Multiple sequence alignment - TraesCS6D01G260500

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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 TraesCS6D01G260500 chr6D 100.000 3955 0 0 1 3955 368112462 368108508 0.000000e+00 7304.0
1 TraesCS6D01G260500 chr6D 91.315 829 54 10 3128 3949 422221283 422220466 0.000000e+00 1116.0
2 TraesCS6D01G260500 chr6D 80.000 295 57 2 2584 2877 355137135 355136842 2.390000e-52 217.0
3 TraesCS6D01G260500 chr6D 75.359 418 91 11 1593 2004 355138138 355137727 1.450000e-44 191.0
4 TraesCS6D01G260500 chr6B 95.608 2823 95 19 322 3128 553413476 553416285 0.000000e+00 4499.0
5 TraesCS6D01G260500 chr6B 93.671 158 7 2 1 155 553413074 553413231 2.380000e-57 233.0
6 TraesCS6D01G260500 chr6B 80.201 298 57 2 2581 2877 522642663 522642959 5.140000e-54 222.0
7 TraesCS6D01G260500 chr6B 81.277 235 38 6 1593 1824 522641669 522641900 6.750000e-43 185.0
8 TraesCS6D01G260500 chr6A 95.043 2784 100 24 373 3128 508716520 508713747 0.000000e+00 4342.0
9 TraesCS6D01G260500 chr6A 73.590 727 157 32 2170 2877 486549543 486550253 3.050000e-61 246.0
10 TraesCS6D01G260500 chr6A 93.038 158 8 1 1 155 508716938 508716781 1.110000e-55 228.0
11 TraesCS6D01G260500 chr6A 76.284 409 83 13 1594 1995 486548964 486549365 5.180000e-49 206.0
12 TraesCS6D01G260500 chr4A 93.939 990 46 8 1057 2041 590935894 590934914 0.000000e+00 1483.0
13 TraesCS6D01G260500 chr5A 91.435 829 59 9 3125 3949 296307053 296306233 0.000000e+00 1127.0
14 TraesCS6D01G260500 chr2D 91.525 826 56 11 3129 3949 119369983 119370799 0.000000e+00 1125.0
15 TraesCS6D01G260500 chr2D 91.205 830 55 13 3125 3949 590062216 590061400 0.000000e+00 1112.0
16 TraesCS6D01G260500 chr2D 95.238 42 2 0 1950 1991 528099398 528099357 2.550000e-07 67.6
17 TraesCS6D01G260500 chr7D 91.505 824 59 7 3127 3949 610765984 610766797 0.000000e+00 1123.0
18 TraesCS6D01G260500 chr3D 91.525 826 52 13 3129 3949 90352148 90351336 0.000000e+00 1122.0
19 TraesCS6D01G260500 chr3D 91.108 821 60 10 3129 3945 182342763 182343574 0.000000e+00 1099.0
20 TraesCS6D01G260500 chr5D 91.616 823 48 13 3129 3948 170318936 170318132 0.000000e+00 1118.0
21 TraesCS6D01G260500 chr1D 91.262 824 57 11 3129 3949 301250368 301251179 0.000000e+00 1109.0
22 TraesCS6D01G260500 chr3B 82.759 87 9 4 1908 1991 42126017 42126100 5.480000e-09 73.1
23 TraesCS6D01G260500 chr3B 88.136 59 7 0 1950 2008 42047467 42047409 1.970000e-08 71.3
24 TraesCS6D01G260500 chr2A 97.619 42 1 0 1950 1991 672945950 672945909 5.480000e-09 73.1


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 TraesCS6D01G260500 chr6D 368108508 368112462 3954 True 7304.0 7304 100.0000 1 3955 1 chr6D.!!$R1 3954
1 TraesCS6D01G260500 chr6D 422220466 422221283 817 True 1116.0 1116 91.3150 3128 3949 1 chr6D.!!$R2 821
