Multiple sequence alignment - TraesCS7A01G404800

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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 TraesCS7A01G404800 chr7A 100.000 3158 0 0 1 3158 587364061 587367218 0.000000e+00 5832.0
1 TraesCS7A01G404800 chr7A 84.942 684 64 15 2503 3149 4555483 4554802 0.000000e+00 656.0
2 TraesCS7A01G404800 chr7A 84.064 502 52 16 2385 2860 610272774 610272275 2.870000e-125 459.0
3 TraesCS7A01G404800 chr7D 95.252 2359 84 14 13 2350 514073959 514076310 0.000000e+00 3711.0
4 TraesCS7A01G404800 chr7B 95.446 2218 83 8 146 2350 544910995 544913207 0.000000e+00 3520.0
5 TraesCS7A01G404800 chr6D 89.273 839 60 9 2350 3158 324791970 324792808 0.000000e+00 1024.0
6 TraesCS7A01G404800 chr6D 73.741 278 53 17 1433 1700 127379947 127379680 1.210000e-14 91.6
7 TraesCS7A01G404800 chr3A 86.920 841 74 16 2351 3158 640500661 640499824 0.000000e+00 911.0
8 TraesCS7A01G404800 chr2D 86.633 793 72 20 2389 3149 433718412 433719202 0.000000e+00 846.0
9 TraesCS7A01G404800 chr2D 85.602 764 74 23 2389 3142 617423394 617422657 0.000000e+00 769.0
10 TraesCS7A01G404800 chr1B 86.336 666 79 8 2503 3158 352516897 352516234 0.000000e+00 715.0
11 TraesCS7A01G404800 chr1B 85.630 508 48 11 2378 2860 662165598 662166105 7.810000e-141 510.0
12 TraesCS7A01G404800 chr4A 84.934 677 68 20 2504 3149 554693948 554694621 0.000000e+00 654.0
13 TraesCS7A01G404800 chr4A 85.075 670 66 19 2510 3149 557668392 557667727 0.000000e+00 652.0
14 TraesCS7A01G404800 chr6A 84.835 666 81 15 2503 3149 294633883 294634547 0.000000e+00 652.0
15 TraesCS7A01G404800 chr4B 84.385 634 56 26 2387 2984 608829542 608828916 1.630000e-162 582.0
16 TraesCS7A01G404800 chr3D 84.840 376 31 14 2389 2739 58364771 58364397 3.870000e-94 355.0


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 TraesCS7A01G404800 chr7A 587364061 587367218 3157 False 5832 5832 100.000 1 3158 1 chr7A.!!$F1 3157
1 TraesCS7A01G404800 chr7A 4554802 4555483 681 True 656 656 84.942 2503 3149 1 chr7A.!!$R1 646
2 TraesCS7A01G404800 chr7D 514073959 514076310 2351 False 3711 3711 95.252 13 2350 1 chr7D.!!$F1 2337
3 TraesCS7A01G404800 chr7B 544910995 544913207 2212 False 3520 3520 95.446 146 2350 1 chr7B.!!$F1 2204
4 TraesCS7A01G404800 chr6D 324791970 324792808 838 False 1024 1024 89.273 2350 3158 1 chr6D.!!$F1 808
5 TraesCS7A01G404800 chr3A 640499824 640500661 837 True 911 911 86.920 2351 3158 1 chr3A.!!$R1 807
6 TraesCS7A01G404800 chr2D 433718412 433719202 790 False 846 846 86.633 2389 3149 1 chr2D.!!$F1 760
7 TraesCS7A01G404800 chr2D 617422657 617423394 737 True 769 769 85.602 2389 3142 1 chr2D.!!$R1 753
8 TraesCS7A01G404800 chr1B 352516234 352516897 663 True 715 715 86.336 2503 3158 1 chr1B.!!$R1 655
9 TraesCS7A01G404800 chr1B 662165598 662166105 507 False 510 510 85.630 2378 2860 1 chr1B.!!$F1 482
