Multiple sequence alignment - TraesCS2B01G284700

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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 TraesCS2B01G284700 chr2B 100.000 2690 0 0 1 2690 391950266 391947577 0.000000e+00 4968.0
1 TraesCS2B01G284700 chr2B 86.709 158 13 8 103 258 95798031 95798182 4.610000e-38 169.0
2 TraesCS2B01G284700 chr2B 95.745 47 2 0 2586 2632 549552597 549552643 2.870000e-10 76.8
3 TraesCS2B01G284700 chr2A 92.567 2489 117 29 228 2690 406662011 406664457 0.000000e+00 3509.0
4 TraesCS2B01G284700 chr2A 91.892 111 7 1 1 111 406661901 406662009 1.290000e-33 154.0
5 TraesCS2B01G284700 chr2D 92.851 2280 114 15 430 2690 323747996 323745747 0.000000e+00 3262.0
6 TraesCS2B01G284700 chr2D 91.429 70 4 1 368 437 323748725 323748658 7.930000e-16 95.3
7 TraesCS2B01G284700 chr6A 98.291 117 2 0 112 228 564730177 564730061 3.510000e-49 206.0
8 TraesCS2B01G284700 chr5B 93.130 131 7 2 111 241 38365241 38365113 9.830000e-45 191.0
9 TraesCS2B01G284700 chr5B 80.682 88 15 2 2586 2673 541127592 541127507 1.730000e-07 67.6
10 TraesCS2B01G284700 chr6B 92.481 133 8 1 101 231 638921021 638920889 3.540000e-44 189.0
11 TraesCS2B01G284700 chr6B 92.913 127 8 1 104 230 35636850 35636975 1.640000e-42 183.0
12 TraesCS2B01G284700 chr5D 94.309 123 7 0 108 230 473359887 473359765 3.540000e-44 189.0
13 TraesCS2B01G284700 chr5D 80.899 89 15 2 2585 2673 452213060 452212974 4.810000e-08 69.4
14 TraesCS2B01G284700 chr5D 88.889 45 5 0 2586 2630 17504154 17504110 3.740000e-04 56.5
15 TraesCS2B01G284700 chr3B 93.496 123 8 0 109 231 513904076 513904198 1.640000e-42 183.0
16 TraesCS2B01G284700 chr3B 92.913 127 7 2 112 237 725714429 725714304 1.640000e-42 183.0
17 TraesCS2B01G284700 chr3B 82.143 112 15 4 2393 2500 280028892 280029002 1.030000e-14 91.6
18 TraesCS2B01G284700 chr4B 90.071 141 12 2 90 228 243726780 243726640 5.920000e-42 182.0
19 TraesCS2B01G284700 chr7D 87.302 126 13 3 2375 2500 412742798 412742920 1.000000e-29 141.0
20 TraesCS2B01G284700 chrUn 76.014 296 50 13 2214 2500 10391110 10390827 1.680000e-27 134.0
21 TraesCS2B01G284700 chr1B 82.143 112 15 5 2393 2500 431150547 431150657 1.030000e-14 91.6
22 TraesCS2B01G284700 chr1B 82.143 112 15 5 2393 2500 612579417 612579307 1.030000e-14 91.6
23 TraesCS2B01G284700 chr1B 84.043 94 12 3 2586 2678 329491872 329491781 1.330000e-13 87.9
24 TraesCS2B01G284700 chr1B 80.851 94 15 3 2585 2676 474111981 474111889 1.340000e-08 71.3
25 TraesCS2B01G284700 chr7B 81.081 111 17 4 2393 2500 34791866 34791975 4.770000e-13 86.1
26 TraesCS2B01G284700 chr1D 81.250 112 16 4 2393 2500 32852785 32852675 4.770000e-13 86.1


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 TraesCS2B01G284700 chr2B 391947577 391950266 2689 True 4968.00 4968 100.0000 1 2690 1 chr2B.!!$R1 2689
1 TraesCS2B01G284700 chr2A 406661901 406664457 2556 False 1831.50 3509 92.2295 1 2690 2 chr2A.!!$F1 2689
