Multiple sequence alignment - TraesCS4A01G022200

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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 TraesCS4A01G022200 chr4A 100.000 3429 0 0 1 3429 15921378 15917950 0.000000e+00 6333
1 TraesCS4A01G022200 chr4A 95.722 2314 67 15 1130 3429 682751395 682753690 0.000000e+00 3696
2 TraesCS4A01G022200 chr4A 90.443 1852 163 13 26 1874 581496457 581494617 0.000000e+00 2427
3 TraesCS4A01G022200 chr4A 93.537 557 30 3 1875 2425 581494579 581494023 0.000000e+00 824
4 TraesCS4A01G022200 chr4A 77.901 181 31 6 2427 2599 671922774 671922595 1.680000e-18 104
5 TraesCS4A01G022200 chr3D 95.014 2447 92 10 995 3429 562559005 562561433 0.000000e+00 3816
6 TraesCS4A01G022200 chr3D 89.391 886 76 10 2421 3298 266652316 266653191 0.000000e+00 1099
7 TraesCS4A01G022200 chr4D 94.942 1997 69 21 994 2981 451038015 451039988 0.000000e+00 3099
8 TraesCS4A01G022200 chr4D 89.611 1877 155 18 9 1874 472683670 472681823 0.000000e+00 2350
9 TraesCS4A01G022200 chr4D 87.037 864 99 13 26 884 451033887 451034742 0.000000e+00 963
10 TraesCS4A01G022200 chr4D 97.327 449 9 3 2980 3428 451040092 451040537 0.000000e+00 760
11 TraesCS4A01G022200 chr4D 89.318 337 29 5 3095 3429 262390676 262390345 1.900000e-112 416
12 TraesCS4A01G022200 chr6D 90.507 1875 161 10 10 1874 420231888 420230021 0.000000e+00 2460
13 TraesCS4A01G022200 chr6D 94.245 556 27 3 1875 2425 420229983 420229428 0.000000e+00 845
14 TraesCS4A01G022200 chr1D 90.295 1762 144 23 124 1872 439791956 439790209 0.000000e+00 2281
15 TraesCS4A01G022200 chr1D 82.099 162 15 9 2669 2816 93831324 93831485 3.590000e-25 126
16 TraesCS4A01G022200 chr5A 87.594 1854 169 27 26 1874 611981731 611979934 0.000000e+00 2093
17 TraesCS4A01G022200 chr5A 94.231 884 47 4 992 1874 124618283 124619163 0.000000e+00 1347
18 TraesCS4A01G022200 chr5A 88.401 888 91 8 11 892 124617387 124618268 0.000000e+00 1059
19 TraesCS4A01G022200 chr5A 93.514 555 28 4 1876 2425 611979895 611979344 0.000000e+00 819
20 TraesCS4A01G022200 chr5B 88.682 1608 138 26 285 1874 604869385 604870966 0.000000e+00 1921
21 TraesCS4A01G022200 chr5D 88.541 1597 134 27 285 1874 441572642 441571088 0.000000e+00 1890
22 TraesCS4A01G022200 chr5D 87.433 939 99 16 285 1215 490440474 490439547 0.000000e+00 1062
23 TraesCS4A01G022200 chr5D 93.165 556 29 7 1875 2425 490438823 490438272 0.000000e+00 808
24 TraesCS4A01G022200 chr5D 92.857 560 30 4 1875 2425 441571050 441570492 0.000000e+00 804
25 TraesCS4A01G022200 chr2B 90.556 1186 78 20 694 1874 733161487 733162643 0.000000e+00 1539
26 TraesCS4A01G022200 chr2B 93.103 1015 50 12 2421 3429 733164559 733165559 0.000000e+00 1469
27 TraesCS4A01G022200 chr7D 92.593 945 65 3 931 1874 44719597 44718657 0.000000e+00 1352
28 TraesCS4A01G022200 chr7D 89.988 829 77 6 47 872 44720419 44719594 0.000000e+00 1066