10 TraesCS7A01G404800 chr4A 554693948 554694621 673 False 654 654 84.934 2504 3149 1 chr4A.!!$F1 645
11 TraesCS7A01G404800 chr4A 557667727 557668392 665 True 652 652 85.075 2510 3149 1 chr4A.!!$R1 639
12 TraesCS7A01G404800 chr6A 294633883 294634547 664 False 652 652 84.835 2503 3149 1 chr6A.!!$F1 646
13 TraesCS7A01G404800 chr4B 608828916 608829542 626 True 582 582 84.385 2387 2984 1 chr4B.!!$R1 597

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
802 819 0.748729 ACGGAGAGACGGATGACTCC 60.749 60.0 0.0 0.0 43.58 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2356 2385 0.110373 CACGCGGCCACTTTTTAGAC 60.11 55.0 12.47 0.0 0.0 2.59 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
50 51 2.789213 TCCAGCCATCGAACAAATTCA 58.211 42.857 0.00 0.00 34.14 2.57
52 53 3.057596 TCCAGCCATCGAACAAATTCAAC 60.058 43.478 0.00 0.00 34.14 3.18
55 56 2.862512 CCATCGAACAAATTCAACCCG 58.137 47.619 0.00 0.00 34.14 5.28
100 111 0.902531 GCTCTACCAGGCAACCACTA 59.097 55.000 0.00 0.00 37.17 2.74
108 119 2.775384 CCAGGCAACCACTAACCCTATA 59.225 50.000 0.00 0.00 37.17 1.31
121 133 9.159364 CCACTAACCCTATAGTAAAAGACAAAC 57.841 37.037 0.00 0.00 34.40 2.93
127 139 8.222637 ACCCTATAGTAAAAGACAAACCAAACT 58.777 33.333 0.00 0.00 0.00 2.66
172 188 4.021544 GGTTACATGAAGGAAACCATGCAA 60.022 41.667 0.00 0.00 42.77 4.08
193 209 0.872021 GACGCCGATGGTGATGAGTC 60.872 60.000 2.95 0.00 36.58 3.36
194 210 1.323271 ACGCCGATGGTGATGAGTCT 61.323 55.000 2.95 0.00 36.58 3.24
198 214 2.101582 GCCGATGGTGATGAGTCTAACT 59.898 50.000 0.00 0.00 0.00 2.24
258 274 1.202568 TCGATCCATCACCATCAGCAC 60.203 52.381 0.00 0.00 0.00 4.40
267 283 2.495669 TCACCATCAGCACGAACAGATA 59.504 45.455 0.00 0.00 0.00 1.98
270 286 3.699538 ACCATCAGCACGAACAGATACTA 59.300 43.478 0.00 0.00 0.00 1.82
330 346 1.476891 TCCTCCGAAGTGCACATACTC 59.523 52.381 21.04 8.75 0.00 2.59
368 384 1.333931 CACAGCTGCTAATGATGCCAG 59.666 52.381 15.27 0.00 0.00 4.85
377 393 3.501445 GCTAATGATGCCAGAGACAATCC 59.499 47.826 0.00 0.00 0.00 3.01
449 465 6.650372 CACCACTTCTTTAGTTCTTTCTTCG 58.350 40.000 0.00 0.00 33.85 3.79
461 477 5.875359 AGTTCTTTCTTCGGTAATTGCCTAG 59.125 40.000 11.07 7.93 0.00 3.02
575 591 0.930310 GCAGTTGCGCGAATCTGATA 59.070 50.000 26.00 0.00 0.00 2.15
775 792 1.518572 CGTTATGGACTTCGGCGCT 60.519 57.895 7.64 0.00 0.00 5.92
802 819 0.748729 ACGGAGAGACGGATGACTCC 60.749 60.000 0.00 0.00 43.58 3.85
813 830 2.545952 CGGATGACTCCAAGGTAATCGG 60.546 54.545 0.00 0.00 42.19 4.18
823 840 1.446618 GGTAATCGGTTGTCGCGGT 60.447 57.895 6.13 0.00 39.05 5.68
867 884 2.158460 AGGAATATGCAAGTTAGGGGCC 60.158 50.000 0.00 0.00 0.00 5.80
877 894 1.124780 GTTAGGGGCCTCCTTCTCTC 58.875 60.000 16.84 2.42 45.47 3.20
1012 1029 4.228097 GCTACATGCAGGTGCGCG 62.228 66.667 15.48 0.00 45.83 6.86
1215 1232 1.931172 GTAAGCCGCGCTAATTTCTCA 59.069 47.619 5.56 0.00 38.25 3.27
