Multiple sequence alignment - TraesCS2A01G533200

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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 TraesCS2A01G533200 chr2A 100.000 3251 0 0 1 3251 749105605 749102355 0.000000e+00 6004.0
1 TraesCS2A01G533200 chr2A 82.609 1265 208 10 996 2251 4293809 4292548 0.000000e+00 1107.0
2 TraesCS2A01G533200 chr2D 95.726 2340 78 16 267 2597 618289321 618286995 0.000000e+00 3747.0
3 TraesCS2A01G533200 chr2D 82.560 1250 207 10 1009 2251 5747602 5748847 0.000000e+00 1090.0
4 TraesCS2A01G533200 chr2D 92.377 669 31 7 2599 3251 618286959 618286295 0.000000e+00 935.0
5 TraesCS2A01G533200 chr2D 97.143 35 1 0 2599 2633 608770111 608770145 3.500000e-05 60.2
6 TraesCS2A01G533200 chr2B 95.264 1499 54 10 839 2325 754928833 754927340 0.000000e+00 2359.0
7 TraesCS2A01G533200 chr2B 81.594 1255 210 17 1009 2251 5628373 5629618 0.000000e+00 1018.0
8 TraesCS2A01G533200 chr2B 88.604 351 27 10 279 625 754931765 754931424 6.490000e-112 414.0
9 TraesCS2A01G533200 chr2B 86.709 158 16 3 675 832 754931411 754931259 1.550000e-38 171.0
10 TraesCS2A01G533200 chr6B 88.030 401 39 8 2858 3251 162562966 162563364 1.770000e-127 466.0
11 TraesCS2A01G533200 chr6B 78.417 278 24 11 2327 2590 162550437 162550692 7.270000e-32 148.0
12 TraesCS2A01G533200 chr3A 87.879 396 39 9 2862 3251 549909415 549909023 1.060000e-124 457.0
13 TraesCS2A01G533200 chr3A 86.538 156 18 3 2639 2793 549909577 549909424 5.580000e-38 169.0
14 TraesCS2A01G533200 chr5B 82.319 526 54 22 2647 3163 18065943 18065448 1.390000e-113 420.0
15 TraesCS2A01G533200 chr5B 87.850 107 11 1 2479 2583 18070476 18070370 1.220000e-24 124.0
16 TraesCS2A01G533200 chr1D 84.932 73 11 0 2787 2859 104527925 104527853 1.250000e-09 75.0
17 TraesCS2A01G533200 chr3B 100.000 35 0 0 2599 2633 783006575 783006609 7.530000e-07 65.8
18 TraesCS2A01G533200 chr5A 100.000 33 0 0 2600 2632 597741399 597741367 9.740000e-06 62.1
19 TraesCS2A01G533200 chr5A 97.222 36 1 0 2598 2633 650556762 650556797 9.740000e-06 62.1
20 TraesCS2A01G533200 chr4B 97.143 35 1 0 2599 2633 167362953 167362919 3.500000e-05 60.2
21 TraesCS2A01G533200 chr3D 96.875 32 1 0 2768 2799 313284726 313284757 2.000000e-03 54.7
22 TraesCS2A01G533200 chr7D 100.000 28 0 0 2910 2937 496775912 496775939 6.000000e-03 52.8


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 TraesCS2A01G533200 chr2A 749102355 749105605 3250 True 6004.000000 6004 100.000000 1 3251 1 chr2A.!!$R2 3250
1 TraesCS2A01G533200 chr2A 4292548 4293809 1261 True 1107.000000 1107 82.609000 996 2251 1 chr2A.!!$R1 1255
2 TraesCS2A01G533200 chr2D 618286295 618289321 3026 True 2341.000000 3747 94.051500 267 3251 2 chr2D.!!$R1 2984
3 TraesCS2A01G533200 chr2D 5747602 5748847 1245 False 1090.000000 1090 82.560000 1009 2251 1 chr2D.!!$F1 1242
4 TraesCS2A01G533200 chr2B 5628373 5629618 1245 False 1018.000000 1018 81.594000 1009 2251 1 chr2B.!!$F1 1242
5 TraesCS2A01G533200 chr2B 754927340 754931765 4425 True 981.333333 2359 90.192333 279 2325 3 chr2B.!!$R1 2046
6 TraesCS2A01G533200 chr3A 549909023 549909577 554 True 313.000000 457 87.208500 2639 3251 2 chr3A.!!$R1 612

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
133 134 0.517316 CCGAGCAAGTTAGTGTTGGC 59.483 55.0 0.00 0.0 0.00 4.52 F
1980 4423 0.101399 ATGTCGACGCTGTCATCCTC 59.899 55.0 11.62 0.0 32.09 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1995 4438 1.582968 CCACTGTGGCACATTGCTC 59.417 57.895 27.0 0.0 44.52 4.26 R
