Multiple sequence alignment - TraesCS4D01G340700

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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 TraesCS4D01G340700 chr4D 100.000 5615 0 0 1 5615 497899536 497893922 0.000000e+00 10370.0
1 TraesCS4D01G340700 chr4D 98.361 61 1 0 3944 4004 9443894 9443834 2.140000e-19 108.0
2 TraesCS4D01G340700 chr4D 92.105 76 6 0 3937 4012 450331546 450331471 2.140000e-19 108.0
3 TraesCS4D01G340700 chr4B 89.912 5809 266 126 1 5615 639127337 639121655 0.000000e+00 7186.0
4 TraesCS4D01G340700 chr4B 96.610 59 2 0 3944 4002 18092030 18091972 1.290000e-16 99.0
5 TraesCS4D01G340700 chr5A 90.167 2329 128 45 601 2885 678206299 678204028 0.000000e+00 2939.0
6 TraesCS4D01G340700 chr5A 91.066 2149 80 34 3128 5231 678203571 678201490 0.000000e+00 2802.0
7 TraesCS4D01G340700 chr5A 92.915 621 25 13 1 609 678207084 678206471 0.000000e+00 885.0
8 TraesCS4D01G340700 chr5A 80.615 325 53 8 5299 5615 616085801 616085479 5.620000e-60 243.0
9 TraesCS4D01G340700 chr5A 82.946 129 12 6 5300 5419 325195153 325195280 2.140000e-19 108.0
10 TraesCS4D01G340700 chr1D 81.327 407 57 10 2486 2884 269728495 269728100 4.220000e-81 313.0
11 TraesCS4D01G340700 chr1D 81.790 324 44 9 5299 5615 99673930 99673615 2.010000e-64 257.0
12 TraesCS4D01G340700 chr1D 78.947 323 55 9 5301 5613 83942046 83942365 2.050000e-49 207.0
13 TraesCS4D01G340700 chr1D 83.969 131 8 7 1748 1878 46117619 46117502 4.600000e-21 113.0
14 TraesCS4D01G340700 chr7D 81.056 322 49 9 5300 5613 453186848 453186531 4.340000e-61 246.0
15 TraesCS4D01G340700 chr7D 79.641 334 57 7 5291 5615 601457876 601457545 4.380000e-56 230.0
16 TraesCS4D01G340700 chr2A 81.115 323 48 10 5301 5613 769783159 769782840 4.340000e-61 246.0
17 TraesCS4D01G340700 chr2A 77.410 332 62 13 5291 5613 693643689 693644016 9.610000e-43 185.0
18 TraesCS4D01G340700 chr6D 80.495 323 51 9 5300 5613 321760769 321760450 2.610000e-58 237.0
19 TraesCS4D01G340700 chr5B 79.751 321 50 12 5303 5613 1415787 1415472 9.470000e-53 219.0
20 TraesCS4D01G340700 chr2D 77.778 324 58 11 5300 5613 599458316 599458635 2.670000e-43 187.0
21 TraesCS4D01G340700 chr4A 94.118 68 4 0 3937 4004 594004218 594004285 2.770000e-18 104.0
22 TraesCS4D01G340700 chr6B 91.667 60 4 1 5232 5291 71282463 71282521 1.300000e-11 82.4
23 TraesCS4D01G340700 chr2B 89.474 57 5 1 5232 5288 748452675 748452730 2.810000e-08 71.3


