Multiple sequence alignment - TraesCS4A01G187900

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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 TraesCS4A01G187900 chr4A 100.000 4141 0 0 1 4141 466924867 466929007 0.000000e+00 7648
1 TraesCS4A01G187900 chr4B 94.594 3422 124 21 744 4135 171028959 171025569 0.000000e+00 5238
2 TraesCS4A01G187900 chr4B 80.800 500 57 19 3 484 171090248 171089770 5.090000e-94 355
3 TraesCS4A01G187900 chr4B 85.024 207 20 9 530 732 171089699 171089500 2.520000e-47 200
4 TraesCS4A01G187900 chr4D 94.060 3064 122 31 4 3029 109913116 109910075 0.000000e+00 4595
5 TraesCS4A01G187900 chr4D 94.571 700 27 6 3383 4071 109909437 109908738 0.000000e+00 1072
6 TraesCS4A01G187900 chr4D 96.538 260 7 2 3025 3284 109910052 109909795 2.960000e-116 429
7 TraesCS4A01G187900 chr5D 83.959 1066 133 25 1159 2192 242356809 242357868 0.000000e+00 987
8 TraesCS4A01G187900 chr5A 87.814 837 95 6 1159 1991 310874921 310874088 0.000000e+00 974
9 TraesCS4A01G187900 chr5B 87.694 837 96 6 1159 1991 259538264 259539097 0.000000e+00 968
10 TraesCS4A01G187900 chr1A 83.413 832 134 4 1159 1988 500343352 500342523 0.000000e+00 769
11 TraesCS4A01G187900 chr1D 83.562 803 130 2 1187 1988 404970783 404969982 0.000000e+00 750
12 TraesCS4A01G187900 chr1B 83.188 803 133 2 1187 1988 544726890 544726089 0.000000e+00 734
13 TraesCS4A01G187900 chr3A 87.902 529 64 0 1159 1687 579552998 579553526 1.260000e-174 623
14 TraesCS4A01G187900 chr3A 77.654 179 40 0 2294 2472 579554290 579554468 4.380000e-20 110
15 TraesCS4A01G187900 chr6B 80.132 302 54 6 1643 1941 717076325 717076027 1.940000e-53 220


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 TraesCS4A01G187900 chr4A 466924867 466929007 4140 False 7648.0 7648 100.000000 1 4141 1 chr4A.!!$F1 4140
1 TraesCS4A01G187900 chr4B 171025569 171028959 3390 True 5238.0 5238 94.594000 744 4135 1 chr4B.!!$R1 3391
2 TraesCS4A01G187900 chr4B 171089500 171090248 748 True 277.5 355 82.912000 3 732 2 chr4B.!!$R2 729
3 TraesCS4A01G187900 chr4D 109908738 109913116 4378 True 2032.0 4595 95.056333 4 4071 3 chr4D.!!$R1 4067
4 TraesCS4A01G187900 chr5D 242356809 242357868 1059 False 987.0 987 83.959000 1159 2192 1 chr5D.!!$F1 1033
5 TraesCS4A01G187900 chr5A 310874088 310874921 833 True 974.0 974 87.814000 1159 1991 1 chr5A.!!$R1 832
6 TraesCS4A01G187900 chr5B 259538264 259539097 833 False 968.0 968 87.694000 1159 1991 1 chr5B.!!$F1 832
7 TraesCS4A01G187900 chr1A 500342523 500343352 829 True 769.0 769 83.413000 1159 1988 1 chr1A.!!$R1 829