2 TraesCS6D01G260500 chr6D 355136842 355138138 1296 True 204.0 217 77.6795 1593 2877 2 chr6D.!!$R3 1284
3 TraesCS6D01G260500 chr6B 553413074 553416285 3211 False 2366.0 4499 94.6395 1 3128 2 chr6B.!!$F2 3127
4 TraesCS6D01G260500 chr6B 522641669 522642959 1290 False 203.5 222 80.7390 1593 2877 2 chr6B.!!$F1 1284
5 TraesCS6D01G260500 chr6A 508713747 508716938 3191 True 2285.0 4342 94.0405 1 3128 2 chr6A.!!$R1 3127
6 TraesCS6D01G260500 chr6A 486548964 486550253 1289 False 226.0 246 74.9370 1594 2877 2 chr6A.!!$F1 1283
7 TraesCS6D01G260500 chr4A 590934914 590935894 980 True 1483.0 1483 93.9390 1057 2041 1 chr4A.!!$R1 984
8 TraesCS6D01G260500 chr5A 296306233 296307053 820 True 1127.0 1127 91.4350 3125 3949 1 chr5A.!!$R1 824
9 TraesCS6D01G260500 chr2D 119369983 119370799 816 False 1125.0 1125 91.5250 3129 3949 1 chr2D.!!$F1 820
10 TraesCS6D01G260500 chr2D 590061400 590062216 816 True 1112.0 1112 91.2050 3125 3949 1 chr2D.!!$R2 824
11 TraesCS6D01G260500 chr7D 610765984 610766797 813 False 1123.0 1123 91.5050 3127 3949 1 chr7D.!!$F1 822
12 TraesCS6D01G260500 chr3D 90351336 90352148 812 True 1122.0 1122 91.5250 3129 3949 1 chr3D.!!$R1 820
13 TraesCS6D01G260500 chr3D 182342763 182343574 811 False 1099.0 1099 91.1080 3129 3945 1 chr3D.!!$F1 816
14 TraesCS6D01G260500 chr5D 170318132 170318936 804 True 1118.0 1118 91.6160 3129 3948 1 chr5D.!!$R1 819
15 TraesCS6D01G260500 chr1D 301250368 301251179 811 False 1109.0 1109 91.2620 3129 3949 1 chr1D.!!$F1 820

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
249 274 0.733909 CGACGATGTCAGCTCTTGCA 60.734 55.0 0.0 0.0 42.74 4.08 F
1089 1204 0.040067 GAAACCCAGCAGTCAAAGCG 60.040 55.0 0.0 0.0 37.01 4.68 F
2096 2399 0.462581 TCCGGAAGATCATGCACAGC 60.463 55.0 0.0 0.0 0.00 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2096 2399 0.108615 CAAGGTACCTGAGCTGGTCG 60.109 60.0 17.14 0.00 41.22 4.79 R
2313 2616 0.601841 AACGACCCGATGTTGGTGTC 60.602 55.0 0.00 0.00 35.85 3.67 R
3445 3764 0.257616 TGCCTATTTCGGAAAGGGGG 59.742 55.0 19.70 15.94 0.00 5.40 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
26 30 1.292992 GGTTTCGTCTTGGTGTCGTT 58.707 50.000 0.00 0.00 0.00 3.85
48 52 2.885861 CTAGAGGTGGCGCTCGTT 59.114 61.111 7.64 0.00 0.00 3.85
59 63 1.798735 CGCTCGTTCCCGTCTTAGA 59.201 57.895 0.00 0.00 35.01 2.10
155 159 6.295123 GGAGGCTTCATCAACGAAGGTATATA 60.295 42.308 0.00 0.00 42.26 0.86
156 160 6.456501 AGGCTTCATCAACGAAGGTATATAC 58.543 40.000 4.14 4.14 42.26 1.47
157 161 6.041637 AGGCTTCATCAACGAAGGTATATACA 59.958 38.462 14.70 0.00 42.26 2.29
158 162 6.145696 GGCTTCATCAACGAAGGTATATACAC 59.854 42.308 14.70 4.51 42.26 2.90
159 163 6.700081 GCTTCATCAACGAAGGTATATACACA 59.300 38.462 14.70 0.00 42.26 3.72
