Multiple sequence alignment - TraesCS4D01G348200

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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 TraesCS4D01G348200 chr4D 100.000 3719 0 0 1 3719 502032697 502036415 0.000000e+00 6868.0
1 TraesCS4D01G348200 chr4D 92.593 54 4 0 756 809 441512354 441512301 1.110000e-10 78.7
2 TraesCS4D01G348200 chr4D 83.133 83 9 3 756 833 401206826 401206908 1.850000e-08 71.3
3 TraesCS4D01G348200 chr5A 95.675 2890 104 9 837 3719 684687190 684690065 0.000000e+00 4625.0
4 TraesCS4D01G348200 chr5A 93.538 1300 75 1 978 2277 661197462 661198752 0.000000e+00 1927.0
5 TraesCS4D01G348200 chr5A 96.429 756 26 1 2275 3030 661207173 661207927 0.000000e+00 1245.0
6 TraesCS4D01G348200 chr5A 93.390 711 40 5 3013 3719 661208275 661208982 0.000000e+00 1046.0
7 TraesCS4D01G348200 chr5A 84.405 731 76 18 1 723 661194728 661195428 0.000000e+00 684.0
8 TraesCS4D01G348200 chr5A 78.010 382 43 23 398 746 684686817 684687190 6.300000e-48 202.0
9 TraesCS4D01G348200 chr5A 88.372 129 8 2 834 955 661195479 661195607 8.320000e-32 148.0
10 TraesCS4D01G348200 chr5A 84.146 82 8 4 756 833 125278268 125278188 1.430000e-09 75.0
11 TraesCS4D01G348200 chr4B 89.979 2884 198 38 872 3719 646137443 646140271 0.000000e+00 3640.0
12 TraesCS4D01G348200 chr7A 86.250 80 9 2 756 833 536511230 536511309 6.620000e-13 86.1
13 TraesCS4D01G348200 chr1D 87.671 73 8 1 756 827 24862827 24862755 2.380000e-12 84.2
14 TraesCS4D01G348200 chr3B 83.750 80 9 4 756 833 219489658 219489581 5.150000e-09 73.1
15 TraesCS4D01G348200 chr3B 82.500 80 10 4 756 833 218003865 218003788 2.400000e-07 67.6
16 TraesCS4D01G348200 chr4A 82.895 76 9 2 756 830 658744839 658744911 8.620000e-07 65.8
17 TraesCS4D01G348200 chr4A 82.895 76 9 2 756 830 658791304 658791376 8.620000e-07 65.8


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 TraesCS4D01G348200 chr4D 502032697 502036415 3718 False 6868.000000 6868 100.000000 1 3719 1 chr4D.!!$F2 3718
1 TraesCS4D01G348200 chr5A 684686817 684690065 3248 False 2413.500000 4625 86.842500 398 3719 2 chr5A.!!$F3 3321
2 TraesCS4D01G348200 chr5A 661207173 661208982 1809 False 1145.500000 1245 94.909500 2275 3719 2 chr5A.!!$F2 1444
3 TraesCS4D01G348200 chr5A 661194728 661198752 4024 False 919.666667 1927 88.771667 1 2277 3 chr5A.!!$F1 2276
4 TraesCS4D01G348200 chr4B 646137443 646140271 2828 False 3640.000000 3640 89.979000 872 3719 1 chr4B.!!$F1 2847

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
316 320 0.038744 CCAGAACACAAGGCATCCCT 59.961 55.0 0.0 0.0 45.77 4.20 F
1752 3651 0.107993 ACATGAGGTGCGGAGATGTG 60.108 55.0 0.0 0.0 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2243 4142 0.040204 AAGGTCCCATTTCCCAGCAG 59.960 55.000 0.00 0.0 0.0 4.24 R
3327 5614 1.414181 CAGCTCCACGGATTCCATAGT 59.586 52.381 3.09 0.0 0.0 2.12 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
22 23 2.751259 GGGTTCGGTTCATTTCCTAACC 59.249 50.000 9.07 9.07 44.73 2.85
