Multiple sequence alignment - TraesCS4B01G243900

Loading Multiple Alignment...

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 TraesCS4B01G243900 chr4B 100.000 6514 0 0 1 6514 505097528 505091015 0.000000e+00 12030.0
1 TraesCS4B01G243900 chr4B 91.089 202 18 0 1764 1965 505095717 505095516 2.310000e-69 274.0
2 TraesCS4B01G243900 chr4B 91.089 202 18 0 1812 2013 505095765 505095564 2.310000e-69 274.0
3 TraesCS4B01G243900 chr4A 94.779 5957 182 44 1 5919 63553328 63547463 0.000000e+00 9158.0
4 TraesCS4B01G243900 chr4A 93.146 321 14 5 6123 6436 63546871 63546552 1.280000e-126 464.0
5 TraesCS4B01G243900 chr4A 95.050 202 10 0 1764 1965 63551542 63551341 1.050000e-82 318.0
6 TraesCS4B01G243900 chr4A 94.271 192 9 1 5916 6105 63547282 63547091 6.390000e-75 292.0
7 TraesCS4B01G243900 chr4A 90.594 202 19 0 1812 2013 63551590 63551389 1.080000e-67 268.0
8 TraesCS4B01G243900 chr4A 92.208 154 12 0 1860 2013 63551590 63551437 1.100000e-52 219.0
9 TraesCS4B01G243900 chr4D 96.000 5200 147 17 994 6162 405783362 405778193 0.000000e+00 8394.0
10 TraesCS4B01G243900 chr4D 88.006 692 33 18 273 954 405784475 405783824 0.000000e+00 773.0
11 TraesCS4B01G243900 chr4D 92.737 358 18 3 6164 6514 405777957 405777601 1.620000e-140 510.0
12 TraesCS4B01G243900 chr4D 89.078 293 11 7 1 281 405787540 405787257 1.740000e-90 344.0
13 TraesCS4B01G243900 chr4D 94.059 202 12 0 1764 1965 405782544 405782343 2.280000e-79 307.0
14 TraesCS4B01G243900 chr4D 91.089 202 18 0 1812 2013 405782592 405782391 2.310000e-69 274.0
15 TraesCS4B01G243900 chr4D 94.805 154 8 0 1764 1917 405782496 405782343 2.350000e-59 241.0
16 TraesCS4B01G243900 chr4D 96.552 58 2 0 1764 1821 405782400 405782343 5.380000e-16 97.1


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 TraesCS4B01G243900 chr4B 505091015 505097528 6513 True 4192.666667 12030 94.059333 1 6514 3 chr4B.!!$R1 6513
1 TraesCS4B01G243900 chr4A 63546552 63553328 6776 True 1786.500000 9158 93.341333 1 6436 6 chr4A.!!$R1 6435
2 TraesCS4B01G243900 chr4D 405777601 405787540 9939 True 1367.512500 8394 92.790750 1 6514 8 chr4D.!!$R1 6513

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
932 3772 0.365523 CACGCATTTCTCCGTACACG 59.634 55.000 0.0 0.0 35.69 4.49 F
2127 5395 0.238289 CACGACAAGATGGTGCCAAC 59.762 55.000 0.0 0.0 29.56 3.77 F
3004 6272 0.112995 TGGTGCTTTCCTTCAGCCAT 59.887 50.000 0.0 0.0 36.33 4.40 F
3792 7060 1.072965 AGTCTTTCAAGGGGTGAGCTG 59.927 52.381 0.0 0.0 37.61 4.24 F
4380 7648 4.809513 GGGGGAGCTGGTTCTAGA 57.190 61.111 0.0 0.0 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2255 5523 0.034670 GCTGGATGAAGTGCCCTTCT 60.035 55.000 10.38 0.0 46.07 2.85 R
3792 7060 0.170561 CAAGCTGTTCCTCATGCTGC 59.829 55.000 0.00 0.0 33.37 5.25 R
4802 8071 1.003233 GCCTACAAGCTGGGTAACTGT 59.997 52.381 0.00 0.0 0.00 3.55 R