160 164 7.306632 GCTTCATCAACGAAGGTATATACACAC 60.307 40.741 14.70 4.25 42.26 3.82
180 192 2.981875 CACATGTGTGCATCATCGATG 58.018 47.619 19.61 19.61 42.37 3.84
181 193 2.610374 CACATGTGTGCATCATCGATGA 59.390 45.455 29.09 29.09 41.31 2.92
182 194 3.250040 CACATGTGTGCATCATCGATGAT 59.750 43.478 30.75 30.75 41.31 2.45
183 195 3.881089 ACATGTGTGCATCATCGATGATT 59.119 39.130 33.13 17.47 44.70 2.57
184 196 4.024302 ACATGTGTGCATCATCGATGATTC 60.024 41.667 33.13 29.04 44.70 2.52
186 198 7.026072 CATGTGTGCATCATCGATGATTCGA 62.026 44.000 33.13 18.66 44.70 3.71
196 208 1.858091 GATGATTCGATGCTGTCCGT 58.142 50.000 0.00 0.00 0.00 4.69
197 209 1.524355 GATGATTCGATGCTGTCCGTG 59.476 52.381 0.00 0.00 0.00 4.94
199 211 0.924090 GATTCGATGCTGTCCGTGTC 59.076 55.000 0.00 0.00 0.00 3.67
201 213 2.812542 TTCGATGCTGTCCGTGTCCG 62.813 60.000 0.00 0.00 0.00 4.79
202 214 2.261671 GATGCTGTCCGTGTCCGT 59.738 61.111 0.00 0.00 0.00 4.69
203 215 2.048222 ATGCTGTCCGTGTCCGTG 60.048 61.111 0.00 0.00 0.00 4.94
204 216 2.765250 GATGCTGTCCGTGTCCGTGT 62.765 60.000 0.00 0.00 0.00 4.49
205 217 2.733593 GCTGTCCGTGTCCGTGTC 60.734 66.667 0.00 0.00 0.00 3.67
206 218 2.049433 CTGTCCGTGTCCGTGTCC 60.049 66.667 0.00 0.00 0.00 4.02
207 219 3.891586 CTGTCCGTGTCCGTGTCCG 62.892 68.421 0.00 0.00 0.00 4.79
208 220 3.969802 GTCCGTGTCCGTGTCCGT 61.970 66.667 0.00 0.00 0.00 4.69
209 221 3.968568 TCCGTGTCCGTGTCCGTG 61.969 66.667 0.00 0.00 0.00 4.94
210 222 3.968568 CCGTGTCCGTGTCCGTGA 61.969 66.667 0.00 0.00 0.00 4.35
223 235 0.885879 TCCGTGAGCGAGTACATGTT 59.114 50.000 2.30 0.00 41.33 2.71
224 236 1.271379 TCCGTGAGCGAGTACATGTTT 59.729 47.619 2.30 0.00 41.33 2.83
225 237 2.488937 TCCGTGAGCGAGTACATGTTTA 59.511 45.455 2.30 0.00 41.33 2.01
226 238 3.129813 TCCGTGAGCGAGTACATGTTTAT 59.870 43.478 2.30 0.00 41.33 1.40
227 239 3.242944 CCGTGAGCGAGTACATGTTTATG 59.757 47.826 2.30 0.00 41.33 1.90
245 270 1.153939 GTGCGACGATGTCAGCTCT 60.154 57.895 0.00 0.00 34.86 4.09
249 274 0.733909 CGACGATGTCAGCTCTTGCA 60.734 55.000 0.00 0.00 42.74 4.08
256 281 1.071228 TGTCAGCTCTTGCATGACTGT 59.929 47.619 16.16 0.00 42.37 3.55
257 282 2.299867 TGTCAGCTCTTGCATGACTGTA 59.700 45.455 16.16 10.84 42.37 2.74
260 285 2.538861 CAGCTCTTGCATGACTGTATCG 59.461 50.000 16.83 2.72 42.74 2.92
262 287 2.537625 GCTCTTGCATGACTGTATCGTC 59.462 50.000 0.00 0.00 39.41 4.20
263 288 3.119291 CTCTTGCATGACTGTATCGTCC 58.881 50.000 0.00 0.00 32.97 4.79
264 289 2.760650 TCTTGCATGACTGTATCGTCCT 59.239 45.455 0.00 0.00 32.97 3.85
265 290 2.871182 TGCATGACTGTATCGTCCTC 57.129 50.000 0.00 0.00 32.97 3.71
268 293 2.287909 GCATGACTGTATCGTCCTCTCC 60.288 54.545 0.00 0.00 32.97 3.71
269 294 2.801077 TGACTGTATCGTCCTCTCCA 57.199 50.000 0.00 0.00 32.97 3.86
270 295 3.298686 TGACTGTATCGTCCTCTCCAT 57.701 47.619 0.00 0.00 32.97 3.41
