Multiple sequence alignment - TraesCS3A01G205300

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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 TraesCS3A01G205300 chr3A 100.000 7157 0 0 1 7157 360833084 360825928 0.000000e+00 13217.0
1 TraesCS3A01G205300 chr3A 95.527 693 30 1 1 692 500896237 500895545 0.000000e+00 1107.0
2 TraesCS3A01G205300 chr3A 92.157 102 4 1 3193 3290 11708179 11708280 2.690000e-29 141.0
3 TraesCS3A01G205300 chr3A 91.176 102 5 1 3193 3290 11682797 11682898 1.250000e-27 135.0
4 TraesCS3A01G205300 chr3B 95.443 2875 92 19 4303 7157 372244094 372241239 0.000000e+00 4547.0
5 TraesCS3A01G205300 chr3B 96.032 1109 31 6 1981 3089 372246298 372245203 0.000000e+00 1792.0
6 TraesCS3A01G205300 chr3B 96.338 983 34 2 3282 4264 372245070 372244090 0.000000e+00 1615.0
7 TraesCS3A01G205300 chr3B 94.828 696 35 1 1 696 564034843 564034149 0.000000e+00 1085.0
8 TraesCS3A01G205300 chr3B 94.684 696 37 0 1 696 51239066 51238371 0.000000e+00 1081.0
9 TraesCS3A01G205300 chr3B 89.294 878 47 13 1147 1982 372247252 372246380 0.000000e+00 1057.0
10 TraesCS3A01G205300 chr3B 93.376 468 16 5 694 1146 372247749 372247282 0.000000e+00 678.0
11 TraesCS3A01G205300 chr3B 97.170 106 3 0 3086 3191 372245175 372245070 5.700000e-41 180.0
12 TraesCS3A01G205300 chr3B 79.545 88 8 7 1383 1461 372246911 372246825 4.000000e-03 54.7
13 TraesCS3A01G205300 chr3D 96.940 2549 56 10 4626 7157 278447053 278449596 0.000000e+00 4255.0
14 TraesCS3A01G205300 chr3D 95.475 1967 38 10 1147 3089 278440166 278442105 0.000000e+00 3092.0
15 TraesCS3A01G205300 chr3D 96.824 1354 35 5 3281 4631 278442284 278443632 0.000000e+00 2255.0
16 TraesCS3A01G205300 chr3D 98.584 353 4 1 694 1046 278439152 278439503 2.190000e-174 623.0
17 TraesCS3A01G205300 chr3D 96.644 149 5 0 3086 3234 278442133 278442281 1.540000e-61 248.0
18 TraesCS3A01G205300 chr3D 89.908 109 5 2 3182 3286 582796856 582796962 1.250000e-27 135.0
19 TraesCS3A01G205300 chr3D 89.286 112 6 3 3193 3299 613073358 613073468 1.250000e-27 135.0
20 TraesCS3A01G205300 chr3D 95.062 81 4 0 4551 4631 278443772 278443852 2.100000e-25 128.0
21 TraesCS3A01G205300 chr3D 100.000 30 0 0 1117 1146 278440107 278440136 1.000000e-03 56.5
22 TraesCS3A01G205300 chr6A 95.520 692 29 2 1 692 475413511 475412822 0.000000e+00 1105.0
23 TraesCS3A01G205300 chr6A 94.476 706 29 7 1 696 84962624 84961919 0.000000e+00 1079.0
24 TraesCS3A01G205300 chr6A 94.798 692 36 0 1 692 416744739 416744048 0.000000e+00 1079.0
25 TraesCS3A01G205300 chr1A 95.157 702 24 8 1 692 100299056 100299757 0.000000e+00 1099.0
26 TraesCS3A01G205300 chr1A 85.163 492 73 0 4693 5184 591149149 591148658 8.290000e-139 505.0
27 TraesCS3A01G205300 chr7A 94.850 699 36 0 1 699 710811732 710811034 0.000000e+00 1092.0