2 TraesCS2B01G284700 chr2D 323745747 323748725 2978 True 1678.65 3262 92.1400 368 2690 2 chr2D.!!$R1 2322

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
130 131 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.0 5.23 0.0 44.66 2.17 F
133 134 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.0 5.23 0.0 44.66 2.24 F
226 227 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.0 13.64 0.0 46.06 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1676 2357 1.133181 TCCCTCTCACATGCCCAACA 61.133 55.000 0.0 0.0 0.0 3.33 R
1682 2363 1.202627 GGTCAGATCCCTCTCACATGC 60.203 57.143 0.0 0.0 0.0 4.06 R
2045 2755 4.275689 TGCTCTGGTTTCTGTTGTTGTATG 59.724 41.667 0.0 0.0 0.0 2.39 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
60 61 7.869016 TGTACTATATATTGCTCGCTTGTTC 57.131 36.000 0.00 0.00 0.00 3.18
66 67 2.099633 TTGCTCGCTTGTTCGTTTTC 57.900 45.000 0.00 0.00 0.00 2.29
80 81 6.773080 TGTTCGTTTTCGTCATAAACTTCAA 58.227 32.000 0.00 0.00 44.46 2.69
82 83 5.425398 TCGTTTTCGTCATAAACTTCAACG 58.575 37.500 0.00 0.00 44.46 4.10
117 118 8.697507 ATCATTTGGAGATAAAACATACTCCC 57.302 34.615 0.00 0.00 45.61 4.30
118 119 7.872138 TCATTTGGAGATAAAACATACTCCCT 58.128 34.615 0.00 0.00 45.61 4.20
119 120 7.993183 TCATTTGGAGATAAAACATACTCCCTC 59.007 37.037 0.00 0.00 45.61 4.30
120 121 5.888982 TGGAGATAAAACATACTCCCTCC 57.111 43.478 0.00 0.00 45.61 4.30
121 122 4.344102 TGGAGATAAAACATACTCCCTCCG 59.656 45.833 0.00 0.00 45.61 4.63
122 123 4.344390 GGAGATAAAACATACTCCCTCCGT 59.656 45.833 0.00 0.00 41.89 4.69
123 124 5.509332 GGAGATAAAACATACTCCCTCCGTC 60.509 48.000 0.00 0.00 41.89 4.79
124 125 4.344390 AGATAAAACATACTCCCTCCGTCC 59.656 45.833 0.00 0.00 0.00 4.79
125 126 0.822164 AAACATACTCCCTCCGTCCG 59.178 55.000 0.00 0.00 0.00 4.79
126 127 1.041447 AACATACTCCCTCCGTCCGG 61.041 60.000 0.00 0.00 0.00 5.14
127 128 1.152819 CATACTCCCTCCGTCCGGA 60.153 63.158 0.00 0.00 42.90 5.14
128 129 0.754217 CATACTCCCTCCGTCCGGAA 60.754 60.000 5.23 0.00 44.66 4.30
129 130 0.187851 ATACTCCCTCCGTCCGGAAT 59.812 55.000 5.23 0.00 44.66 3.01
130 131 0.032813 TACTCCCTCCGTCCGGAATT 60.033 55.000 5.23 0.00 44.66 2.17
131 132 0.032813 ACTCCCTCCGTCCGGAATTA 60.033 55.000 5.23 0.00 44.66 1.40
132 133 0.388294 CTCCCTCCGTCCGGAATTAC 59.612 60.000 5.23 0.00 44.66 1.89
133 134 0.032813 TCCCTCCGTCCGGAATTACT 60.033 55.000 5.23 0.00 44.66 2.24
134 135 0.828677 CCCTCCGTCCGGAATTACTT 59.171 55.000 5.23 0.00 44.66 2.24
135 136 1.472728 CCCTCCGTCCGGAATTACTTG 60.473 57.143 5.23 0.00 44.66 3.16
136 137 1.206371 CCTCCGTCCGGAATTACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
137 138 2.537401 CTCCGTCCGGAATTACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
138 139 1.894466 TCCGTCCGGAATTACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
139 140 2.498481 TCCGTCCGGAATTACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
140 141 3.700539 TCCGTCCGGAATTACTTGTCATA 59.299 43.478 5.23 0.00 42.05 2.15
