Multiple sequence alignment - TraesCS3D01G360900

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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 TraesCS3D01G360900 chr3D 100.000 3482 0 0 1 3482 474449707 474453188 0.000000e+00 6431.0
1 TraesCS3D01G360900 chr3D 85.556 90 9 4 447 534 582135069 582134982 1.330000e-14 91.6
2 TraesCS3D01G360900 chr3A 92.221 2764 133 29 411 3136 616727021 616724302 0.000000e+00 3838.0
3 TraesCS3D01G360900 chr3B 93.021 2522 122 22 1 2484 630867971 630870476 0.000000e+00 3633.0
4 TraesCS3D01G360900 chr3B 86.024 737 64 15 2540 3267 630870923 630871629 0.000000e+00 754.0
5 TraesCS3D01G360900 chr3B 86.528 193 26 0 3290 3482 630871764 630871956 2.720000e-51 213.0
6 TraesCS3D01G360900 chr1A 81.988 1338 206 29 1139 2460 474432170 474430852 0.000000e+00 1103.0
7 TraesCS3D01G360900 chr1D 81.665 1309 212 25 1166 2460 375369492 375368198 0.000000e+00 1062.0
8 TraesCS3D01G360900 chr1D 87.850 107 9 3 3174 3278 349546106 349546002 4.720000e-24 122.0
9 TraesCS3D01G360900 chr1D 88.525 61 6 1 221 281 224572704 224572763 4.820000e-09 73.1
10 TraesCS3D01G360900 chr1B 81.259 1334 220 28 1139 2460 500539551 500540866 0.000000e+00 1051.0
11 TraesCS3D01G360900 chr7D 80.978 184 28 4 3094 3277 555884651 555884827 4.690000e-29 139.0
12 TraesCS3D01G360900 chr4A 81.143 175 27 6 3104 3277 500146347 500146178 6.060000e-28 135.0
13 TraesCS3D01G360900 chr6A 92.500 80 5 1 3202 3280 591950012 591950091 2.840000e-21 113.0
14 TraesCS3D01G360900 chr2D 77.647 170 30 7 3106 3275 640036505 640036666 2.860000e-16 97.1
15 TraesCS3D01G360900 chr2B 83.654 104 16 1 3174 3277 144076864 144076966 2.860000e-16 97.1
16 TraesCS3D01G360900 chr5B 89.333 75 8 0 3202 3276 332293418 332293492 1.030000e-15 95.3
17 TraesCS3D01G360900 chr4D 86.747 83 11 0 3194 3276 85346085 85346167 3.700000e-15 93.5
18 TraesCS3D01G360900 chr2A 85.393 89 11 2 3100 3186 733354125 733354037 1.330000e-14 91.6
19 TraesCS3D01G360900 chr4B 82.353 102 16 2 3194 3295 122317812 122317911 1.720000e-13 87.9
20 TraesCS3D01G360900 chr6B 86.111 72 10 0 3090 3161 11577207 11577278 1.040000e-10 78.7
21 TraesCS3D01G360900 chr7A 77.536 138 19 10 3343 3475 541424733 541424603 4.820000e-09 73.1
22 TraesCS3D01G360900 chr7A 97.368 38 1 0 244 281 118139820 118139783 8.070000e-07 65.8