29 30 5.878116 TCGGTTCATTTCCTAACCACTATTG 59.122 40.000 5.21 0.00 44.49 1.90
33 34 7.812669 GGTTCATTTCCTAACCACTATTGTTTG 59.187 37.037 0.00 0.00 43.84 2.93
35 36 8.106247 TCATTTCCTAACCACTATTGTTTGTC 57.894 34.615 0.00 0.00 0.00 3.18
43 44 4.215399 ACCACTATTGTTTGTCCAATCACG 59.785 41.667 0.00 0.00 36.48 4.35
45 46 3.818210 ACTATTGTTTGTCCAATCACGCA 59.182 39.130 0.00 0.00 36.48 5.24
56 57 5.163513 GTCCAATCACGCAAATCAATCTTT 58.836 37.500 0.00 0.00 0.00 2.52
79 80 1.388547 TTTTTGCTTCCGCTGACAGT 58.611 45.000 3.99 0.00 36.97 3.55
80 81 2.248280 TTTTGCTTCCGCTGACAGTA 57.752 45.000 3.99 0.00 36.97 2.74
102 104 2.875102 TTGAGAGGAGATGGGATCCA 57.125 50.000 15.23 0.00 39.47 3.41
118 120 6.183347 TGGGATCCAGAAAAGAAGAGATTTC 58.817 40.000 15.23 0.00 36.11 2.17
122 124 9.454859 GGATCCAGAAAAGAAGAGATTTCTTTA 57.545 33.333 6.95 1.23 45.07 1.85
127 129 9.771915 CAGAAAAGAAGAGATTTCTTTATCTGC 57.228 33.333 22.84 11.68 45.07 4.26
128 130 9.737844 AGAAAAGAAGAGATTTCTTTATCTGCT 57.262 29.630 13.44 5.91 45.07 4.24
132 134 9.512588 AAGAAGAGATTTCTTTATCTGCTTTCA 57.487 29.630 0.00 0.00 43.63 2.69
133 135 9.683870 AGAAGAGATTTCTTTATCTGCTTTCAT 57.316 29.630 0.00 0.00 43.63 2.57
136 138 8.684520 AGAGATTTCTTTATCTGCTTTCATTGG 58.315 33.333 0.00 0.00 35.06 3.16
137 139 7.779073 AGATTTCTTTATCTGCTTTCATTGGG 58.221 34.615 0.00 0.00 33.68 4.12
138 140 5.920193 TTCTTTATCTGCTTTCATTGGGG 57.080 39.130 0.00 0.00 0.00 4.96
139 141 3.701040 TCTTTATCTGCTTTCATTGGGGC 59.299 43.478 0.00 0.00 0.00 5.80
143 145 1.101331 CTGCTTTCATTGGGGCTCTC 58.899 55.000 0.00 0.00 0.00 3.20
161 163 4.367450 CTCTCCCTTCATCTAAGCTTTCG 58.633 47.826 3.20 0.00 33.49 3.46
169 171 6.019156 CCTTCATCTAAGCTTTCGAGAATCAC 60.019 42.308 3.20 0.00 33.49 3.06
196 198 7.383843 TGTTTTGCTTTTCTTTCGGGAATATTC 59.616 33.333 6.93 6.93 0.00 1.75
272 274 7.278135 AGAGATTTGATTCTTGATCCAATCGA 58.722 34.615 0.00 0.00 45.11 3.59
283 285 5.363979 TGATCCAATCGATACTCTTCTCG 57.636 43.478 0.00 0.00 36.25 4.04
284 286 5.063880 TGATCCAATCGATACTCTTCTCGA 58.936 41.667 0.00 0.00 46.71 4.04
308 312 1.903404 GGGGTGGCCAGAACACAAG 60.903 63.158 5.11 0.00 40.54 3.16
316 320 0.038744 CCAGAACACAAGGCATCCCT 59.961 55.000 0.00 0.00 45.77 4.20
323 327 1.211212 CACAAGGCATCCCTGAGATCA 59.789 52.381 0.00 0.00 41.90 2.92
338 342 2.686915 GAGATCAAGCCAAGGATGTTGG 59.313 50.000 0.00 0.00 42.37 3.77
339 343 2.309755 AGATCAAGCCAAGGATGTTGGA 59.690 45.455 7.99 0.00 42.06 3.53
340 344 1.909700 TCAAGCCAAGGATGTTGGAC 58.090 50.000 7.99 0.00 42.06 4.02
380 385 0.533032 GAGGTGAGGAAGAGGGTTCG 59.467 60.000 0.00 0.00 0.00 3.95
381 386 0.178929 AGGTGAGGAAGAGGGTTCGT 60.179 55.000 0.00 0.00 0.00 3.85
383 388 1.608283 GGTGAGGAAGAGGGTTCGTTG 60.608 57.143 0.00 0.00 0.00 4.10
394 399 1.231958 GGTTCGTTGGTGCGGATGAA 61.232 55.000 0.00 0.00 0.00 2.57
433 438 6.777213 TTGACCTCCTAGAGATTAGACAAC 57.223 41.667 0.00 0.00 0.00 3.32
464 469 2.185867 GCAAGCGTCATCCCCGTA 59.814 61.111 0.00 0.00 0.00 4.02
465 470 1.227556 GCAAGCGTCATCCCCGTAT 60.228 57.895 0.00 0.00 0.00 3.06