141 142 4.049186 CCGTCCGGAATTACTTGTCATAG 58.951 47.826 5.23 0.00 37.50 2.23
142 143 4.202080 CCGTCCGGAATTACTTGTCATAGA 60.202 45.833 5.23 0.00 37.50 1.98
143 144 5.345702 CGTCCGGAATTACTTGTCATAGAA 58.654 41.667 5.23 0.00 0.00 2.10
144 145 5.808540 CGTCCGGAATTACTTGTCATAGAAA 59.191 40.000 5.23 0.00 0.00 2.52
145 146 6.479001 CGTCCGGAATTACTTGTCATAGAAAT 59.521 38.462 5.23 0.00 0.00 2.17
146 147 7.516785 CGTCCGGAATTACTTGTCATAGAAATG 60.517 40.741 5.23 0.00 0.00 2.32
147 148 6.765989 TCCGGAATTACTTGTCATAGAAATGG 59.234 38.462 0.00 0.00 33.61 3.16
148 149 6.765989 CCGGAATTACTTGTCATAGAAATGGA 59.234 38.462 0.00 0.00 33.61 3.41
149 150 7.445402 CCGGAATTACTTGTCATAGAAATGGAT 59.555 37.037 0.00 0.00 33.61 3.41
150 151 9.489084 CGGAATTACTTGTCATAGAAATGGATA 57.511 33.333 0.00 0.00 33.61 2.59
201 202 6.332735 TGTCTAGATACATCAATTCCTCCG 57.667 41.667 0.00 0.00 0.00 4.63
202 203 6.068670 TGTCTAGATACATCAATTCCTCCGA 58.931 40.000 0.00 0.00 0.00 4.55
203 204 6.016192 TGTCTAGATACATCAATTCCTCCGAC 60.016 42.308 0.00 0.00 0.00 4.79
204 205 6.016192 GTCTAGATACATCAATTCCTCCGACA 60.016 42.308 0.00 0.00 0.00 4.35
205 206 5.614324 AGATACATCAATTCCTCCGACAA 57.386 39.130 0.00 0.00 0.00 3.18
206 207 5.605534 AGATACATCAATTCCTCCGACAAG 58.394 41.667 0.00 0.00 0.00 3.16
207 208 3.703001 ACATCAATTCCTCCGACAAGT 57.297 42.857 0.00 0.00 0.00 3.16
208 209 4.819105 ACATCAATTCCTCCGACAAGTA 57.181 40.909 0.00 0.00 0.00 2.24
209 210 5.359194 ACATCAATTCCTCCGACAAGTAT 57.641 39.130 0.00 0.00 0.00 2.12
210 211 5.745227 ACATCAATTCCTCCGACAAGTATT 58.255 37.500 0.00 0.00 0.00 1.89
211 212 6.180472 ACATCAATTCCTCCGACAAGTATTT 58.820 36.000 0.00 0.00 0.00 1.40
212 213 6.316390 ACATCAATTCCTCCGACAAGTATTTC 59.684 38.462 0.00 0.00 0.00 2.17
213 214 5.183228 TCAATTCCTCCGACAAGTATTTCC 58.817 41.667 0.00 0.00 0.00 3.13
214 215 2.953466 TCCTCCGACAAGTATTTCCG 57.047 50.000 0.00 0.00 0.00 4.30
215 216 1.479323 TCCTCCGACAAGTATTTCCGG 59.521 52.381 0.00 0.00 41.36 5.14
216 217 1.479323 CCTCCGACAAGTATTTCCGGA 59.521 52.381 0.00 0.00 45.74 5.14
217 218 2.537401 CTCCGACAAGTATTTCCGGAC 58.463 52.381 1.83 0.00 43.47 4.79
218 219 1.135315 TCCGACAAGTATTTCCGGACG 60.135 52.381 1.83 0.00 43.47 4.79
219 220 1.274596 CGACAAGTATTTCCGGACGG 58.725 55.000 1.83 3.96 0.00 4.79
220 221 1.135315 CGACAAGTATTTCCGGACGGA 60.135 52.381 1.83 9.76 43.52 4.69
221 222 2.537401 GACAAGTATTTCCGGACGGAG 58.463 52.381 13.64 3.15 46.06 4.63
222 223 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
223 224 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
224 225 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
225 226 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
226 227 0.032813 TATTTCCGGACGGAGGGAGT 60.033 55.000 13.64 0.00 46.06 3.85
246 247 9.927081 AGGGAGTATTTATGTTTGAATCAATCT 57.073 29.630 0.00 0.00 0.00 2.40
307 308 9.422196 GACTATAAAATGCAGTAAAGTTAAGCG 57.578 33.333 0.00 0.00 0.00 4.68
372 373 9.431887 GTATTGTGTAAATTCAGGTGACTAAGA 57.568 33.333 0.00 0.00 40.21 2.10
