Multiple sequence alignment - TraesCS6B01G285000

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 TraesCS6B01G285000 chr6B 100.000 3676 0 0 1 3676 513891049 513887374 0.000000e+00 6789.0
1 TraesCS6B01G285000 chr6B 80.222 541 103 4 2117 2655 26004843 26005381 1.590000e-108 403.0
2 TraesCS6B01G285000 chr6B 79.298 541 101 8 2117 2655 26120787 26120256 5.800000e-98 368.0
3 TraesCS6B01G285000 chr6B 90.909 44 3 1 2916 2959 142511034 142511076 1.430000e-04 58.4
4 TraesCS6B01G285000 chr6A 92.706 3071 165 29 644 3676 449667132 449670181 0.000000e+00 4375.0
5 TraesCS6B01G285000 chr6A 82.841 542 87 6 2117 2655 15542665 15543203 7.140000e-132 481.0
6 TraesCS6B01G285000 chr6A 86.275 51 7 0 2910 2960 604890660 604890710 5.130000e-04 56.5
7 TraesCS6B01G285000 chr6D 91.670 2833 147 41 1 2814 312803836 312806598 0.000000e+00 3842.0
8 TraesCS6B01G285000 chr6D 88.404 871 89 6 2811 3676 312812404 312813267 0.000000e+00 1038.0
9 TraesCS6B01G285000 chr2D 78.252 515 96 13 22 531 385374337 385374840 2.130000e-82 316.0
10 TraesCS6B01G285000 chr2D 75.862 232 54 1 150 379 585384929 585384698 2.320000e-22 117.0
11 TraesCS6B01G285000 chr2D 92.982 57 4 0 1387 1443 637445241 637445185 2.350000e-12 84.2
12 TraesCS6B01G285000 chr3B 75.701 535 99 22 1067 1585 708520793 708520274 4.740000e-59 239.0
13 TraesCS6B01G285000 chr3B 77.485 342 63 11 194 532 396732914 396732584 3.750000e-45 193.0
14 TraesCS6B01G285000 chr3D 74.532 534 107 22 1067 1585 536327450 536327969 4.810000e-49 206.0
15 TraesCS6B01G285000 chr7B 78.683 319 57 10 199 514 217620143 217620453 6.220000e-48 202.0
16 TraesCS6B01G285000 chr7B 74.109 533 107 23 1067 1586 507141133 507140619 1.350000e-44 191.0
17 TraesCS6B01G285000 chr1A 78.808 302 51 10 38 333 292850464 292850758 1.350000e-44 191.0
18 TraesCS6B01G285000 chr1A 74.592 429 89 17 38 454 292867039 292867459 1.760000e-38 171.0
19 TraesCS6B01G285000 chr1A 75.065 385 77 16 38 412 292846116 292846491 1.060000e-35 161.0
20 TraesCS6B01G285000 chr1A 77.474 293 49 15 38 322 292871393 292871676 3.800000e-35 159.0
21 TraesCS6B01G285000 chr1A 100.000 28 0 0 2263 2290 57391052 57391025 7.000000e-03 52.8
22 TraesCS6B01G285000 chr7D 73.783 534 107 22 1067 1586 481697519 481697005 2.920000e-41 180.0
23 TraesCS6B01G285000 chr1D 74.414 469 93 20 38 499 225066007 225065559 3.770000e-40 176.0