3167 5676 2.418368 TGTTCGGCTTATTCCTGCAT 57.582 45.000 0.0 0.0 0.00 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
107 108 9.109393 TGATTATATTATTTTGAGCTATCGGGC 57.891 33.333 0.00 0.00 0.00 6.13
108 109 9.331282 GATTATATTATTTTGAGCTATCGGGCT 57.669 33.333 0.00 0.00 46.11 5.19
112 113 7.817418 ATTATTTTGAGCTATCGGGCTAAAA 57.183 32.000 0.00 4.98 43.20 1.52
114 115 4.957759 TTTGAGCTATCGGGCTAAAAAC 57.042 40.909 6.18 0.00 43.20 2.43
115 116 2.914059 TGAGCTATCGGGCTAAAAACC 58.086 47.619 0.00 0.00 43.20 3.27
123 124 1.244816 GGGCTAAAAACCGAGCAAGT 58.755 50.000 0.00 0.00 40.64 3.16
124 125 1.611977 GGGCTAAAAACCGAGCAAGTT 59.388 47.619 0.00 0.00 40.64 2.66
125 126 2.815503 GGGCTAAAAACCGAGCAAGTTA 59.184 45.455 0.00 0.00 40.64 2.24
126 127 3.119955 GGGCTAAAAACCGAGCAAGTTAG 60.120 47.826 0.00 0.00 40.64 2.34
127 128 3.501062 GGCTAAAAACCGAGCAAGTTAGT 59.499 43.478 0.00 0.00 40.64 2.24
128 129 4.464112 GCTAAAAACCGAGCAAGTTAGTG 58.536 43.478 0.00 0.00 38.62 2.74
129 130 4.024302 GCTAAAAACCGAGCAAGTTAGTGT 60.024 41.667 0.00 0.00 38.62 3.55
130 131 4.976224 AAAAACCGAGCAAGTTAGTGTT 57.024 36.364 0.00 0.00 0.00 3.32
131 132 3.963383 AAACCGAGCAAGTTAGTGTTG 57.037 42.857 0.00 0.00 0.00 3.33
132 133 1.878953 ACCGAGCAAGTTAGTGTTGG 58.121 50.000 0.00 0.00 0.00 3.77
133 134 0.517316 CCGAGCAAGTTAGTGTTGGC 59.483 55.000 0.00 0.00 0.00 4.52
134 135 1.512926 CGAGCAAGTTAGTGTTGGCT 58.487 50.000 0.00 0.00 0.00 4.75
135 136 1.461127 CGAGCAAGTTAGTGTTGGCTC 59.539 52.381 0.00 0.00 0.00 4.70
136 137 2.494059 GAGCAAGTTAGTGTTGGCTCA 58.506 47.619 0.00 0.00 32.71 4.26
137 138 2.878406 GAGCAAGTTAGTGTTGGCTCAA 59.122 45.455 0.00 0.00 32.71 3.02
138 139 3.490348 AGCAAGTTAGTGTTGGCTCAAT 58.510 40.909 0.00 0.00 0.00 2.57
139 140 3.891366 AGCAAGTTAGTGTTGGCTCAATT 59.109 39.130 0.00 0.00 0.00 2.32
140 141 5.070001 AGCAAGTTAGTGTTGGCTCAATTA 58.930 37.500 0.00 0.00 0.00 1.40
141 142 5.534654 AGCAAGTTAGTGTTGGCTCAATTAA 59.465 36.000 0.00 0.00 0.00 1.40
142 143 5.858581 GCAAGTTAGTGTTGGCTCAATTAAG 59.141 40.000 0.00 0.00 0.00 1.85
143 144 6.293955 GCAAGTTAGTGTTGGCTCAATTAAGA 60.294 38.462 0.00 0.00 0.00 2.10
144 145 7.575720 GCAAGTTAGTGTTGGCTCAATTAAGAT 60.576 37.037 0.00 0.00 0.00 2.40
145 146 7.617041 AGTTAGTGTTGGCTCAATTAAGATC 57.383 36.000 0.00 0.00 0.00 2.75
146 147 7.168219 AGTTAGTGTTGGCTCAATTAAGATCA 58.832 34.615 0.00 0.00 0.00 2.92
147 148 7.665559 AGTTAGTGTTGGCTCAATTAAGATCAA 59.334 33.333 0.00 0.00 0.00 2.57
148 149 6.899393 AGTGTTGGCTCAATTAAGATCAAA 57.101 33.333 0.00 0.00 0.00 2.69
149 150 7.472334 AGTGTTGGCTCAATTAAGATCAAAT 57.528 32.000 0.00 0.00 0.00 2.32
150 151 7.542025 AGTGTTGGCTCAATTAAGATCAAATC 58.458 34.615 0.00 0.00 0.00 2.17
151 152 7.177216 AGTGTTGGCTCAATTAAGATCAAATCA 59.823 33.333 0.00 0.00 0.00 2.57
152 153 7.977853 GTGTTGGCTCAATTAAGATCAAATCAT 59.022 33.333 0.00 0.00 0.00 2.45
153 154 8.533657 TGTTGGCTCAATTAAGATCAAATCATT 58.466 29.630 0.00 0.00 0.00 2.57
154 155 9.374838 GTTGGCTCAATTAAGATCAAATCATTT 57.625 29.630 0.00 0.00 0.00 2.32
155 156 9.947433 TTGGCTCAATTAAGATCAAATCATTTT 57.053 25.926 0.00 0.00 0.00 1.82
156 157 9.947433 TGGCTCAATTAAGATCAAATCATTTTT 57.053 25.926 0.00 0.00 0.00 1.94
165 166 6.549952 AGATCAAATCATTTTTCAGTCGAGC 58.450 36.000 0.00 0.00 0.00 5.03
166 167 5.947228 TCAAATCATTTTTCAGTCGAGCT 57.053 34.783 0.00 0.00 0.00 4.09