466 471 1.498865 GCAAGCGTCATCCCCGTATG 61.499 60.000 0.00 0.00 0.00 2.39
467 472 0.880278 CAAGCGTCATCCCCGTATGG 60.880 60.000 0.00 0.00 0.00 2.74
479 486 2.683475 GTATGGGGCAGGGCTTGT 59.317 61.111 0.00 0.00 0.00 3.16
480 487 1.000359 GTATGGGGCAGGGCTTGTT 60.000 57.895 0.00 0.00 0.00 2.83
488 495 0.909623 GCAGGGCTTGTTAGGACCTA 59.090 55.000 0.00 0.00 40.86 3.08
525 555 0.460987 CGTGACTCATCTCCTTGCCC 60.461 60.000 0.00 0.00 0.00 5.36
547 577 4.440127 CAAGCATTGCCCCACCGC 62.440 66.667 4.70 0.00 40.39 5.68
565 595 3.273080 CTGCTGGGCGGCTTTTGTC 62.273 63.158 9.56 0.00 0.00 3.18
566 596 3.294493 GCTGGGCGGCTTTTGTCA 61.294 61.111 9.56 0.00 0.00 3.58
575 605 1.299850 GCTTTTGTCAACGGTGCCC 60.300 57.895 0.00 0.00 0.00 5.36
577 607 0.310854 CTTTTGTCAACGGTGCCCTC 59.689 55.000 0.00 0.00 0.00 4.30
613 643 4.890306 GGGAGGGGAGGAGGGAGC 62.890 77.778 0.00 0.00 0.00 4.70
635 665 2.430367 GGCCGTTCTGGTCACCTT 59.570 61.111 0.00 0.00 44.04 3.50
644 674 2.813908 GGTCACCTTGCGCTACCG 60.814 66.667 9.73 0.00 37.57 4.02
658 688 1.207329 GCTACCGGAGTCACCAAAGAT 59.793 52.381 9.46 0.00 38.90 2.40
717 749 5.906113 TGTTGTAGGAAAGTTGCAAAGAA 57.094 34.783 0.00 0.00 0.00 2.52
722 775 9.476202 GTTGTAGGAAAGTTGCAAAGAATATTT 57.524 29.630 0.00 0.00 0.00 1.40
761 821 9.696917 CATAAAACATATAAAAGCATTCCCTCC 57.303 33.333 0.00 0.00 0.00 4.30
762 822 7.732222 AAAACATATAAAAGCATTCCCTCCA 57.268 32.000 0.00 0.00 0.00 3.86
763 823 7.919385 AAACATATAAAAGCATTCCCTCCAT 57.081 32.000 0.00 0.00 0.00 3.41
764 824 7.530426 AACATATAAAAGCATTCCCTCCATC 57.470 36.000 0.00 0.00 0.00 3.51
765 825 6.012745 ACATATAAAAGCATTCCCTCCATCC 58.987 40.000 0.00 0.00 0.00 3.51
766 826 2.165357 AAAAGCATTCCCTCCATCCC 57.835 50.000 0.00 0.00 0.00 3.85
767 827 1.009997 AAAGCATTCCCTCCATCCCA 58.990 50.000 0.00 0.00 0.00 4.37
768 828 1.009997 AAGCATTCCCTCCATCCCAA 58.990 50.000 0.00 0.00 0.00 4.12
769 829 1.009997 AGCATTCCCTCCATCCCAAA 58.990 50.000 0.00 0.00 0.00 3.28
770 830 1.362237 AGCATTCCCTCCATCCCAAAA 59.638 47.619 0.00 0.00 0.00 2.44
771 831 2.022722 AGCATTCCCTCCATCCCAAAAT 60.023 45.455 0.00 0.00 0.00 1.82
772 832 3.207321 AGCATTCCCTCCATCCCAAAATA 59.793 43.478 0.00 0.00 0.00 1.40
773 833 3.966665 GCATTCCCTCCATCCCAAAATAA 59.033 43.478 0.00 0.00 0.00 1.40
774 834 4.039609 GCATTCCCTCCATCCCAAAATAAG 59.960 45.833 0.00 0.00 0.00 1.73
775 835 4.965283 TTCCCTCCATCCCAAAATAAGT 57.035 40.909 0.00 0.00 0.00 2.24
776 836 4.249638 TCCCTCCATCCCAAAATAAGTG 57.750 45.455 0.00 0.00 0.00 3.16
777 837 3.596046 TCCCTCCATCCCAAAATAAGTGT 59.404 43.478 0.00 0.00 0.00 3.55
778 838 3.954258 CCCTCCATCCCAAAATAAGTGTC 59.046 47.826 0.00 0.00 0.00 3.67
779 839 4.325344 CCCTCCATCCCAAAATAAGTGTCT 60.325 45.833 0.00 0.00 0.00 3.41
780 840 4.884164 CCTCCATCCCAAAATAAGTGTCTC 59.116 45.833 0.00 0.00 0.00 3.36
781 841 5.500234 CTCCATCCCAAAATAAGTGTCTCA 58.500 41.667 0.00 0.00 0.00 3.27
782 842 5.886609 TCCATCCCAAAATAAGTGTCTCAA 58.113 37.500 0.00 0.00 0.00 3.02