1220 1237 1.732259 CCGCGCTAATTTCTCACTGTT 59.268 47.619 5.56 0.00 0.00 3.16
1228 1252 6.586463 CGCTAATTTCTCACTGTTTCACTCTA 59.414 38.462 0.00 0.00 0.00 2.43
1241 1265 3.309961 TCACTCTAAACTGAGCTGCTG 57.690 47.619 7.01 0.00 37.58 4.41
1256 1280 2.501128 CTGGGCCGACATCGTGAT 59.499 61.111 0.00 0.00 37.74 3.06
1263 1287 3.179830 GGCCGACATCGTGATATGATAC 58.820 50.000 0.00 0.00 37.74 2.24
1264 1288 2.846550 GCCGACATCGTGATATGATACG 59.153 50.000 0.00 0.00 41.38 3.06
1279 1303 4.627611 TGATACGACTTCTCCTTAACCG 57.372 45.455 0.00 0.00 0.00 4.44
1285 1309 3.919197 CGACTTCTCCTTAACCGTTTCTC 59.081 47.826 0.00 0.00 0.00 2.87
1318 1342 1.379309 GCCCCGGCAGTCCATAAAA 60.379 57.895 0.00 0.00 41.49 1.52
1795 1819 1.002430 CGGAACCCCATCATCATCGAT 59.998 52.381 0.00 0.00 0.00 3.59
1843 1867 2.513666 TGCCGCCATGAATCGGTC 60.514 61.111 17.78 12.43 46.79 4.79
1847 1871 0.877649 CCGCCATGAATCGGTCAGAG 60.878 60.000 11.28 0.00 40.43 3.35
1854 1878 0.247736 GAATCGGTCAGAGCCACAGT 59.752 55.000 0.00 0.00 0.00 3.55
1877 1901 8.971321 CAGTTGTTAATTTCTTGTCAAATCCAG 58.029 33.333 0.00 0.00 0.00 3.86
1915 1939 7.123830 CGGTTTTAGCCTAACAGAATTATTCG 58.876 38.462 0.00 0.00 34.02 3.34
2246 2271 6.239120 CCAAAGATTTTGCTTCTTTCCTCTGA 60.239 38.462 0.00 0.00 40.53 3.27
2336 2365 1.727335 GAACGAGCAAGCACTTACCTC 59.273 52.381 0.00 1.96 0.00 3.85
2356 2385 4.755123 CCTCGCCTTTGTATATACCCAAAG 59.245 45.833 10.38 12.91 44.48 2.77
2374 2403 0.250166 AGTCTAAAAAGTGGCCGCGT 60.250 50.000 11.42 4.31 0.00 6.01
2376 2405 0.533308 TCTAAAAAGTGGCCGCGTGT 60.533 50.000 11.42 0.00 0.00 4.49
2381 2410 0.955905 AAAGTGGCCGCGTGTTAAAT 59.044 45.000 11.42 0.00 0.00 1.40
2383 2412 0.604243 AGTGGCCGCGTGTTAAATGA 60.604 50.000 11.42 0.00 0.00 2.57
2434 2466 2.177394 TGCATGCGAGGTTTTGTCTA 57.823 45.000 14.09 0.00 0.00 2.59
2443 2475 3.673809 CGAGGTTTTGTCTACTAGTGCAC 59.326 47.826 9.40 9.40 0.00 4.57
2451 2483 3.179830 GTCTACTAGTGCACGTGATTGG 58.820 50.000 22.23 7.93 0.00 3.16
2498 2530 2.136298 TCCAGTGGACAACAAAGCAA 57.864 45.000 8.12 0.00 0.00 3.91
2561 2593 5.179368 AGTCATATCTTTCAAACCACGTGTG 59.821 40.000 15.65 6.55 0.00 3.82
2774 2833 3.890756 AGCAACCATGACAACTTTGATGA 59.109 39.130 0.00 0.00 0.00 2.92
2821 2881 2.299013 AGTCGATGTGCAACCACTCTTA 59.701 45.455 0.00 0.00 42.54 2.10
2834 2894 9.158233 TGCAACCACTCTTATAATGTAGTTTAC 57.842 33.333 0.00 0.00 0.00 2.01
2864 2924 8.458052 CACACATATTGATGTTTAGTTGGCTTA 58.542 33.333 0.00 0.00 44.18 3.09
2882 2942 6.213677 TGGCTTATAATGTAGTCTAGTTGCG 58.786 40.000 0.00 0.00 0.00 4.85
2907 2967 4.826733 ACACATTGATGTTTAGTTGGCAGA 59.173 37.500 0.00 0.00 39.39 4.26
2999 3156 0.692476 TGGCAGGACACTAGTTGCAT 59.308 50.000 16.86 0.00 34.02 3.96
3019 3176 1.372582 ACACATATGCTCAGTTGGCG 58.627 50.000 1.58 0.00 0.00 5.69
3020 3177 0.028505 CACATATGCTCAGTTGGCGC 59.971 55.000 0.00 0.00 0.00 6.53