4803 8072 1.279271 AGCCTACAAGCTGGGTAACTG 59.721 52.381 0.00 0.0 42.95 3.16 R
6056 9534 2.595124 ACGACATTGTGTGTGTCTGA 57.405 45.000 0.00 0.0 42.36 3.27 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
32 33 2.887783 TCCCGAATGCAAGCAAACTTTA 59.112 40.909 0.00 0.00 32.29 1.85
76 77 0.755698 TCAGCTTCTACTAGCCCCCG 60.756 60.000 0.00 0.00 42.20 5.73
146 147 1.202952 TGCCAATTGGTAAACTCCGGT 60.203 47.619 25.19 0.00 37.57 5.28
170 171 1.155042 GCAGTTGCTCTCACCTTGAG 58.845 55.000 0.00 0.00 45.59 3.02
276 291 3.679980 CGAATCAAATCGAAGTCTGTGGT 59.320 43.478 0.00 0.00 45.48 4.16
350 3155 1.746517 GACGGGACAAGTCACCAGT 59.253 57.895 2.29 0.00 38.42 4.00
355 3160 1.069090 GACAAGTCACCAGTGCGGA 59.931 57.895 0.00 0.00 38.63 5.54
378 3189 2.512515 GGAGACGCTGATGCCCAC 60.513 66.667 0.00 0.00 35.36 4.61
385 3196 2.313172 GCTGATGCCCACGCTATCG 61.313 63.158 0.00 0.00 42.43 2.92
433 3244 2.637382 TGACCTTTCTGGCTCACACATA 59.363 45.455 0.00 0.00 40.22 2.29
478 3298 3.461773 CCGAGGCCTCCACGACAT 61.462 66.667 27.20 0.00 39.84 3.06
489 3309 1.138859 TCCACGACATGACCCATCATC 59.861 52.381 0.00 0.00 44.13 2.92
490 3310 1.211743 CACGACATGACCCATCATCG 58.788 55.000 0.00 0.00 44.13 3.84
494 3314 1.601759 CATGACCCATCATCGCCCC 60.602 63.158 0.00 0.00 44.13 5.80
495 3315 2.078044 ATGACCCATCATCGCCCCA 61.078 57.895 0.00 0.00 42.15 4.96
496 3316 2.060567 ATGACCCATCATCGCCCCAG 62.061 60.000 0.00 0.00 42.15 4.45
497 3317 2.366837 ACCCATCATCGCCCCAGA 60.367 61.111 0.00 0.00 0.00 3.86
559 3380 3.186047 GTCCACCATCGCCGTTCG 61.186 66.667 0.00 0.00 40.15 3.95
652 3474 3.314635 CGCTTACTACCATCTACGAAGGT 59.685 47.826 0.00 0.00 37.42 3.50
686 3508 3.909258 GACTCCCGCGCGTCAGAAA 62.909 63.158 29.95 5.96 0.00 2.52
748 3574 0.545646 AAGAGAGGAGGAAGCATGGC 59.454 55.000 0.00 0.00 0.00 4.40
819 3650 3.352748 TAGGAGGGGAGTGGCCGA 61.353 66.667 0.00 0.00 37.63 5.54
832 3663 4.605967 GCCGAGAGCGAGCGAGAG 62.606 72.222 0.00 0.00 40.82 3.20
833 3664 4.605967 CCGAGAGCGAGCGAGAGC 62.606 72.222 0.00 0.00 46.69 4.09
869 3700 2.683933 GGGAGGAGTGAGCCGGAA 60.684 66.667 5.05 0.00 0.00 4.30
882 3713 4.735132 CGGAAGGACGCAAGCCGA 62.735 66.667 0.00 0.00 44.43 5.54
883 3714 2.815647 GGAAGGACGCAAGCCGAG 60.816 66.667 0.00 0.00 45.62 4.63
884 3715 2.815647 GAAGGACGCAAGCCGAGG 60.816 66.667 0.00 0.00 45.62 4.63
921 3761 4.088762 CACCTCGCGCACGCATTT 62.089 61.111 16.04 0.00 42.06 2.32
922 3762 3.788766 ACCTCGCGCACGCATTTC 61.789 61.111 16.04 0.00 42.06 2.17
923 3763 3.490759 CCTCGCGCACGCATTTCT 61.491 61.111 16.04 0.00 42.06 2.52
932 3772 0.365523 CACGCATTTCTCCGTACACG 59.634 55.000 0.00 0.00 35.69 4.49
959 3799 2.593026 CGCTCCTTCCTTATCTCTCCT 58.407 52.381 0.00 0.00 0.00 3.69
961 3801 3.571590 GCTCCTTCCTTATCTCTCCTCA 58.428 50.000 0.00 0.00 0.00 3.86
962 3802 3.573967 GCTCCTTCCTTATCTCTCCTCAG 59.426 52.174 0.00 0.00 0.00 3.35
