Multiple sequence alignment - TraesCS1B01G208500

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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 TraesCS1B01G208500 chr1B 100.000 4297 0 0 1 4297 378396076 378400372 0.000000e+00 7936.0
1 TraesCS1B01G208500 chr1B 82.490 257 34 7 1 250 432827602 432827350 9.360000e-52 215.0
2 TraesCS1B01G208500 chr1D 93.874 2726 112 15 1 2723 278511208 278513881 0.000000e+00 4058.0
3 TraesCS1B01G208500 chr1D 92.438 1005 40 13 2822 3794 278513925 278514925 0.000000e+00 1402.0
4 TraesCS1B01G208500 chr1D 94.309 369 13 4 3836 4199 278514920 278515285 3.750000e-155 558.0
5 TraesCS1B01G208500 chr1D 97.917 96 0 2 4202 4297 278515366 278515459 9.560000e-37 165.0
6 TraesCS1B01G208500 chr1A 93.993 2214 72 21 2097 4296 350750800 350752966 0.000000e+00 3295.0
7 TraesCS1B01G208500 chr1A 93.839 1753 90 14 303 2053 350748770 350750506 0.000000e+00 2623.0
8 TraesCS1B01G208500 chr1A 85.762 302 35 7 1734 2030 108155099 108154801 3.230000e-81 313.0
9 TraesCS1B01G208500 chr1A 84.146 246 31 6 1 239 403018327 403018571 9.290000e-57 231.0
10 TraesCS1B01G208500 chr7A 86.093 302 34 6 1734 2030 598473785 598473487 6.930000e-83 318.0
11 TraesCS1B01G208500 chr7A 85.526 304 37 6 1728 2027 317380572 317380872 1.160000e-80 311.0
12 TraesCS1B01G208500 chr7A 82.278 79 12 2 390 467 137443149 137443226 2.770000e-07 67.6
13 TraesCS1B01G208500 chr7A 96.875 32 1 0 1045 1076 71387042 71387073 2.000000e-03 54.7
14 TraesCS1B01G208500 chr3A 85.809 303 38 4 1728 2027 424662398 424662698 2.490000e-82 316.0
15 TraesCS1B01G208500 chr3A 85.762 302 35 7 1734 2030 325451199 325451497 3.230000e-81 313.0
16 TraesCS1B01G208500 chr3A 81.853 259 32 12 2 250 699758884 699758631 2.030000e-48 204.0
17 TraesCS1B01G208500 chr2D 86.047 301 34 7 1731 2027 422089833 422089537 2.490000e-82 316.0
18 TraesCS1B01G208500 chr2B 85.714 301 35 7 1731 2027 494402008 494401712 1.160000e-80 311.0
19 TraesCS1B01G208500 chr7D 82.946 258 34 8 1 250 614109017 614108762 1.550000e-54 224.0
20 TraesCS1B01G208500 chr7D 94.444 36 1 1 1042 1076 289813696 289813731 2.000000e-03 54.7
21 TraesCS1B01G208500 chr5B 82.443 262 35 9 1 256 590584450 590584706 7.230000e-53 219.0
22 TraesCS1B01G208500 chr3B 81.712 257 38 7 1 250 753669516 753669262 5.630000e-49 206.0
23 TraesCS1B01G208500 chr3B 100.000 29 0 0 1048 1076 802681980 802681952 2.000000e-03 54.7
24 TraesCS1B01G208500 chr6D 81.783 258 34 11 2 250 269776536 269776283 2.030000e-48 204.0