3021 3178 1.277739 CATATGCTCAGTTGGCGCG 59.722 57.895 0.00 0.00 0.00 6.86
3022 3179 1.143838 ATATGCTCAGTTGGCGCGA 59.856 52.632 12.10 0.00 0.00 5.87
3023 3180 1.154205 ATATGCTCAGTTGGCGCGAC 61.154 55.000 12.10 8.22 0.00 5.19
3024 3181 2.499756 TATGCTCAGTTGGCGCGACA 62.500 55.000 12.71 12.71 0.00 4.35
3025 3182 3.345808 GCTCAGTTGGCGCGACAA 61.346 61.111 26.47 26.47 0.00 3.18
3026 3183 2.680913 GCTCAGTTGGCGCGACAAT 61.681 57.895 32.77 16.99 32.24 2.71
3027 3184 1.358725 GCTCAGTTGGCGCGACAATA 61.359 55.000 32.77 18.21 32.24 1.90
3028 3185 1.290203 CTCAGTTGGCGCGACAATAT 58.710 50.000 32.77 20.17 32.24 1.28
3029 3186 2.469826 CTCAGTTGGCGCGACAATATA 58.530 47.619 32.77 17.46 32.24 0.86
3030 3187 2.469826 TCAGTTGGCGCGACAATATAG 58.530 47.619 32.77 19.99 32.24 1.31
3031 3188 2.159156 TCAGTTGGCGCGACAATATAGT 60.159 45.455 32.77 8.56 32.24 2.12
3032 3189 2.218759 CAGTTGGCGCGACAATATAGTC 59.781 50.000 32.77 16.92 32.24 2.59
3033 3190 2.100916 AGTTGGCGCGACAATATAGTCT 59.899 45.455 32.77 19.13 36.38 3.24
3034 3191 3.317149 AGTTGGCGCGACAATATAGTCTA 59.683 43.478 32.77 0.57 36.38 2.59
3035 3192 3.554259 TGGCGCGACAATATAGTCTAG 57.446 47.619 15.11 0.00 36.38 2.43
3036 3193 2.882761 TGGCGCGACAATATAGTCTAGT 59.117 45.455 15.11 0.00 36.38 2.57
3037 3194 3.317149 TGGCGCGACAATATAGTCTAGTT 59.683 43.478 15.11 0.00 36.38 2.24
3038 3195 3.669122 GGCGCGACAATATAGTCTAGTTG 59.331 47.826 12.10 6.34 36.38 3.16
3039 3196 3.119792 GCGCGACAATATAGTCTAGTTGC 59.880 47.826 12.10 0.00 36.38 4.17
3040 3197 4.287720 CGCGACAATATAGTCTAGTTGCA 58.712 43.478 0.00 0.00 39.07 4.08
3041 3198 4.146616 CGCGACAATATAGTCTAGTTGCAC 59.853 45.833 0.00 4.16 39.07 4.57
3042 3199 5.041287 GCGACAATATAGTCTAGTTGCACA 58.959 41.667 0.00 0.00 38.98 4.57
3043 3200 5.051641 GCGACAATATAGTCTAGTTGCACAC 60.052 44.000 0.00 0.00 38.98 3.82
3044 3201 6.033966 CGACAATATAGTCTAGTTGCACACA 58.966 40.000 0.00 0.00 36.38 3.72
3045 3202 6.697455 CGACAATATAGTCTAGTTGCACACAT 59.303 38.462 0.00 0.00 36.38 3.21
3046 3203 7.222805 CGACAATATAGTCTAGTTGCACACATT 59.777 37.037 0.00 0.00 36.38 2.71
3047 3204 8.201554 ACAATATAGTCTAGTTGCACACATTG 57.798 34.615 0.00 0.00 0.00 2.82
3048 3205 8.040727 ACAATATAGTCTAGTTGCACACATTGA 58.959 33.333 0.00 0.00 0.00 2.57
3049 3206 9.049523 CAATATAGTCTAGTTGCACACATTGAT 57.950 33.333 0.00 0.00 0.00 2.57
3053 3210 7.928307 AGTCTAGTTGCACACATTGATATTT 57.072 32.000 0.00 0.00 0.00 1.40
3055 3212 9.102757 AGTCTAGTTGCACACATTGATATTTAG 57.897 33.333 0.00 0.00 0.00 1.85
3056 3213 8.883731 GTCTAGTTGCACACATTGATATTTAGT 58.116 33.333 0.00 0.00 0.00 2.24
3057 3214 9.448438 TCTAGTTGCACACATTGATATTTAGTT 57.552 29.630 0.00 0.00 0.00 2.24
3058 3215 9.494479 CTAGTTGCACACATTGATATTTAGTTG 57.506 33.333 0.00 0.00 0.00 3.16
3059 3216 7.315142 AGTTGCACACATTGATATTTAGTTGG 58.685 34.615 0.00 0.00 0.00 3.77