783 843 6.493166 TCCATCCCAAAATAAGTGTCTCAAT 58.507 36.000 0.00 0.00 0.00 2.57
784 844 6.953520 TCCATCCCAAAATAAGTGTCTCAATT 59.046 34.615 0.00 0.00 0.00 2.32
785 845 7.454380 TCCATCCCAAAATAAGTGTCTCAATTT 59.546 33.333 0.00 0.00 0.00 1.82
786 846 8.748412 CCATCCCAAAATAAGTGTCTCAATTTA 58.252 33.333 0.00 0.00 0.00 1.40
787 847 9.793252 CATCCCAAAATAAGTGTCTCAATTTAG 57.207 33.333 0.00 0.00 0.00 1.85
788 848 8.934023 TCCCAAAATAAGTGTCTCAATTTAGT 57.066 30.769 0.00 0.00 0.00 2.24
827 887 7.677454 AGGTTAAGTTACTTATTTTGGGACG 57.323 36.000 5.60 0.00 0.00 4.79
828 888 6.656270 AGGTTAAGTTACTTATTTTGGGACGG 59.344 38.462 5.60 0.00 0.00 4.79
829 889 6.654582 GGTTAAGTTACTTATTTTGGGACGGA 59.345 38.462 5.60 0.00 0.00 4.69
830 890 7.148356 GGTTAAGTTACTTATTTTGGGACGGAG 60.148 40.741 5.60 0.00 0.00 4.63
831 891 4.840271 AGTTACTTATTTTGGGACGGAGG 58.160 43.478 0.00 0.00 0.00 4.30
832 892 2.801077 ACTTATTTTGGGACGGAGGG 57.199 50.000 0.00 0.00 0.00 4.30
833 893 1.990327 ACTTATTTTGGGACGGAGGGT 59.010 47.619 0.00 0.00 0.00 4.34
834 894 3.183801 ACTTATTTTGGGACGGAGGGTA 58.816 45.455 0.00 0.00 0.00 3.69
835 895 3.588396 ACTTATTTTGGGACGGAGGGTAA 59.412 43.478 0.00 0.00 0.00 2.85
836 896 4.043184 ACTTATTTTGGGACGGAGGGTAAA 59.957 41.667 0.00 0.00 0.00 2.01
974 1042 0.736636 CACATCATTGCATCAGCCGT 59.263 50.000 0.00 0.00 41.13 5.68
976 2875 0.309922 CATCATTGCATCAGCCGTCC 59.690 55.000 0.00 0.00 41.13 4.79
1164 3063 4.787280 CTCCTCCGAGCCCACCCT 62.787 72.222 0.00 0.00 0.00 4.34
1255 3154 0.749649 CTACCGCTCCATGCTTCTCT 59.250 55.000 0.00 0.00 40.11 3.10
1287 3186 3.245122 CCAACCCCAACAACTACACCTAT 60.245 47.826 0.00 0.00 0.00 2.57
1296 3195 1.041447 ACTACACCTATCCGCCGCTT 61.041 55.000 0.00 0.00 0.00 4.68
1434 3333 1.587054 CGCGTCACTCCTCTCCTTT 59.413 57.895 0.00 0.00 0.00 3.11
1752 3651 0.107993 ACATGAGGTGCGGAGATGTG 60.108 55.000 0.00 0.00 0.00 3.21
1987 3886 0.904649 CCTGGACTGTATGCCTGTCA 59.095 55.000 0.00 0.00 42.18 3.58
1994 3893 5.104569 TGGACTGTATGCCTGTCAAATATCA 60.105 40.000 6.43 0.00 42.18 2.15
2019 3918 2.158755 ACAGCCCACCATAGAGCATTAC 60.159 50.000 0.00 0.00 0.00 1.89
2025 3924 1.762957 ACCATAGAGCATTACGGCTGT 59.237 47.619 2.42 2.42 45.99 4.40
2037 3936 1.583967 CGGCTGTGTCGTCGATCTC 60.584 63.158 0.00 0.00 32.97 2.75
2040 3939 0.248296 GCTGTGTCGTCGATCTCCTC 60.248 60.000 0.00 0.00 0.00 3.71
2084 3983 2.243221 AGGCATTGGCTCTCATTAAGGT 59.757 45.455 6.96 0.00 40.87 3.50
2202 4101 5.306678 GGAGATACTCAAGTTGGATCCTCAT 59.693 44.000 14.23 0.00 31.08 2.90
2243 4142 7.358765 CGTGTTCTTATCTAATGTCTATGCTGC 60.359 40.741 0.00 0.00 0.00 5.25
2691 4590 0.834612 TCCACCACTTCAAGAACGGT 59.165 50.000 0.00 0.00 0.00 4.83
2739 4638 6.884836 GGTAGGACAAAATCTGAATGGTAAGT 59.115 38.462 0.00 0.00 0.00 2.24
2813 4712 6.878923 CACTACTTTCATTCAACCAGTGGATA 59.121 38.462 18.40 0.00 0.00 2.59
2852 4751 3.914426 AGCAACCTTCGTCCTATTCAT 57.086 42.857 0.00 0.00 0.00 2.57
2881 4780 8.556589 TCATAAGATCCCTTGGTTGAATTAAGA 58.443 33.333 0.00 0.00 33.94 2.10
