Multiple sequence alignment - TraesCS7B01G327800

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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 TraesCS7B01G327800 chr7B 100.000 3209 0 0 1 3209 582278282 582281490 0.000000e+00 5927.0
1 TraesCS7B01G327800 chr7B 97.619 42 1 0 3168 3209 46465112 46465071 4.440000e-09 73.1
2 TraesCS7B01G327800 chr7D 93.509 3189 124 33 1 3162 539485880 539489012 0.000000e+00 4665.0
3 TraesCS7B01G327800 chr7D 92.568 444 20 5 1185 1623 603142787 603142352 2.720000e-175 625.0
4 TraesCS7B01G327800 chrUn 91.609 3206 148 43 1 3168 82944779 82947901 0.000000e+00 4318.0
5 TraesCS7B01G327800 chr4D 93.034 445 25 2 1185 1623 62468580 62468136 0.000000e+00 645.0
6 TraesCS7B01G327800 chr1A 89.640 444 29 7 1185 1623 558476037 558476468 1.680000e-152 549.0
7 TraesCS7B01G327800 chr2A 95.509 334 15 0 1185 1518 773369888 773369555 4.710000e-148 534.0
8 TraesCS7B01G327800 chr2A 92.727 110 2 3 1514 1623 773355391 773355288 1.540000e-33 154.0
9 TraesCS7B01G327800 chr2B 86.275 459 29 19 1165 1623 602256438 602256862 4.850000e-128 468.0
10 TraesCS7B01G327800 chr2B 93.182 44 3 0 3166 3209 54437921 54437964 7.430000e-07 65.8
11 TraesCS7B01G327800 chr6D 97.561 41 1 0 3169 3209 387392089 387392049 1.600000e-08 71.3
12 TraesCS7B01G327800 chr3B 95.455 44 2 0 3166 3209 573643997 573644040 1.600000e-08 71.3
13 TraesCS7B01G327800 chr3A 95.455 44 2 0 3166 3209 729328905 729328948 1.600000e-08 71.3
14 TraesCS7B01G327800 chr2D 95.455 44 2 0 3166 3209 425735920 425735877 1.600000e-08 71.3
15 TraesCS7B01G327800 chr7A 95.122 41 2 0 3169 3209 204276986 204276946 7.430000e-07 65.8
16 TraesCS7B01G327800 chr6B 95.122 41 2 0 3169 3209 578483535 578483495 7.430000e-07 65.8
17 TraesCS7B01G327800 chr1D 93.182 44 3 0 3166 3209 461324568 461324611 7.430000e-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 TraesCS7B01G327800 chr7B 582278282 582281490 3208 False 5927 5927 100.000 1 3209 1 chr7B.!!$F1 3208
1 TraesCS7B01G327800 chr7D 539485880 539489012 3132 False 4665 4665 93.509 1 3162 1 chr7D.!!$F1 3161
2 TraesCS7B01G327800 chrUn 82944779 82947901 3122 False 4318 4318 91.609 1 3168 1 chrUn.!!$F1 3167

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
368 382 0.170784 GAGACGACGAGAGGGGTTTC 59.829 60.0 0.00 0.0 0.00 2.78 F
785 812 0.396139 CACCGCCCCCACTAGTAGTA 60.396 60.0 1.57 0.0 0.00 1.82 F
1146 1176 0.863538 CGAGCGTCTTCTCCATCACG 60.864 60.0 0.00 0.0 35.32 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1584 1614 0.033504 TGCTCTTGTCCTTGACCGTC 59.966 55.000 0.00 0.00 0.00 4.79 R