24 TraesCS6B01G285000 chr1D 93.182 44 3 0 2916 2959 8008032 8008075 8.520000e-07 65.8
25 TraesCS6B01G285000 chr7A 74.044 497 97 21 1103 1586 548585806 548585329 1.360000e-39 174.0
26 TraesCS6B01G285000 chr7A 91.304 46 3 1 2916 2960 537642117 537642162 1.100000e-05 62.1
27 TraesCS6B01G285000 chr5B 76.774 310 50 19 189 484 293949244 293949545 1.770000e-33 154.0
28 TraesCS6B01G285000 chr5B 97.143 35 1 0 468 502 15290542 15290508 3.960000e-05 60.2
29 TraesCS6B01G285000 chr5B 96.875 32 1 0 468 499 49499337 49499306 2.000000e-03 54.7
30 TraesCS6B01G285000 chr4D 84.091 88 12 2 39 125 117653826 117653740 2.350000e-12 84.2
31 TraesCS6B01G285000 chr4D 86.567 67 7 2 67 132 117653655 117653590 5.090000e-09 73.1
32 TraesCS6B01G285000 chr2A 92.982 57 4 0 1387 1443 762568444 762568500 2.350000e-12 84.2
33 TraesCS6B01G285000 chr5D 78.571 98 20 1 436 532 46873284 46873187 3.060000e-06 63.9
34 TraesCS6B01G285000 chr3A 100.000 29 0 0 2932 2960 702538847 702538819 2.000000e-03 54.7


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 TraesCS6B01G285000 chr6B 513887374 513891049 3675 True 6789 6789 100.000 1 3676 1 chr6B.!!$R2 3675
1 TraesCS6B01G285000 chr6B 26004843 26005381 538 False 403 403 80.222 2117 2655 1 chr6B.!!$F1 538
2 TraesCS6B01G285000 chr6B 26120256 26120787 531 True 368 368 79.298 2117 2655 1 chr6B.!!$R1 538
3 TraesCS6B01G285000 chr6A 449667132 449670181 3049 False 4375 4375 92.706 644 3676 1 chr6A.!!$F2 3032
4 TraesCS6B01G285000 chr6A 15542665 15543203 538 False 481 481 82.841 2117 2655 1 chr6A.!!$F1 538
5 TraesCS6B01G285000 chr6D 312803836 312806598 2762 False 3842 3842 91.670 1 2814 1 chr6D.!!$F1 2813
6 TraesCS6B01G285000 chr6D 312812404 312813267 863 False 1038 1038 88.404 2811 3676 1 chr6D.!!$F2 865
7 TraesCS6B01G285000 chr2D 385374337 385374840 503 False 316 316 78.252 22 531 1 chr2D.!!$F1 509
8 TraesCS6B01G285000 chr3B 708520274 708520793 519 True 239 239 75.701 1067 1585 1 chr3B.!!$R2 518
9 TraesCS6B01G285000 chr3D 536327450 536327969 519 False 206 206 74.532 1067 1585 1 chr3D.!!$F1 518

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
183 184 0.036010 CCCACTAGCAACAGACAGGG 60.036 60.0 0.00 0.0 0.00 4.45 F
224 225 0.253044 GTAGGGCATGGAAGACAGCA 59.747 55.0 0.00 0.0 0.00 4.41 F
338 339 0.389817 CTCACGAGGACGGCAAATGA 60.390 55.0 0.00 0.0 44.46 2.57 F
596 598 0.541392 TCATCTGTGTTCCCGGATGG 59.459 55.0 0.73 0.0 44.75 3.51 F
