Multiple sequence alignment - TraesCS2A01G427200

Loading Multiple Alignment...

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 TraesCS2A01G427200 chr2A 100.000 2563 0 0 1 2563 680098534 680095972 0.000000e+00 4734.0
1 TraesCS2A01G427200 chr2B 89.884 1384 86 19 700 2055 640490879 640489522 0.000000e+00 1731.0
2 TraesCS2A01G427200 chr2B 93.831 308 17 2 401 707 640491206 640490900 1.800000e-126 462.0
3 TraesCS2A01G427200 chr2B 85.204 196 26 3 2248 2442 640489333 640489140 5.590000e-47 198.0
4 TraesCS2A01G427200 chr2B 87.786 131 14 2 205 334 549540005 549540134 4.420000e-33 152.0
5 TraesCS2A01G427200 chr2D 92.706 1042 53 7 700 1732 537705586 537704559 0.000000e+00 1482.0
6 TraesCS2A01G427200 chr2D 85.342 730 69 12 2 707 537706322 537705607 0.000000e+00 721.0
7 TraesCS2A01G427200 chr2D 87.965 565 32 9 2022 2563 537696996 537696445 3.600000e-178 634.0
8 TraesCS2A01G427200 chr2D 93.791 306 19 0 1725 2030 537703741 537703436 6.460000e-126 460.0
9 TraesCS2A01G427200 chr7B 89.231 130 12 2 216 344 383714618 383714746 7.340000e-36 161.0
10 TraesCS2A01G427200 chr3B 88.793 116 12 1 217 331 649645640 649645755 9.560000e-30 141.0
11 TraesCS2A01G427200 chr3B 89.583 48 5 0 1793 1840 657596050 657596097 7.660000e-06 62.1
12 TraesCS2A01G427200 chr1B 88.235 119 13 1 219 336 582927088 582927206 9.560000e-30 141.0
13 TraesCS2A01G427200 chr1B 86.777 121 15 1 218 337 17963273 17963153 1.600000e-27 134.0
14 TraesCS2A01G427200 chr1B 84.733 131 18 2 219 348 502961244 502961373 2.070000e-26 130.0
15 TraesCS2A01G427200 chr5B 86.777 121 13 3 219 337 26402377 26402258 5.750000e-27 132.0
16 TraesCS2A01G427200 chr4A 85.385 130 16 3 213 339 618561563 618561434 5.750000e-27 132.0
17 TraesCS2A01G427200 chr3D 85.484 124 16 2 212 334 187938641 187938519 7.440000e-26 128.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G427200 chr2A 680095972 680098534 2562 True 4734.000000 4734 100.000000 1 2563 1 chr2A.!!$R1 2562
1 TraesCS2A01G427200 chr2B 640489140 640491206 2066 True 797.000000 1731 89.639667 401 2442 3 chr2B.!!$R1 2041
2 TraesCS2A01G427200 chr2D 537703436 537706322 2886 True 887.666667 1482 90.613000 2 2030 3 chr2D.!!$R2 2028
3 TraesCS2A01G427200 chr2D 537696445 537696996 551 True 634.000000 634 87.965000 2022 2563 1 chr2D.!!$R1 541

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