2884 4783 6.183347 AGATCCCTTGGTTGAATTAAGACTG 58.817 40.000 0.00 0.00 0.00 3.51
2987 4886 5.415221 TCACATGATTTATACGTCACTGCA 58.585 37.500 0.00 0.00 0.00 4.41
3005 4911 6.070824 TCACTGCAGACTAATTGACCAAGATA 60.071 38.462 23.35 0.00 0.00 1.98
3036 5306 0.179048 TATGATCCCACTGGCGCAAG 60.179 55.000 11.17 11.17 43.44 4.01
3098 5375 7.374975 TCATATACCCCTTCTCTTTACTTGG 57.625 40.000 0.00 0.00 0.00 3.61
3103 5380 4.202472 ACCCCTTCTCTTTACTTGGTTCTG 60.202 45.833 0.00 0.00 0.00 3.02
3105 5382 4.041691 CCCTTCTCTTTACTTGGTTCTGGA 59.958 45.833 0.00 0.00 0.00 3.86
3112 5389 6.055588 TCTTTACTTGGTTCTGGAGTTCAAG 58.944 40.000 0.00 0.00 40.21 3.02
3132 5409 5.699915 TCAAGAGAAAAGAAGCTCTGATGTG 59.300 40.000 0.00 0.00 40.43 3.21
3186 5469 2.618241 TCCTTGTTTGCTGCTGTAACAG 59.382 45.455 0.00 0.00 40.80 3.16
3409 5706 0.624500 TGAAAGGGGAGGGAGGGATG 60.625 60.000 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 4.158384 GCGTGATTGGACAAACAATAGTG 58.842 43.478 0.00 0.00 40.92 2.74
29 30 3.637432 TGATTTGCGTGATTGGACAAAC 58.363 40.909 0.00 0.00 35.06 2.93
33 34 4.361451 AGATTGATTTGCGTGATTGGAC 57.639 40.909 0.00 0.00 0.00 4.02
35 36 5.162794 TCAAAGATTGATTTGCGTGATTGG 58.837 37.500 0.00 0.00 39.51 3.16
66 67 4.245660 TCTCAATTTACTGTCAGCGGAAG 58.754 43.478 0.00 0.00 0.00 3.46
67 68 4.245660 CTCTCAATTTACTGTCAGCGGAA 58.754 43.478 0.00 0.00 0.00 4.30
69 70 2.932614 CCTCTCAATTTACTGTCAGCGG 59.067 50.000 0.00 0.00 0.00 5.52
71 72 5.078411 TCTCCTCTCAATTTACTGTCAGC 57.922 43.478 0.00 0.00 0.00 4.26
72 73 6.047870 CCATCTCCTCTCAATTTACTGTCAG 58.952 44.000 0.00 0.00 0.00 3.51
74 75 5.129485 TCCCATCTCCTCTCAATTTACTGTC 59.871 44.000 0.00 0.00 0.00 3.51
75 76 5.032846 TCCCATCTCCTCTCAATTTACTGT 58.967 41.667 0.00 0.00 0.00 3.55
76 77 5.620738 TCCCATCTCCTCTCAATTTACTG 57.379 43.478 0.00 0.00 0.00 2.74
77 78 5.309282 GGATCCCATCTCCTCTCAATTTACT 59.691 44.000 0.00 0.00 0.00 2.24
79 80 5.226803 TGGATCCCATCTCCTCTCAATTTA 58.773 41.667 9.90 0.00 33.69 1.40
80 81 4.050037 TGGATCCCATCTCCTCTCAATTT 58.950 43.478 9.90 0.00 33.69 1.82
102 104 9.737844 AGCAGATAAAGAAATCTCTTCTTTTCT 57.262 29.630 15.47 14.11 43.84 2.52
118 120 3.703052 AGCCCCAATGAAAGCAGATAAAG 59.297 43.478 0.00 0.00 0.00 1.85
121 123 2.511218 AGAGCCCCAATGAAAGCAGATA 59.489 45.455 0.00 0.00 0.00 1.98
122 124 1.287146 AGAGCCCCAATGAAAGCAGAT 59.713 47.619 0.00 0.00 0.00 2.90
123 125 0.700564 AGAGCCCCAATGAAAGCAGA 59.299 50.000 0.00 0.00 0.00 4.26
124 126 1.101331 GAGAGCCCCAATGAAAGCAG 58.899 55.000 0.00 0.00 0.00 4.24
125 127 0.323725 GGAGAGCCCCAATGAAAGCA 60.324 55.000 0.00 0.00 0.00 3.91
126 128 2.498077 GGAGAGCCCCAATGAAAGC 58.502 57.895 0.00 0.00 0.00 3.51
137 139 2.046292 AGCTTAGATGAAGGGAGAGCC 58.954 52.381 0.00 0.00 35.49 4.70
138 140 3.836365 AAGCTTAGATGAAGGGAGAGC 57.164 47.619 0.00 0.00 35.49 4.09
139 141 4.098654 TCGAAAGCTTAGATGAAGGGAGAG 59.901 45.833 0.00 0.00 35.49 3.20
143 145 4.392921 TCTCGAAAGCTTAGATGAAGGG 57.607 45.455 0.00 0.00 35.49 3.95
145 147 6.756074 AGTGATTCTCGAAAGCTTAGATGAAG 59.244 38.462 0.00 0.00 38.30 3.02