788 792 0.835941 AGCATCACTCATCCCACCTC 59.164 55.0 0.00 0.0 0.00 3.85 F
2264 2310 0.037326 ACACCACGGAGTACATGCTG 60.037 55.0 0.00 0.0 41.61 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1385 0.634465 GGAACCTCTCCCTCCTCTCT 59.366 60.000 0.00 0.00 38.44 3.10 R
1936 1982 0.674895 GTCCTCGTTCTGCTGCCAAT 60.675 55.000 0.00 0.00 0.00 3.16 R
2240 2286 0.818852 TGTACTCCGTGGTGTCGTCA 60.819 55.000 0.00 0.00 0.00 4.35 R
2264 2310 1.796796 GAACGCCATCAGGTTCAGC 59.203 57.895 0.00 0.00 41.60 4.26 R
2630 2683 1.906990 ACTGTAGCACGGTGTAGACT 58.093 50.000 10.24 0.68 36.13 3.24 R
3309 3374 1.076777 ATGGGCCAATCAACTCGGG 60.077 57.895 11.89 0.00 0.00 5.14 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
27 28 4.505217 CCGTCGCTCGCAATGTGC 62.505 66.667 0.00 0.00 40.69 4.57
32 33 3.437795 GCTCGCAATGTGCAGGCT 61.438 61.111 0.61 0.00 45.36 4.58
121 122 0.108520 GTTTGGTCGCGTCATAGGGA 60.109 55.000 5.77 0.00 0.00 4.20
152 153 1.225704 CAGCCCCTTCACTCCATCC 59.774 63.158 0.00 0.00 0.00 3.51
155 156 1.274703 GCCCCTTCACTCCATCCTGA 61.275 60.000 0.00 0.00 0.00 3.86
183 184 0.036010 CCCACTAGCAACAGACAGGG 60.036 60.000 0.00 0.00 0.00 4.45
219 220 2.050144 GGATGAGTAGGGCATGGAAGA 58.950 52.381 0.00 0.00 0.00 2.87
224 225 0.253044 GTAGGGCATGGAAGACAGCA 59.747 55.000 0.00 0.00 0.00 4.41
245 246 1.602237 GGCTCGAGTCCCAAATGGA 59.398 57.895 15.13 0.00 42.41 3.41
254 255 1.181786 TCCCAAATGGATCGGTTTGC 58.818 50.000 13.18 0.00 38.61 3.68
258 259 2.094675 CAAATGGATCGGTTTGCCTCT 58.905 47.619 8.05 0.00 0.00 3.69
285 286 0.609957 TACTCTTCCTCGCCGGTGAA 60.610 55.000 20.06 1.50 0.00 3.18
312 313 3.124636 CCTTCACTTCACGGGTTTTATCG 59.875 47.826 0.00 0.00 0.00 2.92
314 315 1.129811 CACTTCACGGGTTTTATCGCC 59.870 52.381 0.00 0.00 0.00 5.54
334 335 4.717629 CGCTCACGAGGACGGCAA 62.718 66.667 0.00 0.00 43.93 4.52
338 339 0.389817 CTCACGAGGACGGCAAATGA 60.390 55.000 0.00 0.00 44.46 2.57
346 347 1.065709 GGACGGCAAATGAAGGAGGTA 60.066 52.381 0.00 0.00 0.00 3.08
348 349 1.065418 ACGGCAAATGAAGGAGGTAGG 60.065 52.381 0.00 0.00 0.00 3.18
352 353 0.912486 AAATGAAGGAGGTAGGCGCT 59.088 50.000 7.64 0.00 0.00 5.92
372 373 4.016444 GCTGGAAGGGAATAACAATGACA 58.984 43.478 0.00 0.00 0.00 3.58
415 417 0.712380 TAGGTTTAGGTCCGGTCCCT 59.288 55.000 14.60 16.30 36.04 4.20
417 419 0.906282 GGTTTAGGTCCGGTCCCTCA 60.906 60.000 14.60 3.49 33.35 3.86
