Multiple sequence alignment - TraesCS4A01G049700

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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 TraesCS4A01G049700 chr4A 100.000 3923 0 0 1 3923 40445517 40441595 0.000000e+00 7245
1 TraesCS4A01G049700 chr4D 93.733 2553 99 32 1391 3923 423696175 423698686 0.000000e+00 3771
2 TraesCS4A01G049700 chr4D 87.955 880 45 25 527 1389 423695206 423696041 0.000000e+00 981
3 TraesCS4A01G049700 chr4D 87.500 280 17 5 243 518 423694887 423695152 1.370000e-79 307
4 TraesCS4A01G049700 chr4B 95.058 2327 65 19 1508 3804 520224082 520226388 0.000000e+00 3615
5 TraesCS4A01G049700 chr4B 86.909 1016 44 31 408 1390 520222842 520223801 0.000000e+00 1057
6 TraesCS4A01G049700 chr4B 77.713 341 37 24 3 326 520222509 520222827 5.210000e-39 172
7 TraesCS4A01G049700 chr5B 88.848 816 86 3 1890 2703 38364554 38363742 0.000000e+00 998


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 TraesCS4A01G049700 chr4A 40441595 40445517 3922 True 7245.000000 7245 100.000000 1 3923 1 chr4A.!!$R1 3922
1 TraesCS4A01G049700 chr4D 423694887 423698686 3799 False 1686.333333 3771 89.729333 243 3923 3 chr4D.!!$F1 3680
2 TraesCS4A01G049700 chr4B 520222509 520226388 3879 False 1614.666667 3615 86.560000 3 3804 3 chr4B.!!$F1 3801
3 TraesCS4A01G049700 chr5B 38363742 38364554 812 True 998.000000 998 88.848000 1890 2703 1 chr5B.!!$R1 813

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
65 66 0.179018 GGTGCTGTCCCAAGAACTGT 60.179 55.0 0.0 0.0 0.0 3.55 F
1106 1204 0.309612 TGCCGTTTCGCCTTTCTTTC 59.690 50.0 0.0 0.0 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2028 2337 0.610232 ATTGTTCAGCAGCACCCTCC 60.610 55.0 0.0 0.0 0.0 4.30 R
2979 3292 0.322648 TCACTCCTGTCCACATGCAG 59.677 55.0 0.0 0.0 0.0 4.41 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
62 63 1.168714 GATGGTGCTGTCCCAAGAAC 58.831 55.000 0.00 0.00 35.14 3.01
63 64 0.773644 ATGGTGCTGTCCCAAGAACT 59.226 50.000 0.00 0.00 35.14 3.01
64 65 0.179020 TGGTGCTGTCCCAAGAACTG 60.179 55.000 0.00 0.00 0.00 3.16
65 66 0.179018 GGTGCTGTCCCAAGAACTGT 60.179 55.000 0.00 0.00 0.00 3.55
66 67 1.680338 GTGCTGTCCCAAGAACTGTT 58.320 50.000 0.00 0.00 0.00 3.16
67 68 2.024414 GTGCTGTCCCAAGAACTGTTT 58.976 47.619 0.00 0.00 0.00 2.83
68 69 2.033424 GTGCTGTCCCAAGAACTGTTTC 59.967 50.000 0.00 0.00 0.00 2.78
69 70 2.297701 GCTGTCCCAAGAACTGTTTCA 58.702 47.619 0.00 0.00 33.72 2.69
70 71 2.291741 GCTGTCCCAAGAACTGTTTCAG 59.708 50.000 0.00 0.00 37.52 3.02
71 72 3.808728 CTGTCCCAAGAACTGTTTCAGA 58.191 45.455 3.70 0.00 35.18 3.27
72 73 4.392940 CTGTCCCAAGAACTGTTTCAGAT 58.607 43.478 3.70 0.00 35.18 2.90
73 74 4.136796 TGTCCCAAGAACTGTTTCAGATG 58.863 43.478 3.70 0.00 35.18 2.90
74 75 3.057946 GTCCCAAGAACTGTTTCAGATGC 60.058 47.826 3.70 0.00 35.18 3.91
75 76 3.152341 CCCAAGAACTGTTTCAGATGCT 58.848 45.455 3.70 0.00 35.18 3.79
