Multiple sequence alignment - TraesCS1A01G304100

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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 TraesCS1A01G304100 chr1A 100.000 3778 0 0 1 3778 497499596 497495819 0.000000e+00 6977
1 TraesCS1A01G304100 chr1B 90.665 3160 144 56 1 3083 539483461 539480376 0.000000e+00 4061
2 TraesCS1A01G304100 chr1D 93.063 2638 80 33 499 3083 401566339 401563752 0.000000e+00 3762
3 TraesCS1A01G304100 chr4D 96.006 701 28 0 3078 3778 502781469 502780769 0.000000e+00 1140
4 TraesCS1A01G304100 chr3A 95.422 699 31 1 3080 3778 509380826 509381523 0.000000e+00 1112
5 TraesCS1A01G304100 chr3A 79.987 1514 269 23 1275 2766 587552826 587551325 0.000000e+00 1086
6 TraesCS1A01G304100 chr3D 94.986 698 35 0 3081 3778 579166247 579165550 0.000000e+00 1096
7 TraesCS1A01G304100 chr3D 94.864 701 35 1 3078 3778 252331099 252331798 0.000000e+00 1094
8 TraesCS1A01G304100 chr3D 80.270 1110 211 8 1275 2380 445738413 445737308 0.000000e+00 830
9 TraesCS1A01G304100 chr3D 87.919 298 34 2 2470 2766 445737198 445736902 2.160000e-92 350
10 TraesCS1A01G304100 chr7D 94.857 700 35 1 3079 3778 550638839 550638141 0.000000e+00 1092
11 TraesCS1A01G304100 chr5B 94.707 699 37 0 3080 3778 184291901 184291203 0.000000e+00 1086
12 TraesCS1A01G304100 chr6B 94.579 701 38 0 3078 3778 197815471 197816171 0.000000e+00 1085
13 TraesCS1A01G304100 chr5D 94.571 700 38 0 3079 3778 320663549 320662850 0.000000e+00 1083
14 TraesCS1A01G304100 chr4A 94.556 698 38 0 3081 3778 114568901 114568204 0.000000e+00 1079
15 TraesCS1A01G304100 chr3B 79.854 1509 266 32 1275 2766 584576720 584575233 0.000000e+00 1068
16 TraesCS1A01G304100 chr2B 73.282 393 81 18 1684 2058 382911132 382910746 5.120000e-24 122


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 TraesCS1A01G304100 chr1A 497495819 497499596 3777 True 6977 6977 100.0000 1 3778 1 chr1A.!!$R1 3777
1 TraesCS1A01G304100 chr1B 539480376 539483461 3085 True 4061 4061 90.6650 1 3083 1 chr1B.!!$R1 3082
2 TraesCS1A01G304100 chr1D 401563752 401566339 2587 True 3762 3762 93.0630 499 3083 1 chr1D.!!$R1 2584
3 TraesCS1A01G304100 chr4D 502780769 502781469 700 True 1140 1140 96.0060 3078 3778 1 chr4D.!!$R1 700
4 TraesCS1A01G304100 chr3A 509380826 509381523 697 False 1112 1112 95.4220 3080 3778 1 chr3A.!!$F1 698
5 TraesCS1A01G304100 chr3A 587551325 587552826 1501 True 1086 1086 79.9870 1275 2766 1 chr3A.!!$R1 1491
6 TraesCS1A01G304100 chr3D 579165550 579166247 697 True 1096 1096 94.9860 3081 3778 1 chr3D.!!$R1 697
7 TraesCS1A01G304100 chr3D 252331099 252331798 699 False 1094 1094 94.8640 3078 3778 1 chr3D.!!$F1 700
8 TraesCS1A01G304100 chr3D 445736902 445738413 1511 True 590 830 84.0945 1275 2766 2 chr3D.!!$R2 1491
9 TraesCS1A01G304100 chr7D 550638141 550638839 698 True 1092 1092 94.8570 3079 3778 1 chr7D.!!$R1 699