28 TraesCS3A01G205300 chr5A 94.759 706 27 3 1 696 616883089 616883794 0.000000e+00 1090.0
29 TraesCS3A01G205300 chr1B 85.193 493 71 2 4693 5184 685290023 685289532 8.290000e-139 505.0
30 TraesCS3A01G205300 chr1B 88.000 125 9 3 3179 3298 132296913 132296790 7.480000e-30 143.0
31 TraesCS3A01G205300 chr1D 84.016 513 78 4 4674 5184 492641817 492641307 2.320000e-134 490.0
32 TraesCS3A01G205300 chr7D 90.654 107 6 1 3182 3284 41596538 41596644 9.680000e-29 139.0
33 TraesCS3A01G205300 chr5D 91.262 103 5 1 3193 3291 266749450 266749348 3.480000e-28 137.0
34 TraesCS3A01G205300 chr2D 88.393 112 8 2 3180 3286 178280841 178280730 5.830000e-26 130.0
35 TraesCS3A01G205300 chr2D 87.611 113 8 3 3193 3300 206682752 206682641 7.540000e-25 126.0


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 TraesCS3A01G205300 chr3A 360825928 360833084 7156 True 13217.000000 13217 100.000000 1 7157 1 chr3A.!!$R1 7156
1 TraesCS3A01G205300 chr3A 500895545 500896237 692 True 1107.000000 1107 95.527000 1 692 1 chr3A.!!$R2 691
2 TraesCS3A01G205300 chr3B 372241239 372247749 6510 True 1417.671429 4547 92.456857 694 7157 7 chr3B.!!$R3 6463
3 TraesCS3A01G205300 chr3B 564034149 564034843 694 True 1085.000000 1085 94.828000 1 696 1 chr3B.!!$R2 695
4 TraesCS3A01G205300 chr3B 51238371 51239066 695 True 1081.000000 1081 94.684000 1 696 1 chr3B.!!$R1 695
5 TraesCS3A01G205300 chr3D 278439152 278449596 10444 False 1522.500000 4255 97.075571 694 7157 7 chr3D.!!$F3 6463
6 TraesCS3A01G205300 chr6A 475412822 475413511 689 True 1105.000000 1105 95.520000 1 692 1 chr6A.!!$R3 691
7 TraesCS3A01G205300 chr6A 84961919 84962624 705 True 1079.000000 1079 94.476000 1 696 1 chr6A.!!$R1 695
8 TraesCS3A01G205300 chr6A 416744048 416744739 691 True 1079.000000 1079 94.798000 1 692 1 chr6A.!!$R2 691
9 TraesCS3A01G205300 chr1A 100299056 100299757 701 False 1099.000000 1099 95.157000 1 692 1 chr1A.!!$F1 691
10 TraesCS3A01G205300 chr7A 710811034 710811732 698 True 1092.000000 1092 94.850000 1 699 1 chr7A.!!$R1 698
11 TraesCS3A01G205300 chr5A 616883089 616883794 705 False 1090.000000 1090 94.759000 1 696 1 chr5A.!!$F1 695
12 TraesCS3A01G205300 chr1D 492641307 492641817 510 True 490.000000 490 84.016000 4674 5184 1 chr1D.!!$R1 510

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
929 957 2.159198 CCAATCCAATCTTCCGCCTTTG 60.159 50.000 0.0 0.0 0.00 2.77 F
2219 2938 0.033208 TGGGGATTTGGAGGCATGTC 60.033 55.000 0.0 0.0 0.00 3.06 F
2220 2939 0.259938 GGGGATTTGGAGGCATGTCT 59.740 55.000 0.0 0.0 0.00 3.41 F
3772 4529 0.584396 TGTGGCTTAAAACTCGTGCG 59.416 50.000 0.0 0.0 0.00 5.34 F
4198 4956 1.337167 GGTGTTGATGAAGCCAAAGCC 60.337 52.381 0.0 0.0 41.25 4.35 F