1719 1749 1.227089 CAACTCCAGATCGGCCGAG 60.227 63.158 33.87 20.58 33.14 4.63 R
3086 3145 0.040157 CAGCACAATTCACACGGGTG 60.040 55.000 12.84 12.84 46.66 4.61 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
57 63 5.639931 GGCGCCCATGAAATTAAACTAAAAA 59.360 36.000 18.11 0.00 0.00 1.94
81 87 8.922931 AATTTCCCTAGCAAACATTCAAAATT 57.077 26.923 0.00 0.00 0.00 1.82
134 147 1.471287 GTGCCCCGAACTTTGATAACC 59.529 52.381 0.00 0.00 0.00 2.85
135 148 1.100510 GCCCCGAACTTTGATAACCC 58.899 55.000 0.00 0.00 0.00 4.11
136 149 1.614850 GCCCCGAACTTTGATAACCCA 60.615 52.381 0.00 0.00 0.00 4.51
137 150 2.365582 CCCCGAACTTTGATAACCCAG 58.634 52.381 0.00 0.00 0.00 4.45
138 151 2.026636 CCCCGAACTTTGATAACCCAGA 60.027 50.000 0.00 0.00 0.00 3.86
139 152 3.560453 CCCCGAACTTTGATAACCCAGAA 60.560 47.826 0.00 0.00 0.00 3.02
140 153 3.439129 CCCGAACTTTGATAACCCAGAAC 59.561 47.826 0.00 0.00 0.00 3.01
153 166 1.071471 CAGAACGCCAGAACCCACT 59.929 57.895 0.00 0.00 0.00 4.00
168 181 0.322997 CCACTCTCTGTCTCTCCCGT 60.323 60.000 0.00 0.00 0.00 5.28
172 185 1.979155 CTCTGTCTCTCCCGTGCCA 60.979 63.158 0.00 0.00 0.00 4.92
323 337 0.465460 GCACGGGCATTCATTCCCTA 60.465 55.000 3.77 0.00 40.41 3.53
368 382 0.170784 GAGACGACGAGAGGGGTTTC 59.829 60.000 0.00 0.00 0.00 2.78
369 383 1.214853 GACGACGAGAGGGGTTTCC 59.785 63.158 0.00 0.00 0.00 3.13
370 384 2.181021 CGACGAGAGGGGTTTCCG 59.819 66.667 0.00 0.00 41.52 4.30
383 400 0.539986 GTTTCCGATACTGCCCCTGA 59.460 55.000 0.00 0.00 0.00 3.86
402 419 4.449068 CCTGACATGTATGATTAAGACGCC 59.551 45.833 0.00 0.00 0.00 5.68
408 425 6.482308 ACATGTATGATTAAGACGCCCTTAAC 59.518 38.462 11.32 7.62 46.63 2.01
412 429 2.660189 TTAAGACGCCCTTAACTCGG 57.340 50.000 6.53 0.00 41.15 4.63
429 446 0.810031 CGGGGCCAGAACAGTAATCG 60.810 60.000 4.39 0.00 0.00 3.34
432 449 1.429148 GGCCAGAACAGTAATCGCGG 61.429 60.000 6.13 0.00 0.00 6.46
435 452 1.153429 AGAACAGTAATCGCGGCCC 60.153 57.895 6.13 0.00 0.00 5.80
533 550 3.955650 TTCCCTCTCGGAGTAAACAAG 57.044 47.619 4.69 0.00 43.39 3.16
692 719 4.988598 AGCAGTGGGTTCGCCACG 62.989 66.667 5.22 2.68 42.35 4.94
741 768 4.008933 GTGACTCGCTGGCCACCT 62.009 66.667 0.00 0.00 0.00 4.00
782 809 1.380785 CTCACCGCCCCCACTAGTA 60.381 63.158 0.00 0.00 0.00 1.82
783 810 1.380785 TCACCGCCCCCACTAGTAG 60.381 63.158 0.00 0.00 0.00 2.57
784 811 1.684734 CACCGCCCCCACTAGTAGT 60.685 63.158 0.00 0.00 0.00 2.73
785 812 0.396139 CACCGCCCCCACTAGTAGTA 60.396 60.000 1.57 0.00 0.00 1.82
790 817 2.813354 CGCCCCCACTAGTAGTAGTAGG 60.813 59.091 13.63 13.63 37.40 3.18
