58.897 50.000 0.00 0.00 0.00 4.26
400 403 0.389817 CAGATCGGTGACAAAGGCGA 60.390 55.000 0.00 0.00 0.00 5.54
457 460 5.584251 GGAACAATTGCAAAGGAGTTTCAAA 59.416 36.000 1.71 0.00 0.00 2.69
512 516 9.920946 TTGCAAAGTAGATAGGAAGGAAAATAT 57.079 29.630 0.00 0.00 0.00 1.28
572 576 0.322098 CGTGGTGGGGTTATGCAAGA 60.322 55.000 0.00 0.00 0.00 3.02
589 593 1.823470 GACACAGTGCCAACCTGCA 60.823 57.895 0.00 0.00 39.37 4.41
601 605 0.035317 AACCTGCATGTTGAGCGAGA 59.965 50.000 6.57 0.00 33.85 4.04
686 690 3.294038 AGCTATTGCAGGCAATTCTCT 57.706 42.857 22.92 14.58 43.32 3.10
829 834 4.468689 GCTGGACACGGCCCTACC 62.469 72.222 0.00 0.00 43.36 3.18
830 835 3.000819 CTGGACACGGCCCTACCA 61.001 66.667 0.00 0.95 39.03 3.25
831 836 2.527123 TGGACACGGCCCTACCAA 60.527 61.111 0.00 0.00 39.03 3.67
832 837 1.910580 CTGGACACGGCCCTACCAAT 61.911 60.000 0.00 0.00 39.03 3.16
910 919 0.909610 ATTCCCCACCTCTCTCGCAA 60.910 55.000 0.00 0.00 0.00 4.85
1208 1217 1.664151 CTCCCGTCAAGCCGATTTTAC 59.336 52.381 0.00 0.00 0.00 2.01
1219 1228 5.675684 AGCCGATTTTACCCAATGATTTT 57.324 34.783 0.00 0.00 0.00 1.82
1261 1270 3.467374 AGCGGAAGATCTTCTGGATTC 57.533 47.619 34.69 22.59 44.13 2.52
1308 1317 5.581126 TTTAGCTGAATATTGGTGCCTTG 57.419 39.130 0.00 0.00 0.00 3.61
1309 1318 1.753073 AGCTGAATATTGGTGCCTTGC 59.247 47.619 0.00 0.00 0.00 4.01
1347 1356 4.286549 ACCATGGCATTTTCATTCCTTTGA 59.713 37.500 13.04 0.00 0.00 2.69
1366 1375 6.206634 CCTTTGAAATCTTGCTTAGTGGTGTA 59.793 38.462 0.00 0.00 0.00 2.90
1404 1413 3.192001 TGTTTGATGCTGCCTCTGAATTC 59.808 43.478 6.49 0.00 0.00 2.17
1447 1513 4.742438 TCGTGAGTTTTGCAGGTTAATC 57.258 40.909 0.00 0.00 0.00 1.75
1462 1528 3.193479 GGTTAATCTTGCAGAAACTGGGG 59.807 47.826 0.00 0.00 31.21 4.96
1584 1651 6.264518 TCATTCCTATGTTGTACATCGCTCTA 59.735 38.462 0.00 0.00 39.88 2.43
1902 1984 7.497249 GTGGATCATAGTGAAAGCAGTAGATTT 59.503 37.037 0.00 0.00 35.78 2.17
1989 2071 3.999663 GCATTGATAGATGTAGAGTGGCC 59.000 47.826 0.00 0.00 0.00 5.36
1996 2078 0.539051 ATGTAGAGTGGCCACAGAGC 59.461 55.000 36.39 22.81 0.00 4.09
2071 2155 8.511321 TGACACATAAATTGAAATGGAGTGTAC 58.489 33.333 0.00 0.00 37.76 2.90
2188 2272 8.855110 ACTCTTCTATACTAATCTGTGATGTGG 58.145 37.037 0.00 0.00 0.00 4.17
