Multiple sequence alignment - TraesCS1D01G252300

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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 TraesCS1D01G252300 chr1D 100.000 3195 0 0 1 3195 344605024 344608218 0.000000e+00 5901.0
1 TraesCS1D01G252300 chr1D 89.655 58 6 0 1268 1325 68446377 68446434 1.230000e-09 75.0
2 TraesCS1D01G252300 chr1B 92.711 2744 150 22 362 3094 466077345 466074641 0.000000e+00 3914.0
3 TraesCS1D01G252300 chr1B 89.899 99 7 2 3100 3195 466074463 466074365 1.200000e-24 124.0
4 TraesCS1D01G252300 chr1A 93.946 2428 107 14 361 2762 444135698 444138111 0.000000e+00 3633.0
5 TraesCS1D01G252300 chr1A 94.521 438 18 3 2763 3195 444143945 444144381 0.000000e+00 671.0
6 TraesCS1D01G252300 chr1A 85.204 392 35 11 1 372 444135258 444135646 6.470000e-102 381.0
7 TraesCS1D01G252300 chr1A 95.745 47 2 0 1279 1325 66892813 66892859 3.420000e-10 76.8
8 TraesCS1D01G252300 chr6B 86.331 139 19 0 1001 1139 652631344 652631206 5.520000e-33 152.0
9 TraesCS1D01G252300 chr6A 86.331 139 19 0 1001 1139 578887719 578887581 5.520000e-33 152.0
10 TraesCS1D01G252300 chr6D 85.612 139 20 0 1001 1139 432710580 432710442 2.570000e-31 147.0
11 TraesCS1D01G252300 chr3B 82.051 117 21 0 1268 1384 103722465 103722349 2.030000e-17 100.0
12 TraesCS1D01G252300 chr3D 83.962 106 13 4 1268 1371 352367944 352367841 7.290000e-17 99.0
13 TraesCS1D01G252300 chr4B 95.349 43 2 0 1277 1319 601792346 601792388 5.720000e-08 69.4


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 TraesCS1D01G252300 chr1D 344605024 344608218 3194 False 5901 5901 100.000 1 3195 1 chr1D.!!$F2 3194
1 TraesCS1D01G252300 chr1B 466074365 466077345 2980 True 2019 3914 91.305 362 3195 2 chr1B.!!$R1 2833
2 TraesCS1D01G252300 chr1A 444135258 444138111 2853 False 2007 3633 89.575 1 2762 2 chr1A.!!$F3 2761

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
179 180 0.112412 ACACAACCTCCCCACAATCC 59.888 55.0 0.0 0.0 0.00 3.01 F
955 1061 0.317020 GACTCACAACGCAAGGCAAC 60.317 55.0 0.0 0.0 46.39 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1864 0.325203 AAGGGGTTGTTGTGGTTGCT 60.325 50.0 0.0 0.0 0.00 3.91 R
2650 2767 0.178950 ATCGATGCAGAGGCTAGGGA 60.179 55.0 0.0 0.0 41.91 4.20 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 2.543012 CACTTCTGATCATCGATGCACC 59.457 50.000 20.81 11.73 0.00 5.01
