Multiple sequence alignment - TraesCS3A01G167200

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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 TraesCS3A01G167200 chr3A 100.000 4612 0 0 1 4612 172967149 172962538 0.000000e+00 8517.0
1 TraesCS3A01G167200 chr3D 93.616 3650 118 49 132 3729 154182941 154179355 0.000000e+00 5343.0
2 TraesCS3A01G167200 chr3D 89.444 900 46 28 3722 4612 154178542 154177683 0.000000e+00 1090.0
3 TraesCS3A01G167200 chr3D 95.000 140 1 1 1 134 154183921 154183782 1.010000e-51 215.0
4 TraesCS3A01G167200 chr3B 91.886 2502 108 34 129 2590 226786367 226788813 0.000000e+00 3408.0
5 TraesCS3A01G167200 chr3B 92.070 2043 80 37 2585 4612 226789090 226791065 0.000000e+00 2800.0
6 TraesCS3A01G167200 chr3B 100.000 132 0 0 3 134 226786214 226786345 1.280000e-60 244.0
7 TraesCS3A01G167200 chr4A 86.486 111 15 0 2473 2583 671598672 671598782 6.270000e-24 122.0
8 TraesCS3A01G167200 chr6D 90.278 72 5 2 2739 2809 415027746 415027676 4.910000e-15 93.5
9 TraesCS3A01G167200 chr6B 88.889 72 6 2 2739 2809 625779386 625779316 2.290000e-13 87.9
10 TraesCS3A01G167200 chr6A 87.500 72 7 2 2739 2809 560032829 560032759 1.060000e-11 82.4


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 TraesCS3A01G167200 chr3A 172962538 172967149 4611 True 8517.000000 8517 100.000000 1 4612 1 chr3A.!!$R1 4611
1 TraesCS3A01G167200 chr3D 154177683 154183921 6238 True 2216.000000 5343 92.686667 1 4612 3 chr3D.!!$R1 4611
2 TraesCS3A01G167200 chr3B 226786214 226791065 4851 False 2150.666667 3408 94.652000 3 4612 3 chr3B.!!$F1 4609

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
399 1265 0.038618 CAACGGACGGTGTGATCTGA 60.039 55.0 0.83 0.0 0.00 3.27 F
553 1438 0.043310 GCGGTATCAACAACGCGATC 60.043 55.0 15.93 0.0 42.66 3.69 F
2367 3276 0.036010 CCCCGATTGTGAGACTGCTT 60.036 55.0 0.00 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1951 2854 0.033642 GCGATCCCTGGCTAGGTTAC 59.966 60.0 15.86 4.64 42.96 2.50 R
2430 3349 0.172803 ACGGTAAGGTCAGCACGATC 59.827 55.0 0.00 0.00 0.00 3.69 R
3928 5951 0.317103 GGACCGATGACGAGATCACG 60.317 60.0 11.16 11.16 41.24 4.35 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
169 1019 2.939756 ACCGTTTTTCCATTTTGTTGGC 59.060 40.909 0.00 0.00 36.66 4.52
257 1107 6.372659 TGCTGACCTCAATATTCTTTCTCAAC 59.627 38.462 0.00 0.00 0.00 3.18
265 1115 9.467258 CTCAATATTCTTTCTCAACAGCAAAAA 57.533 29.630 0.00 0.00 0.00 1.94