847 874 1.814634 GCCGCTACCACTAGAGCTCTA 60.815 57.143 22.01 22.01 36.50 2.43
904 931 3.577649 ACAAATCGATCACACTCTCGT 57.422 42.857 0.00 0.00 36.33 4.18
951 978 3.374058 CGCCATTGTTTATCTCCTCGTTT 59.626 43.478 0.00 0.00 0.00 3.60
1146 1176 0.863538 CGAGCGTCTTCTCCATCACG 60.864 60.000 0.00 0.00 35.32 4.35
1440 1470 1.441729 CGTGGATACGTGGCTGGAT 59.558 57.895 0.00 0.00 44.99 3.41
1638 1668 4.106925 CCTGCACCTGCTCCCTCC 62.107 72.222 0.00 0.00 42.66 4.30
1735 1765 3.532155 GCTCGGCCGATCTGGAGT 61.532 66.667 31.19 0.00 42.00 3.85
1861 1891 3.636313 GATCCCGTGGCGTTCGACA 62.636 63.158 0.00 0.00 0.00 4.35
1980 2010 0.246360 ATCTGATGTTCGTGCGGTCA 59.754 50.000 0.00 0.00 0.00 4.02
1995 2025 0.610174 GGTCAGAGATGCTGGTGACA 59.390 55.000 3.92 0.00 44.98 3.58
2007 2037 3.371063 GTGACAGAGACCGGGCGA 61.371 66.667 6.32 0.00 0.00 5.54
2253 2283 2.450476 AGGCATCCGCATTTTCTTTCT 58.550 42.857 0.00 0.00 41.24 2.52
2302 2332 2.286025 CGTTATTACGGGGCAGTAAAGC 59.714 50.000 8.48 0.00 43.94 3.51
2303 2333 2.228138 TATTACGGGGCAGTAAAGCG 57.772 50.000 8.48 0.00 39.65 4.68
2304 2334 0.251073 ATTACGGGGCAGTAAAGCGT 59.749 50.000 8.48 0.00 39.65 5.07
2305 2335 0.390209 TTACGGGGCAGTAAAGCGTC 60.390 55.000 2.91 0.00 34.08 5.19
2306 2336 1.534336 TACGGGGCAGTAAAGCGTCA 61.534 55.000 0.00 0.00 34.64 4.35
2307 2337 2.388232 CGGGGCAGTAAAGCGTCAC 61.388 63.158 0.00 0.00 34.64 3.67
2309 2339 1.302192 GGGCAGTAAAGCGTCACCA 60.302 57.895 0.00 0.00 34.64 4.17
2310 2340 1.298859 GGGCAGTAAAGCGTCACCAG 61.299 60.000 0.00 0.00 34.64 4.00
2325 2356 2.348998 CAGGCACTCCAGTGGGTC 59.651 66.667 9.92 0.00 45.72 4.46
2521 2559 4.408821 TGCGGATGGGAGCCACAC 62.409 66.667 0.00 0.00 35.80 3.82
2719 2771 2.737180 CCGCGTGCCTGGATCTAT 59.263 61.111 4.92 0.00 0.00 1.98
2833 2889 4.114794 CCTGGTTTGTCTTTTGCTTTCTG 58.885 43.478 0.00 0.00 0.00 3.02
2841 2897 1.615392 CTTTTGCTTTCTGGTGGAGGG 59.385 52.381 0.00 0.00 0.00 4.30
2843 2899 1.065410 TTGCTTTCTGGTGGAGGGGA 61.065 55.000 0.00 0.00 0.00 4.81
2982 3041 0.742505 TAACGGCTAGGGATCACACG 59.257 55.000 0.00 0.00 0.00 4.49
3032 3091 4.978083 GGACTTATCCGTTCACAGACTA 57.022 45.455 0.00 0.00 34.48 2.59
3034 3093 4.352887 GACTTATCCGTTCACAGACTAGC 58.647 47.826 0.00 0.00 0.00 3.42
3035 3094 3.762288 ACTTATCCGTTCACAGACTAGCA 59.238 43.478 0.00 0.00 0.00 3.49
3076 3135 1.451387 GCCCATCCTGTGTTACCCG 60.451 63.158 0.00 0.00 0.00 5.28
3077 3136 1.988015 CCCATCCTGTGTTACCCGT 59.012 57.895 0.00 0.00 0.00 5.28
3078 3137 0.392461 CCCATCCTGTGTTACCCGTG 60.392 60.000 0.00 0.00 0.00 4.94
3079 3138 1.024579 CCATCCTGTGTTACCCGTGC 61.025 60.000 0.00 0.00 0.00 5.34