23 TraesCS3D01G360900 chr7A 97.368 38 1 0 244 281 118141841 118141804 8.070000e-07 65.8


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 TraesCS3D01G360900 chr3D 474449707 474453188 3481 False 6431.000000 6431 100.000000 1 3482 1 chr3D.!!$F1 3481
1 TraesCS3D01G360900 chr3A 616724302 616727021 2719 True 3838.000000 3838 92.221000 411 3136 1 chr3A.!!$R1 2725
2 TraesCS3D01G360900 chr3B 630867971 630871956 3985 False 1533.333333 3633 88.524333 1 3482 3 chr3B.!!$F1 3481
3 TraesCS3D01G360900 chr1A 474430852 474432170 1318 True 1103.000000 1103 81.988000 1139 2460 1 chr1A.!!$R1 1321
4 TraesCS3D01G360900 chr1D 375368198 375369492 1294 True 1062.000000 1062 81.665000 1166 2460 1 chr1D.!!$R2 1294
5 TraesCS3D01G360900 chr1B 500539551 500540866 1315 False 1051.000000 1051 81.259000 1139 2460 1 chr1B.!!$F1 1321

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
994 1051 0.10852 GGTGGTAGCAATCGGTCGAA 60.109 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2663 3136 1.108776 TCGCCGCCTAAACTAGTCAT 58.891 50.0 0.0 0.0 0.0 3.06 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
39 40 1.453197 CCATAGAACCGGGTTGGGC 60.453 63.158 18.88 2.77 44.64 5.36
58 59 1.003355 AGTCCCACAAGACGCATGG 60.003 57.895 0.00 0.00 41.83 3.66
109 115 7.475137 TGTTTTGATCATTTACTAAAGGGGG 57.525 36.000 0.00 0.00 0.00 5.40
112 118 8.372459 GTTTTGATCATTTACTAAAGGGGGTTT 58.628 33.333 0.00 0.00 0.00 3.27
119 125 3.468071 ACTAAAGGGGGTTTGGGATTC 57.532 47.619 0.00 0.00 30.95 2.52
123 129 0.916809 AGGGGGTTTGGGATTCTACG 59.083 55.000 0.00 0.00 0.00 3.51
131 137 5.180271 GGTTTGGGATTCTACGTTCATACA 58.820 41.667 0.00 0.00 0.00 2.29
132 138 5.064325 GGTTTGGGATTCTACGTTCATACAC 59.936 44.000 0.00 0.00 0.00 2.90
133 139 4.395959 TGGGATTCTACGTTCATACACC 57.604 45.455 0.00 0.00 0.00 4.16
134 140 3.181484 TGGGATTCTACGTTCATACACCG 60.181 47.826 0.00 0.00 0.00 4.94
135 141 2.793232 GGATTCTACGTTCATACACCGC 59.207 50.000 0.00 0.00 0.00 5.68
136 142 2.282701 TTCTACGTTCATACACCGCC 57.717 50.000 0.00 0.00 0.00 6.13
137 143 0.457035 TCTACGTTCATACACCGCCC 59.543 55.000 0.00 0.00 0.00 6.13
138 144 0.173935 CTACGTTCATACACCGCCCA 59.826 55.000 0.00 0.00 0.00 5.36
139 145 0.108709 TACGTTCATACACCGCCCAC 60.109 55.000 0.00 0.00 0.00 4.61
140 146 2.104253 CGTTCATACACCGCCCACC 61.104 63.158 0.00 0.00 0.00 4.61
