Multiple sequence alignment - TraesCS6D01G162000

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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 TraesCS6D01G162000 chr6D 100.000 3139 0 0 1 3139 140191404 140188266 0.000000e+00 5797.0
1 TraesCS6D01G162000 chr6B 94.248 1530 69 13 693 2209 240308927 240307404 0.000000e+00 2320.0
2 TraesCS6D01G162000 chr6B 87.302 441 55 1 2700 3139 655262564 655262124 1.300000e-138 503.0
3 TraesCS6D01G162000 chr6B 81.425 393 43 11 302 687 240309427 240309058 8.510000e-76 294.0
4 TraesCS6D01G162000 chr6A 95.318 897 28 3 1404 2286 184739876 184738980 0.000000e+00 1411.0
5 TraesCS6D01G162000 chr6A 96.682 633 15 4 772 1401 184740910 184740281 0.000000e+00 1048.0
6 TraesCS6D01G162000 chr6A 85.116 692 70 18 5 685 184742084 184741415 0.000000e+00 676.0
7 TraesCS6D01G162000 chr6A 92.105 152 7 2 2282 2428 184736169 184736018 3.170000e-50 209.0
8 TraesCS6D01G162000 chr6A 97.674 43 1 0 690 732 184741286 184741244 1.210000e-09 75.0
9 TraesCS6D01G162000 chr4D 92.275 712 49 5 2426 3136 46114488 46115194 0.000000e+00 1005.0
10 TraesCS6D01G162000 chr4B 90.295 711 60 7 2427 3135 639484409 639485112 0.000000e+00 922.0
11 TraesCS6D01G162000 chr7B 90.042 713 65 6 2427 3136 558326392 558327101 0.000000e+00 918.0
12 TraesCS6D01G162000 chr7B 89.140 709 72 5 2427 3134 532205071 532204367 0.000000e+00 878.0
13 TraesCS6D01G162000 chr7B 92.157 51 4 0 1561 1611 526867534 526867584 4.340000e-09 73.1
14 TraesCS6D01G162000 chr3B 89.859 710 68 4 2428 3136 603493053 603493759 0.000000e+00 909.0
15 TraesCS6D01G162000 chr3B 92.453 159 9 3 2428 2585 755436636 755436792 1.130000e-54 224.0
16 TraesCS6D01G162000 chr1D 86.332 717 91 6 2422 3136 274956848 274956137 0.000000e+00 774.0
17 TraesCS6D01G162000 chr1D 86.689 601 69 9 2538 3136 42070 41479 0.000000e+00 656.0
18 TraesCS6D01G162000 chr5D 87.624 606 70 5 2427 3029 450225244 450225847 0.000000e+00 699.0
19 TraesCS6D01G162000 chr7D 92.157 51 4 0 1561 1611 498498127 498498177 4.340000e-09 73.1
20 TraesCS6D01G162000 chr7A 95.556 45 2 0 1567 1611 564281676 564281720 4.340000e-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 TraesCS6D01G162000 chr6D 140188266 140191404 3138 True 5797.0 5797 100.0000 1 3139 1 chr6D.!!$R1 3138
1 TraesCS6D01G162000 chr6B 240307404 240309427 2023 True 1307.0 2320 87.8365 302 2209 2 chr6B.!!$R2 1907
2 TraesCS6D01G162000 chr6A 184736018 184742084 6066 True 683.8 1411 93.3790 5 2428 5 chr6A.!!$R1 2423