3060 3217 5.649557 TGCACACATTGATATTTAGTTGGC 58.350 37.500 0.00 0.00 0.00 4.52
3061 3218 5.184671 TGCACACATTGATATTTAGTTGGCA 59.815 36.000 0.00 0.00 0.00 4.92
3062 3219 5.745294 GCACACATTGATATTTAGTTGGCAG 59.255 40.000 0.00 0.00 0.00 4.85
3063 3220 6.267817 CACACATTGATATTTAGTTGGCAGG 58.732 40.000 0.00 0.00 0.00 4.85
3064 3221 6.095300 CACACATTGATATTTAGTTGGCAGGA 59.905 38.462 0.00 0.00 0.00 3.86
3065 3222 6.095440 ACACATTGATATTTAGTTGGCAGGAC 59.905 38.462 0.00 0.00 0.00 3.85
3066 3223 6.319658 CACATTGATATTTAGTTGGCAGGACT 59.680 38.462 0.00 0.00 0.00 3.85
3067 3224 7.498900 CACATTGATATTTAGTTGGCAGGACTA 59.501 37.037 0.00 0.00 0.00 2.59
3068 3225 8.220559 ACATTGATATTTAGTTGGCAGGACTAT 58.779 33.333 0.15 0.00 30.30 2.12
3069 3226 9.071276 CATTGATATTTAGTTGGCAGGACTATT 57.929 33.333 0.15 0.00 30.30 1.73
3070 3227 9.646522 ATTGATATTTAGTTGGCAGGACTATTT 57.353 29.630 0.15 0.00 30.30 1.40
3071 3228 8.450578 TGATATTTAGTTGGCAGGACTATTTG 57.549 34.615 0.15 0.00 30.30 2.32
3072 3229 7.502226 TGATATTTAGTTGGCAGGACTATTTGG 59.498 37.037 0.15 0.00 30.30 3.28
3077 3234 1.005805 TGGCAGGACTATTTGGCACAT 59.994 47.619 0.00 0.00 43.78 3.21
3086 3243 6.013032 AGGACTATTTGGCACATATATGCTCT 60.013 38.462 12.79 0.00 45.38 4.09
3091 3248 4.420522 TGGCACATATATGCTCTGTTGA 57.579 40.909 12.79 0.00 45.38 3.18
3095 3252 3.803778 CACATATATGCTCTGTTGACGCA 59.196 43.478 12.79 0.00 38.14 5.24
3109 3266 4.174009 GTTGACGCAGCAATCTAGTCTAA 58.826 43.478 0.00 0.00 33.26 2.10
3125 3282 5.362556 AGTCTAATTGCACACACATTGAC 57.637 39.130 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 4.599047 TTTGTTCGATGGCTGGAATTTT 57.401 36.364 0.00 0.00 0.00 1.82
31 32 3.244976 GTTGAATTTGTTCGATGGCTGG 58.755 45.455 0.00 0.00 0.00 4.85
38 39 4.634184 TTTTCGGGTTGAATTTGTTCGA 57.366 36.364 0.00 0.00 36.22 3.71
100 111 8.853126 GTTTGGTTTGTCTTTTACTATAGGGTT 58.147 33.333 4.43 0.00 0.00 4.11
108 119 9.719355 ATTTTTCAGTTTGGTTTGTCTTTTACT 57.281 25.926 0.00 0.00 0.00 2.24
144 156 6.195600 TGGTTTCCTTCATGTAACCTTAGT 57.804 37.500 0.00 0.00 40.50 2.24
151 167 4.220382 CCTTGCATGGTTTCCTTCATGTAA 59.780 41.667 10.48 0.00 41.30 2.41
156 172 2.238521 GTCCTTGCATGGTTTCCTTCA 58.761 47.619 17.54 0.00 0.00 3.02
172 188 2.021068 CTCATCACCATCGGCGTCCT 62.021 60.000 6.85 0.00 0.00 3.85
193 209 5.954296 TCCCGAAACCGATCTATAGTTAG 57.046 43.478 0.00 0.00 0.00 2.34
194 210 6.906157 AATCCCGAAACCGATCTATAGTTA 57.094 37.500 0.00 0.00 0.00 2.24
198 214 6.164417 TGAAAATCCCGAAACCGATCTATA 57.836 37.500 0.00 0.00 0.00 1.31
232 248 4.635223 TGATGGTGATGGATCGAATCTTC 58.365 43.478 8.11 0.00 0.00 2.87
258 274 2.512885 ACACGCGTTAGTATCTGTTCG 58.487 47.619 10.22 0.00 0.00 3.95
267 283 2.838386 ATATGTCGACACGCGTTAGT 57.162 45.000 22.71 5.15 41.80 2.24
270 286 2.713011 GACTATATGTCGACACGCGTT 58.287 47.619 22.71 7.17 41.80 4.84
291 307 3.139077 GGAAACACACGACCTTTGATCT 58.861 45.455 0.00 0.00 0.00 2.75