29 TraesCS4A01G022200 chr7D 90.881 329 23 5 3102 3429 545213338 545213660 5.260000e-118 435
30 TraesCS4A01G022200 chr4B 96.135 828 27 5 2606 3429 564155407 564156233 0.000000e+00 1347
31 TraesCS4A01G022200 chr4B 95.652 621 16 7 1961 2577 564152535 564153148 0.000000e+00 987
32 TraesCS4A01G022200 chr4B 77.957 186 32 5 2422 2599 338507240 338507056 1.300000e-19 108
33 TraesCS4A01G022200 chr7A 89.378 932 87 7 10 934 47298450 47297524 0.000000e+00 1162
34 TraesCS4A01G022200 chr7A 83.333 288 30 13 2545 2816 354946883 354947168 2.040000e-62 250
35 TraesCS4A01G022200 chr7B 85.124 363 32 14 2472 2816 530665624 530665982 5.440000e-93 351
36 TraesCS4A01G022200 chrUn 87.925 265 29 2 3022 3284 87853778 87853515 3.320000e-80 309
37 TraesCS4A01G022200 chr2A 84.561 285 43 1 751 1035 743368648 743368931 7.250000e-72 281
38 TraesCS4A01G022200 chr1A 82.303 356 23 21 2477 2816 335873083 335873414 4.360000e-69 272
39 TraesCS4A01G022200 chr3B 78.453 181 30 5 2427 2599 279752788 279752967 3.620000e-20 110


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 TraesCS4A01G022200 chr4A 15917950 15921378 3428 True 6333.000000 6333 100.0000 1 3429 1 chr4A.!!$R1 3428
1 TraesCS4A01G022200 chr4A 682751395 682753690 2295 False 3696.000000 3696 95.7220 1130 3429 1 chr4A.!!$F1 2299
2 TraesCS4A01G022200 chr4A 581494023 581496457 2434 True 1625.500000 2427 91.9900 26 2425 2 chr4A.!!$R3 2399
3 TraesCS4A01G022200 chr3D 562559005 562561433 2428 False 3816.000000 3816 95.0140 995 3429 1 chr3D.!!$F2 2434
4 TraesCS4A01G022200 chr3D 266652316 266653191 875 False 1099.000000 1099 89.3910 2421 3298 1 chr3D.!!$F1 877
5 TraesCS4A01G022200 chr4D 472681823 472683670 1847 True 2350.000000 2350 89.6110 9 1874 1 chr4D.!!$R2 1865
6 TraesCS4A01G022200 chr4D 451033887 451040537 6650 False 1607.333333 3099 93.1020 26 3428 3 chr4D.!!$F1 3402
7 TraesCS4A01G022200 chr6D 420229428 420231888 2460 True 1652.500000 2460 92.3760 10 2425 2 chr6D.!!$R1 2415
8 TraesCS4A01G022200 chr1D 439790209 439791956 1747 True 2281.000000 2281 90.2950 124 1872 1 chr1D.!!$R1 1748
9 TraesCS4A01G022200 chr5A 611979344 611981731 2387 True 1456.000000 2093 90.5540 26 2425 2 chr5A.!!$R1 2399
10 TraesCS4A01G022200 chr5A 124617387 124619163 1776 False 1203.000000 1347 91.3160 11 1874 2 chr5A.!!$F1 1863
11 TraesCS4A01G022200 chr5B 604869385 604870966 1581 False 1921.000000 1921 88.6820 285 1874 1 chr5B.!!$F1 1589
12 TraesCS4A01G022200 chr5D 441570492 441572642 2150 True 1347.000000 1890 90.6990 285 2425 2 chr5D.!!$R1 2140
13 TraesCS4A01G022200 chr5D 490438272 490440474 2202 True 935.000000 1062 90.2990 285 2425 2 chr5D.!!$R2 2140
14 TraesCS4A01G022200 chr2B 733161487 733165559 4072 False 1504.000000 1539 91.8295 694 3429 2 chr2B.!!$F1 2735
15 TraesCS4A01G022200 chr7D 44718657 44720419 1762 True 1209.000000 1352 91.2905 47 1874 2 chr7D.!!$R1 1827