3 TraesCS6D01G162000 chr4D 46114488 46115194 706 False 1005.0 1005 92.2750 2426 3136 1 chr4D.!!$F1 710
4 TraesCS6D01G162000 chr4B 639484409 639485112 703 False 922.0 922 90.2950 2427 3135 1 chr4B.!!$F1 708
5 TraesCS6D01G162000 chr7B 558326392 558327101 709 False 918.0 918 90.0420 2427 3136 1 chr7B.!!$F2 709
6 TraesCS6D01G162000 chr7B 532204367 532205071 704 True 878.0 878 89.1400 2427 3134 1 chr7B.!!$R1 707
7 TraesCS6D01G162000 chr3B 603493053 603493759 706 False 909.0 909 89.8590 2428 3136 1 chr3B.!!$F1 708
8 TraesCS6D01G162000 chr1D 274956137 274956848 711 True 774.0 774 86.3320 2422 3136 1 chr1D.!!$R2 714
9 TraesCS6D01G162000 chr1D 41479 42070 591 True 656.0 656 86.6890 2538 3136 1 chr1D.!!$R1 598
10 TraesCS6D01G162000 chr5D 450225244 450225847 603 False 699.0 699 87.6240 2427 3029 1 chr5D.!!$F1 602

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
543 556 0.107945 GCTCATGAAGGGCGTCTCTT 60.108 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2449 6150 0.963962 TCAGTTAAAGCCGGACGTCT 59.036 50.0 16.46 0.0 0.0 4.18 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
22 23 1.605710 GTGCAATCTGCTCAGTGTGTT 59.394 47.619 0.00 0.00 45.31 3.32
41 42 8.084073 AGTGTGTTGTAAATTGATTCATGAAGG 58.916 33.333 14.54 0.00 0.00 3.46
67 68 4.817517 ACACTAAAGGTCCAATGTCTACG 58.182 43.478 0.00 0.00 0.00 3.51
68 69 3.617263 CACTAAAGGTCCAATGTCTACGC 59.383 47.826 0.00 0.00 0.00 4.42
79 80 4.142622 CCAATGTCTACGCACATGTTCATT 60.143 41.667 0.00 0.00 37.07 2.57
95 96 9.599866 ACATGTTCATTACGAGATTTCTATCAA 57.400 29.630 0.00 0.00 32.95 2.57
106 107 7.437862 ACGAGATTTCTATCAAATCTTGAGCTC 59.562 37.037 22.77 6.82 44.94 4.09
107 108 7.437565 CGAGATTTCTATCAAATCTTGAGCTCA 59.562 37.037 13.74 13.74 44.94 4.26
112 113 8.571461 TTCTATCAAATCTTGAGCTCACAAAT 57.429 30.769 18.03 7.38 43.98 2.32
157 158 2.730382 AGGATCATGCATGCAACTCAA 58.270 42.857 26.68 8.83 0.00 3.02
173 174 3.936564 ACTCAAGTGAGAGCTTGGATTC 58.063 45.455 15.15 0.00 44.74 2.52
175 176 2.005451 CAAGTGAGAGCTTGGATTCCG 58.995 52.381 0.00 0.00 41.41 4.30
180 181 0.980231 AGAGCTTGGATTCCGCCTCT 60.980 55.000 11.61 11.61 0.00 3.69
181 182 0.753262 GAGCTTGGATTCCGCCTCTA 59.247 55.000 0.00 0.00 0.00 2.43
201 203 8.281212 CCTCTAGTGGCACTGTAAAAATTAAT 57.719 34.615 29.65 1.20 0.00 1.40
204 206 9.727859 TCTAGTGGCACTGTAAAAATTAATGTA 57.272 29.630 29.65 2.91 0.00 2.29