25 TraesCS1B01G208500 chr5D 81.855 248 32 11 1 239 393733340 393733097 3.390000e-46 196.0
26 TraesCS1B01G208500 chr6A 100.000 29 0 0 1048 1076 437566533 437566505 2.000000e-03 54.7
27 TraesCS1B01G208500 chr5A 100.000 29 0 0 1048 1076 8490134 8490106 2.000000e-03 54.7


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 TraesCS1B01G208500 chr1B 378396076 378400372 4296 False 7936.00 7936 100.0000 1 4297 1 chr1B.!!$F1 4296
1 TraesCS1B01G208500 chr1D 278511208 278515459 4251 False 1545.75 4058 94.6345 1 4297 4 chr1D.!!$F1 4296
2 TraesCS1B01G208500 chr1A 350748770 350752966 4196 False 2959.00 3295 93.9160 303 4296 2 chr1A.!!$F2 3993

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
562 563 0.036306 GGTCCACCCGTCATTGAGTT 59.964 55.000 0.00 0.00 0.00 3.01 F
648 650 1.460273 CGGCTAGGAGGCTCTCTTCC 61.460 65.000 15.23 12.36 38.85 3.46 F
745 747 1.609501 AACAGACGGCTAGGAGGCA 60.610 57.895 0.00 0.00 41.44 4.75 F
2034 2038 1.413118 CCAAAGGAGGCCAAACTGTT 58.587 50.000 5.01 0.00 0.00 3.16 F
3173 3431 0.468648 CCCTCAAGGTACCGATTCCC 59.531 60.000 6.18 0.00 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1455 1457 0.325933 TGACCTCCGAGGACGTCTTA 59.674 55.000 21.89 0.0 37.67 2.10 R
1678 1680 1.401931 GCAACAGCACGCAATCATTCT 60.402 47.619 0.00 0.0 0.00 2.40 R
2584 2838 1.439679 GTTTGACGAAGGGGCTACAG 58.560 55.000 0.00 0.0 0.00 2.74 R
3176 3434 0.180406 ACGACTTGGCCTTGTTGTCT 59.820 50.000 3.32 0.0 0.00 3.41 R
3996 4287 1.067354 CCCAGTTCTGCATTTGAAGCC 60.067 52.381 0.00 0.0 0.00 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
75 76 3.861341 CTCATTTGGAGCTCCGGAA 57.139 52.632 27.43 23.26 36.69 4.30
117 118 1.078143 GGCTCGGAATTCCAGCTGT 60.078 57.895 30.75 0.00 38.95 4.40
119 120 1.424493 GCTCGGAATTCCAGCTGTCG 61.424 60.000 27.75 13.93 37.27 4.35
161 162 7.064609 CGGTGTATCTTGCATTTTAAGAGAGAA 59.935 37.037 0.00 0.00 37.56 2.87
239 240 7.540745 ACAATAATAGGAAACACGATGCAAAAC 59.459 33.333 0.00 0.00 0.00 2.43
240 241 5.446143 AATAGGAAACACGATGCAAAACA 57.554 34.783 0.00 0.00 0.00 2.83
303 304 2.272146 GTGCCACCCGTCATGGAT 59.728 61.111 0.00 0.00 42.00 3.41
306 307 1.594293 GCCACCCGTCATGGATACG 60.594 63.158 0.00 0.00 42.00 3.06
355 356 1.822990 GTCCACCTGTCATCGACCTTA 59.177 52.381 0.00 0.00 0.00 2.69
399 400 1.712018 CGTCTGGGCAGATCGTACGA 61.712 60.000 21.93 21.93 39.97 3.43
403 404 1.359475 GGGCAGATCGTACGACTCC 59.641 63.158 22.14 17.50 0.00 3.85