8 TraesCS4A01G187900 chr1D 404969982 404970783 801 True 750.0 750 83.562000 1187 1988 1 chr1D.!!$R1 801
9 TraesCS4A01G187900 chr1B 544726089 544726890 801 True 734.0 734 83.188000 1187 1988 1 chr1B.!!$R1 801
10 TraesCS4A01G187900 chr3A 579552998 579554468 1470 False 366.5 623 82.778000 1159 2472 2 chr3A.!!$F1 1313

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
820 873 0.037303 TGAGGAAGCAAGGGAGCAAG 59.963 55.0 0.00 0.0 36.85 4.01 F
981 1058 1.033746 CGGTTCTCCATGCATGCCTT 61.034 55.0 21.69 0.0 0.00 4.35 F
2078 2382 0.321564 TTGAGTTGCCAGATCACCCG 60.322 55.0 0.00 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2023 2305 1.210478 AGGCCATAAGCTTCGACACAT 59.790 47.619 5.01 0.0 43.05 3.21 R
2273 2583 2.957680 TGAAAGCACACACACCATCAAT 59.042 40.909 0.00 0.0 0.00 2.57 R
3340 3684 0.250901 ATGTGCAGGTGGGAGACAAC 60.251 55.000 0.00 0.0 36.91 3.32 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
53 57 7.823310 AGATAGATGAATGCCTGCTAAATGTAG 59.177 37.037 0.00 0.00 0.00 2.74
119 123 3.364764 GCTTTTGCGCAGGATGATCTATC 60.365 47.826 11.31 0.00 34.25 2.08
214 219 6.102663 GGTTTACGATGAGAGCTGCATATAT 58.897 40.000 1.02 0.00 0.00 0.86
215 220 6.591834 GGTTTACGATGAGAGCTGCATATATT 59.408 38.462 1.02 0.00 0.00 1.28
216 221 7.412346 GGTTTACGATGAGAGCTGCATATATTG 60.412 40.741 1.02 0.00 0.00 1.90
217 222 5.144692 ACGATGAGAGCTGCATATATTGT 57.855 39.130 1.02 0.00 0.00 2.71
218 223 6.272822 ACGATGAGAGCTGCATATATTGTA 57.727 37.500 1.02 0.00 0.00 2.41
219 224 6.328714 ACGATGAGAGCTGCATATATTGTAG 58.671 40.000 1.02 0.00 40.70 2.74
220 225 6.151817 ACGATGAGAGCTGCATATATTGTAGA 59.848 38.462 1.02 0.00 40.21 2.59
221 226 7.147932 ACGATGAGAGCTGCATATATTGTAGAT 60.148 37.037 1.02 1.87 40.21 1.98
222 227 7.705752 CGATGAGAGCTGCATATATTGTAGATT 59.294 37.037 1.02 0.00 40.21 2.40
228 233 9.429359 GAGCTGCATATATTGTAGATTTGTAGT 57.571 33.333 1.02 0.00 40.21 2.73
255 260 2.262211 GTCTCATGCGAAATTTTGGCC 58.738 47.619 12.72 0.00 33.01 5.36
271 276 1.273267 TGGCCAGGTGTCTCTAGTCAT 60.273 52.381 0.00 0.00 0.00 3.06
284 289 9.593134 GTGTCTCTAGTCATTTCTCAACATAAT 57.407 33.333 0.00 0.00 0.00 1.28
291 296 8.037382 AGTCATTTCTCAACATAATCACTGTG 57.963 34.615 0.17 0.17 0.00 3.66
294 299 9.500785 TCATTTCTCAACATAATCACTGTGTAA 57.499 29.630 7.79 0.00 0.00 2.41
298 303 9.936759 TTCTCAACATAATCACTGTGTAATACA 57.063 29.630 7.79 0.00 37.78 2.29
315 320 6.486657 TGTAATACAGCCATCTTATTTGGAGC 59.513 38.462 0.00 0.00 36.26 4.70
400 421 3.864003 GCGTGGAGGATTACTCTGTAAAC 59.136 47.826 0.00 0.00 45.83 2.01
401 422 4.430908 CGTGGAGGATTACTCTGTAAACC 58.569 47.826 8.19 8.19 45.83 3.27