10 TraesCS1A01G304100 chr5B 184291203 184291901 698 True 1086 1086 94.7070 3080 3778 1 chr5B.!!$R1 698
11 TraesCS1A01G304100 chr6B 197815471 197816171 700 False 1085 1085 94.5790 3078 3778 1 chr6B.!!$F1 700
12 TraesCS1A01G304100 chr5D 320662850 320663549 699 True 1083 1083 94.5710 3079 3778 1 chr5D.!!$R1 699
13 TraesCS1A01G304100 chr4A 114568204 114568901 697 True 1079 1079 94.5560 3081 3778 1 chr4A.!!$R1 697
14 TraesCS1A01G304100 chr3B 584575233 584576720 1487 True 1068 1068 79.8540 1275 2766 1 chr3B.!!$R1 1491

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
173 200 0.457166 TCGGTTTGCGAGATACACGG 60.457 55.000 0.0 0.0 0.00 4.94 F
729 768 0.461961 CCGGTCTCCACATCCTTCTC 59.538 60.000 0.0 0.0 0.00 2.87 F
741 782 0.898789 TCCTTCTCCACACCGTCCTC 60.899 60.000 0.0 0.0 0.00 3.71 F
2211 2290 1.003355 CAGCGACCAGGTGTTCCAT 60.003 57.895 0.0 0.0 42.98 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1131 1210 0.888736 TGCCCACGATGTTCTTGGTG 60.889 55.000 0.0 0.0 34.30 4.17 R
2211 2290 0.875728 CGTCGCCCATTTGGTTGTAA 59.124 50.000 0.0 0.0 36.04 2.41 R
2441 2555 3.193903 CACATGCATCAACTCCATTTCCA 59.806 43.478 0.0 0.0 0.00 3.53 R
3586 3710 1.760613 CATGGGAAGAAGCCAATGCAT 59.239 47.619 0.0 0.0 41.13 3.96 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
23 24 5.328691 CAAGTTACTTCGAACAAAAGCACA 58.671 37.500 0.00 0.00 0.00 4.57
28 29 3.130340 ACTTCGAACAAAAGCACACCAAT 59.870 39.130 0.00 0.00 0.00 3.16
50 51 1.360192 GAGTGCAGTGGTTTGGTGC 59.640 57.895 0.00 0.00 37.73 5.01
65 66 1.220749 GTGCTCGGGCTACATGGAA 59.779 57.895 9.62 0.00 39.59 3.53
143 154 7.867445 TTGACATATGCATGTATACTACACG 57.133 36.000 10.16 0.00 45.58 4.49
156 183 8.551122 TGTATACTACACGTGAAAATACATCG 57.449 34.615 25.01 0.00 32.89 3.84
157 184 7.644945 TGTATACTACACGTGAAAATACATCGG 59.355 37.037 25.01 0.00 32.89 4.18
162 189 3.602062 CACGTGAAAATACATCGGTTTGC 59.398 43.478 10.90 0.00 0.00 3.68
172 199 1.255342 CATCGGTTTGCGAGATACACG 59.745 52.381 0.00 0.00 0.00 4.49
173 200 0.457166 TCGGTTTGCGAGATACACGG 60.457 55.000 0.00 0.00 0.00 4.94
181 208 2.230508 TGCGAGATACACGGAAAGAAGT 59.769 45.455 0.00 0.00 0.00 3.01
187 218 6.073980 CGAGATACACGGAAAGAAGTGAAAAA 60.074 38.462 2.42 0.00 40.56 1.94
192 223 4.904154 CACGGAAAGAAGTGAAAAATCGTC 59.096 41.667 0.00 0.00 40.56 4.20
194 225 4.464112 GGAAAGAAGTGAAAAATCGTCGG 58.536 43.478 0.00 0.00 0.00 4.79
197 228 4.727235 AGAAGTGAAAAATCGTCGGTTC 57.273 40.909 0.00 0.00 0.00 3.62
202 233 7.980099 AGAAGTGAAAAATCGTCGGTTCTATAT 59.020 33.333 0.00 0.00 0.00 0.86
203 234 9.241317 GAAGTGAAAAATCGTCGGTTCTATATA 57.759 33.333 0.00 0.00 0.00 0.86
204 235 8.798748 AGTGAAAAATCGTCGGTTCTATATAG 57.201 34.615 3.10 3.10 0.00 1.31
205 236 8.627403 AGTGAAAAATCGTCGGTTCTATATAGA 58.373 33.333 8.44 8.44 0.00 1.98