964 3804 3.052566 TCCTTCCTTATCTCTCCTCAGCA 60.053 47.826 0.00 0.00 0.00 4.41
967 3807 2.037901 CCTTATCTCTCCTCAGCAGCA 58.962 52.381 0.00 0.00 0.00 4.41
975 3819 3.714001 CTCAGCAGCAGCCCCTCA 61.714 66.667 0.00 0.00 43.56 3.86
980 3824 3.655211 CAGCAGCCCCTCACCCTT 61.655 66.667 0.00 0.00 0.00 3.95
988 3832 3.068691 CCTCACCCTTCTCGGCGA 61.069 66.667 10.14 10.14 0.00 5.54
1065 4327 2.017559 GCGACAGGCGGAGGTTCTAT 62.018 60.000 0.00 0.00 41.29 1.98
1676 4944 1.283321 GAAAGTGGATTCTCCTGGGCT 59.717 52.381 0.00 0.00 37.46 5.19
1778 5046 3.317993 GCAGAAGCAGGGAAAGTAACAAA 59.682 43.478 0.00 0.00 41.58 2.83
1845 5113 3.818961 AACACACAGCATGAGAAATCG 57.181 42.857 0.00 0.00 39.69 3.34
1955 5223 4.063689 GAGAAATCAGCATCGGATGTCAT 58.936 43.478 18.54 6.30 32.45 3.06
1956 5224 3.813724 AGAAATCAGCATCGGATGTCATG 59.186 43.478 18.54 14.45 32.45 3.07
1974 5242 3.566322 TCATGGGGAAAGTAACAAACACG 59.434 43.478 0.00 0.00 0.00 4.49
1988 5256 3.243501 ACAAACACGCAGCATGAGAAATT 60.244 39.130 0.00 0.00 38.60 1.82
2040 5308 0.392729 GAGATGAAGCTGCCAGTGCT 60.393 55.000 0.00 0.00 43.32 4.40
2056 5324 1.537202 GTGCTGTTGATCAAGGTGGAC 59.463 52.381 8.80 9.42 0.00 4.02
2097 5365 3.869272 CTGGAAGCGCGGCATGAC 61.869 66.667 8.83 0.00 0.00 3.06
2127 5395 0.238289 CACGACAAGATGGTGCCAAC 59.762 55.000 0.00 0.00 29.56 3.77
2144 5412 2.359107 CGCTGCTGATGTGGGTGT 60.359 61.111 0.00 0.00 0.00 4.16
2169 5437 3.387374 AGAGCACTTCATCTGGTATCCTG 59.613 47.826 0.00 0.00 0.00 3.86
2185 5453 0.471617 CCTGAAGGAGGCTACCATGG 59.528 60.000 11.19 11.19 34.01 3.66
2186 5454 1.500474 CTGAAGGAGGCTACCATGGA 58.500 55.000 21.47 0.67 0.00 3.41
2187 5455 1.839994 CTGAAGGAGGCTACCATGGAA 59.160 52.381 21.47 0.00 0.00 3.53
2188 5456 1.839994 TGAAGGAGGCTACCATGGAAG 59.160 52.381 21.47 0.00 0.00 3.46
2189 5457 2.119495 GAAGGAGGCTACCATGGAAGA 58.881 52.381 21.47 1.83 0.00 2.87
2190 5458 2.270434 AGGAGGCTACCATGGAAGAA 57.730 50.000 21.47 0.00 0.00 2.52
2191 5459 2.122768 AGGAGGCTACCATGGAAGAAG 58.877 52.381 21.47 10.97 0.00 2.85
2192 5460 1.840635 GGAGGCTACCATGGAAGAAGT 59.159 52.381 21.47 0.00 0.00 3.01
2193 5461 2.420687 GGAGGCTACCATGGAAGAAGTG 60.421 54.545 21.47 1.11 0.00 3.16
2194 5462 1.561542 AGGCTACCATGGAAGAAGTGG 59.438 52.381 21.47 0.00 38.96 4.00
2195 5463 1.559682 GGCTACCATGGAAGAAGTGGA 59.440 52.381 21.47 0.00 36.82 4.02
2196 5464 2.420687 GGCTACCATGGAAGAAGTGGAG 60.421 54.545 21.47 0.00 36.82 3.86
2197 5465 2.501723 GCTACCATGGAAGAAGTGGAGA 59.498 50.000 21.47 0.00 36.82 3.71
2198 5466 3.680196 GCTACCATGGAAGAAGTGGAGAC 60.680 52.174 21.47 0.00 36.82 3.36
2199 5467 2.625639 ACCATGGAAGAAGTGGAGACT 58.374 47.619 21.47 0.00 36.82 3.24
2200 5468 3.791320 ACCATGGAAGAAGTGGAGACTA 58.209 45.455 21.47 0.00 36.82 2.59
2201 5469 3.515901 ACCATGGAAGAAGTGGAGACTAC 59.484 47.826 21.47 0.00 36.82 2.73
2202 5470 3.118592 CCATGGAAGAAGTGGAGACTACC 60.119 52.174 5.56 0.00 34.94 3.18