3080 3139 0.036388 CATCCTGTGTTACCCGTGCT 60.036 55.000 0.00 0.00 0.00 4.40
3081 3140 0.249398 ATCCTGTGTTACCCGTGCTC 59.751 55.000 0.00 0.00 0.00 4.26
3082 3141 1.116536 TCCTGTGTTACCCGTGCTCA 61.117 55.000 0.00 0.00 0.00 4.26
3083 3142 0.036388 CCTGTGTTACCCGTGCTCAT 60.036 55.000 0.00 0.00 0.00 2.90
3084 3143 1.610624 CCTGTGTTACCCGTGCTCATT 60.611 52.381 0.00 0.00 0.00 2.57
3085 3144 2.151202 CTGTGTTACCCGTGCTCATTT 58.849 47.619 0.00 0.00 0.00 2.32
3086 3145 2.147958 TGTGTTACCCGTGCTCATTTC 58.852 47.619 0.00 0.00 0.00 2.17
3087 3146 2.147958 GTGTTACCCGTGCTCATTTCA 58.852 47.619 0.00 0.00 0.00 2.69
3088 3147 2.095919 GTGTTACCCGTGCTCATTTCAC 60.096 50.000 0.00 0.00 0.00 3.18
3089 3148 1.467342 GTTACCCGTGCTCATTTCACC 59.533 52.381 0.00 0.00 0.00 4.02
3090 3149 0.035820 TACCCGTGCTCATTTCACCC 60.036 55.000 0.00 0.00 0.00 4.61
3118 3177 1.527034 TGTGCTGGACTTCATTGCTC 58.473 50.000 0.00 0.00 0.00 4.26
3119 3178 1.202794 TGTGCTGGACTTCATTGCTCA 60.203 47.619 0.00 0.00 0.00 4.26
3121 3180 2.097142 GTGCTGGACTTCATTGCTCATC 59.903 50.000 0.00 0.00 0.00 2.92
3122 3181 2.290450 TGCTGGACTTCATTGCTCATCA 60.290 45.455 0.00 0.00 0.00 3.07
3162 3226 2.043227 AGAAGAGGCGGGATCTTAAGG 58.957 52.381 1.85 0.00 37.14 2.69
3163 3227 2.040178 GAAGAGGCGGGATCTTAAGGA 58.960 52.381 1.85 0.00 37.14 3.36
3164 3228 1.710816 AGAGGCGGGATCTTAAGGAG 58.289 55.000 1.85 0.00 0.00 3.69
3168 3232 1.538419 GGCGGGATCTTAAGGAGAACG 60.538 57.143 1.85 3.25 38.06 3.95
3169 3233 1.538419 GCGGGATCTTAAGGAGAACGG 60.538 57.143 1.85 0.00 38.06 4.44
3170 3234 1.068741 CGGGATCTTAAGGAGAACGGG 59.931 57.143 1.85 0.00 38.06 5.28
3171 3235 1.202663 GGGATCTTAAGGAGAACGGGC 60.203 57.143 1.85 0.00 38.06 6.13
3172 3236 1.763545 GGATCTTAAGGAGAACGGGCT 59.236 52.381 1.85 0.00 38.06 5.19
3173 3237 2.170817 GGATCTTAAGGAGAACGGGCTT 59.829 50.000 1.85 0.00 38.06 4.35
3174 3238 2.762535 TCTTAAGGAGAACGGGCTTG 57.237 50.000 1.85 0.00 0.00 4.01
3175 3239 1.087501 CTTAAGGAGAACGGGCTTGC 58.912 55.000 0.00 0.00 0.00 4.01
3176 3240 0.690762 TTAAGGAGAACGGGCTTGCT 59.309 50.000 0.00 0.00 0.00 3.91
3177 3241 1.563924 TAAGGAGAACGGGCTTGCTA 58.436 50.000 0.00 0.00 0.00 3.49
3178 3242 0.690762 AAGGAGAACGGGCTTGCTAA 59.309 50.000 0.00 0.00 0.00 3.09
3179 3243 0.690762 AGGAGAACGGGCTTGCTAAA 59.309 50.000 0.00 0.00 0.00 1.85
3180 3244 1.073284 AGGAGAACGGGCTTGCTAAAA 59.927 47.619 0.00 0.00 0.00 1.52
3181 3245 1.199327 GGAGAACGGGCTTGCTAAAAC 59.801 52.381 0.00 0.00 0.00 2.43
3182 3246 2.152016 GAGAACGGGCTTGCTAAAACT 58.848 47.619 0.00 0.00 0.00 2.66