214 216 9.853555 CTGTAAAAATTAATGTAGATGGTGCAA 57.146 29.630 0.00 0.00 0.00 4.08
233 235 3.442977 GCAATGAGCAGAAGTGGAAAGAT 59.557 43.478 0.00 0.00 44.79 2.40
235 237 5.220815 GCAATGAGCAGAAGTGGAAAGATAG 60.221 44.000 0.00 0.00 44.79 2.08
238 240 2.507471 AGCAGAAGTGGAAAGATAGGGG 59.493 50.000 0.00 0.00 0.00 4.79
240 242 2.239654 CAGAAGTGGAAAGATAGGGGCA 59.760 50.000 0.00 0.00 0.00 5.36
245 247 1.839994 TGGAAAGATAGGGGCAGTCAG 59.160 52.381 0.00 0.00 0.00 3.51
259 261 2.554142 CAGTCAGTGCAGTTTGTCTGA 58.446 47.619 11.83 6.34 46.27 3.27
260 262 3.136763 CAGTCAGTGCAGTTTGTCTGAT 58.863 45.455 11.83 0.00 46.27 2.90
261 263 3.059120 CAGTCAGTGCAGTTTGTCTGATG 60.059 47.826 11.83 6.20 46.27 3.07
263 265 2.158769 TCAGTGCAGTTTGTCTGATGGT 60.159 45.455 0.00 0.00 46.27 3.55
264 266 3.070878 TCAGTGCAGTTTGTCTGATGGTA 59.929 43.478 0.00 0.00 46.27 3.25
265 267 4.005650 CAGTGCAGTTTGTCTGATGGTAT 58.994 43.478 0.00 0.00 46.27 2.73
266 268 5.046663 TCAGTGCAGTTTGTCTGATGGTATA 60.047 40.000 0.00 0.00 46.27 1.47
268 270 4.572389 GTGCAGTTTGTCTGATGGTATAGG 59.428 45.833 0.00 0.00 46.27 2.57
276 279 9.046296 GTTTGTCTGATGGTATAGGAGTTTATG 57.954 37.037 0.00 0.00 0.00 1.90
279 282 9.078990 TGTCTGATGGTATAGGAGTTTATGTAG 57.921 37.037 0.00 0.00 0.00 2.74
300 303 2.554462 GGTTCTTCTGCTTTGGTCCTTC 59.446 50.000 0.00 0.00 0.00 3.46
350 354 1.537202 GCTCTGGCTTGTCGTGAATTT 59.463 47.619 0.00 0.00 35.22 1.82
355 359 2.293122 TGGCTTGTCGTGAATTTCTTGG 59.707 45.455 0.00 0.00 0.00 3.61
357 361 2.922335 GCTTGTCGTGAATTTCTTGGCC 60.922 50.000 0.00 0.00 0.00 5.36
359 363 3.410631 TGTCGTGAATTTCTTGGCCTA 57.589 42.857 3.32 0.00 0.00 3.93
370 374 0.804989 CTTGGCCTAGCAAAAGACCG 59.195 55.000 3.32 0.00 0.00 4.79
372 376 2.750888 GGCCTAGCAAAAGACCGCG 61.751 63.158 0.00 0.00 0.00 6.46
415 419 6.567050 TCGCTTCGGATTGTAAGTTAGTTAT 58.433 36.000 0.00 0.00 0.00 1.89
453 457 6.502863 AGGTACTTTAGGACCCATTAGTTCAA 59.497 38.462 7.55 0.00 36.27 2.69
482 495 6.206438 TCAACAGGACGATGATTGATTTTGAA 59.794 34.615 0.00 0.00 0.00 2.69
483 496 6.764308 ACAGGACGATGATTGATTTTGAAT 57.236 33.333 0.00 0.00 0.00 2.57
486 499 6.039047 CAGGACGATGATTGATTTTGAATCCT 59.961 38.462 0.00 0.00 31.84 3.24
487 500 6.039047 AGGACGATGATTGATTTTGAATCCTG 59.961 38.462 0.00 0.00 30.55 3.86
488 501 6.183360 GGACGATGATTGATTTTGAATCCTGT 60.183 38.462 0.00 0.00 0.00 4.00
489 502 6.789262 ACGATGATTGATTTTGAATCCTGTC 58.211 36.000 0.00 0.00 0.00 3.51
490 503 5.905733 CGATGATTGATTTTGAATCCTGTCG 59.094 40.000 0.00 0.00 0.00 4.35