2203 5471 3.254093 TGGAAGAAGTGGAGACTACCA 57.746 47.619 0.00 0.00 37.63 3.25
2204 5472 3.791320 TGGAAGAAGTGGAGACTACCAT 58.209 45.455 0.00 0.00 42.17 3.55
2205 5473 3.515502 TGGAAGAAGTGGAGACTACCATG 59.484 47.826 0.00 0.00 42.17 3.66
2221 5489 3.480470 ACCATGGAAGAAGTGACAACAG 58.520 45.455 21.47 0.00 0.00 3.16
2276 5544 0.333993 AAGGGCACTTCATCCAGCAT 59.666 50.000 0.00 0.00 28.54 3.79
2298 5566 4.843220 ACAAAAAGAATCACTGCAGGAG 57.157 40.909 19.93 10.48 0.00 3.69
2320 5588 2.550830 AGTAATGGCATTAGGCGAGG 57.449 50.000 19.79 0.00 46.16 4.63
2407 5675 3.904136 AAGAAGCAACAGATGGAAACG 57.096 42.857 0.00 0.00 0.00 3.60
2442 5710 1.269517 GGTGTTGGAAATTGCGCTTCA 60.270 47.619 9.73 0.00 0.00 3.02
2506 5774 8.728337 ATATGTAGATGTAGCTGCCAATATTG 57.272 34.615 8.58 8.58 0.00 1.90
2517 5785 0.669619 CCAATATTGCAGATGCGCCA 59.330 50.000 10.11 0.00 45.83 5.69
2565 5833 2.191128 AGGAAGTGGTGCATGAAGAC 57.809 50.000 0.00 0.00 0.00 3.01
2670 5938 5.052481 ACAGTAACCACGAAAGAACTAACC 58.948 41.667 0.00 0.00 0.00 2.85
2742 6010 5.110598 CAGGAAGATGTCATGACTTCTCTG 58.889 45.833 32.66 29.88 42.66 3.35
2915 6183 9.449719 AACTGAAGTTGTAGAAGAAAAAGAAGA 57.550 29.630 0.00 0.00 36.80 2.87
3000 6268 2.039084 AGGTACTGGTGCTTTCCTTCAG 59.961 50.000 0.00 0.00 37.18 3.02
3004 6272 0.112995 TGGTGCTTTCCTTCAGCCAT 59.887 50.000 0.00 0.00 36.33 4.40
3137 6405 1.350019 GGCAGGTGGTGGTACTTTAGT 59.650 52.381 0.00 0.00 0.00 2.24
3215 6483 3.802948 ATCTACAAGCACTACTTCCGG 57.197 47.619 0.00 0.00 36.04 5.14
3252 6520 4.421131 ACACACTCAAGATAGGGAGACTT 58.579 43.478 0.00 0.00 35.17 3.01
3305 6573 6.983906 ACAGGATCCTGAATTCAAAAGTTT 57.016 33.333 41.91 16.68 46.30 2.66
3483 6751 3.194116 GGTCATTGGACAATTGTGAGCAT 59.806 43.478 17.58 0.00 46.17 3.79
3558 6826 2.237392 AGGATGGCAAGTAGAGTTGTCC 59.763 50.000 0.00 2.41 30.53 4.02
3573 6841 7.726033 AGAGTTGTCCTCAAACATATCTACT 57.274 36.000 0.00 0.00 43.12 2.57
3741 7009 5.780282 TGGATTGGGACATAGTAGACATAGG 59.220 44.000 0.00 0.00 39.30 2.57
3792 7060 1.072965 AGTCTTTCAAGGGGTGAGCTG 59.927 52.381 0.00 0.00 37.61 4.24
4380 7648 4.809513 GGGGGAGCTGGTTCTAGA 57.190 61.111 0.00 0.00 0.00 2.43
4798 8067 6.489700 TGCTTGATCTTCAAACCAATAACAGA 59.510 34.615 0.00 0.00 35.73 3.41
4799 8068 7.177216 TGCTTGATCTTCAAACCAATAACAGAT 59.823 33.333 0.00 0.00 35.73 2.90
4800 8069 8.031277 GCTTGATCTTCAAACCAATAACAGATT 58.969 33.333 0.00 0.00 35.73 2.40
4901 8170 4.178540 GGTGTAAATACGAGTGCAAGCTA 58.821 43.478 0.00 0.00 0.00 3.32
4903 8172 5.276868 GGTGTAAATACGAGTGCAAGCTATG 60.277 44.000 0.00 0.00 0.00 2.23
4906 8175 6.761242 TGTAAATACGAGTGCAAGCTATGATT 59.239 34.615 0.00 0.00 0.00 2.57
4932 8201 7.443879 TGATCGGCAAATTATATCTTGCTAACA 59.556 33.333 15.21 8.79 45.79 2.41
5135 8404 3.398318 TCTACTACTGGGAGCCAATCA 57.602 47.619 0.00 0.00 30.80 2.57
