Multiple sequence alignment - TraesCS4A01G168800

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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 TraesCS4A01G168800 chr4A 100.000 5145 0 0 1 5145 423154190 423159334 0.000000e+00 9502.0
1 TraesCS4A01G168800 chr4D 95.070 3489 117 23 1704 5145 136186770 136183290 0.000000e+00 5439.0
2 TraesCS4A01G168800 chr4D 94.885 1310 26 4 433 1709 136188203 136186902 0.000000e+00 2010.0
3 TraesCS4A01G168800 chr4D 93.720 207 13 0 228 434 136188444 136188238 1.390000e-80 311.0
4 TraesCS4A01G168800 chr4D 93.564 202 12 1 3 203 136188641 136188440 3.010000e-77 300.0
5 TraesCS4A01G168800 chr4B 93.272 2185 99 15 3004 5145 195462567 195460388 0.000000e+00 3177.0
6 TraesCS4A01G168800 chr4B 95.706 1304 43 4 1704 3007 195463934 195462644 0.000000e+00 2085.0
7 TraesCS4A01G168800 chr4B 95.805 739 16 3 971 1708 195464792 195464068 0.000000e+00 1179.0
8 TraesCS4A01G168800 chr4B 91.096 438 29 5 1 434 195465793 195465362 7.420000e-163 584.0
9 TraesCS4A01G168800 chr4B 91.393 244 20 1 434 677 195465326 195465084 2.970000e-87 333.0
10 TraesCS4A01G168800 chr4B 100.000 39 0 0 827 865 195464885 195464847 7.150000e-09 73.1
11 TraesCS4A01G168800 chr5D 83.628 226 37 0 1483 1708 116174511 116174286 4.040000e-51 213.0
12 TraesCS4A01G168800 chr5D 73.858 394 83 16 2377 2757 116173373 116172987 6.950000e-29 139.0
13 TraesCS4A01G168800 chr5B 83.628 226 37 0 1483 1708 128218645 128218420 4.040000e-51 213.0
14 TraesCS4A01G168800 chr5B 82.759 116 20 0 2377 2492 128217501 128217386 2.530000e-18 104.0
15 TraesCS4A01G168800 chr5A 83.186 226 38 0 1483 1708 123712419 123712194 1.880000e-49 207.0
16 TraesCS4A01G168800 chr5A 74.177 395 80 16 2377 2757 123711289 123710903 1.490000e-30 145.0


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 TraesCS4A01G168800 chr4A 423154190 423159334 5144 False 9502.000000 9502 100.000000 1 5145 1 chr4A.!!$F1 5144
1 TraesCS4A01G168800 chr4D 136183290 136188641 5351 True 2015.000000 5439 94.309750 3 5145 4 chr4D.!!$R1 5142
2 TraesCS4A01G168800 chr4B 195460388 195465793 5405 True 1238.516667 3177 94.545333 1 5145 6 chr4B.!!$R1 5144

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
788 915 0.179150 CTCCTTCGCTTCTCCTGTCG 60.179 60.0 0.00 0.00 0.0 4.35 F
1122 1250 0.320683 TGTCATGTGTCGCTCTTGGG 60.321 55.0 0.00 0.00 0.0 4.12 F
2610 2875 0.109342 CTTATCGATGGCCAGGGCTT 59.891 55.0 13.05 8.01 41.6 4.35 F