410 411 2.605854 ATCGTACGACTCCCCTCGCT 62.606 60.000 22.14 0.00 37.15 4.93
467 468 6.309757 CAGACAACTGGGAAGCTCTCTTCA 62.310 50.000 7.27 0.00 42.37 3.02
516 517 2.583319 ACTCATCATGGACGCGCG 60.583 61.111 30.96 30.96 0.00 6.86
561 562 1.677552 GGTCCACCCGTCATTGAGT 59.322 57.895 0.00 0.00 0.00 3.41
562 563 0.036306 GGTCCACCCGTCATTGAGTT 59.964 55.000 0.00 0.00 0.00 3.01
574 576 3.502211 GTCATTGAGTTGTCCGGTTGATT 59.498 43.478 0.00 0.00 0.00 2.57
607 609 2.612115 CCCCCAAGAGCCTCCTGT 60.612 66.667 0.00 0.00 0.00 4.00
648 650 1.460273 CGGCTAGGAGGCTCTCTTCC 61.460 65.000 15.23 12.36 38.85 3.46
745 747 1.609501 AACAGACGGCTAGGAGGCA 60.610 57.895 0.00 0.00 41.44 4.75
805 807 6.441274 CACGCCGTTCTTTATATAGGAGTAA 58.559 40.000 0.00 0.00 30.94 2.24
822 824 7.704578 AGGAGTAATATATGATACGCACACT 57.295 36.000 0.00 0.00 0.00 3.55
823 825 8.803397 AGGAGTAATATATGATACGCACACTA 57.197 34.615 0.00 0.00 0.00 2.74
1164 1166 3.474570 GGAGGCAGCCCACTCGAT 61.475 66.667 8.22 0.00 34.58 3.59
1525 1527 2.044946 AGGCTTCCAATCCCACGC 60.045 61.111 0.00 0.00 0.00 5.34
1602 1604 3.072915 TCCCACTTCTTGCTCTCAATCAA 59.927 43.478 0.00 0.00 0.00 2.57
1677 1679 8.707938 ATGCTTTATTTGAATTTTAGCCACTC 57.292 30.769 0.00 0.00 0.00 3.51
1678 1680 7.665690 TGCTTTATTTGAATTTTAGCCACTCA 58.334 30.769 0.00 0.00 0.00 3.41
1798 1801 8.789767 AGGAAAATCATAGGAAGTGAGATAGA 57.210 34.615 0.00 0.00 0.00 1.98
1853 1857 7.994425 TGTCATTTGAAGCATAGGTAGAAAA 57.006 32.000 0.00 0.00 0.00 2.29
1962 1966 3.532641 AACCAAAGAGCTCCAAAGGAT 57.467 42.857 10.93 0.00 0.00 3.24
2034 2038 1.413118 CCAAAGGAGGCCAAACTGTT 58.587 50.000 5.01 0.00 0.00 3.16
2060 2064 6.917217 AGCAGTCAACTTCTTATAATGCTC 57.083 37.500 0.00 0.00 36.85 4.26
2141 2395 2.901839 GGGGTCCAGTCAGTTACTTGTA 59.098 50.000 0.00 0.00 35.76 2.41
2142 2396 3.306571 GGGGTCCAGTCAGTTACTTGTAC 60.307 52.174 0.00 0.00 35.76 2.90
2143 2397 3.577415 GGGTCCAGTCAGTTACTTGTACT 59.423 47.826 0.00 0.00 35.76 2.73
2144 2398 4.040095 GGGTCCAGTCAGTTACTTGTACTT 59.960 45.833 0.00 0.00 35.76 2.24
2331 2585 5.600696 ACTCCATTTGCTTCGTTTTCATTT 58.399 33.333 0.00 0.00 0.00 2.32
2400 2654 2.037772 ACAGACCTGCTTCTCGTCAATT 59.962 45.455 0.00 0.00 0.00 2.32
2761 3016 3.669536 TCAACAGACGCATTTGATACCA 58.330 40.909 0.00 0.00 0.00 3.25
2770 3025 3.606846 CGCATTTGATACCAGTATTGCCG 60.607 47.826 6.61 0.88 0.00 5.69
2795 3050 4.985538 ACCTGTCATTCTCCTAGTTACG 57.014 45.455 0.00 0.00 0.00 3.18
2799 3054 4.084287 TGTCATTCTCCTAGTTACGGTGT 58.916 43.478 0.00 0.00 0.00 4.16