206 237 8.903723 GTGAAAAATCGTCGGTTCTATATAGAG 58.096 37.037 12.16 2.29 33.21 2.43
211 242 8.845413 AATCGTCGGTTCTATATAGAGTAGTT 57.155 34.615 12.16 0.26 33.21 2.24
214 245 9.416794 TCGTCGGTTCTATATAGAGTAGTTAAG 57.583 37.037 12.16 3.15 33.21 1.85
227 258 7.328277 AGAGTAGTTAAGAGAGCACATACTG 57.672 40.000 0.00 0.00 0.00 2.74
246 279 7.283127 ACATACTGTTCACTGTGTTCAAAATCT 59.717 33.333 7.79 0.00 0.00 2.40
247 280 6.124088 ACTGTTCACTGTGTTCAAAATCTC 57.876 37.500 7.79 0.00 0.00 2.75
248 281 5.066505 ACTGTTCACTGTGTTCAAAATCTCC 59.933 40.000 7.79 0.00 0.00 3.71
250 283 5.417266 TGTTCACTGTGTTCAAAATCTCCAA 59.583 36.000 7.79 0.00 0.00 3.53
292 325 2.348666 AGCTCGCGTGTCAATGTATTTC 59.651 45.455 5.77 0.00 0.00 2.17
315 348 9.544314 TTTCGTCATAAAAATTTACGTACATGG 57.456 29.630 9.54 0.00 0.00 3.66
316 349 8.476657 TCGTCATAAAAATTTACGTACATGGA 57.523 30.769 9.54 0.00 0.00 3.41
317 350 8.597227 TCGTCATAAAAATTTACGTACATGGAG 58.403 33.333 9.54 0.00 0.00 3.86
322 355 6.693315 AAAATTTACGTACATGGAGATGGG 57.307 37.500 0.00 0.00 33.39 4.00
327 360 4.122337 ACGTACATGGAGATGGGGTATA 57.878 45.455 0.00 0.00 33.39 1.47
332 365 3.846588 ACATGGAGATGGGGTATACATCC 59.153 47.826 5.01 6.39 44.45 3.51
348 381 8.692710 GGTATACATCCGTATGATATTCTGGAA 58.307 37.037 5.01 0.00 38.79 3.53
351 384 7.912056 ACATCCGTATGATATTCTGGAAATG 57.088 36.000 0.00 0.00 36.54 2.32
356 389 9.839817 TCCGTATGATATTCTGGAAATGTTTTA 57.160 29.630 0.00 0.00 0.00 1.52
450 489 2.153039 GCATTTCTGCGCCAAAACC 58.847 52.632 4.18 0.00 38.92 3.27
472 511 3.875727 CTGTCAACATGGCAGGATCTAAG 59.124 47.826 5.99 0.00 45.77 2.18
588 627 3.106407 GCGGCGAGACAGACACAC 61.106 66.667 12.98 0.00 0.00 3.82
596 635 0.603065 AGACAGACACACGCTGCATA 59.397 50.000 0.00 0.00 36.86 3.14
630 669 2.781595 TTTCTCGGCACCGCTCCTTC 62.782 60.000 3.66 0.00 39.59 3.46
721 760 3.923645 ACCTCCCCGGTCTCCACA 61.924 66.667 0.00 0.00 44.93 4.17
722 761 2.365635 CCTCCCCGGTCTCCACAT 60.366 66.667 0.00 0.00 0.00 3.21
723 762 2.435693 CCTCCCCGGTCTCCACATC 61.436 68.421 0.00 0.00 0.00 3.06
724 763 2.365105 TCCCCGGTCTCCACATCC 60.365 66.667 0.00 0.00 0.00 3.51
725 764 2.365635 CCCCGGTCTCCACATCCT 60.366 66.667 0.00 0.00 0.00 3.24
726 765 1.995626 CCCCGGTCTCCACATCCTT 60.996 63.158 0.00 0.00 0.00 3.36
728 767 0.978146 CCCGGTCTCCACATCCTTCT 60.978 60.000 0.00 0.00 0.00 2.85
729 768 0.461961 CCGGTCTCCACATCCTTCTC 59.538 60.000 0.00 0.00 0.00 2.87
731 770 1.573108 GGTCTCCACATCCTTCTCCA 58.427 55.000 0.00 0.00 0.00 3.86
741 782 0.898789 TCCTTCTCCACACCGTCCTC 60.899 60.000 0.00 0.00 0.00 3.71
743 784 1.152419 TTCTCCACACCGTCCTCCA 60.152 57.895 0.00 0.00 0.00 3.86
746 787 4.016706 CCACACCGTCCTCCACCC 62.017 72.222 0.00 0.00 0.00 4.61
747 788 4.016706 CACACCGTCCTCCACCCC 62.017 72.222 0.00 0.00 0.00 4.95
748 789 4.250170 ACACCGTCCTCCACCCCT 62.250 66.667 0.00 0.00 0.00 4.79