3171 3526 2.814336 GGGAATTCAACTGACACACCTC 59.186 50.0 7.93 0.00 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2372 2637 0.458889 CCACAATTGGCCATTGCGAG 60.459 55.0 20.93 13.88 45.74 5.03 R
2773 3038 0.678950 TCACACCTCGTGCATGAAGA 59.321 50.0 11.53 1.71 45.92 2.87 R
3490 3849 0.671472 TGGTGCTGTCTTCGATGCAG 60.671 55.0 14.24 14.24 36.03 4.41 R
5094 5500 0.865111 CGATGGCAAAACACGTCTGA 59.135 50.0 0.00 0.00 0.00 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
41 42 8.127150 AGGTGCTTTTGAGAAAAATATAAGCT 57.873 30.769 0.00 0.00 37.85 3.74
107 109 2.123033 GCCCAACCAAACACCCCT 60.123 61.111 0.00 0.00 0.00 4.79
108 110 1.154221 GCCCAACCAAACACCCCTA 59.846 57.895 0.00 0.00 0.00 3.53
110 112 1.627864 CCCAACCAAACACCCCTAAG 58.372 55.000 0.00 0.00 0.00 2.18
112 114 2.673258 CCAACCAAACACCCCTAAGTT 58.327 47.619 0.00 0.00 0.00 2.66
113 115 3.436761 CCCAACCAAACACCCCTAAGTTA 60.437 47.826 0.00 0.00 0.00 2.24
133 137 5.071519 AGTTAGTGGATAGATCTGCAGCAAT 59.928 40.000 9.47 0.00 0.00 3.56
140 144 6.013984 TGGATAGATCTGCAGCAATGAGAATA 60.014 38.462 9.47 0.00 0.00 1.75
170 174 6.037500 TGAGAAGCTCGAATGGTGAAATAATG 59.962 38.462 0.00 0.00 32.35 1.90
207 211 2.031682 CACCTTCTTTCTTGCAAGGACG 60.032 50.000 25.73 15.68 39.36 4.79
210 214 1.967319 TCTTTCTTGCAAGGACGCTT 58.033 45.000 25.73 0.00 0.00 4.68
213 217 1.967319 TTCTTGCAAGGACGCTTTCT 58.033 45.000 25.73 0.00 0.00 2.52
250 254 7.938563 ATGCAATATCTAAAGAAGTCTCGTC 57.061 36.000 0.00 0.00 0.00 4.20
346 351 4.575885 ACTCGCTAAGCAATAAAGAACCA 58.424 39.130 0.00 0.00 0.00 3.67
416 421 6.426328 GCTGGAGGATAGAGAATGTTGTATTG 59.574 42.308 0.00 0.00 0.00 1.90
545 586 2.184385 TCGTTCCGATCTACGCTTTC 57.816 50.000 6.92 0.00 41.07 2.62
569 610 3.076621 TCGTCTTTGGTTCGCTCTAGTA 58.923 45.455 0.00 0.00 0.00 1.82
596 637 1.174078 TCGTCGCTAGTTGGTCCACA 61.174 55.000 0.00 0.00 0.00 4.17
606 647 6.016527 CGCTAGTTGGTCCACAGATATAGTTA 60.017 42.308 0.00 0.00 0.00 2.24
788 915 0.179150 CTCCTTCGCTTCTCCTGTCG 60.179 60.000 0.00 0.00 0.00 4.35
816 943 4.828925 GCAGCAGCCGGACTCCTC 62.829 72.222 5.05 0.00 33.58 3.71
908 1035 2.875672 GCTACCTTGTTGACTGCATCCA 60.876 50.000 0.00 0.00 0.00 3.41
1107 1235 1.374631 GCTGCTCCGTGATGTGTCA 60.375 57.895 0.00 0.00 0.00 3.58
1108 1236 0.742281 GCTGCTCCGTGATGTGTCAT 60.742 55.000 0.00 0.00 36.60 3.06
1109 1237 1.004595 CTGCTCCGTGATGTGTCATG 58.995 55.000 0.00 0.00 40.38 3.07
1110 1238 0.321346 TGCTCCGTGATGTGTCATGT 59.679 50.000 0.00 0.00 39.29 3.21
1111 1239 0.723414 GCTCCGTGATGTGTCATGTG 59.277 55.000 0.00 0.00 39.29 3.21
1112 1240 1.941209 GCTCCGTGATGTGTCATGTGT 60.941 52.381 0.00 0.00 39.29 3.72