491 504 6.238184 CGATGATTGATTTTGAATCCTGTCGA 60.238 38.462 0.00 0.00 34.05 4.20
492 505 7.519488 CGATGATTGATTTTGAATCCTGTCGAT 60.519 37.037 0.00 0.00 34.05 3.59
493 506 6.788243 TGATTGATTTTGAATCCTGTCGATG 58.212 36.000 0.00 0.00 0.00 3.84
494 507 6.598850 TGATTGATTTTGAATCCTGTCGATGA 59.401 34.615 0.00 0.00 0.00 2.92
495 508 7.283807 TGATTGATTTTGAATCCTGTCGATGAT 59.716 33.333 0.00 0.00 0.00 2.45
496 509 6.609237 TGATTTTGAATCCTGTCGATGATC 57.391 37.500 0.00 0.00 0.00 2.92
497 510 6.351711 TGATTTTGAATCCTGTCGATGATCT 58.648 36.000 0.00 0.00 0.00 2.75
498 511 7.500141 TGATTTTGAATCCTGTCGATGATCTA 58.500 34.615 0.00 0.00 0.00 1.98
499 512 7.986889 TGATTTTGAATCCTGTCGATGATCTAA 59.013 33.333 0.00 0.00 0.00 2.10
500 513 8.737168 ATTTTGAATCCTGTCGATGATCTAAA 57.263 30.769 0.00 0.00 0.00 1.85
501 514 8.560355 TTTTGAATCCTGTCGATGATCTAAAA 57.440 30.769 0.00 1.63 0.00 1.52
502 515 8.560355 TTTGAATCCTGTCGATGATCTAAAAA 57.440 30.769 0.00 0.00 0.00 1.94
543 556 0.107945 GCTCATGAAGGGCGTCTCTT 60.108 55.000 0.00 0.00 0.00 2.85
580 593 5.050431 GCACAATTTAGCGAAACATGGTTTT 60.050 36.000 0.00 0.00 0.00 2.43
586 599 9.968870 AATTTAGCGAAACATGGTTTTAACTTA 57.031 25.926 0.00 0.00 0.00 2.24
593 613 7.534239 CGAAACATGGTTTTAACTTAGAAGAGC 59.466 37.037 0.00 0.00 0.00 4.09
634 654 1.761449 ACCCGCATGATGCAAATGTA 58.239 45.000 18.47 0.00 45.36 2.29
678 698 4.889409 TGATCAATAGAAGCATGTTTCCCC 59.111 41.667 17.56 0.00 0.00 4.81
771 1232 2.919602 TCCTGGCTAATGAAGAGGGTTT 59.080 45.455 0.00 0.00 0.00 3.27
806 1270 9.598517 GCTCCATTTTTCATTTCCACATATTTA 57.401 29.630 0.00 0.00 0.00 1.40
827 1291 1.710816 TTTGCGGGGATTTCCACTTT 58.289 45.000 0.00 0.00 37.25 2.66
939 1404 3.121030 CCCACTGCGAGAAAGGCG 61.121 66.667 0.00 0.00 0.00 5.52
1032 1497 1.355971 ACATGTCCATGCGACGTTAC 58.644 50.000 7.18 0.00 45.23 2.50
1110 1575 2.658593 CCGGCGCTCCTCGTATTG 60.659 66.667 7.64 0.00 41.07 1.90
1410 2277 2.103263 GGTAAGCCATCGTCAAGAGGAT 59.897 50.000 0.00 0.00 36.47 3.24
1453 2322 2.254546 TTGGCTCACATGAAGTCGTT 57.745 45.000 0.00 0.00 0.00 3.85
1650 2531 4.060038 CGAAGTACCCCACGGCGT 62.060 66.667 6.77 6.77 0.00 5.68
1691 2572 4.338539 AGCGTCGCGGAGTCGTTT 62.339 61.111 12.30 0.00 38.89 3.60
1862 2743 1.144057 GATCGACCGGCTCAATGGT 59.856 57.895 0.00 0.00 42.42 3.55
1958 2839 2.747686 GGGCTGGAGAACGTGGAA 59.252 61.111 0.00 0.00 0.00 3.53
2154 3035 0.807667 ATGATTCGTCCGTCTGCTGC 60.808 55.000 0.00 0.00 0.00 5.25