294 310 2.557317 GAGGAAACACACGACCTTTGA 58.443 47.619 0.00 0.00 32.53 2.69
303 319 0.586802 GCACTTCGGAGGAAACACAC 59.413 55.000 0.00 0.00 0.00 3.82
330 346 0.595567 TGGGTCAACGACGAAACGAG 60.596 55.000 0.00 0.00 37.03 4.18
368 384 1.464997 GTTTCGTGGCTGGATTGTCTC 59.535 52.381 0.00 0.00 0.00 3.36
461 477 6.797033 GTGTATGATTGAGTAGTGTTGTTTGC 59.203 38.462 0.00 0.00 0.00 3.68
567 583 3.472652 ACGAGCTCGAGAGTATCAGATT 58.527 45.455 40.58 12.21 43.02 2.40
575 591 1.654317 AATCGTACGAGCTCGAGAGT 58.346 50.000 40.58 28.99 43.02 3.24
671 687 0.322997 CAACCAGGGGAAACGCCATA 60.323 55.000 7.53 0.00 46.15 2.74
775 792 2.242572 CGTCTCTCCGTCGGCGATA 61.243 63.158 12.93 0.00 41.33 2.92
802 819 0.368907 CGCGACAACCGATTACCTTG 59.631 55.000 0.00 0.00 41.76 3.61
813 830 1.958417 CATGGTTAAACCGCGACAAC 58.042 50.000 8.23 5.59 42.58 3.32
867 884 4.769345 ATAAAAGCCTGGAGAGAAGGAG 57.231 45.455 0.00 0.00 36.91 3.69
877 894 1.676006 CACGCCCTTATAAAAGCCTGG 59.324 52.381 0.00 0.00 0.00 4.45
1068 1085 0.250684 TGCTGGCGAAGTTGATCCAA 60.251 50.000 0.00 0.00 0.00 3.53
1215 1232 5.053145 CAGCTCAGTTTAGAGTGAAACAGT 58.947 41.667 2.23 0.00 41.00 3.55
1220 1237 3.555795 CCAGCAGCTCAGTTTAGAGTGAA 60.556 47.826 0.00 0.00 37.94 3.18
1228 1252 2.282745 GGCCCAGCAGCTCAGTTT 60.283 61.111 0.00 0.00 0.00 2.66
1241 1265 0.317160 TCATATCACGATGTCGGCCC 59.683 55.000 7.38 0.00 44.95 5.80
1256 1280 5.824624 ACGGTTAAGGAGAAGTCGTATCATA 59.175 40.000 0.00 0.00 0.00 2.15
1263 1287 3.910648 AGAAACGGTTAAGGAGAAGTCG 58.089 45.455 0.00 0.00 0.00 4.18
1264 1288 3.919197 CGAGAAACGGTTAAGGAGAAGTC 59.081 47.826 0.00 0.00 38.46 3.01
1279 1303 0.108567 GGAGCAGAGTCCCGAGAAAC 60.109 60.000 0.00 0.00 0.00 2.78
1302 1326 1.379527 GAGTTTTATGGACTGCCGGG 58.620 55.000 2.18 0.00 36.79 5.73
1312 1336 1.060308 CACGCGCCCGAGTTTTATG 59.940 57.895 5.73 0.00 38.29 1.90
1462 1486 2.300967 GGAGCCCTGGATGTGGACA 61.301 63.158 0.00 0.00 0.00 4.02
1795 1819 0.708209 TGTAGGGGCAGTACTCCTGA 59.292 55.000 11.06 0.00 44.49 3.86
1843 1867 5.695851 AGAAATTAACAACTGTGGCTCTG 57.304 39.130 0.00 0.00 0.00 3.35
1847 1871 5.587289 TGACAAGAAATTAACAACTGTGGC 58.413 37.500 0.00 0.00 0.00 5.01
1854 1878 8.690884 TGTCTGGATTTGACAAGAAATTAACAA 58.309 29.630 0.00 0.00 40.89 2.83
1898 1922 4.260784 CCTGCACGAATAATTCTGTTAGGC 60.261 45.833 0.00 0.00 0.00 3.93
2356 2385 0.110373 CACGCGGCCACTTTTTAGAC 60.110 55.000 12.47 0.00 0.00 2.59
2374 2403 5.437263 GTCGCTCGTTCTTTTCATTTAACA 58.563 37.500 0.00 0.00 0.00 2.41
2376 2405 4.376615 CGGTCGCTCGTTCTTTTCATTTAA 60.377 41.667 0.00 0.00 0.00 1.52
2381 2410 0.942410 CCGGTCGCTCGTTCTTTTCA 60.942 55.000 0.00 0.00 0.00 2.69
2383 2412 2.315386 GCCGGTCGCTCGTTCTTTT 61.315 57.895 1.90 0.00 0.00 2.27
2434 2466 1.343142 TGACCAATCACGTGCACTAGT 59.657 47.619 16.19 3.07 0.00 2.57