3183 3247 2.152016 AGAACGGGCTTGCTAAAACTC 58.848 47.619 0.00 0.00 0.00 3.01
3184 3248 1.877443 GAACGGGCTTGCTAAAACTCA 59.123 47.619 0.00 0.00 0.00 3.41
3185 3249 1.523758 ACGGGCTTGCTAAAACTCAG 58.476 50.000 0.00 0.00 0.00 3.35
3186 3250 1.202770 ACGGGCTTGCTAAAACTCAGT 60.203 47.619 0.00 0.00 0.00 3.41
3187 3251 1.464997 CGGGCTTGCTAAAACTCAGTC 59.535 52.381 0.00 0.00 0.00 3.51
3188 3252 1.464997 GGGCTTGCTAAAACTCAGTCG 59.535 52.381 0.00 0.00 0.00 4.18
3189 3253 2.413837 GGCTTGCTAAAACTCAGTCGA 58.586 47.619 0.00 0.00 0.00 4.20
3190 3254 2.157863 GGCTTGCTAAAACTCAGTCGAC 59.842 50.000 7.70 7.70 0.00 4.20
3191 3255 3.060602 GCTTGCTAAAACTCAGTCGACT 58.939 45.455 13.58 13.58 0.00 4.18
3192 3256 3.120854 GCTTGCTAAAACTCAGTCGACTG 60.121 47.826 34.76 34.76 45.08 3.51
3206 3270 6.727824 CAGTCGACTGAGATTTAACCAATT 57.272 37.500 36.73 0.00 46.59 2.32
3207 3271 6.766084 CAGTCGACTGAGATTTAACCAATTC 58.234 40.000 36.73 0.00 46.59 2.17
3208 3272 6.591834 CAGTCGACTGAGATTTAACCAATTCT 59.408 38.462 36.73 0.00 46.59 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 63 8.922931 AAATTTTGAATGTTTGCTAGGGAAAT 57.077 26.923 0.00 0.00 0.00 2.17
134 147 1.966451 GTGGGTTCTGGCGTTCTGG 60.966 63.158 0.00 0.00 0.00 3.86
135 148 0.951040 GAGTGGGTTCTGGCGTTCTG 60.951 60.000 0.00 0.00 0.00 3.02
136 149 1.122019 AGAGTGGGTTCTGGCGTTCT 61.122 55.000 0.00 0.00 0.00 3.01
137 150 0.670854 GAGAGTGGGTTCTGGCGTTC 60.671 60.000 0.00 0.00 0.00 3.95
138 151 1.122019 AGAGAGTGGGTTCTGGCGTT 61.122 55.000 0.00 0.00 0.00 4.84
139 152 1.534235 AGAGAGTGGGTTCTGGCGT 60.534 57.895 0.00 0.00 0.00 5.68
140 153 1.079543 CAGAGAGTGGGTTCTGGCG 60.080 63.158 0.00 0.00 37.70 5.69
153 166 1.679305 GGCACGGGAGAGACAGAGA 60.679 63.158 0.00 0.00 0.00 3.10
168 181 4.912395 GTGGGGTTGGCAGTGGCA 62.912 66.667 16.56 16.56 43.71 4.92
172 185 4.643387 GAGCGTGGGGTTGGCAGT 62.643 66.667 0.00 0.00 0.00 4.40
235 249 1.583495 CTCGGTCACTGACACGGCTA 61.583 60.000 11.34 0.00 33.68 3.93
238 252 2.258591 CCTCGGTCACTGACACGG 59.741 66.667 11.34 4.24 33.68 4.94
280 294 4.820744 AAAGGATGGGCCGCGCAT 62.821 61.111 21.80 21.80 43.43 4.73
368 382 0.250038 CATGTCAGGGGCAGTATCGG 60.250 60.000 0.00 0.00 0.00 4.18
369 383 0.465705 ACATGTCAGGGGCAGTATCG 59.534 55.000 0.00 0.00 0.00 2.92
370 384 3.324846 TCATACATGTCAGGGGCAGTATC 59.675 47.826 0.00 0.00 0.00 2.24
383 400 4.689612 AGGGCGTCTTAATCATACATGT 57.310 40.909 2.69 2.69 0.00 3.21
402 419 0.392595 GTTCTGGCCCCGAGTTAAGG 60.393 60.000 0.00 0.00 0.00 2.69
408 425 0.541863 ATTACTGTTCTGGCCCCGAG 59.458 55.000 0.00 0.00 0.00 4.63