167 168 7.550551 AGATCAAATCATTTTTCAGTCGAGCTA 59.449 33.333 0.00 0.00 0.00 3.32
168 169 7.615582 TCAAATCATTTTTCAGTCGAGCTAT 57.384 32.000 0.00 0.00 0.00 2.97
169 170 8.716646 TCAAATCATTTTTCAGTCGAGCTATA 57.283 30.769 0.00 0.00 0.00 1.31
170 171 9.330063 TCAAATCATTTTTCAGTCGAGCTATAT 57.670 29.630 0.00 0.00 0.00 0.86
173 174 7.853377 TCATTTTTCAGTCGAGCTATATACG 57.147 36.000 0.00 0.00 0.00 3.06
174 175 7.645402 TCATTTTTCAGTCGAGCTATATACGA 58.355 34.615 0.00 0.00 0.00 3.43
183 184 5.358090 TCGAGCTATATACGACATCCTAGG 58.642 45.833 0.82 0.82 0.00 3.02
184 185 4.512198 CGAGCTATATACGACATCCTAGGG 59.488 50.000 9.46 0.00 0.00 3.53
185 186 5.682659 GAGCTATATACGACATCCTAGGGA 58.317 45.833 9.46 0.00 35.55 4.20
186 187 6.075949 AGCTATATACGACATCCTAGGGAA 57.924 41.667 9.46 0.00 34.34 3.97
187 188 5.887035 AGCTATATACGACATCCTAGGGAAC 59.113 44.000 9.46 0.00 34.34 3.62
189 190 6.038492 GCTATATACGACATCCTAGGGAACTC 59.962 46.154 9.46 0.00 43.67 3.01
190 191 2.526888 ACGACATCCTAGGGAACTCA 57.473 50.000 9.46 0.00 43.67 3.41
191 192 3.033659 ACGACATCCTAGGGAACTCAT 57.966 47.619 9.46 0.00 43.67 2.90
192 193 3.375699 ACGACATCCTAGGGAACTCATT 58.624 45.455 9.46 0.00 43.67 2.57
193 194 3.775316 ACGACATCCTAGGGAACTCATTT 59.225 43.478 9.46 0.00 43.67 2.32
194 195 4.960469 ACGACATCCTAGGGAACTCATTTA 59.040 41.667 9.46 0.00 43.67 1.40
195 196 5.602978 ACGACATCCTAGGGAACTCATTTAT 59.397 40.000 9.46 0.00 43.67 1.40
196 197 6.099845 ACGACATCCTAGGGAACTCATTTATT 59.900 38.462 9.46 0.00 43.67 1.40
197 198 6.992715 CGACATCCTAGGGAACTCATTTATTT 59.007 38.462 9.46 0.00 43.67 1.40
198 199 7.499232 CGACATCCTAGGGAACTCATTTATTTT 59.501 37.037 9.46 0.00 43.67 1.82
199 200 9.190317 GACATCCTAGGGAACTCATTTATTTTT 57.810 33.333 9.46 0.00 43.67 1.94
221 222 7.781548 TTTTTAGCCGGTCTTGAATATCTAC 57.218 36.000 1.90 0.00 0.00 2.59
222 223 6.726490 TTTAGCCGGTCTTGAATATCTACT 57.274 37.500 1.90 0.00 0.00 2.57
223 224 7.828508 TTTAGCCGGTCTTGAATATCTACTA 57.171 36.000 1.90 0.00 0.00 1.82
224 225 5.708877 AGCCGGTCTTGAATATCTACTAC 57.291 43.478 1.90 0.00 0.00 2.73
225 226 5.386924 AGCCGGTCTTGAATATCTACTACT 58.613 41.667 1.90 0.00 0.00 2.57
226 227 5.834204 AGCCGGTCTTGAATATCTACTACTT 59.166 40.000 1.90 0.00 0.00 2.24
227 228 7.002879 AGCCGGTCTTGAATATCTACTACTTA 58.997 38.462 1.90 0.00 0.00 2.24
228 229 7.504911 AGCCGGTCTTGAATATCTACTACTTAA 59.495 37.037 1.90 0.00 0.00 1.85
229 230 8.139989 GCCGGTCTTGAATATCTACTACTTAAA 58.860 37.037 1.90 0.00 0.00 1.52
252 253 8.763049 AAAATAAGTAGCATTCTTTTCTTGCC 57.237 30.769 0.00 0.00 37.07 4.52
253 254 7.466746 AATAAGTAGCATTCTTTTCTTGCCA 57.533 32.000 0.00 0.00 37.07 4.92
254 255 5.382618 AAGTAGCATTCTTTTCTTGCCAG 57.617 39.130 0.00 0.00 37.07 4.85
255 256 3.760684 AGTAGCATTCTTTTCTTGCCAGG 59.239 43.478 0.00 0.00 37.07 4.45
256 257 2.601905 AGCATTCTTTTCTTGCCAGGT 58.398 42.857 0.00 0.00 37.07 4.00
257 258 3.766545 AGCATTCTTTTCTTGCCAGGTA 58.233 40.909 0.00 0.00 37.07 3.08
258 259 3.760684 AGCATTCTTTTCTTGCCAGGTAG 59.239 43.478 0.00 0.00 37.07 3.18
259 260 3.758554 GCATTCTTTTCTTGCCAGGTAGA 59.241 43.478 0.00 0.00 0.00 2.59
260 261 4.218417 GCATTCTTTTCTTGCCAGGTAGAA 59.782 41.667 2.87 2.87 0.00 2.10
261 262 5.703876 CATTCTTTTCTTGCCAGGTAGAAC 58.296 41.667 5.83 0.00 30.53 3.01
262 263 3.751518 TCTTTTCTTGCCAGGTAGAACC 58.248 45.455 5.83 0.00 38.99 3.62
263 264 2.178912 TTTCTTGCCAGGTAGAACCG 57.821 50.000 5.83 0.00 44.90 4.44