931 981 0.467384 CTCTCGTCCTCCCATTGCAT 59.533 55.0 0.0 0.0 0.0 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2168 3060 0.101759 TATCGTGTGCCCTAGCGTTC 59.898 55.0 0.0 0.0 44.31 3.95 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
30 31 2.818432 CAGCTGACATCTTTTGAAGGCT 59.182 45.455 8.42 0.00 0.00 4.58
65 66 9.746711 GAGCAAATATAATAAGTGATGTAAGCG 57.253 33.333 0.00 0.00 0.00 4.68
66 67 9.489084 AGCAAATATAATAAGTGATGTAAGCGA 57.511 29.630 0.00 0.00 0.00 4.93
67 68 9.746711 GCAAATATAATAAGTGATGTAAGCGAG 57.253 33.333 0.00 0.00 0.00 5.03
74 75 8.581057 AATAAGTGATGTAAGCGAGATGTAAG 57.419 34.615 0.00 0.00 0.00 2.34
141 142 8.879227 AGATAAAAGAGAATAGAAGCAGGCTAT 58.121 33.333 0.00 0.00 0.00 2.97
145 146 8.434589 AAAGAGAATAGAAGCAGGCTATAGAT 57.565 34.615 3.21 0.00 0.00 1.98
159 160 7.361286 GCAGGCTATAGATTAATAACCAGTTGC 60.361 40.741 3.21 0.00 0.00 4.17
198 199 3.648009 CTTTGTGAGAGAGTGAGGTGAC 58.352 50.000 0.00 0.00 0.00 3.67
226 227 9.046296 CATGTATCAACAAAGTAATACTCCCTC 57.954 37.037 0.00 0.00 39.58 4.30
227 228 7.562135 TGTATCAACAAAGTAATACTCCCTCC 58.438 38.462 0.00 0.00 30.91 4.30
228 229 6.893020 ATCAACAAAGTAATACTCCCTCCT 57.107 37.500 0.00 0.00 0.00 3.69
229 230 6.697641 TCAACAAAGTAATACTCCCTCCTT 57.302 37.500 0.00 0.00 0.00 3.36
234 235 6.612049 ACAAAGTAATACTCCCTCCTTCTAGG 59.388 42.308 0.00 0.00 36.46 3.02
244 245 5.209659 TCCCTCCTTCTAGGAATACTTGTC 58.790 45.833 0.00 0.00 45.28 3.18
248 249 4.888239 TCCTTCTAGGAATACTTGTCGGAG 59.112 45.833 0.00 0.00 42.51 4.63
252 253 6.205101 TCTAGGAATACTTGTCGGAGAAAC 57.795 41.667 0.00 0.00 39.69 2.78
253 254 3.846360 AGGAATACTTGTCGGAGAAACG 58.154 45.455 0.00 0.00 39.69 3.60
264 265 4.393680 TGTCGGAGAAACGGATAAAAATGG 59.606 41.667 0.00 0.00 39.69 3.16
270 271 7.041372 CGGAGAAACGGATAAAAATGGATGTAT 60.041 37.037 0.00 0.00 0.00 2.29
271 272 8.076178 GGAGAAACGGATAAAAATGGATGTATG 58.924 37.037 0.00 0.00 0.00 2.39
277 281 9.052759 ACGGATAAAAATGGATGTATGTAGAAC 57.947 33.333 0.00 0.00 0.00 3.01
289 293 9.962783 GGATGTATGTAGAACTAAAATACGTCT 57.037 33.333 21.43 0.00 32.61 4.18
309 314 7.681903 ACGTCTAAATACATTCATTTTCCGAC 58.318 34.615 0.00 0.00 30.84 4.79
325 330 9.571810 CATTTTCCGACAAATATTTTCAGATGA 57.428 29.630 0.00 0.00 0.00 2.92
327 332 9.624697 TTTTCCGACAAATATTTTCAGATGAAG 57.375 29.630 0.00 0.00 35.21 3.02
420 441 9.838339 ACATTATATAGCTATTAACCATGCTCC 57.162 33.333 12.39 0.00 37.02 4.70