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 TraesCS4D01G340700 chr4D 497893922 497899536 5614 True 10370.000000 10370 100.000000 1 5615 1 chr4D.!!$R3 5614
1 TraesCS4D01G340700 chr4B 639121655 639127337 5682 True 7186.000000 7186 89.912000 1 5615 1 chr4B.!!$R2 5614
2 TraesCS4D01G340700 chr5A 678201490 678207084 5594 True 2208.666667 2939 91.382667 1 5231 3 chr5A.!!$R2 5230

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
747 957 0.673437 CTGCTCAGTCCTAGCTAGCC 59.327 60.0 15.74 7.82 40.73 3.93 F
1933 2219 0.394216 CCATCATGGTTGCCGGAAGA 60.394 55.0 5.05 0.00 31.35 2.87 F
2900 3288 0.682852 AAGTAGCAGTACCGCACCAA 59.317 50.0 3.48 0.00 0.00 3.67 F
3321 3887 0.108207 ACGATCGATCCCTACGGACT 59.892 55.0 24.34 0.00 42.48 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2392 2716 0.533308 GGTGTGGTAACTTGTGCGGA 60.533 55.0 0.0 0.0 37.61 5.54 R
2906 3294 0.109179 TGCATGGCACGAAAAGATGC 60.109 50.0 0.0 0.0 39.90 3.91 R
3819 4417 0.527565 ACATGGCAACCGATTGAAGC 59.472 50.0 0.0 0.0 38.15 3.86 R
5039 5698 0.468226 TCCCCTACACAATCATCCGC 59.532 55.0 0.0 0.0 0.00 5.54 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
31 32 2.223525 CGAAAGAGGCCGGTCTAACTAG 60.224 54.545 9.57 0.00 0.00 2.57
41 42 3.002451 CCGGTCTAACTAGTCTCACATCG 59.998 52.174 0.00 0.00 0.00 3.84
46 47 3.972950 AACTAGTCTCACATCGATCCG 57.027 47.619 0.00 0.00 0.00 4.18
71 72 7.097192 GTCCACACACACAGAAGAAGATTATA 58.903 38.462 0.00 0.00 0.00 0.98
76 77 7.766278 ACACACACAGAAGAAGATTATATCCAC 59.234 37.037 0.00 0.00 0.00 4.02
171 178 4.504916 CAGCAGGGCGAGACCGAG 62.505 72.222 0.00 0.00 40.62 4.63
172 179 4.742649 AGCAGGGCGAGACCGAGA 62.743 66.667 0.00 0.00 40.62 4.04
173 180 4.200283 GCAGGGCGAGACCGAGAG 62.200 72.222 0.00 0.00 40.62 3.20
174 181 2.438614 CAGGGCGAGACCGAGAGA 60.439 66.667 0.00 0.00 40.62 3.10
175 182 2.438795 AGGGCGAGACCGAGAGAC 60.439 66.667 0.00 0.00 40.62 3.36
192 202 3.708631 AGAGACAGAGAGAGAGAGAGAGG 59.291 52.174 0.00 0.00 0.00 3.69
301 314 3.785122 GACCACCACCACACACCCC 62.785 68.421 0.00 0.00 0.00 4.95
302 315 4.947147 CCACCACCACACACCCCG 62.947 72.222 0.00 0.00 0.00 5.73
303 316 4.947147 CACCACCACACACCCCGG 62.947 72.222 0.00 0.00 0.00 5.73
501 517 3.742882 GCTGGCTTTTCATCCTGTTTTTC 59.257 43.478 0.00 0.00 0.00 2.29
713 913 3.631686 CAGTAGCTAGCTCTCTGTGATGT 59.368 47.826 27.53 5.98 0.00 3.06
745 955 4.935352 ATTTCTGCTCAGTCCTAGCTAG 57.065 45.455 14.20 14.20 40.73 3.42