2189 2273 8.996651 TCTTCTATACTAATCTGTGATGTGGA 57.003 34.615 0.00 0.00 0.00 4.02
2190 2274 8.851145 TCTTCTATACTAATCTGTGATGTGGAC 58.149 37.037 0.00 0.00 0.00 4.02
2191 2275 8.768501 TTCTATACTAATCTGTGATGTGGACT 57.231 34.615 0.00 0.00 0.00 3.85
2192 2276 8.768501 TCTATACTAATCTGTGATGTGGACTT 57.231 34.615 0.00 0.00 0.00 3.01
2193 2277 9.201989 TCTATACTAATCTGTGATGTGGACTTT 57.798 33.333 0.00 0.00 0.00 2.66
2198 2282 8.758829 ACTAATCTGTGATGTGGACTTTATACA 58.241 33.333 0.00 0.00 0.00 2.29
2199 2283 9.599866 CTAATCTGTGATGTGGACTTTATACAA 57.400 33.333 0.00 0.00 0.00 2.41
2200 2284 7.849804 ATCTGTGATGTGGACTTTATACAAC 57.150 36.000 0.00 0.00 0.00 3.32
2201 2285 5.867174 TCTGTGATGTGGACTTTATACAACG 59.133 40.000 0.00 0.00 0.00 4.10
2202 2286 5.785243 TGTGATGTGGACTTTATACAACGA 58.215 37.500 0.00 0.00 0.00 3.85
2203 2287 6.403049 TGTGATGTGGACTTTATACAACGAT 58.597 36.000 0.00 0.00 0.00 3.73
2204 2288 6.312672 TGTGATGTGGACTTTATACAACGATG 59.687 38.462 0.00 0.00 0.00 3.84
2205 2289 5.293324 TGATGTGGACTTTATACAACGATGC 59.707 40.000 0.00 0.00 0.00 3.91
2206 2290 3.615056 TGTGGACTTTATACAACGATGCG 59.385 43.478 0.00 0.00 0.00 4.73
2207 2291 3.615496 GTGGACTTTATACAACGATGCGT 59.385 43.478 0.00 0.00 43.97 5.24
2208 2292 3.615056 TGGACTTTATACAACGATGCGTG 59.385 43.478 0.00 0.00 39.99 5.34
2209 2293 3.861113 GGACTTTATACAACGATGCGTGA 59.139 43.478 0.00 0.00 39.99 4.35
2210 2294 4.026804 GGACTTTATACAACGATGCGTGAG 60.027 45.833 0.00 0.00 39.99 3.51
2211 2295 4.491676 ACTTTATACAACGATGCGTGAGT 58.508 39.130 0.00 0.00 39.99 3.41
2212 2296 5.643664 ACTTTATACAACGATGCGTGAGTA 58.356 37.500 0.00 0.00 39.99 2.59
2213 2297 6.270815 ACTTTATACAACGATGCGTGAGTAT 58.729 36.000 16.71 16.71 39.99 2.12
2214 2298 6.755141 ACTTTATACAACGATGCGTGAGTATT 59.245 34.615 17.32 7.62 39.99 1.89
2215 2299 7.277098 ACTTTATACAACGATGCGTGAGTATTT 59.723 33.333 17.32 4.84 39.99 1.40
2216 2300 7.528481 TTATACAACGATGCGTGAGTATTTT 57.472 32.000 17.32 4.35 39.99 1.82
2217 2301 4.065423 ACAACGATGCGTGAGTATTTTG 57.935 40.909 0.00 0.00 39.99 2.44
2218 2302 3.496884 ACAACGATGCGTGAGTATTTTGT 59.503 39.130 0.00 0.00 39.99 2.83
2219 2303 3.991605 ACGATGCGTGAGTATTTTGTC 57.008 42.857 0.00 0.00 39.18 3.18