529 551 4.403432 ACTTACCCTTGATTAATCGACGGA 59.597 41.667 21.25 7.72 0.00 4.69
549 571 4.386049 CGGACGGTATCAAATATCTTCTGC 59.614 45.833 0.00 0.00 0.00 4.26
673 695 3.067742 ACAGGTCATGTAGGTATACGTGC 59.932 47.826 8.32 7.47 45.03 5.34
674 696 2.626743 AGGTCATGTAGGTATACGTGCC 59.373 50.000 8.32 0.00 45.03 5.01
678 700 3.004002 TCATGTAGGTATACGTGCCTTCG 59.996 47.826 12.24 0.00 45.03 3.79
679 701 2.368439 TGTAGGTATACGTGCCTTCGT 58.632 47.619 12.24 4.36 41.15 3.85
680 702 6.202969 TCATGTAGGTATACGTGCCTTCGTA 61.203 44.000 12.24 7.99 45.03 3.43
681 703 3.312421 TGTAGGTATACGTGCCTTCGTAC 59.688 47.826 12.24 6.46 46.43 3.67
761 811 5.321959 TCGACCGTACATTACCACATAAA 57.678 39.130 0.00 0.00 0.00 1.40
786 836 2.049063 GACAACTCTCCGCGCACT 60.049 61.111 8.75 0.00 0.00 4.40
790 840 3.923563 AACTCTCCGCGCACTGCTC 62.924 63.158 8.75 0.00 43.27 4.26
927 977 1.617947 GCACCTCTCGTCCTCCCATT 61.618 60.000 0.00 0.00 0.00 3.16
929 979 1.144936 CCTCTCGTCCTCCCATTGC 59.855 63.158 0.00 0.00 0.00 3.56
931 981 0.467384 CTCTCGTCCTCCCATTGCAT 59.533 55.000 0.00 0.00 0.00 3.96
1020 1070 0.108585 TGGCTTCTTCTTCCGTGCTT 59.891 50.000 0.00 0.00 0.00 3.91
1193 1243 1.202417 AGCAGTACCGTTCGATCATGG 60.202 52.381 0.00 0.00 0.00 3.66
1195 1245 0.104304 AGTACCGTTCGATCATGGCC 59.896 55.000 0.00 0.00 0.00 5.36
1230 1280 2.267188 TTACGTACGCTGCTGGTTAG 57.733 50.000 16.72 0.00 0.00 2.34
1235 1289 0.169672 TACGCTGCTGGTTAGTCGTC 59.830 55.000 0.00 0.00 32.25 4.20
1238 1292 0.458716 GCTGCTGGTTAGTCGTCCTC 60.459 60.000 0.00 0.00 0.00 3.71
1241 1295 1.174783 GCTGGTTAGTCGTCCTCTGA 58.825 55.000 0.00 0.00 0.00 3.27
1264 1318 6.264067 TGAGATATGCTGACCGAGATATATGG 59.736 42.308 0.00 0.00 0.00 2.74
1301 1355 4.742201 AACGACGCTGCGGATGCT 62.742 61.111 26.95 4.10 43.34 3.79
1535 1589 2.126071 ATCACGGACAAGGTCGCG 60.126 61.111 0.00 0.00 34.33 5.87
1537 1591 4.351938 CACGGACAAGGTCGCGGA 62.352 66.667 6.13 0.00 33.16 5.54
1558 1612 0.601057 GCGGCCAAAAAGGAAGCTAA 59.399 50.000 2.24 0.00 41.22 3.09
1589 1643 3.129813 ACAATGCGTTGACTAGTCCGATA 59.870 43.478 25.13 10.08 38.71 2.92
1620 1674 9.519191 TCTCTCAATTCATTTTCCATTGTAAGA 57.481 29.630 0.00 0.00 31.08 2.10
1623 1677 9.362539 CTCAATTCATTTTCCATTGTAAGAAGG 57.637 33.333 0.00 0.00 31.08 3.46
1624 1678 8.313292 TCAATTCATTTTCCATTGTAAGAAGGG 58.687 33.333 0.00 0.00 31.08 3.95