5139 8408 1.952296 CTACTGGGAGCCAATCAATGC 59.048 52.381 0.00 0.00 30.80 3.56
5276 8545 3.492313 CAATGAAGCACGTAAAGAAGCC 58.508 45.455 0.00 0.00 0.00 4.35
5684 8953 7.393234 TCAAATGTTACCCAGTATCTTCCTTTG 59.607 37.037 0.00 0.00 0.00 2.77
5694 8988 9.442047 CCCAGTATCTTCCTTTGATAATACATC 57.558 37.037 0.00 0.00 0.00 3.06
5848 9142 3.058016 ACATGCATGAGTTCTGTTTTCCG 60.058 43.478 32.75 0.59 0.00 4.30
5873 9167 6.206634 GGATGTAAGTTTCTGTGAAATGGACA 59.793 38.462 0.00 2.42 0.00 4.02
5877 9171 8.474025 TGTAAGTTTCTGTGAAATGGACAAAAT 58.526 29.630 0.00 0.00 0.00 1.82
6028 9506 2.296792 TGCAGCTACTTTGCACTTTCA 58.703 42.857 0.00 0.00 45.89 2.69
6056 9534 8.472007 TCCTATTTGAACAGTTTACCACAATT 57.528 30.769 0.00 0.00 0.00 2.32
6081 9561 5.389642 GACACACACAATGTCGTATATGG 57.610 43.478 0.00 0.00 40.64 2.74
6093 9573 9.920826 CAATGTCGTATATGGTTATCATAATGC 57.079 33.333 0.00 0.00 41.23 3.56
6161 9843 8.039603 TGCTAGACTAATGTGGTGTATTTTTG 57.960 34.615 0.00 0.00 0.00 2.44
6254 10172 2.952978 GGAGAGAGGAACTTCTATCGCA 59.047 50.000 3.33 0.00 41.55 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 7.645002 ACTACTCCTCCACTAGTTTATTCTCT 58.355 38.462 0.00 0.00 0.00 3.10
76 77 1.235724 CACCAGTTTTTCCTCCGTCC 58.764 55.000 0.00 0.00 0.00 4.79
126 127 1.202952 ACCGGAGTTTACCAATTGGCA 60.203 47.619 24.79 9.21 39.32 4.92
182 183 9.822727 TTTCTGAATTTATTAAGAAGGGGTTCT 57.177 29.630 3.19 0.00 38.24 3.01
192 193 9.189156 TCCCACCAGATTTCTGAATTTATTAAG 57.811 33.333 9.15 0.00 46.59 1.85
213 216 1.237285 ATGTTGCGTGCTTCTCCCAC 61.237 55.000 0.00 0.00 0.00 4.61
237 252 3.518992 TTCGAAGGGGAAAATGGAGTT 57.481 42.857 0.00 0.00 0.00 3.01
276 291 0.687757 ATCGGCCAAGTGGAGCTCTA 60.688 55.000 14.64 4.15 37.39 2.43
303 3108 3.760684 GCAAATCCAGATTCCAGTGAAGT 59.239 43.478 0.00 0.00 33.05 3.01
306 3111 2.358957 CGCAAATCCAGATTCCAGTGA 58.641 47.619 0.00 0.00 0.00 3.41
355 3160 2.043852 ATCAGCGTCTCCCGACCT 60.044 61.111 0.00 0.00 39.56 3.85
385 3196 3.862063 CTGGCGTTTGCGTGCAGAC 62.862 63.158 5.51 5.51 44.10 3.51
388 3199 3.947841 GACTGGCGTTTGCGTGCA 61.948 61.111 0.00 0.00 44.10 4.57
433 3244 0.247736 GTGCGGTGGTCTGATCTCTT 59.752 55.000 0.00 0.00 0.00 2.85
478 3298 2.690510 TGGGGCGATGATGGGTCA 60.691 61.111 0.00 0.00 39.04 4.02
680 3502 2.747686 GAGGCCCGTGGTTTCTGA 59.252 61.111 0.00 0.00 0.00 3.27
802 3628 3.352748 TCGGCCACTCCCCTCCTA 61.353 66.667 2.24 0.00 0.00 2.94
833 3664 4.089757 TCTTCCTCCCTCCCCCGG 62.090 72.222 0.00 0.00 0.00 5.73
834 3665 2.444895 CTCTTCCTCCCTCCCCCG 60.445 72.222 0.00 0.00 0.00 5.73
835 3666 2.040359 CCTCTTCCTCCCTCCCCC 60.040 72.222 0.00 0.00 0.00 5.40
836 3667 2.040359 CCCTCTTCCTCCCTCCCC 60.040 72.222 0.00 0.00 0.00 4.81
837 3668 2.040359 CCCCTCTTCCTCCCTCCC 60.040 72.222 0.00 0.00 0.00 4.30
838 3669 1.074850 CTCCCCTCTTCCTCCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
921 3761 3.376078 GGTGGGCGTGTACGGAGA 61.376 66.667 6.55 0.00 40.23 3.71