2801 3056 5.124457 TGTCATTCTCCTAGTTACGGTGTAC 59.876 44.000 0.00 0.00 0.00 2.90
2814 3069 7.655490 AGTTACGGTGTACATAGGATGATAAC 58.345 38.462 0.00 1.74 0.00 1.89
2815 3070 7.504911 AGTTACGGTGTACATAGGATGATAACT 59.495 37.037 0.00 3.82 0.00 2.24
2816 3071 6.726490 ACGGTGTACATAGGATGATAACTT 57.274 37.500 0.00 0.00 0.00 2.66
2817 3072 6.513180 ACGGTGTACATAGGATGATAACTTG 58.487 40.000 0.00 0.00 0.00 3.16
2818 3073 6.322969 ACGGTGTACATAGGATGATAACTTGA 59.677 38.462 0.00 0.00 0.00 3.02
2819 3074 7.015292 ACGGTGTACATAGGATGATAACTTGAT 59.985 37.037 0.00 0.00 0.00 2.57
2820 3075 8.520351 CGGTGTACATAGGATGATAACTTGATA 58.480 37.037 0.00 0.00 0.00 2.15
2842 3097 8.461222 TGATAAGCAAATCTCTTGTACCAAATG 58.539 33.333 0.00 0.00 0.00 2.32
2865 3120 2.710377 TGAGGTGCACATCATGGTTAC 58.290 47.619 28.88 2.76 31.11 2.50
3029 3287 4.466726 CAGCCTCCTGAGATATCATCATCA 59.533 45.833 5.32 0.00 41.77 3.07
3140 3398 1.202806 GCTAGCATTGCAGGGTCCATA 60.203 52.381 10.63 0.00 0.00 2.74
3173 3431 0.468648 CCCTCAAGGTACCGATTCCC 59.531 60.000 6.18 0.00 0.00 3.97
3251 3509 2.286365 TTTCAAAAGGCGATGGAGGT 57.714 45.000 0.00 0.00 0.00 3.85
3440 3701 7.011389 TCTGGCAGAATCAACTAAATATTGTCG 59.989 37.037 16.28 0.00 0.00 4.35
3463 3724 2.961526 TGGAGTCTCCATACGCTTTC 57.038 50.000 18.15 0.00 42.67 2.62
3478 3739 2.784347 GCTTTCTGCTCCTTGGTAACT 58.216 47.619 0.00 0.00 38.95 2.24
3479 3740 3.616560 CGCTTTCTGCTCCTTGGTAACTA 60.617 47.826 0.00 0.00 40.11 2.24
3480 3741 3.685272 GCTTTCTGCTCCTTGGTAACTAC 59.315 47.826 0.00 0.00 38.95 2.73
3481 3742 3.587797 TTCTGCTCCTTGGTAACTACG 57.412 47.619 0.00 0.00 37.61 3.51
3521 3782 6.638873 TGTGTTATTAAAAAGGAATGTGCACG 59.361 34.615 13.13 0.00 0.00 5.34
3522 3783 6.858993 GTGTTATTAAAAAGGAATGTGCACGA 59.141 34.615 13.13 1.58 0.00 4.35
3552 3813 5.007385 TCGTAAGAGTATTTTCTGCTCCC 57.993 43.478 0.00 0.00 45.01 4.30
3642 3931 6.112058 GGATTCAGTTATTGCTTCTGAGTCT 58.888 40.000 13.47 0.00 41.41 3.24
3689 3978 8.327941 TGATCCTCTTTAGTTCAATCAAACTG 57.672 34.615 0.00 0.00 39.74 3.16
3787 4077 6.866010 TCACAAATTTGCATCGCTAGATAT 57.134 33.333 18.12 0.00 34.85 1.63
3796 4086 8.552083 TTTGCATCGCTAGATATATTTCACAT 57.448 30.769 0.00 0.00 34.85 3.21
3799 4089 9.651913 TGCATCGCTAGATATATTTCACATAAA 57.348 29.630 0.00 0.00 34.85 1.40
3811 4101 8.915057 ATATTTCACATAAATCTGGACTGGAG 57.085 34.615 0.00 0.00 0.00 3.86
3812 4102 4.760530 TCACATAAATCTGGACTGGAGG 57.239 45.455 0.00 0.00 0.00 4.30