499 1169 0.165944 GGAAGCCATGAAACACGTCG 59.834 55.000 0.00 0.00 0.00 5.12
579 1249 2.178912 TCCCCAACTAACAAAGAGCG 57.821 50.000 0.00 0.00 0.00 5.03
769 1441 0.895559 CAAGCTGGGGGTCAAAGGAC 60.896 60.000 0.00 0.00 43.55 3.85
931 1603 3.448301 CCAGATCTCAAGCTCTCAACTCT 59.552 47.826 0.00 0.00 0.00 3.24
999 1671 1.967066 GCTAGAAGCAGGGCTCTATCA 59.033 52.381 0.00 0.00 41.89 2.15
1193 1874 2.445682 AAGCTCACTCCCTACTCGAT 57.554 50.000 0.00 0.00 0.00 3.59
1194 1875 1.975660 AGCTCACTCCCTACTCGATC 58.024 55.000 0.00 0.00 0.00 3.69
1195 1876 1.493022 AGCTCACTCCCTACTCGATCT 59.507 52.381 0.00 0.00 0.00 2.75
1196 1877 2.706723 AGCTCACTCCCTACTCGATCTA 59.293 50.000 0.00 0.00 0.00 1.98
1207 1888 4.693566 CCTACTCGATCTACTAGCTCTTGG 59.306 50.000 0.00 0.00 0.00 3.61
1209 1890 2.881513 CTCGATCTACTAGCTCTTGGCA 59.118 50.000 0.00 0.00 44.79 4.92
1392 2073 4.335647 AAGCTCACCACTGCCGGG 62.336 66.667 2.18 0.00 0.00 5.73
1458 2139 0.468226 TGAAGCTCCAGGTGAACGTT 59.532 50.000 0.00 0.00 0.00 3.99
1676 2357 2.363276 CATGGGCATGGCTGTGGT 60.363 61.111 19.78 0.00 35.24 4.16
1682 2363 2.934570 GCATGGCTGTGGTGTTGGG 61.935 63.158 0.00 0.00 0.00 4.12
1732 2413 3.758425 GGTACCAAGGCTTAGTTTTGGA 58.242 45.455 18.65 5.11 43.15 3.53
1733 2414 3.756963 GGTACCAAGGCTTAGTTTTGGAG 59.243 47.826 18.65 0.00 43.15 3.86
1734 2415 3.595190 ACCAAGGCTTAGTTTTGGAGT 57.405 42.857 18.65 0.91 43.15 3.85
1735 2416 3.222603 ACCAAGGCTTAGTTTTGGAGTG 58.777 45.455 18.65 0.00 43.15 3.51
1736 2417 3.222603 CCAAGGCTTAGTTTTGGAGTGT 58.777 45.455 0.00 0.00 43.15 3.55
1737 2418 3.636764 CCAAGGCTTAGTTTTGGAGTGTT 59.363 43.478 0.00 0.00 43.15 3.32
1738 2419 4.099419 CCAAGGCTTAGTTTTGGAGTGTTT 59.901 41.667 0.00 0.00 43.15 2.83
1739 2420 5.300792 CCAAGGCTTAGTTTTGGAGTGTTTA 59.699 40.000 0.00 0.00 43.15 2.01
1740 2421 6.183360 CCAAGGCTTAGTTTTGGAGTGTTTAA 60.183 38.462 0.00 0.00 43.15 1.52
1741 2422 6.635030 AGGCTTAGTTTTGGAGTGTTTAAG 57.365 37.500 0.00 0.00 0.00 1.85
1742 2423 6.127101 AGGCTTAGTTTTGGAGTGTTTAAGT 58.873 36.000 0.00 0.00 0.00 2.24
1743 2424 6.262496 AGGCTTAGTTTTGGAGTGTTTAAGTC 59.738 38.462 0.00 0.00 0.00 3.01
1744 2425 6.262496 GGCTTAGTTTTGGAGTGTTTAAGTCT 59.738 38.462 0.00 0.00 0.00 3.24
2014 2724 1.407618 GTCCTGTTGGTTGGTTGGTTC 59.592 52.381 0.00 0.00 34.23 3.62
2029 2739 4.370917 GTTGGTTCGTTGGACTAGTAACA 58.629 43.478 8.79 2.99 0.00 2.41
2045 2755 4.310769 AGTAACATGTCTCTGTTCAGCAC 58.689 43.478 0.00 0.00 39.88 4.40
2141 2851 6.653320 ACATTGCCTATTCGTTAAGTGAGAAA 59.347 34.615 0.00 0.00 0.00 2.52
2176 2889 7.568199 AATATATGTACAAAGAGTTGGTGCC 57.432 36.000 0.00 0.00 39.22 5.01
2203 2916 0.775542 GGGGAACACACCTAAACCCT 59.224 55.000 0.00 0.00 37.66 4.34
2204 2917 1.271762 GGGGAACACACCTAAACCCTC 60.272 57.143 0.00 0.00 37.66 4.30
2205 2918 1.422402 GGGAACACACCTAAACCCTCA 59.578 52.381 0.00 0.00 35.03 3.86
2209 2922 4.941873 GGAACACACCTAAACCCTCATAAG 59.058 45.833 0.00 0.00 0.00 1.73