746 956 1.686355 TCTGCTCAGTCCTAGCTAGC 58.314 55.000 15.74 6.62 40.73 3.42
747 957 0.673437 CTGCTCAGTCCTAGCTAGCC 59.327 60.000 15.74 7.82 40.73 3.93
796 1014 4.202121 TGGCGATAGGAGTGACTAATCAAC 60.202 45.833 0.00 0.00 36.31 3.18
798 1016 4.979197 GCGATAGGAGTGACTAATCAACTG 59.021 45.833 0.00 0.00 36.31 3.16
800 1018 5.508153 CGATAGGAGTGACTAATCAACTGGG 60.508 48.000 0.00 0.00 36.31 4.45
801 1019 3.521727 AGGAGTGACTAATCAACTGGGT 58.478 45.455 0.00 0.00 36.31 4.51
818 1038 1.021968 GGTGCCGTCTGTTCTTGTTT 58.978 50.000 0.00 0.00 0.00 2.83
820 1040 2.159296 GGTGCCGTCTGTTCTTGTTTTT 60.159 45.455 0.00 0.00 0.00 1.94
1047 1292 2.278013 GACTACTTCTCGGCGGCG 60.278 66.667 27.15 27.15 0.00 6.46
1083 1328 1.600076 GCTCATGCCGCAGATGGAT 60.600 57.895 0.00 0.00 0.00 3.41
1281 1526 2.361119 GCAGCATCATCAACATCACCAT 59.639 45.455 0.00 0.00 0.00 3.55
1287 1532 2.501316 TCATCAACATCACCATCCGAGT 59.499 45.455 0.00 0.00 0.00 4.18
1377 1637 1.806351 CTCGTCTCAGCAGCAGCAG 60.806 63.158 3.17 0.00 45.49 4.24
1378 1638 3.488978 CGTCTCAGCAGCAGCAGC 61.489 66.667 3.17 0.46 45.49 5.25
1379 1639 2.358369 GTCTCAGCAGCAGCAGCA 60.358 61.111 12.92 0.00 45.49 4.41
1380 1640 2.047179 TCTCAGCAGCAGCAGCAG 60.047 61.111 12.92 3.97 45.49 4.24
1533 1793 3.075005 TACTGCAGCCTCCCGGTC 61.075 66.667 15.27 0.00 0.00 4.79
1542 1802 2.102357 CTCCCGGTCGACATCACG 59.898 66.667 18.91 11.34 0.00 4.35
1898 2178 0.673437 TTACGGGAAAGGTCGTCGTT 59.327 50.000 0.00 0.00 40.31 3.85
1933 2219 0.394216 CCATCATGGTTGCCGGAAGA 60.394 55.000 5.05 0.00 31.35 2.87
2303 2622 1.227468 ATGCAGCTCGATCGCACAT 60.227 52.632 11.09 6.31 38.73 3.21
2369 2693 5.009010 CACTGTTACATTGCCCATCCTAATC 59.991 44.000 0.00 0.00 0.00 1.75
2383 2707 6.040842 CCCATCCTAATCAACCAATTTACTGG 59.959 42.308 0.00 0.00 42.68 4.00
2407 2737 5.004448 TCAATTAATCCGCACAAGTTACCA 58.996 37.500 0.00 0.00 0.00 3.25
2711 3044 3.809013 CCGGGGATGACAAGGGGG 61.809 72.222 0.00 0.00 0.00 5.40
2894 3227 1.098050 ACCCGTAAGTAGCAGTACCG 58.902 55.000 0.00 0.00 0.00 4.02
2900 3288 0.682852 AAGTAGCAGTACCGCACCAA 59.317 50.000 3.48 0.00 0.00 3.67
2903 3291 2.100916 AGTAGCAGTACCGCACCAATAG 59.899 50.000 3.48 0.00 0.00 1.73
2906 3294 1.396996 GCAGTACCGCACCAATAGTTG 59.603 52.381 0.00 0.00 0.00 3.16
2914 3302 3.367292 CCGCACCAATAGTTGCATCTTTT 60.367 43.478 1.93 0.00 0.00 2.27
2916 3304 3.853671 GCACCAATAGTTGCATCTTTTCG 59.146 43.478 1.93 0.00 0.00 3.46