2309 6005 9.793259 TCTATAGTTGATCATATTTTTCACCCC 57.207 33.333 0.00 0.00 0.00 4.95
2371 6071 7.582667 AAAGGCCGAAAGCAATATATTAAGT 57.417 32.000 0.00 0.00 46.50 2.24
2379 6079 8.604035 CGAAAGCAATATATTAAGTGTCACAGT 58.396 33.333 5.62 0.00 0.00 3.55
2380 6080 9.922305 GAAAGCAATATATTAAGTGTCACAGTC 57.078 33.333 5.62 0.00 0.00 3.51
2382 6082 7.796054 AGCAATATATTAAGTGTCACAGTCCT 58.204 34.615 5.62 0.00 0.00 3.85
2384 6084 9.542462 GCAATATATTAAGTGTCACAGTCCTTA 57.458 33.333 5.62 0.00 0.00 2.69
2390 6091 3.454375 AGTGTCACAGTCCTTACAAACG 58.546 45.455 5.62 0.00 0.00 3.60
2398 6099 2.364324 AGTCCTTACAAACGCTCTCACA 59.636 45.455 0.00 0.00 0.00 3.58
2408 6109 2.139118 ACGCTCTCACAGAAAAGAAGC 58.861 47.619 0.00 0.00 0.00 3.86
2451 6152 5.618056 TTTTAGAACGAAGACGCTAGAGA 57.382 39.130 0.00 0.00 43.96 3.10
2479 6180 5.279056 CCGGCTTTAACTGAATAAAACCCAA 60.279 40.000 0.00 0.00 30.58 4.12
2495 6196 0.881118 CCAAAACAGGCAGCGTACAT 59.119 50.000 0.00 0.00 0.00 2.29
2568 6270 2.899900 GAGGGGAGCAAGTTTTGGATTT 59.100 45.455 0.00 0.00 0.00 2.17
2570 6272 2.632512 GGGGAGCAAGTTTTGGATTTCA 59.367 45.455 0.00 0.00 0.00 2.69
2594 6296 0.669318 CGTAGCCGGCTGAAACAGAA 60.669 55.000 38.98 13.89 32.44 3.02
2698 6403 0.387367 GACGAAGACGAGCAAGAGCA 60.387 55.000 0.00 0.00 42.55 4.26
2761 6466 1.128136 CACTGCTGCAAGAAGATGACG 59.872 52.381 3.02 0.00 45.09 4.35
2824 6529 6.472887 TCCCTCAATAGTAAGTTTGTTCCTG 58.527 40.000 0.00 0.00 0.00 3.86
2878 6584 0.878523 AACACCACATGACACGTCGG 60.879 55.000 0.00 0.00 0.00 4.79
3079 6787 0.793861 GCGTTTGGCTATGTTGACGA 59.206 50.000 0.00 0.00 39.11 4.20
3098 6806 2.011222 GAACGTGGGAAGTTTGTCACA 58.989 47.619 0.00 0.00 31.14 3.58
3107 6815 3.119495 GGAAGTTTGTCACAACACAGCTT 60.119 43.478 0.00 0.00 34.35 3.74
3112 6820 0.304705 GTCACAACACAGCTTCCACG 59.695 55.000 0.00 0.00 0.00 4.94
3117 6825 2.687935 ACAACACAGCTTCCACGAAAAT 59.312 40.909 0.00 0.00 0.00 1.82
3124 6832 6.077838 CACAGCTTCCACGAAAATACTTTAC 58.922 40.000 0.00 0.00 0.00 2.01
3136 6844 3.821421 ATACTTTACTCTTGAGGGGCG 57.179 47.619 2.55 0.00 0.00 6.13
3137 6845 1.640917 ACTTTACTCTTGAGGGGCGA 58.359 50.000 2.55 0.00 0.00 5.54
3138 6846 1.275573 ACTTTACTCTTGAGGGGCGAC 59.724 52.381 2.55 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 8.291740 TCATGAATCAATTTACAACACACTGAG 58.708 33.333 0.00 0.00 0.00 3.35
22 23 6.072230 TGTTCGCCTTCATGAATCAATTTACA 60.072 34.615 8.96 5.42 0.00 2.41