412 433 9.685828 GATTACTCTGTAAACCATGTAGAGATC 57.314 37.037 0.00 0.00 38.53 2.75
420 441 7.706607 TGTAAACCATGTAGAGATCTTGAATCG 59.293 37.037 0.00 0.00 0.00 3.34
427 448 6.556212 TGTAGAGATCTTGAATCGTCAGAAC 58.444 40.000 0.00 0.00 34.49 3.01
429 450 5.649557 AGAGATCTTGAATCGTCAGAACAG 58.350 41.667 0.00 0.00 34.49 3.16
430 451 5.417266 AGAGATCTTGAATCGTCAGAACAGA 59.583 40.000 0.00 0.00 34.49 3.41
431 452 6.096705 AGAGATCTTGAATCGTCAGAACAGAT 59.903 38.462 0.00 0.00 34.49 2.90
433 454 3.928992 TCTTGAATCGTCAGAACAGATGC 59.071 43.478 0.00 0.00 34.49 3.91
448 472 3.891366 ACAGATGCTGTTTTAGTTGCCTT 59.109 39.130 0.00 0.00 42.59 4.35
455 479 5.105310 TGCTGTTTTAGTTGCCTTTTTGGTA 60.105 36.000 0.00 0.00 38.35 3.25
458 482 7.011950 GCTGTTTTAGTTGCCTTTTTGGTAAAT 59.988 33.333 0.00 0.00 41.99 1.40
474 498 5.053145 TGGTAAATTTTCATTGGTGTGTGC 58.947 37.500 0.00 0.00 0.00 4.57
487 511 4.256110 TGGTGTGTGCATAGAGATTGAAG 58.744 43.478 0.00 0.00 0.00 3.02
493 517 4.713814 TGTGCATAGAGATTGAAGAGTCCT 59.286 41.667 0.00 0.00 0.00 3.85
497 521 5.163364 GCATAGAGATTGAAGAGTCCTGGAA 60.163 44.000 0.00 0.00 0.00 3.53
511 542 2.173356 TCCTGGAACCTTATGGATGCTG 59.827 50.000 0.81 0.00 37.04 4.41
518 549 5.163237 GGAACCTTATGGATGCTGTAGGTAA 60.163 44.000 0.81 0.00 35.05 2.85
519 550 5.291905 ACCTTATGGATGCTGTAGGTAAC 57.708 43.478 0.81 0.00 34.39 2.50
527 558 4.141937 GGATGCTGTAGGTAACACAGATGA 60.142 45.833 12.69 0.00 43.81 2.92
596 643 8.905702 GCCTGCAGAACGATATATTTTATTTTG 58.094 33.333 17.39 0.00 0.00 2.44
664 711 7.738345 ACCGCAACATTTTAAAAATAGCAATC 58.262 30.769 4.44 0.00 0.00 2.67
687 734 4.009675 TGAACTCACTTCCATAATGTGCC 58.990 43.478 0.00 0.00 0.00 5.01
746 797 8.778059 AGAGTTGTATTAGTATCAAAATGGGGA 58.222 33.333 0.00 0.00 0.00 4.81
813 866 1.163554 GAGCAAGTGAGGAAGCAAGG 58.836 55.000 0.00 0.00 0.00 3.61
814 867 0.251077 AGCAAGTGAGGAAGCAAGGG 60.251 55.000 0.00 0.00 0.00 3.95
815 868 0.250901 GCAAGTGAGGAAGCAAGGGA 60.251 55.000 0.00 0.00 0.00 4.20
816 869 1.818642 CAAGTGAGGAAGCAAGGGAG 58.181 55.000 0.00 0.00 0.00 4.30
817 870 0.037447 AAGTGAGGAAGCAAGGGAGC 59.963 55.000 0.00 0.00 0.00 4.70
818 871 1.130054 AGTGAGGAAGCAAGGGAGCA 61.130 55.000 0.00 0.00 36.85 4.26
819 872 0.250901 GTGAGGAAGCAAGGGAGCAA 60.251 55.000 0.00 0.00 36.85 3.91
820 873 0.037303 TGAGGAAGCAAGGGAGCAAG 59.963 55.000 0.00 0.00 36.85 4.01
836 901 2.072298 GCAAGCAAGCTATATCCGGAG 58.928 52.381 11.34 0.00 0.00 4.63
902 967 5.412594 TCCAAATCCATCTTTTTCTCTGTCG 59.587 40.000 0.00 0.00 0.00 4.35
981 1058 1.033746 CGGTTCTCCATGCATGCCTT 61.034 55.000 21.69 0.00 0.00 4.35