271 296 3.215151 TGACTGTATCGTCCTCTCCATC 58.785 50.000 0.00 0.00 32.97 3.51
273 298 3.218453 ACTGTATCGTCCTCTCCATCTG 58.782 50.000 0.00 0.00 0.00 2.90
276 301 3.632604 TGTATCGTCCTCTCCATCTGTTC 59.367 47.826 0.00 0.00 0.00 3.18
279 304 3.099905 TCGTCCTCTCCATCTGTTCATT 58.900 45.455 0.00 0.00 0.00 2.57
280 305 3.131223 TCGTCCTCTCCATCTGTTCATTC 59.869 47.826 0.00 0.00 0.00 2.67
293 321 6.564709 TCTGTTCATTCTTTCACCATTCTG 57.435 37.500 0.00 0.00 0.00 3.02
294 322 6.064060 TCTGTTCATTCTTTCACCATTCTGT 58.936 36.000 0.00 0.00 0.00 3.41
336 430 1.789751 CTGCTGTGCATGTACCACG 59.210 57.895 11.66 1.42 38.13 4.94
349 443 3.467226 CCACGCGTGGGACCCTAT 61.467 66.667 43.64 0.68 46.81 2.57
361 455 4.162509 GTGGGACCCTATAGGATTATGCTC 59.837 50.000 21.07 3.29 39.89 4.26
362 456 4.202890 TGGGACCCTATAGGATTATGCTCA 60.203 45.833 21.07 5.77 39.89 4.26
363 457 4.162509 GGGACCCTATAGGATTATGCTCAC 59.837 50.000 21.07 1.59 39.89 3.51
377 472 7.201956 GGATTATGCTCACTATACCATCCCTAG 60.202 44.444 0.00 0.00 0.00 3.02
379 474 4.408276 TGCTCACTATACCATCCCTAGAC 58.592 47.826 0.00 0.00 0.00 2.59
382 477 5.057843 TCACTATACCATCCCTAGACGTT 57.942 43.478 0.00 0.00 0.00 3.99
452 557 4.575236 CCAGTAGTATACACGCTTCTGAGA 59.425 45.833 5.50 0.00 46.26 3.27
508 613 2.232452 CCGTCTCCACTTTGTCTGATCT 59.768 50.000 0.00 0.00 0.00 2.75
509 614 3.249091 CGTCTCCACTTTGTCTGATCTG 58.751 50.000 0.00 0.00 0.00 2.90
510 615 2.999355 GTCTCCACTTTGTCTGATCTGC 59.001 50.000 0.00 0.00 0.00 4.26
511 616 2.902486 TCTCCACTTTGTCTGATCTGCT 59.098 45.455 0.00 0.00 0.00 4.24
512 617 3.326006 TCTCCACTTTGTCTGATCTGCTT 59.674 43.478 0.00 0.00 0.00 3.91
513 618 4.528206 TCTCCACTTTGTCTGATCTGCTTA 59.472 41.667 0.00 0.00 0.00 3.09
540 648 8.075574 TGCTAAACAAACTGATCATGTTAAGTG 58.924 33.333 12.37 9.06 36.33 3.16
559 667 9.543018 GTTAAGTGGAAATAATGTCTTCTTTCG 57.457 33.333 0.00 0.00 31.56 3.46
560 668 6.183309 AGTGGAAATAATGTCTTCTTTCGC 57.817 37.500 0.00 0.00 31.56 4.70
562 670 6.206634 AGTGGAAATAATGTCTTCTTTCGCAA 59.793 34.615 0.00 0.00 31.56 4.85
615 723 1.024046 TGGTCGCATGGTTTCATCCG 61.024 55.000 0.00 0.00 35.98 4.18
653 761 3.447586 TCGCAGGTTGAACTAATCTAGCT 59.552 43.478 0.00 0.00 41.31 3.32
681 789 2.945008 TCAAGCCTCACACAAAGAAGTG 59.055 45.455 0.00 0.00 44.93 3.16
913 1028 6.434340 GTGTTGGTTAGGAATCTCAAGGATTT 59.566 38.462 0.00 0.00 43.90 2.17
915 1030 7.508977 TGTTGGTTAGGAATCTCAAGGATTTTT 59.491 33.333 0.00 0.00 43.90 1.94
1089 1204 0.040067 GAAACCCAGCAGTCAAAGCG 60.040 55.000 0.00 0.00 37.01 4.68
1092 1207 0.886490 ACCCAGCAGTCAAAGCGAAG 60.886 55.000 0.00 0.00 37.01 3.79
1207 1326 8.453238 TGTCTATGAGTTAACTGGATCTAGAC 57.547 38.462 14.14 18.24 0.00 2.59
1228 1347 5.184864 AGACTCTGATCGAGATTTCTTGTGT 59.815 40.000 17.60 1.99 42.62 3.72