16 TraesCS4A01G022200 chr4B 564152535 564156233 3698 False 1167.000000 1347 95.8935 1961 3429 2 chr4B.!!$F1 1468
17 TraesCS4A01G022200 chr7A 47297524 47298450 926 True 1162.000000 1162 89.3780 10 934 1 chr7A.!!$R1 924

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
898 4337 0.170339 GAGTTAATTTGGCGGCGCTT 59.830 50.000 32.30 20.02 0.00 4.68 F
929 4454 0.671472 CGAGGAGCATGTGCAGTGAA 60.671 55.000 7.83 0.00 45.16 3.18 F
1111 4637 1.304952 CTCCACCTCGTCTCTCCCT 59.695 63.158 0.00 0.00 0.00 4.20 F
2063 5682 1.337167 TGATCTTCCGCACAGTGACAG 60.337 52.381 4.15 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 5618 1.271054 CCTGCAGTAGCCAACAGACTT 60.271 52.381 13.81 0.0 41.13 3.01 R
2098 5717 1.377202 GGTGAATCTCAGCGCCCAA 60.377 57.895 2.29 0.0 35.04 4.12 R
2205 7107 3.392616 ACAACAATGATAGCCCTAGGGAG 59.607 47.826 33.21 6.3 37.50 4.30 R
3134 10646 2.291209 ATTGACCTGTTGCCATGTCA 57.709 45.000 0.00 0.0 42.25 3.58 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
46 51 7.337689 TGGATTTAGTTGATTGTGATCTTGAGG 59.662 37.037 0.00 0.00 33.28 3.86
47 52 7.554118 GGATTTAGTTGATTGTGATCTTGAGGA 59.446 37.037 0.00 0.00 33.28 3.71
48 53 7.912056 TTTAGTTGATTGTGATCTTGAGGAG 57.088 36.000 0.00 0.00 33.28 3.69
56 64 6.462552 TTGTGATCTTGAGGAGATAGTCAG 57.537 41.667 0.00 0.00 45.17 3.51
72 80 3.632333 AGTCAGAGATGTTCGGTGGATA 58.368 45.455 0.00 0.00 0.00 2.59
144 152 9.971922 GAACCAAATTTCTCTATGATTTATGGG 57.028 33.333 0.00 0.00 0.00 4.00
145 153 9.713684 AACCAAATTTCTCTATGATTTATGGGA 57.286 29.630 0.00 0.00 0.00 4.37
146 154 9.887862 ACCAAATTTCTCTATGATTTATGGGAT 57.112 29.630 0.00 0.00 0.00 3.85
176 184 9.561069 AGTTGGATATAATTAGGTGATTGTGTC 57.439 33.333 0.00 0.00 0.00 3.67
177 185 9.561069 GTTGGATATAATTAGGTGATTGTGTCT 57.439 33.333 0.00 0.00 0.00 3.41
179 187 9.559732 TGGATATAATTAGGTGATTGTGTCTTG 57.440 33.333 0.00 0.00 0.00 3.02
180 188 9.778741 GGATATAATTAGGTGATTGTGTCTTGA 57.221 33.333 0.00 0.00 0.00 3.02
184 192 7.621428 AATTAGGTGATTGTGTCTTGAGATG 57.379 36.000 0.00 0.00 0.00 2.90
185 193 4.897509 AGGTGATTGTGTCTTGAGATGA 57.102 40.909 0.00 0.00 0.00 2.92
186 194 5.432680 AGGTGATTGTGTCTTGAGATGAT 57.567 39.130 0.00 0.00 0.00 2.45
187 195 6.550938 AGGTGATTGTGTCTTGAGATGATA 57.449 37.500 0.00 0.00 0.00 2.15
188 196 6.950842 AGGTGATTGTGTCTTGAGATGATAA 58.049 36.000 0.00 0.00 0.00 1.75
189 197 7.571919 AGGTGATTGTGTCTTGAGATGATAAT 58.428 34.615 0.00 0.00 0.00 1.28
190 198 7.714377 AGGTGATTGTGTCTTGAGATGATAATC 59.286 37.037 0.00 0.00 0.00 1.75
191 199 7.496920 GGTGATTGTGTCTTGAGATGATAATCA 59.503 37.037 0.00 0.00 31.23 2.57
192 200 8.886719 GTGATTGTGTCTTGAGATGATAATCAA 58.113 33.333 12.47 0.00 33.31 2.57
193 201 9.452287 TGATTGTGTCTTGAGATGATAATCAAA 57.548 29.630 10.19 0.00 35.14 2.69
205 213 9.903682 GAGATGATAATCAAATATGTTTGGTGG 57.096 33.333 14.11 0.00 43.85 4.61