2930 3318 3.832276 TCTTTTCGTGCCATGCATTAAC 58.168 40.909 0.00 0.00 41.91 2.01
3120 3594 6.714810 AGCACATTGAATTGGTAGTCAGTTAA 59.285 34.615 0.00 0.00 28.99 2.01
3122 3596 8.028938 GCACATTGAATTGGTAGTCAGTTAATT 58.971 33.333 0.00 0.00 28.99 1.40
3209 3761 3.489059 GGACCACAATTATGTTGGCATCG 60.489 47.826 0.00 0.00 37.82 3.84
3313 3879 1.133598 TGTGTGTGTACGATCGATCCC 59.866 52.381 24.34 8.42 0.00 3.85
3319 3885 1.070601 TGTACGATCGATCCCTACGGA 59.929 52.381 24.34 1.76 44.33 4.69
3320 3886 1.462670 GTACGATCGATCCCTACGGAC 59.537 57.143 24.34 11.14 42.48 4.79
3321 3887 0.108207 ACGATCGATCCCTACGGACT 59.892 55.000 24.34 0.00 42.48 3.85
3322 3888 1.345741 ACGATCGATCCCTACGGACTA 59.654 52.381 24.34 0.00 42.48 2.59
3327 3893 2.028294 TCGATCCCTACGGACTAGCTAG 60.028 54.545 19.44 19.44 42.48 3.42
3330 3896 0.894642 CCCTACGGACTAGCTAGGGC 60.895 65.000 24.35 15.24 40.28 5.19
3522 4112 0.786581 GCTGGATATGTGACGCATCG 59.213 55.000 4.40 0.00 38.94 3.84
3523 4113 1.602920 GCTGGATATGTGACGCATCGA 60.603 52.381 4.40 0.00 38.94 3.59
3529 4119 5.105756 TGGATATGTGACGCATCGATCTTAT 60.106 40.000 4.40 0.00 38.94 1.73
3551 4141 9.272901 CTTATTGTGTGATGTGTAAATTAACCG 57.727 33.333 0.00 0.00 0.00 4.44
3586 4176 7.013750 TGTTTGAGTGGACAAAGCATAAACATA 59.986 33.333 0.00 0.00 39.83 2.29
3687 4285 4.740741 TGTGATCGTACCAAAATGTGTG 57.259 40.909 0.00 0.00 0.00 3.82
3768 4366 2.401766 ACGGAGCCAGGTACGTACG 61.402 63.158 18.98 15.01 37.85 3.67
3769 4367 2.401766 CGGAGCCAGGTACGTACGT 61.402 63.158 25.98 25.98 0.00 3.57
3819 4417 1.592669 GCCCATCTCCATCGTCACG 60.593 63.158 0.00 0.00 0.00 4.35
3840 4438 2.086869 CTTCAATCGGTTGCCATGTCT 58.913 47.619 2.72 0.00 35.26 3.41
4317 4939 2.768344 GGCCAGGGAGGATTCGGA 60.768 66.667 0.00 0.00 41.22 4.55
4605 5230 1.816863 TTCACCTGCTCCGTGACCTC 61.817 60.000 1.31 0.00 39.89 3.85
4665 5294 4.688419 CAAGCGCTGGTTGCACGG 62.688 66.667 12.58 0.00 43.06 4.94
4686 5318 3.147595 CCATCCACGGCGAGGAGA 61.148 66.667 28.69 9.65 38.83 3.71
4688 5320 3.148279 ATCCACGGCGAGGAGACC 61.148 66.667 28.69 0.00 38.83 3.85
4689 5321 3.957435 ATCCACGGCGAGGAGACCA 62.957 63.158 28.69 8.15 38.83 4.02
4692 5324 2.915659 ACGGCGAGGAGACCAACA 60.916 61.111 16.62 0.00 0.00 3.33
4695 5327 2.435059 GCGAGGAGACCAACAGCC 60.435 66.667 0.00 0.00 0.00 4.85
4747 5385 2.224450 ACCTGTACCAGTTTACCTGCAC 60.224 50.000 0.00 0.00 40.06 4.57
4748 5386 2.224426 CCTGTACCAGTTTACCTGCACA 60.224 50.000 0.00 0.00 40.06 4.57