23 24 2.141517 CTTCTGATCATCGATGCACCC 58.858 52.381 20.81 9.40 0.00 4.61
24 25 0.394192 TCTGATCATCGATGCACCCC 59.606 55.000 20.81 7.75 0.00 4.95
43 44 1.565305 CTGTCTCGCTGATGTTAGCC 58.435 55.000 0.00 0.00 40.59 3.93
111 112 1.936547 CTCGGTCAAGCTAGATTTGGC 59.063 52.381 0.00 0.00 0.00 4.52
128 129 4.100479 CCTTGCTGGCATTCACCA 57.900 55.556 0.00 0.00 38.29 4.17
160 161 3.749064 GAGGAGTGCCGCGTCTCA 61.749 66.667 19.27 7.09 39.96 3.27
179 180 0.112412 ACACAACCTCCCCACAATCC 59.888 55.000 0.00 0.00 0.00 3.01
188 189 1.535204 CCCCACAATCCAGCCAACAC 61.535 60.000 0.00 0.00 0.00 3.32
190 191 0.540365 CCACAATCCAGCCAACACCT 60.540 55.000 0.00 0.00 0.00 4.00
191 192 0.599558 CACAATCCAGCCAACACCTG 59.400 55.000 0.00 0.00 0.00 4.00
192 193 0.478072 ACAATCCAGCCAACACCTGA 59.522 50.000 0.00 0.00 32.03 3.86
194 195 2.308570 ACAATCCAGCCAACACCTGATA 59.691 45.455 0.00 0.00 32.03 2.15
203 223 4.410228 AGCCAACACCTGATACATCTATGT 59.590 41.667 0.63 0.63 44.48 2.29
216 236 9.952030 TGATACATCTATGTTTGACCAAGTTTA 57.048 29.630 0.12 0.00 41.97 2.01
232 252 9.665264 GACCAAGTTTACAAGAAAAAGTATGAG 57.335 33.333 0.00 0.00 0.00 2.90
235 255 9.683069 CAAGTTTACAAGAAAAAGTATGAGCAT 57.317 29.630 0.00 0.00 0.00 3.79
254 274 9.836864 ATGAGCATCTACAATATGAAGTAAACA 57.163 29.630 0.00 0.00 34.92 2.83
316 336 6.991531 AGTAATTTTGCATTGTGGTTGTTGAT 59.008 30.769 0.00 0.00 0.00 2.57
344 364 8.934023 TTTCCTCTATAAACTTGGTCAAATGT 57.066 30.769 0.00 0.00 0.00 2.71
346 366 9.444600 TTCCTCTATAAACTTGGTCAAATGTAC 57.555 33.333 0.00 0.00 0.00 2.90
358 378 8.705048 TTGGTCAAATGTACAAAAAGTTAACC 57.295 30.769 0.00 2.15 0.00 2.85
359 379 7.837863 TGGTCAAATGTACAAAAAGTTAACCA 58.162 30.769 0.00 4.67 0.00 3.67
398 480 6.943718 ACACCTTATATTTTTGAAACGGAGGA 59.056 34.615 0.00 0.00 0.00 3.71
552 642 0.539986 TCTTATCCCTGGGCGTGTTC 59.460 55.000 8.22 0.00 0.00 3.18
590 685 2.563702 GGTCACTCTCTAGACCCTACG 58.436 57.143 0.00 0.00 46.79 3.51
597 692 4.101430 ACTCTCTAGACCCTACGTTCCTAG 59.899 50.000 0.00 0.00 0.00 3.02
600 695 5.663106 TCTCTAGACCCTACGTTCCTAGTAA 59.337 44.000 0.00 0.00 0.00 2.24
601 696 6.156949 TCTCTAGACCCTACGTTCCTAGTAAA 59.843 42.308 0.00 0.00 0.00 2.01
602 697 6.904626 TCTAGACCCTACGTTCCTAGTAAAT 58.095 40.000 0.00 0.00 0.00 1.40
603 698 6.995091 TCTAGACCCTACGTTCCTAGTAAATC 59.005 42.308 0.00 0.00 0.00 2.17