1113 1241 1.995484 CTCCGTGATGTGTCATGTGTC 59.005 52.381 0.00 0.00 39.29 3.67
1122 1250 0.320683 TGTCATGTGTCGCTCTTGGG 60.321 55.000 0.00 0.00 0.00 4.12
1351 1479 5.237815 AGAGCGATGTTTTGATGTGTAAGA 58.762 37.500 0.00 0.00 0.00 2.10
1660 1788 0.610232 GCTTCAACCTCACCAGCCAT 60.610 55.000 0.00 0.00 0.00 4.40
1749 2014 4.240096 GCATTTGCATTGAACTGCTAGTT 58.760 39.130 0.00 1.82 42.75 2.24
1857 2122 3.244875 TGTGCAATGTGAGGTCATAGGTT 60.245 43.478 0.00 0.00 0.00 3.50
1889 2154 1.129811 CGGGAAACGCCAATGTAGTTC 59.870 52.381 0.00 0.00 38.95 3.01
1909 2174 1.001487 CGATTGTGCTCTTTGTTGGCA 60.001 47.619 0.00 0.00 0.00 4.92
1930 2195 1.471676 CGCTAGACGGCAGAGGAAATT 60.472 52.381 0.00 0.00 38.44 1.82
2050 2315 1.985159 ACCTGTTTGATGTGAGGGCTA 59.015 47.619 0.00 0.00 0.00 3.93
2053 2318 3.370846 CCTGTTTGATGTGAGGGCTATGA 60.371 47.826 0.00 0.00 0.00 2.15
2103 2368 3.696051 TGTTTTGAAGTCAAGCTGCTCTT 59.304 39.130 1.00 1.68 37.15 2.85
2151 2416 1.632965 ATGCTGCTCTGATGCTCCCA 61.633 55.000 0.00 0.00 0.00 4.37
2170 2435 3.319755 CCACAAAGATTGCGATTGCTTT 58.680 40.909 6.47 0.00 43.34 3.51
2177 2442 2.500509 TTGCGATTGCTTTTCGGTTT 57.499 40.000 6.47 0.00 43.34 3.27
2305 2570 8.286800 TCGTCGAAAACAATTTGTTCTTCATAT 58.713 29.630 14.80 0.00 40.14 1.78
2372 2637 2.177233 TGTCCCCTCACTATAGGAGTCC 59.823 54.545 0.00 0.00 39.15 3.85
2512 2777 9.111613 TGGTAATTTTCTTGTTATATGTACGGG 57.888 33.333 0.00 0.00 0.00 5.28
2514 2779 7.875327 AATTTTCTTGTTATATGTACGGGCT 57.125 32.000 0.00 0.00 0.00 5.19
2539 2804 9.520204 CTTTGACTATGTCACATTTGTTTTTCT 57.480 29.630 0.00 0.00 42.60 2.52
2610 2875 0.109342 CTTATCGATGGCCAGGGCTT 59.891 55.000 13.05 8.01 41.60 4.35
2817 3082 5.670485 TCCGTGAGTGTTATTTGAGCATAT 58.330 37.500 0.00 0.00 0.00 1.78
2818 3083 6.811954 TCCGTGAGTGTTATTTGAGCATATA 58.188 36.000 0.00 0.00 0.00 0.86
2819 3084 6.700081 TCCGTGAGTGTTATTTGAGCATATAC 59.300 38.462 0.00 0.00 0.00 1.47
2820 3085 6.701841 CCGTGAGTGTTATTTGAGCATATACT 59.298 38.462 0.00 0.00 0.00 2.12
2821 3086 7.865889 CCGTGAGTGTTATTTGAGCATATACTA 59.134 37.037 0.00 0.00 0.00 1.82
2822 3087 9.244799 CGTGAGTGTTATTTGAGCATATACTAA 57.755 33.333 0.00 0.00 0.00 2.24
3006 3361 9.760077 ATATGTATTTTGCACAGTAGTACTACC 57.240 33.333 25.97 13.34 36.75 3.18
3155 3510 7.242322 ACTACTAGAAGTTTTTCGAGGGAAT 57.758 36.000 0.00 0.00 39.51 3.01
3171 3526 2.814336 GGGAATTCAACTGACACACCTC 59.186 50.000 7.93 0.00 0.00 3.85
3248 3605 9.655769 CTCGAATCATTGTATTAAGAAACATGG 57.344 33.333 0.00 0.00 0.00 3.66
3424 3783 4.777366 TCATTCTGTCTCCACTCCATAACA 59.223 41.667 0.00 0.00 0.00 2.41