1655 1709 7.494211 AGAATGCATATACGTACTTTGGTACA 58.506 34.615 0.00 0.00 46.15 2.90
1675 1734 7.495934 TGGTACAAGAAGAGATAAAATAGCTGC 59.504 37.037 0.00 0.00 31.92 5.25
1705 1764 2.364324 TCTGACATACAGGATTACCGCC 59.636 50.000 0.00 0.00 45.76 6.13
1807 2699 1.798735 GAGTCGGTCGATTCGTGGA 59.201 57.895 5.89 0.00 0.00 4.02
1831 2723 0.612453 GGAAGGAGGAGACGAGGTGT 60.612 60.000 0.00 0.00 0.00 4.16
1965 2857 2.520069 GTCTCAGGAGAAGGTGAGTCA 58.480 52.381 0.00 0.00 40.97 3.41
2001 2893 4.097361 GTGGGACCGGGAAGGCTC 62.097 72.222 6.32 0.00 46.52 4.70
2094 2986 1.333881 CGTCGATCCTAACAGCGGTAG 60.334 57.143 0.00 0.00 0.00 3.18
2117 3009 4.572909 AGGGGAGTACGTGAAATTTGTAC 58.427 43.478 0.00 2.28 38.94 2.90
2132 3024 4.959631 TTTGTACTCGATGAAACGTCAC 57.040 40.909 0.00 0.00 36.31 3.67
2143 3035 2.199236 GAAACGTCACGTGAGGAAACT 58.801 47.619 36.89 20.66 41.87 2.66
2144 3036 3.181488 TGAAACGTCACGTGAGGAAACTA 60.181 43.478 36.89 19.34 39.61 2.24
2145 3037 2.701073 ACGTCACGTGAGGAAACTAG 57.299 50.000 36.89 15.93 39.18 2.57
2146 3038 1.268899 ACGTCACGTGAGGAAACTAGG 59.731 52.381 36.89 14.93 39.18 3.02
2147 3039 1.538512 CGTCACGTGAGGAAACTAGGA 59.461 52.381 29.41 0.00 44.43 2.94
2148 3040 2.030540 CGTCACGTGAGGAAACTAGGAA 60.031 50.000 29.41 0.00 44.43 3.36
2149 3041 3.551454 CGTCACGTGAGGAAACTAGGAAA 60.551 47.826 29.41 0.00 44.43 3.13
2150 3042 3.739810 GTCACGTGAGGAAACTAGGAAAC 59.260 47.826 20.73 0.00 44.43 2.78
2168 3060 1.867363 ACTAGGGGACTTAGGCACAG 58.133 55.000 0.00 0.00 43.67 3.66
2176 3068 2.531206 GACTTAGGCACAGAACGCTAG 58.469 52.381 0.00 0.00 0.00 3.42
2177 3069 1.204941 ACTTAGGCACAGAACGCTAGG 59.795 52.381 0.00 0.00 0.00 3.02
2183 3075 1.004918 ACAGAACGCTAGGGCACAC 60.005 57.895 6.73 0.00 38.60 3.82
2198 3090 3.746492 GGGCACACGATATATTCAGGTTC 59.254 47.826 0.00 0.00 0.00 3.62
2203 3095 4.345257 ACACGATATATTCAGGTTCAGGCT 59.655 41.667 0.00 0.00 0.00 4.58
2213 3105 2.026822 CAGGTTCAGGCTCCTAATGTGT 60.027 50.000 0.00 0.00 32.26 3.72
2220 3112 4.160439 TCAGGCTCCTAATGTGTGTAAGAG 59.840 45.833 0.00 0.00 0.00 2.85
2225 3117 4.616553 TCCTAATGTGTGTAAGAGCCCTA 58.383 43.478 0.00 0.00 0.00 3.53
2232 3124 2.185387 GTGTAAGAGCCCTACTTCCCA 58.815 52.381 0.00 0.00 0.00 4.37
2274 3236 5.335740 GGAGAACAGAGAACTACAATGTCGA 60.336 44.000 0.00 0.00 0.00 4.20
2296 3258 1.606889 AGGGACTCGGCGAGTTCTT 60.607 57.895 38.55 32.56 43.53 2.52
2297 3259 1.446272 GGGACTCGGCGAGTTCTTG 60.446 63.158 38.55 17.83 43.53 3.02