2023 2305 4.450053 TGATTCATGCGTCATATGGTTCA 58.550 39.130 2.13 0.00 0.00 3.18
2078 2382 0.321564 TTGAGTTGCCAGATCACCCG 60.322 55.000 0.00 0.00 0.00 5.28
2230 2540 6.398234 TCTCCTCATATCTAGCTGTTGAAC 57.602 41.667 0.00 0.00 0.00 3.18
2273 2583 2.016318 CAGTTTGTCAGGCACTCAACA 58.984 47.619 0.00 0.00 34.60 3.33
2512 2825 2.223021 CGATAACACGGTTCCATTGCAG 60.223 50.000 0.00 0.00 0.00 4.41
2518 2831 1.308069 CGGTTCCATTGCAGGACAGG 61.308 60.000 0.00 0.00 37.42 4.00
2599 2912 5.044558 GGATTGATTGACTACGAGGAGTTC 58.955 45.833 0.00 0.00 0.00 3.01
2742 3055 9.187455 GTAGCTGAATTCTGTAGTTTAGATAGC 57.813 37.037 13.17 5.95 0.00 2.97
2889 3204 4.019860 AGGCTGACACTGACAATGTAAGAT 60.020 41.667 5.56 0.00 30.87 2.40
3006 3323 3.838244 AGCCAGTTTACTCAGTTGACA 57.162 42.857 0.00 0.00 0.00 3.58
3286 3630 5.900865 ACTTACTAGTTGCTGAGGAGTAC 57.099 43.478 0.00 0.00 0.00 2.73
3289 3633 2.826725 ACTAGTTGCTGAGGAGTACCAC 59.173 50.000 0.00 0.00 38.94 4.16
3340 3684 5.018809 TGAATTTGGGGAAGAAAGATGGAG 58.981 41.667 0.00 0.00 0.00 3.86
3382 3993 8.898761 ACATTTTTGTCATCTTGTACACTTACA 58.101 29.630 0.00 0.00 36.36 2.41
3383 3994 9.169468 CATTTTTGTCATCTTGTACACTTACAC 57.831 33.333 0.00 0.00 37.97 2.90
3384 3995 7.851387 TTTTGTCATCTTGTACACTTACACA 57.149 32.000 0.00 0.00 37.97 3.72
3385 3996 6.838198 TTGTCATCTTGTACACTTACACAC 57.162 37.500 0.00 0.00 37.97 3.82
3386 3997 6.156748 TGTCATCTTGTACACTTACACACT 57.843 37.500 0.00 0.00 37.97 3.55
3387 3998 6.578944 TGTCATCTTGTACACTTACACACTT 58.421 36.000 0.00 0.00 37.97 3.16
3388 3999 7.718525 TGTCATCTTGTACACTTACACACTTA 58.281 34.615 0.00 0.00 37.97 2.24
3389 4000 7.650504 TGTCATCTTGTACACTTACACACTTAC 59.349 37.037 0.00 0.00 37.97 2.34
3468 4079 1.681166 GCCTCTGCTGATGTGGTTGAT 60.681 52.381 0.00 0.00 33.53 2.57
3541 4156 8.729756 TCACCAACAATTTCAAGACTACATATG 58.270 33.333 0.00 0.00 0.00 1.78
3563 4178 5.402630 TGGTATATAGTGAGGCCAGATGAA 58.597 41.667 5.01 0.00 0.00 2.57
3640 4255 8.840321 GCTTATGTTACACCAGATGAATACAAT 58.160 33.333 0.00 0.00 0.00 2.71
3729 4344 8.408043 TTGGTTTGTCATTACAGAGAATTGAT 57.592 30.769 0.00 0.00 36.83 2.57
3730 4345 7.819644 TGGTTTGTCATTACAGAGAATTGATG 58.180 34.615 0.00 0.00 36.83 3.07
3807 4426 4.130857 TGGTCGCAACTTCATCAAACTTA 58.869 39.130 0.00 0.00 0.00 2.24
3818 4437 5.512942 TCATCAAACTTACTCCATCCCAA 57.487 39.130 0.00 0.00 0.00 4.12
3927 4550 3.093814 TGAGGTCGCTACTTATTGGACA 58.906 45.455 0.00 0.00 0.00 4.02
3942 4565 5.540400 ATTGGACAATTTGCTATGGGATG 57.460 39.130 0.00 0.00 0.00 3.51
3962 4585 0.250209 CATCAGCGGAATCTCCCAGG 60.250 60.000 0.00 0.00 31.13 4.45
4010 4634 1.226547 GAGCGCTTCTCACCTCGAG 60.227 63.158 13.26 5.13 43.80 4.04