516 518 9.997482 GTAATTTGTTTGACTAGTTGAAACTCA 57.003 29.630 22.29 14.11 40.37 3.41
526 528 8.208224 TGACTAGTTGAAACTCACCTTGAAATA 58.792 33.333 0.00 0.00 40.37 1.40
538 540 8.571336 ACTCACCTTGAAATATATGCAAATAGC 58.429 33.333 0.00 0.00 45.96 2.97
551 553 4.503741 GCAAATAGCAACTCACCTTGAA 57.496 40.909 0.00 0.00 44.79 2.69
552 554 4.870363 GCAAATAGCAACTCACCTTGAAA 58.130 39.130 0.00 0.00 44.79 2.69
553 555 5.473039 GCAAATAGCAACTCACCTTGAAAT 58.527 37.500 0.00 0.00 44.79 2.17
554 556 6.620678 GCAAATAGCAACTCACCTTGAAATA 58.379 36.000 0.00 0.00 44.79 1.40
555 557 7.260603 GCAAATAGCAACTCACCTTGAAATAT 58.739 34.615 0.00 0.00 44.79 1.28
556 558 8.405531 GCAAATAGCAACTCACCTTGAAATATA 58.594 33.333 0.00 0.00 44.79 0.86
559 561 6.382869 AGCAACTCACCTTGAAATATATGC 57.617 37.500 0.00 0.00 0.00 3.14
560 562 5.887598 AGCAACTCACCTTGAAATATATGCA 59.112 36.000 0.00 0.00 0.00 3.96
561 563 6.377996 AGCAACTCACCTTGAAATATATGCAA 59.622 34.615 0.00 0.00 0.00 4.08
562 564 7.035004 GCAACTCACCTTGAAATATATGCAAA 58.965 34.615 0.00 0.00 0.00 3.68
563 565 7.707893 GCAACTCACCTTGAAATATATGCAAAT 59.292 33.333 0.00 0.00 0.00 2.32
581 583 1.333177 ATAGCACCGACTCCCTCATC 58.667 55.000 0.00 0.00 0.00 2.92
589 591 1.134965 CGACTCCCTCATCTGTGTTCC 60.135 57.143 0.00 0.00 0.00 3.62
596 598 0.541392 TCATCTGTGTTCCCGGATGG 59.459 55.000 0.73 0.00 44.75 3.51
788 792 0.835941 AGCATCACTCATCCCACCTC 59.164 55.000 0.00 0.00 0.00 3.85
986 997 5.865085 TCATGACACTAGGTGCTTAAGTTT 58.135 37.500 4.02 0.00 36.98 2.66
1157 1171 1.202580 CCTGAATCTCAAGGCCTACCG 60.203 57.143 5.16 0.00 42.76 4.02
1639 1659 4.913335 AATTAAGCCATGCATGAGACAG 57.087 40.909 28.31 11.71 0.00 3.51
1659 1691 5.846203 ACAGTGCATGCATTCTTTAACTTT 58.154 33.333 25.64 3.51 0.00 2.66
1662 1694 7.086376 CAGTGCATGCATTCTTTAACTTTACT 58.914 34.615 25.64 7.78 0.00 2.24
1665 1697 9.573133 GTGCATGCATTCTTTAACTTTACTTAT 57.427 29.630 25.64 0.00 0.00 1.73
1735 1768 4.660168 AGCTGAACAGAAGATCCAAACAT 58.340 39.130 5.97 0.00 0.00 2.71
1748 1781 3.826524 TCCAAACATCAAAGTGTAGCCA 58.173 40.909 0.00 0.00 0.00 4.75
1804 1837 7.308435 AGCAATGTAGTTGATGCTTTACTTTC 58.692 34.615 0.00 0.00 46.36 2.62
1805 1838 7.175641 AGCAATGTAGTTGATGCTTTACTTTCT 59.824 33.333 0.00 0.00 46.36 2.52
1806 1839 7.272084 GCAATGTAGTTGATGCTTTACTTTCTG 59.728 37.037 0.00 0.00 40.37 3.02
1809 1852 4.401925 AGTTGATGCTTTACTTTCTGGCT 58.598 39.130 0.00 0.00 0.00 4.75