206 214 9.645128 AGATGATAATCAAATATGTTTGGTGGA 57.355 29.630 14.11 1.02 43.85 4.02
214 222 9.645128 ATCAAATATGTTTGGTGGATTATGAGA 57.355 29.630 14.11 0.00 43.85 3.27
215 223 9.645128 TCAAATATGTTTGGTGGATTATGAGAT 57.355 29.630 14.11 0.00 43.85 2.75
221 229 8.292444 TGTTTGGTGGATTATGAGATTTTAGG 57.708 34.615 0.00 0.00 0.00 2.69
222 230 7.893302 TGTTTGGTGGATTATGAGATTTTAGGT 59.107 33.333 0.00 0.00 0.00 3.08
223 231 8.406297 GTTTGGTGGATTATGAGATTTTAGGTC 58.594 37.037 0.00 0.00 0.00 3.85
224 232 7.451731 TGGTGGATTATGAGATTTTAGGTCT 57.548 36.000 0.00 0.00 0.00 3.85
225 233 8.561536 TGGTGGATTATGAGATTTTAGGTCTA 57.438 34.615 0.00 0.00 0.00 2.59
226 234 8.651389 TGGTGGATTATGAGATTTTAGGTCTAG 58.349 37.037 0.00 0.00 0.00 2.43
227 235 8.652290 GGTGGATTATGAGATTTTAGGTCTAGT 58.348 37.037 0.00 0.00 0.00 2.57
228 236 9.482627 GTGGATTATGAGATTTTAGGTCTAGTG 57.517 37.037 0.00 0.00 0.00 2.74
229 237 8.651389 TGGATTATGAGATTTTAGGTCTAGTGG 58.349 37.037 0.00 0.00 0.00 4.00
230 238 8.871125 GGATTATGAGATTTTAGGTCTAGTGGA 58.129 37.037 0.00 0.00 0.00 4.02
233 241 7.921041 ATGAGATTTTAGGTCTAGTGGATGA 57.079 36.000 0.00 0.00 0.00 2.92
234 242 7.353414 TGAGATTTTAGGTCTAGTGGATGAG 57.647 40.000 0.00 0.00 0.00 2.90
235 243 6.168270 AGATTTTAGGTCTAGTGGATGAGC 57.832 41.667 0.00 0.00 0.00 4.26
236 244 5.663106 AGATTTTAGGTCTAGTGGATGAGCA 59.337 40.000 0.00 0.00 33.63 4.26
237 245 5.957771 TTTTAGGTCTAGTGGATGAGCAT 57.042 39.130 0.00 0.00 33.63 3.79
238 246 4.944619 TTAGGTCTAGTGGATGAGCATG 57.055 45.455 0.00 0.00 33.63 4.06
239 247 2.045524 AGGTCTAGTGGATGAGCATGG 58.954 52.381 0.00 0.00 33.63 3.66
240 248 1.765314 GGTCTAGTGGATGAGCATGGT 59.235 52.381 0.00 0.00 0.00 3.55
241 249 2.484417 GGTCTAGTGGATGAGCATGGTG 60.484 54.545 0.00 0.00 0.00 4.17
242 250 2.432146 GTCTAGTGGATGAGCATGGTGA 59.568 50.000 0.00 0.00 0.00 4.02
243 251 3.070734 GTCTAGTGGATGAGCATGGTGAT 59.929 47.826 0.00 0.00 0.00 3.06
244 252 3.713248 TCTAGTGGATGAGCATGGTGATT 59.287 43.478 0.00 0.00 0.00 2.57
245 253 4.901250 TCTAGTGGATGAGCATGGTGATTA 59.099 41.667 0.00 0.00 0.00 1.75
246 254 3.813443 AGTGGATGAGCATGGTGATTAC 58.187 45.455 0.00 3.41 0.00 1.89
247 255 3.457380 AGTGGATGAGCATGGTGATTACT 59.543 43.478 0.00 5.79 0.00 2.24
248 256 4.655649 AGTGGATGAGCATGGTGATTACTA 59.344 41.667 0.00 0.00 0.00 1.82
249 257 5.309020 AGTGGATGAGCATGGTGATTACTAT 59.691 40.000 0.00 0.00 0.00 2.12
250 258 6.498303 AGTGGATGAGCATGGTGATTACTATA 59.502 38.462 0.00 0.00 0.00 1.31
251 259 7.181665 AGTGGATGAGCATGGTGATTACTATAT 59.818 37.037 0.00 0.00 0.00 0.86
252 260 7.826252 GTGGATGAGCATGGTGATTACTATATT 59.174 37.037 0.00 0.00 0.00 1.28
253 261 7.825761 TGGATGAGCATGGTGATTACTATATTG 59.174 37.037 0.00 0.00 0.00 1.90
254 262 7.281774 GGATGAGCATGGTGATTACTATATTGG 59.718 40.741 0.00 0.00 0.00 3.16
255 263 7.078249 TGAGCATGGTGATTACTATATTGGT 57.922 36.000 0.00 0.00 0.00 3.67