144 150 4.752594 ATACACCGCCCACCCCCT 62.753 66.667 0.00 0.00 0.00 4.79
367 396 8.122330 TCGCATTAATATGAACAGTCAAATCAC 58.878 33.333 0.00 0.00 37.30 3.06
371 400 6.801539 AATATGAACAGTCAAATCACGTGT 57.198 33.333 16.51 0.00 37.30 4.49
388 417 3.451178 ACGTGTCAATATGCTACTCCCTT 59.549 43.478 0.00 0.00 0.00 3.95
389 418 4.081087 ACGTGTCAATATGCTACTCCCTTT 60.081 41.667 0.00 0.00 0.00 3.11
393 422 4.816925 GTCAATATGCTACTCCCTTTGTCC 59.183 45.833 0.00 0.00 0.00 4.02
434 463 4.946784 ATCACGTGCCAATTTTCTACTC 57.053 40.909 11.67 0.00 0.00 2.59
443 472 4.323868 GCCAATTTTCTACTCCCTCTGTCT 60.324 45.833 0.00 0.00 0.00 3.41
445 474 3.963428 TTTTCTACTCCCTCTGTCTGC 57.037 47.619 0.00 0.00 0.00 4.26
456 486 4.962362 TCCCTCTGTCTGCAATACTTATCA 59.038 41.667 0.00 0.00 0.00 2.15
515 546 3.802722 GCGTCTAGATGCATCCATTTC 57.197 47.619 28.27 9.30 42.66 2.17
518 549 3.244353 CGTCTAGATGCATCCATTTCCCT 60.244 47.826 23.06 4.58 0.00 4.20
519 550 4.021104 CGTCTAGATGCATCCATTTCCCTA 60.021 45.833 23.06 5.55 0.00 3.53
531 562 6.995511 TCCATTTCCCTAACAAGTATTTCG 57.004 37.500 0.00 0.00 0.00 3.46
536 567 3.839490 TCCCTAACAAGTATTTCGGGACA 59.161 43.478 0.00 0.00 34.46 4.02
544 575 3.178865 AGTATTTCGGGACAAAGGGAGA 58.821 45.455 0.00 0.00 0.00 3.71
557 588 7.290481 GGGACAAAGGGAGAGAGTAGTTATTAT 59.710 40.741 0.00 0.00 0.00 1.28
558 589 8.361889 GGACAAAGGGAGAGAGTAGTTATTATC 58.638 40.741 0.00 0.00 0.00 1.75
559 590 8.840200 ACAAAGGGAGAGAGTAGTTATTATCA 57.160 34.615 0.00 0.00 0.00 2.15
560 591 8.919145 ACAAAGGGAGAGAGTAGTTATTATCAG 58.081 37.037 0.00 0.00 0.00 2.90
575 606 9.490083 AGTTATTATCAGTAACTAGGAACACCT 57.510 33.333 0.00 0.00 39.81 4.00
604 635 8.492673 AAGAGTTCGAATATTTTATGTGCAGA 57.507 30.769 0.00 0.00 0.00 4.26
649 680 4.907269 TGCTCCTAATCACCATCCTAATCA 59.093 41.667 0.00 0.00 0.00 2.57
657 688 9.650539 CTAATCACCATCCTAATCAGTAATCAG 57.349 37.037 0.00 0.00 0.00 2.90
658 689 7.623999 ATCACCATCCTAATCAGTAATCAGT 57.376 36.000 0.00 0.00 0.00 3.41
730 761 1.881973 AGGCACAAGCATAACACACAG 59.118 47.619 0.00 0.00 44.61 3.66
810 852 7.635089 GCCCAGAGAATATCCAAAACAGTAGTA 60.635 40.741 0.00 0.00 0.00 1.82
888 930 1.339727 CCTATATAAACCGCCCCAGCC 60.340 57.143 0.00 0.00 34.57 4.85
986 1043 1.746615 CAGCAGCGGTGGTAGCAAT 60.747 57.895 20.00 0.00 37.01 3.56
989 1046 2.173669 CAGCGGTGGTAGCAATCGG 61.174 63.158 6.74 4.05 37.01 4.18