4027 4651 5.007724 ACCTCGAGAAAATCCATTTATTCGC 59.992 40.000 15.71 0.00 36.52 4.70
4028 4652 5.418310 TCGAGAAAATCCATTTATTCGCC 57.582 39.130 10.79 0.00 36.52 5.54
4048 4674 4.498513 CGCCGAATATCAGTGGTGTAGTTA 60.499 45.833 0.00 0.00 0.00 2.24
4074 4700 6.040878 AGTCTAGTTAATTCACCGGAAATCG 58.959 40.000 9.46 0.00 36.43 3.34
4076 4702 6.312180 GTCTAGTTAATTCACCGGAAATCGTT 59.688 38.462 9.46 0.00 36.43 3.85
4115 4741 5.164620 TGAGTACAAGGAGATGCATGAAA 57.835 39.130 2.46 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 57 6.463360 TCCTTGTTCTGAATAAAAATTGGCC 58.537 36.000 0.00 0.00 0.00 5.36
151 156 7.130681 TGTAAACCCTTCCAAAATTGTGATT 57.869 32.000 0.00 0.00 0.00 2.57
214 219 8.201464 TGAGACAACTTGACTACAAATCTACAA 58.799 33.333 0.00 0.00 35.49 2.41
215 220 7.722363 TGAGACAACTTGACTACAAATCTACA 58.278 34.615 0.00 0.00 35.49 2.74
216 221 8.651588 CATGAGACAACTTGACTACAAATCTAC 58.348 37.037 0.00 0.00 35.49 2.59
217 222 7.331934 GCATGAGACAACTTGACTACAAATCTA 59.668 37.037 0.00 0.00 35.49 1.98
218 223 6.148480 GCATGAGACAACTTGACTACAAATCT 59.852 38.462 0.00 0.00 35.49 2.40
219 224 6.310197 GCATGAGACAACTTGACTACAAATC 58.690 40.000 0.00 0.00 35.49 2.17
220 225 5.106948 CGCATGAGACAACTTGACTACAAAT 60.107 40.000 0.00 0.00 35.49 2.32
221 226 4.211164 CGCATGAGACAACTTGACTACAAA 59.789 41.667 0.00 0.00 35.49 2.83
222 227 3.740832 CGCATGAGACAACTTGACTACAA 59.259 43.478 0.00 0.00 34.65 2.41
228 233 5.437289 AAATTTCGCATGAGACAACTTGA 57.563 34.783 0.00 0.00 0.00 3.02
238 243 1.067000 CCTGGCCAAAATTTCGCATGA 60.067 47.619 7.01 0.00 0.00 3.07
255 260 5.651387 TGAGAAATGACTAGAGACACCTG 57.349 43.478 0.00 0.00 0.00 4.00
291 296 6.712547 AGCTCCAAATAAGATGGCTGTATTAC 59.287 38.462 0.00 0.00 37.88 1.89
294 299 5.316158 AGCTCCAAATAAGATGGCTGTAT 57.684 39.130 0.00 0.00 37.88 2.29
295 300 4.778213 AGCTCCAAATAAGATGGCTGTA 57.222 40.909 0.00 0.00 37.88 2.74
296 301 3.659183 AGCTCCAAATAAGATGGCTGT 57.341 42.857 0.00 0.00 37.88 4.40
298 303 4.080129 TCTGAAGCTCCAAATAAGATGGCT 60.080 41.667 0.00 0.00 37.88 4.75
299 304 4.202441 TCTGAAGCTCCAAATAAGATGGC 58.798 43.478 0.00 0.00 37.88 4.40
300 305 4.820716 CCTCTGAAGCTCCAAATAAGATGG 59.179 45.833 0.00 0.00 39.41 3.51
301 306 4.275443 GCCTCTGAAGCTCCAAATAAGATG 59.725 45.833 0.00 0.00 0.00 2.90
400 421 5.836347 TGACGATTCAAGATCTCTACATGG 58.164 41.667 0.00 0.00 0.00 3.66
401 422 6.733145 TCTGACGATTCAAGATCTCTACATG 58.267 40.000 0.00 0.00 0.00 3.21
412 433 3.931468 AGCATCTGTTCTGACGATTCAAG 59.069 43.478 0.00 0.00 0.00 3.02
448 472 7.414540 GCACACACCAATGAAAATTTACCAAAA 60.415 33.333 0.00 0.00 0.00 2.44