4799 5437 1.075536 CCCCTAAGCTTTTGGTGGTCT 59.924 52.381 3.20 0.00 0.00 3.85
4849 5487 4.444838 CACGGTCGATCGGGGCAA 62.445 66.667 23.84 0.00 0.00 4.52
4924 5566 8.792830 ATGTTGCACATTAATTAGAGTACTGT 57.207 30.769 0.00 0.00 34.67 3.55
4932 5574 2.743636 TTAGAGTACTGTGCACCAGC 57.256 50.000 15.69 1.95 45.68 4.85
4933 5575 0.526211 TAGAGTACTGTGCACCAGCG 59.474 55.000 15.69 2.64 45.68 5.18
4934 5576 1.738099 GAGTACTGTGCACCAGCGG 60.738 63.158 15.69 0.00 45.68 5.52
5037 5696 3.296709 ATGTATCGATCGGCCGGCC 62.297 63.158 36.69 36.69 0.00 6.13
5038 5697 3.986006 GTATCGATCGGCCGGCCA 61.986 66.667 42.78 30.05 35.37 5.36
5039 5698 3.680786 TATCGATCGGCCGGCCAG 61.681 66.667 42.78 33.39 35.37 4.85
5051 5710 2.827051 CGGCCAGCGGATGATTGTG 61.827 63.158 2.24 0.00 0.00 3.33
5255 5914 2.685897 AGAGTGTGCGTTTGGCTTTAAA 59.314 40.909 0.00 0.00 44.05 1.52
5265 5924 6.128282 TGCGTTTGGCTTTAAAATTTGTTCAA 60.128 30.769 0.00 0.00 44.05 2.69
5294 5953 7.800300 AAAGTGTACTTCTATCTTCCCTCTT 57.200 36.000 0.00 0.00 34.61 2.85
5297 5956 6.605594 AGTGTACTTCTATCTTCCCTCTTGAG 59.394 42.308 0.00 0.00 0.00 3.02
5302 5961 4.735369 TCTATCTTCCCTCTTGAGCTAGG 58.265 47.826 0.00 0.00 0.00 3.02
5307 5966 1.834263 TCCCTCTTGAGCTAGGCTTTC 59.166 52.381 0.00 0.00 39.88 2.62
5366 6031 6.827727 ACCAAGTACCGATAGCAAATAAGAT 58.172 36.000 0.00 0.00 0.00 2.40
5393 6058 2.625823 CCACACCACAATCACGCCC 61.626 63.158 0.00 0.00 0.00 6.13
5396 6061 1.285641 CACCACAATCACGCCCAAC 59.714 57.895 0.00 0.00 0.00 3.77
5404 6069 3.052036 CAATCACGCCCAACAAAGAAAG 58.948 45.455 0.00 0.00 0.00 2.62
5411 6076 4.099419 ACGCCCAACAAAGAAAGAAGAAAT 59.901 37.500 0.00 0.00 0.00 2.17
5444 6109 1.359459 CGGGTGGCGAACTAAGAAGC 61.359 60.000 0.00 0.00 0.00 3.86
5452 6117 2.793933 GCGAACTAAGAAGCCGTCGTAT 60.794 50.000 0.00 0.00 31.15 3.06
5576 6241 4.912187 GGCAAGAAATTTGAAGAACGAGTC 59.088 41.667 0.00 0.00 0.00 3.36
5588 6253 0.307760 AACGAGTCAAAAGCTTGCCG 59.692 50.000 0.00 0.38 32.14 5.69
5590 6255 1.441016 GAGTCAAAAGCTTGCCGCG 60.441 57.895 0.00 0.00 45.59 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 0.738975 TGGACGGATCGATGTGAGAC 59.261 55.000 0.54 0.00 0.00 3.36
41 42 0.317160 TCTGTGTGTGTGGACGGATC 59.683 55.000 0.00 0.00 0.00 3.36
46 47 3.179443 TCTTCTTCTGTGTGTGTGGAC 57.821 47.619 0.00 0.00 0.00 4.02
71 72 3.091633 CAGGTTTTGGAGATGGTGGAT 57.908 47.619 0.00 0.00 0.00 3.41