76 77 3.190118 CCCAAGAACTGTTTCAGATGCTC 59.810 47.826 3.70 0.00 35.18 4.26
77 78 4.070716 CCAAGAACTGTTTCAGATGCTCT 58.929 43.478 3.70 0.00 35.18 4.09
81 82 4.874966 AGAACTGTTTCAGATGCTCTATGC 59.125 41.667 3.70 0.00 37.42 3.14
87 88 7.391554 ACTGTTTCAGATGCTCTATGCTTTTAA 59.608 33.333 3.70 0.00 37.62 1.52
100 101 9.922305 CTCTATGCTTTTAATAACGAGGAAAAG 57.078 33.333 0.00 0.00 40.35 2.27
102 103 6.887626 TGCTTTTAATAACGAGGAAAAGGT 57.112 33.333 7.76 0.00 38.66 3.50
105 106 8.848182 TGCTTTTAATAACGAGGAAAAGGTAAA 58.152 29.630 7.76 0.00 38.66 2.01
112 113 4.529897 ACGAGGAAAAGGTAAAAAGTGGT 58.470 39.130 0.00 0.00 0.00 4.16
116 117 6.465439 AGGAAAAGGTAAAAAGTGGTTCAG 57.535 37.500 0.00 0.00 0.00 3.02
121 122 8.942338 AAAAGGTAAAAAGTGGTTCAGATTTC 57.058 30.769 0.00 0.00 0.00 2.17
127 128 0.804989 GTGGTTCAGATTTCCGCCTG 59.195 55.000 0.00 0.00 0.00 4.85
135 136 2.229784 CAGATTTCCGCCTGCTTCTTTT 59.770 45.455 0.00 0.00 0.00 2.27
137 138 2.507339 TTTCCGCCTGCTTCTTTTTG 57.493 45.000 0.00 0.00 0.00 2.44
139 140 1.909700 TCCGCCTGCTTCTTTTTGAT 58.090 45.000 0.00 0.00 0.00 2.57
140 141 1.812571 TCCGCCTGCTTCTTTTTGATC 59.187 47.619 0.00 0.00 0.00 2.92
141 142 1.541147 CCGCCTGCTTCTTTTTGATCA 59.459 47.619 0.00 0.00 0.00 2.92
143 144 3.367703 CCGCCTGCTTCTTTTTGATCATT 60.368 43.478 0.00 0.00 0.00 2.57
144 145 4.240096 CGCCTGCTTCTTTTTGATCATTT 58.760 39.130 0.00 0.00 0.00 2.32
145 146 5.401550 CGCCTGCTTCTTTTTGATCATTTA 58.598 37.500 0.00 0.00 0.00 1.40
146 147 6.038356 CGCCTGCTTCTTTTTGATCATTTAT 58.962 36.000 0.00 0.00 0.00 1.40
148 149 7.701924 CGCCTGCTTCTTTTTGATCATTTATTA 59.298 33.333 0.00 0.00 0.00 0.98
149 150 8.811378 GCCTGCTTCTTTTTGATCATTTATTAC 58.189 33.333 0.00 0.00 0.00 1.89
196 212 6.889301 AATGCGATGTGGATATTTGATCTT 57.111 33.333 0.00 0.00 0.00 2.40
202 218 5.823209 TGTGGATATTTGATCTTGCTGTG 57.177 39.130 0.00 0.00 0.00 3.66
204 220 5.124297 TGTGGATATTTGATCTTGCTGTGTG 59.876 40.000 0.00 0.00 0.00 3.82
210 226 2.518836 GATCTTGCTGTGTGCCGTGC 62.519 60.000 0.00 0.00 42.00 5.34
212 228 3.531920 CTTGCTGTGTGCCGTGCTG 62.532 63.158 0.00 0.00 42.00 4.41
239 255 2.171448 GTCAGCCTGTCAGGGTATCATT 59.829 50.000 22.96 0.00 45.88 2.57
240 256 2.435805 TCAGCCTGTCAGGGTATCATTC 59.564 50.000 22.96 2.06 45.88 2.67
241 257 2.171237 CAGCCTGTCAGGGTATCATTCA 59.829 50.000 22.96 0.00 45.88 2.57
250 266 2.146342 GGGTATCATTCATCAGTGGCG 58.854 52.381 0.00 0.00 0.00 5.69
276 292 1.505425 GTGTTGTCCGGTACCAGAAC 58.495 55.000 13.54 8.89 0.00 3.01
359 375 1.445095 GCATCAGGAGCGGATGACT 59.555 57.895 12.71 0.00 43.80 3.41
364 380 2.107953 GGAGCGGATGACTGGAGC 59.892 66.667 0.00 0.00 0.00 4.70
368 384 2.580815 CGGATGACTGGAGCTGCA 59.419 61.111 7.99 7.99 0.00 4.41
372 388 1.367659 GATGACTGGAGCTGCAGTTC 58.632 55.000 36.94 28.04 0.00 3.01
390 406 5.402568 GCAGTTCGCGATAAGAATATCTGAA 59.597 40.000 10.88 0.00 36.55 3.02
395 411 4.324669 CGCGATAAGAATATCTGAACGCAT 59.675 41.667 16.42 0.00 39.66 4.73