2224 2937 6.611642 ACCCTCATAAGAGCAAGTACAATAGA 59.388 38.462 0.00 0.00 40.68 1.98
2229 2942 5.428184 AAGAGCAAGTACAATAGAAGGCT 57.572 39.130 0.00 0.00 0.00 4.58
2230 2943 6.546428 AAGAGCAAGTACAATAGAAGGCTA 57.454 37.500 0.00 0.00 0.00 3.93
2231 2944 6.739331 AGAGCAAGTACAATAGAAGGCTAT 57.261 37.500 0.00 0.00 38.98 2.97
2232 2945 7.841282 AGAGCAAGTACAATAGAAGGCTATA 57.159 36.000 0.00 0.00 36.31 1.31
2233 2946 8.251383 AGAGCAAGTACAATAGAAGGCTATAA 57.749 34.615 0.00 0.00 36.31 0.98
2234 2947 8.364142 AGAGCAAGTACAATAGAAGGCTATAAG 58.636 37.037 0.00 0.00 36.31 1.73
2235 2948 6.931840 AGCAAGTACAATAGAAGGCTATAAGC 59.068 38.462 0.00 0.00 41.46 3.09
2257 2984 7.592885 AGCCTGCTTATATGACATTTTTGAT 57.407 32.000 0.00 0.00 0.00 2.57
2365 3097 7.996098 TTAATACCAAGAAAAAGTGGAGAGG 57.004 36.000 0.00 0.00 38.36 3.69
2415 3147 6.618196 ACCCAACCTTATAGCCAACTCTATTA 59.382 38.462 0.00 0.00 32.07 0.98
2457 3189 5.232838 GCTAACTTTTGATAACATGCCATGC 59.767 40.000 4.17 0.00 0.00 4.06
2467 3199 1.422781 ACATGCCATGCCTACATAGCT 59.577 47.619 4.17 0.00 41.00 3.32
2506 3238 7.875327 TTATTAACCATGCTCTAAAGAACCC 57.125 36.000 0.00 0.00 0.00 4.11
2563 3295 0.040067 GGGCACTTTGAAAGTCTGCG 60.040 55.000 7.75 0.00 40.46 5.18
2570 3302 0.394938 TTGAAAGTCTGCGCCCACTA 59.605 50.000 4.18 0.00 0.00 2.74
2606 3338 8.914328 TCAATGTTGTGATTAATTAGCACATG 57.086 30.769 18.22 14.66 41.60 3.21
2650 3382 3.826524 TGCTGAAACCTTCATGTGGTTA 58.173 40.909 20.23 9.62 45.99 2.85
2666 3398 0.600782 GTTACCTTCCGCAACCGACA 60.601 55.000 0.00 0.00 36.29 4.35
2668 3400 2.438951 TACCTTCCGCAACCGACACC 62.439 60.000 0.00 0.00 36.29 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 6.453643 AACGAACAAGCGAGCAATATATAG 57.546 37.500 0.00 0.00 34.83 1.31
60 61 5.332594 GTCGTTGAAGTTTATGACGAAAACG 59.667 40.000 0.00 0.00 43.28 3.60
66 67 5.176958 AGGAAAGTCGTTGAAGTTTATGACG 59.823 40.000 5.94 0.00 35.84 4.35
80 81 6.049955 TCTCCAAATGATTAGGAAAGTCGT 57.950 37.500 0.00 0.00 0.00 4.34
111 112 0.032813 AATTCCGGACGGAGGGAGTA 60.033 55.000 13.64 0.00 46.06 2.59
112 113 0.032813 TAATTCCGGACGGAGGGAGT 60.033 55.000 13.64 1.45 46.06 3.85
113 114 0.388294 GTAATTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
114 115 0.032813 AGTAATTCCGGACGGAGGGA 60.033 55.000 13.64 0.00 46.06 4.20
115 116 0.828677 AAGTAATTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
116 117 1.206371 ACAAGTAATTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
117 118 2.094390 TGACAAGTAATTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
118 119 1.894466 TGACAAGTAATTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
119 120 2.373540 TGACAAGTAATTCCGGACGG 57.626 50.000 1.83 3.96 0.00 4.79
120 121 4.928601 TCTATGACAAGTAATTCCGGACG 58.071 43.478 1.83 0.00 0.00 4.79
121 122 7.254795 CCATTTCTATGACAAGTAATTCCGGAC 60.255 40.741 1.83 0.00 33.37 4.79
122 123 6.765989 CCATTTCTATGACAAGTAATTCCGGA 59.234 38.462 0.00 0.00 33.37 5.14
123 124 6.765989 TCCATTTCTATGACAAGTAATTCCGG 59.234 38.462 0.00 0.00 33.37 5.14