1448 1567 1.675310 CACCTGCGCCATCTTCCAA 60.675 57.895 4.18 0.00 0.00 3.53
1504 1623 7.402811 TCGATCGTAATACAGGCTTATTTTG 57.597 36.000 15.94 2.82 0.00 2.44
1505 1624 6.982141 TCGATCGTAATACAGGCTTATTTTGT 59.018 34.615 15.94 0.00 0.00 2.83
1538 1670 6.470278 TGTTCTGATCTGAACTTGTGATGAT 58.530 36.000 32.51 0.00 44.63 2.45
1544 1676 3.054875 TCTGAACTTGTGATGATCAGGGG 60.055 47.826 0.09 0.00 38.39 4.79
2096 2399 0.462581 TCCGGAAGATCATGCACAGC 60.463 55.000 0.00 0.00 0.00 4.40
2252 2555 1.687054 CCCATCTGGATGTGCACCATT 60.687 52.381 15.69 0.00 37.11 3.16
2313 2616 1.379044 GAGCAAGGGACCACCATGG 60.379 63.158 11.19 11.19 45.02 3.66
2378 2687 0.317160 TGTTCGACATCCTCAGCGTT 59.683 50.000 0.00 0.00 0.00 4.84
3136 3449 5.413309 AGACCAAGAGTTCTCGAAATCAT 57.587 39.130 9.40 0.00 37.82 2.45
3169 3482 6.431198 AAAGAAGTACTCGTTGCAAAGAAA 57.569 33.333 15.91 4.93 0.00 2.52
3170 3483 6.619801 AAGAAGTACTCGTTGCAAAGAAAT 57.380 33.333 15.91 9.74 0.00 2.17
3172 3485 7.724305 AGAAGTACTCGTTGCAAAGAAATAA 57.276 32.000 15.91 0.00 0.00 1.40
3188 3501 9.546428 CAAAGAAATAATCCACTTTTTCAGGTT 57.454 29.630 0.00 0.00 31.94 3.50
3196 3509 3.506810 CACTTTTTCAGGTTGCGACAAA 58.493 40.909 6.39 0.00 0.00 2.83
3199 3512 2.132740 TTTCAGGTTGCGACAAATGC 57.867 45.000 6.39 0.00 0.00 3.56
3240 3553 2.582052 TGTCGCAATCTGGGAGTTTTT 58.418 42.857 0.00 0.00 40.09 1.94
3446 3765 4.935630 CGGAAGCACGGTTTTTCC 57.064 55.556 9.36 9.36 37.58 3.13
3459 3779 2.635915 GGTTTTTCCCCCTTTCCGAAAT 59.364 45.455 0.00 0.00 0.00 2.17
3504 3824 1.753930 TCATAACCGTGCCTCTCGTA 58.246 50.000 0.00 0.00 0.00 3.43
3515 3835 2.037251 TGCCTCTCGTAGAAGCAAAACT 59.963 45.455 5.91 0.00 34.84 2.66
3535 3855 4.363999 ACTGTGACTCTCGTGAAAGAAAG 58.636 43.478 0.00 0.00 0.00 2.62
3550 3870 7.149031 CGTGAAAGAAAGAAAAACAGAAAACGT 60.149 33.333 0.00 0.00 0.00 3.99
3950 4298 3.169198 GTGCTTCTCGCGAAAGGG 58.831 61.111 23.14 9.35 43.27 3.95
3951 4299 2.047274 TGCTTCTCGCGAAAGGGG 60.047 61.111 23.14 9.02 45.20 4.79
3952 4300 2.264794 GCTTCTCGCGAAAGGGGA 59.735 61.111 23.14 10.96 45.20 4.81
3953 4301 1.375523 GCTTCTCGCGAAAGGGGAA 60.376 57.895 23.14 16.45 45.20 3.97
3954 4302 0.953960 GCTTCTCGCGAAAGGGGAAA 60.954 55.000 23.14 6.50 45.20 3.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.180456 TCTAGCCCGAACGACACCAA 61.180 55.000 0.00 0.00 0.00 3.67
72 76 0.389166 ACGAGCGCTTCAGAAAGGAG 60.389 55.000 13.26 0.00 32.79 3.69
159 163 5.219702 ATCATCGATGATGCACACATGTGT 61.220 41.667 34.29 25.76 45.27 3.72
160 164 3.250040 ATCATCGATGATGCACACATGTG 59.750 43.478 34.29 24.25 45.27 3.21
177 189 1.524355 CACGGACAGCATCGAATCATC 59.476 52.381 0.00 0.00 0.00 2.92
178 190 1.134699 ACACGGACAGCATCGAATCAT 60.135 47.619 0.00 0.00 0.00 2.45
179 191 0.246360 ACACGGACAGCATCGAATCA 59.754 50.000 0.00 0.00 0.00 2.57