264 265 1.053424 TTCTTGCCAGGTAGAACCGT 58.947 50.000 2.87 0.00 44.90 4.83
265 266 0.606604 TCTTGCCAGGTAGAACCGTC 59.393 55.000 0.00 0.00 44.90 4.79
276 277 1.368374 GAACCGTCGGTGTTTTGCG 60.368 57.895 19.67 0.00 35.34 4.85
414 416 2.291741 GCATCGATGAAAGATTGGACCC 59.708 50.000 29.20 2.35 0.00 4.46
482 484 8.723311 ACTTTTTGTATTTTGATTGATGCATGG 58.277 29.630 2.46 0.00 0.00 3.66
483 485 8.618702 TTTTTGTATTTTGATTGATGCATGGT 57.381 26.923 2.46 0.00 0.00 3.55
484 486 8.618702 TTTTGTATTTTGATTGATGCATGGTT 57.381 26.923 2.46 0.00 0.00 3.67
485 487 7.598189 TTGTATTTTGATTGATGCATGGTTG 57.402 32.000 2.46 0.00 0.00 3.77
511 513 5.295152 CAGAAAGCCAGAAAGCTCAATTTT 58.705 37.500 0.00 0.00 44.11 1.82
573 579 1.388547 GCACAAGGAGGTTTGACACA 58.611 50.000 0.00 0.00 0.00 3.72
584 590 5.220796 GGAGGTTTGACACACTGTTAGAAAC 60.221 44.000 0.00 0.00 0.00 2.78
640 646 7.565768 CCTAGTCCTTTTTCTCTAATACTCCCT 59.434 40.741 0.00 0.00 0.00 4.20
641 647 7.189079 AGTCCTTTTTCTCTAATACTCCCTG 57.811 40.000 0.00 0.00 0.00 4.45
659 665 7.287810 ACTCCCTGTGTAAACTTTTGTAAGAT 58.712 34.615 0.00 0.00 35.30 2.40
780 786 2.660802 GCAGCTTTGCATGGGCTT 59.339 55.556 5.95 0.00 41.91 4.35
806 813 4.996122 TGCATTAAGATTTGTGCTTTTGGG 59.004 37.500 0.00 0.00 38.37 4.12
834 841 0.606944 AAATTTGAGGTGCCGCCGTA 60.607 50.000 0.00 0.00 43.70 4.02
878 3304 1.206849 CTTCCACTCAGCCTTCTCCTC 59.793 57.143 0.00 0.00 0.00 3.71
894 3320 7.518188 CCTTCTCCTCCTATATTTAAAAGCCA 58.482 38.462 0.00 0.00 0.00 4.75
895 3321 8.166726 CCTTCTCCTCCTATATTTAAAAGCCAT 58.833 37.037 0.00 0.00 0.00 4.40
898 3324 9.393786 TCTCCTCCTATATTTAAAAGCCATAGT 57.606 33.333 0.00 0.00 0.00 2.12
1419 3862 1.212935 GGTGCCCAGATGGAGTACATT 59.787 52.381 0.00 0.00 40.72 2.71
1539 3982 2.992689 TACAAGTCCGGCGAGCCA 60.993 61.111 9.30 0.00 35.37 4.75
1731 4174 4.020617 TGGCTCCCGCTCTGGTTG 62.021 66.667 0.00 0.00 35.15 3.77
1954 4397 3.002583 TGCTCTCCGATGGCACCA 61.003 61.111 0.00 0.00 0.00 4.17
1980 4423 0.101399 ATGTCGACGCTGTCATCCTC 59.899 55.000 11.62 0.00 32.09 3.71
2289 4736 7.466996 GCTTTCAATCTAGATGTTCCTCATGTG 60.467 40.741 5.86 0.00 36.83 3.21
2319 4766 1.352352 CTGGAATTGTGTGGAGAGGGT 59.648 52.381 0.00 0.00 0.00 4.34
2355 4805 4.219725 GGCTATTGGTAAGTTGGCTGAAAA 59.780 41.667 0.00 0.00 0.00 2.29
2381 4831 2.223971 ACTTGGGTCAGTGTGTAAGTCG 60.224 50.000 0.00 0.00 0.00 4.18
2382 4832 1.694844 TGGGTCAGTGTGTAAGTCGA 58.305 50.000 0.00 0.00 0.00 4.20
2385 4835 3.070446 TGGGTCAGTGTGTAAGTCGATTT 59.930 43.478 0.00 0.00 0.00 2.17
2476 4926 1.379916 CAGGGCCTTGATCCACACA 59.620 57.895 9.80 0.00 0.00 3.72
2477 4927 0.962356 CAGGGCCTTGATCCACACAC 60.962 60.000 9.80 0.00 0.00 3.82
2478 4928 1.074775 GGGCCTTGATCCACACACA 59.925 57.895 0.84 0.00 0.00 3.72
2523 4973 0.442310 CGTACGTGCCATCCTGTTTG 59.558 55.000 7.22 0.00 0.00 2.93
2534 4984 4.280819 CCATCCTGTTTGGTATGGTTCAT 58.719 43.478 0.00 0.00 38.04 2.57
2571 5021 3.478857 AATCACAGTCACCGGTGTTTA 57.521 42.857 32.74 12.72 37.90 2.01
2597 5047 8.848182 AGTTACTTTATTACTCTATCTGTCCCG 58.152 37.037 0.00 0.00 0.00 5.14
2660 5144 1.973281 CGCCATTGCCCAGTGTCTT 60.973 57.895 0.00 0.00 0.00 3.01
2675 5159 4.864806 CAGTGTCTTTCTATGCATACGTGT 59.135 41.667 1.16 0.00 0.00 4.49
2699 5184 3.532542 ACGCTGGAAGGTTAAAGATAGC 58.467 45.455 0.00 0.00 0.00 2.97
2718 5217 2.556622 AGCCTTTTCAAATGTGTACGGG 59.443 45.455 0.00 0.00 0.00 5.28
2780 5279 6.215515 AGCTATGTACCTATTACTCCCTCA 57.784 41.667 0.00 0.00 0.00 3.86