2220 2304 2.671396 ACGATGCGTGAGTATTTTGTCC 59.329 45.455 0.00 0.00 39.18 4.02
2221 2305 2.930040 CGATGCGTGAGTATTTTGTCCT 59.070 45.455 0.00 0.00 36.23 3.85
2222 2306 3.242091 CGATGCGTGAGTATTTTGTCCTG 60.242 47.826 0.00 0.00 36.23 3.86
2223 2307 2.422597 TGCGTGAGTATTTTGTCCTGG 58.577 47.619 0.00 0.00 0.00 4.45
2224 2308 1.130561 GCGTGAGTATTTTGTCCTGGC 59.869 52.381 0.00 0.00 0.00 4.85
2225 2309 2.422597 CGTGAGTATTTTGTCCTGGCA 58.577 47.619 0.00 0.00 0.00 4.92
2226 2310 2.159627 CGTGAGTATTTTGTCCTGGCAC 59.840 50.000 0.00 0.00 0.00 5.01
2227 2311 2.488153 GTGAGTATTTTGTCCTGGCACC 59.512 50.000 0.00 0.00 0.00 5.01
2228 2312 2.375174 TGAGTATTTTGTCCTGGCACCT 59.625 45.455 0.00 0.00 0.00 4.00
2229 2313 2.749621 GAGTATTTTGTCCTGGCACCTG 59.250 50.000 0.00 0.00 0.00 4.00
2230 2314 1.202348 GTATTTTGTCCTGGCACCTGC 59.798 52.381 0.00 0.00 41.14 4.85
2231 2315 0.178953 ATTTTGTCCTGGCACCTGCT 60.179 50.000 0.00 0.00 41.70 4.24
2232 2316 0.476338 TTTTGTCCTGGCACCTGCTA 59.524 50.000 0.00 0.00 41.70 3.49
2233 2317 0.476338 TTTGTCCTGGCACCTGCTAA 59.524 50.000 0.00 0.00 41.70 3.09
2234 2318 0.698238 TTGTCCTGGCACCTGCTAAT 59.302 50.000 0.00 0.00 41.70 1.73
2235 2319 1.578897 TGTCCTGGCACCTGCTAATA 58.421 50.000 0.00 0.00 41.70 0.98
2236 2320 1.209504 TGTCCTGGCACCTGCTAATAC 59.790 52.381 0.00 0.00 41.70 1.89
2237 2321 1.209504 GTCCTGGCACCTGCTAATACA 59.790 52.381 0.00 0.00 41.70 2.29
2238 2322 2.126882 TCCTGGCACCTGCTAATACAT 58.873 47.619 0.00 0.00 41.70 2.29
2239 2323 2.158769 TCCTGGCACCTGCTAATACATG 60.159 50.000 0.00 0.00 41.70 3.21
2289 2373 7.716560 TCTGCATGTTATGAACTACAGCATATT 59.283 33.333 0.00 0.00 32.30 1.28
2302 2386 3.758554 ACAGCATATTGTTTGGTCCTGTC 59.241 43.478 0.00 0.00 0.00 3.51
2312 2396 0.404040 TGGTCCTGTCCCATTGTTCC 59.596 55.000 0.00 0.00 0.00 3.62
2318 2402 1.535462 CTGTCCCATTGTTCCGTTGAC 59.465 52.381 0.00 0.00 0.00 3.18
2422 2506 3.118408 ACTTTGAAGACCACTACAGCACA 60.118 43.478 0.00 0.00 0.00 4.57
2696 2780 4.641396 ACAGTAGTTATCAACTGCAGCAA 58.359 39.130 15.27 0.00 45.65 3.91
2713 2797 3.437741 CAGCAACAGTCAGCATTCACATA 59.562 43.478 1.25 0.00 0.00 2.29
2853 2940 2.694628 TGCTGAGGTGTGCATTTTTCTT 59.305 40.909 0.00 0.00 33.94 2.52
2854 2941 3.243501 TGCTGAGGTGTGCATTTTTCTTC 60.244 43.478 0.00 0.00 33.94 2.87