290 1140 6.153067 AGAATTGTTCGTTGTTCAACAAACA 58.847 32.000 15.26 15.26 43.79 2.83
301 1151 6.773976 TGTTCAACAAACAAAAGAGAGGAT 57.226 33.333 0.00 0.00 44.83 3.24
334 1184 3.378112 TGTGCACAACAAAAGAGAAGAGG 59.622 43.478 19.28 0.00 35.24 3.69
392 1258 0.457853 CATCGATCAACGGACGGTGT 60.458 55.000 9.77 0.00 42.82 4.16
399 1265 0.038618 CAACGGACGGTGTGATCTGA 60.039 55.000 0.83 0.00 0.00 3.27
423 1289 0.617820 ACGCAGGGTTGGATAGACCT 60.618 55.000 0.00 0.00 39.86 3.85
426 1292 2.368875 CGCAGGGTTGGATAGACCTTAT 59.631 50.000 0.00 0.00 39.86 1.73
429 1295 5.306394 GCAGGGTTGGATAGACCTTATTAC 58.694 45.833 0.00 0.00 39.86 1.89
430 1296 5.071923 GCAGGGTTGGATAGACCTTATTACT 59.928 44.000 0.00 0.00 39.86 2.24
431 1297 6.269307 GCAGGGTTGGATAGACCTTATTACTA 59.731 42.308 0.00 0.00 39.86 1.82
432 1298 7.668492 CAGGGTTGGATAGACCTTATTACTAC 58.332 42.308 0.00 0.00 39.86 2.73
433 1299 6.786461 AGGGTTGGATAGACCTTATTACTACC 59.214 42.308 0.00 0.00 39.86 3.18
437 1303 5.015515 GGATAGACCTTATTACTACCGCCT 58.984 45.833 0.00 0.00 35.41 5.52
438 1304 5.105837 GGATAGACCTTATTACTACCGCCTG 60.106 48.000 0.00 0.00 35.41 4.85
439 1305 3.639952 AGACCTTATTACTACCGCCTGT 58.360 45.455 0.00 0.00 0.00 4.00
440 1306 4.796606 AGACCTTATTACTACCGCCTGTA 58.203 43.478 0.00 0.00 0.00 2.74
487 1372 8.208903 GCTACTCCTAGTAAACATTTCCCATTA 58.791 37.037 0.00 0.00 29.00 1.90
511 1396 2.400408 GCGAAAATGTGCGTGTTACTTG 59.600 45.455 0.00 0.00 0.00 3.16
514 1399 4.605594 CGAAAATGTGCGTGTTACTTGTAC 59.394 41.667 0.00 0.00 0.00 2.90
518 1403 1.717645 GTGCGTGTTACTTGTACGAGG 59.282 52.381 14.75 0.00 40.01 4.63
553 1438 0.043310 GCGGTATCAACAACGCGATC 60.043 55.000 15.93 0.00 42.66 3.69
563 1448 4.024472 TCAACAACGCGATCTTGAAAATCA 60.024 37.500 15.93 0.00 0.00 2.57
616 1501 1.154395 GAAAAAGGAGACGCAGCGC 60.154 57.895 16.61 8.00 0.00 5.92
726 1618 2.434658 GAAAAGTTGCAAGCCGGGGG 62.435 60.000 2.18 0.00 0.00 5.40
984 1876 1.713647 AGACTTCAGACTCCTCCCTCA 59.286 52.381 0.00 0.00 0.00 3.86
1025 1917 2.293246 TCTTTCTCTCTCCCTCTCCCT 58.707 52.381 0.00 0.00 0.00 4.20
1026 1918 2.243736 TCTTTCTCTCTCCCTCTCCCTC 59.756 54.545 0.00 0.00 0.00 4.30
1027 1919 1.994399 TTCTCTCTCCCTCTCCCTCT 58.006 55.000 0.00 0.00 0.00 3.69
1028 1920 1.518367 TCTCTCTCCCTCTCCCTCTC 58.482 60.000 0.00 0.00 0.00 3.20
1029 1921 0.478507 CTCTCTCCCTCTCCCTCTCC 59.521 65.000 0.00 0.00 0.00 3.71
1030 1922 0.996762 TCTCTCCCTCTCCCTCTCCC 60.997 65.000 0.00 0.00 0.00 4.30