256 264 6.936335 TGAGCATGGTGATTACTATATTGGTG 59.064 38.462 0.00 0.00 0.00 4.17
257 265 6.240894 AGCATGGTGATTACTATATTGGTGG 58.759 40.000 0.00 0.00 0.00 4.61
258 266 6.044287 AGCATGGTGATTACTATATTGGTGGA 59.956 38.462 0.00 0.00 0.00 4.02
259 267 6.886459 GCATGGTGATTACTATATTGGTGGAT 59.114 38.462 0.00 0.00 0.00 3.41
260 268 8.046708 GCATGGTGATTACTATATTGGTGGATA 58.953 37.037 0.00 0.00 0.00 2.59
261 269 9.383519 CATGGTGATTACTATATTGGTGGATAC 57.616 37.037 0.00 0.00 0.00 2.24
307 3261 8.364142 TGGAACAATTTGGATTTAGTTAAGTGG 58.636 33.333 0.78 0.00 31.92 4.00
429 3392 6.929049 TGGATTATGCGAATTTAGGTCTAGTG 59.071 38.462 0.00 0.00 0.00 2.74
643 4076 6.545666 TGGACAATTTGCATATAGTTAGGTGG 59.454 38.462 0.00 0.00 0.00 4.61
654 4087 9.284968 GCATATAGTTAGGTGGTTGTGATATTT 57.715 33.333 0.00 0.00 0.00 1.40
691 4124 8.786826 TCCGTGATTTATGAGATTTTAGTTGT 57.213 30.769 0.00 0.00 0.00 3.32
692 4125 8.664798 TCCGTGATTTATGAGATTTTAGTTGTG 58.335 33.333 0.00 0.00 0.00 3.33
712 4145 8.691797 AGTTGTGTTTATTTAGGTGATTGTGTT 58.308 29.630 0.00 0.00 0.00 3.32
740 4173 8.593679 TGAGAAGATAGTCAAAGATGTTTGGTA 58.406 33.333 14.72 7.86 42.98 3.25
898 4337 0.170339 GAGTTAATTTGGCGGCGCTT 59.830 50.000 32.30 20.02 0.00 4.68
928 4453 1.079612 CGAGGAGCATGTGCAGTGA 60.080 57.895 7.83 0.00 45.16 3.41
929 4454 0.671472 CGAGGAGCATGTGCAGTGAA 60.671 55.000 7.83 0.00 45.16 3.18
989 4514 4.947147 GGGCGGTGACACCTGCAA 62.947 66.667 29.54 0.00 38.76 4.08
1059 4584 2.397413 CTTCCCGGCACAACAGGAGT 62.397 60.000 0.00 0.00 35.22 3.85
1102 4628 1.672356 CAGGTTTGCCTCCACCTCG 60.672 63.158 0.00 0.00 44.97 4.63
1111 4637 1.304952 CTCCACCTCGTCTCTCCCT 59.695 63.158 0.00 0.00 0.00 4.20
1602 5174 4.400529 TCTACACTGACAAGTCTTTGCA 57.599 40.909 1.53 0.00 37.85 4.08
1896 5509 3.906720 TGGACCTGAAGTATGCCTAAC 57.093 47.619 0.00 0.00 0.00 2.34
2003 5618 3.071892 ACAGTTTATCCGTTTGAGACCCA 59.928 43.478 0.00 0.00 0.00 4.51
2063 5682 1.337167 TGATCTTCCGCACAGTGACAG 60.337 52.381 4.15 0.00 0.00 3.51
2318 7226 9.057089 AGTGTACTTTGTTCTTATTTCTGAAGG 57.943 33.333 0.00 0.00 0.00 3.46
2343 7251 7.352719 AGCTTACTGAATCTCGTTTTAACTG 57.647 36.000 0.00 0.00 0.00 3.16
2346 7254 7.063074 GCTTACTGAATCTCGTTTTAACTGCTA 59.937 37.037 0.00 0.00 0.00 3.49
2470 7611 4.969484 TCTCCCTCTTGTTAACCTTTGTC 58.031 43.478 2.48 0.00 0.00 3.18
2567 7708 6.732154 CAGTGAAGAGCTTTCTTTCATTTGA 58.268 36.000 9.17 0.00 0.00 2.69
2590 9972 9.797642 TTGATTACCTACATATCTTGATTGCAT 57.202 29.630 0.00 0.00 0.00 3.96
2719 10109 2.299867 CCACAAGGCTTGCCTAACAAAT 59.700 45.455 26.45 1.06 37.96 2.32
2725 10115 2.562738 GGCTTGCCTAACAAATGTTCCT 59.437 45.455 4.11 0.00 37.96 3.36
3275 10787 4.968719 TCATCTGTGCTCCCTATTTTCCTA 59.031 41.667 0.00 0.00 0.00 2.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.196039 CCATTGCAAATCTCCACCATGAA 59.804 43.478 1.71 0.00 0.00 2.57
1 2 2.761767 CCATTGCAAATCTCCACCATGA 59.238 45.455 1.71 0.00 0.00 3.07