2316 3278 2.355115 GGGCGTGGAGATTTGGGT 59.645 61.111 0.00 0.00 0.00 4.51
2332 3294 7.614494 AGATTTGGGTGTTTTAGGATCAATTG 58.386 34.615 0.00 0.00 0.00 2.32
2333 3295 6.739331 TTTGGGTGTTTTAGGATCAATTGT 57.261 33.333 5.13 0.00 0.00 2.71
2348 3310 6.263168 GGATCAATTGTGTATGTCTAAAGGGG 59.737 42.308 5.13 0.00 0.00 4.79
2415 3378 4.669318 CACCCTACACATACAAGTCTACG 58.331 47.826 0.00 0.00 0.00 3.51
2429 3392 4.906747 AGTCTACGGGAGTATAGGTAGG 57.093 50.000 0.00 0.00 45.62 3.18
2457 3437 9.452287 GAAAGTAAAGAGTAGAGTTAGAGAGGA 57.548 37.037 0.00 0.00 0.00 3.71
2476 3456 7.350389 AGAGAGGAGTATAGGTAGTGGAAAGTA 59.650 40.741 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.404224 AGATGTCAGCTGCTATGATGG 57.596 47.619 9.47 0.00 0.00 3.51
9 10 2.818432 AGCCTTCAAAAGATGTCAGCTG 59.182 45.455 7.63 7.63 30.90 4.24
30 31 9.770097 CACTTATTATATTTGCTCTCAAGGAGA 57.230 33.333 0.00 0.00 44.45 3.71
112 113 7.714813 GCCTGCTTCTATTCTCTTTTATCTTCT 59.285 37.037 0.00 0.00 0.00 2.85
114 115 7.572814 AGCCTGCTTCTATTCTCTTTTATCTT 58.427 34.615 0.00 0.00 0.00 2.40
118 119 9.368416 TCTATAGCCTGCTTCTATTCTCTTTTA 57.632 33.333 0.00 0.00 0.00 1.52
141 142 6.828273 ACATGCTGCAACTGGTTATTAATCTA 59.172 34.615 6.36 0.00 0.00 1.98
145 146 4.617995 GCACATGCTGCAACTGGTTATTAA 60.618 41.667 6.36 0.00 46.29 1.40
159 160 4.230603 CCACTAGGGCACATGCTG 57.769 61.111 3.48 0.00 41.70 4.41
174 175 1.345741 CCTCACTCTCTCACAAAGCCA 59.654 52.381 0.00 0.00 0.00 4.75
198 199 9.046296 GGGAGTATTACTTTGTTGATACATGAG 57.954 37.037 0.00 0.00 33.44 2.90
200 201 8.964476 AGGGAGTATTACTTTGTTGATACATG 57.036 34.615 0.00 0.00 33.44 3.21
226 227 4.888239 TCTCCGACAAGTATTCCTAGAAGG 59.112 45.833 0.00 0.00 36.46 3.46
227 228 6.452494 TTCTCCGACAAGTATTCCTAGAAG 57.548 41.667 0.00 0.00 0.00 2.85
228 229 6.624423 CGTTTCTCCGACAAGTATTCCTAGAA 60.624 42.308 0.00 0.00 0.00 2.10
229 230 5.163683 CGTTTCTCCGACAAGTATTCCTAGA 60.164 44.000 0.00 0.00 0.00 2.43
234 235 3.841643 TCCGTTTCTCCGACAAGTATTC 58.158 45.455 0.00 0.00 0.00 1.75
244 245 5.065988 ACATCCATTTTTATCCGTTTCTCCG 59.934 40.000 0.00 0.00 0.00 4.63
248 249 9.878599 CTACATACATCCATTTTTATCCGTTTC 57.121 33.333 0.00 0.00 0.00 2.78
252 253 9.273016 AGTTCTACATACATCCATTTTTATCCG 57.727 33.333 0.00 0.00 0.00 4.18
298 302 9.571810 CATCTGAAAATATTTGTCGGAAAATGA 57.428 29.630 17.91 3.93 32.16 2.57