1187 2079 2.677902 CGGCTTCCTGAACTTGCTATCA 60.678 50.000 0.00 0.00 0.00 2.15
1310 2205 1.731720 AGAACATGAAGAAGAGCCGC 58.268 50.000 0.00 0.00 0.00 6.53
1429 2324 1.339151 ACCGCTTCTTCACCCATTCTC 60.339 52.381 0.00 0.00 0.00 2.87
1433 2328 3.369471 CGCTTCTTCACCCATTCTCCTTA 60.369 47.826 0.00 0.00 0.00 2.69
1447 2342 6.830838 CCATTCTCCTTACTTCTTAAATGGCT 59.169 38.462 0.00 0.00 36.54 4.75
1455 2350 7.201652 CCTTACTTCTTAAATGGCTAGACTTGC 60.202 40.741 0.00 0.00 0.00 4.01
1463 2358 1.298014 GCTAGACTTGCCAGCAGGT 59.702 57.895 7.15 7.15 38.99 4.00
1470 2365 2.758979 GACTTGCCAGCAGGTACTACTA 59.241 50.000 7.44 0.00 36.37 1.82
1478 2373 5.169295 CCAGCAGGTACTACTACTTGTTTC 58.831 45.833 0.00 0.00 36.02 2.78
1482 2377 6.151480 AGCAGGTACTACTACTTGTTTCTCTC 59.849 42.308 0.00 0.00 36.02 3.20
1505 2408 9.043079 TCTCTATATACGGCGATCTAATACTTG 57.957 37.037 16.62 0.00 0.00 3.16
1528 2431 1.485124 TTCGATCCTGCAGCTCCTTA 58.515 50.000 8.66 0.00 0.00 2.69
1639 2542 2.287248 GGCGAGGTACGTAGTTATCCAC 60.287 54.545 0.00 0.00 37.78 4.02
1650 2553 3.802948 AGTTATCCACGATCTGTCCAC 57.197 47.619 0.00 0.00 0.00 4.02
1651 2554 3.096852 AGTTATCCACGATCTGTCCACA 58.903 45.455 0.00 0.00 0.00 4.17
1652 2555 3.119101 AGTTATCCACGATCTGTCCACAC 60.119 47.826 0.00 0.00 0.00 3.82
1653 2556 1.266178 ATCCACGATCTGTCCACACA 58.734 50.000 0.00 0.00 0.00 3.72
1654 2557 1.044611 TCCACGATCTGTCCACACAA 58.955 50.000 0.00 0.00 29.82 3.33
1655 2558 1.623311 TCCACGATCTGTCCACACAAT 59.377 47.619 0.00 0.00 29.82 2.71
1950 2853 5.848833 CCCACGAGGTACTATTCTTACTT 57.151 43.478 0.00 0.00 41.55 2.24
1951 2854 5.589192 CCCACGAGGTACTATTCTTACTTG 58.411 45.833 0.00 0.00 41.55 3.16
1961 2867 8.140628 GGTACTATTCTTACTTGTAACCTAGCC 58.859 40.741 0.00 0.00 0.00 3.93
2004 2910 6.271488 TGGCCAAGAAATTTACTGAATCAG 57.729 37.500 0.61 8.98 37.52 2.90
2331 3240 3.644399 GAAGGCCCGTGTCTCCGTC 62.644 68.421 0.00 0.00 0.00 4.79
2365 3274 2.109126 GCCCCGATTGTGAGACTGC 61.109 63.158 0.00 0.00 0.00 4.40
2366 3275 1.599047 CCCCGATTGTGAGACTGCT 59.401 57.895 0.00 0.00 0.00 4.24
2367 3276 0.036010 CCCCGATTGTGAGACTGCTT 60.036 55.000 0.00 0.00 0.00 3.91
2430 3349 5.661056 TCTTGAGTAGTCCTTGTGTATGG 57.339 43.478 0.00 0.00 0.00 2.74
2680 3881 5.589050 GGGGTGTATGATTGGTCTAACTTTC 59.411 44.000 0.00 0.00 0.00 2.62
2809 4010 1.456892 CATGGCCATGGCATCCACT 60.457 57.895 36.56 12.09 45.69 4.00
2839 4040 3.260483 GCGTCCATGCTGCTCTCG 61.260 66.667 0.00 0.45 0.00 4.04