2797 5296 7.787028 ACTCCCTCAGTCTCAAAATAAGTATC 58.213 38.462 0.00 0.00 0.00 2.24
2885 5385 7.068593 GGGGAATATTAGCTAATAATGCATGCA 59.931 37.037 25.90 25.04 35.63 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
81 82 9.109393 GCCCGATAGCTCAAAATAATATAATCA 57.891 33.333 0.00 0.00 0.00 2.57
82 83 9.331282 AGCCCGATAGCTCAAAATAATATAATC 57.669 33.333 0.00 0.00 39.48 1.75
86 87 9.515226 TTTTAGCCCGATAGCTCAAAATAATAT 57.485 29.630 0.00 0.00 43.67 1.28
87 88 8.911918 TTTTAGCCCGATAGCTCAAAATAATA 57.088 30.769 0.00 0.00 43.67 0.98
88 89 7.817418 TTTTAGCCCGATAGCTCAAAATAAT 57.183 32.000 0.00 0.00 43.67 1.28
89 90 7.415877 GGTTTTTAGCCCGATAGCTCAAAATAA 60.416 37.037 13.47 0.00 43.80 1.40
90 91 6.038936 GGTTTTTAGCCCGATAGCTCAAAATA 59.961 38.462 13.47 0.05 43.80 1.40
91 92 5.163550 GGTTTTTAGCCCGATAGCTCAAAAT 60.164 40.000 13.47 0.00 43.80 1.82
92 93 4.157105 GGTTTTTAGCCCGATAGCTCAAAA 59.843 41.667 0.00 8.91 43.67 2.44
93 94 3.692593 GGTTTTTAGCCCGATAGCTCAAA 59.307 43.478 0.00 0.00 43.67 2.69
94 95 3.275999 GGTTTTTAGCCCGATAGCTCAA 58.724 45.455 0.00 0.00 43.67 3.02
95 96 2.914059 GGTTTTTAGCCCGATAGCTCA 58.086 47.619 0.00 0.00 43.67 4.26
103 104 0.168128 CTTGCTCGGTTTTTAGCCCG 59.832 55.000 0.00 0.00 45.55 6.13
104 105 1.244816 ACTTGCTCGGTTTTTAGCCC 58.755 50.000 0.00 0.00 37.97 5.19
105 106 3.501062 ACTAACTTGCTCGGTTTTTAGCC 59.499 43.478 0.00 0.00 37.97 3.93
106 107 4.024302 ACACTAACTTGCTCGGTTTTTAGC 60.024 41.667 0.00 0.00 39.25 3.09
107 108 5.668558 ACACTAACTTGCTCGGTTTTTAG 57.331 39.130 0.00 0.00 0.00 1.85
108 109 5.220892 CCAACACTAACTTGCTCGGTTTTTA 60.221 40.000 0.00 0.00 0.00 1.52
109 110 4.439563 CCAACACTAACTTGCTCGGTTTTT 60.440 41.667 0.00 0.00 0.00 1.94
110 111 3.066203 CCAACACTAACTTGCTCGGTTTT 59.934 43.478 0.00 0.00 0.00 2.43
111 112 2.616842 CCAACACTAACTTGCTCGGTTT 59.383 45.455 0.00 0.00 0.00 3.27
112 113 2.218603 CCAACACTAACTTGCTCGGTT 58.781 47.619 0.00 0.00 0.00 4.44
113 114 1.878953 CCAACACTAACTTGCTCGGT 58.121 50.000 0.00 0.00 0.00 4.69
114 115 0.517316 GCCAACACTAACTTGCTCGG 59.483 55.000 0.00 0.00 0.00 4.63
115 116 1.461127 GAGCCAACACTAACTTGCTCG 59.539 52.381 0.00 0.00 0.00 5.03
116 117 2.494059 TGAGCCAACACTAACTTGCTC 58.506 47.619 0.00 0.00 0.00 4.26
117 118 2.638480 TGAGCCAACACTAACTTGCT 57.362 45.000 0.00 0.00 0.00 3.91
118 119 3.923017 ATTGAGCCAACACTAACTTGC 57.077 42.857 0.00 0.00 0.00 4.01
119 120 7.202016 TCTTAATTGAGCCAACACTAACTTG 57.798 36.000 0.00 0.00 0.00 3.16
120 121 7.665559 TGATCTTAATTGAGCCAACACTAACTT 59.334 33.333 0.00 0.00 0.00 2.66
121 122 7.168219 TGATCTTAATTGAGCCAACACTAACT 58.832 34.615 0.00 0.00 0.00 2.24
122 123 7.377766 TGATCTTAATTGAGCCAACACTAAC 57.622 36.000 0.00 0.00 0.00 2.34
123 124 7.994425 TTGATCTTAATTGAGCCAACACTAA 57.006 32.000 0.00 0.00 0.00 2.24
124 125 7.994425 TTTGATCTTAATTGAGCCAACACTA 57.006 32.000 0.00 0.00 0.00 2.74
125 126 6.899393 TTTGATCTTAATTGAGCCAACACT 57.101 33.333 0.00 0.00 0.00 3.55
126 127 7.315142 TGATTTGATCTTAATTGAGCCAACAC 58.685 34.615 0.00 4.15 0.00 3.32
127 128 7.465353 TGATTTGATCTTAATTGAGCCAACA 57.535 32.000 0.00 0.77 0.00 3.33
128 129 8.937634 AATGATTTGATCTTAATTGAGCCAAC 57.062 30.769 0.00 0.00 0.00 3.77
129 130 9.947433 AAAATGATTTGATCTTAATTGAGCCAA 57.053 25.926 0.00 0.00 0.00 4.52
130 131 9.947433 AAAAATGATTTGATCTTAATTGAGCCA 57.053 25.926 0.00 0.00 0.00 4.75
139 140 8.177663 GCTCGACTGAAAAATGATTTGATCTTA 58.822 33.333 0.00 0.00 0.00 2.10