5718 9903 0.460109 TGACATCCGGTGCTTCATCG 60.460 55.000 0.0 0.0 37.76 3.84 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2771 3491 0.035152 TGATCATCCCCAGCACACAC 60.035 55.000 0.0 0.00 0.00 3.82 R
3753 4510 0.584396 CGCACGAGTTTTAAGCCACA 59.416 50.000 0.0 0.00 0.00 4.17 R
4268 5026 3.094484 AGAGTAGCTGGTAGAAGCACT 57.906 47.619 0.0 0.73 46.08 4.40 R
5718 9903 3.118542 CAAAGTTGCTTGCTCAAAGTCC 58.881 45.455 0.0 0.00 38.25 3.85 R
5961 10146 0.178975 TTTGGGTTCCGCTCATGGTT 60.179 50.000 0.0 0.00 0.00 3.67 R
6791 11003 1.870055 GACTACGTGGAAGTGGCCGA 61.870 60.000 5.7 0.00 0.00 5.54 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
76 78 5.657474 ACCTTGATGAACATCATGAAATGC 58.343 37.500 23.06 0.00 46.21 3.56
204 206 3.363970 CGCATACACGCTTTTCTTCAAGT 60.364 43.478 0.00 0.00 0.00 3.16
582 604 6.385759 AGTTTAAAGGTTGGATTTGAGGGTTT 59.614 34.615 0.00 0.00 0.00 3.27
587 609 5.464069 AGGTTGGATTTGAGGGTTTTAGTT 58.536 37.500 0.00 0.00 0.00 2.24
615 637 9.740710 TTTCCCCTGTTTTTCAATCTTTAAAAA 57.259 25.926 0.00 0.00 33.41 1.94
692 714 7.365384 GGTTTAGGGGTTCTACTAGTAATGCTT 60.365 40.741 3.76 0.00 0.00 3.91
929 957 2.159198 CCAATCCAATCTTCCGCCTTTG 60.159 50.000 0.00 0.00 0.00 2.77
1239 1847 6.889198 TCAGGTTAGTTAATCCTCCTGATTG 58.111 40.000 14.16 0.00 43.97 2.67
1241 1849 6.540189 CAGGTTAGTTAATCCTCCTGATTGTG 59.460 42.308 11.63 0.00 43.57 3.33
1242 1850 5.823045 GGTTAGTTAATCCTCCTGATTGTGG 59.177 44.000 0.00 0.00 43.57 4.17
1243 1851 6.352737 GGTTAGTTAATCCTCCTGATTGTGGA 60.353 42.308 0.00 0.00 43.57 4.02
1244 1852 5.983333 AGTTAATCCTCCTGATTGTGGAT 57.017 39.130 0.00 0.00 43.57 3.41
1245 1853 5.688807 AGTTAATCCTCCTGATTGTGGATG 58.311 41.667 0.00 0.00 43.57 3.51
1246 1854 2.653234 ATCCTCCTGATTGTGGATGC 57.347 50.000 0.00 0.00 37.85 3.91
1247 1855 1.588239 TCCTCCTGATTGTGGATGCT 58.412 50.000 0.00 0.00 32.56 3.79
1248 1856 1.918262 TCCTCCTGATTGTGGATGCTT 59.082 47.619 0.00 0.00 32.56 3.91
1261 1869 4.771577 TGTGGATGCTTGTGTAATGGATTT 59.228 37.500 0.00 0.00 0.00 2.17
1325 1933 9.629878 TTTGTAGGTATTGGAAAGTTTAAGTCA 57.370 29.630 0.00 0.00 0.00 3.41
1438 2046 7.755591 TCAGAAAGATTTATGATTGACAGTGC 58.244 34.615 0.00 0.00 33.88 4.40
1574 2184 0.751643 CTACCAAATCCCGGGCCAAG 60.752 60.000 18.49 5.66 0.00 3.61
1600 2210 8.062448 GCGCTAAACACTTGTAATTATTCTAGG 58.938 37.037 0.00 0.00 0.00 3.02
1689 2299 6.130298 TGTTTGGTCTTAGTTTCACATGTG 57.870 37.500 20.18 20.18 0.00 3.21
1771 2389 1.922545 GATTTGCTTCGCCATCTTTGC 59.077 47.619 0.00 0.00 0.00 3.68
1821 2439 8.669946 TGCATCGACAATAATAATCTACCAAA 57.330 30.769 0.00 0.00 0.00 3.28
1899 2535 4.371855 TCGCTTACTTCGATCAACATCT 57.628 40.909 0.00 0.00 0.00 2.90
1929 2565 3.364889 TCCCAATACGACAGCTAATCG 57.635 47.619 15.92 15.92 45.17 3.34
2026 2745 0.033366 CCATGTGTCGGATGCGGATA 59.967 55.000 6.82 0.00 0.00 2.59