152 154 6.658831 CAAAACAGTGATTCTCGAAAGCTTA 58.341 36.000 0.00 0.00 0.00 3.09
161 163 7.305648 CGAAAGAAAAGCAAAACAGTGATTCTC 60.306 37.037 0.00 0.00 0.00 2.87
169 171 4.040445 TCCCGAAAGAAAAGCAAAACAG 57.960 40.909 0.00 0.00 0.00 3.16
196 198 8.279970 TGATTAAAGGTAAAGTCATGACATGG 57.720 34.615 27.02 0.00 0.00 3.66
241 243 8.721479 TGGATCAAGAATCAAATCTCTATTCCT 58.279 33.333 0.00 0.00 35.96 3.36
242 244 8.915057 TGGATCAAGAATCAAATCTCTATTCC 57.085 34.615 0.00 0.00 35.96 3.01
283 285 1.779061 TTCTGGCCACCCCTCAACTC 61.779 60.000 0.00 0.00 0.00 3.01
284 286 1.774217 TTCTGGCCACCCCTCAACT 60.774 57.895 0.00 0.00 0.00 3.16
286 288 2.081787 TGTTCTGGCCACCCCTCAA 61.082 57.895 0.00 0.00 0.00 3.02
308 312 0.536915 GGCTTGATCTCAGGGATGCC 60.537 60.000 0.00 0.00 35.07 4.40
316 320 3.349927 CAACATCCTTGGCTTGATCTCA 58.650 45.455 0.00 0.00 0.00 3.27
323 327 0.609131 CGGTCCAACATCCTTGGCTT 60.609 55.000 0.00 0.00 39.38 4.35
357 362 2.289467 ACCCTCTTCCTCACCTCTAGA 58.711 52.381 0.00 0.00 0.00 2.43
359 364 2.620886 CGAACCCTCTTCCTCACCTCTA 60.621 54.545 0.00 0.00 0.00 2.43
380 385 0.036388 TCCTCTTCATCCGCACCAAC 60.036 55.000 0.00 0.00 0.00 3.77
381 386 0.250234 CTCCTCTTCATCCGCACCAA 59.750 55.000 0.00 0.00 0.00 3.67
383 388 1.144936 CCTCCTCTTCATCCGCACC 59.855 63.158 0.00 0.00 0.00 5.01
418 423 2.617308 TCGGGCGTTGTCTAATCTCTAG 59.383 50.000 0.00 0.00 0.00 2.43
419 424 2.617308 CTCGGGCGTTGTCTAATCTCTA 59.383 50.000 0.00 0.00 0.00 2.43
420 425 1.405821 CTCGGGCGTTGTCTAATCTCT 59.594 52.381 0.00 0.00 0.00 3.10
464 469 1.307647 CTAACAAGCCCTGCCCCAT 59.692 57.895 0.00 0.00 0.00 4.00
465 470 2.763215 CTAACAAGCCCTGCCCCA 59.237 61.111 0.00 0.00 0.00 4.96
466 471 2.043953 CCTAACAAGCCCTGCCCC 60.044 66.667 0.00 0.00 0.00 5.80
467 472 1.378646 GTCCTAACAAGCCCTGCCC 60.379 63.158 0.00 0.00 0.00 5.36
470 476 2.168728 GACTAGGTCCTAACAAGCCCTG 59.831 54.545 0.00 0.00 0.00 4.45
479 486 2.842496 TCTGTCTCCGACTAGGTCCTAA 59.158 50.000 0.00 0.00 41.99 2.69
480 487 2.475155 TCTGTCTCCGACTAGGTCCTA 58.525 52.381 0.00 0.00 41.99 2.94
488 495 1.407979 ACGTTGTTTCTGTCTCCGACT 59.592 47.619 0.00 0.00 33.15 4.18
500 507 3.753294 AGGAGATGAGTCACGTTGTTT 57.247 42.857 0.00 0.00 0.00 2.83
507 514 0.460987 CGGGCAAGGAGATGAGTCAC 60.461 60.000 0.00 0.00 0.00 3.67
508 515 0.614697 TCGGGCAAGGAGATGAGTCA 60.615 55.000 0.00 0.00 0.00 3.41
525 555 0.667184 GTGGGGCAATGCTTGTTTCG 60.667 55.000 4.82 0.00 0.00 3.46
547 577 3.273080 GACAAAAGCCGCCCAGCAG 62.273 63.158 0.00 0.00 34.23 4.24
550 580 1.007387 GTTGACAAAAGCCGCCCAG 60.007 57.895 0.00 0.00 0.00 4.45
591 621 4.179599 CTCCTCCCCTCCCCTCCC 62.180 77.778 0.00 0.00 0.00 4.30
592 622 4.179599 CCTCCTCCCCTCCCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
593 623 4.179599 CCCTCCTCCCCTCCCCTC 62.180 77.778 0.00 0.00 0.00 4.30
613 643 2.358737 GACCAGAACGGCCACCAG 60.359 66.667 2.24 0.00 39.03 4.00
634 664 2.260434 GTGACTCCGGTAGCGCAA 59.740 61.111 11.47 0.00 0.00 4.85