2855 2942 3.005155 GCTGAGGTGTGCATTTTTCTTCT 59.995 43.478 0.00 0.00 0.00 2.85
3039 3126 4.270008 GAAGGCAAACTGCTTATAAGGGA 58.730 43.478 14.28 0.00 44.28 4.20
3075 3162 1.339055 ACTGTCATGGACGTTGATGGG 60.339 52.381 7.63 2.96 34.95 4.00
3097 3184 4.415735 GAAGAATCCAAGGCAATCGAAAC 58.584 43.478 0.00 0.00 0.00 2.78
3120 3207 0.874607 GATATCGGCCGAAGCAACGT 60.875 55.000 34.66 16.71 42.56 3.99
3261 3348 1.156645 CGGCTGTATCAAGGCTGAGC 61.157 60.000 0.00 0.00 40.47 4.26
3303 3390 0.249031 GCATAACCTTTGGCCATCGC 60.249 55.000 6.09 0.00 0.00 4.58
3390 3477 7.386848 CCAGAAGCAAATTGACAATTCTTCAAT 59.613 33.333 27.44 15.38 44.00 2.57
3779 3907 3.249189 TGGCCAGGACACCAGGTC 61.249 66.667 0.00 0.00 46.20 3.85
3827 3955 0.461548 CGTGCTGGAAGATCTGCCTA 59.538 55.000 21.10 6.51 34.07 3.93
3859 3987 4.452733 CGCCGTTCCCCTGGAGAC 62.453 72.222 0.00 0.00 31.21 3.36
3882 4010 2.273449 CTGATGTGGGAGGTGGGC 59.727 66.667 0.00 0.00 0.00 5.36
3883 4011 3.338250 TGATGTGGGAGGTGGGCC 61.338 66.667 0.00 0.00 0.00 5.80
3900 4028 2.100410 CTTCTCGCGCTCGCTACA 59.900 61.111 5.56 0.00 39.32 2.74
3901 4029 1.514228 CTTCTCGCGCTCGCTACAA 60.514 57.895 5.56 1.33 39.32 2.41
3902 4030 1.071019 CTTCTCGCGCTCGCTACAAA 61.071 55.000 5.56 1.30 39.32 2.83
3903 4031 0.457853 TTCTCGCGCTCGCTACAAAT 60.458 50.000 5.56 0.00 39.32 2.32
4006 4135 6.668541 ATCCAAAAATGTACACGATCTCAG 57.331 37.500 0.00 0.00 0.00 3.35
4181 4313 7.043722 TCAGAAACGTTTATGTGCATGAAAAAC 60.044 33.333 28.89 6.37 31.69 2.43
4192 4324 8.836268 ATGTGCATGAAAAACTATTCACAAAT 57.164 26.923 0.00 0.00 41.78 2.32
4193 4325 8.659925 TGTGCATGAAAAACTATTCACAAATT 57.340 26.923 0.00 0.00 41.78 1.82
4339 4477 9.521503 TGAATTTGAACATTGTTCACGAAATTA 57.478 25.926 27.43 16.43 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 6.939132 TCGATCTATCTTAGAAGTTCCGTT 57.061 37.500 0.00 0.00 38.50 4.44
81 82 7.045126 TGACAATTTAACCATCGGACTTTTT 57.955 32.000 0.00 0.00 0.00 1.94
131 133 4.314121 TGGCTTTTTCCATCATTTTTCCG 58.686 39.130 0.00 0.00 0.00 4.30
169 171 5.712152 AAACTTCCATCAACATTGACCTC 57.288 39.130 0.00 0.00 40.49 3.85
226 228 6.356186 TCTTCCATCATGATCTCGAATCAT 57.644 37.500 4.86 13.79 39.16 2.45
258 260 4.184629 GCGGTATATAATCCCAAGCTGAG 58.815 47.826 0.00 0.00 0.00 3.35