396 412 5.511729 CGCGATAAGAATATCTGAACGCATA 59.488 40.000 16.42 0.00 39.66 3.14
398 414 7.253783 CGCGATAAGAATATCTGAACGCATAAT 60.254 37.037 16.42 0.00 39.66 1.28
399 415 7.843204 GCGATAAGAATATCTGAACGCATAATG 59.157 37.037 12.76 0.00 39.57 1.90
400 416 9.076596 CGATAAGAATATCTGAACGCATAATGA 57.923 33.333 0.00 0.00 36.55 2.57
402 418 7.426929 AAGAATATCTGAACGCATAATGACC 57.573 36.000 0.00 0.00 0.00 4.02
403 419 6.524734 AGAATATCTGAACGCATAATGACCA 58.475 36.000 0.00 0.00 0.00 4.02
404 420 6.648310 AGAATATCTGAACGCATAATGACCAG 59.352 38.462 0.00 0.00 0.00 4.00
405 421 3.610040 TCTGAACGCATAATGACCAGT 57.390 42.857 0.00 0.00 0.00 4.00
406 422 4.729227 TCTGAACGCATAATGACCAGTA 57.271 40.909 0.00 0.00 0.00 2.74
407 423 4.682787 TCTGAACGCATAATGACCAGTAG 58.317 43.478 0.00 0.00 0.00 2.57
412 428 3.702548 ACGCATAATGACCAGTAGTACCA 59.297 43.478 0.00 0.00 0.00 3.25
608 674 1.758862 AGCTGCCAGCAAAGTTTTTCT 59.241 42.857 20.53 0.00 45.56 2.52
719 785 0.465460 TGCTTCGCTGGGTTTCAACT 60.465 50.000 0.00 0.00 0.00 3.16
720 786 0.668535 GCTTCGCTGGGTTTCAACTT 59.331 50.000 0.00 0.00 0.00 2.66
721 787 1.067060 GCTTCGCTGGGTTTCAACTTT 59.933 47.619 0.00 0.00 0.00 2.66
722 788 2.858646 GCTTCGCTGGGTTTCAACTTTC 60.859 50.000 0.00 0.00 0.00 2.62
723 789 2.045561 TCGCTGGGTTTCAACTTTCA 57.954 45.000 0.00 0.00 0.00 2.69
724 790 2.370349 TCGCTGGGTTTCAACTTTCAA 58.630 42.857 0.00 0.00 0.00 2.69
725 791 2.098443 TCGCTGGGTTTCAACTTTCAAC 59.902 45.455 0.00 0.00 0.00 3.18
731 797 3.951680 GGGTTTCAACTTTCAACAGAGGA 59.048 43.478 0.00 0.00 0.00 3.71
778 844 4.692475 CGCCGTTTCCCCCGAGTT 62.692 66.667 0.00 0.00 0.00 3.01
779 845 2.664398 GCCGTTTCCCCCGAGTTA 59.336 61.111 0.00 0.00 0.00 2.24
780 846 1.003476 GCCGTTTCCCCCGAGTTAA 60.003 57.895 0.00 0.00 0.00 2.01
781 847 0.393402 GCCGTTTCCCCCGAGTTAAT 60.393 55.000 0.00 0.00 0.00 1.40
782 848 1.134431 GCCGTTTCCCCCGAGTTAATA 60.134 52.381 0.00 0.00 0.00 0.98
918 985 1.000771 GCCCTTCTCTTTCCCACCC 60.001 63.158 0.00 0.00 0.00 4.61
919 986 1.501654 GCCCTTCTCTTTCCCACCCT 61.502 60.000 0.00 0.00 0.00 4.34
1068 1166 1.304952 CGAGGAGGTCCAGGAGTCT 59.695 63.158 0.00 0.00 38.89 3.24
1101 1199 4.025401 CGCTGCCGTTTCGCCTTT 62.025 61.111 0.00 0.00 0.00 3.11
1102 1200 2.126850 GCTGCCGTTTCGCCTTTC 60.127 61.111 0.00 0.00 0.00 2.62
1105 1203 0.310854 CTGCCGTTTCGCCTTTCTTT 59.689 50.000 0.00 0.00 0.00 2.52
1106 1204 0.309612 TGCCGTTTCGCCTTTCTTTC 59.690 50.000 0.00 0.00 0.00 2.62
1155 1260 9.244799 GTTCTTATGGATCTCGTTTTTGTTTTT 57.755 29.630 0.00 0.00 0.00 1.94
1192 1297 1.583054 GCAGGATGGAATCGGTGTAC 58.417 55.000 0.00 0.00 46.86 2.90
1438 1678 5.939883 AGTCATTGTGCTGAAATACTGCTTA 59.060 36.000 0.00 0.00 42.58 3.09
1474 1782 4.968719 TGTAGATGTGGGTGTGATTAGGAT 59.031 41.667 0.00 0.00 0.00 3.24
1478 1786 5.608437 AGATGTGGGTGTGATTAGGATGTAT 59.392 40.000 0.00 0.00 0.00 2.29