3127 4328 3.239861 CCAGTCCAAGTTCTCTGGC 57.760 57.895 0.00 0.00 40.43 4.85
3145 4346 2.037620 GCCTGCAGATGTCCTCCGAT 62.038 60.000 17.39 0.00 0.00 4.18
3259 4460 1.890041 CGCGGACCCAAACTTCACA 60.890 57.895 0.00 0.00 0.00 3.58
3419 4620 0.389817 CAGCGAGACCCAATGAACGA 60.390 55.000 0.00 0.00 0.00 3.85
3434 4635 0.748450 AACGACCTGGTCAAGTTCGA 59.252 50.000 25.42 0.00 32.09 3.71
3454 4656 5.611374 TCGAAAAGAGTTGAGAAACCAGAT 58.389 37.500 0.00 0.00 0.00 2.90
3455 4657 6.755206 TCGAAAAGAGTTGAGAAACCAGATA 58.245 36.000 0.00 0.00 0.00 1.98
3456 4658 6.645415 TCGAAAAGAGTTGAGAAACCAGATAC 59.355 38.462 0.00 0.00 0.00 2.24
3517 4719 5.248640 TCTTCTTTGGTCAGGATTAGCTTG 58.751 41.667 0.00 0.00 0.00 4.01
3527 4729 2.159366 AGGATTAGCTTGTCGAGACGTG 60.159 50.000 0.00 0.00 0.00 4.49
3645 4850 3.181510 CCTTAGTTCTTTTTCCATCGCCG 60.182 47.826 0.00 0.00 0.00 6.46
3710 4915 9.763837 ATAGTAATAAGTAAAATAATGGCCCCC 57.236 33.333 0.00 0.00 0.00 5.40
3711 4916 7.597327 AGTAATAAGTAAAATAATGGCCCCCA 58.403 34.615 0.00 0.00 38.19 4.96
3712 4917 6.740944 AATAAGTAAAATAATGGCCCCCAC 57.259 37.500 0.00 0.00 35.80 4.61
3713 4918 3.040655 AGTAAAATAATGGCCCCCACC 57.959 47.619 0.00 0.00 35.80 4.61
3714 4919 2.590137 AGTAAAATAATGGCCCCCACCT 59.410 45.455 0.00 0.00 35.80 4.00
3715 4920 2.174685 AAAATAATGGCCCCCACCTC 57.825 50.000 0.00 0.00 35.80 3.85
3716 4921 0.106217 AAATAATGGCCCCCACCTCG 60.106 55.000 0.00 0.00 35.80 4.63
3717 4922 2.006805 AATAATGGCCCCCACCTCGG 62.007 60.000 0.00 0.00 35.80 4.63
3752 5773 4.410448 GCTAGTCAAAGCAGAAGAAATGC 58.590 43.478 0.00 0.00 42.30 3.56
3776 5798 3.440522 GGGGTAAAGAACAATGACAGCTC 59.559 47.826 0.00 0.00 0.00 4.09
3813 5835 4.536364 ACGTGTTTGTTCACATCTTGAG 57.464 40.909 0.00 0.00 38.12 3.02
3840 5863 1.925972 GCACCCCTCTCCCCTTTCT 60.926 63.158 0.00 0.00 0.00 2.52
3843 5866 2.684499 CCCCTCTCCCCTTTCTGGC 61.684 68.421 0.00 0.00 0.00 4.85
3844 5867 1.617839 CCCTCTCCCCTTTCTGGCT 60.618 63.158 0.00 0.00 0.00 4.75
3906 5929 1.781025 TTCAAACAAGTCGCTGCCCG 61.781 55.000 0.00 0.00 38.61 6.13
4024 6047 0.036164 TGGTCAGTTCGTCCCCATTG 59.964 55.000 0.00 0.00 0.00 2.82
4025 6048 0.323629 GGTCAGTTCGTCCCCATTGA 59.676 55.000 0.00 0.00 0.00 2.57
4027 6050 1.804748 GTCAGTTCGTCCCCATTGAAC 59.195 52.381 0.00 0.00 41.71 3.18
4028 6051 1.418264 TCAGTTCGTCCCCATTGAACA 59.582 47.619 7.03 0.00 43.36 3.18
4029 6052 1.806542 CAGTTCGTCCCCATTGAACAG 59.193 52.381 7.03 0.00 43.36 3.16
4030 6053 1.420138 AGTTCGTCCCCATTGAACAGT 59.580 47.619 7.03 0.00 43.36 3.55