299 303 9.571810 TCATCTGAAAATATTTGTCGGAAAATG 57.428 29.630 17.91 14.15 32.16 2.32
306 311 7.066284 ACTCCCTTCATCTGAAAATATTTGTCG 59.934 37.037 0.39 0.00 33.07 4.35
309 314 9.177608 TGTACTCCCTTCATCTGAAAATATTTG 57.822 33.333 0.39 0.00 33.07 2.32
382 387 9.690913 ATAGCTATATAATGTTGCCATGTCATT 57.309 29.630 3.84 0.57 36.12 2.57
388 393 9.973661 TGGTTAATAGCTATATAATGTTGCCAT 57.026 29.630 6.68 0.00 0.00 4.40
391 396 9.722056 GCATGGTTAATAGCTATATAATGTTGC 57.278 33.333 6.68 7.92 0.00 4.17
398 403 6.837048 TCGGGAGCATGGTTAATAGCTATATA 59.163 38.462 6.68 0.00 37.48 0.86
529 551 7.896811 TGATAGCAGAAGATATTTGATACCGT 58.103 34.615 0.00 0.00 0.00 4.83
678 700 2.181021 CCCACCAGCGTCTCGTAC 59.819 66.667 0.00 0.00 0.00 3.67
679 701 2.482796 TACCCCACCAGCGTCTCGTA 62.483 60.000 0.00 0.00 0.00 3.43
680 702 3.873679 TACCCCACCAGCGTCTCGT 62.874 63.158 0.00 0.00 0.00 4.18
681 703 2.558554 CTTACCCCACCAGCGTCTCG 62.559 65.000 0.00 0.00 0.00 4.04
686 708 2.436646 CTGCTTACCCCACCAGCG 60.437 66.667 0.00 0.00 36.24 5.18
689 711 1.559065 GGTAGCTGCTTACCCCACCA 61.559 60.000 7.79 0.00 37.68 4.17
761 811 0.314302 CGGAGAGTTGTCGACAAGGT 59.686 55.000 30.38 20.59 36.39 3.50
786 836 0.179020 CAAGGTTCTGTGGTGGAGCA 60.179 55.000 0.00 0.00 0.00 4.26
790 840 0.105964 TCGACAAGGTTCTGTGGTGG 59.894 55.000 0.00 0.00 0.00 4.61
859 909 4.785453 GCGAAGGGTGAGCTGGGG 62.785 72.222 0.00 0.00 0.00 4.96
864 914 4.475135 GAGGGGCGAAGGGTGAGC 62.475 72.222 0.00 0.00 0.00 4.26
889 939 2.610374 TGCATCGTCGTTTTTATAGGCC 59.390 45.455 0.00 0.00 0.00 5.19
927 977 1.001048 GTGAGCTTCACTTGCAATGCA 60.001 47.619 2.72 2.72 43.73 3.96
956 1006 0.767060 GATGGGTGGGTAGGGTAGGG 60.767 65.000 0.00 0.00 0.00 3.53
1168 1218 2.879462 GAACGGTACTGCTCGCGG 60.879 66.667 6.13 0.00 0.00 6.46
1193 1243 4.219033 CGTAAAAATAATCGGCATGAGGC 58.781 43.478 0.00 0.00 43.74 4.70
1195 1245 6.062646 CGTACGTAAAAATAATCGGCATGAG 58.937 40.000 7.22 0.00 0.00 2.90
1208 1258 1.868469 ACCAGCAGCGTACGTAAAAA 58.132 45.000 17.90 0.00 0.00 1.94
1230 1280 2.881513 TCAGCATATCTCAGAGGACGAC 59.118 50.000 0.00 0.00 0.00 4.34
1235 1289 2.228582 CTCGGTCAGCATATCTCAGAGG 59.771 54.545 0.00 0.00 0.00 3.69
1238 1292 5.833406 ATATCTCGGTCAGCATATCTCAG 57.167 43.478 0.00 0.00 0.00 3.35
1241 1295 5.538053 CCCATATATCTCGGTCAGCATATCT 59.462 44.000 0.00 0.00 0.00 1.98
1264 1318 3.323758 TACGCCTGTCCCATGCACC 62.324 63.158 0.00 0.00 0.00 5.01