167 174 2.430694 TCTCTCTCTCTCTGTCTCTCGG 59.569 54.545 0.00 0.00 0.00 4.63
170 177 3.708631 CCTCTCTCTCTCTCTCTGTCTCT 59.291 52.174 0.00 0.00 0.00 3.10
171 178 3.181461 CCCTCTCTCTCTCTCTCTGTCTC 60.181 56.522 0.00 0.00 0.00 3.36
172 179 2.774234 CCCTCTCTCTCTCTCTCTGTCT 59.226 54.545 0.00 0.00 0.00 3.41
173 180 2.771943 TCCCTCTCTCTCTCTCTCTGTC 59.228 54.545 0.00 0.00 0.00 3.51
174 181 2.845659 TCCCTCTCTCTCTCTCTCTGT 58.154 52.381 0.00 0.00 0.00 3.41
175 182 3.931907 TTCCCTCTCTCTCTCTCTCTG 57.068 52.381 0.00 0.00 0.00 3.35
192 202 9.316730 GCTTCTTCTGATATGATATGAGATTCC 57.683 37.037 2.49 0.00 0.00 3.01
501 517 1.994463 CTTTGGTCTGGAGGGGAGG 59.006 63.158 0.00 0.00 0.00 4.30
704 904 8.244113 CAGAAATACTACTACACACATCACAGA 58.756 37.037 0.00 0.00 0.00 3.41
705 905 7.009631 GCAGAAATACTACTACACACATCACAG 59.990 40.741 0.00 0.00 0.00 3.66
713 913 6.127703 GGACTGAGCAGAAATACTACTACACA 60.128 42.308 4.21 0.00 0.00 3.72
745 955 5.788450 TCTATCAAGCTAGCTAATCAAGGC 58.212 41.667 19.70 0.00 0.00 4.35
746 956 7.609960 TGATCTATCAAGCTAGCTAATCAAGG 58.390 38.462 19.70 5.76 33.08 3.61
747 957 8.306038 ACTGATCTATCAAGCTAGCTAATCAAG 58.694 37.037 19.70 12.06 36.18 3.02
796 1014 1.071471 AAGAACAGACGGCACCCAG 59.929 57.895 0.00 0.00 0.00 4.45
798 1016 0.818040 AACAAGAACAGACGGCACCC 60.818 55.000 0.00 0.00 0.00 4.61
800 1018 2.844122 AAAACAAGAACAGACGGCAC 57.156 45.000 0.00 0.00 0.00 5.01
818 1038 3.003897 CGGACGACCAAATCTTTCCAAAA 59.996 43.478 4.48 0.00 35.59 2.44
820 1040 2.147958 CGGACGACCAAATCTTTCCAA 58.852 47.619 4.48 0.00 35.59 3.53
1108 1353 2.503061 CTCCATCCCGGACTGCAG 59.497 66.667 13.48 13.48 39.64 4.41
1324 1572 4.731503 GTGCAGCTGCGCGACTTG 62.732 66.667 34.12 2.78 45.83 3.16
1573 1833 2.561885 GTCTTGCTGCTGCTGCTG 59.438 61.111 27.67 20.66 40.48 4.41
1574 1834 3.048475 CGTCTTGCTGCTGCTGCT 61.048 61.111 27.67 0.00 40.48 4.24
1575 1835 3.024782 CTCGTCTTGCTGCTGCTGC 62.025 63.158 22.51 22.51 40.48 5.25
1576 1836 2.389020 CCTCGTCTTGCTGCTGCTG 61.389 63.158 17.00 9.59 40.48 4.41
1577 1837 2.047465 CCTCGTCTTGCTGCTGCT 60.047 61.111 17.00 0.00 40.48 4.24
1578 1838 3.797546 GCCTCGTCTTGCTGCTGC 61.798 66.667 8.89 8.89 40.20 5.25
1579 1839 3.123620 GGCCTCGTCTTGCTGCTG 61.124 66.667 0.00 0.00 0.00 4.41
1580 1840 4.749310 CGGCCTCGTCTTGCTGCT 62.749 66.667 0.00 0.00 0.00 4.24
1957 2243 1.823899 CCCAAGAATAGCGCCCCAC 60.824 63.158 2.29 0.00 0.00 4.61
1963 2249 1.376609 GGTGTGGCCCAAGAATAGCG 61.377 60.000 0.00 0.00 0.00 4.26