4031 6054 2.635915 AGTTCGTCCCCATTGAACAGTA 59.364 45.455 7.03 0.00 43.36 2.74
4032 6055 3.000727 GTTCGTCCCCATTGAACAGTAG 58.999 50.000 0.00 0.00 41.20 2.57
4033 6056 1.553248 TCGTCCCCATTGAACAGTAGG 59.447 52.381 0.00 0.00 0.00 3.18
4051 6074 3.526931 AGGAGTACATCACATGGTTCG 57.473 47.619 0.00 0.00 33.60 3.95
4114 6141 2.472816 GAGTTTGAACACGTACGGGAA 58.527 47.619 27.01 5.08 0.00 3.97
4120 6147 0.677842 AACACGTACGGGAAAGCTCT 59.322 50.000 27.01 0.00 0.00 4.09
4195 6222 1.082690 GCAGTCTGAGTTAAGCTGGC 58.917 55.000 3.32 0.00 0.00 4.85
4196 6223 1.731720 CAGTCTGAGTTAAGCTGGCC 58.268 55.000 0.00 0.00 0.00 5.36
4202 6229 0.393132 GAGTTAAGCTGGCCTGGGTC 60.393 60.000 12.06 0.00 0.00 4.46
4205 6232 2.484287 TTAAGCTGGCCTGGGTCTGC 62.484 60.000 13.87 13.87 43.45 4.26
4212 6239 4.421515 CCTGGGTCTGCCTGCCTG 62.422 72.222 0.00 0.00 34.45 4.85
4213 6240 4.421515 CTGGGTCTGCCTGCCTGG 62.422 72.222 0.00 0.00 39.35 4.45
4338 6371 1.570979 GAAGGGGAGAAATCATGGGGT 59.429 52.381 0.00 0.00 0.00 4.95
4401 6445 2.502080 CGCGTCGTCTGTGGACTC 60.502 66.667 0.00 0.00 40.10 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
169 1019 2.557056 TCCTCCCATTAGATTACTCGCG 59.443 50.000 0.00 0.00 0.00 5.87
278 1128 6.563422 CATCCTCTCTTTTGTTTGTTGAACA 58.437 36.000 0.00 0.00 46.19 3.18
279 1129 5.460091 GCATCCTCTCTTTTGTTTGTTGAAC 59.540 40.000 0.00 0.00 38.78 3.18
280 1130 5.451798 GGCATCCTCTCTTTTGTTTGTTGAA 60.452 40.000 0.00 0.00 0.00 2.69
281 1131 4.037923 GGCATCCTCTCTTTTGTTTGTTGA 59.962 41.667 0.00 0.00 0.00 3.18
282 1132 4.301628 GGCATCCTCTCTTTTGTTTGTTG 58.698 43.478 0.00 0.00 0.00 3.33
290 1140 4.821532 AATATGGGGCATCCTCTCTTTT 57.178 40.909 0.00 0.00 36.20 2.27
298 1148 1.069049 GTGCACAAATATGGGGCATCC 59.931 52.381 13.17 0.00 41.13 3.51
301 1151 1.274728 GTTGTGCACAAATATGGGGCA 59.725 47.619 32.61 5.04 38.24 5.36
358 1213 0.652592 CGATGTCTCGCCATTTCACC 59.347 55.000 0.00 0.00 38.20 4.02
359 1214 1.640428 TCGATGTCTCGCCATTTCAC 58.360 50.000 0.00 0.00 44.65 3.18
372 1238 0.457853 CACCGTCCGTTGATCGATGT 60.458 55.000 0.54 0.00 42.86 3.06
381 1247 0.038526 GTCAGATCACACCGTCCGTT 60.039 55.000 0.00 0.00 0.00 4.44
383 1249 1.514228 CGTCAGATCACACCGTCCG 60.514 63.158 0.00 0.00 0.00 4.79
384 1250 1.805945 GCGTCAGATCACACCGTCC 60.806 63.158 0.00 0.00 0.00 4.79
392 1258 2.125952 CTGCGTGGCGTCAGATCA 60.126 61.111 0.00 0.00 34.71 2.92
414 1280 5.015515 AGGCGGTAGTAATAAGGTCTATCC 58.984 45.833 0.00 0.00 0.00 2.59