455 479 6.757237 TCTATGCACACACCAATGAAAATTT 58.243 32.000 0.00 0.00 0.00 1.82
458 482 5.069318 TCTCTATGCACACACCAATGAAAA 58.931 37.500 0.00 0.00 0.00 2.29
474 498 6.279882 GTTCCAGGACTCTTCAATCTCTATG 58.720 44.000 0.00 0.00 0.00 2.23
487 511 3.745797 GCATCCATAAGGTTCCAGGACTC 60.746 52.174 0.00 0.00 35.89 3.36
493 517 3.136443 CCTACAGCATCCATAAGGTTCCA 59.864 47.826 0.00 0.00 35.89 3.53
497 521 4.719773 TGTTACCTACAGCATCCATAAGGT 59.280 41.667 0.00 0.00 40.38 3.50
511 542 7.172532 TCAACATTTGTCATCTGTGTTACCTAC 59.827 37.037 0.00 0.00 32.27 3.18
518 549 5.469760 TCGATTCAACATTTGTCATCTGTGT 59.530 36.000 0.00 0.00 0.00 3.72
519 550 5.791974 GTCGATTCAACATTTGTCATCTGTG 59.208 40.000 0.00 0.00 0.00 3.66
607 654 5.339695 GGGGTGATCATCCTAAAGGTTTACA 60.340 44.000 24.26 0.00 36.34 2.41
608 655 5.131067 GGGGTGATCATCCTAAAGGTTTAC 58.869 45.833 24.26 0.00 36.34 2.01
609 656 4.791334 TGGGGTGATCATCCTAAAGGTTTA 59.209 41.667 24.26 0.00 36.34 2.01
612 659 2.858644 TGGGGTGATCATCCTAAAGGT 58.141 47.619 24.26 0.00 36.34 3.50
614 661 4.510167 ACTTGGGGTGATCATCCTAAAG 57.490 45.455 26.49 26.49 31.37 1.85
653 700 6.716628 TGGAAGTGAGTTCAGATTGCTATTTT 59.283 34.615 2.06 0.00 36.82 1.82
654 701 6.240894 TGGAAGTGAGTTCAGATTGCTATTT 58.759 36.000 2.06 0.00 36.82 1.40
655 702 5.809001 TGGAAGTGAGTTCAGATTGCTATT 58.191 37.500 2.06 0.00 36.82 1.73
664 711 4.095483 GGCACATTATGGAAGTGAGTTCAG 59.905 45.833 2.06 0.00 36.82 3.02
669 716 6.769822 AGATAAAGGCACATTATGGAAGTGAG 59.230 38.462 0.00 0.00 32.01 3.51
723 771 8.747538 ACTCCCCATTTTGATACTAATACAAC 57.252 34.615 0.00 0.00 0.00 3.32
729 777 6.126594 CCTGGTACTCCCCATTTTGATACTAA 60.127 42.308 0.00 0.00 33.00 2.24
746 797 1.542187 GGCCGTCAGTTCCTGGTACT 61.542 60.000 0.00 0.00 31.51 2.73
762 813 4.501400 GGTCAATGTTTTATAGCCATGGCC 60.501 45.833 33.14 16.18 43.17 5.36
813 866 2.072298 CGGATATAGCTTGCTTGCTCC 58.928 52.381 7.26 4.06 42.97 4.70
814 867 2.072298 CCGGATATAGCTTGCTTGCTC 58.928 52.381 0.00 0.00 42.97 4.26
815 868 1.694150 TCCGGATATAGCTTGCTTGCT 59.306 47.619 0.00 8.85 46.11 3.91
816 869 2.072298 CTCCGGATATAGCTTGCTTGC 58.928 52.381 3.57 0.00 0.00 4.01
817 870 3.321497 GACTCCGGATATAGCTTGCTTG 58.679 50.000 3.57 0.00 0.00 4.01
818 871 2.300437 GGACTCCGGATATAGCTTGCTT 59.700 50.000 3.57 0.00 0.00 3.91
819 872 1.896465 GGACTCCGGATATAGCTTGCT 59.104 52.381 3.57 0.00 0.00 3.91
820 873 1.402984 CGGACTCCGGATATAGCTTGC 60.403 57.143 3.57 0.00 44.15 4.01
902 967 0.463620 TGGTTGGAAAGCCTTTGTGC 59.536 50.000 0.00 0.00 45.42 4.57
1498 1575 2.893398 CTCCGTGTAGTGGCCCTC 59.107 66.667 0.00 0.00 0.00 4.30