2218 2937 0.413037 TTGGGGATTTGGAGGCATGT 59.587 50.000 0.00 0.00 0.00 3.21
2219 2938 0.033208 TGGGGATTTGGAGGCATGTC 60.033 55.000 0.00 0.00 0.00 3.06
2220 2939 0.259938 GGGGATTTGGAGGCATGTCT 59.740 55.000 0.00 0.00 0.00 3.41
2221 2940 1.396653 GGGATTTGGAGGCATGTCTG 58.603 55.000 3.48 0.00 0.00 3.51
2222 2941 1.064463 GGGATTTGGAGGCATGTCTGA 60.064 52.381 3.48 0.00 0.00 3.27
2223 2942 2.295885 GGATTTGGAGGCATGTCTGAG 58.704 52.381 3.48 0.00 0.00 3.35
2224 2943 2.092753 GGATTTGGAGGCATGTCTGAGA 60.093 50.000 3.48 0.00 0.00 3.27
2225 2944 2.479566 TTTGGAGGCATGTCTGAGAC 57.520 50.000 3.48 5.47 0.00 3.36
2455 3174 1.675720 GCAGCCTCCTCTCCTCTGAC 61.676 65.000 0.00 0.00 0.00 3.51
2672 3391 8.207545 ACCTTTTATTTGCATTAAAACAGTCCA 58.792 29.630 9.74 0.00 0.00 4.02
2755 3475 6.965607 TCTCGGGGATAATTCTTTTACCTTT 58.034 36.000 0.00 0.00 0.00 3.11
3225 3976 7.041644 CGTCCCAAAATAAGTGACTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
3241 3992 9.991906 ACTCAACTTTATACTAACTTTAGCACA 57.008 29.630 0.00 0.00 34.09 4.57
3252 4003 8.502105 ACTAACTTTAGCACAAAGTACAAAGT 57.498 30.769 14.60 12.66 39.36 2.66
3253 4004 8.953313 ACTAACTTTAGCACAAAGTACAAAGTT 58.047 29.630 14.60 16.07 44.21 2.66
3254 4005 9.221775 CTAACTTTAGCACAAAGTACAAAGTTG 57.778 33.333 18.99 10.25 42.79 3.16
3255 4006 7.385778 ACTTTAGCACAAAGTACAAAGTTGA 57.614 32.000 13.11 0.00 38.58 3.18
3256 4007 7.472543 ACTTTAGCACAAAGTACAAAGTTGAG 58.527 34.615 13.11 0.00 38.58 3.02
3257 4008 6.995511 TTAGCACAAAGTACAAAGTTGAGT 57.004 33.333 0.00 0.00 0.00 3.41
3258 4009 5.485662 AGCACAAAGTACAAAGTTGAGTC 57.514 39.130 0.00 0.00 0.00 3.36
3259 4010 4.941263 AGCACAAAGTACAAAGTTGAGTCA 59.059 37.500 0.00 0.00 0.00 3.41
3260 4011 5.028375 GCACAAAGTACAAAGTTGAGTCAC 58.972 41.667 0.00 0.00 0.00 3.67
3261 4012 5.163754 GCACAAAGTACAAAGTTGAGTCACT 60.164 40.000 0.00 0.00 0.00 3.41
3262 4013 6.622896 GCACAAAGTACAAAGTTGAGTCACTT 60.623 38.462 0.00 0.00 38.74 3.16
3263 4014 7.413657 GCACAAAGTACAAAGTTGAGTCACTTA 60.414 37.037 0.00 0.00 35.87 2.24
3264 4015 8.612619 CACAAAGTACAAAGTTGAGTCACTTAT 58.387 33.333 0.00 0.00 35.87 1.73
3265 4016 9.174166 ACAAAGTACAAAGTTGAGTCACTTATT 57.826 29.630 0.00 0.00 35.87 1.40
3269 4020 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
3270 4021 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
3271 4022 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
3272 4023 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3273 4024 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
3274 4025 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
3275 4026 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
3276 4027 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