993 1050 1.514087 GGTGGTAGCAATCGGTCGA 59.486 57.895 0.00 0.00 0.00 4.20
994 1051 0.108520 GGTGGTAGCAATCGGTCGAA 60.109 55.000 0.00 0.00 0.00 3.71
1200 1260 3.746949 CTCCGACCTGCCCATGCTC 62.747 68.421 0.00 0.00 38.71 4.26
1389 1452 4.814294 GCCGGCGTCGAGTTCCAT 62.814 66.667 12.58 0.00 39.00 3.41
1458 1521 4.083862 GACGTCCCCACCAGGCTC 62.084 72.222 3.51 0.00 0.00 4.70
1827 1890 4.404098 ATGGCCAACCGTCGGTCC 62.404 66.667 19.16 15.36 39.70 4.46
1878 1941 2.755469 ATGGCGCATGACCCCAAC 60.755 61.111 10.83 0.00 31.43 3.77
1879 1942 3.582242 ATGGCGCATGACCCCAACA 62.582 57.895 10.83 0.00 31.43 3.33
1880 1943 2.988684 GGCGCATGACCCCAACAA 60.989 61.111 10.83 0.00 0.00 2.83
2491 2554 3.616956 ACCTGTTGTGATCATCGATGT 57.383 42.857 24.09 12.20 0.00 3.06
2492 2555 4.736126 ACCTGTTGTGATCATCGATGTA 57.264 40.909 24.09 12.00 0.00 2.29
2493 2556 4.433615 ACCTGTTGTGATCATCGATGTAC 58.566 43.478 24.09 20.01 0.00 2.90
2494 2557 3.804325 CCTGTTGTGATCATCGATGTACC 59.196 47.826 24.09 14.53 0.00 3.34
2663 3136 2.230508 CTGGTACTCGTAGTGCTTGGAA 59.769 50.000 0.00 0.00 31.18 3.53
2678 3151 3.309954 GCTTGGAATGACTAGTTTAGGCG 59.690 47.826 0.00 0.00 36.27 5.52
2712 3187 3.781965 TGAAGGAGATGGATGGATTGTGA 59.218 43.478 0.00 0.00 0.00 3.58
2723 3198 5.010282 GGATGGATTGTGAAACTGGTAACT 58.990 41.667 0.00 0.00 38.04 2.24
2762 3237 3.698029 AGTGTTTGATTGCACAGTGTC 57.302 42.857 1.61 0.00 38.02 3.67
2841 3316 3.181479 GGAAGACACACACAGTACAGACA 60.181 47.826 0.00 0.00 0.00 3.41
2844 3324 5.122512 AGACACACACAGTACAGACATAC 57.877 43.478 0.00 0.00 0.00 2.39
2851 3331 4.142665 ACACAGTACAGACATACTACTGCG 60.143 45.833 0.00 0.00 38.22 5.18
2887 3367 3.566322 CCTAATCGCACACTAGCTAGACT 59.434 47.826 27.45 8.35 0.00 3.24
2964 3444 6.458342 CGGCTTAACAAATAATTCCTCCTCAC 60.458 42.308 0.00 0.00 0.00 3.51
2974 3454 4.056125 CTCCTCACTCCGTGCGCA 62.056 66.667 5.66 5.66 32.98 6.09
2998 3478 5.094134 GTCCAGTAATGTACTTCAGTCGTC 58.906 45.833 0.00 0.00 36.76 4.20
3016 3496 7.117236 TCAGTCGTCTCAAAACATAAACCATAC 59.883 37.037 0.00 0.00 0.00 2.39
3019 3499 7.062138 GTCGTCTCAAAACATAAACCATACGTA 59.938 37.037 0.00 0.00 0.00 3.57
3020 3500 7.274033 TCGTCTCAAAACATAAACCATACGTAG 59.726 37.037 0.08 0.00 0.00 3.51
3035 3515 7.778083 ACCATACGTAGATACATCTGTTTGAA 58.222 34.615 0.08 0.00 37.76 2.69
3044 3524 4.795970 ACATCTGTTTGAACGTCAAGTC 57.204 40.909 0.00 0.00 37.70 3.01