1986 2272 3.606687 GGAATAGAGGTTTCCGAAAGCA 58.393 45.455 21.78 5.18 41.18 3.91
2056 2355 2.185867 GTTGCTGCATGGCCATGG 59.814 61.111 39.72 27.67 39.16 3.66
2303 2622 2.588596 CAGTGCTGTGCCGTGACA 60.589 61.111 0.00 0.00 0.00 3.58
2383 2707 5.106475 TGGTAACTTGTGCGGATTAATTGAC 60.106 40.000 0.00 0.00 37.61 3.18
2384 2708 5.004448 TGGTAACTTGTGCGGATTAATTGA 58.996 37.500 0.00 0.00 37.61 2.57
2385 2709 5.092781 GTGGTAACTTGTGCGGATTAATTG 58.907 41.667 0.00 0.00 37.61 2.32
2386 2710 4.762765 TGTGGTAACTTGTGCGGATTAATT 59.237 37.500 0.00 0.00 37.61 1.40
2387 2711 4.155280 GTGTGGTAACTTGTGCGGATTAAT 59.845 41.667 0.00 0.00 37.61 1.40
2388 2712 3.499157 GTGTGGTAACTTGTGCGGATTAA 59.501 43.478 0.00 0.00 37.61 1.40
2390 2714 1.877443 GTGTGGTAACTTGTGCGGATT 59.123 47.619 0.00 0.00 37.61 3.01
2392 2716 0.533308 GGTGTGGTAACTTGTGCGGA 60.533 55.000 0.00 0.00 37.61 5.54
2407 2737 1.877443 GTAACAATGAACTGCCGGTGT 59.123 47.619 1.90 0.00 0.00 4.16
2663 2996 3.316573 CTTCTCCCCGAGCGCCTTT 62.317 63.158 2.29 0.00 0.00 3.11
2777 3110 0.466739 GGCTGTCCATCATCATGCCA 60.467 55.000 0.00 0.00 38.79 4.92
2894 3227 3.853671 CGAAAAGATGCAACTATTGGTGC 59.146 43.478 10.44 10.44 0.00 5.01
2900 3288 3.081061 TGGCACGAAAAGATGCAACTAT 58.919 40.909 0.00 0.00 43.93 2.12
2903 3291 1.987770 CATGGCACGAAAAGATGCAAC 59.012 47.619 0.00 0.00 43.93 4.17
2906 3294 0.109179 TGCATGGCACGAAAAGATGC 60.109 50.000 0.00 0.00 39.90 3.91
2914 3302 0.322906 TGGGTTAATGCATGGCACGA 60.323 50.000 0.00 0.00 43.04 4.35
2916 3304 1.274728 TGTTGGGTTAATGCATGGCAC 59.725 47.619 0.00 0.00 43.04 5.01
2930 3318 3.614092 AGCTGATGACATAACTGTTGGG 58.386 45.455 2.69 0.00 35.14 4.12
3025 3499 9.657419 ACATTGCATCGATTTACATGATCTATA 57.343 29.630 0.00 0.00 0.00 1.31
3041 3515 3.678915 TGCTCAATGTACATTGCATCG 57.321 42.857 34.12 24.06 45.77 3.84
3177 3729 6.189859 ACATAATTGTGGTCCTGATGAACAT 58.810 36.000 7.15 0.00 44.11 2.71
3179 3731 6.324819 CAACATAATTGTGGTCCTGATGAAC 58.675 40.000 7.15 0.00 35.83 3.18
3184 3736 3.088532 GCCAACATAATTGTGGTCCTGA 58.911 45.455 7.15 0.00 35.83 3.86
3283 3845 2.799978 CGTACACACACACACATGACAT 59.200 45.455 0.00 0.00 0.00 3.06
3313 3879 0.534652 ACGCCCTAGCTAGTCCGTAG 60.535 60.000 25.26 9.14 36.60 3.51
3319 3885 1.265454 AAGCCAACGCCCTAGCTAGT 61.265 55.000 19.31 0.00 34.49 2.57
3320 3886 0.750850 TAAGCCAACGCCCTAGCTAG 59.249 55.000 14.20 14.20 34.49 3.42