922 3762 4.446413 GGGTGGGCGTGTACGGAG 62.446 72.222 6.55 0.00 40.23 4.63
959 3799 4.025858 GTGAGGGGCTGCTGCTGA 62.026 66.667 15.64 0.00 39.59 4.26
964 3804 3.334054 GAAGGGTGAGGGGCTGCT 61.334 66.667 0.00 0.00 0.00 4.24
967 3807 2.685380 CGAGAAGGGTGAGGGGCT 60.685 66.667 0.00 0.00 0.00 5.19
973 3817 3.760035 GCTCGCCGAGAAGGGTGA 61.760 66.667 20.05 0.00 44.02 4.02
1676 4944 6.495181 AGTTCTCAAATCCACTCTTAGTCTCA 59.505 38.462 0.00 0.00 0.00 3.27
1778 5046 1.736126 CTGATTTCTCATGCTGCGTGT 59.264 47.619 20.33 1.67 0.00 4.49
1845 5113 1.524621 CCCTGTGACATCCGATGCC 60.525 63.158 8.36 0.00 0.00 4.40
1955 5223 1.677052 GCGTGTTTGTTACTTTCCCCA 59.323 47.619 0.00 0.00 0.00 4.96
1956 5224 1.677052 TGCGTGTTTGTTACTTTCCCC 59.323 47.619 0.00 0.00 0.00 4.81
1974 5242 3.552541 CGATGCTAATTTCTCATGCTGC 58.447 45.455 0.00 0.00 0.00 5.25
1988 5256 2.654863 TCTCTGTGACATCCGATGCTA 58.345 47.619 8.36 0.00 0.00 3.49
2040 5308 2.550855 GCTCTGTCCACCTTGATCAACA 60.551 50.000 3.38 0.00 0.00 3.33
2056 5324 0.749649 ATAGCGGAGGAAGTGCTCTG 59.250 55.000 4.39 4.39 40.06 3.35
2097 5365 0.506932 CTTGTCGTGTAACCACTGCG 59.493 55.000 0.00 0.00 39.55 5.18
2099 5367 2.736721 CCATCTTGTCGTGTAACCACTG 59.263 50.000 0.00 0.00 39.55 3.66
2127 5395 2.359107 ACACCCACATCAGCAGCG 60.359 61.111 0.00 0.00 0.00 5.18
2144 5412 0.689055 ACCAGATGAAGTGCTCTGCA 59.311 50.000 0.00 0.00 38.03 4.41
2169 5437 2.119495 TCTTCCATGGTAGCCTCCTTC 58.881 52.381 12.58 0.00 0.00 3.46
2185 5453 3.769844 TCCATGGTAGTCTCCACTTCTTC 59.230 47.826 12.58 0.00 40.51 2.87
2186 5454 3.791320 TCCATGGTAGTCTCCACTTCTT 58.209 45.455 12.58 0.00 40.51 2.52
2187 5455 3.474798 TCCATGGTAGTCTCCACTTCT 57.525 47.619 12.58 0.00 40.51 2.85
2188 5456 3.769844 TCTTCCATGGTAGTCTCCACTTC 59.230 47.826 17.07 0.00 40.51 3.01
2189 5457 3.791320 TCTTCCATGGTAGTCTCCACTT 58.209 45.455 17.07 0.00 40.51 3.16
2190 5458 3.474798 TCTTCCATGGTAGTCTCCACT 57.525 47.619 17.07 0.00 40.51 4.00
2191 5459 3.515901 ACTTCTTCCATGGTAGTCTCCAC 59.484 47.826 17.07 0.00 40.51 4.02
2192 5460 3.515502 CACTTCTTCCATGGTAGTCTCCA 59.484 47.826 17.07 0.00 42.01 3.86
2193 5461 3.769844 TCACTTCTTCCATGGTAGTCTCC 59.230 47.826 17.07 0.00 0.00 3.71
2194 5462 4.220821 TGTCACTTCTTCCATGGTAGTCTC 59.779 45.833 17.07 9.37 0.00 3.36
2195 5463 4.160329 TGTCACTTCTTCCATGGTAGTCT 58.840 43.478 17.07 0.00 0.00 3.24
2196 5464 4.537135 TGTCACTTCTTCCATGGTAGTC 57.463 45.455 17.07 5.06 0.00 2.59
2197 5465 4.102524 TGTTGTCACTTCTTCCATGGTAGT 59.897 41.667 17.07 10.99 0.00 2.73
2198 5466 4.641396 TGTTGTCACTTCTTCCATGGTAG 58.359 43.478 12.58 12.27 0.00 3.18
2199 5467 4.346709 TCTGTTGTCACTTCTTCCATGGTA 59.653 41.667 12.58 0.02 0.00 3.25
2200 5468 3.136443 TCTGTTGTCACTTCTTCCATGGT 59.864 43.478 12.58 0.00 0.00 3.55
2201 5469 3.743521 TCTGTTGTCACTTCTTCCATGG 58.256 45.455 4.97 4.97 0.00 3.66