2443 2475 6.092092 TGAAAGCATTTAATGACCAATCACG 58.908 36.000 9.36 0.00 39.27 4.35
2482 2514 4.734398 TGAATTTGCTTTGTTGTCCACT 57.266 36.364 0.00 0.00 0.00 4.00
2561 2593 3.198872 GTGAAGACGGATCTGAATTCCC 58.801 50.000 9.00 0.00 34.48 3.97
2650 2682 7.773224 TGCATAATACAGTACTAAAGTTGGCAT 59.227 33.333 0.00 0.00 0.00 4.40
2653 2685 9.162764 AGTTGCATAATACAGTACTAAAGTTGG 57.837 33.333 0.00 0.00 0.00 3.77
2672 2729 5.291128 GCACGATGTAGTACTAAAGTTGCAT 59.709 40.000 3.61 2.70 0.00 3.96
2760 2819 5.368145 ACTAGTTGCTCATCAAAGTTGTCA 58.632 37.500 0.00 0.00 36.26 3.58
2774 2833 4.272991 CGTCGAGGTAATAGACTAGTTGCT 59.727 45.833 0.00 0.00 31.82 3.91
2821 2881 9.542462 AATATGTGTGCGAGTAAACTACATTAT 57.458 29.630 0.00 0.00 0.00 1.28
2834 2894 6.349973 ACTAAACATCAATATGTGTGCGAG 57.650 37.500 0.00 0.00 45.79 5.03
2864 2924 4.804139 GTGTGCGCAACTAGACTACATTAT 59.196 41.667 14.00 0.00 0.00 1.28
2882 2942 3.674753 GCCAACTAAACATCAATGTGTGC 59.325 43.478 0.00 0.00 41.61 4.57
2939 3006 7.172532 TGTGTGCAACTAGACTAAATTACAAGG 59.827 37.037 0.00 0.00 38.04 3.61
2999 3156 2.549926 CGCCAACTGAGCATATGTGTA 58.450 47.619 4.29 0.00 0.00 2.90
3011 3168 2.201732 ACTATATTGTCGCGCCAACTG 58.798 47.619 4.03 0.00 0.00 3.16
3019 3176 5.041287 TGTGCAACTAGACTATATTGTCGC 58.959 41.667 10.95 8.79 38.82 5.19
3020 3177 6.033966 TGTGTGCAACTAGACTATATTGTCG 58.966 40.000 10.95 2.03 38.82 4.35
3021 3178 8.331022 CAATGTGTGCAACTAGACTATATTGTC 58.669 37.037 9.01 9.01 38.04 3.18
3022 3179 8.040727 TCAATGTGTGCAACTAGACTATATTGT 58.959 33.333 0.00 0.00 38.04 2.71
3023 3180 8.424274 TCAATGTGTGCAACTAGACTATATTG 57.576 34.615 0.00 0.00 38.04 1.90
3027 3184 9.618890 AAATATCAATGTGTGCAACTAGACTAT 57.381 29.630 0.00 0.00 38.04 2.12
3029 3186 7.928307 AAATATCAATGTGTGCAACTAGACT 57.072 32.000 0.00 0.00 38.04 3.24
3030 3187 8.883731 ACTAAATATCAATGTGTGCAACTAGAC 58.116 33.333 0.00 0.00 38.04 2.59
3031 3188 9.448438 AACTAAATATCAATGTGTGCAACTAGA 57.552 29.630 0.00 0.00 38.04 2.43
3032 3189 9.494479 CAACTAAATATCAATGTGTGCAACTAG 57.506 33.333 0.00 0.00 38.04 2.57
3033 3190 8.458052 CCAACTAAATATCAATGTGTGCAACTA 58.542 33.333 0.00 0.00 38.04 2.24
3034 3191 7.315142 CCAACTAAATATCAATGTGTGCAACT 58.685 34.615 0.00 0.00 38.04 3.16
3035 3192 6.034898 GCCAACTAAATATCAATGTGTGCAAC 59.965 38.462 0.00 0.00 37.35 4.17
3036 3193 6.098679 GCCAACTAAATATCAATGTGTGCAA 58.901 36.000 0.00 0.00 0.00 4.08
3037 3194 5.184671 TGCCAACTAAATATCAATGTGTGCA 59.815 36.000 0.00 0.00 0.00 4.57
3038 3195 5.649557 TGCCAACTAAATATCAATGTGTGC 58.350 37.500 0.00 0.00 0.00 4.57
3039 3196 6.095300 TCCTGCCAACTAAATATCAATGTGTG 59.905 38.462 0.00 0.00 0.00 3.82
3040 3197 6.095440 GTCCTGCCAACTAAATATCAATGTGT 59.905 38.462 0.00 0.00 0.00 3.72
3041 3198 6.319658 AGTCCTGCCAACTAAATATCAATGTG 59.680 38.462 0.00 0.00 0.00 3.21
3042 3199 6.426587 AGTCCTGCCAACTAAATATCAATGT 58.573 36.000 0.00 0.00 0.00 2.71