604 699 5.764432 AGACCCTACGTTCCTAGTAAATCT 58.236 41.667 0.00 0.00 0.00 2.40
605 700 6.904626 AGACCCTACGTTCCTAGTAAATCTA 58.095 40.000 0.00 0.00 0.00 1.98
606 701 7.349598 AGACCCTACGTTCCTAGTAAATCTAA 58.650 38.462 0.00 0.00 0.00 2.10
644 741 2.940410 CTGGTTTTCAACGTACAGGTGT 59.060 45.455 0.00 0.00 39.03 4.16
667 766 1.905637 TACACTCCTCGTCTGCTCAA 58.094 50.000 0.00 0.00 0.00 3.02
749 852 3.091318 GCATGAGCAGCATAGGTGT 57.909 52.632 0.00 0.00 41.58 4.16
785 888 6.340962 ACAATAAAAGGGCTTCCAAAGTAC 57.659 37.500 0.00 0.00 0.00 2.73
786 889 6.075315 ACAATAAAAGGGCTTCCAAAGTACT 58.925 36.000 0.00 0.00 0.00 2.73
787 890 6.208797 ACAATAAAAGGGCTTCCAAAGTACTC 59.791 38.462 0.00 0.00 0.00 2.59
895 1001 3.521727 TCTGCTCCTATAAATCCCTCCC 58.478 50.000 0.00 0.00 0.00 4.30
955 1061 0.317020 GACTCACAACGCAAGGCAAC 60.317 55.000 0.00 0.00 46.39 4.17
956 1062 1.029408 ACTCACAACGCAAGGCAACA 61.029 50.000 0.00 0.00 46.39 3.33
969 1075 1.202114 AGGCAACACAACACAACACAG 59.798 47.619 0.00 0.00 41.41 3.66
1149 1257 6.828273 CACACAAGATTGGTAATTATCTCCCA 59.172 38.462 0.00 0.00 30.95 4.37
1420 1532 5.278758 GCAGGTACACATACAAACACCAAAT 60.279 40.000 0.00 0.00 32.40 2.32
1478 1591 2.264005 TGTTTGTGCTAATCCGGTGT 57.736 45.000 0.00 0.00 0.00 4.16
1751 1864 2.202236 GAACCCCCTCAGCAGCATCA 62.202 60.000 0.00 0.00 0.00 3.07
1828 1941 0.951558 CCACCCACAGTAACAACAGC 59.048 55.000 0.00 0.00 0.00 4.40
1952 2065 1.893062 CAGATGGAGACGACAGCCA 59.107 57.895 0.00 0.00 35.91 4.75
1955 2068 1.888436 GATGGAGACGACAGCCACCA 61.888 60.000 2.09 0.00 33.93 4.17
1956 2069 1.267574 ATGGAGACGACAGCCACCAT 61.268 55.000 0.00 0.00 33.93 3.55
1957 2070 1.448540 GGAGACGACAGCCACCATG 60.449 63.158 0.00 0.00 0.00 3.66
2041 2157 0.682855 AGGAGCTTCTCTACAGCGCT 60.683 55.000 2.64 2.64 42.55 5.92
2062 2178 2.947890 GACGACGACGACCGACAGT 61.948 63.158 15.32 5.56 42.66 3.55
2104 2220 1.137872 GTGGACTGGTGGAGCTATGAG 59.862 57.143 0.00 0.00 0.00 2.90
2112 2228 1.071128 GGAGCTATGAGCAGGGCAG 59.929 63.158 0.64 0.00 45.56 4.85
2171 2287 1.835494 CTCGGTTCTCCAGGACTACA 58.165 55.000 0.00 0.00 0.00 2.74
2173 2289 0.170561 CGGTTCTCCAGGACTACACG 59.829 60.000 0.00 0.00 0.00 4.49
2174 2290 1.254954 GGTTCTCCAGGACTACACGT 58.745 55.000 0.00 0.00 0.00 4.49
2220 2336 5.367945 AAGTGTGAAGAGGACCAAGTTAA 57.632 39.130 0.00 0.00 0.00 2.01
2281 2397 6.538742 TCTTGTAAGAGTCCAAAGAAACTGTG 59.461 38.462 0.00 0.00 0.00 3.66