41 42 2.812011 ACATTGGACCTTTAGTGTTCGC 59.188 45.455 0.00 0.00 0.00 4.70
67 68 6.111768 AGAAATCTCGTAATGAACATGTGC 57.888 37.500 0.00 0.00 0.00 4.57
68 69 9.034544 TGATAGAAATCTCGTAATGAACATGTG 57.965 33.333 0.00 0.00 32.93 3.21
79 80 8.417106 AGCTCAAGATTTGATAGAAATCTCGTA 58.583 33.333 9.50 0.26 43.87 3.43
95 96 4.660168 ACAGGATTTGTGAGCTCAAGATT 58.340 39.130 20.19 6.35 38.99 2.40
157 158 0.107945 GCGGAATCCAAGCTCTCACT 60.108 55.000 0.00 0.00 0.00 3.41
180 181 9.727859 TCTACATTAATTTTTACAGTGCCACTA 57.272 29.630 0.00 0.00 0.00 2.74
181 182 8.630054 TCTACATTAATTTTTACAGTGCCACT 57.370 30.769 0.00 0.00 0.00 4.00
188 190 9.853555 TTGCACCATCTACATTAATTTTTACAG 57.146 29.630 0.00 0.00 0.00 2.74
196 198 6.323203 GCTCATTGCACCATCTACATTAAT 57.677 37.500 0.00 0.00 42.31 1.40
214 216 4.141528 CCCTATCTTTCCACTTCTGCTCAT 60.142 45.833 0.00 0.00 0.00 2.90
226 228 1.840635 ACTGACTGCCCCTATCTTTCC 59.159 52.381 0.00 0.00 0.00 3.13
233 235 1.127567 AACTGCACTGACTGCCCCTA 61.128 55.000 0.00 0.00 46.51 3.53
235 237 1.529244 AAACTGCACTGACTGCCCC 60.529 57.895 0.00 0.00 46.51 5.80
240 242 2.988010 TCAGACAAACTGCACTGACT 57.012 45.000 0.00 0.00 45.38 3.41
245 247 4.572389 CCTATACCATCAGACAAACTGCAC 59.428 45.833 0.00 0.00 45.38 4.57
255 257 8.232412 ACCTACATAAACTCCTATACCATCAGA 58.768 37.037 0.00 0.00 0.00 3.27
257 259 8.792830 AACCTACATAAACTCCTATACCATCA 57.207 34.615 0.00 0.00 0.00 3.07
258 260 9.091220 AGAACCTACATAAACTCCTATACCATC 57.909 37.037 0.00 0.00 0.00 3.51
259 261 9.448587 AAGAACCTACATAAACTCCTATACCAT 57.551 33.333 0.00 0.00 0.00 3.55
260 262 8.849543 AAGAACCTACATAAACTCCTATACCA 57.150 34.615 0.00 0.00 0.00 3.25
261 263 9.145442 AGAAGAACCTACATAAACTCCTATACC 57.855 37.037 0.00 0.00 0.00 2.73
263 265 8.639761 GCAGAAGAACCTACATAAACTCCTATA 58.360 37.037 0.00 0.00 0.00 1.31
264 266 7.345914 AGCAGAAGAACCTACATAAACTCCTAT 59.654 37.037 0.00 0.00 0.00 2.57
265 267 6.668283 AGCAGAAGAACCTACATAAACTCCTA 59.332 38.462 0.00 0.00 0.00 2.94
266 268 5.485708 AGCAGAAGAACCTACATAAACTCCT 59.514 40.000 0.00 0.00 0.00 3.69
268 270 7.361286 CCAAAGCAGAAGAACCTACATAAACTC 60.361 40.741 0.00 0.00 0.00 3.01
276 279 3.075148 GGACCAAAGCAGAAGAACCTAC 58.925 50.000 0.00 0.00 0.00 3.18
279 282 2.278332 AGGACCAAAGCAGAAGAACC 57.722 50.000 0.00 0.00 0.00 3.62
300 303 2.124570 CGGCTCAACCATCCCAGG 60.125 66.667 0.00 0.00 39.03 4.45
350 354 1.610624 CGGTCTTTTGCTAGGCCAAGA 60.611 52.381 5.01 0.21 40.01 3.02