3549 3908 3.490348 CCATCTCAGTGAAAAGTGGGTT 58.510 45.455 0.00 0.00 0.00 4.11
3685 4044 4.314121 GGATCTCAGGTATTCATGCTGAC 58.686 47.826 0.00 0.00 0.00 3.51
3724 4083 6.003950 TGGTTCTGATAAAGGGTTCTCTTTG 58.996 40.000 7.80 0.00 37.51 2.77
3764 4123 5.568023 CGTGGAGGTTACATAAAGGAAGTGA 60.568 44.000 0.00 0.00 0.00 3.41
3862 4221 3.942829 TGATTTTGATCCGTCTGAGCTT 58.057 40.909 0.00 0.00 0.00 3.74
3923 4282 1.879380 CAAACATCTCGGTTGCAGGAA 59.121 47.619 0.00 0.00 0.00 3.36
3930 4289 5.418840 ACATCTCGGTTGCAGGAATTTTATT 59.581 36.000 0.00 0.00 0.00 1.40
3941 4300 8.359875 TGCAGGAATTTTATTAGGAATTGACA 57.640 30.769 0.00 0.00 0.00 3.58
3961 4320 4.517285 ACAGTGATCCATTTACTGCGATT 58.483 39.130 9.43 0.00 44.22 3.34
3999 4358 5.000012 AGTTTCTCGATAACTGATTCGCT 58.000 39.130 11.09 0.00 34.68 4.93
4054 4413 2.361119 TGGATACTCGGAATCGGTCTTG 59.639 50.000 0.00 0.00 36.95 3.02
4129 4488 2.832129 CTCCCTTCCTAGTTACAGTGCA 59.168 50.000 0.00 0.00 0.00 4.57
4134 4493 4.262463 CCTTCCTAGTTACAGTGCACTTGA 60.262 45.833 18.94 4.78 0.00 3.02
4186 4547 4.903638 TCATACTTCGCTTTTCTTGTCG 57.096 40.909 0.00 0.00 0.00 4.35
4215 4576 9.959749 GTCCTTGTACAATTCAGAAACATTAAA 57.040 29.630 9.13 0.00 0.00 1.52
4229 4590 7.007723 AGAAACATTAAACCTTCACCACCATA 58.992 34.615 0.00 0.00 0.00 2.74
4375 4760 7.692460 ACAGCTACATTTCTTCATTCAATCA 57.308 32.000 0.00 0.00 0.00 2.57
4422 4808 0.808125 TGTGTGCACAACAGTTGTCC 59.192 50.000 23.59 8.30 43.23 4.02
4447 4833 8.471609 CCTTTGGTTATAAATTATCCAACCGTT 58.528 33.333 11.12 0.00 41.27 4.44
4448 4834 9.863845 CTTTGGTTATAAATTATCCAACCGTTT 57.136 29.630 11.12 0.00 41.27 3.60
4528 4916 5.913137 TCACATGTTTTCTTGGAGTTTGT 57.087 34.783 0.00 0.00 0.00 2.83
4565 4953 1.134159 GTAGAGCCAGACGTCTCCCTA 60.134 57.143 16.96 11.25 0.00 3.53
4601 4989 6.902341 TGCTGTCAGATGAGTTGTTAATTTC 58.098 36.000 3.32 0.00 0.00 2.17
4644 5032 1.416401 TCTCCCGGGCTCATTCATTAC 59.584 52.381 18.49 0.00 0.00 1.89
4690 5078 1.064758 TGTACTCCAATGGGGTCATGC 60.065 52.381 8.69 0.00 38.11 4.06
4735 5123 0.178981 ACTGCCACCTGTTGCTGAAT 60.179 50.000 7.14 0.00 0.00 2.57
4755 5143 8.233190 GCTGAATAGCTGATAAATACATGTTCC 58.767 37.037 2.30 0.00 46.57 3.62
4816 5204 6.601332 TGTACACTTTTGGAGGAATCTCTTT 58.399 36.000 0.00 0.00 39.86 2.52
4884 5272 1.518325 TGGACGCAATAGGTGTTGTG 58.482 50.000 0.00 0.00 41.19 3.33
5070 5476 1.364171 CCGACTAAGGGCATCTCCG 59.636 63.158 0.00 0.00 34.94 4.63
5072 5478 0.962489 CGACTAAGGGCATCTCCGAT 59.038 55.000 0.00 0.00 34.94 4.18
5085 5491 4.082523 CCGATGCTGACCCCGTGT 62.083 66.667 0.00 0.00 0.00 4.49