2370 2486 7.228706 CAACAAAGGTATGTAAGAACAGGTTCT 59.771 37.037 8.82 8.82 41.14 3.01
2371 2487 7.228706 AACAAAGGTATGTAAGAACAGGTTCTG 59.771 37.037 14.88 0.00 39.69 3.02
2429 2545 5.669477 AGAACAGATAAGAGGAACATGAGC 58.331 41.667 0.00 0.00 0.00 4.26
2466 2582 8.713271 GCTTGTAGTACATATATCCTCTTTTGC 58.287 37.037 3.28 0.00 0.00 3.68
2508 2625 4.380973 GGAAACTCTGACATCATCGACTCA 60.381 45.833 0.00 0.00 0.00 3.41
2579 2696 0.601311 GCTATCCATCGTCAGTGGGC 60.601 60.000 0.00 0.00 37.34 5.36
2584 2701 0.882042 CCATCGTCAGTGGGCTATGC 60.882 60.000 0.00 0.00 32.98 3.14
2650 2767 7.283127 ACTGTATTCTTGAAACACAGACACAAT 59.717 33.333 23.28 7.67 39.13 2.71
2706 2823 5.999044 AGTGGAGCATTATTCATCAACTCT 58.001 37.500 0.00 0.00 0.00 3.24
2765 2882 0.320160 AACCGGCCTACAGAACGAAC 60.320 55.000 0.00 0.00 0.00 3.95
2790 2907 5.409520 TGACAACATCTGATCAACAGCTAAC 59.590 40.000 0.00 0.00 45.38 2.34
2828 2945 3.402110 TGACATCACATGGTTCACTGTC 58.598 45.455 0.00 2.31 33.79 3.51
2830 2947 2.106338 ACATCACATGGTTCACTGTCCA 59.894 45.455 0.00 0.00 38.14 4.02
2840 2957 3.003689 GGTTCACTGTCCAACATGAACAG 59.996 47.826 22.21 9.88 42.08 3.16
2855 2972 3.797039 TGAACAGATATGTAGCACAGCC 58.203 45.455 0.00 0.00 0.00 4.85
2874 2991 1.541233 CCGATGCTGGTTAGATCACCC 60.541 57.143 0.00 0.00 35.73 4.61
2897 3014 6.366061 CCCTTCACTAAAATGCAGTTTTTAGC 59.634 38.462 23.33 0.00 46.20 3.09
2901 3018 2.415697 AAATGCAGTTTTTAGCGCGT 57.584 40.000 8.43 0.00 0.00 6.01
2911 3028 4.565564 AGTTTTTAGCGCGTACCTCAATAG 59.434 41.667 8.43 0.00 0.00 1.73
2936 3053 3.641437 TGCAAAATTCCTTGTCCGAAG 57.359 42.857 0.00 0.00 0.00 3.79
2939 3056 4.229876 GCAAAATTCCTTGTCCGAAGAAG 58.770 43.478 0.00 0.00 0.00 2.85
2999 3116 5.310409 TCCCAATTATAAGAGCAGGAAGG 57.690 43.478 0.00 0.00 0.00 3.46
3012 3129 3.010420 GCAGGAAGGGTCAGAACATAAC 58.990 50.000 0.00 0.00 0.00 1.89
3017 3134 7.112779 CAGGAAGGGTCAGAACATAACTATTT 58.887 38.462 0.00 0.00 0.00 1.40
3025 3142 8.258708 GGTCAGAACATAACTATTTACCTGAGT 58.741 37.037 0.00 0.00 0.00 3.41
3041 3158 1.078848 AGTTGGATGTCGCTCTGGC 60.079 57.895 0.00 0.00 0.00 4.85
3049 3166 3.785859 TCGCTCTGGCCCATCACC 61.786 66.667 0.00 0.00 34.44 4.02
3051 3168 2.679716 GCTCTGGCCCATCACCTT 59.320 61.111 0.00 0.00 0.00 3.50
3061 3179 3.119137 GGCCCATCACCTTCATTAACAAC 60.119 47.826 0.00 0.00 0.00 3.32