2202 5470 4.818546 ACTTCTGTTGTCACTTCTTCCATG 59.181 41.667 0.00 0.00 0.00 3.66
2203 5471 5.041191 ACTTCTGTTGTCACTTCTTCCAT 57.959 39.130 0.00 0.00 0.00 3.41
2204 5472 4.487714 ACTTCTGTTGTCACTTCTTCCA 57.512 40.909 0.00 0.00 0.00 3.53
2205 5473 5.162000 CAACTTCTGTTGTCACTTCTTCC 57.838 43.478 1.22 0.00 46.08 3.46
2221 5489 3.054878 CAGCAATGGCAGTTTCAACTTC 58.945 45.455 0.00 0.00 44.61 3.01
2255 5523 0.034670 GCTGGATGAAGTGCCCTTCT 60.035 55.000 10.38 0.00 46.07 2.85
2276 5544 4.761739 CCTCCTGCAGTGATTCTTTTTGTA 59.238 41.667 13.81 0.00 0.00 2.41
2298 5566 3.326747 CTCGCCTAATGCCATTACTACC 58.673 50.000 0.00 0.00 36.24 3.18
2320 5588 6.798315 AACAATATCATCATCACTAGCAGC 57.202 37.500 0.00 0.00 0.00 5.25
2423 5691 2.132740 TGAAGCGCAATTTCCAACAC 57.867 45.000 11.47 0.00 0.00 3.32
2431 5699 2.880890 GGATACTGGATGAAGCGCAATT 59.119 45.455 11.47 0.00 0.00 2.32
2506 5774 1.138247 CCTCTTTTGGCGCATCTGC 59.862 57.895 10.83 0.00 37.78 4.26
2517 5785 6.205658 GCATACTGAAAGAACTGACCTCTTTT 59.794 38.462 0.00 0.00 41.96 2.27
2552 5820 0.105778 TGTGTCGTCTTCATGCACCA 59.894 50.000 0.00 0.00 0.00 4.17
2565 5833 3.156334 GCAGTTAGCGGTGTGTCG 58.844 61.111 0.00 0.00 0.00 4.35
2613 5881 1.688735 TCCTCCAGCATAACGGATGAG 59.311 52.381 3.92 0.00 37.82 2.90
2681 5949 1.067565 TGCTCTTTCCAGCTACGTCAG 60.068 52.381 0.00 0.00 40.39 3.51
2742 6010 6.560253 TTAATTTCTTGAGACTCTTGGCAC 57.440 37.500 3.68 0.00 0.00 5.01
2915 6183 5.455392 CAACGATTTCATTCTCAACTGCTT 58.545 37.500 0.00 0.00 0.00 3.91
3000 6268 4.082125 CCTTAATATGGTCCTTGGATGGC 58.918 47.826 0.00 0.00 0.00 4.40
3004 6272 7.079700 TCAGTATCCTTAATATGGTCCTTGGA 58.920 38.462 0.00 0.00 0.00 3.53
3039 6307 5.989477 TCCATAATCAGATCCAAAGTCGTT 58.011 37.500 0.00 0.00 0.00 3.85
3078 6346 7.724061 TCAAATGCTATACCCTTTCCTTTATCC 59.276 37.037 0.00 0.00 0.00 2.59
3137 6405 2.576191 CCTATGTCAAAACCTCTCCCCA 59.424 50.000 0.00 0.00 0.00 4.96
3215 6483 3.406764 AGTGTGTCATCTTCCTGCTTTC 58.593 45.455 0.00 0.00 0.00 2.62
3252 6520 5.221722 ACCTGACAAGCTTAGTGAAAGATCA 60.222 40.000 0.00 0.00 37.38 2.92
3305 6573 3.423539 CAGAATCAGGTCTGGGAACAA 57.576 47.619 0.00 0.00 41.21 2.83
3483 6751 5.043737 ACAAAGGTTTACTGCCTACTGAA 57.956 39.130 0.00 0.00 34.81 3.02
3558 6826 7.786030 TCCCTTTCTCAGTAGATATGTTTGAG 58.214 38.462 7.40 7.40 37.27 3.02
3573 6841 1.665137 GGGTAGGGTTCCCTTTCTCA 58.335 55.000 16.05 0.00 41.58 3.27
3741 7009 0.894141 TCTCTCTTGTGAGCTGCCTC 59.106 55.000 0.00 0.00 40.03 4.70
3792 7060 0.170561 CAAGCTGTTCCTCATGCTGC 59.829 55.000 0.00 0.00 33.37 5.25
3879 7147 3.520721 TCATCTCTTGAAGCATCCTTCCA 59.479 43.478 0.00 0.00 45.53 3.53
4106 7374 4.581824 CCAAATCAGGTGTAGCAATGCTAT 59.418 41.667 18.63 0.00 43.30 2.97
4146 7414 2.421073 TGAGAGATTGCGGCATTTCAAG 59.579 45.455 2.28 0.00 0.00 3.02
4177 7445 5.241403 TCACAATCAACCACTGGTAGAAT 57.759 39.130 0.00 0.00 33.12 2.40