124 125 7.786178 TCCATTTCTATGACAAGTAATTCCG 57.214 36.000 0.00 0.00 33.37 4.30
175 176 8.690884 CGGAGGAATTGATGTATCTAGACATAT 58.309 37.037 0.00 0.00 40.18 1.78
176 177 7.888546 TCGGAGGAATTGATGTATCTAGACATA 59.111 37.037 0.00 0.00 40.18 2.29
177 178 6.721668 TCGGAGGAATTGATGTATCTAGACAT 59.278 38.462 0.00 0.00 42.82 3.06
178 179 6.016192 GTCGGAGGAATTGATGTATCTAGACA 60.016 42.308 0.00 0.00 0.00 3.41
179 180 6.016192 TGTCGGAGGAATTGATGTATCTAGAC 60.016 42.308 0.00 0.00 0.00 2.59
180 181 6.068670 TGTCGGAGGAATTGATGTATCTAGA 58.931 40.000 0.00 0.00 0.00 2.43
181 182 6.332735 TGTCGGAGGAATTGATGTATCTAG 57.667 41.667 0.00 0.00 0.00 2.43
182 183 6.323996 ACTTGTCGGAGGAATTGATGTATCTA 59.676 38.462 0.00 0.00 0.00 1.98
183 184 5.129485 ACTTGTCGGAGGAATTGATGTATCT 59.871 40.000 0.00 0.00 0.00 1.98
184 185 5.360591 ACTTGTCGGAGGAATTGATGTATC 58.639 41.667 0.00 0.00 0.00 2.24
185 186 5.359194 ACTTGTCGGAGGAATTGATGTAT 57.641 39.130 0.00 0.00 0.00 2.29
186 187 4.819105 ACTTGTCGGAGGAATTGATGTA 57.181 40.909 0.00 0.00 0.00 2.29
187 188 3.703001 ACTTGTCGGAGGAATTGATGT 57.297 42.857 0.00 0.00 0.00 3.06
188 189 6.238484 GGAAATACTTGTCGGAGGAATTGATG 60.238 42.308 0.00 0.00 0.00 3.07
189 190 5.823045 GGAAATACTTGTCGGAGGAATTGAT 59.177 40.000 0.00 0.00 0.00 2.57
190 191 5.183228 GGAAATACTTGTCGGAGGAATTGA 58.817 41.667 0.00 0.00 0.00 2.57
191 192 4.034048 CGGAAATACTTGTCGGAGGAATTG 59.966 45.833 0.00 0.00 0.00 2.32
192 193 4.189231 CGGAAATACTTGTCGGAGGAATT 58.811 43.478 0.00 0.00 0.00 2.17
193 194 3.431766 CCGGAAATACTTGTCGGAGGAAT 60.432 47.826 0.00 0.00 42.94 3.01
194 195 2.093869 CCGGAAATACTTGTCGGAGGAA 60.094 50.000 0.00 0.00 42.94 3.36
195 196 1.479323 CCGGAAATACTTGTCGGAGGA 59.521 52.381 0.00 0.00 42.94 3.71
196 197 1.479323 TCCGGAAATACTTGTCGGAGG 59.521 52.381 0.00 0.00 43.84 4.30
197 198 2.953466 TCCGGAAATACTTGTCGGAG 57.047 50.000 0.00 0.00 43.84 4.63
198 199 1.135315 CGTCCGGAAATACTTGTCGGA 60.135 52.381 5.23 0.00 46.06 4.55
199 200 1.274596 CGTCCGGAAATACTTGTCGG 58.725 55.000 5.23 0.00 41.80 4.79
200 201 1.135315 TCCGTCCGGAAATACTTGTCG 60.135 52.381 5.23 1.25 42.05 4.35
201 202 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
202 203 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
203 204 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
204 205 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
205 206 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
206 207 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
207 208 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
208 209 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
209 210 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
210 211 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
211 212 0.032813 AAATACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
212 213 1.696063 TAAATACTCCCTCCGTCCGG 58.304 55.000 0.00 0.00 0.00 5.14
213 214 2.626743 ACATAAATACTCCCTCCGTCCG 59.373 50.000 0.00 0.00 0.00 4.79