3063 3181 4.085733 CCCATCACCTTCATTAACAACCA 58.914 43.478 0.00 0.00 0.00 3.67
3066 3184 3.761897 TCACCTTCATTAACAACCAGGG 58.238 45.455 0.00 0.00 0.00 4.45
3081 3199 5.768164 ACAACCAGGGTTTCTACAATAACAG 59.232 40.000 0.00 0.00 36.00 3.16
3083 3201 4.042934 ACCAGGGTTTCTACAATAACAGCT 59.957 41.667 0.00 0.00 0.00 4.24
3087 3205 6.037610 CAGGGTTTCTACAATAACAGCTGATC 59.962 42.308 23.35 0.00 0.00 2.92
3094 3212 5.426689 ACAATAACAGCTGATCTCTTGGA 57.573 39.130 23.35 0.00 0.00 3.53
3095 3213 5.181748 ACAATAACAGCTGATCTCTTGGAC 58.818 41.667 23.35 0.00 0.00 4.02
3098 3388 3.996921 ACAGCTGATCTCTTGGACAAT 57.003 42.857 23.35 0.00 0.00 2.71
3144 3437 5.365403 TGGAAAATAGTTTACTGTTGCCG 57.635 39.130 0.00 0.00 30.43 5.69
3146 3439 4.456566 GGAAAATAGTTTACTGTTGCCGGA 59.543 41.667 5.05 0.00 0.00 5.14
3180 3473 1.847737 TGGTTCCTACACCAAACCAGT 59.152 47.619 2.19 0.00 45.62 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.395686 AGGGGTGCATCGATGATCAG 59.604 55.000 29.20 2.09 0.00 2.90
14 15 2.202797 CGAGACAGGGGTGCATCG 60.203 66.667 0.00 0.00 0.00 3.84
22 23 1.804372 GCTAACATCAGCGAGACAGGG 60.804 57.143 0.00 0.00 0.00 4.45
23 24 1.565305 GCTAACATCAGCGAGACAGG 58.435 55.000 0.00 0.00 0.00 4.00
24 25 1.565305 GGCTAACATCAGCGAGACAG 58.435 55.000 0.00 0.00 42.76 3.51
98 99 2.097825 CAGCAAGGCCAAATCTAGCTT 58.902 47.619 5.01 0.00 0.00 3.74
128 129 2.055042 CCTCCGCCTCACTACTGCT 61.055 63.158 0.00 0.00 0.00 4.24
131 132 0.681564 CACTCCTCCGCCTCACTACT 60.682 60.000 0.00 0.00 0.00 2.57
132 133 1.810532 CACTCCTCCGCCTCACTAC 59.189 63.158 0.00 0.00 0.00 2.73
134 135 3.386237 GCACTCCTCCGCCTCACT 61.386 66.667 0.00 0.00 0.00 3.41
160 161 0.112412 GGATTGTGGGGAGGTTGTGT 59.888 55.000 0.00 0.00 0.00 3.72
179 180 3.272574 AGATGTATCAGGTGTTGGCTG 57.727 47.619 0.00 0.00 0.00 4.85
188 189 7.050377 ACTTGGTCAAACATAGATGTATCAGG 58.950 38.462 0.00 0.00 40.80 3.86
190 191 8.862325 AAACTTGGTCAAACATAGATGTATCA 57.138 30.769 0.00 0.00 40.80 2.15
192 193 9.733556 TGTAAACTTGGTCAAACATAGATGTAT 57.266 29.630 0.00 0.00 40.80 2.29
194 195 8.458573 TTGTAAACTTGGTCAAACATAGATGT 57.541 30.769 0.00 0.00 44.20 3.06
216 236 8.621532 TTGTAGATGCTCATACTTTTTCTTGT 57.378 30.769 0.00 0.00 0.00 3.16
294 314 6.696441 AATCAACAACCACAATGCAAAATT 57.304 29.167 0.00 0.00 0.00 1.82
300 320 6.165577 AGGAAATAATCAACAACCACAATGC 58.834 36.000 0.00 0.00 0.00 3.56