3048 3528 5.811399 TCTGTTTGAACGTCAAGTCATTT 57.189 34.783 0.00 0.00 37.70 2.32
3094 3578 3.858247 ACTAATGGCCGAGTACTTTGAC 58.142 45.455 0.00 0.00 0.00 3.18
3102 3586 1.798813 CGAGTACTTTGACAAGGGTGC 59.201 52.381 0.00 3.38 33.82 5.01
3120 3604 2.226912 GTGCGGCTAGATCTTAGTCGAT 59.773 50.000 22.13 0.00 44.51 3.59
3136 3620 4.487002 GTCGATTGAGACTTAACGAAGC 57.513 45.455 0.00 0.00 38.09 3.86
3137 3621 3.303760 GTCGATTGAGACTTAACGAAGCC 59.696 47.826 0.00 0.00 38.09 4.35
3138 3622 3.192844 TCGATTGAGACTTAACGAAGCCT 59.807 43.478 0.00 0.00 35.97 4.58
3139 3623 3.927142 CGATTGAGACTTAACGAAGCCTT 59.073 43.478 0.00 0.00 35.97 4.35
3140 3624 5.100259 CGATTGAGACTTAACGAAGCCTTA 58.900 41.667 0.00 0.00 35.97 2.69
3143 3627 5.056894 TGAGACTTAACGAAGCCTTAGTC 57.943 43.478 0.00 0.00 35.97 2.59
3147 3631 5.010820 AGACTTAACGAAGCCTTAGTCAAGT 59.989 40.000 6.00 6.00 35.97 3.16
3255 3739 6.576662 TGACTGAGACTTCGTTAAATCTCT 57.423 37.500 0.00 0.00 38.72 3.10
3256 3740 7.683437 TGACTGAGACTTCGTTAAATCTCTA 57.317 36.000 0.00 0.00 38.72 2.43
3259 3743 8.282455 ACTGAGACTTCGTTAAATCTCTATCA 57.718 34.615 0.00 0.00 38.72 2.15
3278 3777 8.027524 TCTATCAACTGAGATTTAGCAATCCT 57.972 34.615 0.00 0.00 39.95 3.24
3323 3919 8.091449 ACTCATTCTGATTCGGTTTATAGGATC 58.909 37.037 0.00 0.00 0.00 3.36
3325 3921 5.386958 TCTGATTCGGTTTATAGGATCGG 57.613 43.478 0.00 0.00 0.00 4.18
3331 3927 2.490991 GGTTTATAGGATCGGTGTGGC 58.509 52.381 0.00 0.00 0.00 5.01
3334 3930 1.629043 TATAGGATCGGTGTGGCCTC 58.371 55.000 3.32 0.00 34.25 4.70
3336 3932 1.043116 TAGGATCGGTGTGGCCTCTG 61.043 60.000 3.32 0.00 34.25 3.35
3337 3933 2.660064 GGATCGGTGTGGCCTCTGT 61.660 63.158 3.32 0.00 34.25 3.41
3343 3939 1.004440 GTGTGGCCTCTGTGTCCTC 60.004 63.158 3.32 0.00 0.00 3.71
3345 3941 1.294780 GTGGCCTCTGTGTCCTCAG 59.705 63.158 3.32 0.00 36.85 3.35
3356 3952 4.058817 CTGTGTCCTCAGTTTGACTAACC 58.941 47.826 0.00 0.00 37.46 2.85
3357 3953 3.709653 TGTGTCCTCAGTTTGACTAACCT 59.290 43.478 0.00 0.00 37.46 3.50
3367 3963 7.728148 TCAGTTTGACTAACCTACATGTGTTA 58.272 34.615 9.11 8.50 37.46 2.41
3397 3993 7.396907 ACCATCAAAAGTGTATCATTGGATTCA 59.603 33.333 0.00 0.00 34.89 2.57
3433 4029 7.442969 ACAATTTTCAGACACATAGTTTCGGTA 59.557 33.333 0.00 0.00 0.00 4.02
3434 4030 7.596749 ATTTTCAGACACATAGTTTCGGTAG 57.403 36.000 0.00 0.00 0.00 3.18