430 1296 1.003812 ACATTTTGGCTACAGGCGGTA 59.996 47.619 0.00 0.00 44.42 4.02
431 1297 0.251165 ACATTTTGGCTACAGGCGGT 60.251 50.000 0.00 0.00 44.42 5.68
432 1298 0.887933 AACATTTTGGCTACAGGCGG 59.112 50.000 0.00 0.00 44.42 6.13
433 1299 1.402720 CCAACATTTTGGCTACAGGCG 60.403 52.381 0.00 0.00 46.09 5.52
443 1309 7.926018 AGGAGTAGCTTTTTAACCAACATTTTG 59.074 33.333 0.00 0.00 0.00 2.44
444 1310 8.018537 AGGAGTAGCTTTTTAACCAACATTTT 57.981 30.769 0.00 0.00 0.00 1.82
460 1345 5.724854 TGGGAAATGTTTACTAGGAGTAGCT 59.275 40.000 0.00 0.00 31.47 3.32
466 1351 7.012894 CGCAATAATGGGAAATGTTTACTAGGA 59.987 37.037 0.00 0.00 41.79 2.94
487 1372 2.132740 AACACGCACATTTTCGCAAT 57.867 40.000 0.00 0.00 0.00 3.56
553 1438 4.379813 CCTGTCGGTCCAATGATTTTCAAG 60.380 45.833 0.00 0.00 0.00 3.02
563 1448 1.079127 CTTCGCCTGTCGGTCCAAT 60.079 57.895 0.00 0.00 39.05 3.16
616 1501 2.637025 CAACAAAGCGACGTGGGG 59.363 61.111 0.00 0.00 0.00 4.96
620 1510 2.323105 CGTGCAACAAAGCGACGT 59.677 55.556 0.00 0.00 35.74 4.34
726 1618 0.110010 GCTTGTCTGCGCTTTTCCTC 60.110 55.000 9.73 0.00 0.00 3.71
830 1722 4.247612 GGACGACGACCCGATCCG 62.248 72.222 0.00 0.00 0.00 4.18
1025 1917 2.015726 GGGGAGAGGGAGAGGGAGA 61.016 68.421 0.00 0.00 0.00 3.71
1026 1918 2.018086 AGGGGAGAGGGAGAGGGAG 61.018 68.421 0.00 0.00 0.00 4.30
1027 1919 2.015726 GAGGGGAGAGGGAGAGGGA 61.016 68.421 0.00 0.00 0.00 4.20
1028 1920 2.612251 GAGGGGAGAGGGAGAGGG 59.388 72.222 0.00 0.00 0.00 4.30
1029 1921 2.197324 CGAGGGGAGAGGGAGAGG 59.803 72.222 0.00 0.00 0.00 3.69
1030 1922 2.197324 CCGAGGGGAGAGGGAGAG 59.803 72.222 0.00 0.00 34.06 3.20
1173 2065 1.009829 GCCGGTGATAGCAAGTTCAG 58.990 55.000 1.90 0.00 0.00 3.02
1325 2220 3.220999 CTTGTGGTCCTCCGCGTCA 62.221 63.158 4.92 0.00 46.30 4.35
1429 2324 7.201652 GCAAGTCTAGCCATTTAAGAAGTAAGG 60.202 40.741 0.00 0.00 0.00 2.69
1447 2342 1.938585 AGTACCTGCTGGCAAGTCTA 58.061 50.000 9.95 0.00 36.63 2.59
1455 2350 4.803098 AACAAGTAGTAGTACCTGCTGG 57.197 45.455 8.29 8.29 39.83 4.85
1470 2365 5.530171 TCGCCGTATATAGAGAGAAACAAGT 59.470 40.000 0.00 0.00 0.00 3.16
1478 2373 8.821147 AGTATTAGATCGCCGTATATAGAGAG 57.179 38.462 0.00 0.00 0.00 3.20
1482 2377 6.856938 GGCAAGTATTAGATCGCCGTATATAG 59.143 42.308 0.00 0.00 0.00 1.31
1505 2408 1.435408 GAGCTGCAGGATCGAAAGGC 61.435 60.000 17.12 0.00 0.00 4.35
1528 2431 2.095978 CTCCTCGTGTTGTTCCCGGT 62.096 60.000 0.00 0.00 0.00 5.28