3813 4103 3.118261 TCACATAAATCTGGACTGGAGGC 60.118 47.826 0.00 0.00 0.00 4.70
3814 4104 3.118112 CACATAAATCTGGACTGGAGGCT 60.118 47.826 0.00 0.00 0.00 4.58
3815 4105 3.118112 ACATAAATCTGGACTGGAGGCTG 60.118 47.826 0.00 0.00 0.00 4.85
3816 4106 1.366319 AAATCTGGACTGGAGGCTGT 58.634 50.000 0.00 0.00 0.00 4.40
3817 4107 0.617413 AATCTGGACTGGAGGCTGTG 59.383 55.000 0.00 0.00 0.00 3.66
3818 4108 1.270414 ATCTGGACTGGAGGCTGTGG 61.270 60.000 0.00 0.00 0.00 4.17
3819 4109 3.618780 CTGGACTGGAGGCTGTGGC 62.619 68.421 0.00 0.00 37.82 5.01
3830 4120 1.980772 GCTGTGGCCTGCTTGGAAT 60.981 57.895 3.32 0.00 38.35 3.01
3839 4129 3.055602 GGCCTGCTTGGAATCAGAATTTT 60.056 43.478 0.00 0.00 38.35 1.82
3866 4157 6.825610 ACAAAAATGCAAGGGAATCAAACTA 58.174 32.000 0.00 0.00 0.00 2.24
3891 4182 3.782046 CGATCAACTGTTCCTTCCGTAT 58.218 45.455 0.00 0.00 0.00 3.06
3969 4260 1.067354 CAGAACTGGGAAAATGGCAGC 60.067 52.381 0.00 0.00 0.00 5.25
4015 4306 1.891150 AGGCTTCAAATGCAGAACTGG 59.109 47.619 3.99 0.00 0.00 4.00
4141 4432 5.888901 TCCACCTTTTCTCTCTAGTAGACA 58.111 41.667 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 9.696917 AAATGAGCTGAAAATTTACGAAGAATT 57.303 25.926 0.00 0.00 0.00 2.17
57 58 2.113860 TTTCCGGAGCTCCAAATGAG 57.886 50.000 31.67 14.37 44.47 2.90
96 97 1.221840 GCTGGAATTCCGAGCCTGA 59.778 57.895 26.08 7.67 39.43 3.86
100 101 1.424493 CGACAGCTGGAATTCCGAGC 61.424 60.000 27.77 27.77 39.11 5.03
104 105 0.960364 TTGCCGACAGCTGGAATTCC 60.960 55.000 19.93 18.17 44.23 3.01
117 118 0.391130 CGAAAGAGGGACATTGCCGA 60.391 55.000 0.00 0.00 30.73 5.54
119 120 0.322546 ACCGAAAGAGGGACATTGCC 60.323 55.000 0.00 0.00 35.02 4.52
214 215 7.540400 TGTTTTGCATCGTGTTTCCTATTATTG 59.460 33.333 0.00 0.00 0.00 1.90
223 224 4.290155 ACATCTGTTTTGCATCGTGTTTC 58.710 39.130 0.00 0.00 0.00 2.78
233 234 5.030295 CGGATTGTGATACATCTGTTTTGC 58.970 41.667 0.00 0.00 0.00 3.68
239 240 2.222678 GCAGCGGATTGTGATACATCTG 59.777 50.000 0.00 0.00 0.00 2.90
240 241 2.158914 TGCAGCGGATTGTGATACATCT 60.159 45.455 0.00 0.00 0.00 2.90
303 304 4.525576 CGCTACAGTCGGCGCGTA 62.526 66.667 8.43 2.62 44.64 4.42
342 343 3.025978 ACCGGTTATAAGGTCGATGACA 58.974 45.455 0.00 0.00 35.50 3.58
399 400 4.824515 CTCGGGAGCGAGGGGAGT 62.825 72.222 0.00 0.00 32.81 3.85
440 441 1.212935 AGCTTCCCAGTTGTCTGTTGT 59.787 47.619 0.00 0.00 39.82 3.32
467 468 1.076533 CGCAATCGCTACAGTTCGGT 61.077 55.000 0.00 0.00 35.30 4.69
490 491 1.114627 CCATGATGAGTGGACCGAGA 58.885 55.000 0.00 0.00 39.12 4.04