180 192 0.924090 GACACGGACAGCATCGAATC 59.076 55.000 0.00 0.00 0.00 2.52
181 193 0.460284 GGACACGGACAGCATCGAAT 60.460 55.000 0.00 0.00 0.00 3.34
182 194 1.080093 GGACACGGACAGCATCGAA 60.080 57.895 0.00 0.00 0.00 3.71
183 195 2.571757 GGACACGGACAGCATCGA 59.428 61.111 0.00 0.00 0.00 3.59
184 196 2.880879 CGGACACGGACAGCATCG 60.881 66.667 0.00 0.00 36.18 3.84
186 198 2.048222 CACGGACACGGACAGCAT 60.048 61.111 0.00 0.00 46.48 3.79
189 201 2.049433 GGACACGGACACGGACAG 60.049 66.667 0.00 0.00 46.48 3.51
190 202 3.968568 CGGACACGGACACGGACA 61.969 66.667 0.00 0.00 46.48 4.02
191 203 3.969802 ACGGACACGGACACGGAC 61.970 66.667 0.00 0.00 46.48 4.79
192 204 3.968568 CACGGACACGGACACGGA 61.969 66.667 0.00 0.00 46.48 4.69
194 206 2.428569 CTCACGGACACGGACACG 60.429 66.667 0.00 0.00 46.48 4.49
195 207 2.733593 GCTCACGGACACGGACAC 60.734 66.667 0.00 0.00 46.48 3.67
196 208 4.337060 CGCTCACGGACACGGACA 62.337 66.667 0.00 0.00 46.48 4.02
197 209 3.948086 CTCGCTCACGGACACGGAC 62.948 68.421 0.00 0.00 46.48 4.79
199 211 2.683859 TACTCGCTCACGGACACGG 61.684 63.158 0.00 0.00 46.48 4.94
201 213 0.170561 ATGTACTCGCTCACGGACAC 59.829 55.000 0.00 0.00 40.63 3.67
202 214 0.170339 CATGTACTCGCTCACGGACA 59.830 55.000 0.00 0.00 40.63 4.02
203 215 0.170561 ACATGTACTCGCTCACGGAC 59.829 55.000 0.00 0.00 40.63 4.79
204 216 0.885879 AACATGTACTCGCTCACGGA 59.114 50.000 0.00 0.00 40.63 4.69
205 217 1.710013 AAACATGTACTCGCTCACGG 58.290 50.000 0.00 0.00 40.63 4.94
206 218 3.857665 ACATAAACATGTACTCGCTCACG 59.142 43.478 0.00 0.00 35.00 4.35
207 219 4.492570 GCACATAAACATGTACTCGCTCAC 60.493 45.833 0.00 0.00 32.74 3.51
208 220 3.616821 GCACATAAACATGTACTCGCTCA 59.383 43.478 0.00 0.00 32.74 4.26
209 221 3.301835 CGCACATAAACATGTACTCGCTC 60.302 47.826 0.00 0.00 32.74 5.03
210 222 2.603110 CGCACATAAACATGTACTCGCT 59.397 45.455 0.00 0.00 32.74 4.93
223 235 1.135112 AGCTGACATCGTCGCACATAA 60.135 47.619 11.48 0.00 35.68 1.90
224 236 0.455815 AGCTGACATCGTCGCACATA 59.544 50.000 11.48 0.00 35.68 2.29
225 237 0.803768 GAGCTGACATCGTCGCACAT 60.804 55.000 0.00 0.00 35.68 3.21
226 238 1.444383 GAGCTGACATCGTCGCACA 60.444 57.895 0.00 0.00 35.68 4.57
227 239 0.734253 AAGAGCTGACATCGTCGCAC 60.734 55.000 0.00 6.88 35.68 5.34
232 257 1.066645 TCATGCAAGAGCTGACATCGT 60.067 47.619 0.00 0.00 42.74 3.73
245 270 2.760650 AGAGGACGATACAGTCATGCAA 59.239 45.455 0.00 0.00 42.62 4.08
249 274 3.298686 TGGAGAGGACGATACAGTCAT 57.701 47.619 0.00 0.00 42.62 3.06
256 281 3.898482 TGAACAGATGGAGAGGACGATA 58.102 45.455 0.00 0.00 0.00 2.92
257 282 2.739943 TGAACAGATGGAGAGGACGAT 58.260 47.619 0.00 0.00 0.00 3.73
260 285 4.751767 AGAATGAACAGATGGAGAGGAC 57.248 45.455 0.00 0.00 0.00 3.85
262 287 5.353678 GTGAAAGAATGAACAGATGGAGAGG 59.646 44.000 0.00 0.00 0.00 3.69