5113 5519 0.865111 TCAGACGTGTTTTGCCATCG 59.135 50.000 0.00 0.00 0.00 3.84
5116 5522 2.095768 CAGACGTGTTTTGCCATCGAAT 60.096 45.455 0.00 0.00 0.00 3.34
5121 5527 2.487762 GTGTTTTGCCATCGAATGAGGA 59.512 45.455 0.00 0.00 0.00 3.71
5140 5546 0.034767 ACCTGTATCGGTCTGTCGGA 60.035 55.000 0.00 0.00 29.14 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
107 109 5.598417 TGCTGCAGATCTATCCACTAACTTA 59.402 40.000 20.43 0.00 0.00 2.24
108 110 4.406972 TGCTGCAGATCTATCCACTAACTT 59.593 41.667 20.43 0.00 0.00 2.66
110 112 4.327982 TGCTGCAGATCTATCCACTAAC 57.672 45.455 20.43 0.00 0.00 2.34
112 114 4.590222 TCATTGCTGCAGATCTATCCACTA 59.410 41.667 20.43 0.00 0.00 2.74
113 115 3.390311 TCATTGCTGCAGATCTATCCACT 59.610 43.478 20.43 0.00 0.00 4.00
133 137 6.025749 TCGAGCTTCTCAAAACTATTCTCA 57.974 37.500 0.00 0.00 0.00 3.27
140 144 3.499918 CACCATTCGAGCTTCTCAAAACT 59.500 43.478 0.00 0.00 0.00 2.66
170 174 4.757149 AGAAGGTGCTTACATGAAGTGAAC 59.243 41.667 0.00 0.50 37.49 3.18
184 188 1.959282 CCTTGCAAGAAAGAAGGTGCT 59.041 47.619 28.05 0.00 37.87 4.40
249 253 5.131642 AGAGATAACTCCATTGCAAGGATGA 59.868 40.000 13.66 1.03 43.53 2.92
250 254 5.374921 AGAGATAACTCCATTGCAAGGATG 58.625 41.667 13.66 7.19 43.53 3.51
416 421 4.715896 TCACTACTACGACGAACATGAAC 58.284 43.478 0.00 0.00 0.00 3.18
424 429 0.725686 GCTGCTCACTACTACGACGA 59.274 55.000 0.00 0.00 0.00 4.20
545 586 0.721718 GAGCGAACCAAAGACGATGG 59.278 55.000 0.00 0.00 43.84 3.51
569 610 3.057033 ACCAACTAGCGACGACTACAAAT 60.057 43.478 0.00 0.00 0.00 2.32
606 647 7.966812 TGCATGTGGTACAGAGAATATTAGAT 58.033 34.615 0.00 0.00 41.80 1.98
1107 1235 0.687354 AGAACCCAAGAGCGACACAT 59.313 50.000 0.00 0.00 0.00 3.21
1108 1236 0.033504 GAGAACCCAAGAGCGACACA 59.966 55.000 0.00 0.00 0.00 3.72
1109 1237 1.009389 CGAGAACCCAAGAGCGACAC 61.009 60.000 0.00 0.00 0.00 3.67
1110 1238 1.289066 CGAGAACCCAAGAGCGACA 59.711 57.895 0.00 0.00 0.00 4.35
1111 1239 0.319641 AACGAGAACCCAAGAGCGAC 60.320 55.000 0.00 0.00 0.00 5.19
1112 1240 0.391597 AAACGAGAACCCAAGAGCGA 59.608 50.000 0.00 0.00 0.00 4.93
1113 1241 1.069906 CAAAACGAGAACCCAAGAGCG 60.070 52.381 0.00 0.00 0.00 5.03
1122 1250 3.626028 ATCAAGCACCAAAACGAGAAC 57.374 42.857 0.00 0.00 0.00 3.01
1351 1479 6.514947 TGAACACAGCAAGAAATTAGCATTT 58.485 32.000 0.00 0.00 35.12 2.32
1660 1788 0.992695 TCTCGAGGAAGAGGGTGAGA 59.007 55.000 13.56 0.00 38.71 3.27
1694 1822 0.672342 ATGTATACCTCCGTGCCGAC 59.328 55.000 0.00 0.00 0.00 4.79
1700 1828 6.518537 GCTGAAAAGGATATGTATACCTCCGT 60.519 42.308 0.00 0.16 33.16 4.69