749 790 3.391382 CACCGTCCTCCACCCCTC 61.391 72.222 0.00 0.00 0.00 4.30
750 791 4.716977 ACCGTCCTCCACCCCTCC 62.717 72.222 0.00 0.00 0.00 4.30
788 832 3.326006 TCTTCCATGGCATCCTCATAGAC 59.674 47.826 6.96 0.00 0.00 2.59
789 833 1.980765 TCCATGGCATCCTCATAGACC 59.019 52.381 6.96 0.00 0.00 3.85
790 834 1.701292 CCATGGCATCCTCATAGACCA 59.299 52.381 0.00 0.00 0.00 4.02
828 872 3.340034 CCCGCAACTCCTACATTACAAA 58.660 45.455 0.00 0.00 0.00 2.83
850 894 2.210524 CTTCAAGGTACGCACGCACG 62.211 60.000 0.00 0.00 39.50 5.34
909 985 5.453266 CCGATCAATTCATTCGAATGTGTTG 59.547 40.000 31.49 30.82 41.12 3.33
999 1078 1.200020 CTGCCACCGATCTTGGTTTTC 59.800 52.381 10.93 0.00 41.38 2.29
1024 1103 2.321060 CGACGATGACAATGCGCC 59.679 61.111 4.18 0.00 0.00 6.53
1774 1853 2.189521 CCCACACGATACAGGGCC 59.810 66.667 0.00 0.00 33.91 5.80
2211 2290 1.003355 CAGCGACCAGGTGTTCCAT 60.003 57.895 0.00 0.00 42.98 3.41
2220 2299 3.226777 CCAGGTGTTCCATTACAACCAA 58.773 45.455 0.00 0.00 36.36 3.67
2399 2505 3.409026 ACCCTAAGTTCTTGTGCTCAG 57.591 47.619 0.00 0.00 0.00 3.35
2438 2552 3.211963 GGCGGCGCTGATGGAATT 61.212 61.111 32.30 0.00 0.00 2.17
2439 2553 1.891919 GGCGGCGCTGATGGAATTA 60.892 57.895 32.30 0.00 0.00 1.40
2440 2554 1.444119 GGCGGCGCTGATGGAATTAA 61.444 55.000 32.30 0.00 0.00 1.40
2441 2555 0.593128 GCGGCGCTGATGGAATTAAT 59.407 50.000 26.86 0.00 0.00 1.40
2849 2964 1.747709 TGTACACGAGGAGGTCTAGC 58.252 55.000 0.00 0.00 0.00 3.42
2850 2965 1.281287 TGTACACGAGGAGGTCTAGCT 59.719 52.381 0.00 0.00 0.00 3.32
2851 2966 2.502947 TGTACACGAGGAGGTCTAGCTA 59.497 50.000 0.00 0.00 0.00 3.32
2853 2968 1.134037 ACACGAGGAGGTCTAGCTAGG 60.134 57.143 20.58 4.50 0.00 3.02
2859 2974 2.838225 GGTCTAGCTAGGCCGCCA 60.838 66.667 27.94 0.62 38.47 5.69
2954 3072 7.244898 TGTGTAATTGTGTTACTGTTGTTGTC 58.755 34.615 0.00 0.00 0.00 3.18
2974 3092 2.739913 TCGTTCTTGGCGATCGATTTTT 59.260 40.909 21.57 0.00 38.53 1.94
3022 3144 3.052944 TGATTAAGCATGGGGGCTAGTTT 60.053 43.478 0.00 0.00 45.07 2.66
3055 3177 7.881142 TCAAAAGAACAAAGACAGAAGAAACA 58.119 30.769 0.00 0.00 0.00 2.83
3059 3181 8.964476 AAGAACAAAGACAGAAGAAACATAGA 57.036 30.769 0.00 0.00 0.00 1.98
3060 3182 8.371770 AGAACAAAGACAGAAGAAACATAGAC 57.628 34.615 0.00 0.00 0.00 2.59
3064 3186 7.873505 ACAAAGACAGAAGAAACATAGACTACC 59.126 37.037 0.00 0.00 0.00 3.18
3091 3215 4.929819 AAGAAAATTAGGGCGTGTTTGT 57.070 36.364 0.00 0.00 0.00 2.83
3097 3221 3.423996 TTAGGGCGTGTTTGTTTTCAC 57.576 42.857 0.00 0.00 0.00 3.18
3101 3225 3.444388 AGGGCGTGTTTGTTTTCACTTTA 59.556 39.130 0.00 0.00 33.07 1.85
3138 3262 1.559682 GCATACCCTTCTCAACCCAGA 59.440 52.381 0.00 0.00 0.00 3.86
3169 3293 1.375551 AAAACAGGCCCTAATACGCG 58.624 50.000 3.53 3.53 0.00 6.01
3181 3305 5.165676 CCCTAATACGCGATATGCAACTTA 58.834 41.667 15.93 0.00 46.97 2.24
3223 3347 3.965347 AGTCCCTGCATTAGGTAATACGT 59.035 43.478 0.00 0.00 45.80 3.57