263 288 5.353678 GGTGAAAGAATGAACAGATGGAGAG 59.646 44.000 0.00 0.00 0.00 3.20
264 289 5.221904 TGGTGAAAGAATGAACAGATGGAGA 60.222 40.000 0.00 0.00 0.00 3.71
265 290 5.005740 TGGTGAAAGAATGAACAGATGGAG 58.994 41.667 0.00 0.00 0.00 3.86
268 293 7.027760 CAGAATGGTGAAAGAATGAACAGATG 58.972 38.462 0.00 0.00 0.00 2.90
269 294 6.718454 ACAGAATGGTGAAAGAATGAACAGAT 59.282 34.615 0.00 0.00 43.62 2.90
270 295 6.016860 CACAGAATGGTGAAAGAATGAACAGA 60.017 38.462 0.00 0.00 43.62 3.41
271 296 6.016860 TCACAGAATGGTGAAAGAATGAACAG 60.017 38.462 0.00 0.00 44.34 3.16
273 298 6.317789 TCACAGAATGGTGAAAGAATGAAC 57.682 37.500 0.00 0.00 44.34 3.18
293 321 4.595116 CTCGAATCAAAGCATTCCATCAC 58.405 43.478 0.00 0.00 30.03 3.06
294 322 3.065786 GCTCGAATCAAAGCATTCCATCA 59.934 43.478 0.41 0.00 38.42 3.07
301 329 0.376152 CAGCGCTCGAATCAAAGCAT 59.624 50.000 7.13 0.00 38.45 3.79
304 332 0.247576 CAGCAGCGCTCGAATCAAAG 60.248 55.000 7.13 0.00 36.40 2.77
336 430 1.349067 AATCCTATAGGGTCCCACGC 58.651 55.000 18.97 0.00 36.25 5.34
349 443 6.611642 GGGATGGTATAGTGAGCATAATCCTA 59.388 42.308 0.00 0.00 37.66 2.94
361 455 4.583489 ACAACGTCTAGGGATGGTATAGTG 59.417 45.833 0.00 0.00 33.05 2.74
362 456 4.801164 ACAACGTCTAGGGATGGTATAGT 58.199 43.478 0.00 0.00 33.05 2.12
363 457 5.071370 AGACAACGTCTAGGGATGGTATAG 58.929 45.833 0.00 0.00 41.51 1.31
377 472 8.035394 ACATATATATCCATCCAAGACAACGTC 58.965 37.037 0.00 0.00 0.00 4.34
379 474 8.777865 AACATATATATCCATCCAAGACAACG 57.222 34.615 0.00 0.00 0.00 4.10
424 529 5.526846 AGAAGCGTGTATACTACTGGTACTC 59.473 44.000 4.17 0.00 32.72 2.59
452 557 1.485480 CCATGCACTGTCTGATCTCCT 59.515 52.381 0.00 0.00 0.00 3.69
508 613 6.816134 TGATCAGTTTGTTTAGCATAAGCA 57.184 33.333 0.00 0.00 45.49 3.91
509 614 7.253422 ACATGATCAGTTTGTTTAGCATAAGC 58.747 34.615 0.00 0.00 42.56 3.09
513 618 8.796475 ACTTAACATGATCAGTTTGTTTAGCAT 58.204 29.630 19.26 5.72 34.85 3.79
537 645 5.705441 TGCGAAAGAAGACATTATTTCCACT 59.295 36.000 3.34 0.00 41.48 4.00
540 648 7.867445 TTTTGCGAAAGAAGACATTATTTCC 57.133 32.000 0.00 0.00 41.48 3.13
575 683 7.432252 CGACCACTGCCAAATTATATTTCTTTC 59.568 37.037 0.00 0.00 0.00 2.62
578 686 5.221048 GCGACCACTGCCAAATTATATTTCT 60.221 40.000 0.00 0.00 0.00 2.52
582 690 3.550820 TGCGACCACTGCCAAATTATAT 58.449 40.909 0.00 0.00 0.00 0.86
587 695 1.597797 CCATGCGACCACTGCCAAAT 61.598 55.000 0.00 0.00 0.00 2.32
615 723 1.272781 GCGAGTACAGCTCATGTCAC 58.727 55.000 6.15 0.00 44.33 3.67
681 789 0.784778 CTGCAGGAAGTTTCGTCGAC 59.215 55.000 5.57 5.18 0.00 4.20
749 857 3.097877 TCAGCGTGCAATCATACTAGG 57.902 47.619 0.00 0.00 0.00 3.02
890 1005 7.468141 AAAATCCTTGAGATTCCTAACCAAC 57.532 36.000 0.00 0.00 44.75 3.77
926 1041 6.925165 GCTCCATCACAAAATTCAGAAGAAAA 59.075 34.615 0.00 0.00 37.29 2.29