301 321 7.605449 AGAGGAAATAATCAACAACCACAATG 58.395 34.615 0.00 0.00 0.00 2.82
304 324 9.967451 TTATAGAGGAAATAATCAACAACCACA 57.033 29.630 0.00 0.00 0.00 4.17
335 355 8.880878 ATGGTTAACTTTTTGTACATTTGACC 57.119 30.769 5.42 3.06 0.00 4.02
442 525 4.906065 GCATGACTGCTAATCAATCCAA 57.094 40.909 0.00 0.00 45.32 3.53
471 561 4.329638 TCCTTTAGAATCCCATGGCAAA 57.670 40.909 6.09 0.00 0.00 3.68
600 695 7.657761 CCAGCTCCTATGAACGTAAATTAGATT 59.342 37.037 0.00 0.00 0.00 2.40
601 696 7.155328 CCAGCTCCTATGAACGTAAATTAGAT 58.845 38.462 0.00 0.00 0.00 1.98
602 697 6.097839 ACCAGCTCCTATGAACGTAAATTAGA 59.902 38.462 0.00 0.00 0.00 2.10
603 698 6.281405 ACCAGCTCCTATGAACGTAAATTAG 58.719 40.000 0.00 0.00 0.00 1.73
604 699 6.229936 ACCAGCTCCTATGAACGTAAATTA 57.770 37.500 0.00 0.00 0.00 1.40
605 700 5.099042 ACCAGCTCCTATGAACGTAAATT 57.901 39.130 0.00 0.00 0.00 1.82
606 701 4.755266 ACCAGCTCCTATGAACGTAAAT 57.245 40.909 0.00 0.00 0.00 1.40
617 714 2.922740 ACGTTGAAAACCAGCTCCTA 57.077 45.000 0.00 0.00 46.28 2.94
644 741 1.961394 AGCAGACGAGGAGTGTAACAA 59.039 47.619 0.00 0.00 41.43 2.83
749 852 3.436577 TTTATTGTTACCTTGGCCGGA 57.563 42.857 5.05 0.00 0.00 5.14
785 888 2.492090 CCGGCTCTTCTCGTGGAG 59.508 66.667 0.00 0.00 0.00 3.86
786 889 3.760035 GCCGGCTCTTCTCGTGGA 61.760 66.667 22.15 0.00 0.00 4.02
787 890 3.997064 CTGCCGGCTCTTCTCGTGG 62.997 68.421 29.70 0.93 0.00 4.94
895 1001 2.972505 GATGTGGTATGCGCGGGG 60.973 66.667 8.83 0.00 0.00 5.73
905 1011 1.063266 AGTTGGTTTGGGTGATGTGGT 60.063 47.619 0.00 0.00 0.00 4.16
955 1061 1.467883 CCTGTGCTGTGTTGTGTTGTG 60.468 52.381 0.00 0.00 0.00 3.33
956 1062 0.810648 CCTGTGCTGTGTTGTGTTGT 59.189 50.000 0.00 0.00 0.00 3.32
969 1075 4.017877 GCGTGTGTGAGCCTGTGC 62.018 66.667 0.00 0.00 37.95 4.57
985 1091 1.269726 CCCCATTGAAGTTGTGTGTGC 60.270 52.381 0.00 0.00 0.00 4.57
1120 1228 6.663093 AGATAATTACCAATCTTGTGTGGCAA 59.337 34.615 0.00 0.00 38.58 4.52
1149 1257 9.175312 GATGCTTGGATGATGAACATATATCTT 57.825 33.333 0.00 0.00 39.56 2.40
1420 1532 5.781306 TGTGGAGACTACATTAGTGGGTTAA 59.219 40.000 0.00 0.00 39.59 2.01
1478 1591 2.455557 CCTGGTTGGTTAATCATGGCA 58.544 47.619 0.00 0.00 0.00 4.92
1534 1647 3.553105 AGTAGTTTTTGACGTCGTTGTCC 59.447 43.478 11.62 0.00 38.11 4.02
1549 1662 3.118038 TGAGCTTGGTGTTCCAGTAGTTT 60.118 43.478 0.00 0.00 45.22 2.66