1860 1903 2.167281 TGCACCACTTTAGCTTTTTGCA 59.833 40.909 0.00 0.00 45.94 4.08
1865 1908 3.245990 CCACTTTAGCTTTTTGCAAGTGC 59.754 43.478 0.00 5.78 46.02 4.40
1936 1982 1.173043 AATGGTACGGACGGACGTTA 58.827 50.000 11.73 0.96 46.25 3.18
1986 2032 1.408266 GGATGGTGTGGCGGTTTCTAT 60.408 52.381 0.00 0.00 0.00 1.98
2112 2158 2.353145 CTCCGGATTACGCGGTCG 60.353 66.667 12.47 6.45 42.52 4.79
2207 2253 1.489649 CTCCTGGACATCAGCTTCCAT 59.510 52.381 5.33 0.00 41.20 3.41
2264 2310 0.037326 ACACCACGGAGTACATGCTG 60.037 55.000 0.00 0.00 41.61 4.41
2289 2335 3.989698 CTGATGGCGTTCGAGCGGT 62.990 63.158 23.12 0.00 38.18 5.68
2460 2506 1.874345 GATGTCGAGGGACGTGGTGT 61.874 60.000 0.00 0.00 46.49 4.16
2665 2718 1.556911 ACAGTTCTACCAGGATGCCAG 59.443 52.381 0.00 0.00 31.97 4.85
2687 2740 5.004922 GCACCAGCTAGCTTATATCTAGG 57.995 47.826 16.46 13.13 37.91 3.02
2688 2741 4.679372 GCACCAGCTAGCTTATATCTAGGC 60.679 50.000 16.46 5.18 37.91 3.93
2689 2742 4.464244 CACCAGCTAGCTTATATCTAGGCA 59.536 45.833 16.46 0.00 35.30 4.75
2690 2743 5.128499 CACCAGCTAGCTTATATCTAGGCAT 59.872 44.000 16.46 0.00 35.30 4.40
2691 2744 5.362430 ACCAGCTAGCTTATATCTAGGCATC 59.638 44.000 16.46 0.00 35.30 3.91
2692 2745 5.598005 CCAGCTAGCTTATATCTAGGCATCT 59.402 44.000 16.46 0.00 35.30 2.90
2775 2828 2.851263 TCACGGTGTGGCTTTTATCT 57.149 45.000 8.17 0.00 33.87 1.98
2806 2859 6.486253 TTTAGTTGCATCAGTTCATGACTC 57.514 37.500 0.00 0.00 41.91 3.36
2817 2870 5.873164 TCAGTTCATGACTCTGATGACATTG 59.127 40.000 19.59 0.73 36.10 2.82
2826 2882 6.170846 ACTCTGATGACATTGCTCATATGA 57.829 37.500 5.07 5.07 30.62 2.15
2885 2941 2.232941 TCAACTTACCGGGTAGCTCTTG 59.767 50.000 6.32 7.68 0.00 3.02
2901 2957 0.916358 CTTGTCCTCATCCCTGGGGT 60.916 60.000 14.00 1.30 44.22 4.95
2908 2964 3.336997 TCCTCATCCCTGGGGTAGTATAG 59.663 52.174 14.00 0.00 44.22 1.31
2914 2970 5.280998 TCCCTGGGGTAGTATAGAATACC 57.719 47.826 14.00 5.44 40.69 2.73
2928 2984 8.907050 AGTATAGAATACCACTCCCTCTTATCT 58.093 37.037 0.00 0.00 0.00 1.98
3002 3061 2.037511 CCCACAACATGAACAAGGCAAT 59.962 45.455 0.00 0.00 0.00 3.56
3006 3065 4.992319 CACAACATGAACAAGGCAATCAAT 59.008 37.500 0.00 0.00 0.00 2.57
3007 3066 5.467399 CACAACATGAACAAGGCAATCAATT 59.533 36.000 0.00 0.00 0.00 2.32
3101 3165 3.788227 TCAACACTATTGAACCAGGCT 57.212 42.857 0.00 0.00 0.00 4.58
3138 3202 2.356382 CCGCAAAGGTTGTCACTTGTTA 59.644 45.455 0.00 0.00 34.51 2.41