930 1045 5.381174 TGCTCCATCACAAAATTCAGAAG 57.619 39.130 0.00 0.00 0.00 2.85
962 1077 4.390297 GGTGAATTCTCTGAACCTTCTTCG 59.610 45.833 7.05 0.00 0.00 3.79
1008 1123 1.519455 CTTGGGATCGACGGTGCTC 60.519 63.158 0.00 0.00 0.00 4.26
1089 1204 6.201226 GAAGATTTCCATTTCCCAGTCTTC 57.799 41.667 0.00 0.00 35.24 2.87
1149 1264 5.124457 GTGTCTGTGGCATATGAAGAACAAT 59.876 40.000 6.97 0.00 0.00 2.71
1204 1323 5.184864 ACACAAGAAATCTCGATCAGAGTCT 59.815 40.000 12.27 8.77 46.86 3.24
1228 1347 6.822667 AGTTAACTGCATCATCATCAACAA 57.177 33.333 7.48 0.00 0.00 2.83
1448 1567 3.318275 AGCGTACCGTGACATAGATCATT 59.682 43.478 0.00 0.00 0.00 2.57
1504 1623 7.629027 GTTCAGATCAGAACAATCCAAAAAC 57.371 36.000 22.09 0.00 45.53 2.43
1538 1670 1.555075 GACAGTATCACAAGCCCCTGA 59.445 52.381 0.00 0.00 0.00 3.86
2052 2355 2.228343 CGGACTCCTTGTAAGACTCGTT 59.772 50.000 0.00 0.00 0.00 3.85
2096 2399 0.108615 CAAGGTACCTGAGCTGGTCG 60.109 60.000 17.14 0.00 41.22 4.79
2252 2555 1.338973 GTGAACACCACCGAGTAGACA 59.661 52.381 0.00 0.00 39.86 3.41
2313 2616 0.601841 AACGACCCGATGTTGGTGTC 60.602 55.000 0.00 0.00 35.85 3.67
2405 2714 3.952508 ATGACCGGCACCAGCACA 61.953 61.111 0.00 0.00 44.61 4.57
3145 3458 6.431198 TTCTTTGCAACGAGTACTTCTTTT 57.569 33.333 0.00 0.00 0.00 2.27
3146 3459 6.431198 TTTCTTTGCAACGAGTACTTCTTT 57.569 33.333 0.00 0.00 0.00 2.52
3147 3460 6.619801 ATTTCTTTGCAACGAGTACTTCTT 57.380 33.333 0.00 0.00 0.00 2.52
3148 3461 7.724305 TTATTTCTTTGCAACGAGTACTTCT 57.276 32.000 0.00 0.00 0.00 2.85
3149 3462 7.692705 GGATTATTTCTTTGCAACGAGTACTTC 59.307 37.037 0.00 0.00 0.00 3.01
3150 3463 7.174253 TGGATTATTTCTTTGCAACGAGTACTT 59.826 33.333 0.00 0.00 0.00 2.24
3169 3482 4.764823 TCGCAACCTGAAAAAGTGGATTAT 59.235 37.500 0.00 0.00 0.00 1.28
3170 3483 4.023536 GTCGCAACCTGAAAAAGTGGATTA 60.024 41.667 0.00 0.00 0.00 1.75
3172 3485 2.293399 GTCGCAACCTGAAAAAGTGGAT 59.707 45.455 0.00 0.00 0.00 3.41
3218 3531 2.270352 AACTCCCAGATTGCGACAAA 57.730 45.000 0.00 0.00 0.00 2.83
3270 3585 4.751098 ACGCACGGTTTAAGAGATAAAACA 59.249 37.500 0.00 0.00 40.57 2.83
3432 3750 0.397957 AAGGGGGAAAAACCGTGCTT 60.398 50.000 0.00 0.00 40.11 3.91
3445 3764 0.257616 TGCCTATTTCGGAAAGGGGG 59.742 55.000 19.70 15.94 0.00 5.40
3446 3765 1.389555 GTGCCTATTTCGGAAAGGGG 58.610 55.000 19.70 17.73 0.00 4.79
3479 3799 2.093658 AGAGGCACGGTTATGATTTCGT 60.094 45.455 0.00 0.00 36.19 3.85
3488 3808 1.741706 CTTCTACGAGAGGCACGGTTA 59.258 52.381 0.00 0.00 34.93 2.85
3504 3824 3.126831 CGAGAGTCACAGTTTTGCTTCT 58.873 45.455 0.00 0.00 0.00 2.85
3688 4022 0.856641 GTGCTTACGCGAAAGTCACA 59.143 50.000 15.93 0.00 39.65 3.58
3809 4146 3.645975 ACGGTTGTGCTTTCGCGG 61.646 61.111 6.13 0.00 39.65 6.46


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

AutoCloner maintained by Alex Coulton.