1716 1905 1.579932 CTCCGGCGCGATGTAGTAT 59.420 57.895 12.10 0.00 0.00 2.12
2023 2305 1.210478 AGGCCATAAGCTTCGACACAT 59.790 47.619 5.01 0.00 43.05 3.21
2078 2382 3.254892 GTCTCCGTCTTCTTTGATCCAC 58.745 50.000 0.00 0.00 0.00 4.02
2230 2540 5.921976 TGCAATCTAAGCATTGTTTGTTCAG 59.078 36.000 0.00 0.00 37.02 3.02
2273 2583 2.957680 TGAAAGCACACACACCATCAAT 59.042 40.909 0.00 0.00 0.00 2.57
2512 2825 7.874528 AGATGAATTTTGATGAAAAACCTGTCC 59.125 33.333 0.00 0.00 40.51 4.02
2771 3084 7.665559 TCTCTTGTTATGTACCTGCAAGATTTT 59.334 33.333 14.98 0.00 42.76 1.82
2910 3225 4.794248 TCAGATTGCGTATGTGTAATGC 57.206 40.909 0.00 0.00 0.00 3.56
3019 3336 6.947733 CCTCCCATCCTATATGTGCAATAAAA 59.052 38.462 0.00 0.00 0.00 1.52
3340 3684 0.250901 ATGTGCAGGTGGGAGACAAC 60.251 55.000 0.00 0.00 36.91 3.32
3382 3993 5.705441 CACCACCAACATCTTATGTAAGTGT 59.295 40.000 15.51 2.22 44.07 3.55
3383 3994 5.391950 GCACCACCAACATCTTATGTAAGTG 60.392 44.000 12.18 12.18 44.07 3.16
3384 3995 4.700213 GCACCACCAACATCTTATGTAAGT 59.300 41.667 0.16 0.00 44.07 2.24
3385 3996 4.201812 CGCACCACCAACATCTTATGTAAG 60.202 45.833 0.00 0.00 44.07 2.34
3386 3997 3.687212 CGCACCACCAACATCTTATGTAA 59.313 43.478 0.00 0.00 44.07 2.41
3387 3998 3.266636 CGCACCACCAACATCTTATGTA 58.733 45.455 0.00 0.00 44.07 2.29
3389 4000 1.202177 GCGCACCACCAACATCTTATG 60.202 52.381 0.30 0.00 0.00 1.90
3468 4079 6.732487 TCTAGTCCTCTATGTTTCTTCTCCA 58.268 40.000 0.00 0.00 0.00 3.86
3541 4156 6.552445 ATTCATCTGGCCTCACTATATACC 57.448 41.667 3.32 0.00 0.00 2.73
3807 4426 5.255397 TGTTCATTTACTTGGGATGGAGT 57.745 39.130 0.00 0.00 0.00 3.85
3818 4437 6.484288 TCACATCCTGGATTGTTCATTTACT 58.516 36.000 6.42 0.00 0.00 2.24
3927 4550 3.006537 GCTGATGCATCCCATAGCAAATT 59.993 43.478 24.35 0.00 44.88 1.82
3942 4565 0.883814 CTGGGAGATTCCGCTGATGC 60.884 60.000 0.00 0.00 37.43 3.91
4010 4634 8.020819 TGATATTCGGCGAATAAATGGATTTTC 58.979 33.333 36.83 27.20 37.92 2.29
4015 4639 5.408299 CACTGATATTCGGCGAATAAATGGA 59.592 40.000 36.83 21.54 37.92 3.41
4016 4640 5.390885 CCACTGATATTCGGCGAATAAATGG 60.391 44.000 36.83 32.49 37.92 3.16
4027 4651 7.039882 ACTTTAACTACACCACTGATATTCGG 58.960 38.462 0.00 0.00 0.00 4.30
4028 4652 7.974501 AGACTTTAACTACACCACTGATATTCG 59.025 37.037 0.00 0.00 0.00 3.34
4048 4674 7.064253 CGATTTCCGGTGAATTAACTAGACTTT 59.936 37.037 0.00 0.00 33.91 2.66
4074 4700 8.523658 TGTACTCATAGTATGGCATCATAGAAC 58.476 37.037 1.65 0.00 36.62 3.01
4076 4702 8.650143 TTGTACTCATAGTATGGCATCATAGA 57.350 34.615 1.65 0.00 36.62 1.98


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

AutoCloner maintained by Alex Coulton.