3474 4070 5.526115 TGTTAGTCAAAACTGACGACCTAG 58.474 41.667 0.00 0.00 43.17 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.535335 GGTTCTATGGCGACTGGTCA 59.465 55.000 0.00 0.00 32.67 4.02
39 40 1.300971 CCATGCGTCTTGTGGGACTG 61.301 60.000 0.00 0.00 34.38 3.51
58 59 3.248171 GTCACACCGAGCGATCGC 61.248 66.667 32.15 32.15 42.33 4.58
69 70 2.396590 AACATATCCACCGGTCACAC 57.603 50.000 2.59 0.00 0.00 3.82
109 115 5.064325 GGTGTATGAACGTAGAATCCCAAAC 59.936 44.000 0.00 0.00 0.00 2.93
112 118 3.181484 CGGTGTATGAACGTAGAATCCCA 60.181 47.826 0.00 0.00 0.00 4.37
119 125 0.173935 TGGGCGGTGTATGAACGTAG 59.826 55.000 0.00 0.00 0.00 3.51
123 129 1.747745 GGGTGGGCGGTGTATGAAC 60.748 63.158 0.00 0.00 0.00 3.18
202 212 1.441738 GGCCGGTTAAAGCGACTTAA 58.558 50.000 1.90 0.00 42.41 1.85
203 213 0.391528 GGGCCGGTTAAAGCGACTTA 60.392 55.000 1.90 0.00 42.41 2.24
207 217 1.450669 GATGGGCCGGTTAAAGCGA 60.451 57.895 1.90 0.00 42.41 4.93
303 332 8.729805 ATGTTTGCCAAATAAAAACTTTCTCA 57.270 26.923 0.00 0.00 35.35 3.27
340 369 8.122330 TGATTTGACTGTTCATATTAATGCGAC 58.878 33.333 0.00 0.00 32.76 5.19
342 371 7.110628 CGTGATTTGACTGTTCATATTAATGCG 59.889 37.037 0.00 0.00 32.76 4.73
367 396 3.735237 AGGGAGTAGCATATTGACACG 57.265 47.619 0.00 0.00 0.00 4.49
371 400 4.473196 TGGACAAAGGGAGTAGCATATTGA 59.527 41.667 0.00 0.00 0.00 2.57
393 422 9.825972 ACGTGATTTGTTTGATAAGTATTTCTG 57.174 29.630 0.00 0.00 0.00 3.02
434 463 5.282055 TGATAAGTATTGCAGACAGAGGG 57.718 43.478 3.91 0.00 0.00 4.30
473 503 8.213518 ACGCATTTTAGTTTCAGATACATCAT 57.786 30.769 0.00 0.00 0.00 2.45
482 512 6.183360 TGCATCTAGACGCATTTTAGTTTCAG 60.183 38.462 9.88 0.00 31.95 3.02
484 514 6.106877 TGCATCTAGACGCATTTTAGTTTC 57.893 37.500 9.88 0.00 31.95 2.78
495 525 2.481952 GGAAATGGATGCATCTAGACGC 59.518 50.000 25.28 3.27 0.00 5.19
515 546 4.210724 TGTCCCGAAATACTTGTTAGGG 57.789 45.455 0.00 0.00 38.73 3.53
518 549 5.005094 CCCTTTGTCCCGAAATACTTGTTA 58.995 41.667 0.00 0.00 0.00 2.41
519 550 3.824443 CCCTTTGTCCCGAAATACTTGTT 59.176 43.478 0.00 0.00 0.00 2.83
531 562 2.822697 ACTACTCTCTCCCTTTGTCCC 58.177 52.381 0.00 0.00 0.00 4.46
557 588 4.122337 TGGAGGTGTTCCTAGTTACTGA 57.878 45.455 0.00 0.00 46.92 3.41
558 589 4.884668 TTGGAGGTGTTCCTAGTTACTG 57.115 45.455 0.00 0.00 46.92 2.74
559 590 5.152934 TCTTTGGAGGTGTTCCTAGTTACT 58.847 41.667 0.00 0.00 46.92 2.24