3170 3235 2.031333 ACTAGTCTTGTCACCGACGAAC 60.031 50.000 0.00 0.00 34.95 3.95
3218 3283 4.715297 GGGAATCAGAGTCTAGGGTTACAA 59.285 45.833 0.00 0.00 0.00 2.41
3237 3302 7.603784 GGTTACAAGTTCTAATTCGGTTAGGAA 59.396 37.037 8.11 0.00 40.21 3.36
3239 3304 5.642491 ACAAGTTCTAATTCGGTTAGGAAGC 59.358 40.000 8.11 0.00 40.21 3.86
3240 3305 5.416271 AGTTCTAATTCGGTTAGGAAGCA 57.584 39.130 8.11 0.00 40.21 3.91
3253 3318 1.447838 GAAGCATCCTTCGGACGCA 60.448 57.895 3.68 0.00 43.97 5.24
3309 3374 2.672996 ACGTTGTGAGGCCATGGC 60.673 61.111 29.47 29.47 41.06 4.40
3347 3412 0.391966 GACATAACCGACCTAGGGGC 59.608 60.000 14.81 3.61 35.63 5.80
3373 3438 2.570302 GGTTAGCTCCTGGTAAGGTGAA 59.430 50.000 0.00 0.00 44.82 3.18
3441 3506 4.020617 CCGGCTGCTTCCTGGTCA 62.021 66.667 0.00 0.00 0.00 4.02
3504 3569 1.168714 GAAGCCGGTTCATGAAGCTT 58.831 50.000 29.27 27.12 45.97 3.74
3571 3636 2.060275 TCATCCCATGAAGCCTGCTAT 58.940 47.619 0.00 0.00 36.11 2.97
3587 3652 4.502105 TGCTATTGCAGGTTGATTCCTA 57.498 40.909 0.00 0.00 45.31 2.94
3660 3725 1.348036 GGACCAGGCTCTAACACAACT 59.652 52.381 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 71 1.582968 GCGTAGGACGGACAACTGA 59.417 57.895 0.70 0.00 42.82 3.41
152 153 0.108615 CTAGTGGGCGTGAGGTTCAG 60.109 60.000 0.00 0.00 0.00 3.02
155 156 1.764571 TTGCTAGTGGGCGTGAGGTT 61.765 55.000 0.00 0.00 34.52 3.50
183 184 4.838486 CCTCGTCGGAGTCAGCGC 62.838 72.222 0.00 0.00 38.70 5.92
224 225 1.616628 ATTTGGGACTCGAGCCCCT 60.617 57.895 33.46 14.42 45.40 4.79
245 246 2.026822 AGAACATGAGAGGCAAACCGAT 60.027 45.455 0.00 0.00 42.76 4.18
251 252 4.081420 GGAAGAGTAGAACATGAGAGGCAA 60.081 45.833 0.00 0.00 0.00 4.52
254 255 4.036262 CGAGGAAGAGTAGAACATGAGAGG 59.964 50.000 0.00 0.00 0.00 3.69
258 259 2.427453 GGCGAGGAAGAGTAGAACATGA 59.573 50.000 0.00 0.00 0.00 3.07
285 286 0.606401 CCCGTGAAGTGAAGGTGCAT 60.606 55.000 0.00 0.00 0.00 3.96
334 335 0.179000 CAGCGCCTACCTCCTTCATT 59.821 55.000 2.29 0.00 0.00 2.57
338 339 1.612442 TTCCAGCGCCTACCTCCTT 60.612 57.895 2.29 0.00 0.00 3.36
346 347 0.107165 GTTATTCCCTTCCAGCGCCT 60.107 55.000 2.29 0.00 0.00 5.52
348 349 1.459450 TTGTTATTCCCTTCCAGCGC 58.541 50.000 0.00 0.00 0.00 5.92
352 353 4.955450 CCATGTCATTGTTATTCCCTTCCA 59.045 41.667 0.00 0.00 0.00 3.53
362 363 2.679639 GCCCTCGTCCATGTCATTGTTA 60.680 50.000 0.00 0.00 0.00 2.41
480 482 9.409312 CTAGTCAAACAAATTACATGCAAATCA 57.591 29.630 0.00 0.00 0.00 2.57