3277 4028 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3278 4029 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
3279 4030 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3328 4079 7.201929 CCCTAGTCCTAAACTCCTGATTACTTC 60.202 44.444 0.00 0.00 39.55 3.01
3360 4115 6.903883 TTTCTTTATTGCTCGTGGACTATC 57.096 37.500 0.00 0.00 0.00 2.08
3361 4116 5.592104 TCTTTATTGCTCGTGGACTATCA 57.408 39.130 0.00 0.00 0.00 2.15
3362 4117 5.592054 TCTTTATTGCTCGTGGACTATCAG 58.408 41.667 0.00 0.00 0.00 2.90
3363 4118 5.127194 TCTTTATTGCTCGTGGACTATCAGT 59.873 40.000 0.00 0.00 0.00 3.41
3525 4280 2.905415 TGTTCCATTGGAAGCAGGAT 57.095 45.000 18.49 0.00 42.88 3.24
3527 4282 2.225091 TGTTCCATTGGAAGCAGGATGT 60.225 45.455 18.49 0.00 42.88 3.06
3528 4283 2.133281 TCCATTGGAAGCAGGATGTG 57.867 50.000 1.94 0.00 39.31 3.21
3710 4467 6.092955 AGTTTACAGTTACGTTCCATCTGA 57.907 37.500 0.00 0.00 0.00 3.27
3772 4529 0.584396 TGTGGCTTAAAACTCGTGCG 59.416 50.000 0.00 0.00 0.00 5.34
4198 4956 1.337167 GGTGTTGATGAAGCCAAAGCC 60.337 52.381 0.00 0.00 41.25 4.35
4245 5003 3.241067 TCGAGATCCAAAGGTAAACCG 57.759 47.619 0.00 0.00 42.08 4.44
4290 5048 3.835395 AGTGCTTCTACCAGCTACTCTTT 59.165 43.478 0.00 0.00 40.79 2.52
4291 5049 4.081917 AGTGCTTCTACCAGCTACTCTTTC 60.082 45.833 0.00 0.00 40.79 2.62
4292 5050 4.081917 GTGCTTCTACCAGCTACTCTTTCT 60.082 45.833 0.00 0.00 40.79 2.52
4357 5115 5.299279 TGCTATGGATTAACTTTTGCCTAGC 59.701 40.000 0.00 0.00 0.00 3.42
4462 5220 7.452880 TGAATAGCTTGCTTAATTCAACACT 57.547 32.000 14.69 0.00 35.88 3.55
4481 5239 4.081752 ACACTGTTGTTTGATTTTGCCAGA 60.082 37.500 0.00 0.00 28.43 3.86
4616 5594 6.770785 AGAAATGAGTTGTTAGCCACTGTTTA 59.229 34.615 0.00 0.00 0.00 2.01
5200 9385 9.114952 TCAAAGGTAATTTTGGGAATTTTTGTC 57.885 29.630 0.00 0.00 38.33 3.18
5208 9393 2.890311 TGGGAATTTTTGTCGTCATGCT 59.110 40.909 0.00 0.00 0.00 3.79
5209 9394 4.075682 TGGGAATTTTTGTCGTCATGCTA 58.924 39.130 0.00 0.00 0.00 3.49
5325 9510 2.042162 ACCAGGATTTTCAGGTGCTGAT 59.958 45.455 0.00 0.00 40.39 2.90
5718 9903 0.460109 TGACATCCGGTGCTTCATCG 60.460 55.000 0.00 0.00 37.76 3.84
6075 10260 2.599645 CTTCACCCCCATCTCCAGCG 62.600 65.000 0.00 0.00 0.00 5.18
6338 10523 5.165676 CACATGGAGGAAAATTCACACATG 58.834 41.667 15.42 15.42 0.00 3.21
6474 10673 8.196771 TGGTCATGAAAGTTGCCAATAATATTC 58.803 33.333 0.00 0.00 0.00 1.75
6488 10687 3.482156 AATATTCTGCTCATCAGCCGT 57.518 42.857 0.00 0.00 46.26 5.68
6515 10714 3.751518 TGAGATTGAGATCCCATGCATG 58.248 45.455 20.19 20.19 32.44 4.06
6525 10724 1.750206 TCCCATGCATGCACACATTAC 59.250 47.619 25.37 0.00 32.87 1.89
6547 10759 3.056891 CGAAGGAAGCTAAAATGGCCAAA 60.057 43.478 10.96 0.00 0.00 3.28
6548 10760 4.498241 GAAGGAAGCTAAAATGGCCAAAG 58.502 43.478 10.96 6.46 0.00 2.77