345 347 5.063017 TGATTAAGGGTAGATCCGTCTCT 57.937 43.478 0.00 0.00 35.87 3.10
384 387 0.249120 TGATCGCCTTTGTCACCGAT 59.751 50.000 0.00 0.00 42.43 4.18
400 403 7.226523 CGATCTATCAATAGACGAGAGGATGAT 59.773 40.741 1.89 0.00 41.77 2.45
457 460 3.395941 ACTTCTCTGTTCCCTTTCATGGT 59.604 43.478 0.00 0.00 0.00 3.55
512 516 2.837591 TGGGCAAGACTATGAGCTAACA 59.162 45.455 0.00 0.00 0.00 2.41
572 576 2.275089 TGCAGGTTGGCACTGTGT 59.725 55.556 9.86 0.00 39.25 3.72
589 593 0.035317 TGCAAGGTCTCGCTCAACAT 59.965 50.000 0.00 0.00 0.00 2.71
601 605 1.796459 GTTCGTACAATCGTGCAAGGT 59.204 47.619 0.00 0.00 0.00 3.50
668 672 3.003482 GCTGAGAGAATTGCCTGCAATAG 59.997 47.826 17.01 10.81 44.86 1.73
698 702 9.687210 TCGTATGGATAAAATATATGATACGCC 57.313 33.333 0.00 0.00 38.06 5.68
754 759 7.161404 AGCCCAGGAATTTGAATTAGTTTTTC 58.839 34.615 0.00 0.00 0.00 2.29
829 834 0.029834 GGTGCTGCGCTTATGGATTG 59.970 55.000 9.73 0.00 0.00 2.67
830 835 0.107017 AGGTGCTGCGCTTATGGATT 60.107 50.000 9.73 0.00 0.00 3.01
831 836 0.816825 CAGGTGCTGCGCTTATGGAT 60.817 55.000 9.73 0.00 0.00 3.41
832 837 1.450134 CAGGTGCTGCGCTTATGGA 60.450 57.895 9.73 0.00 0.00 3.41
910 919 2.043450 CCTCCCGGAGAGACAGCT 60.043 66.667 16.69 0.00 46.50 4.24
1208 1217 9.602568 TCATGAACAATCAATAAAATCATTGGG 57.397 29.630 0.00 0.00 39.49 4.12
1219 1228 5.463392 GCTAGACGCTCATGAACAATCAATA 59.537 40.000 0.00 0.00 35.78 1.90
1227 1236 0.100682 TCCGCTAGACGCTCATGAAC 59.899 55.000 0.00 0.00 41.76 3.18
1261 1270 2.423538 GGTTTGATTTGGGGATCTGTCG 59.576 50.000 0.00 0.00 0.00 4.35
1308 1317 3.132824 CCATGGTTTATTCCTTCAAGGGC 59.867 47.826 2.75 0.00 35.59 5.19
1309 1318 3.132824 GCCATGGTTTATTCCTTCAAGGG 59.867 47.826 14.67 0.00 35.59 3.95
1347 1356 5.242795 AGGTACACCACTAAGCAAGATTT 57.757 39.130 0.38 0.00 38.89 2.17
1447 1513 2.278330 GGCCCCCAGTTTCTGCAAG 61.278 63.158 0.00 0.00 0.00 4.01
1462 1528 4.083862 GAGTCCACGGTCAGGGCC 62.084 72.222 0.00 0.00 0.00 5.80
1477 1544 5.652994 AGCTACTCTAAGTTCCTTGTGAG 57.347 43.478 0.00 0.00 34.31 3.51
1584 1651 5.538433 ACACATGCCAAACCACTTAAGTATT 59.462 36.000 8.04 3.13 0.00 1.89
1788 1855 9.832445 AATGAATACGAAACCATGTAGATACTT 57.168 29.630 0.00 0.00 0.00 2.24