412 429 1.429148 CGCGATTACTGTTCTGGCCC 61.429 60.000 0.00 0.00 0.00 5.80
415 432 1.429148 GGCCGCGATTACTGTTCTGG 61.429 60.000 8.23 0.00 0.00 3.86
429 446 0.463116 TTAAGAATCGAAGGGGCCGC 60.463 55.000 12.88 12.88 0.00 6.53
432 449 2.287009 CGCATTTAAGAATCGAAGGGGC 60.287 50.000 0.00 0.00 0.00 5.80
435 452 3.673746 TGCGCATTTAAGAATCGAAGG 57.326 42.857 5.66 0.00 0.00 3.46
501 518 0.887836 AGAGGGAAAACGAAACGGGC 60.888 55.000 0.00 0.00 0.00 6.13
625 647 2.363018 CCAGAGAGGGAGTGGCGA 60.363 66.667 0.00 0.00 0.00 5.54
680 707 2.030862 GTAACCGTGGCGAACCCA 59.969 61.111 0.00 0.00 42.79 4.51
686 713 3.475774 GTGAGCGTAACCGTGGCG 61.476 66.667 0.00 0.00 36.15 5.69
782 809 2.092103 CAGAGCCACTCCTCCTACTACT 60.092 54.545 0.00 0.00 32.17 2.57
783 810 2.303175 CAGAGCCACTCCTCCTACTAC 58.697 57.143 0.00 0.00 32.17 2.73
784 811 1.215673 CCAGAGCCACTCCTCCTACTA 59.784 57.143 0.00 0.00 32.17 1.82
785 812 0.032615 CCAGAGCCACTCCTCCTACT 60.033 60.000 0.00 0.00 32.17 2.57
790 817 2.583520 CAGCCAGAGCCACTCCTC 59.416 66.667 0.00 0.00 41.25 3.71
847 874 3.305881 GGTAATAATAGCGGCGGAGACTT 60.306 47.826 9.78 0.00 0.00 3.01
1146 1176 0.179124 CGTAGAGCAGCAGGAGGAAC 60.179 60.000 0.00 0.00 0.00 3.62
1404 1434 2.732016 CACTCGACGTGGAACCCA 59.268 61.111 0.86 0.00 40.02 4.51
1584 1614 0.033504 TGCTCTTGTCCTTGACCGTC 59.966 55.000 0.00 0.00 0.00 4.79
1719 1749 1.227089 CAACTCCAGATCGGCCGAG 60.227 63.158 33.87 20.58 33.14 4.63
1735 1765 2.285368 ACCATCGCCTCCTCCCAA 60.285 61.111 0.00 0.00 0.00 4.12
1980 2010 1.824230 GTCTCTGTCACCAGCATCTCT 59.176 52.381 0.00 0.00 38.66 3.10
1995 2025 1.528776 GGAGTATCGCCCGGTCTCT 60.529 63.158 0.00 0.00 34.37 3.10
2007 2037 3.917760 GCGGCCGAGCAGGAGTAT 61.918 66.667 33.48 0.00 45.00 2.12
2230 2260 4.462483 AGAAAGAAAATGCGGATGCCTTTA 59.538 37.500 9.99 0.00 37.87 1.85
2292 2322 1.298859 CCTGGTGACGCTTTACTGCC 61.299 60.000 0.00 0.00 0.00 4.85
2302 2332 2.047844 CTGGAGTGCCTGGTGACG 60.048 66.667 0.00 0.00 34.31 4.35
2303 2333 1.302033 CACTGGAGTGCCTGGTGAC 60.302 63.158 0.00 0.00 39.31 3.67
2304 2334 2.519622 CCACTGGAGTGCCTGGTGA 61.520 63.158 0.91 0.00 44.34 4.02
2305 2335 2.033141 CCACTGGAGTGCCTGGTG 59.967 66.667 0.91 0.00 44.34 4.17
2306 2336 3.252284 CCCACTGGAGTGCCTGGT 61.252 66.667 0.91 0.00 44.34 4.00
2307 2337 3.252284 ACCCACTGGAGTGCCTGG 61.252 66.667 0.91 0.66 44.34 4.45
2309 2339 2.930562 GGACCCACTGGAGTGCCT 60.931 66.667 0.91 0.00 44.34 4.75
2310 2340 3.249189 TGGACCCACTGGAGTGCC 61.249 66.667 0.91 0.00 44.34 5.01
2521 2559 2.126888 GCACACACGCCGGAATTG 60.127 61.111 5.05 0.00 0.00 2.32