6549 10761 3.510459 AGGAAGCTAAAATGGCCAAAGT 58.490 40.909 10.96 0.00 0.00 2.66
6550 10762 4.672899 AGGAAGCTAAAATGGCCAAAGTA 58.327 39.130 10.96 0.35 0.00 2.24
6551 10763 4.706962 AGGAAGCTAAAATGGCCAAAGTAG 59.293 41.667 10.96 12.43 0.00 2.57
6552 10764 4.142160 GGAAGCTAAAATGGCCAAAGTAGG 60.142 45.833 10.96 0.00 0.00 3.18
6871 11083 2.064581 GTCCTGTATCCACCGGGCT 61.065 63.158 6.32 0.00 31.39 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
204 206 5.529581 TGCATCCTTAATCTCACGATGTA 57.470 39.130 0.00 0.00 34.21 2.29
512 534 2.621070 TCTAGTCTTTGCCTCAACCCT 58.379 47.619 0.00 0.00 0.00 4.34
587 609 9.740710 TTTAAAGATTGAAAAACAGGGGAAAAA 57.259 25.926 0.00 0.00 0.00 1.94
591 613 9.336171 CATTTTTAAAGATTGAAAAACAGGGGA 57.664 29.630 3.25 0.00 37.35 4.81
625 647 8.515414 GCAGTTTTAAGAATTGAGAAGTACCAT 58.485 33.333 0.00 0.00 0.00 3.55
640 662 9.396022 CCTCAAATCCTTATAGCAGTTTTAAGA 57.604 33.333 0.00 0.00 0.00 2.10
929 957 2.034221 AGGGAAGCAGAAACGCCC 59.966 61.111 0.00 0.00 39.12 6.13
1023 1051 8.974060 AGAAAGTTAATAGAAAACACACCTGA 57.026 30.769 0.00 0.00 0.00 3.86
1093 1122 3.254960 CTCCCTCCTATCCCATCACAAT 58.745 50.000 0.00 0.00 0.00 2.71
1155 1745 9.262358 CTTATAAGGTCACAACTAGAATTAGCC 57.738 37.037 4.42 0.00 0.00 3.93
1239 1847 4.989279 AATCCATTACACAAGCATCCAC 57.011 40.909 0.00 0.00 0.00 4.02
1241 1849 8.947055 AAATAAAATCCATTACACAAGCATCC 57.053 30.769 0.00 0.00 0.00 3.51
1243 1851 9.723601 ACAAAATAAAATCCATTACACAAGCAT 57.276 25.926 0.00 0.00 0.00 3.79
1325 1933 1.696097 AACTGACACAAGCCGGTCCT 61.696 55.000 1.90 0.00 33.09 3.85
1438 2046 2.107141 GTCGAATCCTGGCTCCGG 59.893 66.667 0.00 0.00 0.00 5.14
1574 2184 8.062448 CCTAGAATAATTACAAGTGTTTAGCGC 58.938 37.037 0.00 0.00 0.00 5.92
1689 2299 0.952984 AGAAAGAACAGAGCGCTGCC 60.953 55.000 18.48 9.71 46.26 4.85
1771 2389 3.490348 ACTTGTTCTTCCAACCCATCAG 58.510 45.455 0.00 0.00 0.00 2.90
1821 2439 3.554934 TGTTGGCACATTTGAAGAGACT 58.445 40.909 0.00 0.00 39.30 3.24
1929 2565 2.915463 CTCGTTATCGTGTGTGGTTCTC 59.085 50.000 0.00 0.00 38.33 2.87
2026 2745 0.043940 ATCTGGAGAGGCTCACCCTT 59.956 55.000 25.34 9.55 46.60 3.95
2119 2838 4.631740 TCCACCACCGCCTCCAGA 62.632 66.667 0.00 0.00 0.00 3.86
2218 2937 5.708230 GGAAGTAGAAACTCAGAGTCTCAGA 59.292 44.000 6.67 0.00 33.75 3.27
2219 2938 5.710099 AGGAAGTAGAAACTCAGAGTCTCAG 59.290 44.000 6.67 0.00 33.75 3.35
2220 2939 5.475220 CAGGAAGTAGAAACTCAGAGTCTCA 59.525 44.000 6.67 0.00 33.75 3.27
2221 2940 5.105917 CCAGGAAGTAGAAACTCAGAGTCTC 60.106 48.000 2.72 0.00 33.75 3.36
2222 2941 4.770010 CCAGGAAGTAGAAACTCAGAGTCT 59.230 45.833 2.72 0.00 33.75 3.24
2223 2942 4.767928 TCCAGGAAGTAGAAACTCAGAGTC 59.232 45.833 2.72 0.00 33.75 3.36
2224 2943 4.742012 TCCAGGAAGTAGAAACTCAGAGT 58.258 43.478 0.00 0.00 33.75 3.24