1790 1857 9.864034 CAAATGAATACGAAACCATGTAGATAC 57.136 33.333 0.00 0.00 0.00 2.24
1795 1862 8.330466 AGTTCAAATGAATACGAAACCATGTA 57.670 30.769 0.00 0.00 36.33 2.29
1902 1984 8.698210 ATACTACACGTATAGGAATGGAAACAA 58.302 33.333 5.74 0.00 39.62 2.83
1966 2048 3.677121 GCCACTCTACATCTATCAATGCG 59.323 47.826 0.00 0.00 0.00 4.73
1989 2071 7.165812 GTGTTTGTTTAACTATGTTGCTCTGTG 59.834 37.037 0.00 0.00 37.64 3.66
2044 2128 8.125978 ACACTCCATTTCAATTTATGTGTCAT 57.874 30.769 0.00 0.00 31.64 3.06
2045 2129 7.523293 ACACTCCATTTCAATTTATGTGTCA 57.477 32.000 0.00 0.00 31.64 3.58
2071 2155 7.867752 TGTGTCTGATGATGCAAATACATATG 58.132 34.615 0.00 0.00 0.00 1.78
2176 2260 6.535150 CGTTGTATAAAGTCCACATCACAGAT 59.465 38.462 0.00 0.00 0.00 2.90
2182 2266 5.556382 CGCATCGTTGTATAAAGTCCACATC 60.556 44.000 0.00 0.00 0.00 3.06
2186 2270 3.615056 CACGCATCGTTGTATAAAGTCCA 59.385 43.478 0.00 0.00 38.32 4.02
2187 2271 3.861113 TCACGCATCGTTGTATAAAGTCC 59.139 43.478 0.00 0.00 38.32 3.85
2188 2272 4.561606 ACTCACGCATCGTTGTATAAAGTC 59.438 41.667 0.00 0.00 38.32 3.01
2189 2273 4.491676 ACTCACGCATCGTTGTATAAAGT 58.508 39.130 0.00 0.00 38.32 2.66
2190 2274 6.749216 ATACTCACGCATCGTTGTATAAAG 57.251 37.500 10.73 0.00 38.32 1.85
2191 2275 7.528481 AAATACTCACGCATCGTTGTATAAA 57.472 32.000 12.00 0.00 38.32 1.40
2192 2276 7.063662 ACAAAATACTCACGCATCGTTGTATAA 59.936 33.333 12.00 0.00 38.32 0.98
2193 2277 6.532302 ACAAAATACTCACGCATCGTTGTATA 59.468 34.615 12.00 0.00 38.32 1.47
2194 2278 5.350365 ACAAAATACTCACGCATCGTTGTAT 59.650 36.000 8.13 8.13 38.32 2.29
2195 2279 4.687018 ACAAAATACTCACGCATCGTTGTA 59.313 37.500 0.00 0.00 38.32 2.41
2196 2280 3.496884 ACAAAATACTCACGCATCGTTGT 59.503 39.130 0.00 0.00 38.32 3.32
2197 2281 4.065423 ACAAAATACTCACGCATCGTTG 57.935 40.909 0.00 0.00 38.32 4.10
2198 2282 3.124636 GGACAAAATACTCACGCATCGTT 59.875 43.478 0.00 0.00 38.32 3.85
2199 2283 2.671396 GGACAAAATACTCACGCATCGT 59.329 45.455 0.00 0.00 42.36 3.73
2200 2284 2.930040 AGGACAAAATACTCACGCATCG 59.070 45.455 0.00 0.00 0.00 3.84
2201 2285 3.063997 CCAGGACAAAATACTCACGCATC 59.936 47.826 0.00 0.00 0.00 3.91
2202 2286 3.009723 CCAGGACAAAATACTCACGCAT 58.990 45.455 0.00 0.00 0.00 4.73
2203 2287 2.422597 CCAGGACAAAATACTCACGCA 58.577 47.619 0.00 0.00 0.00 5.24