1751 1864 0.325203 AAGGGGTTGTTGTGGTTGCT 60.325 50.000 0.00 0.00 0.00 3.91
1813 1926 3.119673 TGTTGTTGCTGTTGTTACTGTGG 60.120 43.478 0.00 0.00 0.00 4.17
1828 1941 1.921887 CTGCTGTTGCTGTTGTTGTTG 59.078 47.619 0.00 0.00 40.48 3.33
1916 2029 4.379243 CTGCTGTCCGCCGAGGTT 62.379 66.667 0.00 0.00 41.99 3.50
2041 2157 2.430075 TCGGTCGTCGTCGTCGTA 60.430 61.111 11.41 0.00 40.32 3.43
2062 2178 2.661537 CCTTGCTGCGTGACGACA 60.662 61.111 10.10 5.49 0.00 4.35
2171 2287 0.892755 ATGTCATACACCACGGACGT 59.107 50.000 0.00 0.00 33.04 4.34
2173 2289 1.999735 CACATGTCATACACCACGGAC 59.000 52.381 0.00 0.00 0.00 4.79
2174 2290 1.896465 TCACATGTCATACACCACGGA 59.104 47.619 0.00 0.00 0.00 4.69
2176 2292 3.063485 TGTTCACATGTCATACACCACG 58.937 45.455 0.00 0.00 0.00 4.94
2220 2336 5.679606 ACAAATCCCTATTACCACCCCTAAT 59.320 40.000 0.00 0.00 0.00 1.73
2370 2486 3.118629 TGCCAAGTTACATTTGTTTGCCA 60.119 39.130 0.00 0.00 0.00 4.92
2371 2487 3.247411 GTGCCAAGTTACATTTGTTTGCC 59.753 43.478 0.00 0.00 0.00 4.52
2429 2545 3.505680 TGTACTACAAGCCTTGCAAATGG 59.494 43.478 3.88 0.00 0.00 3.16
2495 2612 2.728007 TCAGTCCTGAGTCGATGATGT 58.272 47.619 0.00 0.00 34.14 3.06
2508 2625 1.147817 AGGGGCATTGTTTTCAGTCCT 59.852 47.619 0.00 0.00 0.00 3.85
2579 2696 4.051922 GGACAGTATGAAGGTTCGCATAG 58.948 47.826 0.00 0.00 39.69 2.23
2650 2767 0.178950 ATCGATGCAGAGGCTAGGGA 60.179 55.000 0.00 0.00 41.91 4.20
2675 2792 5.316167 TGAATAATGCTCCACTCTTGTGTT 58.684 37.500 0.00 0.00 42.34 3.32
2681 2798 5.999044 AGTTGATGAATAATGCTCCACTCT 58.001 37.500 0.00 0.00 0.00 3.24
2682 2799 6.054295 AGAGTTGATGAATAATGCTCCACTC 58.946 40.000 0.00 0.00 33.09 3.51
2706 2823 5.641783 TTGCATGCTTTCTTATGTAGCAA 57.358 34.783 20.33 0.00 46.78 3.91
2765 2882 4.001652 AGCTGTTGATCAGATGTTGTCAG 58.998 43.478 0.00 0.00 46.27 3.51
2809 2926 2.106338 TGGACAGTGAACCATGTGATGT 59.894 45.455 0.00 0.00 0.00 3.06
2828 2945 5.585844 TGTGCTACATATCTGTTCATGTTGG 59.414 40.000 0.00 0.00 36.74 3.77
2830 2947 5.295292 GCTGTGCTACATATCTGTTCATGTT 59.705 40.000 0.00 0.00 36.74 2.71
2840 2957 1.728971 GCATCGGCTGTGCTACATATC 59.271 52.381 11.41 0.00 39.45 1.63
2855 2972 1.414181 AGGGTGATCTAACCAGCATCG 59.586 52.381 4.72 0.00 42.47 3.84
2862 2979 6.183360 GCATTTTAGTGAAGGGTGATCTAACC 60.183 42.308 0.00 0.00 39.71 2.85
2897 3014 2.281762 GCAACTTCTATTGAGGTACGCG 59.718 50.000 3.53 3.53 31.98 6.01