2547 2589 3.178540 AAGCCGCCGAAACCTCACT 62.179 57.895 0.00 0.00 0.00 3.41
2671 2723 5.972935 ACAACTTGTACAAAAGAAAAGGGG 58.027 37.500 10.03 0.00 0.00 4.79
2672 2724 6.871492 ACAACAACTTGTACAAAAGAAAAGGG 59.129 34.615 10.03 0.00 38.95 3.95
2719 2771 1.748879 GCCGCTTTAGCATCCACCA 60.749 57.895 2.29 0.00 42.21 4.17
2833 2889 0.041386 ACTACTCACTCCCCTCCACC 59.959 60.000 0.00 0.00 0.00 4.61
2841 2897 2.419324 CTCACGTGGTACTACTCACTCC 59.581 54.545 17.00 0.00 0.00 3.85
2843 2899 2.039480 TCCTCACGTGGTACTACTCACT 59.961 50.000 17.00 0.00 0.00 3.41
2982 3041 8.373256 GCAACAGAACAAAAGAAGTTAAGAAAC 58.627 33.333 0.00 0.00 35.72 2.78
3029 3088 1.776662 TTAGCGAGGACCATGCTAGT 58.223 50.000 14.91 0.00 41.75 2.57
3032 3091 0.107654 GGTTTAGCGAGGACCATGCT 60.108 55.000 14.11 14.11 42.58 3.79
3034 3093 3.853104 TGGTTTAGCGAGGACCATG 57.147 52.632 0.00 0.00 38.47 3.66
3076 3135 2.629002 ACACGGGTGAAATGAGCAC 58.371 52.632 5.71 0.00 35.56 4.40
3086 3145 0.040157 CAGCACAATTCACACGGGTG 60.040 55.000 12.84 12.84 46.66 4.61
3087 3146 1.172180 CCAGCACAATTCACACGGGT 61.172 55.000 0.00 0.00 0.00 5.28
3088 3147 0.888736 TCCAGCACAATTCACACGGG 60.889 55.000 0.00 0.00 0.00 5.28
3089 3148 0.238289 GTCCAGCACAATTCACACGG 59.762 55.000 0.00 0.00 0.00 4.94
3090 3149 1.229428 AGTCCAGCACAATTCACACG 58.771 50.000 0.00 0.00 0.00 4.49
3118 3177 2.932614 CCGAAGCTAAGAACACCTGATG 59.067 50.000 0.00 0.00 0.00 3.07
3119 3178 2.567615 ACCGAAGCTAAGAACACCTGAT 59.432 45.455 0.00 0.00 0.00 2.90
3121 3180 2.457366 ACCGAAGCTAAGAACACCTG 57.543 50.000 0.00 0.00 0.00 4.00
3122 3181 3.830755 TCTTACCGAAGCTAAGAACACCT 59.169 43.478 0.00 0.00 32.21 4.00
3150 3214 1.068741 CCCGTTCTCCTTAAGATCCCG 59.931 57.143 3.36 0.00 32.82 5.14
3162 3226 2.152016 AGTTTTAGCAAGCCCGTTCTC 58.848 47.619 0.00 0.00 0.00 2.87
3163 3227 2.152016 GAGTTTTAGCAAGCCCGTTCT 58.848 47.619 0.00 0.00 0.00 3.01
3164 3228 1.877443 TGAGTTTTAGCAAGCCCGTTC 59.123 47.619 0.00 0.00 0.00 3.95
3168 3232 1.464997 CGACTGAGTTTTAGCAAGCCC 59.535 52.381 0.00 0.00 0.00 5.19
3169 3233 2.157863 GTCGACTGAGTTTTAGCAAGCC 59.842 50.000 8.70 0.00 0.00 4.35
3170 3234 3.060602 AGTCGACTGAGTTTTAGCAAGC 58.939 45.455 19.30 0.00 0.00 4.01
3171 3235 4.637574 CAGTCGACTGAGTTTTAGCAAG 57.362 45.455 36.73 7.99 46.59 4.01
3183 3247 6.591834 AGAATTGGTTAAATCTCAGTCGACTG 59.408 38.462 34.76 34.76 45.08 3.51
3184 3248 6.702329 AGAATTGGTTAAATCTCAGTCGACT 58.298 36.000 13.58 13.58 0.00 4.18
3185 3249 6.969828 AGAATTGGTTAAATCTCAGTCGAC 57.030 37.500 7.70 7.70 0.00 4.20


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

AutoCloner maintained by Alex Coulton.