1639 2542 5.582269 AGATTGTAATTGTGTGGACAGATCG 59.418 40.000 0.00 0.00 32.26 3.69
1650 2553 6.191534 GACGAGATCGAGATTGTAATTGTG 57.808 41.667 9.58 0.00 43.02 3.33
1950 2853 1.410004 CGATCCCTGGCTAGGTTACA 58.590 55.000 15.86 0.00 42.96 2.41
1951 2854 0.033642 GCGATCCCTGGCTAGGTTAC 59.966 60.000 15.86 4.64 42.96 2.50
1961 2867 2.932614 CAAGTCAAACTAGCGATCCCTG 59.067 50.000 0.00 0.00 0.00 4.45
1969 2875 2.504367 TCTTGGCCAAGTCAAACTAGC 58.496 47.619 37.97 0.00 39.38 3.42
2004 2910 8.570488 TCCTAATAAAAACGGAAAAAGAGGAAC 58.430 33.333 0.00 0.00 0.00 3.62
2274 3183 1.601419 CTTGCTGGTCATGGCCCTTG 61.601 60.000 15.27 5.28 0.00 3.61
2367 3276 9.347240 ACAAGAAAATGATCAAGAAGAAGAAGA 57.653 29.630 0.00 0.00 0.00 2.87
2430 3349 0.172803 ACGGTAAGGTCAGCACGATC 59.827 55.000 0.00 0.00 0.00 3.69
2680 3881 3.976793 ATGGCATCACGCATAAAGAAG 57.023 42.857 0.00 0.00 45.17 2.85
2821 4022 3.260483 GAGAGCAGCATGGACGCG 61.260 66.667 3.53 3.53 35.86 6.01
2869 4070 1.558756 AGGAAGTTGGAGCTCATGAGG 59.441 52.381 23.89 6.34 0.00 3.86
2959 4160 3.371063 TGGGTGAGGTCGAGCGTC 61.371 66.667 9.28 7.92 0.00 5.19
3127 4328 0.467384 AATCGGAGGACATCTGCAGG 59.533 55.000 15.13 0.36 33.93 4.85
3370 4571 3.044986 GTTGCTCGTCGTGTTGTTACTA 58.955 45.455 0.00 0.00 0.00 1.82
3419 4620 3.118371 ACTCTTTTCGAACTTGACCAGGT 60.118 43.478 0.00 0.00 0.00 4.00
3434 4635 7.604545 GCTAGTATCTGGTTTCTCAACTCTTTT 59.395 37.037 0.00 0.00 32.90 2.27
3454 4656 7.486647 GTGTATAACTTGCAACCTAGCTAGTA 58.513 38.462 19.31 2.49 46.96 1.82
3456 4658 5.459107 CGTGTATAACTTGCAACCTAGCTAG 59.541 44.000 14.20 14.20 41.97 3.42
3517 4719 1.849097 AACCAAAGACACGTCTCGAC 58.151 50.000 0.00 0.00 39.39 4.20
3645 4850 3.441572 ACAGTGAAATATCAACAGCTGCC 59.558 43.478 15.27 0.00 37.30 4.85
3710 4915 5.398603 AGCATAGAAATATCTCCGAGGTG 57.601 43.478 0.00 0.00 37.10 4.00
3711 4916 6.249951 ACTAGCATAGAAATATCTCCGAGGT 58.750 40.000 0.00 0.00 42.77 3.85
3712 4917 6.375736 TGACTAGCATAGAAATATCTCCGAGG 59.624 42.308 0.00 0.00 42.77 4.63
3713 4918 7.384439 TGACTAGCATAGAAATATCTCCGAG 57.616 40.000 0.00 0.00 42.77 4.63
3714 4919 7.761038 TTGACTAGCATAGAAATATCTCCGA 57.239 36.000 0.00 0.00 42.77 4.55
3715 4920 7.062839 GCTTTGACTAGCATAGAAATATCTCCG 59.937 40.741 8.16 0.00 42.77 4.63
3716 4921 7.875041 TGCTTTGACTAGCATAGAAATATCTCC 59.125 37.037 0.00 0.00 45.72 3.71
3717 4922 8.824159 TGCTTTGACTAGCATAGAAATATCTC 57.176 34.615 0.00 0.00 45.72 2.75
3752 5773 2.747446 CTGTCATTGTTCTTTACCCCCG 59.253 50.000 0.00 0.00 0.00 5.73