635 665 3.755628 GGTGACTCCGGTAGCGCA 61.756 66.667 11.47 0.00 0.00 6.09
644 674 2.069273 CGTGTCATCTTTGGTGACTCC 58.931 52.381 11.52 2.89 44.80 3.85
748 808 1.009997 TGGGATGGAGGGAATGCTTT 58.990 50.000 0.00 0.00 0.00 3.51
749 809 1.009997 TTGGGATGGAGGGAATGCTT 58.990 50.000 0.00 0.00 0.00 3.91
750 810 1.009997 TTTGGGATGGAGGGAATGCT 58.990 50.000 0.00 0.00 0.00 3.79
751 811 1.864669 TTTTGGGATGGAGGGAATGC 58.135 50.000 0.00 0.00 0.00 3.56
752 812 5.069516 CACTTATTTTGGGATGGAGGGAATG 59.930 44.000 0.00 0.00 0.00 2.67
753 813 5.211201 CACTTATTTTGGGATGGAGGGAAT 58.789 41.667 0.00 0.00 0.00 3.01
754 814 4.045334 ACACTTATTTTGGGATGGAGGGAA 59.955 41.667 0.00 0.00 0.00 3.97
755 815 3.596046 ACACTTATTTTGGGATGGAGGGA 59.404 43.478 0.00 0.00 0.00 4.20
756 816 3.954258 GACACTTATTTTGGGATGGAGGG 59.046 47.826 0.00 0.00 0.00 4.30
757 817 4.860022 AGACACTTATTTTGGGATGGAGG 58.140 43.478 0.00 0.00 0.00 4.30
758 818 5.500234 TGAGACACTTATTTTGGGATGGAG 58.500 41.667 0.00 0.00 0.00 3.86
759 819 5.512942 TGAGACACTTATTTTGGGATGGA 57.487 39.130 0.00 0.00 0.00 3.41
760 820 6.780457 ATTGAGACACTTATTTTGGGATGG 57.220 37.500 0.00 0.00 0.00 3.51
761 821 9.793252 CTAAATTGAGACACTTATTTTGGGATG 57.207 33.333 0.00 0.00 0.00 3.51
762 822 9.533831 ACTAAATTGAGACACTTATTTTGGGAT 57.466 29.630 0.00 0.00 0.00 3.85
763 823 8.934023 ACTAAATTGAGACACTTATTTTGGGA 57.066 30.769 0.00 0.00 0.00 4.37
801 861 9.218440 CGTCCCAAAATAAGTAACTTAACCTTA 57.782 33.333 0.00 0.00 29.35 2.69
802 862 7.175467 CCGTCCCAAAATAAGTAACTTAACCTT 59.825 37.037 0.00 0.00 29.35 3.50
803 863 6.656270 CCGTCCCAAAATAAGTAACTTAACCT 59.344 38.462 0.00 0.00 29.35 3.50
804 864 6.654582 TCCGTCCCAAAATAAGTAACTTAACC 59.345 38.462 0.00 0.00 29.35 2.85
805 865 7.148356 CCTCCGTCCCAAAATAAGTAACTTAAC 60.148 40.741 0.00 0.00 29.35 2.01
806 866 6.880529 CCTCCGTCCCAAAATAAGTAACTTAA 59.119 38.462 0.00 0.00 29.35 1.85
807 867 6.408869 CCTCCGTCCCAAAATAAGTAACTTA 58.591 40.000 0.00 0.00 0.00 2.24
808 868 5.250982 CCTCCGTCCCAAAATAAGTAACTT 58.749 41.667 0.00 0.00 0.00 2.66
809 869 4.324022 CCCTCCGTCCCAAAATAAGTAACT 60.324 45.833 0.00 0.00 0.00 2.24
810 870 3.943381 CCCTCCGTCCCAAAATAAGTAAC 59.057 47.826 0.00 0.00 0.00 2.50
811 871 3.588396 ACCCTCCGTCCCAAAATAAGTAA 59.412 43.478 0.00 0.00 0.00 2.24
812 872 3.183801 ACCCTCCGTCCCAAAATAAGTA 58.816 45.455 0.00 0.00 0.00 2.24
813 873 1.990327 ACCCTCCGTCCCAAAATAAGT 59.010 47.619 0.00 0.00 0.00 2.24
814 874 2.801077 ACCCTCCGTCCCAAAATAAG 57.199 50.000 0.00 0.00 0.00 1.73
815 875 4.334552 GTTTACCCTCCGTCCCAAAATAA 58.665 43.478 0.00 0.00 0.00 1.40
816 876 3.619487 CGTTTACCCTCCGTCCCAAAATA 60.619 47.826 0.00 0.00 0.00 1.40
817 877 2.799017 GTTTACCCTCCGTCCCAAAAT 58.201 47.619 0.00 0.00 0.00 1.82
818 878 1.542987 CGTTTACCCTCCGTCCCAAAA 60.543 52.381 0.00 0.00 0.00 2.44
819 879 0.035176 CGTTTACCCTCCGTCCCAAA 59.965 55.000 0.00 0.00 0.00 3.28
820 880 1.120795 ACGTTTACCCTCCGTCCCAA 61.121 55.000 0.00 0.00 0.00 4.12
821 881 1.533753 ACGTTTACCCTCCGTCCCA 60.534 57.895 0.00 0.00 0.00 4.37