2 3 2.761767 TCCATTGCAAATCTCCACCATG 59.238 45.455 1.71 0.00 0.00 3.66
5 6 4.476628 AAATCCATTGCAAATCTCCACC 57.523 40.909 1.71 0.00 0.00 4.61
6 7 6.212888 ACTAAATCCATTGCAAATCTCCAC 57.787 37.500 1.71 0.00 0.00 4.02
16 17 7.486647 AGATCACAATCAACTAAATCCATTGC 58.513 34.615 0.00 0.00 34.07 3.56
46 51 4.261405 CCACCGAACATCTCTGACTATCTC 60.261 50.000 0.00 0.00 0.00 2.75
47 52 3.634448 CCACCGAACATCTCTGACTATCT 59.366 47.826 0.00 0.00 0.00 1.98
48 53 3.632604 TCCACCGAACATCTCTGACTATC 59.367 47.826 0.00 0.00 0.00 2.08
56 64 8.608844 AGATTAATTTATCCACCGAACATCTC 57.391 34.615 0.89 0.00 0.00 2.75
99 107 8.642935 TTGGTTCAATATCACAATCACCTAAA 57.357 30.769 0.00 0.00 0.00 1.85
150 158 9.561069 GACACAATCACCTAATTATATCCAACT 57.439 33.333 0.00 0.00 0.00 3.16
151 159 9.561069 AGACACAATCACCTAATTATATCCAAC 57.439 33.333 0.00 0.00 0.00 3.77
153 161 9.559732 CAAGACACAATCACCTAATTATATCCA 57.440 33.333 0.00 0.00 0.00 3.41
154 162 9.778741 TCAAGACACAATCACCTAATTATATCC 57.221 33.333 0.00 0.00 0.00 2.59
158 166 9.334947 CATCTCAAGACACAATCACCTAATTAT 57.665 33.333 0.00 0.00 0.00 1.28
159 167 8.539544 TCATCTCAAGACACAATCACCTAATTA 58.460 33.333 0.00 0.00 0.00 1.40
160 168 7.397221 TCATCTCAAGACACAATCACCTAATT 58.603 34.615 0.00 0.00 0.00 1.40
161 169 6.950842 TCATCTCAAGACACAATCACCTAAT 58.049 36.000 0.00 0.00 0.00 1.73
162 170 6.358974 TCATCTCAAGACACAATCACCTAA 57.641 37.500 0.00 0.00 0.00 2.69
163 171 6.550938 ATCATCTCAAGACACAATCACCTA 57.449 37.500 0.00 0.00 0.00 3.08
164 172 4.897509 TCATCTCAAGACACAATCACCT 57.102 40.909 0.00 0.00 0.00 4.00
165 173 7.496920 TGATTATCATCTCAAGACACAATCACC 59.503 37.037 0.00 0.00 0.00 4.02
166 174 8.429493 TGATTATCATCTCAAGACACAATCAC 57.571 34.615 0.00 0.00 0.00 3.06
167 175 9.452287 TTTGATTATCATCTCAAGACACAATCA 57.548 29.630 0.00 0.00 33.25 2.57
195 203 8.917088 CCTAAAATCTCATAATCCACCAAACAT 58.083 33.333 0.00 0.00 0.00 2.71
196 204 7.893302 ACCTAAAATCTCATAATCCACCAAACA 59.107 33.333 0.00 0.00 0.00 2.83
197 205 8.293699 ACCTAAAATCTCATAATCCACCAAAC 57.706 34.615 0.00 0.00 0.00 2.93
198 206 8.336235 AGACCTAAAATCTCATAATCCACCAAA 58.664 33.333 0.00 0.00 0.00 3.28
199 207 7.872138 AGACCTAAAATCTCATAATCCACCAA 58.128 34.615 0.00 0.00 0.00 3.67
200 208 7.451731 AGACCTAAAATCTCATAATCCACCA 57.548 36.000 0.00 0.00 0.00 4.17
201 209 8.652290 ACTAGACCTAAAATCTCATAATCCACC 58.348 37.037 0.00 0.00 0.00 4.61
202 210 9.482627 CACTAGACCTAAAATCTCATAATCCAC 57.517 37.037 0.00 0.00 0.00 4.02
203 211 8.651389 CCACTAGACCTAAAATCTCATAATCCA 58.349 37.037 0.00 0.00 0.00 3.41
204 212 8.871125 TCCACTAGACCTAAAATCTCATAATCC 58.129 37.037 0.00 0.00 0.00 3.01
207 215 9.434275 TCATCCACTAGACCTAAAATCTCATAA 57.566 33.333 0.00 0.00 0.00 1.90
208 216 9.083422 CTCATCCACTAGACCTAAAATCTCATA 57.917 37.037 0.00 0.00 0.00 2.15
209 217 7.472663 GCTCATCCACTAGACCTAAAATCTCAT 60.473 40.741 0.00 0.00 0.00 2.90