3317 3441 6.202188 GCGTACATGTTGTGCTTACCTTATAT 59.798 38.462 2.30 0.00 30.49 0.86
3326 3450 7.907841 TGTGCTTACCTTATATCCTAGTTGA 57.092 36.000 0.00 0.00 0.00 3.18
3447 3571 1.899814 ACTGACGATCCACCTTAGCAA 59.100 47.619 0.00 0.00 0.00 3.91
3448 3572 2.501723 ACTGACGATCCACCTTAGCAAT 59.498 45.455 0.00 0.00 0.00 3.56
3586 3710 4.394439 TGTTGCTATACGATGCCACTTA 57.606 40.909 0.00 0.00 0.00 2.24
3622 3746 4.376223 TCCCATGAACTATAAACCCCTGA 58.624 43.478 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.003897 TCGGTATTGGTGTGCTTTTGTTC 59.996 43.478 0.00 0.00 0.00 3.18
23 24 0.036388 CCACTGCACTCGGTATTGGT 60.036 55.000 0.00 0.00 29.07 3.67
28 29 0.250124 CCAAACCACTGCACTCGGTA 60.250 55.000 0.00 0.00 31.12 4.02
50 51 0.462047 GGTGTTCCATGTAGCCCGAG 60.462 60.000 0.00 0.00 0.00 4.63
65 66 4.993029 TTGAATGTTTCGGAAAAGGTGT 57.007 36.364 4.46 0.00 0.00 4.16
133 144 7.706159 ACCGATGTATTTTCACGTGTAGTATA 58.294 34.615 16.51 5.36 0.00 1.47
134 145 6.567050 ACCGATGTATTTTCACGTGTAGTAT 58.433 36.000 16.51 6.31 0.00 2.12
143 154 4.073169 TCGCAAACCGATGTATTTTCAC 57.927 40.909 0.00 0.00 41.89 3.18
155 182 0.457166 TCCGTGTATCTCGCAAACCG 60.457 55.000 0.00 0.00 38.61 4.44
156 183 1.717194 TTCCGTGTATCTCGCAAACC 58.283 50.000 0.00 0.00 0.00 3.27
157 184 2.991190 TCTTTCCGTGTATCTCGCAAAC 59.009 45.455 0.00 0.00 0.00 2.93
162 189 4.092771 TCACTTCTTTCCGTGTATCTCG 57.907 45.455 0.00 0.00 33.07 4.04
172 199 4.024302 ACCGACGATTTTTCACTTCTTTCC 60.024 41.667 0.00 0.00 0.00 3.13
173 200 5.091910 ACCGACGATTTTTCACTTCTTTC 57.908 39.130 0.00 0.00 0.00 2.62
177 204 4.727235 AGAACCGACGATTTTTCACTTC 57.273 40.909 0.00 0.00 0.00 3.01
181 208 8.627403 ACTCTATATAGAACCGACGATTTTTCA 58.373 33.333 13.41 0.00 0.00 2.69
187 218 9.935241 TTAACTACTCTATATAGAACCGACGAT 57.065 33.333 13.41 0.00 0.00 3.73
202 233 8.439993 CAGTATGTGCTCTCTTAACTACTCTA 57.560 38.462 0.00 0.00 0.00 2.43
203 234 7.328277 CAGTATGTGCTCTCTTAACTACTCT 57.672 40.000 0.00 0.00 0.00 3.24
223 254 6.260050 GGAGATTTTGAACACAGTGAACAGTA 59.740 38.462 7.81 0.05 0.00 2.74
227 258 5.499139 TGGAGATTTTGAACACAGTGAAC 57.501 39.130 7.81 1.17 0.00 3.18
266 299 0.738975 ATTGACACGCGAGCTAGCTA 59.261 50.000 19.38 0.00 34.40 3.32
267 300 0.803768 CATTGACACGCGAGCTAGCT 60.804 55.000 19.45 19.45 34.40 3.32
268 301 1.078759 ACATTGACACGCGAGCTAGC 61.079 55.000 15.93 6.62 0.00 3.42
269 302 2.188837 TACATTGACACGCGAGCTAG 57.811 50.000 15.93 0.00 0.00 3.42
270 303 2.863401 ATACATTGACACGCGAGCTA 57.137 45.000 15.93 0.00 0.00 3.32
292 325 8.597227 TCTCCATGTACGTAAATTTTTATGACG 58.403 33.333 8.50 8.50 34.54 4.35
306 339 2.464796 TACCCCATCTCCATGTACGT 57.535 50.000 0.00 0.00 0.00 3.57
308 341 5.104900 GGATGTATACCCCATCTCCATGTAC 60.105 48.000 0.00 0.00 38.95 2.90
309 342 5.030147 GGATGTATACCCCATCTCCATGTA 58.970 45.833 0.00 0.00 38.95 2.29