516 517 1.922545 GTACGAATTGGTACAGTCGGC 59.077 52.381 21.64 0.00 46.99 5.54
528 529 0.392060 GGACCCTTGGCGTACGAATT 60.392 55.000 21.65 0.00 0.00 2.17
648 650 2.905935 TTCCTAGGCTCGTCGAGGGG 62.906 65.000 23.09 2.31 31.58 4.79
820 822 7.751450 TTTCTCCCTGAAATTCGCACGTAGT 62.751 44.000 0.00 0.00 39.95 2.73
821 823 1.927174 CTCCCTGAAATTCGCACGTAG 59.073 52.381 0.00 0.00 0.00 3.51
822 824 1.546923 TCTCCCTGAAATTCGCACGTA 59.453 47.619 0.00 0.00 0.00 3.57
823 825 0.320374 TCTCCCTGAAATTCGCACGT 59.680 50.000 0.00 0.00 0.00 4.49
1390 1392 2.364961 CTCCTCCCTCCCCTCGTT 59.635 66.667 0.00 0.00 0.00 3.85
1455 1457 0.325933 TGACCTCCGAGGACGTCTTA 59.674 55.000 21.89 0.00 37.67 2.10
1459 1461 2.361357 CCTGACCTCCGAGGACGT 60.361 66.667 21.89 0.00 37.67 4.34
1602 1604 7.046652 TCGAAGTAGTGAGTACTAGCAAGTAT 58.953 38.462 0.00 0.00 41.50 2.12
1677 1679 2.247637 CAACAGCACGCAATCATTCTG 58.752 47.619 0.00 0.00 0.00 3.02
1678 1680 1.401931 GCAACAGCACGCAATCATTCT 60.402 47.619 0.00 0.00 0.00 2.40
1853 1857 9.566432 GACATTATCCTAGACTCAATGGAAAAT 57.434 33.333 0.00 0.00 32.20 1.82
1939 1943 2.546584 CCTTTGGAGCTCTTTGGTTTGC 60.547 50.000 14.64 0.00 0.00 3.68
1992 1996 8.691661 TGGCTTATAGGATTTTTGTAGGAATC 57.308 34.615 0.00 0.00 0.00 2.52
2034 2038 8.792830 AGCATTATAAGAAGTTGACTGCTTAA 57.207 30.769 14.04 3.29 44.80 1.85
2141 2395 6.374333 CCATGCACAATTAAGTAGGTACAAGT 59.626 38.462 0.00 0.00 0.00 3.16
2142 2396 6.374333 ACCATGCACAATTAAGTAGGTACAAG 59.626 38.462 0.00 0.00 0.00 3.16
2143 2397 6.242396 ACCATGCACAATTAAGTAGGTACAA 58.758 36.000 0.00 0.00 0.00 2.41
2144 2398 5.811190 ACCATGCACAATTAAGTAGGTACA 58.189 37.500 0.00 0.00 0.00 2.90
2510 2764 7.088589 AGCAAATGTAACTAGCGAAATGATT 57.911 32.000 0.00 0.00 0.00 2.57
2511 2765 6.683974 AGCAAATGTAACTAGCGAAATGAT 57.316 33.333 0.00 0.00 0.00 2.45
2584 2838 1.439679 GTTTGACGAAGGGGCTACAG 58.560 55.000 0.00 0.00 0.00 2.74
2761 3016 0.464452 GACAGGTAGGCGGCAATACT 59.536 55.000 13.08 0.10 0.00 2.12
2770 3025 3.301274 ACTAGGAGAATGACAGGTAGGC 58.699 50.000 0.00 0.00 0.00 3.93
2814 3069 7.615582 TGGTACAAGAGATTTGCTTATCAAG 57.384 36.000 0.00 0.00 32.70 3.02
2832 3087 3.067461 GTGCACCTCAAACATTTGGTACA 59.933 43.478 5.22 0.00 38.66 2.90
2842 3097 1.888512 ACCATGATGTGCACCTCAAAC 59.111 47.619 25.50 2.24 0.00 2.93
2865 3120 8.103948 ACTGATGAAACATCCAAGTCTTTTAG 57.896 34.615 8.87 0.00 0.00 1.85
3029 3287 5.452077 GGCGATCTGTTCAGGTAGATTTACT 60.452 44.000 0.00 0.00 33.97 2.24