210 218 6.183360 GCTCATCCACTAGACCTAAAATCTCA 60.183 42.308 0.00 0.00 0.00 3.27
211 219 6.183360 TGCTCATCCACTAGACCTAAAATCTC 60.183 42.308 0.00 0.00 0.00 2.75
212 220 5.663106 TGCTCATCCACTAGACCTAAAATCT 59.337 40.000 0.00 0.00 0.00 2.40
213 221 5.918608 TGCTCATCCACTAGACCTAAAATC 58.081 41.667 0.00 0.00 0.00 2.17
214 222 5.957771 TGCTCATCCACTAGACCTAAAAT 57.042 39.130 0.00 0.00 0.00 1.82
215 223 5.396772 CCATGCTCATCCACTAGACCTAAAA 60.397 44.000 0.00 0.00 0.00 1.52
216 224 4.101585 CCATGCTCATCCACTAGACCTAAA 59.898 45.833 0.00 0.00 0.00 1.85
217 225 3.643320 CCATGCTCATCCACTAGACCTAA 59.357 47.826 0.00 0.00 0.00 2.69
218 226 3.234353 CCATGCTCATCCACTAGACCTA 58.766 50.000 0.00 0.00 0.00 3.08
219 227 2.045524 CCATGCTCATCCACTAGACCT 58.954 52.381 0.00 0.00 0.00 3.85
220 228 1.765314 ACCATGCTCATCCACTAGACC 59.235 52.381 0.00 0.00 0.00 3.85
221 229 2.432146 TCACCATGCTCATCCACTAGAC 59.568 50.000 0.00 0.00 0.00 2.59
222 230 2.750814 TCACCATGCTCATCCACTAGA 58.249 47.619 0.00 0.00 0.00 2.43
223 231 3.766068 ATCACCATGCTCATCCACTAG 57.234 47.619 0.00 0.00 0.00 2.57
224 232 4.655649 AGTAATCACCATGCTCATCCACTA 59.344 41.667 0.00 0.00 0.00 2.74
225 233 3.457380 AGTAATCACCATGCTCATCCACT 59.543 43.478 0.00 0.00 0.00 4.00
226 234 3.813443 AGTAATCACCATGCTCATCCAC 58.187 45.455 0.00 0.00 0.00 4.02
227 235 5.830799 ATAGTAATCACCATGCTCATCCA 57.169 39.130 0.00 0.00 0.00 3.41
228 236 7.281774 CCAATATAGTAATCACCATGCTCATCC 59.718 40.741 0.00 0.00 0.00 3.51
229 237 7.826252 ACCAATATAGTAATCACCATGCTCATC 59.174 37.037 0.00 0.00 0.00 2.92
230 238 7.609146 CACCAATATAGTAATCACCATGCTCAT 59.391 37.037 0.00 0.00 0.00 2.90
231 239 6.936335 CACCAATATAGTAATCACCATGCTCA 59.064 38.462 0.00 0.00 0.00 4.26
232 240 6.372659 CCACCAATATAGTAATCACCATGCTC 59.627 42.308 0.00 0.00 0.00 4.26
233 241 6.044287 TCCACCAATATAGTAATCACCATGCT 59.956 38.462 0.00 0.00 0.00 3.79
234 242 6.237901 TCCACCAATATAGTAATCACCATGC 58.762 40.000 0.00 0.00 0.00 4.06
235 243 9.383519 GTATCCACCAATATAGTAATCACCATG 57.616 37.037 0.00 0.00 0.00 3.66
236 244 9.111519 TGTATCCACCAATATAGTAATCACCAT 57.888 33.333 0.00 0.00 0.00 3.55
237 245 8.372459 GTGTATCCACCAATATAGTAATCACCA 58.628 37.037 0.00 0.00 35.44 4.17
238 246 8.372459 TGTGTATCCACCAATATAGTAATCACC 58.628 37.037 0.00 0.00 41.09 4.02
239 247 9.944376 ATGTGTATCCACCAATATAGTAATCAC 57.056 33.333 0.00 0.00 41.09 3.06
280 288 9.757227 CACTTAACTAAATCCAAATTGTTCCAA 57.243 29.630 0.00 0.00 0.00 3.53
281 289 8.364142 CCACTTAACTAAATCCAAATTGTTCCA 58.636 33.333 0.00 0.00 0.00 3.53
282 290 8.364894 ACCACTTAACTAAATCCAAATTGTTCC 58.635 33.333 0.00 0.00 0.00 3.62
283 291 9.758651 AACCACTTAACTAAATCCAAATTGTTC 57.241 29.630 0.00 0.00 0.00 3.18
303 3257 3.897239 TGGTCAAAAGATCACAACCACT 58.103 40.909 0.00 0.00 32.08 4.00
307 3261 8.764287 CCTAAAATTTGGTCAAAAGATCACAAC 58.236 33.333 0.00 0.00 33.56 3.32