355 359 2.033194 ACGCGGTCTTTTGCTAGGC 61.033 57.895 12.47 0.00 0.00 3.93
357 361 1.132640 GCACGCGGTCTTTTGCTAG 59.867 57.895 12.47 0.00 32.00 3.42
359 363 2.591715 AGCACGCGGTCTTTTGCT 60.592 55.556 12.47 12.89 40.53 3.91
370 374 0.026803 CTTTATCCGCTGAAGCACGC 59.973 55.000 2.79 0.00 42.21 5.34
372 376 2.219674 CGATCTTTATCCGCTGAAGCAC 59.780 50.000 2.79 0.00 42.21 4.40
415 419 9.444600 GTCCTAAAGTACCTTTGTTGATATCAA 57.555 33.333 14.23 14.23 35.21 2.57
435 439 7.206789 TGATCATTGAACTAATGGGTCCTAA 57.793 36.000 0.00 0.00 45.05 2.69
453 457 5.027293 TCAATCATCGTCCTGTTGATCAT 57.973 39.130 0.00 0.00 36.27 2.45
501 514 7.056006 AGCAAAAGGACAGGATTCAAATTTTT 58.944 30.769 0.00 0.00 0.00 1.94
502 515 6.594744 AGCAAAAGGACAGGATTCAAATTTT 58.405 32.000 0.00 0.00 0.00 1.82
503 516 6.178607 AGCAAAAGGACAGGATTCAAATTT 57.821 33.333 0.00 0.00 0.00 1.82
504 517 5.305128 TGAGCAAAAGGACAGGATTCAAATT 59.695 36.000 0.00 0.00 0.00 1.82
505 518 4.834496 TGAGCAAAAGGACAGGATTCAAAT 59.166 37.500 0.00 0.00 0.00 2.32
506 519 4.214310 TGAGCAAAAGGACAGGATTCAAA 58.786 39.130 0.00 0.00 0.00 2.69
507 520 3.831323 TGAGCAAAAGGACAGGATTCAA 58.169 40.909 0.00 0.00 0.00 2.69
508 521 3.507162 TGAGCAAAAGGACAGGATTCA 57.493 42.857 0.00 0.00 0.00 2.57
509 522 4.012374 TCATGAGCAAAAGGACAGGATTC 58.988 43.478 0.00 0.00 0.00 2.52
510 523 4.038271 TCATGAGCAAAAGGACAGGATT 57.962 40.909 0.00 0.00 0.00 3.01
511 524 3.726557 TCATGAGCAAAAGGACAGGAT 57.273 42.857 0.00 0.00 0.00 3.24
512 525 3.415212 CTTCATGAGCAAAAGGACAGGA 58.585 45.455 0.00 0.00 0.00 3.86
513 526 2.490903 CCTTCATGAGCAAAAGGACAGG 59.509 50.000 4.60 0.00 41.78 4.00
514 527 2.490903 CCCTTCATGAGCAAAAGGACAG 59.509 50.000 11.32 0.00 41.78 3.51
517 530 1.549203 GCCCTTCATGAGCAAAAGGA 58.451 50.000 11.32 0.00 41.78 3.36
520 533 0.881118 GACGCCCTTCATGAGCAAAA 59.119 50.000 6.28 0.00 0.00 2.44
543 556 2.346766 ATTGTGCGCCTCCATATTGA 57.653 45.000 4.18 0.00 0.00 2.57
580 593 1.814394 TGGCGACGCTCTTCTAAGTTA 59.186 47.619 20.77 0.00 0.00 2.24
586 599 2.992114 AGGTGGCGACGCTCTTCT 60.992 61.111 20.77 9.46 41.78 2.85
634 654 9.246670 TGATCATTCATCAAGTTTACAGGAATT 57.753 29.630 0.00 0.00 38.68 2.17
654 674 5.537674 GGGGAAACATGCTTCTATTGATCAT 59.462 40.000 8.66 0.00 0.00 2.45
687 708 3.012518 GGTCATGATTGGTTGGAGAGTG 58.987 50.000 0.00 0.00 0.00 3.51
688 709 2.025887 GGGTCATGATTGGTTGGAGAGT 60.026 50.000 0.00 0.00 0.00 3.24
741 1202 0.107017 ATTAGCCAGGATGCAGCGTT 60.107 50.000 0.00 0.00 31.97 4.84