3776 5798 0.385751 ACGTAGATGAGCATCCGGTG 59.614 55.000 0.00 0.00 38.58 4.94
3822 5844 1.925972 AGAAAGGGGAGAGGGGTGC 60.926 63.158 0.00 0.00 0.00 5.01
3840 5863 0.322975 GCCAAGACAAGAGAGAGCCA 59.677 55.000 0.00 0.00 0.00 4.75
3843 5866 3.399440 ACAAGCCAAGACAAGAGAGAG 57.601 47.619 0.00 0.00 0.00 3.20
3844 5867 3.845781 AACAAGCCAAGACAAGAGAGA 57.154 42.857 0.00 0.00 0.00 3.10
3912 5935 1.006825 CACGTTCACATCCGAGCGAA 61.007 55.000 4.21 0.00 41.52 4.70
3928 5951 0.317103 GGACCGATGACGAGATCACG 60.317 60.000 11.16 11.16 41.24 4.35
4024 6047 5.105310 ACCATGTGATGTACTCCTACTGTTC 60.105 44.000 0.00 0.00 0.00 3.18
4025 6048 4.777896 ACCATGTGATGTACTCCTACTGTT 59.222 41.667 0.00 0.00 0.00 3.16
4027 6050 5.344743 AACCATGTGATGTACTCCTACTG 57.655 43.478 0.00 0.00 0.00 2.74
4028 6051 4.098044 CGAACCATGTGATGTACTCCTACT 59.902 45.833 0.00 0.00 0.00 2.57
4029 6052 4.142227 ACGAACCATGTGATGTACTCCTAC 60.142 45.833 0.00 0.00 0.00 3.18
4030 6053 4.021229 ACGAACCATGTGATGTACTCCTA 58.979 43.478 0.00 0.00 0.00 2.94
4031 6054 2.832129 ACGAACCATGTGATGTACTCCT 59.168 45.455 0.00 0.00 0.00 3.69
4032 6055 2.930040 CACGAACCATGTGATGTACTCC 59.070 50.000 0.00 0.00 39.73 3.85
4033 6056 2.348666 GCACGAACCATGTGATGTACTC 59.651 50.000 0.00 0.00 39.73 2.59
4096 6123 2.600556 GCTTTCCCGTACGTGTTCAAAC 60.601 50.000 15.21 0.00 0.00 2.93
4114 6141 1.756950 CCCCATGCATGCAGAGCTT 60.757 57.895 26.69 5.62 0.00 3.74
4120 6147 2.756691 GTGCTCCCCATGCATGCA 60.757 61.111 25.04 25.04 42.69 3.96
4195 6222 4.421515 CAGGCAGGCAGACCCAGG 62.422 72.222 0.00 0.00 36.11 4.45
4196 6223 4.421515 CCAGGCAGGCAGACCCAG 62.422 72.222 0.00 0.00 36.11 4.45
4216 6243 3.989698 CTACGCACCAGGCAGGACG 62.990 68.421 1.67 8.71 45.17 4.79
4217 6244 2.125512 CTACGCACCAGGCAGGAC 60.126 66.667 1.67 0.00 45.17 3.85
4218 6245 4.082523 GCTACGCACCAGGCAGGA 62.083 66.667 1.67 0.00 45.17 3.86
4264 6291 1.299648 CGCCATGAGTTTCCCTCCA 59.700 57.895 0.00 0.00 39.65 3.86
4290 6317 4.669809 ATTTTCCCCGTGCCGCCA 62.670 61.111 0.00 0.00 0.00 5.69
4338 6371 4.794439 CGTGCCGTGCCAGATCGA 62.794 66.667 0.00 0.00 0.00 3.59
4445 6489 1.833934 TAATCGCCTCCCCCGGTAC 60.834 63.158 0.00 0.00 0.00 3.34
4446 6490 1.833934 GTAATCGCCTCCCCCGGTA 60.834 63.158 0.00 0.00 0.00 4.02
4447 6491 3.159347 GTAATCGCCTCCCCCGGT 61.159 66.667 0.00 0.00 0.00 5.28


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

AutoCloner maintained by Alex Coulton.