1741 2006 7.416964 AGATGCCTATCCTAATAACTAGCAG 57.583 40.000 0.00 0.00 33.64 4.24
1749 2014 6.962311 ACTGATTGGAGATGCCTATCCTAATA 59.038 38.462 4.24 0.00 45.02 0.98
1870 2135 1.129811 CGAACTACATTGGCGTTTCCC 59.870 52.381 0.00 0.00 0.00 3.97
1889 2154 1.001487 TGCCAACAAAGAGCACAATCG 60.001 47.619 0.00 0.00 0.00 3.34
1909 2174 1.248785 TTTCCTCTGCCGTCTAGCGT 61.249 55.000 5.97 0.00 39.32 5.07
1930 2195 3.070878 TGCTGATCGGGTATTTGCATAGA 59.929 43.478 3.14 0.00 0.00 1.98
2103 2368 7.707464 CCATGCTCTGTTCATGCATAATTAAAA 59.293 33.333 0.00 0.00 44.39 1.52
2151 2416 3.670055 CGAAAAGCAATCGCAATCTTTGT 59.330 39.130 0.00 0.00 42.27 2.83
2372 2637 0.458889 CCACAATTGGCCATTGCGAG 60.459 55.000 20.93 13.88 45.74 5.03
2512 2777 7.698836 AAAACAAATGTGACATAGTCAAAGC 57.301 32.000 0.00 0.00 44.49 3.51
2539 2804 3.729462 GCACGCAACAGTTGTCAAAACTA 60.729 43.478 14.88 0.00 0.00 2.24
2610 2875 2.104111 CGAAGCCAATCCCACCATACTA 59.896 50.000 0.00 0.00 0.00 1.82
2698 2963 7.492344 GGTGAGTTCAAAAATGTCAAGTTTGAT 59.508 33.333 12.55 2.78 40.08 2.57
2773 3038 0.678950 TCACACCTCGTGCATGAAGA 59.321 50.000 11.53 1.71 45.92 2.87
2795 3060 5.991328 ATATGCTCAAATAACACTCACGG 57.009 39.130 0.00 0.00 0.00 4.94
2820 3085 9.628746 GGAAAACAAACAAAACAGTAAGAGTTA 57.371 29.630 0.00 0.00 0.00 2.24
2821 3086 8.145122 TGGAAAACAAACAAAACAGTAAGAGTT 58.855 29.630 0.00 0.00 0.00 3.01
2822 3087 7.662897 TGGAAAACAAACAAAACAGTAAGAGT 58.337 30.769 0.00 0.00 0.00 3.24
2823 3088 7.201435 GCTGGAAAACAAACAAAACAGTAAGAG 60.201 37.037 0.00 0.00 0.00 2.85
2824 3089 6.588373 GCTGGAAAACAAACAAAACAGTAAGA 59.412 34.615 0.00 0.00 0.00 2.10
2825 3090 6.367422 TGCTGGAAAACAAACAAAACAGTAAG 59.633 34.615 0.00 0.00 0.00 2.34
2826 3091 6.223852 TGCTGGAAAACAAACAAAACAGTAA 58.776 32.000 0.00 0.00 0.00 2.24
2952 3227 4.630894 TCACCAAACAATGTGTGAAGAC 57.369 40.909 4.88 0.00 36.74 3.01
3155 3510 4.487714 AGAAAGAGGTGTGTCAGTTGAA 57.512 40.909 0.00 0.00 0.00 2.69
3171 3526 6.391227 ACCACAAATACCACAGAAAGAAAG 57.609 37.500 0.00 0.00 0.00 2.62
3248 3605 5.627135 TGCATAGGGCCTTTTAAGTATACC 58.373 41.667 13.45 0.00 43.89 2.73
3459 3818 7.835682 TCAAACATGAATCTGGATAAGGAATGT 59.164 33.333 0.00 0.00 0.00 2.71
3490 3849 0.671472 TGGTGCTGTCTTCGATGCAG 60.671 55.000 14.24 14.24 36.03 4.41
3549 3908 2.851263 AGAAATGCCGTACTTGTCCA 57.149 45.000 0.00 0.00 0.00 4.02
3685 4044 4.408921 TCAGAACCATGTATCCTTAGGTGG 59.591 45.833 0.00 0.29 31.86 4.61
3739 4098 4.529377 ACTTCCTTTATGTAACCTCCACGA 59.471 41.667 0.00 0.00 0.00 4.35
3764 4123 7.017353 ACCATCCATTTCTACATCTGAGATGAT 59.983 37.037 27.73 14.52 32.28 2.45