482 484 9.762933 AACTAGTCAAACAAATTACATGCAAAT 57.237 25.926 0.00 0.00 0.00 2.32
492 494 7.973944 GGTGAGTTTCAACTAGTCAAACAAATT 59.026 33.333 22.92 9.76 39.88 1.82
496 498 5.741011 AGGTGAGTTTCAACTAGTCAAACA 58.259 37.500 22.92 8.75 43.79 2.83
540 542 8.571336 GCTATTTGCATATATTTCAAGGTGAGT 58.429 33.333 0.00 0.00 42.31 3.41
541 543 8.961294 GCTATTTGCATATATTTCAAGGTGAG 57.039 34.615 0.00 0.00 42.31 3.51
558 560 0.107654 AGGGAGTCGGTGCTATTTGC 60.108 55.000 0.00 0.00 43.25 3.68
559 561 1.207089 TGAGGGAGTCGGTGCTATTTG 59.793 52.381 0.00 0.00 0.00 2.32
560 562 1.568504 TGAGGGAGTCGGTGCTATTT 58.431 50.000 0.00 0.00 0.00 1.40
561 563 1.689273 GATGAGGGAGTCGGTGCTATT 59.311 52.381 0.00 0.00 0.00 1.73
562 564 1.133325 AGATGAGGGAGTCGGTGCTAT 60.133 52.381 0.00 0.00 0.00 2.97
563 565 0.259065 AGATGAGGGAGTCGGTGCTA 59.741 55.000 0.00 0.00 0.00 3.49
564 566 1.000993 AGATGAGGGAGTCGGTGCT 59.999 57.895 0.00 0.00 0.00 4.40
565 567 1.142748 CAGATGAGGGAGTCGGTGC 59.857 63.158 0.00 0.00 0.00 5.01
570 572 1.208293 GGGAACACAGATGAGGGAGTC 59.792 57.143 0.00 0.00 0.00 3.36
572 574 0.176680 CGGGAACACAGATGAGGGAG 59.823 60.000 0.00 0.00 0.00 4.30
788 792 0.109365 CCAGCACTCTGACAGAGACG 60.109 60.000 34.00 24.71 45.07 4.18
986 997 0.671472 CGCCATCTGAGTCACTTGCA 60.671 55.000 0.00 0.00 0.00 4.08
1275 1289 3.060615 ACGGCCGCTACGAACTCT 61.061 61.111 28.58 0.00 34.93 3.24
1371 1385 0.634465 GGAACCTCTCCCTCCTCTCT 59.366 60.000 0.00 0.00 38.44 3.10
1639 1659 7.873739 AAGTAAAGTTAAAGAATGCATGCAC 57.126 32.000 25.37 11.79 0.00 4.57
1709 1741 6.017109 TGTTTGGATCTTCTGTTCAGCTTTAC 60.017 38.462 0.00 0.00 0.00 2.01
1735 1768 4.469657 AGAACCATTTGGCTACACTTTGA 58.530 39.130 0.00 0.00 39.32 2.69
1797 1830 8.508883 TTTTTGTACTACAAGCCAGAAAGTAA 57.491 30.769 1.95 0.00 39.53 2.24
1835 1878 7.190256 GCAAAAAGCTAAAGTGGTGCACTTG 62.190 44.000 17.98 9.32 45.97 3.16
1837 1880 3.737972 GCAAAAAGCTAAAGTGGTGCACT 60.738 43.478 17.98 0.00 43.00 4.40
1838 1881 2.539688 GCAAAAAGCTAAAGTGGTGCAC 59.460 45.455 8.80 8.80 41.15 4.57
1839 1882 2.167281 TGCAAAAAGCTAAAGTGGTGCA 59.833 40.909 0.00 0.00 45.94 4.57
1840 1883 2.820330 TGCAAAAAGCTAAAGTGGTGC 58.180 42.857 0.00 0.00 45.94 5.01
1841 1884 4.268405 CACTTGCAAAAAGCTAAAGTGGTG 59.732 41.667 0.00 0.00 45.93 4.17
1842 1885 4.432712 CACTTGCAAAAAGCTAAAGTGGT 58.567 39.130 0.00 0.00 45.93 4.16