1484 1792 5.462405 GGTGTGATTAGGATGTATCGAGTC 58.538 45.833 0.00 0.00 0.00 3.36
1488 1796 6.490040 TGTGATTAGGATGTATCGAGTCATGA 59.510 38.462 9.34 0.00 0.00 3.07
1504 1812 4.020307 AGTCATGAAAAATTGCCCCGAAAT 60.020 37.500 0.00 0.00 0.00 2.17
1505 1813 5.186797 AGTCATGAAAAATTGCCCCGAAATA 59.813 36.000 0.00 0.00 0.00 1.40
1506 1814 5.290885 GTCATGAAAAATTGCCCCGAAATAC 59.709 40.000 0.00 0.00 0.00 1.89
1513 1822 3.426787 TTGCCCCGAAATACTGAAGAA 57.573 42.857 0.00 0.00 0.00 2.52
1523 1832 6.090898 CCGAAATACTGAAGAAGTTGGTACAG 59.909 42.308 0.00 0.00 42.39 2.74
1647 1956 2.294791 GGATACGAGAGCACTGCATAGT 59.705 50.000 3.30 0.92 37.75 2.12
1758 2067 3.004524 GCTGGATTCATTTGGATGAGAGC 59.995 47.826 0.00 0.00 42.90 4.09
1783 2092 4.736896 ACGACCTCGCGGCTTTCC 62.737 66.667 6.13 0.00 44.43 3.13
1809 2118 1.952367 GCAACCCCTCCTCAACATCAG 60.952 57.143 0.00 0.00 0.00 2.90
1830 2139 5.878116 TCAGGATAAAGTTGTTACAATCCCG 59.122 40.000 10.10 2.32 33.87 5.14
2481 2794 1.065102 CGGCCTGCTCAATTGATTCTG 59.935 52.381 8.96 7.95 0.00 3.02
2669 2982 0.451783 CATTGCGCCCTAAGTTGGTC 59.548 55.000 4.18 0.00 0.00 4.02
2672 2985 0.321298 TGCGCCCTAAGTTGGTCTTC 60.321 55.000 4.18 0.00 37.56 2.87
2821 3134 8.991783 AAGTGATGACTTGATCCAATCATAAT 57.008 30.769 0.00 0.00 41.12 1.28
2832 3145 9.713684 TTGATCCAATCATAATTTTCTTAGGGT 57.286 29.630 0.00 0.00 39.39 4.34
2833 3146 9.354673 TGATCCAATCATAATTTTCTTAGGGTC 57.645 33.333 0.00 0.00 33.59 4.46
2834 3147 7.801716 TCCAATCATAATTTTCTTAGGGTCG 57.198 36.000 0.00 0.00 0.00 4.79
2835 3148 6.262273 TCCAATCATAATTTTCTTAGGGTCGC 59.738 38.462 0.00 0.00 0.00 5.19
2836 3149 6.438763 CAATCATAATTTTCTTAGGGTCGCC 58.561 40.000 0.00 0.00 0.00 5.54
2837 3150 5.105567 TCATAATTTTCTTAGGGTCGCCA 57.894 39.130 0.00 0.00 0.00 5.69
2838 3151 4.879545 TCATAATTTTCTTAGGGTCGCCAC 59.120 41.667 0.00 0.00 0.00 5.01
2839 3152 3.434940 AATTTTCTTAGGGTCGCCACT 57.565 42.857 0.00 0.00 0.00 4.00
2840 3153 2.943036 TTTTCTTAGGGTCGCCACTT 57.057 45.000 0.00 0.00 0.00 3.16
2841 3154 4.563140 ATTTTCTTAGGGTCGCCACTTA 57.437 40.909 0.00 0.00 0.00 2.24
2854 3167 5.971202 GGTCGCCACTTATTATTCAATGTTG 59.029 40.000 0.00 0.00 0.00 3.33
2946 3259 0.527113 TTTGCATGGGCTCGTGATTG 59.473 50.000 10.85 0.00 41.91 2.67
2979 3292 2.301346 CCCCACCAGATCAGCATAAAC 58.699 52.381 0.00 0.00 0.00 2.01
3097 3410 1.438651 GAGCAATTCACCACGCTACA 58.561 50.000 0.00 0.00 34.12 2.74
3142 3455 0.178068 GGATATGCACTGGACGGTGT 59.822 55.000 12.43 0.00 39.21 4.16
3143 3456 1.290203 GATATGCACTGGACGGTGTG 58.710 55.000 12.43 0.00 39.21 3.82
3144 3457 0.613260 ATATGCACTGGACGGTGTGT 59.387 50.000 12.43 4.85 39.21 3.72
3146 3459 3.649986 GCACTGGACGGTGTGTGC 61.650 66.667 12.43 11.87 46.66 4.57
3147 3460 3.337889 CACTGGACGGTGTGTGCG 61.338 66.667 3.12 0.00 42.78 5.34
3168 3487 4.168760 CGCGCATGATGTATCTCAAGATA 58.831 43.478 8.75 0.00 36.05 1.98
3192 3511 2.766263 AGTTCTCACAGTGACCAGTTGA 59.234 45.455 0.00 0.00 0.00 3.18