3853 4212 1.066858 TCAATCACCGGAAGCTCAGAC 60.067 52.381 9.46 0.00 0.00 3.51
3884 4243 7.841282 TGTTTGTTCCCACCATATTCTTTAA 57.159 32.000 0.00 0.00 0.00 1.52
3923 4282 9.699410 TGGATCACTGTCAATTCCTAATAAAAT 57.301 29.630 0.00 0.00 0.00 1.82
3930 4289 7.770433 CAGTAAATGGATCACTGTCAATTCCTA 59.230 37.037 0.00 0.00 35.91 2.94
3941 4300 4.201950 GCAAATCGCAGTAAATGGATCACT 60.202 41.667 0.00 0.00 41.79 3.41
3961 4320 4.473444 AGAAACTGAGATTGGAAAGGCAA 58.527 39.130 0.00 0.00 0.00 4.52
3998 4357 3.039252 AGACCAGGGACTAGAATGGAG 57.961 52.381 0.00 0.00 36.02 3.86
3999 4358 3.107601 CAAGACCAGGGACTAGAATGGA 58.892 50.000 0.00 0.00 36.02 3.41
4129 4488 3.701205 TGTGACTATGCCACATCAAGT 57.299 42.857 0.00 0.00 39.36 3.16
4169 4530 1.261619 CTGCGACAAGAAAAGCGAAGT 59.738 47.619 0.00 0.00 0.00 3.01
4186 4547 5.008613 TGTTTCTGAATTGTACAAGGACTGC 59.991 40.000 14.65 0.00 0.00 4.40
4257 4619 6.566079 ACCCTGATATGATTCTTCTTGACA 57.434 37.500 0.00 0.00 0.00 3.58
4395 4781 3.743714 TTGTGCACACAAGCCCTAT 57.256 47.368 21.56 0.00 45.42 2.57
4422 4808 9.863845 AAACGGTTGGATAATTTATAACCAAAG 57.136 29.630 16.16 12.64 41.29 2.77
4495 4883 9.559958 CCAAGAAAACATGTGATACTGTTTATC 57.440 33.333 0.00 3.02 42.98 1.75
4503 4891 7.425606 ACAAACTCCAAGAAAACATGTGATAC 58.574 34.615 0.00 0.00 0.00 2.24
4504 4892 7.284261 TGACAAACTCCAAGAAAACATGTGATA 59.716 33.333 0.00 0.00 0.00 2.15
4528 4916 3.308401 TCTACATTCATAGCCAGGCTGA 58.692 45.455 25.59 12.05 40.10 4.26
4565 4953 9.236006 ACTCATCTGACAGCAAATTATTTAACT 57.764 29.630 0.00 0.00 0.00 2.24
4644 5032 1.063174 GCAGCAAGGACAAGCTAATCG 59.937 52.381 0.00 0.00 39.50 3.34
4690 5078 1.317613 TTGCACAGTTGGCAACCTAG 58.682 50.000 25.81 18.09 45.57 3.02
4735 5123 7.441836 ACATCGGAACATGTATTTATCAGCTA 58.558 34.615 0.00 0.00 35.10 3.32
4755 5143 2.079158 ACCAGCTCAACATCAACATCG 58.921 47.619 0.00 0.00 0.00 3.84
4816 5204 8.912988 ACAGGTTTATTTTTCTTCTTGACATCA 58.087 29.630 0.00 0.00 0.00 3.07
4837 5225 3.011708 AGAATAATGAAGCCCCAACAGGT 59.988 43.478 0.00 0.00 0.00 4.00
4884 5272 4.509600 GCCTAAGCACTCTGATGACAATAC 59.490 45.833 0.00 0.00 39.53 1.89
5035 5441 3.137913 AGTCGGCTAGAATAGGACACCTA 59.862 47.826 0.00 0.00 39.70 3.08
5037 5443 2.308690 AGTCGGCTAGAATAGGACACC 58.691 52.381 0.00 0.00 39.70 4.16
5093 5499 1.262950 CGATGGCAAAACACGTCTGAA 59.737 47.619 0.00 0.00 0.00 3.02
5094 5500 0.865111 CGATGGCAAAACACGTCTGA 59.135 50.000 0.00 0.00 0.00 3.27


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

AutoCloner maintained by Alex Coulton.