1301 1355 1.514087 GTCGATGGCCTTGTCGGTA 59.486 57.895 20.23 4.99 38.34 4.02
1535 1589 2.472232 CTTCCTTTTTGGCCGCGTCC 62.472 60.000 4.92 0.42 35.26 4.79
1537 1591 3.039134 CTTCCTTTTTGGCCGCGT 58.961 55.556 4.92 0.00 35.26 6.01
1558 1612 4.315803 AGTCAACGCATTGTTAGCTTAGT 58.684 39.130 0.00 0.00 39.29 2.24
1570 1624 3.318275 ACATATCGGACTAGTCAACGCAT 59.682 43.478 23.91 14.98 0.00 4.73
1572 1626 3.351020 ACATATCGGACTAGTCAACGC 57.649 47.619 23.91 6.03 0.00 4.84
1620 1674 6.354130 ACGTATATGCATTCTTACAACCCTT 58.646 36.000 3.54 0.00 0.00 3.95
1621 1675 5.925509 ACGTATATGCATTCTTACAACCCT 58.074 37.500 3.54 0.00 0.00 4.34
1622 1676 6.927381 AGTACGTATATGCATTCTTACAACCC 59.073 38.462 3.54 0.00 0.00 4.11
1623 1677 7.941795 AGTACGTATATGCATTCTTACAACC 57.058 36.000 3.54 0.00 0.00 3.77
1624 1678 9.632969 CAAAGTACGTATATGCATTCTTACAAC 57.367 33.333 3.54 6.53 0.00 3.32
1667 1726 9.956720 GTATGTCAGAAAATAAATGCAGCTATT 57.043 29.630 0.00 0.00 0.00 1.73
1705 1764 7.081349 TCTTTATTGCGTTTGACATTAACAGG 58.919 34.615 0.00 0.00 0.00 4.00
1807 2699 2.452505 CTCGTCTCCTCCTTCCTTCTT 58.547 52.381 0.00 0.00 0.00 2.52
1831 2723 1.202710 TCGTCTTTTGCCTTGGTGCTA 60.203 47.619 0.00 0.00 0.00 3.49
1843 2735 2.048503 CCGGCTCCGTCGTCTTTT 60.049 61.111 7.59 0.00 37.81 2.27
1931 2823 4.927782 AGACGTTGCGGCAAGGCA 62.928 61.111 29.12 1.43 37.34 4.75
1939 2831 0.734253 CCTTCTCCTGAGACGTTGCG 60.734 60.000 0.00 0.00 37.14 4.85
1965 2857 2.424302 CCCGAACCGTCAACCACT 59.576 61.111 0.00 0.00 0.00 4.00
2007 2899 3.249799 TGAAGTGTAACAGGTGCATTTCG 59.750 43.478 7.19 0.00 41.43 3.46
2060 2952 6.404712 AGGATCGACGTAAAATCTTTCAAC 57.595 37.500 0.00 0.00 0.00 3.18
2061 2953 7.599621 TGTTAGGATCGACGTAAAATCTTTCAA 59.400 33.333 0.00 0.00 31.99 2.69
2063 2955 7.515957 TGTTAGGATCGACGTAAAATCTTTC 57.484 36.000 0.00 0.00 31.99 2.62
2064 2956 6.035758 GCTGTTAGGATCGACGTAAAATCTTT 59.964 38.462 0.00 0.00 31.99 2.52
2065 2957 5.519206 GCTGTTAGGATCGACGTAAAATCTT 59.481 40.000 0.00 0.00 31.99 2.40
2094 2986 3.671716 ACAAATTTCACGTACTCCCCTC 58.328 45.455 0.00 0.00 0.00 4.30
2117 3009 1.644295 CTCACGTGACGTTTCATCGAG 59.356 52.381 15.76 7.22 38.32 4.04
2122 3014 1.928503 GTTTCCTCACGTGACGTTTCA 59.071 47.619 15.76 0.00 38.32 2.69
2132 3024 4.381718 CCCTAGTTTCCTAGTTTCCTCACG 60.382 50.000 0.00 0.00 39.29 4.35
2143 3035 3.013188 TGCCTAAGTCCCCTAGTTTCCTA 59.987 47.826 0.00 0.00 0.00 2.94