312 345 3.107601 CGGATGTATACCCCATCTCCAT 58.892 50.000 0.00 0.00 38.95 3.41
313 346 2.158219 ACGGATGTATACCCCATCTCCA 60.158 50.000 0.00 0.00 38.95 3.86
314 347 2.537143 ACGGATGTATACCCCATCTCC 58.463 52.381 0.00 0.00 38.95 3.71
315 348 4.954202 TCATACGGATGTATACCCCATCTC 59.046 45.833 7.68 0.00 39.28 2.75
316 349 4.942944 TCATACGGATGTATACCCCATCT 58.057 43.478 7.68 0.00 39.28 2.90
317 350 5.871396 ATCATACGGATGTATACCCCATC 57.129 43.478 7.68 0.00 39.28 3.51
322 355 8.234136 TCCAGAATATCATACGGATGTATACC 57.766 38.462 7.68 2.13 39.28 2.73
327 360 7.453393 ACATTTCCAGAATATCATACGGATGT 58.547 34.615 7.68 0.00 36.72 3.06
394 433 7.308348 CGGGCTACATGAAGTTCTTCTTAAAAA 60.308 37.037 12.74 0.00 36.40 1.94
395 434 6.148811 CGGGCTACATGAAGTTCTTCTTAAAA 59.851 38.462 12.74 0.00 36.40 1.52
396 435 5.642063 CGGGCTACATGAAGTTCTTCTTAAA 59.358 40.000 12.74 0.00 36.40 1.52
397 436 5.046878 TCGGGCTACATGAAGTTCTTCTTAA 60.047 40.000 12.74 0.00 36.40 1.85
398 437 4.464951 TCGGGCTACATGAAGTTCTTCTTA 59.535 41.667 12.74 2.87 36.40 2.10
402 441 2.678190 GCTCGGGCTACATGAAGTTCTT 60.678 50.000 0.00 0.00 35.22 2.52
404 443 1.291132 GCTCGGGCTACATGAAGTTC 58.709 55.000 0.00 0.00 35.22 3.01
405 444 0.613260 TGCTCGGGCTACATGAAGTT 59.387 50.000 9.62 0.00 39.59 2.66
406 445 0.108138 GTGCTCGGGCTACATGAAGT 60.108 55.000 9.62 0.00 39.59 3.01
408 447 0.323302 TTGTGCTCGGGCTACATGAA 59.677 50.000 9.62 0.00 39.59 2.57
409 448 0.323302 TTTGTGCTCGGGCTACATGA 59.677 50.000 9.62 0.90 39.59 3.07
418 457 2.061028 GAAATGCCTTTTTGTGCTCGG 58.939 47.619 0.00 0.00 0.00 4.63
450 489 2.414994 AGATCCTGCCATGTTGACAG 57.585 50.000 0.00 0.00 0.00 3.51
464 503 1.228094 GCAGCCAGCCCTTAGATCC 60.228 63.158 0.00 0.00 37.23 3.36
493 532 3.360340 GACAGCCCAGCACAGCAC 61.360 66.667 0.00 0.00 0.00 4.40
494 533 4.648626 GGACAGCCCAGCACAGCA 62.649 66.667 0.00 0.00 34.14 4.41
495 534 4.341783 AGGACAGCCCAGCACAGC 62.342 66.667 0.00 0.00 37.41 4.40
496 535 2.359602 CAGGACAGCCCAGCACAG 60.360 66.667 0.00 0.00 37.41 3.66
497 536 3.957586 CCAGGACAGCCCAGCACA 61.958 66.667 0.00 0.00 37.41 4.57
545 584 1.404315 CCGCTCTGTCCCTGTTTAGAC 60.404 57.143 0.00 0.00 0.00 2.59
596 635 1.678970 GAAATGGCCGGAAGCAGGT 60.679 57.895 5.05 0.00 46.50 4.00
649 688 3.306780 CCGTGGCAGGGATTTATAGGTAG 60.307 52.174 21.34 0.00 0.00 3.18
650 689 2.635915 CCGTGGCAGGGATTTATAGGTA 59.364 50.000 21.34 0.00 0.00 3.08
652 691 1.882352 GCCGTGGCAGGGATTTATAGG 60.882 57.143 29.20 0.23 41.49 2.57
674 713 4.733725 TTCGGGGTGAGGAGGGGG 62.734 72.222 0.00 0.00 0.00 5.40
681 720 3.787001 GGGGAGCTTCGGGGTGAG 61.787 72.222 0.00 0.00 0.00 3.51
719 758 0.608640 GACGGTGTGGAGAAGGATGT 59.391 55.000 0.00 0.00 0.00 3.06
720 759 0.108138 GGACGGTGTGGAGAAGGATG 60.108 60.000 0.00 0.00 0.00 3.51
721 760 0.252284 AGGACGGTGTGGAGAAGGAT 60.252 55.000 0.00 0.00 0.00 3.24