140 141 7.025963 GCTCGACTGAAAAATGATTTGATCTT 58.974 34.615 0.00 0.00 0.00 2.40
141 142 6.373774 AGCTCGACTGAAAAATGATTTGATCT 59.626 34.615 0.00 0.00 0.00 2.75
142 143 6.549952 AGCTCGACTGAAAAATGATTTGATC 58.450 36.000 0.00 0.00 0.00 2.92
143 144 6.506500 AGCTCGACTGAAAAATGATTTGAT 57.493 33.333 0.00 0.00 0.00 2.57
144 145 5.947228 AGCTCGACTGAAAAATGATTTGA 57.053 34.783 0.00 0.00 0.00 2.69
147 148 8.916654 CGTATATAGCTCGACTGAAAAATGATT 58.083 33.333 0.00 0.00 0.00 2.57
148 149 8.297426 TCGTATATAGCTCGACTGAAAAATGAT 58.703 33.333 0.00 0.00 0.00 2.45
149 150 7.590322 GTCGTATATAGCTCGACTGAAAAATGA 59.410 37.037 15.39 0.00 46.54 2.57
150 151 7.712119 GTCGTATATAGCTCGACTGAAAAATG 58.288 38.462 15.39 0.00 46.54 2.32
151 152 7.854934 GTCGTATATAGCTCGACTGAAAAAT 57.145 36.000 15.39 0.00 46.54 1.82
160 161 5.358090 CCTAGGATGTCGTATATAGCTCGA 58.642 45.833 1.05 0.00 0.00 4.04
161 162 4.512198 CCCTAGGATGTCGTATATAGCTCG 59.488 50.000 11.48 0.00 0.00 5.03
162 163 5.682659 TCCCTAGGATGTCGTATATAGCTC 58.317 45.833 11.48 0.00 0.00 4.09
163 164 5.712084 TCCCTAGGATGTCGTATATAGCT 57.288 43.478 11.48 0.00 0.00 3.32
164 165 5.887035 AGTTCCCTAGGATGTCGTATATAGC 59.113 44.000 11.48 0.00 0.00 2.97
165 166 7.110810 TGAGTTCCCTAGGATGTCGTATATAG 58.889 42.308 11.48 0.00 0.00 1.31
166 167 7.024345 TGAGTTCCCTAGGATGTCGTATATA 57.976 40.000 11.48 0.00 0.00 0.86
167 168 5.888901 TGAGTTCCCTAGGATGTCGTATAT 58.111 41.667 11.48 0.00 0.00 0.86
168 169 5.314718 TGAGTTCCCTAGGATGTCGTATA 57.685 43.478 11.48 0.00 0.00 1.47
169 170 4.180377 TGAGTTCCCTAGGATGTCGTAT 57.820 45.455 11.48 0.00 0.00 3.06
170 171 3.657398 TGAGTTCCCTAGGATGTCGTA 57.343 47.619 11.48 0.00 0.00 3.43
171 172 2.526888 TGAGTTCCCTAGGATGTCGT 57.473 50.000 11.48 0.00 0.00 4.34
172 173 4.408182 AAATGAGTTCCCTAGGATGTCG 57.592 45.455 11.48 0.00 0.00 4.35
173 174 8.753497 AAAATAAATGAGTTCCCTAGGATGTC 57.247 34.615 11.48 1.85 0.00 3.06
197 198 7.562135 AGTAGATATTCAAGACCGGCTAAAAA 58.438 34.615 0.00 0.00 0.00 1.94
198 199 7.120923 AGTAGATATTCAAGACCGGCTAAAA 57.879 36.000 0.00 0.00 0.00 1.52
199 200 6.726490 AGTAGATATTCAAGACCGGCTAAA 57.274 37.500 0.00 0.00 0.00 1.85
200 201 7.002879 AGTAGTAGATATTCAAGACCGGCTAA 58.997 38.462 0.00 0.00 0.00 3.09
201 202 6.540995 AGTAGTAGATATTCAAGACCGGCTA 58.459 40.000 0.00 0.00 0.00 3.93
202 203 5.386924 AGTAGTAGATATTCAAGACCGGCT 58.613 41.667 0.00 0.00 0.00 5.52
203 204 5.708877 AGTAGTAGATATTCAAGACCGGC 57.291 43.478 0.00 0.00 0.00 6.13
226 227 9.855021 GGCAAGAAAAGAATGCTACTTATTTTA 57.145 29.630 0.00 0.00 39.94 1.52
227 228 8.367156 TGGCAAGAAAAGAATGCTACTTATTTT 58.633 29.630 0.00 0.00 39.94 1.82
228 229 7.895759 TGGCAAGAAAAGAATGCTACTTATTT 58.104 30.769 0.00 0.00 39.94 1.40
229 230 7.363268 CCTGGCAAGAAAAGAATGCTACTTATT 60.363 37.037 0.00 0.00 39.94 1.40
230 231 6.096001 CCTGGCAAGAAAAGAATGCTACTTAT 59.904 38.462 0.00 0.00 39.94 1.73
231 232 5.415701 CCTGGCAAGAAAAGAATGCTACTTA 59.584 40.000 0.00 0.00 39.94 2.24
232 233 4.219288 CCTGGCAAGAAAAGAATGCTACTT 59.781 41.667 0.00 0.00 39.94 2.24
233 234 3.760684 CCTGGCAAGAAAAGAATGCTACT 59.239 43.478 0.00 0.00 39.94 2.57
234 235 3.507622 ACCTGGCAAGAAAAGAATGCTAC 59.492 43.478 0.00 0.00 39.94 3.58
235 236 3.766545 ACCTGGCAAGAAAAGAATGCTA 58.233 40.909 0.00 0.00 39.94 3.49
236 237 2.601905 ACCTGGCAAGAAAAGAATGCT 58.398 42.857 0.00 0.00 39.94 3.79
237 238 3.758554 TCTACCTGGCAAGAAAAGAATGC 59.241 43.478 0.00 0.00 39.33 3.56