2225 2944 5.163457 GGATCCAGGAAGTAGAAACTCAGAG 60.163 48.000 6.95 0.00 33.75 3.35
2672 3391 5.605540 AAATAGACCATAATGGCCCTCAT 57.394 39.130 0.00 0.00 42.67 2.90
2724 3443 2.867109 ATTATCCCCGAGAGCAATGG 57.133 50.000 0.00 0.00 0.00 3.16
2771 3491 0.035152 TGATCATCCCCAGCACACAC 60.035 55.000 0.00 0.00 0.00 3.82
2773 3493 1.679680 CATTGATCATCCCCAGCACAC 59.320 52.381 0.00 0.00 0.00 3.82
2802 3522 4.221703 CCTCTCATGTAAGTTCCTGAGTGT 59.778 45.833 0.00 0.00 37.12 3.55
3191 3942 2.341846 TATTTTGGGACGGATGGAGC 57.658 50.000 0.00 0.00 0.00 4.70
3196 3947 4.019681 TGAGTCACTTATTTTGGGACGGAT 60.020 41.667 0.00 0.00 33.84 4.18
3234 3985 6.596106 TGACTCAACTTTGTACTTTGTGCTAA 59.404 34.615 0.00 0.00 0.00 3.09
3236 3987 4.941263 TGACTCAACTTTGTACTTTGTGCT 59.059 37.500 0.00 0.00 0.00 4.40
3237 3988 5.028375 GTGACTCAACTTTGTACTTTGTGC 58.972 41.667 0.00 0.00 0.00 4.57
3238 3989 6.422776 AGTGACTCAACTTTGTACTTTGTG 57.577 37.500 0.00 0.00 0.00 3.33
3239 3990 8.732746 ATAAGTGACTCAACTTTGTACTTTGT 57.267 30.769 0.00 0.00 40.77 2.83
3243 3994 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
3244 3995 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
3245 3996 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3246 3997 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3247 3998 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
3248 3999 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3249 4000 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3250 4001 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3251 4002 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3252 4003 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3253 4004 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
3254 4005 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
3255 4006 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
3256 4007 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
3257 4008 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
3258 4009 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3259 4010 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3260 4011 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3261 4012 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3262 4013 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3263 4014 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
3264 4015 1.961133 ATACTCCCTCCGTCCCAAAA 58.039 50.000 0.00 0.00 0.00 2.44
3265 4016 2.852714 TATACTCCCTCCGTCCCAAA 57.147 50.000 0.00 0.00 0.00 3.28
3266 4017 2.090943 ACATATACTCCCTCCGTCCCAA 60.091 50.000 0.00 0.00 0.00 4.12
3267 4018 1.502039 ACATATACTCCCTCCGTCCCA 59.498 52.381 0.00 0.00 0.00 4.37
3268 4019 2.305858 ACATATACTCCCTCCGTCCC 57.694 55.000 0.00 0.00 0.00 4.46