722 761 0.898789 GAGGACGGTGTGGAGAAGGA 60.899 60.000 0.00 0.00 0.00 3.36
723 762 1.592223 GAGGACGGTGTGGAGAAGG 59.408 63.158 0.00 0.00 0.00 3.46
724 763 1.185618 TGGAGGACGGTGTGGAGAAG 61.186 60.000 0.00 0.00 0.00 2.85
725 764 1.152419 TGGAGGACGGTGTGGAGAA 60.152 57.895 0.00 0.00 0.00 2.87
726 765 1.906824 GTGGAGGACGGTGTGGAGA 60.907 63.158 0.00 0.00 0.00 3.71
728 767 2.920912 GGTGGAGGACGGTGTGGA 60.921 66.667 0.00 0.00 0.00 4.02
729 768 4.016706 GGGTGGAGGACGGTGTGG 62.017 72.222 0.00 0.00 0.00 4.17
731 770 4.250170 AGGGGTGGAGGACGGTGT 62.250 66.667 0.00 0.00 0.00 4.16
741 782 3.182263 TGGTTGTGGGAGGGGTGG 61.182 66.667 0.00 0.00 0.00 4.61
743 784 2.858974 CCTGGTTGTGGGAGGGGT 60.859 66.667 0.00 0.00 0.00 4.95
746 787 2.531685 TCCCCTGGTTGTGGGAGG 60.532 66.667 0.00 0.00 46.01 4.30
749 790 3.546714 GACGTCCCCTGGTTGTGGG 62.547 68.421 3.51 0.00 44.19 4.61
750 791 2.032071 GACGTCCCCTGGTTGTGG 59.968 66.667 3.51 0.00 0.00 4.17
777 821 1.295292 AGGTGGGTGGTCTATGAGGAT 59.705 52.381 0.00 0.00 0.00 3.24
788 832 3.873812 GGCGGGATAGGTGGGTGG 61.874 72.222 0.00 0.00 0.00 4.61
789 833 4.235762 CGGCGGGATAGGTGGGTG 62.236 72.222 0.00 0.00 0.00 4.61
828 872 0.739813 GCGTGCGTACCTTGAAGGAT 60.740 55.000 19.83 4.89 37.67 3.24
850 894 2.099062 CGACGATTTGCAGGCTGC 59.901 61.111 31.91 31.91 45.29 5.25
857 933 1.012234 GCATCCGACGACGATTTGC 60.012 57.895 9.28 10.58 42.66 3.68
909 985 4.284378 GCTCTCTGCATCACAAAATACC 57.716 45.455 0.00 0.00 42.31 2.73
999 1078 1.613270 TTGTCATCGTCGTCGTCATG 58.387 50.000 1.33 0.00 38.33 3.07
1131 1210 0.888736 TGCCCACGATGTTCTTGGTG 60.889 55.000 0.00 0.00 34.30 4.17
1260 1339 2.035442 GCCGTTCCAGGTGAAGAGC 61.035 63.158 0.00 0.00 32.37 4.09
2106 2185 2.659016 CTGAGCTTGCCCTCGACA 59.341 61.111 0.00 0.00 34.56 4.35
2209 2288 2.730715 CGTCGCCCATTTGGTTGTAATG 60.731 50.000 0.00 0.00 36.04 1.90
2211 2290 0.875728 CGTCGCCCATTTGGTTGTAA 59.124 50.000 0.00 0.00 36.04 2.41
2438 2552 5.657745 ACATGCATCAACTCCATTTCCATTA 59.342 36.000 0.00 0.00 0.00 1.90
2439 2553 4.468510 ACATGCATCAACTCCATTTCCATT 59.531 37.500 0.00 0.00 0.00 3.16
2440 2554 4.028131 ACATGCATCAACTCCATTTCCAT 58.972 39.130 0.00 0.00 0.00 3.41
2441 2555 3.193903 CACATGCATCAACTCCATTTCCA 59.806 43.478 0.00 0.00 0.00 3.53
2819 2934 6.127168 ACCTCCTCGTGTACATCAATCATTTA 60.127 38.462 0.00 0.00 0.00 1.40
2821 2936 4.162320 ACCTCCTCGTGTACATCAATCATT 59.838 41.667 0.00 0.00 0.00 2.57
2822 2937 3.706594 ACCTCCTCGTGTACATCAATCAT 59.293 43.478 0.00 0.00 0.00 2.45
2823 2938 3.096852 ACCTCCTCGTGTACATCAATCA 58.903 45.455 0.00 0.00 0.00 2.57
2824 2939 3.381908 AGACCTCCTCGTGTACATCAATC 59.618 47.826 0.00 0.00 0.00 2.67
2825 2940 3.366396 AGACCTCCTCGTGTACATCAAT 58.634 45.455 0.00 0.00 0.00 2.57
2826 2941 2.803956 AGACCTCCTCGTGTACATCAA 58.196 47.619 0.00 0.00 0.00 2.57
2849 2964 1.690219 AACTCATCCTGGCGGCCTAG 61.690 60.000 21.46 15.04 0.00 3.02