214 215 4.684484 AACATAAATACTCCCTCCGTCC 57.316 45.455 0.00 0.00 0.00 4.79
215 216 5.667466 TCAAACATAAATACTCCCTCCGTC 58.333 41.667 0.00 0.00 0.00 4.79
216 217 5.687166 TCAAACATAAATACTCCCTCCGT 57.313 39.130 0.00 0.00 0.00 4.69
217 218 6.765989 TGATTCAAACATAAATACTCCCTCCG 59.234 38.462 0.00 0.00 0.00 4.63
218 219 8.519799 TTGATTCAAACATAAATACTCCCTCC 57.480 34.615 0.00 0.00 0.00 4.30
220 221 9.927081 AGATTGATTCAAACATAAATACTCCCT 57.073 29.630 2.68 0.00 0.00 4.20
286 287 6.804770 TCCGCTTAACTTTACTGCATTTTA 57.195 33.333 0.00 0.00 0.00 1.52
394 395 8.989653 TTACTTTTGTTCTTCATTTTCGGTTT 57.010 26.923 0.00 0.00 0.00 3.27
550 1220 5.269505 TGTTAGTTGGGGATGTTTGTTTG 57.730 39.130 0.00 0.00 0.00 2.93
591 1261 6.260936 GCTACTCATTGGTAGTACATTGCATT 59.739 38.462 2.06 0.00 40.70 3.56
601 1271 4.891992 ACAACTGCTACTCATTGGTAGT 57.108 40.909 11.50 0.37 40.70 2.73
602 1272 5.237815 TCAACAACTGCTACTCATTGGTAG 58.762 41.667 7.54 7.54 41.31 3.18
603 1273 5.222079 TCAACAACTGCTACTCATTGGTA 57.778 39.130 0.00 0.00 0.00 3.25
604 1274 4.067896 CTCAACAACTGCTACTCATTGGT 58.932 43.478 0.00 0.00 0.00 3.67
651 1321 5.118203 CAGAAAAGAAAATGCTTAGCACTGC 59.882 40.000 9.82 0.00 43.04 4.40
783 1455 0.996762 AACTGGGAAGGGGTTGGTGA 60.997 55.000 0.00 0.00 0.00 4.02
892 1564 1.414181 CTGGGACGATTGTGGAGCTAT 59.586 52.381 0.00 0.00 0.00 2.97
931 1603 1.066858 GTTTGAGATGCGAGGTGAGGA 60.067 52.381 0.00 0.00 0.00 3.71
992 1664 3.317149 CACCACCATTGCCATTGATAGAG 59.683 47.826 0.00 0.00 0.00 2.43
999 1671 1.269012 CCTTCACCACCATTGCCATT 58.731 50.000 0.00 0.00 0.00 3.16
1207 1888 5.578727 CGGTTCTTGATATAATCCTAGCTGC 59.421 44.000 0.00 0.00 0.00 5.25
1209 1890 6.071278 GGTCGGTTCTTGATATAATCCTAGCT 60.071 42.308 0.00 0.00 0.00 3.32
1334 2015 1.278238 GTATCTGGCGACGACTTTGG 58.722 55.000 0.65 0.00 0.00 3.28
1546 2227 4.056125 CAGCTGCTCGTCGGTGGA 62.056 66.667 0.00 0.00 0.00 4.02
1587 2268 2.737376 GAACTGGGCGTCGGTGTC 60.737 66.667 0.00 0.00 34.67 3.67
1632 2313 4.812476 ACCGCAGCGCTCGCATTA 62.812 61.111 24.54 0.00 44.88 1.90
1676 2357 1.133181 TCCCTCTCACATGCCCAACA 61.133 55.000 0.00 0.00 0.00 3.33
1682 2363 1.202627 GGTCAGATCCCTCTCACATGC 60.203 57.143 0.00 0.00 0.00 4.06
1724 2405 9.403583 TGATTAAGACTTAAACACTCCAAAACT 57.596 29.630 11.57 0.00 0.00 2.66
1727 2408 9.349713 ACATGATTAAGACTTAAACACTCCAAA 57.650 29.630 17.23 0.00 31.94 3.28
1728 2409 8.918202 ACATGATTAAGACTTAAACACTCCAA 57.082 30.769 17.23 0.00 31.94 3.53
1729 2410 7.330946 CGACATGATTAAGACTTAAACACTCCA 59.669 37.037 17.23 7.60 31.94 3.86
1730 2411 7.544566 TCGACATGATTAAGACTTAAACACTCC 59.455 37.037 17.23 9.79 31.94 3.85
1731 2412 8.462143 TCGACATGATTAAGACTTAAACACTC 57.538 34.615 17.23 13.80 31.94 3.51
1734 2415 9.863845 TGTATCGACATGATTAAGACTTAAACA 57.136 29.630 17.21 17.21 38.57 2.83
1739 2420 8.338259 GCAAATGTATCGACATGATTAAGACTT 58.662 33.333 0.00 0.00 45.93 3.01
1740 2421 7.306807 CGCAAATGTATCGACATGATTAAGACT 60.307 37.037 0.00 0.00 45.93 3.24