2144 3036 2.225805 TGCCTAAGTCCCCTAGTTTCCT 60.226 50.000 0.00 0.00 0.00 3.36
2145 3037 2.093075 GTGCCTAAGTCCCCTAGTTTCC 60.093 54.545 0.00 0.00 0.00 3.13
2146 3038 2.570302 TGTGCCTAAGTCCCCTAGTTTC 59.430 50.000 0.00 0.00 0.00 2.78
2147 3039 2.572104 CTGTGCCTAAGTCCCCTAGTTT 59.428 50.000 0.00 0.00 0.00 2.66
2148 3040 2.188817 CTGTGCCTAAGTCCCCTAGTT 58.811 52.381 0.00 0.00 0.00 2.24
2149 3041 1.361543 TCTGTGCCTAAGTCCCCTAGT 59.638 52.381 0.00 0.00 0.00 2.57
2150 3042 2.160721 TCTGTGCCTAAGTCCCCTAG 57.839 55.000 0.00 0.00 0.00 3.02
2168 3060 0.101759 TATCGTGTGCCCTAGCGTTC 59.898 55.000 0.00 0.00 44.31 3.95
2176 3068 3.402628 ACCTGAATATATCGTGTGCCC 57.597 47.619 0.00 0.00 0.00 5.36
2177 3069 4.377021 TGAACCTGAATATATCGTGTGCC 58.623 43.478 0.00 0.00 0.00 5.01
2183 3075 4.221703 AGGAGCCTGAACCTGAATATATCG 59.778 45.833 0.00 0.00 34.99 2.92
2198 3090 4.437239 CTCTTACACACATTAGGAGCCTG 58.563 47.826 0.00 0.00 0.00 4.85
2203 3095 3.450904 AGGGCTCTTACACACATTAGGA 58.549 45.455 0.00 0.00 0.00 2.94
2213 3105 2.185387 GTGGGAAGTAGGGCTCTTACA 58.815 52.381 0.00 0.00 0.00 2.41
2220 3112 1.581223 AGTAAGGTGGGAAGTAGGGC 58.419 55.000 0.00 0.00 0.00 5.19
2225 3117 5.312443 ACAAGGAAATAGTAAGGTGGGAAGT 59.688 40.000 0.00 0.00 0.00 3.01
2232 3124 6.043938 TGTTCTCCACAAGGAAATAGTAAGGT 59.956 38.462 0.00 0.00 45.19 3.50
2274 3236 4.824515 CTCGCCGAGTCCCTCCCT 62.825 72.222 5.82 0.00 0.00 4.20
2296 3258 2.745884 CAAATCTCCACGCCCGCA 60.746 61.111 0.00 0.00 0.00 5.69
2297 3259 3.508840 CCAAATCTCCACGCCCGC 61.509 66.667 0.00 0.00 0.00 6.13
2316 3278 8.862325 AGACATACACAATTGATCCTAAAACA 57.138 30.769 13.59 0.00 0.00 2.83
2332 3294 5.454897 GGAGATTCCCCCTTTAGACATACAC 60.455 48.000 0.00 0.00 0.00 2.90
2333 3295 4.658901 GGAGATTCCCCCTTTAGACATACA 59.341 45.833 0.00 0.00 0.00 2.29
2348 3310 4.403752 AGCTTAAAATTGCCAGGAGATTCC 59.596 41.667 0.00 0.00 36.58 3.01
2415 3378 4.210611 ACTTTCCCCTACCTATACTCCC 57.789 50.000 0.00 0.00 0.00 4.30
2429 3392 8.578448 TCTCTAACTCTACTCTTTACTTTCCC 57.422 38.462 0.00 0.00 0.00 3.97
2463 3443 7.660208 TCTGTGAAATCTTTACTTTCCACTACC 59.340 37.037 0.00 0.00 32.75 3.18
2498 3478 8.481314 TGATTGCATCACTCTAAATCTACTCTT 58.519 33.333 0.00 0.00 33.59 2.85
2514 3494 3.460527 GAGCACCCAAGTGATTGCATCA 61.461 50.000 0.00 0.00 44.27 3.07


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

AutoCloner maintained by Alex Coulton.