3043 3200 6.949352 AGTCCTGCCAACTAAATATCAATG 57.051 37.500 0.00 0.00 0.00 2.82
3044 3201 9.646522 AAATAGTCCTGCCAACTAAATATCAAT 57.353 29.630 0.00 0.00 33.19 2.57
3045 3202 8.902806 CAAATAGTCCTGCCAACTAAATATCAA 58.097 33.333 0.00 0.00 33.19 2.57
3046 3203 7.502226 CCAAATAGTCCTGCCAACTAAATATCA 59.498 37.037 0.00 0.00 33.19 2.15
3047 3204 7.522236 GCCAAATAGTCCTGCCAACTAAATATC 60.522 40.741 0.00 0.00 33.19 1.63
3048 3205 6.265422 GCCAAATAGTCCTGCCAACTAAATAT 59.735 38.462 0.00 0.00 33.19 1.28
3049 3206 5.592688 GCCAAATAGTCCTGCCAACTAAATA 59.407 40.000 0.00 0.00 33.19 1.40
3050 3207 4.402474 GCCAAATAGTCCTGCCAACTAAAT 59.598 41.667 0.00 0.00 33.19 1.40
3051 3208 3.761752 GCCAAATAGTCCTGCCAACTAAA 59.238 43.478 0.00 0.00 33.19 1.85
3052 3209 3.245087 TGCCAAATAGTCCTGCCAACTAA 60.245 43.478 0.00 0.00 33.19 2.24
3053 3210 2.307392 TGCCAAATAGTCCTGCCAACTA 59.693 45.455 0.00 0.00 33.94 2.24
3054 3211 1.075374 TGCCAAATAGTCCTGCCAACT 59.925 47.619 0.00 0.00 0.00 3.16
3055 3212 1.202348 GTGCCAAATAGTCCTGCCAAC 59.798 52.381 0.00 0.00 0.00 3.77
3056 3213 1.202989 TGTGCCAAATAGTCCTGCCAA 60.203 47.619 0.00 0.00 0.00 4.52
3057 3214 0.403655 TGTGCCAAATAGTCCTGCCA 59.596 50.000 0.00 0.00 0.00 4.92
3058 3215 1.767759 ATGTGCCAAATAGTCCTGCC 58.232 50.000 0.00 0.00 0.00 4.85
3059 3216 5.392380 GCATATATGTGCCAAATAGTCCTGC 60.392 44.000 13.10 0.00 39.18 4.85
3060 3217 5.942236 AGCATATATGTGCCAAATAGTCCTG 59.058 40.000 19.57 0.00 46.19 3.86
3061 3218 6.013032 AGAGCATATATGTGCCAAATAGTCCT 60.013 38.462 19.57 0.00 46.19 3.85
3062 3219 6.093219 CAGAGCATATATGTGCCAAATAGTCC 59.907 42.308 19.57 0.58 46.19 3.85
3063 3220 6.652481 ACAGAGCATATATGTGCCAAATAGTC 59.348 38.462 19.57 9.60 46.19 2.59
3064 3221 6.537355 ACAGAGCATATATGTGCCAAATAGT 58.463 36.000 19.57 8.36 46.19 2.12
3065 3222 7.173735 TCAACAGAGCATATATGTGCCAAATAG 59.826 37.037 19.57 7.75 46.19 1.73
3066 3223 6.997476 TCAACAGAGCATATATGTGCCAAATA 59.003 34.615 19.57 0.00 46.19 1.40
3067 3224 5.829391 TCAACAGAGCATATATGTGCCAAAT 59.171 36.000 19.57 2.31 46.19 2.32
3068 3225 5.066375 GTCAACAGAGCATATATGTGCCAAA 59.934 40.000 19.57 0.00 46.19 3.28
3069 3226 4.576053 GTCAACAGAGCATATATGTGCCAA 59.424 41.667 19.57 0.00 46.19 4.52
3070 3227 4.129380 GTCAACAGAGCATATATGTGCCA 58.871 43.478 19.57 0.00 46.19 4.92
3071 3228 3.185188 CGTCAACAGAGCATATATGTGCC 59.815 47.826 19.57 11.75 46.19 5.01
3072 3229 3.363378 GCGTCAACAGAGCATATATGTGC 60.363 47.826 16.01 16.01 45.38 4.57
3077 3234 2.159114 TGCTGCGTCAACAGAGCATATA 60.159 45.455 0.00 0.00 40.25 0.86
3086 3243 2.029020 AGACTAGATTGCTGCGTCAACA 60.029 45.455 0.00 0.00 31.97 3.33
3109 3266 3.435105 AAACGTCAATGTGTGTGCAAT 57.565 38.095 0.00 0.00 0.00 3.56
3125 3282 1.878953 AGTGTCCTGCCAACTAAACG 58.121 50.000 0.00 0.00 0.00 3.60


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

AutoCloner maintained by Alex Coulton.