4380 7648 4.949238 TGCATTTCATTAGTACCATGTGCT 59.051 37.500 13.51 0.00 32.46 4.40
4695 7963 3.611057 GCAAGAACTGAACAAGCATGGAG 60.611 47.826 0.00 0.00 0.00 3.86
4798 8067 5.497474 CCTACAAGCTGGGTAACTGTTAAT 58.503 41.667 1.10 0.00 0.00 1.40
4799 8068 4.804934 GCCTACAAGCTGGGTAACTGTTAA 60.805 45.833 1.10 0.00 0.00 2.01
4800 8069 3.307199 GCCTACAAGCTGGGTAACTGTTA 60.307 47.826 0.00 0.00 0.00 2.41
4801 8070 2.552373 GCCTACAAGCTGGGTAACTGTT 60.552 50.000 0.00 0.00 0.00 3.16
4802 8071 1.003233 GCCTACAAGCTGGGTAACTGT 59.997 52.381 0.00 0.00 0.00 3.55
4803 8072 1.279271 AGCCTACAAGCTGGGTAACTG 59.721 52.381 0.00 0.00 42.95 3.16
4804 8073 1.657804 AGCCTACAAGCTGGGTAACT 58.342 50.000 0.00 0.00 42.95 2.24
4805 8074 2.491675 AAGCCTACAAGCTGGGTAAC 57.508 50.000 0.00 0.00 44.11 2.50
4901 8170 7.972277 GCAAGATATAATTTGCCGATCAATCAT 59.028 33.333 11.51 0.00 42.88 2.45
4903 8172 7.731556 GCAAGATATAATTTGCCGATCAATC 57.268 36.000 11.51 0.00 42.88 2.67
4932 8201 7.009179 TGTCATCTGGAATTAGAAACAGAGT 57.991 36.000 0.00 0.00 42.55 3.24
5135 8404 7.363268 CCAGTTTCAGCTATTTTTCTAGGCATT 60.363 37.037 0.00 0.00 0.00 3.56
5139 8408 7.872113 ATCCAGTTTCAGCTATTTTTCTAGG 57.128 36.000 0.00 0.00 0.00 3.02
5170 8439 6.480763 TCAGAAACTGGCTTATTATTGACCA 58.519 36.000 0.00 0.00 31.51 4.02
5276 8545 6.074623 CCATCACGATATTTTTCAGACTCTCG 60.075 42.308 0.00 0.00 0.00 4.04
5411 8680 5.176590 GCTGAGAAATTGATGGTACGATCTC 59.823 44.000 17.41 7.92 0.00 2.75
5694 8988 8.461222 TGTAGATATGTCAGCTTCAAAAATTGG 58.539 33.333 0.00 0.00 0.00 3.16
5697 8991 8.565896 TGTGTAGATATGTCAGCTTCAAAAAT 57.434 30.769 0.00 0.00 0.00 1.82
5823 9117 6.088824 GGAAAACAGAACTCATGCATGTAAG 58.911 40.000 25.43 18.58 0.00 2.34
5848 9142 6.206634 TGTCCATTTCACAGAAACTTACATCC 59.793 38.462 0.00 0.00 0.00 3.51
5877 9171 7.893658 ACCTTCGAAGAGAATCAGTTACTTTA 58.106 34.615 26.61 0.00 38.43 1.85
5883 9177 5.215252 TGAACCTTCGAAGAGAATCAGTT 57.785 39.130 26.61 18.20 38.43 3.16
5893 9187 6.969828 AATTTAGTAGCTGAACCTTCGAAG 57.030 37.500 18.51 18.51 0.00 3.79
6028 9506 8.472007 TGTGGTAAACTGTTCAAATAGGAAAT 57.528 30.769 0.00 0.00 0.00 2.17
6056 9534 2.595124 ACGACATTGTGTGTGTCTGA 57.405 45.000 0.00 0.00 42.36 3.27
6081 9561 6.624352 TTGCTCCTTCTGCATTATGATAAC 57.376 37.500 0.00 0.00 40.34 1.89
6093 9573 3.385755 CCCCCAAAATATTGCTCCTTCTG 59.614 47.826 0.00 0.00 35.10 3.02
6161 9843 5.353123 TCAATCCAGTAAACGTTCATTAGGC 59.647 40.000 0.00 0.00 0.00 3.93
6254 10172 6.343716 TGGCACAACATTATCAATGAACTT 57.656 33.333 5.92 0.00 42.01 2.66
6363 10288 8.647796 AGGACATATGTTTCCGATACAAGATAA 58.352 33.333 10.30 0.00 36.95 1.75
6366 10291 6.479972 AGGACATATGTTTCCGATACAAGA 57.520 37.500 10.30 0.00 36.95 3.02
6483 10408 8.776061 AAGAAGAATGAGCCTATAACTCTAGT 57.224 34.615 4.55 0.00 35.12 2.57


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

AutoCloner maintained by Alex Coulton.