3225 3544 3.153919 TGGTATGCCCTGAACTTCAAAC 58.846 45.455 0.00 0.00 0.00 2.93
3258 3577 2.009042 GCACTAGTGGTCATGCAGGTC 61.009 57.143 23.95 0.00 38.00 3.85
3259 3578 1.276138 CACTAGTGGTCATGCAGGTCA 59.724 52.381 15.49 0.00 0.00 4.02
3260 3579 1.552337 ACTAGTGGTCATGCAGGTCAG 59.448 52.381 0.00 0.00 0.00 3.51
3261 3580 0.904649 TAGTGGTCATGCAGGTCAGG 59.095 55.000 0.00 0.00 0.00 3.86
3262 3581 1.130054 AGTGGTCATGCAGGTCAGGT 61.130 55.000 0.00 0.00 0.00 4.00
3270 3589 1.743252 GCAGGTCAGGTGCAGCTAC 60.743 63.158 19.71 15.93 40.86 3.58
3277 3596 0.035317 CAGGTGCAGCTACCAACAGA 59.965 55.000 19.71 0.00 43.37 3.41
3283 3602 1.541147 GCAGCTACCAACAGAAATGCA 59.459 47.619 0.00 0.00 32.79 3.96
3633 3952 9.139174 CATAAAAAGCCATAAACTGGTTTGTAG 57.861 33.333 8.73 0.00 46.70 2.74
3704 4043 0.959372 CCAGCCCTGTTGCTCTCTTG 60.959 60.000 0.00 0.00 40.32 3.02
3804 4148 4.523943 TGCAGTCAAGCACCTCAAATAAAT 59.476 37.500 0.00 0.00 40.11 1.40
3808 4152 7.761249 GCAGTCAAGCACCTCAAATAAATAAAT 59.239 33.333 0.00 0.00 0.00 1.40
3893 4237 5.121611 TGTCGTGCTATTTGGTAGACAATTG 59.878 40.000 3.24 3.24 39.21 2.32
3914 4258 9.226606 CAATTGTACTTACTGAAACCCAATAGA 57.773 33.333 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.891366 CACAAAACTGGGACCTGATTTCT 59.109 43.478 2.02 0.00 0.00 2.52
3 4 3.005791 CCACAAAACTGGGACCTGATTTC 59.994 47.826 2.02 0.00 0.00 2.17
5 6 2.597455 CCACAAAACTGGGACCTGATT 58.403 47.619 2.02 0.00 0.00 2.57
6 7 2.292828 CCACAAAACTGGGACCTGAT 57.707 50.000 2.02 0.00 0.00 2.90
7 8 3.819245 CCACAAAACTGGGACCTGA 57.181 52.632 2.02 0.00 0.00 3.86
14 15 1.133482 AGGAAGACCCCACAAAACTGG 60.133 52.381 0.00 0.00 36.73 4.00
15 16 1.956477 CAGGAAGACCCCACAAAACTG 59.044 52.381 0.00 0.00 36.73 3.16
16 17 1.569072 ACAGGAAGACCCCACAAAACT 59.431 47.619 0.00 0.00 36.73 2.66
26 27 2.162681 CATCCCAACAACAGGAAGACC 58.837 52.381 0.00 0.00 35.30 3.85
73 74 7.478520 TTCCTCGTTATTAAAAGCATAGAGC 57.521 36.000 0.00 0.00 46.19 4.09
74 75 9.922305 CTTTTCCTCGTTATTAAAAGCATAGAG 57.078 33.333 0.00 0.00 33.60 2.43
75 76 8.889717 CCTTTTCCTCGTTATTAAAAGCATAGA 58.110 33.333 0.00 0.00 37.52 1.98
76 77 8.674607 ACCTTTTCCTCGTTATTAAAAGCATAG 58.325 33.333 0.00 0.00 37.52 2.23
77 78 8.570068 ACCTTTTCCTCGTTATTAAAAGCATA 57.430 30.769 0.00 0.00 37.52 3.14
87 88 6.774170 ACCACTTTTTACCTTTTCCTCGTTAT 59.226 34.615 0.00 0.00 0.00 1.89
91 92 5.066764 TGAACCACTTTTTACCTTTTCCTCG 59.933 40.000 0.00 0.00 0.00 4.63
100 101 5.458015 CGGAAATCTGAACCACTTTTTACC 58.542 41.667 0.00 0.00 0.00 2.85
102 103 4.022676 GGCGGAAATCTGAACCACTTTTTA 60.023 41.667 0.00 0.00 0.00 1.52
105 106 1.886542 GGCGGAAATCTGAACCACTTT 59.113 47.619 0.00 0.00 0.00 2.66
112 113 1.003580 AGAAGCAGGCGGAAATCTGAA 59.996 47.619 0.00 0.00 33.11 3.02
116 117 2.989166 CAAAAAGAAGCAGGCGGAAATC 59.011 45.455 0.00 0.00 0.00 2.17
121 122 1.541147 TGATCAAAAAGAAGCAGGCGG 59.459 47.619 0.00 0.00 0.00 6.13