2901 3018 7.669722 AGGAATTTTGCAACTTCTATTGAGGTA 59.330 33.333 16.45 0.00 31.98 3.08
2911 3028 3.735746 CGGACAAGGAATTTTGCAACTTC 59.264 43.478 0.00 5.49 0.00 3.01
2936 3053 6.917217 AGCATGCTTAGAATAAGACACTTC 57.083 37.500 16.30 0.00 0.00 3.01
2939 3056 7.539712 TGTAAGCATGCTTAGAATAAGACAC 57.460 36.000 34.78 23.28 38.95 3.67
2999 3116 8.258708 ACTCAGGTAAATAGTTATGTTCTGACC 58.741 37.037 0.00 0.00 0.00 4.02
3012 3129 4.508124 GCGACATCCAACTCAGGTAAATAG 59.492 45.833 0.00 0.00 0.00 1.73
3017 3134 1.476891 GAGCGACATCCAACTCAGGTA 59.523 52.381 0.00 0.00 0.00 3.08
3025 3142 2.268920 GGCCAGAGCGACATCCAA 59.731 61.111 0.00 0.00 41.24 3.53
3041 3158 4.085733 TGGTTGTTAATGAAGGTGATGGG 58.914 43.478 0.00 0.00 0.00 4.00
3049 3166 6.488683 TGTAGAAACCCTGGTTGTTAATGAAG 59.511 38.462 1.58 0.00 38.47 3.02
3051 3168 5.942961 TGTAGAAACCCTGGTTGTTAATGA 58.057 37.500 1.58 0.00 38.47 2.57
3061 3179 4.396166 CAGCTGTTATTGTAGAAACCCTGG 59.604 45.833 5.25 0.00 0.00 4.45
3063 3181 5.499004 TCAGCTGTTATTGTAGAAACCCT 57.501 39.130 14.67 0.00 0.00 4.34
3066 3184 8.386606 CAAGAGATCAGCTGTTATTGTAGAAAC 58.613 37.037 14.67 0.00 0.00 2.78
3081 3199 5.009410 CCCAAATATTGTCCAAGAGATCAGC 59.991 44.000 0.00 0.00 0.00 4.26
3083 3201 6.325993 TCCCAAATATTGTCCAAGAGATCA 57.674 37.500 0.00 0.00 0.00 2.92
3087 3205 6.780457 ACATTCCCAAATATTGTCCAAGAG 57.220 37.500 0.00 0.00 0.00 2.85
3119 3409 6.866248 CGGCAACAGTAAACTATTTTCCATTT 59.134 34.615 0.00 0.00 0.00 2.32
3122 3412 4.216687 CCGGCAACAGTAAACTATTTTCCA 59.783 41.667 0.00 0.00 0.00 3.53
3124 3417 5.616488 TCCGGCAACAGTAAACTATTTTC 57.384 39.130 0.00 0.00 0.00 2.29
3125 3418 6.584185 AATCCGGCAACAGTAAACTATTTT 57.416 33.333 0.00 0.00 0.00 1.82
3128 3421 6.202188 CGATTAATCCGGCAACAGTAAACTAT 59.798 38.462 9.87 0.00 0.00 2.12
3129 3422 5.521010 CGATTAATCCGGCAACAGTAAACTA 59.479 40.000 9.87 0.00 0.00 2.24
3133 3426 3.866910 GTCGATTAATCCGGCAACAGTAA 59.133 43.478 9.87 0.00 0.00 2.24
3136 3429 2.276201 TGTCGATTAATCCGGCAACAG 58.724 47.619 9.87 0.00 38.78 3.16
3142 3435 3.202906 ACCACAATGTCGATTAATCCGG 58.797 45.455 9.87 0.00 0.00 5.14
3144 3437 4.881850 AGGAACCACAATGTCGATTAATCC 59.118 41.667 9.87 0.00 0.00 3.01
3146 3439 6.315393 GTGTAGGAACCACAATGTCGATTAAT 59.685 38.462 0.00 0.00 33.00 1.40


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

AutoCloner maintained by Alex Coulton.