238 239 5.335976 GGTTCTACCTGGCAAGAAAAGAATG 60.336 44.000 12.24 0.00 34.73 2.67
239 240 4.767409 GGTTCTACCTGGCAAGAAAAGAAT 59.233 41.667 12.24 0.00 34.73 2.40
240 241 4.142038 GGTTCTACCTGGCAAGAAAAGAA 58.858 43.478 12.24 0.00 34.73 2.52
241 242 3.751518 GGTTCTACCTGGCAAGAAAAGA 58.248 45.455 12.24 0.00 34.73 2.52
242 243 2.484264 CGGTTCTACCTGGCAAGAAAAG 59.516 50.000 12.24 7.11 35.66 2.27
243 244 2.158726 ACGGTTCTACCTGGCAAGAAAA 60.159 45.455 12.24 0.00 35.66 2.29
244 245 1.418637 ACGGTTCTACCTGGCAAGAAA 59.581 47.619 12.24 0.00 35.66 2.52
245 246 1.001633 GACGGTTCTACCTGGCAAGAA 59.998 52.381 7.75 7.75 35.66 2.52
246 247 0.606604 GACGGTTCTACCTGGCAAGA 59.393 55.000 0.00 0.00 35.66 3.02
247 248 0.736325 CGACGGTTCTACCTGGCAAG 60.736 60.000 0.00 0.00 35.66 4.01
248 249 1.290955 CGACGGTTCTACCTGGCAA 59.709 57.895 0.00 0.00 35.66 4.52
249 250 2.642254 CCGACGGTTCTACCTGGCA 61.642 63.158 5.48 0.00 35.66 4.92
250 251 2.183555 CCGACGGTTCTACCTGGC 59.816 66.667 5.48 0.00 35.66 4.85
251 252 1.214589 CACCGACGGTTCTACCTGG 59.785 63.158 19.02 0.00 35.66 4.45
252 253 0.316204 AACACCGACGGTTCTACCTG 59.684 55.000 19.02 6.84 35.66 4.00
253 254 1.043022 AAACACCGACGGTTCTACCT 58.957 50.000 19.02 0.00 35.66 3.08
254 255 1.528161 CAAAACACCGACGGTTCTACC 59.472 52.381 19.02 0.00 31.02 3.18
255 256 1.070376 GCAAAACACCGACGGTTCTAC 60.070 52.381 19.02 1.05 31.02 2.59
256 257 1.219646 GCAAAACACCGACGGTTCTA 58.780 50.000 19.02 0.00 31.02 2.10
257 258 1.768112 CGCAAAACACCGACGGTTCT 61.768 55.000 19.02 4.01 31.02 3.01
258 259 1.368374 CGCAAAACACCGACGGTTC 60.368 57.895 19.02 1.66 31.02 3.62
259 260 2.107903 ACGCAAAACACCGACGGTT 61.108 52.632 19.02 6.33 31.02 4.44
260 261 2.512057 ACGCAAAACACCGACGGT 60.512 55.556 15.37 15.37 35.62 4.83
261 262 2.052590 CACGCAAAACACCGACGG 60.053 61.111 13.61 13.61 0.00 4.79
262 263 0.521659 AAACACGCAAAACACCGACG 60.522 50.000 0.00 0.00 0.00 5.12
263 264 1.319079 CAAAACACGCAAAACACCGAC 59.681 47.619 0.00 0.00 0.00 4.79
264 265 1.618861 CAAAACACGCAAAACACCGA 58.381 45.000 0.00 0.00 0.00 4.69
265 266 0.024364 GCAAAACACGCAAAACACCG 59.976 50.000 0.00 0.00 0.00 4.94
276 277 1.732405 GCGCCCAGATAAGCAAAACAC 60.732 52.381 0.00 0.00 0.00 3.32
301 302 2.508526 GGCAAAGACAACTGACAGGAT 58.491 47.619 7.51 0.00 0.00 3.24
302 303 1.476833 GGGCAAAGACAACTGACAGGA 60.477 52.381 7.51 0.00 0.00 3.86
304 305 1.972872 AGGGCAAAGACAACTGACAG 58.027 50.000 0.00 0.00 0.00 3.51
376 377 7.911727 TCATCGATGCAACATCAATCTTAAAAG 59.088 33.333 20.81 0.00 0.00 2.27
414 416 2.285256 GCTGTAGACGCGTCATTGATTG 60.285 50.000 37.85 21.44 0.00 2.67
482 484 0.030638 TTTCTGGCTTTCTGCGCAAC 59.969 50.000 13.05 0.00 44.05 4.17
483 485 0.311790 CTTTCTGGCTTTCTGCGCAA 59.688 50.000 13.05 0.00 44.05 4.85
484 486 1.951510 CTTTCTGGCTTTCTGCGCA 59.048 52.632 10.98 10.98 44.05 6.09
485 487 1.443363 GCTTTCTGGCTTTCTGCGC 60.443 57.895 0.00 0.00 44.05 6.09
486 488 0.167689 GAGCTTTCTGGCTTTCTGCG 59.832 55.000 0.00 0.00 43.20 5.18
565 571 5.492895 TCCAGTTTCTAACAGTGTGTCAAA 58.507 37.500 0.00 0.00 0.00 2.69
573 579 4.953579 TGGCTTTTTCCAGTTTCTAACAGT 59.046 37.500 0.00 0.00 0.00 3.55
584 590 5.013568 TGCATGATAATGGCTTTTTCCAG 57.986 39.130 0.00 0.00 39.89 3.86
659 665 7.331193 GTGAAGAAAGCTTAAGGATCTAAACGA 59.669 37.037 0.00 0.00 33.61 3.85
780 786 7.333921 CCCAAAAGCACAAATCTTAATGCATAA 59.666 33.333 0.00 0.00 40.63 1.90