3173 3431 0.535102 ACTTGGCCTTGTTGTCTCCG 60.535 55.000 3.32 0.00 0.00 4.63
3176 3434 0.180406 ACGACTTGGCCTTGTTGTCT 59.820 50.000 3.32 0.00 0.00 3.41
3251 3509 1.610363 TGGCAAGAATAAACACGCCA 58.390 45.000 0.00 0.00 46.80 5.69
3353 3611 1.026718 ATGCTCCGTTGTAGGCTTGC 61.027 55.000 0.00 0.00 0.00 4.01
3458 3719 2.784347 AGTTACCAAGGAGCAGAAAGC 58.216 47.619 0.00 0.00 46.19 3.51
3463 3724 3.442977 ACTACGTAGTTACCAAGGAGCAG 59.557 47.826 22.45 0.00 37.78 4.24
3552 3813 3.334583 TGGTTTAGTTGGCTGAGCTAG 57.665 47.619 3.72 0.00 0.00 3.42
3561 3822 6.156519 GCTCAGGTAATTTTGGTTTAGTTGG 58.843 40.000 0.00 0.00 0.00 3.77
3625 3914 3.944087 ACCCAGACTCAGAAGCAATAAC 58.056 45.455 0.00 0.00 0.00 1.89
3787 4077 7.282585 CCTCCAGTCCAGATTTATGTGAAATA 58.717 38.462 0.00 0.00 0.00 1.40
3796 4086 2.237143 CACAGCCTCCAGTCCAGATTTA 59.763 50.000 0.00 0.00 0.00 1.40
3799 4089 1.270414 CCACAGCCTCCAGTCCAGAT 61.270 60.000 0.00 0.00 0.00 2.90
3812 4102 1.941999 GATTCCAAGCAGGCCACAGC 61.942 60.000 5.01 6.06 37.29 4.40
3813 4103 0.609957 TGATTCCAAGCAGGCCACAG 60.610 55.000 5.01 0.00 37.29 3.66
3814 4104 0.609957 CTGATTCCAAGCAGGCCACA 60.610 55.000 5.01 0.00 38.70 4.17
3815 4105 0.322816 TCTGATTCCAAGCAGGCCAC 60.323 55.000 5.01 0.00 42.43 5.01
3816 4106 0.405198 TTCTGATTCCAAGCAGGCCA 59.595 50.000 5.01 0.00 42.43 5.36
3817 4107 1.772836 ATTCTGATTCCAAGCAGGCC 58.227 50.000 4.79 0.00 42.43 5.19
3818 4108 3.881937 AAATTCTGATTCCAAGCAGGC 57.118 42.857 4.79 0.00 42.43 4.85
3819 4109 7.999679 TGTATAAAATTCTGATTCCAAGCAGG 58.000 34.615 4.79 0.00 42.43 4.85
3820 4110 9.859427 TTTGTATAAAATTCTGATTCCAAGCAG 57.141 29.630 0.00 0.00 43.47 4.24
3830 4120 9.434420 CCCTTGCATTTTTGTATAAAATTCTGA 57.566 29.630 0.00 0.00 35.82 3.27
3839 4129 8.592809 AGTTTGATTCCCTTGCATTTTTGTATA 58.407 29.630 0.00 0.00 0.00 1.47
3866 4157 2.814336 GGAAGGAACAGTTGATCGCTTT 59.186 45.455 0.00 0.00 0.00 3.51
3891 4182 4.467795 AGATGTACCTTAAGCAAGCTCTCA 59.532 41.667 0.00 0.00 0.00 3.27
3969 4260 6.166279 ACAGGTGTCAGTTAATGTAGATGTG 58.834 40.000 0.00 0.00 0.00 3.21
3996 4287 1.067354 CCCAGTTCTGCATTTGAAGCC 60.067 52.381 0.00 0.00 0.00 4.35
4015 4306 2.731968 CGTTGTGTTGCTGCCATATTCC 60.732 50.000 0.00 0.00 0.00 3.01
4141 4432 6.322201 CAGGGAAATGCCTCTGTAATTATGTT 59.678 38.462 0.00 0.00 36.66 2.71
4250 4625 8.610248 TTGTATCTTCAAGTCAACCGATAAAA 57.390 30.769 0.00 0.00 0.00 1.52


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

AutoCloner maintained by Alex Coulton.