167 178 8.791327 TCAAATATCCACATCGCATTATACAT 57.209 30.769 0.00 0.00 0.00 2.29
169 180 9.102757 AGATCAAATATCCACATCGCATTATAC 57.897 33.333 0.00 0.00 0.00 1.47
170 181 9.671279 AAGATCAAATATCCACATCGCATTATA 57.329 29.630 0.00 0.00 0.00 0.98
182 193 4.096833 GCACACAGCAAGATCAAATATCCA 59.903 41.667 0.00 0.00 44.79 3.41
202 218 2.027625 GACACTACCAGCACGGCAC 61.028 63.158 0.00 0.00 39.03 5.01
204 220 1.738099 CTGACACTACCAGCACGGC 60.738 63.158 0.00 0.00 39.03 5.68
210 226 0.969149 TGACAGGCTGACACTACCAG 59.031 55.000 23.66 0.00 34.88 4.00
212 228 0.247736 CCTGACAGGCTGACACTACC 59.752 60.000 23.66 1.70 0.00 3.18
233 249 3.721035 CAGACGCCACTGATGAATGATA 58.279 45.455 0.00 0.00 39.94 2.15
250 266 3.041940 CCGGACAACACGGCAGAC 61.042 66.667 0.00 0.00 45.34 3.51
260 276 2.253610 AGATGTTCTGGTACCGGACAA 58.746 47.619 23.57 14.41 0.00 3.18
355 371 1.005748 CGAACTGCAGCTCCAGTCA 60.006 57.895 11.57 0.00 44.86 3.41
359 375 1.944234 TATCGCGAACTGCAGCTCCA 61.944 55.000 15.24 0.00 46.97 3.86
364 380 4.920340 AGATATTCTTATCGCGAACTGCAG 59.080 41.667 15.24 13.48 46.97 4.41
368 384 5.625721 CGTTCAGATATTCTTATCGCGAACT 59.374 40.000 15.24 0.00 42.51 3.01
372 388 3.668656 TGCGTTCAGATATTCTTATCGCG 59.331 43.478 0.00 0.00 39.42 5.87
390 406 3.702548 TGGTACTACTGGTCATTATGCGT 59.297 43.478 0.00 0.00 0.00 5.24
395 411 5.720041 AGCTTTCTGGTACTACTGGTCATTA 59.280 40.000 0.00 0.00 0.00 1.90
396 412 4.532521 AGCTTTCTGGTACTACTGGTCATT 59.467 41.667 0.00 0.00 0.00 2.57
398 414 3.258372 CAGCTTTCTGGTACTACTGGTCA 59.742 47.826 0.00 0.00 36.68 4.02
399 415 3.851098 CAGCTTTCTGGTACTACTGGTC 58.149 50.000 0.00 0.00 36.68 4.02
400 416 3.963428 CAGCTTTCTGGTACTACTGGT 57.037 47.619 0.00 0.00 36.68 4.00
412 428 4.768583 CTTATCTCTTGCTCCAGCTTTCT 58.231 43.478 0.00 0.00 42.66 2.52
497 519 3.744719 CCGACGGCGACCTCAAGA 61.745 66.667 15.16 0.00 40.82 3.02
534 575 0.818445 GCAGGTGCTGATCTGGATGG 60.818 60.000 1.46 0.00 38.21 3.51
557 623 2.527624 TGCTGTGCCCCTCTCTGT 60.528 61.111 0.00 0.00 0.00 3.41
608 674 2.938838 TCGCCCCTCAGAAAAGAAAAA 58.061 42.857 0.00 0.00 0.00 1.94
719 785 4.263068 GGATGTTCCTCTCCTCTGTTGAAA 60.263 45.833 0.00 0.00 32.53 2.69
720 786 3.261897 GGATGTTCCTCTCCTCTGTTGAA 59.738 47.826 0.00 0.00 32.53 2.69
721 787 2.834549 GGATGTTCCTCTCCTCTGTTGA 59.165 50.000 0.00 0.00 32.53 3.18
722 788 2.836981 AGGATGTTCCTCTCCTCTGTTG 59.163 50.000 0.00 0.00 45.66 3.33
723 789 2.836981 CAGGATGTTCCTCTCCTCTGTT 59.163 50.000 0.00 0.00 45.66 3.16
724 790 2.465813 CAGGATGTTCCTCTCCTCTGT 58.534 52.381 0.00 0.00 45.66 3.41
778 844 8.836413 GCTGGCGGCTATTTATTGATTATATTA 58.164 33.333 11.99 0.00 38.06 0.98
779 845 7.201821 GGCTGGCGGCTATTTATTGATTATATT 60.202 37.037 19.30 0.00 41.46 1.28
780 846 6.263168 GGCTGGCGGCTATTTATTGATTATAT 59.737 38.462 19.30 0.00 41.46 0.86
781 847 5.588648 GGCTGGCGGCTATTTATTGATTATA 59.411 40.000 19.30 0.00 41.46 0.98