3321 3887 1.420430 ATAAGCCAACGCCCTAGCTA 58.580 50.000 0.00 0.00 34.49 3.32
3322 3888 0.546598 AATAAGCCAACGCCCTAGCT 59.453 50.000 0.00 0.00 37.10 3.32
3327 3893 2.573920 TTGGAATAAGCCAACGCCC 58.426 52.632 0.00 0.00 42.75 6.13
3529 4119 5.048643 CCCGGTTAATTTACACATCACACAA 60.049 40.000 0.00 0.00 0.00 3.33
3551 4141 1.133915 TCCACTCAAACACACTTCCCC 60.134 52.381 0.00 0.00 0.00 4.81
3687 4285 1.546476 CTCGGATACCTGCAGGGATAC 59.454 57.143 35.42 32.09 39.37 2.24
3802 4400 1.592669 GCGTGACGATGGAGATGGG 60.593 63.158 10.10 0.00 0.00 4.00
3819 4417 0.527565 ACATGGCAACCGATTGAAGC 59.472 50.000 0.00 0.00 38.15 3.86
4379 5001 2.431771 CGATGTTCACACCGCCGA 60.432 61.111 0.00 0.00 0.00 5.54
4611 5236 1.517257 CAGACGACCGGCAGATCAC 60.517 63.158 0.00 0.00 0.00 3.06
4806 5444 2.873367 CTGCGTACGTATCAGGCAG 58.127 57.895 17.90 19.27 45.21 4.85
4849 5487 4.415332 CGGCAGCCGTACGTGTCT 62.415 66.667 26.69 5.34 42.73 3.41
4933 5575 2.755469 TACGTACTCACCGCCCCC 60.755 66.667 0.00 0.00 0.00 5.40
4934 5576 2.491621 GTACGTACTCACCGCCCC 59.508 66.667 18.47 0.00 0.00 5.80
5037 5696 1.586422 CCCTACACAATCATCCGCTG 58.414 55.000 0.00 0.00 0.00 5.18
5038 5697 0.469917 CCCCTACACAATCATCCGCT 59.530 55.000 0.00 0.00 0.00 5.52
5039 5698 0.468226 TCCCCTACACAATCATCCGC 59.532 55.000 0.00 0.00 0.00 5.54
5051 5710 1.823041 CGAGTCTCCGGTCCCCTAC 60.823 68.421 0.00 0.00 0.00 3.18
5270 5929 7.455008 TCAAGAGGGAAGATAGAAGTACACTTT 59.545 37.037 0.00 0.00 36.11 2.66
5271 5930 6.954684 TCAAGAGGGAAGATAGAAGTACACTT 59.045 38.462 0.00 0.00 39.23 3.16
5281 5940 3.258123 GCCTAGCTCAAGAGGGAAGATAG 59.742 52.174 2.46 0.00 33.04 2.08
5342 6001 6.229936 TCTTATTTGCTATCGGTACTTGGT 57.770 37.500 0.00 0.00 0.00 3.67
5380 6045 0.387202 TTTGTTGGGCGTGATTGTGG 59.613 50.000 0.00 0.00 0.00 4.17
5404 6069 5.451381 CCCGGTGGCCTTTTTATATTTCTTC 60.451 44.000 3.32 0.00 0.00 2.87
5411 6076 2.131776 CACCCGGTGGCCTTTTTATA 57.868 50.000 9.99 0.00 33.59 0.98
5433 6098 3.114065 CCATACGACGGCTTCTTAGTTC 58.886 50.000 0.00 0.00 0.00 3.01
5473 6138 0.905357 ATGGACGCACTCCTAGCTTT 59.095 50.000 0.00 0.00 40.26 3.51
5484 6149 2.123248 TTGGGCTTCTCATGGACGCA 62.123 55.000 12.43 2.40 40.43 5.24
5576 6241 3.206211 TTCCCGCGGCAAGCTTTTG 62.206 57.895 22.85 2.11 45.59 2.44
5590 6255 2.158813 TGGTGATTAAGCGGATCTTCCC 60.159 50.000 0.00 0.00 36.25 3.97


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

AutoCloner maintained by Alex Coulton.