3269 4020 5.997384 AATAACATATACTCCCTCCGTCC 57.003 43.478 0.00 0.00 0.00 4.79
3271 4022 9.931698 TGATATAATAACATATACTCCCTCCGT 57.068 33.333 0.00 0.00 0.00 4.69
3328 4079 8.586273 CCACGAGCAATAAAGAAAAACATATTG 58.414 33.333 0.00 0.00 38.28 1.90
3346 4097 1.472878 GTGACTGATAGTCCACGAGCA 59.527 52.381 6.52 0.00 44.44 4.26
3710 4467 1.202903 GGAATGATGCTCAGGCTCCAT 60.203 52.381 0.00 0.00 39.59 3.41
3753 4510 0.584396 CGCACGAGTTTTAAGCCACA 59.416 50.000 0.00 0.00 0.00 4.17
4268 5026 3.094484 AGAGTAGCTGGTAGAAGCACT 57.906 47.619 0.00 0.73 46.08 4.40
4290 5048 8.347004 TCAATTGTCAATGGTTTATTGCTAGA 57.653 30.769 5.13 0.00 44.69 2.43
4291 5049 8.984891 TTCAATTGTCAATGGTTTATTGCTAG 57.015 30.769 5.13 0.00 44.69 3.42
4328 5086 2.256117 AGTTAATCCATAGCACCGGC 57.744 50.000 0.00 0.00 41.61 6.13
4462 5220 5.336150 TCTTCTGGCAAAATCAAACAACA 57.664 34.783 0.00 0.00 0.00 3.33
4481 5239 6.127026 ACACTAAGAAGACAACAAGACCTCTT 60.127 38.462 0.00 0.00 36.45 2.85
4597 5575 5.238650 ACACATAAACAGTGGCTAACAACTC 59.761 40.000 0.00 0.00 41.21 3.01
4616 5594 6.070538 GGACTGGATATAGCAAGGATACACAT 60.071 42.308 0.00 0.00 41.41 3.21
4902 9086 5.161358 TGAATATGATACAAGGCGATCGTC 58.839 41.667 12.83 12.83 0.00 4.20
5325 9510 3.820467 CCACATTCACCAAGTTAGCAAGA 59.180 43.478 0.00 0.00 0.00 3.02
5718 9903 3.118542 CAAAGTTGCTTGCTCAAAGTCC 58.881 45.455 0.00 0.00 38.25 3.85
5961 10146 0.178975 TTTGGGTTCCGCTCATGGTT 60.179 50.000 0.00 0.00 0.00 3.67
6338 10523 1.017387 GCTAACATGTGCCTGCTACC 58.983 55.000 0.00 0.00 0.00 3.18
6488 10687 3.031013 TGGGATCTCAATCTCAGCGTTA 58.969 45.455 0.00 0.00 37.47 3.18
6515 10714 2.076863 AGCTTCCTTCGTAATGTGTGC 58.923 47.619 0.00 0.00 0.00 4.57
6525 10724 2.091541 TGGCCATTTTAGCTTCCTTCG 58.908 47.619 0.00 0.00 0.00 3.79
6548 10760 9.478768 GGTAGATTTGATCTAAAACTAGCCTAC 57.521 37.037 16.84 0.00 41.98 3.18
6549 10761 9.209048 TGGTAGATTTGATCTAAAACTAGCCTA 57.791 33.333 20.64 10.44 44.66 3.93
6550 10762 8.090788 TGGTAGATTTGATCTAAAACTAGCCT 57.909 34.615 20.64 6.08 44.66 4.58
6551 10763 8.778358 CATGGTAGATTTGATCTAAAACTAGCC 58.222 37.037 20.64 16.40 44.66 3.93
6552 10764 9.331282 ACATGGTAGATTTGATCTAAAACTAGC 57.669 33.333 18.78 18.78 45.10 3.42
6647 10859 2.024414 GGAGGTGGTCATGTTTATGCC 58.976 52.381 0.00 0.00 34.21 4.40
6703 10915 2.822701 GATTTCGGGTGGGGCGAC 60.823 66.667 0.00 0.00 0.00 5.19
6791 11003 1.870055 GACTACGTGGAAGTGGCCGA 61.870 60.000 5.70 0.00 0.00 5.54
6859 11071 4.175337 GCTGCAGCCCGGTGGATA 62.175 66.667 28.76 0.00 34.31 2.59
7018 11230 2.599597 GCCATGAGGATGTGCCCT 59.400 61.111 0.00 0.00 39.77 5.19
7121 11333 4.891727 CTTCGCCATCGACCCCGG 62.892 72.222 0.00 0.00 45.43 5.73


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

AutoCloner maintained by Alex Coulton.