2204 2288 1.130561 GCCAGGACAAAATACTCACGC 59.869 52.381 0.00 0.00 0.00 5.34
2205 2289 2.159627 GTGCCAGGACAAAATACTCACG 59.840 50.000 0.00 0.00 0.00 4.35
2206 2290 2.488153 GGTGCCAGGACAAAATACTCAC 59.512 50.000 0.00 0.00 0.00 3.51
2207 2291 2.375174 AGGTGCCAGGACAAAATACTCA 59.625 45.455 0.00 0.00 0.00 3.41
2208 2292 2.749621 CAGGTGCCAGGACAAAATACTC 59.250 50.000 0.00 0.00 0.00 2.59
2209 2293 2.795329 CAGGTGCCAGGACAAAATACT 58.205 47.619 0.00 0.00 0.00 2.12
2210 2294 1.202348 GCAGGTGCCAGGACAAAATAC 59.798 52.381 0.00 0.00 34.31 1.89
2211 2295 1.075374 AGCAGGTGCCAGGACAAAATA 59.925 47.619 0.00 0.00 43.38 1.40
2212 2296 0.178953 AGCAGGTGCCAGGACAAAAT 60.179 50.000 0.00 0.00 43.38 1.82
2213 2297 0.476338 TAGCAGGTGCCAGGACAAAA 59.524 50.000 0.00 0.00 43.38 2.44
2214 2298 0.476338 TTAGCAGGTGCCAGGACAAA 59.524 50.000 0.00 0.00 43.38 2.83
2215 2299 0.698238 ATTAGCAGGTGCCAGGACAA 59.302 50.000 0.00 0.00 43.38 3.18
2216 2300 1.209504 GTATTAGCAGGTGCCAGGACA 59.790 52.381 0.00 0.00 43.38 4.02
2217 2301 1.209504 TGTATTAGCAGGTGCCAGGAC 59.790 52.381 0.00 0.00 43.38 3.85
2218 2302 1.578897 TGTATTAGCAGGTGCCAGGA 58.421 50.000 0.00 0.00 43.38 3.86
2219 2303 2.224606 CATGTATTAGCAGGTGCCAGG 58.775 52.381 0.00 0.00 43.38 4.45
2220 2304 1.605710 GCATGTATTAGCAGGTGCCAG 59.394 52.381 0.00 0.00 43.38 4.85
2221 2305 1.212688 AGCATGTATTAGCAGGTGCCA 59.787 47.619 0.00 0.00 43.38 4.92
2222 2306 1.605710 CAGCATGTATTAGCAGGTGCC 59.394 52.381 0.00 0.00 43.38 5.01
2302 2386 1.806542 CTGAGTCAACGGAACAATGGG 59.193 52.381 0.00 0.00 0.00 4.00
2312 2396 6.525121 TTTAGACAAATGACTGAGTCAACG 57.475 37.500 20.26 12.81 45.96 4.10
2318 2402 7.579726 CAGGAGTTTTTAGACAAATGACTGAG 58.420 38.462 0.00 0.00 0.00 3.35
2584 2668 9.509855 CGGCTATTGTGCAATTTAAGTAATAAA 57.490 29.630 2.56 0.00 34.86 1.40
2673 2757 5.400066 TGCTGCAGTTGATAACTACTGTA 57.600 39.130 16.64 9.91 46.10 2.74
2674 2758 4.271696 TGCTGCAGTTGATAACTACTGT 57.728 40.909 16.64 0.00 46.10 3.55
2675 2759 4.452114 TGTTGCTGCAGTTGATAACTACTG 59.548 41.667 16.64 9.64 46.73 2.74
2676 2760 4.641396 TGTTGCTGCAGTTGATAACTACT 58.359 39.130 16.64 0.00 40.46 2.57
2677 2761 4.452455 ACTGTTGCTGCAGTTGATAACTAC 59.548 41.667 16.64 4.38 46.45 2.73