341 3296 5.447624 AACTAAATCCAACCAAAACCTCG 57.552 39.130 0.00 0.00 0.00 4.63
429 3392 2.825532 ACAATAACCAACATGCTCACCC 59.174 45.455 0.00 0.00 0.00 4.61
549 3981 6.992063 ACAATCAACTAACTGATCCATCAC 57.008 37.500 0.00 0.00 34.90 3.06
657 4090 7.921786 TCTCATAAATCACGGAGAAATTTGT 57.078 32.000 0.00 0.00 33.73 2.83
691 4124 9.743057 CTCAAAACACAATCACCTAAATAAACA 57.257 29.630 0.00 0.00 0.00 2.83
692 4125 9.959749 TCTCAAAACACAATCACCTAAATAAAC 57.040 29.630 0.00 0.00 0.00 2.01
697 4130 7.873719 TCTTCTCAAAACACAATCACCTAAA 57.126 32.000 0.00 0.00 0.00 1.85
712 4145 8.786898 CCAAACATCTTTGACTATCTTCTCAAA 58.213 33.333 0.00 0.00 39.43 2.69
821 4260 6.103997 CAGTCGGCTAACTAAATCCAAGTTA 58.896 40.000 0.00 0.00 38.18 2.24
824 4263 4.330074 CACAGTCGGCTAACTAAATCCAAG 59.670 45.833 0.00 0.00 0.00 3.61
898 4337 1.658686 GCTCCTCGAGGAAGAAGCGA 61.659 60.000 32.94 10.24 44.91 4.93
965 4490 4.308458 TGTCACCGCCCACCTTCG 62.308 66.667 0.00 0.00 0.00 3.79
977 4502 3.924238 CACAAGTTGCAGGTGTCAC 57.076 52.632 1.81 0.00 0.00 3.67
989 4514 0.819259 AGTCGCCATTGTGCACAAGT 60.819 50.000 33.44 20.26 39.47 3.16
1102 4628 1.564348 AGTGAGAGAGGAGGGAGAGAC 59.436 57.143 0.00 0.00 0.00 3.36
1111 4637 1.283613 GGAGACCAGAGTGAGAGAGGA 59.716 57.143 0.00 0.00 0.00 3.71
1602 5174 1.288633 TCACCATGGCAATCCTGGAAT 59.711 47.619 13.04 0.00 35.74 3.01
1874 5450 4.381411 GTTAGGCATACTTCAGGTCCATC 58.619 47.826 0.00 0.00 0.00 3.51
1967 5582 8.426489 ACGGATAAACTGTATGCTTCCTAATTA 58.574 33.333 0.00 0.00 36.20 1.40
2003 5618 1.271054 CCTGCAGTAGCCAACAGACTT 60.271 52.381 13.81 0.00 41.13 3.01
2063 5682 2.440409 TCTTGAAGCCAGCAAATCTCC 58.560 47.619 0.00 0.00 0.00 3.71
2098 5717 1.377202 GGTGAATCTCAGCGCCCAA 60.377 57.895 2.29 0.00 35.04 4.12
2205 7107 3.392616 ACAACAATGATAGCCCTAGGGAG 59.607 47.826 33.21 6.30 37.50 4.30
2318 7226 7.449027 CAGTTAAAACGAGATTCAGTAAGCTC 58.551 38.462 0.00 0.00 43.29 4.09
2343 7251 3.965347 TGACTGAAATAGGGTAGGGTAGC 59.035 47.826 0.00 0.00 0.00 3.58
2346 7254 5.071923 GCTATTGACTGAAATAGGGTAGGGT 59.928 44.000 13.06 0.00 39.53 4.34
2470 7611 8.843262 TCATGTTTATAGCATCAAAATGAGAGG 58.157 33.333 0.00 0.00 34.61 3.69
2567 7708 9.970553 ATCATGCAATCAAGATATGTAGGTAAT 57.029 29.630 0.00 0.00 0.00 1.89
2610 9993 3.460103 GGGCATTTGCATTCCTAACATG 58.540 45.455 4.74 0.00 44.36 3.21
2830 10229 8.263940 TGCTCTAAAACCAGACATATGTTTAC 57.736 34.615 10.30 0.00 32.26 2.01
2843 10242 6.478512 AACCTGAAATTTGCTCTAAAACCA 57.521 33.333 0.00 0.00 0.00 3.67
2940 10339 5.241506 CCCATTCCAAAACGACTGCATATAT 59.758 40.000 0.00 0.00 0.00 0.86
3035 10547 8.255206 CCCAAGGAAAAATTACAAACCTATACC 58.745 37.037 0.00 0.00 0.00 2.73
3134 10646 2.291209 ATTGACCTGTTGCCATGTCA 57.709 45.000 0.00 0.00 42.25 3.58
3275 10787 2.573462 TGGCTTCATTCTTAGTGGAGCT 59.427 45.455 6.39 0.00 45.57 4.09


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

AutoCloner maintained by Alex Coulton.