822 882 1.079612 CACGTTTACCCTCCGTCCC 60.080 63.158 0.00 0.00 31.46 4.46
823 883 1.739196 GCACGTTTACCCTCCGTCC 60.739 63.158 0.00 0.00 31.46 4.79
824 884 0.390735 ATGCACGTTTACCCTCCGTC 60.391 55.000 0.00 0.00 31.46 4.79
825 885 0.035739 AATGCACGTTTACCCTCCGT 59.964 50.000 0.00 0.00 34.71 4.69
826 886 0.446222 CAATGCACGTTTACCCTCCG 59.554 55.000 0.00 0.00 0.00 4.63
827 887 0.170339 GCAATGCACGTTTACCCTCC 59.830 55.000 0.00 0.00 0.00 4.30
828 888 1.165270 AGCAATGCACGTTTACCCTC 58.835 50.000 8.35 0.00 0.00 4.30
829 889 1.539827 GAAGCAATGCACGTTTACCCT 59.460 47.619 8.35 0.00 0.00 4.34
830 890 1.727857 CGAAGCAATGCACGTTTACCC 60.728 52.381 8.35 0.00 0.00 3.69
831 891 1.069500 ACGAAGCAATGCACGTTTACC 60.069 47.619 20.16 0.00 39.57 2.85
832 892 2.309898 ACGAAGCAATGCACGTTTAC 57.690 45.000 20.16 0.00 39.57 2.01
834 894 3.936585 AACGAAGCAATGCACGTTT 57.063 42.105 26.79 16.43 45.00 3.60
836 896 1.064803 TGAAAACGAAGCAATGCACGT 59.935 42.857 20.16 20.16 42.63 4.49
1164 3063 2.370849 GGTGTTGTAGGAGAAGGTGGAA 59.629 50.000 0.00 0.00 0.00 3.53
1386 3285 4.710167 TCGCGGGAGTCGAGACCA 62.710 66.667 6.13 0.00 42.44 4.02
1605 3504 4.200283 GAGACGAGGGCGAGCAGG 62.200 72.222 0.00 0.00 41.64 4.85
1987 3886 4.518278 TGGTGGGCTGTACATGATATTT 57.482 40.909 0.00 0.00 0.00 1.40
1994 3893 1.417890 GCTCTATGGTGGGCTGTACAT 59.582 52.381 0.00 0.00 0.00 2.29
2019 3918 1.583967 GAGATCGACGACACAGCCG 60.584 63.158 0.00 0.00 0.00 5.52
2243 4142 0.040204 AAGGTCCCATTTCCCAGCAG 59.960 55.000 0.00 0.00 0.00 4.24
2834 4733 5.359756 TGATCATGAATAGGACGAAGGTTG 58.640 41.667 0.00 0.00 0.00 3.77
2881 4780 4.930963 TGCATTTCATTCGTGAAAACAGT 58.069 34.783 7.57 0.00 40.60 3.55
2884 4783 5.061311 CCATCTGCATTTCATTCGTGAAAAC 59.939 40.000 7.57 4.59 40.60 2.43
2902 4801 5.061179 TGAAGTACATGATCATGCCATCTG 58.939 41.667 31.17 11.70 42.39 2.90
2987 4886 5.426833 AGCCAGTATCTTGGTCAATTAGTCT 59.573 40.000 0.00 0.00 40.49 3.24
3005 4911 4.910304 AGTGGGATCATAATCTTAGCCAGT 59.090 41.667 0.00 0.00 32.12 4.00
3036 5306 3.910648 AGACTTACGTTAGGTGAACAGC 58.089 45.455 6.52 0.00 37.99 4.40
3098 5375 6.512578 GCTTCTTTTCTCTTGAACTCCAGAAC 60.513 42.308 0.00 0.00 31.02 3.01
3103 5380 5.179182 CAGAGCTTCTTTTCTCTTGAACTCC 59.821 44.000 0.00 0.00 37.56 3.85
3105 5382 5.923204 TCAGAGCTTCTTTTCTCTTGAACT 58.077 37.500 0.00 0.00 37.56 3.01
3112 5389 4.573900 TCCACATCAGAGCTTCTTTTCTC 58.426 43.478 0.00 0.00 0.00 2.87
3167 5446 3.969117 TCTGTTACAGCAGCAAACAAG 57.031 42.857 7.61 4.82 36.49 3.16
3327 5614 1.414181 CAGCTCCACGGATTCCATAGT 59.586 52.381 3.09 0.00 0.00 2.12
3371 5668 2.038952 TCATCTTTCCTGTGGTGGACTG 59.961 50.000 0.00 0.00 35.58 3.51
3409 5706 5.637006 TGGGTATGACACAAAAATAGTGC 57.363 39.130 0.00 0.00 40.59 4.40
3537 5836 4.717877 TGTTGTGGATCACAGTGAAATCT 58.282 39.130 7.50 0.00 45.39 2.40
3548 5847 3.527253 ACCCCTTGATATGTTGTGGATCA 59.473 43.478 0.00 0.00 0.00 2.92
3694 6003 4.218635 TCCTCAGCTATGTCCATAATCGAC 59.781 45.833 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.