806 813 5.389411 GCGGCACCTCAAATTTAAAATGTTC 60.389 40.000 0.00 0.00 0.00 3.18
834 841 1.471676 GGTGGAGAGATGCGATTCGTT 60.472 52.381 8.03 0.00 0.00 3.85
894 3320 6.259608 GCTGAATGCTGATGAACAAGTACTAT 59.740 38.462 0.00 0.00 38.95 2.12
895 3321 5.582269 GCTGAATGCTGATGAACAAGTACTA 59.418 40.000 0.00 0.00 38.95 1.82
896 3322 4.394300 GCTGAATGCTGATGAACAAGTACT 59.606 41.667 0.00 0.00 38.95 2.73
898 3324 4.325972 TGCTGAATGCTGATGAACAAGTA 58.674 39.130 0.00 0.00 43.37 2.24
900 3326 3.842732 TGCTGAATGCTGATGAACAAG 57.157 42.857 0.00 0.00 43.37 3.16
901 3327 3.613193 GCTTGCTGAATGCTGATGAACAA 60.613 43.478 0.00 0.00 43.37 2.83
902 3328 2.094906 GCTTGCTGAATGCTGATGAACA 60.095 45.455 0.00 0.00 43.37 3.18
903 3329 2.163815 AGCTTGCTGAATGCTGATGAAC 59.836 45.455 0.00 0.00 43.37 3.18
904 3330 2.443416 AGCTTGCTGAATGCTGATGAA 58.557 42.857 0.00 0.00 43.37 2.57
935 3366 1.821136 AGTGAGCTTAATTTGCTGGGC 59.179 47.619 9.85 1.89 41.30 5.36
1233 3676 2.783288 CGGGTAGCTCTCCGGGAAC 61.783 68.421 17.01 0.00 42.32 3.62
1539 3982 2.098233 CACGCGCTTCCCGTTGTAT 61.098 57.895 5.73 0.00 36.69 2.29
1995 4438 1.582968 CCACTGTGGCACATTGCTC 59.417 57.895 27.00 0.00 44.52 4.26
2155 4598 2.596851 GCTGGCAGAGGTCCTTGGA 61.597 63.158 20.86 0.00 0.00 3.53
2274 4721 3.307975 CCCAAGTCACATGAGGAACATCT 60.308 47.826 0.00 0.00 37.07 2.90
2289 4736 2.162681 CACAATTCCAGGACCCAAGTC 58.837 52.381 0.00 0.00 42.73 3.01
2319 4766 2.423660 CCAATAGCCGGTCCCCAAAATA 60.424 50.000 1.90 0.00 0.00 1.40
2355 4805 2.802719 ACACACTGACCCAAGTTTTGT 58.197 42.857 0.00 0.00 0.00 2.83
2394 4844 9.529325 AAATCAACTTAAACAGGCTAAGAAAAC 57.471 29.630 1.89 0.00 31.91 2.43
2395 4845 9.528018 CAAATCAACTTAAACAGGCTAAGAAAA 57.472 29.630 1.89 0.00 31.91 2.29
2476 4926 3.009723 CGAGCAGATAAACCCAATGTGT 58.990 45.455 0.00 0.00 0.00 3.72
2477 4927 2.223340 GCGAGCAGATAAACCCAATGTG 60.223 50.000 0.00 0.00 0.00 3.21
2478 4928 2.017049 GCGAGCAGATAAACCCAATGT 58.983 47.619 0.00 0.00 0.00 2.71
2523 4973 4.873827 ACATAACACGTGATGAACCATACC 59.126 41.667 25.01 0.00 0.00 2.73
2534 4984 6.480651 ACTGTGATTACAAACATAACACGTGA 59.519 34.615 25.01 0.00 36.14 4.35
2571 5021 8.848182 CGGGACAGATAGAGTAATAAAGTAACT 58.152 37.037 0.00 0.00 0.00 2.24
2604 5088 6.866770 TCCCTTCGTTTCATAATATAAGAGCG 59.133 38.462 0.00 0.00 0.00 5.03
2619 5103 6.423001 GCGATAATGTAATACTCCCTTCGTTT 59.577 38.462 0.00 0.00 0.00 3.60
2620 5104 5.924825 GCGATAATGTAATACTCCCTTCGTT 59.075 40.000 0.00 0.00 0.00 3.85
2623 5107 5.790593 TGGCGATAATGTAATACTCCCTTC 58.209 41.667 0.00 0.00 0.00 3.46
2637 5121 1.321474 CACTGGGCAATGGCGATAAT 58.679 50.000 0.00 0.00 42.47 1.28
2660 5144 2.804647 CGTCCACACGTATGCATAGAA 58.195 47.619 6.67 0.00 41.42 2.10
2675 5159 1.695242 TCTTTAACCTTCCAGCGTCCA 59.305 47.619 0.00 0.00 0.00 4.02
2699 5184 4.295051 CAACCCGTACACATTTGAAAAGG 58.705 43.478 0.00 0.00 0.00 3.11
2854 5353 7.041098 GCATTATTAGCTAATATTCCCCCATCG 60.041 40.741 23.50 9.31 0.00 3.84
3057 5560 5.596361 TGCCACAATTCTTCCTTAGAAAACA 59.404 36.000 0.00 0.00 45.62 2.83
3122 5631 9.593134 TTCTATGTAAGTTGTGTGCAAATTTTT 57.407 25.926 0.00 0.00 39.49 1.94
3164 5673 3.509575 TGTTCGGCTTATTCCTGCATTTT 59.490 39.130 0.00 0.00 0.00 1.82
3167 5676 2.418368 TGTTCGGCTTATTCCTGCAT 57.582 45.000 0.00 0.00 0.00 3.96
3168 5677 2.418368 ATGTTCGGCTTATTCCTGCA 57.582 45.000 0.00 0.00 0.00 4.41
3172 5682 4.067972 TCCACTATGTTCGGCTTATTCC 57.932 45.455 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.