2696 2780 6.042638 AGTAACTATGTGAATGCTGACTGT 57.957 37.500 0.00 0.00 0.00 3.55
2713 2797 8.958060 TCCATTAGCTGAATAGGATAGTAACT 57.042 34.615 0.00 0.00 0.00 2.24
2778 2862 5.543507 TTTGCATGTGTCAAACCCTAATT 57.456 34.783 0.00 0.00 0.00 1.40
2795 2879 5.531659 TCCAAGTTAGTTCGGTAAATTTGCA 59.468 36.000 8.59 0.00 0.00 4.08
2853 2940 6.018262 CCAAACATTCGTACTGTTTCAGAAGA 60.018 38.462 8.34 0.00 43.15 2.87
2854 2941 6.136071 CCAAACATTCGTACTGTTTCAGAAG 58.864 40.000 8.34 0.00 43.15 2.85
2855 2942 5.587043 ACCAAACATTCGTACTGTTTCAGAA 59.413 36.000 8.34 0.00 43.15 3.02
2976 3063 2.281761 CGCTGGGAAGGTTGTGCT 60.282 61.111 0.00 0.00 0.00 4.40
3039 3126 4.678256 TGACAGTATCCCTTGTCTCTTCT 58.322 43.478 6.24 0.00 43.15 2.85
3075 3162 4.415735 GTTTCGATTGCCTTGGATTCTTC 58.584 43.478 0.00 0.00 0.00 2.87
3120 3207 4.753516 TTCTTTCGGCTCCTTATGATCA 57.246 40.909 0.00 0.00 0.00 2.92
3171 3258 3.815962 CCTCCTTCTCATGATGCTCATTG 59.184 47.826 0.00 0.00 34.28 2.82
3177 3264 0.182061 TGGCCTCCTTCTCATGATGC 59.818 55.000 3.32 0.00 0.00 3.91
3183 3270 0.117140 TCTCCTTGGCCTCCTTCTCA 59.883 55.000 3.32 0.00 0.00 3.27
3261 3348 0.957395 AAGGCACCGAATCTGCAGTG 60.957 55.000 14.67 5.32 36.27 3.66
3303 3390 0.038526 AAGTAAGACCACGAGCACGG 60.039 55.000 8.74 0.00 44.46 4.94
3496 3583 2.185004 TAGCAGGCAGAAGACCAAAC 57.815 50.000 0.00 0.00 0.00 2.93
3669 3797 3.249559 GCTCGATTTTCCATCACTCCATC 59.750 47.826 0.00 0.00 0.00 3.51
3779 3907 1.465777 TCAAACAGTCTCATGCATGCG 59.534 47.619 22.25 16.40 0.00 4.73
3795 3923 1.000385 CCAGCACGGCTTTCATTCAAA 60.000 47.619 0.00 0.00 36.40 2.69
3859 3987 2.513204 CTCCCACATCAGCGCAGG 60.513 66.667 11.47 0.20 0.00 4.85
3866 3994 3.338250 GGCCCACCTCCCACATCA 61.338 66.667 0.00 0.00 0.00 3.07
4138 4270 7.759433 ACGTTTCTGATTTCACAAACATTTTCT 59.241 29.630 10.63 0.00 35.42 2.52
4139 4271 7.894847 ACGTTTCTGATTTCACAAACATTTTC 58.105 30.769 10.63 0.00 35.42 2.29
4140 4272 7.826260 ACGTTTCTGATTTCACAAACATTTT 57.174 28.000 10.63 0.00 35.42 1.82
4154 4286 5.878332 TCATGCACATAAACGTTTCTGAT 57.122 34.783 27.12 10.63 0.00 2.90
4156 4288 6.746104 TTTTCATGCACATAAACGTTTCTG 57.254 33.333 18.42 19.93 0.00 3.02


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

AutoCloner maintained by Alex Coulton.