771 1232 2.108075 TGAAAAATGGAGCCTGTCAGGA 59.892 45.455 23.77 1.24 37.67 3.86
806 1270 1.937191 AGTGGAAATCCCCGCAAAAT 58.063 45.000 0.00 0.00 39.12 1.82
939 1404 2.582728 TTTCATCGATGGCCATTTGC 57.417 45.000 21.84 6.23 40.16 3.68
1032 1497 1.730902 CAGGACGATGATAGGCGCG 60.731 63.158 0.00 0.00 0.00 6.86
1107 1572 3.310860 GACGGTGGAGTCGCCCAAT 62.311 63.158 0.00 0.00 40.35 3.16
1433 2302 2.479566 ACGACTTCATGTGAGCCAAT 57.520 45.000 0.00 0.00 0.00 3.16
1674 2555 4.338539 AAACGACTCCGCGACGCT 62.339 61.111 19.02 0.00 39.95 5.07
1931 2812 2.046411 TCCAGCCCGTACGACGTA 60.046 61.111 18.76 2.97 40.58 3.57
1932 2813 3.437795 CTCCAGCCCGTACGACGT 61.438 66.667 18.76 5.52 40.58 4.34
2170 3051 5.982324 ACGATCACATTTGATGATTCGATG 58.018 37.500 9.02 0.00 42.95 3.84
2306 6002 7.425606 CCTATCAAAAATGAAAGAATACGGGG 58.574 38.462 0.00 0.00 0.00 5.73
2371 6071 2.159014 AGCGTTTGTAAGGACTGTGACA 60.159 45.455 0.00 0.00 0.00 3.58
2379 6079 2.626266 TCTGTGAGAGCGTTTGTAAGGA 59.374 45.455 0.00 0.00 0.00 3.36
2380 6080 3.026630 TCTGTGAGAGCGTTTGTAAGG 57.973 47.619 0.00 0.00 0.00 2.69
2382 6082 5.113383 TCTTTTCTGTGAGAGCGTTTGTAA 58.887 37.500 0.00 0.00 0.00 2.41
2384 6084 3.531538 TCTTTTCTGTGAGAGCGTTTGT 58.468 40.909 0.00 0.00 0.00 2.83
2385 6085 4.521943 CTTCTTTTCTGTGAGAGCGTTTG 58.478 43.478 0.00 0.00 0.00 2.93
2386 6086 3.002759 GCTTCTTTTCTGTGAGAGCGTTT 59.997 43.478 0.00 0.00 0.00 3.60
2390 6091 4.752101 TGTAAGCTTCTTTTCTGTGAGAGC 59.248 41.667 0.00 0.00 0.00 4.09
2398 6099 8.414629 AGAATTTGGATGTAAGCTTCTTTTCT 57.585 30.769 0.00 0.00 0.00 2.52
2449 6150 0.963962 TCAGTTAAAGCCGGACGTCT 59.036 50.000 16.46 0.00 0.00 4.18
2451 6152 2.467566 ATTCAGTTAAAGCCGGACGT 57.532 45.000 5.05 0.00 0.00 4.34
2479 6180 1.001974 TCTCATGTACGCTGCCTGTTT 59.998 47.619 0.00 0.00 0.00 2.83
2495 6196 6.871492 TGATGCGTTGTAAGACTTTATTCTCA 59.129 34.615 0.00 0.00 0.00 3.27
2761 6466 3.307674 TGCTGACGTGATTTTCAAATGC 58.692 40.909 0.00 0.00 0.00 3.56
2824 6529 1.952296 CTCTGGGCACTTTGGCATATC 59.048 52.381 1.86 0.00 45.76 1.63
3079 6787 2.116827 TGTGACAAACTTCCCACGTT 57.883 45.000 0.00 0.00 32.58 3.99
3098 6806 4.134563 AGTATTTTCGTGGAAGCTGTGTT 58.865 39.130 0.00 0.00 0.00 3.32
3107 6815 6.872020 CCTCAAGAGTAAAGTATTTTCGTGGA 59.128 38.462 0.00 0.00 40.09 4.02
3112 6820 5.064834 CGCCCCTCAAGAGTAAAGTATTTTC 59.935 44.000 0.00 0.00 40.09 2.29
3117 6825 2.494870 GTCGCCCCTCAAGAGTAAAGTA 59.505 50.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.