782 848 4.399303 GGCTGGCGGCTATTTATTGATTAT 59.601 41.667 19.30 0.00 41.46 1.28
918 985 2.978010 ACCTTTGCGGTTGCGGAG 60.978 61.111 0.00 0.00 46.37 4.63
1005 1103 3.164011 CAGCGGTCGAACGACGTC 61.164 66.667 29.97 8.82 45.41 4.34
1101 1199 6.163135 ACCGAAGAAGAAGAAGAAGAAAGA 57.837 37.500 0.00 0.00 0.00 2.52
1102 1200 6.073494 GGAACCGAAGAAGAAGAAGAAGAAAG 60.073 42.308 0.00 0.00 0.00 2.62
1105 1203 4.558898 CGGAACCGAAGAAGAAGAAGAAGA 60.559 45.833 7.53 0.00 42.83 2.87
1106 1204 3.675698 CGGAACCGAAGAAGAAGAAGAAG 59.324 47.826 7.53 0.00 42.83 2.85
1155 1260 1.372499 CGAGGTCGCGAACAGGAAA 60.372 57.895 28.31 0.00 0.00 3.13
1168 1273 1.443407 CGATTCCATCCTGCGAGGT 59.557 57.895 0.00 0.00 36.53 3.85
1192 1297 2.224475 CCTCTCCTGCACCCATATCTTG 60.224 54.545 0.00 0.00 0.00 3.02
1389 1494 7.639113 TGTAAGCAGAAGAAAGGAAAGAAAA 57.361 32.000 0.00 0.00 0.00 2.29
1425 1665 7.452880 AAATGCAGTCTTAAGCAGTATTTCA 57.547 32.000 0.00 0.00 44.94 2.69
1426 1666 9.443283 CATAAATGCAGTCTTAAGCAGTATTTC 57.557 33.333 15.34 0.00 44.94 2.17
1438 1678 5.824624 CCCACATCTACATAAATGCAGTCTT 59.175 40.000 0.00 0.00 0.00 3.01
1474 1782 5.163663 GGGCAATTTTTCATGACTCGATACA 60.164 40.000 0.00 0.00 0.00 2.29
1478 1786 2.491693 GGGGCAATTTTTCATGACTCGA 59.508 45.455 0.00 0.00 0.00 4.04
1484 1792 5.291614 CAGTATTTCGGGGCAATTTTTCATG 59.708 40.000 0.00 0.00 0.00 3.07
1488 1796 5.245075 TCTTCAGTATTTCGGGGCAATTTTT 59.755 36.000 0.00 0.00 0.00 1.94
1504 1812 4.502604 GCACCTGTACCAACTTCTTCAGTA 60.503 45.833 0.00 0.00 32.94 2.74
1505 1813 3.744530 GCACCTGTACCAACTTCTTCAGT 60.745 47.826 0.00 0.00 37.30 3.41
1506 1814 2.808543 GCACCTGTACCAACTTCTTCAG 59.191 50.000 0.00 0.00 0.00 3.02
1513 1822 1.136828 TGAAGGCACCTGTACCAACT 58.863 50.000 0.00 0.00 0.00 3.16
1523 1832 1.202818 AGGTTCTGAGTTGAAGGCACC 60.203 52.381 0.00 0.00 0.00 5.01
1647 1956 1.068885 CCAATCGCCGCAACAAAGTTA 60.069 47.619 0.00 0.00 0.00 2.24
1783 2092 1.500474 TGAGGAGGGGTTGCAGATAG 58.500 55.000 0.00 0.00 0.00 2.08
1809 2118 5.878669 AGACGGGATTGTAACAACTTTATCC 59.121 40.000 0.00 0.00 0.00 2.59
1830 2139 1.202580 ACCTGAATATCGCCAGCAGAC 60.203 52.381 0.00 0.00 0.00 3.51
1863 2172 5.945784 TGAGATATTTTTCCTCACCCTTGTG 59.054 40.000 0.00 0.00 44.18 3.33
2028 2337 0.610232 ATTGTTCAGCAGCACCCTCC 60.610 55.000 0.00 0.00 0.00 4.30
2088 2397 1.237954 TTGGCAATCCGCACGCTTTA 61.238 50.000 0.00 0.00 45.17 1.85
2481 2794 2.849880 TGAGAACAGCAAGTGCAAAC 57.150 45.000 6.00 0.00 45.16 2.93
2669 2982 4.396166 GTGTGGTGGAATGTGGAATAGAAG 59.604 45.833 0.00 0.00 0.00 2.85
2672 2985 3.684908 TGTGTGGTGGAATGTGGAATAG 58.315 45.455 0.00 0.00 0.00 1.73
2747 3060 5.774498 ACTCAAAATTCACCTGAAACTCC 57.226 39.130 0.00 0.00 37.61 3.85
2757 3070 7.985634 TGCAAGTTTTCTACTCAAAATTCAC 57.014 32.000 0.00 0.00 35.54 3.18
2821 3134 2.943036 AAGTGGCGACCCTAAGAAAA 57.057 45.000 0.00 0.00 0.00 2.29
2829 3142 4.578928 ACATTGAATAATAAGTGGCGACCC 59.421 41.667 0.00 0.00 0.00 4.46