2850 2965 1.271840 AAACTCATCCTGGCGGCCTA 61.272 55.000 21.46 6.15 0.00 3.93
2851 2966 2.606587 AAACTCATCCTGGCGGCCT 61.607 57.895 21.46 0.00 0.00 5.19
2853 2968 1.244019 AACAAACTCATCCTGGCGGC 61.244 55.000 0.00 0.00 0.00 6.53
2855 2970 1.200020 GGAAACAAACTCATCCTGGCG 59.800 52.381 0.00 0.00 0.00 5.69
2857 2972 2.504367 ACGGAAACAAACTCATCCTGG 58.496 47.619 0.00 0.00 0.00 4.45
2858 2973 5.880054 ATAACGGAAACAAACTCATCCTG 57.120 39.130 0.00 0.00 0.00 3.86
2859 2974 5.768164 ACAATAACGGAAACAAACTCATCCT 59.232 36.000 0.00 0.00 0.00 3.24
2896 3014 5.847111 ATGGAGTACGTACACACATACAT 57.153 39.130 26.55 14.91 0.00 2.29
2897 3015 5.416639 AGAATGGAGTACGTACACACATACA 59.583 40.000 26.55 13.28 0.00 2.29
2898 3016 5.888105 AGAATGGAGTACGTACACACATAC 58.112 41.667 26.55 7.78 0.00 2.39
2899 3017 6.071784 ACAAGAATGGAGTACGTACACACATA 60.072 38.462 26.55 9.25 0.00 2.29
2900 3018 5.168569 CAAGAATGGAGTACGTACACACAT 58.831 41.667 26.55 21.72 0.00 3.21
2901 3019 4.038282 ACAAGAATGGAGTACGTACACACA 59.962 41.667 26.55 20.60 0.00 3.72
2902 3020 4.384846 CACAAGAATGGAGTACGTACACAC 59.615 45.833 26.55 16.05 0.00 3.82
2903 3021 4.038282 ACACAAGAATGGAGTACGTACACA 59.962 41.667 26.55 23.20 0.00 3.72
2954 3072 2.806288 AAAATCGATCGCCAAGAACG 57.194 45.000 11.09 0.00 44.98 3.95
3022 3144 2.746279 TTGTTCTTTTGAGAGGGGCA 57.254 45.000 0.00 0.00 0.00 5.36
3055 3177 9.907229 CCTAATTTTCTTTCCAAGGTAGTCTAT 57.093 33.333 0.00 0.00 0.00 1.98
3058 3180 6.127703 GCCCTAATTTTCTTTCCAAGGTAGTC 60.128 42.308 0.00 0.00 0.00 2.59
3059 3181 5.715279 GCCCTAATTTTCTTTCCAAGGTAGT 59.285 40.000 0.00 0.00 0.00 2.73
3060 3182 5.163652 CGCCCTAATTTTCTTTCCAAGGTAG 60.164 44.000 0.00 0.00 0.00 3.18
3064 3186 4.022329 ACACGCCCTAATTTTCTTTCCAAG 60.022 41.667 0.00 0.00 0.00 3.61
3091 3215 6.044046 TGCGACTACTGTTCTAAAGTGAAAA 58.956 36.000 0.00 0.00 0.00 2.29
3097 3221 4.388773 TGCAATGCGACTACTGTTCTAAAG 59.611 41.667 0.00 0.00 0.00 1.85
3101 3225 2.455674 TGCAATGCGACTACTGTTCT 57.544 45.000 0.00 0.00 0.00 3.01
3138 3262 2.893489 GGCCTGTTTTTCCTCAATCAGT 59.107 45.455 0.00 0.00 0.00 3.41
3181 3305 2.226962 AGAGATGCAGGCAACCAAAT 57.773 45.000 0.00 0.00 37.17 2.32
3223 3347 3.677424 GCCAACCAAACAAAGTGCACTTA 60.677 43.478 31.31 0.00 34.61 2.24
3317 3441 3.451178 GTGGGTAAGCTCATCAACTAGGA 59.549 47.826 0.00 0.00 0.00 2.94
3326 3450 4.202441 GTGATCATTGTGGGTAAGCTCAT 58.798 43.478 0.00 0.00 0.00 2.90
3447 3571 4.099419 GGTTGGAGTTGTCAAAGTGGAAAT 59.901 41.667 0.00 0.00 0.00 2.17
3448 3572 3.445805 GGTTGGAGTTGTCAAAGTGGAAA 59.554 43.478 0.00 0.00 0.00 3.13
3586 3710 1.760613 CATGGGAAGAAGCCAATGCAT 59.239 47.619 0.00 0.00 41.13 3.96
3622 3746 2.346803 CCGTGTTCATCGATGAGGTTT 58.653 47.619 25.95 0.00 38.19 3.27


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

AutoCloner maintained by Alex Coulton.