1741 2422 6.787515 CGCAAATGTATCGACATGATTAAGAC 59.212 38.462 0.00 0.00 45.93 3.01
1742 2423 6.073819 CCGCAAATGTATCGACATGATTAAGA 60.074 38.462 0.00 0.00 45.93 2.10
1743 2424 6.073369 CCGCAAATGTATCGACATGATTAAG 58.927 40.000 0.00 0.00 45.93 1.85
1744 2425 5.755861 TCCGCAAATGTATCGACATGATTAA 59.244 36.000 0.00 0.00 45.93 1.40
2014 2724 5.096169 CAGAGACATGTTACTAGTCCAACG 58.904 45.833 0.00 0.00 32.82 4.10
2029 2739 4.541973 TGTATGTGCTGAACAGAGACAT 57.458 40.909 17.49 17.49 43.64 3.06
2045 2755 4.275689 TGCTCTGGTTTCTGTTGTTGTATG 59.724 41.667 0.00 0.00 0.00 2.39
2203 2916 6.986817 GCCTTCTATTGTACTTGCTCTTATGA 59.013 38.462 0.00 0.00 0.00 2.15
2204 2917 6.989169 AGCCTTCTATTGTACTTGCTCTTATG 59.011 38.462 0.00 0.00 0.00 1.90
2205 2918 7.130681 AGCCTTCTATTGTACTTGCTCTTAT 57.869 36.000 0.00 0.00 0.00 1.73
2209 2922 7.117092 GCTTATAGCCTTCTATTGTACTTGCTC 59.883 40.741 0.00 0.00 36.86 4.26
2230 2943 9.135189 TCAAAAATGTCATATAAGCAGGCTTAT 57.865 29.630 24.89 24.89 46.97 1.73
2231 2944 8.518430 TCAAAAATGTCATATAAGCAGGCTTA 57.482 30.769 15.39 15.39 41.95 3.09
2232 2945 7.408756 TCAAAAATGTCATATAAGCAGGCTT 57.591 32.000 11.70 11.70 39.83 4.35
2233 2946 7.592885 ATCAAAAATGTCATATAAGCAGGCT 57.407 32.000 0.00 0.00 0.00 4.58
2234 2947 9.918630 ATAATCAAAAATGTCATATAAGCAGGC 57.081 29.630 0.00 0.00 0.00 4.85
2283 3010 7.171447 CTCTTGCATTAGAGCACTTATGTAC 57.829 40.000 11.00 0.00 45.61 2.90
2309 3040 3.440872 CCTAGAAGCACGTGTAGAGACTT 59.559 47.826 18.38 10.41 0.00 3.01
2338 3069 8.990163 TCTCCACTTTTTCTTGGTATTAAACT 57.010 30.769 0.00 0.00 34.19 2.66
2347 3078 4.276926 CACTTCCTCTCCACTTTTTCTTGG 59.723 45.833 0.00 0.00 0.00 3.61
2348 3079 4.276926 CCACTTCCTCTCCACTTTTTCTTG 59.723 45.833 0.00 0.00 0.00 3.02
2440 3172 4.276642 TGTAGGCATGGCATGTTATCAAA 58.723 39.130 26.94 6.37 0.00 2.69
2452 3184 3.070018 GTTGCTAGCTATGTAGGCATGG 58.930 50.000 17.23 0.00 36.58 3.66
2457 3189 2.760374 GCCAGTTGCTAGCTATGTAGG 58.240 52.381 17.23 11.12 36.87 3.18
2505 3237 3.689649 GGCAACACCTCAGTAATACTTGG 59.310 47.826 7.43 7.43 34.51 3.61
2506 3238 3.370978 CGGCAACACCTCAGTAATACTTG 59.629 47.826 0.00 0.00 35.61 3.16
2538 3270 1.215423 ACTTTCAAAGTGCCCTGGACT 59.785 47.619 0.68 0.00 41.01 3.85
2542 3274 1.000938 GCAGACTTTCAAAGTGCCCTG 60.001 52.381 7.75 10.08 43.03 4.45
2543 3275 1.322442 GCAGACTTTCAAAGTGCCCT 58.678 50.000 7.75 0.00 43.03 5.19
2563 3295 3.281727 TGAGGACATCAAATAGTGGGC 57.718 47.619 0.00 0.00 34.02 5.36
2632 3364 4.447138 AGGTAACCACATGAAGGTTTCA 57.553 40.909 24.78 11.20 46.85 2.69
2633 3365 4.217767 GGAAGGTAACCACATGAAGGTTTC 59.782 45.833 24.78 20.60 46.85 2.78
2650 3382 2.280592 GTGTCGGTTGCGGAAGGT 60.281 61.111 0.00 0.00 0.00 3.50
2666 3398 0.812412 GCGACGCTAGAGAGAGAGGT 60.812 60.000 13.73 0.00 0.00 3.85
2668 3400 1.149361 ACGCGACGCTAGAGAGAGAG 61.149 60.000 15.93 0.12 0.00 3.20


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

AutoCloner maintained by Alex Coulton.