2830 3143 5.751243 ACATTGAATAATAAGTGGCGACC 57.249 39.130 0.00 0.00 0.00 4.79
2831 3144 6.551736 ACAACATTGAATAATAAGTGGCGAC 58.448 36.000 0.00 0.00 0.00 5.19
2832 3145 6.751514 ACAACATTGAATAATAAGTGGCGA 57.248 33.333 0.00 0.00 0.00 5.54
2833 3146 9.594038 GTATACAACATTGAATAATAAGTGGCG 57.406 33.333 0.00 0.00 0.00 5.69
2841 3154 9.905713 AGGTGTGAGTATACAACATTGAATAAT 57.094 29.630 12.81 0.00 40.72 1.28
2854 3167 7.871463 ACAAGAAACAGTAAGGTGTGAGTATAC 59.129 37.037 0.00 0.00 0.00 1.47
2863 3176 6.289064 AGGAAGTACAAGAAACAGTAAGGTG 58.711 40.000 0.00 0.00 0.00 4.00
2979 3292 0.322648 TCACTCCTGTCCACATGCAG 59.677 55.000 0.00 0.00 0.00 4.41
3017 3330 1.672356 AGTCTGCCATGGTTCGCAC 60.672 57.895 14.67 3.61 0.00 5.34
3020 3333 1.197721 GAAACAGTCTGCCATGGTTCG 59.802 52.381 14.67 2.05 33.77 3.95
3050 3363 7.062605 ACGATCATTCTTCATTTGTTTCAATGC 59.937 33.333 0.00 0.00 0.00 3.56
3142 3455 0.530431 AGATACATCATGCGCGCACA 60.530 50.000 39.05 26.64 0.00 4.57
3143 3456 0.162507 GAGATACATCATGCGCGCAC 59.837 55.000 39.05 21.15 0.00 5.34
3144 3457 0.249405 TGAGATACATCATGCGCGCA 60.249 50.000 38.27 38.27 0.00 6.09
3146 3459 2.397549 TCTTGAGATACATCATGCGCG 58.602 47.619 0.00 0.00 0.00 6.86
3147 3460 5.809051 TGATATCTTGAGATACATCATGCGC 59.191 40.000 0.00 0.00 39.57 6.09
3154 3473 9.140874 TGTGAGAACTGATATCTTGAGATACAT 57.859 33.333 3.98 0.00 39.57 2.29
3168 3487 2.968574 ACTGGTCACTGTGAGAACTGAT 59.031 45.455 11.41 0.00 0.00 2.90
3192 3511 3.023832 GGGCATACCATTAAGCACAAGT 58.976 45.455 0.00 0.00 39.85 3.16
3225 3544 1.759445 ACTAGTGCAGCATGACCCTAG 59.241 52.381 13.10 13.10 39.69 3.02
3258 3577 0.035317 TCTGTTGGTAGCTGCACCTG 59.965 55.000 17.81 8.94 39.50 4.00
3259 3578 0.764890 TTCTGTTGGTAGCTGCACCT 59.235 50.000 17.81 0.00 39.50 4.00
3260 3579 1.604604 TTTCTGTTGGTAGCTGCACC 58.395 50.000 3.61 8.30 39.20 5.01
3261 3580 2.669391 GCATTTCTGTTGGTAGCTGCAC 60.669 50.000 3.61 0.00 0.00 4.57
3262 3581 1.541147 GCATTTCTGTTGGTAGCTGCA 59.459 47.619 3.61 0.00 0.00 4.41
3270 3589 1.962807 TCCCAGTTGCATTTCTGTTGG 59.037 47.619 11.28 7.65 0.00 3.77
3277 3596 1.526575 CGGCACTCCCAGTTGCATTT 61.527 55.000 0.00 0.00 0.00 2.32
3283 3602 2.743718 CAGTCGGCACTCCCAGTT 59.256 61.111 0.00 0.00 0.00 3.16
3633 3952 0.033781 CAGGAGCTAGAGATGCCAGC 59.966 60.000 0.00 0.00 35.49 4.85
3734 4078 1.134848 GGTTGCAGCACCTTGACAAAA 60.135 47.619 2.05 0.00 33.50 2.44
3740 4084 1.521450 CTCCTGGTTGCAGCACCTTG 61.521 60.000 8.97 2.43 37.75 3.61
3804 4148 5.223449 CAGGAGTCCCGGCTATTTATTTA 57.777 43.478 5.25 0.00 37.58 1.40
3861 4205 8.198778 TCTACCAAATAGCACGACAACATTATA 58.801 33.333 0.00 0.00 0.00 0.98
3862 4206 7.011109 GTCTACCAAATAGCACGACAACATTAT 59.989 37.037 0.00 0.00 0.00 1.28
3863 4207 6.311935 GTCTACCAAATAGCACGACAACATTA 59.688 38.462 0.00 0.00 0.00 1.90
3864 4208 5.121768 GTCTACCAAATAGCACGACAACATT 59.878 40.000 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.