1845 1888 4.391405 AGCACTTGCAAAAAGCTAAAGT 57.609 36.364 15.72 0.00 45.94 2.66
1846 1889 5.922544 ACATAGCACTTGCAAAAAGCTAAAG 59.077 36.000 22.81 20.25 45.94 1.85
1847 1890 5.691305 CACATAGCACTTGCAAAAAGCTAAA 59.309 36.000 22.81 10.30 45.94 1.85
1848 1891 5.221880 CACATAGCACTTGCAAAAAGCTAA 58.778 37.500 22.81 12.05 45.94 3.09
1849 1892 4.797471 CACATAGCACTTGCAAAAAGCTA 58.203 39.130 21.83 21.83 45.94 3.32
1850 1893 3.645884 CACATAGCACTTGCAAAAAGCT 58.354 40.909 19.59 19.59 45.94 3.74
1851 1894 2.156310 GCACATAGCACTTGCAAAAAGC 59.844 45.455 0.00 4.92 45.16 3.51
1865 1908 6.016443 TCAGTGTGAGATCTATCAGCACATAG 60.016 42.308 15.00 11.40 42.22 2.23
1936 1982 0.674895 GTCCTCGTTCTGCTGCCAAT 60.675 55.000 0.00 0.00 0.00 3.16
1974 2020 2.737881 CCGGGGATAGAAACCGCCA 61.738 63.158 0.00 0.00 45.93 5.69
1975 2021 2.110420 CCGGGGATAGAAACCGCC 59.890 66.667 0.00 0.00 45.93 6.13
2039 2085 2.835431 CTCCGGCGGAGGATGTCT 60.835 66.667 41.24 0.00 45.43 3.41
2162 2208 2.125106 GTCCGGCTCCGCTTGAAT 60.125 61.111 0.00 0.00 38.24 2.57
2240 2286 0.818852 TGTACTCCGTGGTGTCGTCA 60.819 55.000 0.00 0.00 0.00 4.35
2264 2310 1.796796 GAACGCCATCAGGTTCAGC 59.203 57.895 0.00 0.00 41.60 4.26
2546 2599 2.548920 GCTCTTGAAGTAGGTGTGCACT 60.549 50.000 19.41 0.00 0.00 4.40
2630 2683 1.906990 ACTGTAGCACGGTGTAGACT 58.093 50.000 10.24 0.68 36.13 3.24
2665 2718 4.679372 GCCTAGATATAAGCTAGCTGGTGC 60.679 50.000 20.16 7.36 35.19 5.01
2806 2859 6.401153 CGACATCATATGAGCAATGTCATCAG 60.401 42.308 25.69 13.03 45.24 2.90
2817 2870 8.076714 TCATTTTTCTACGACATCATATGAGC 57.923 34.615 11.78 2.58 0.00 4.26
2885 2941 0.031010 ACTACCCCAGGGATGAGGAC 60.031 60.000 7.25 0.00 38.96 3.85
2979 3035 1.993956 CCTTGTTCATGTTGTGGGGA 58.006 50.000 0.00 0.00 0.00 4.81
3072 3136 5.705441 GGTTCAATAGTGTTGATGGACTGAA 59.295 40.000 2.90 0.00 0.00 3.02
3101 3165 1.757118 TGCGGTGGAAAAATCAAACCA 59.243 42.857 0.00 0.00 0.00 3.67
3170 3235 3.361977 CCTTCCGGCCCACAAACG 61.362 66.667 0.00 0.00 0.00 3.60
3218 3283 5.416271 TGCTTCCTAACCGAATTAGAACT 57.584 39.130 7.71 0.00 42.75 3.01
3253 3318 3.131577 TGGAGTACAAGACACGACAACTT 59.868 43.478 0.00 0.00 0.00 2.66
3309 3374 1.076777 ATGGGCCAATCAACTCGGG 60.077 57.895 11.89 0.00 0.00 5.14
3441 3506 2.037136 GCGCCAGCAGATCAACACT 61.037 57.895 0.00 0.00 44.35 3.55
3504 3569 6.653526 ACATCAACAATTCAAGAACATGGA 57.346 33.333 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.