560 591 5.011840 ACTCTTTGGAGGTGTTCCTAGTTAC 59.988 44.000 0.00 0.00 46.92 2.50
568 599 3.107642 TCGAACTCTTTGGAGGTGTTC 57.892 47.619 0.00 0.00 40.00 3.18
575 606 8.181573 GCACATAAAATATTCGAACTCTTTGGA 58.818 33.333 0.00 0.00 0.00 3.53
604 635 2.621055 TCAGCGTTAGCCAATTTGTTGT 59.379 40.909 0.00 0.00 46.67 3.32
730 761 7.396540 AATCAGATAAAGGAACAACCACATC 57.603 36.000 0.00 0.00 42.04 3.06
810 852 6.041069 GCATCAGTACCTTCTCTACCAGTAAT 59.959 42.308 0.00 0.00 0.00 1.89
888 930 0.533531 TTGTGCTGGACAGTGAGCAG 60.534 55.000 5.30 0.00 45.70 4.24
917 959 1.228862 CCAAGGAGGTGGTTTGGGG 60.229 63.158 0.00 0.00 38.12 4.96
989 1046 1.003839 TGAGCCATGGGTGTTCGAC 60.004 57.895 23.86 6.11 0.00 4.20
993 1050 0.682209 GCATCTGAGCCATGGGTGTT 60.682 55.000 23.86 0.00 0.00 3.32
994 1051 1.077212 GCATCTGAGCCATGGGTGT 60.077 57.895 23.86 1.24 0.00 4.16
1200 1260 1.489481 TCTGGATGTAGTGGCAGGAG 58.511 55.000 0.00 0.00 0.00 3.69
1458 1521 1.074951 GGGGAACAGGTCCTTGGTG 59.925 63.158 3.92 0.00 46.92 4.17
1524 1587 1.739562 GAGCACGGTGAGCTGGAAG 60.740 63.158 13.29 0.00 43.58 3.46
1878 1941 3.121030 CGCGCCTCCTGGTTCTTG 61.121 66.667 0.00 0.00 35.27 3.02
2124 2187 2.882777 CTCGCGTGCAGCTTCGAT 60.883 61.111 5.77 0.00 45.59 3.59
2494 2557 3.782443 GCACTGACCGGTAGGGGG 61.782 72.222 7.34 2.42 43.47 5.40
2550 3016 2.044806 ATGTCATGGCGGCCCTACTC 62.045 60.000 17.97 4.07 0.00 2.59
2663 3136 1.108776 TCGCCGCCTAAACTAGTCAT 58.891 50.000 0.00 0.00 0.00 3.06
2678 3151 3.793144 CCTTCAGCAAGCGTCGCC 61.793 66.667 14.86 0.00 0.00 5.54
2712 3187 7.343574 ACAACCTTATTTCCAAGTTACCAGTTT 59.656 33.333 0.00 0.00 0.00 2.66
2723 3198 6.783708 ACACTTTCACAACCTTATTTCCAA 57.216 33.333 0.00 0.00 0.00 3.53
2762 3237 3.452474 GATCGACAAGGAGAACTCATGG 58.548 50.000 4.23 0.00 0.00 3.66
2841 3316 4.835927 GCTGGTGCGCAGTAGTAT 57.164 55.556 12.22 0.00 0.00 2.12
2862 3342 1.683917 AGCTAGTGTGCGATTAGGAGG 59.316 52.381 0.00 0.00 38.13 4.30
2887 3367 8.981659 TCAAGGATCTACTTCATGTCTTAATCA 58.018 33.333 0.00 0.00 0.00 2.57
2964 3444 2.486636 TTACTGGACTGCGCACGGAG 62.487 60.000 5.66 10.15 39.56 4.63
3016 3496 5.798434 TGACGTTCAAACAGATGTATCTACG 59.202 40.000 9.72 9.72 37.40 3.51
3019 3499 6.223852 ACTTGACGTTCAAACAGATGTATCT 58.776 36.000 0.00 0.00 35.73 1.98
3020 3500 6.145534 TGACTTGACGTTCAAACAGATGTATC 59.854 38.462 0.00 0.00 35.73 2.24
3035 3515 1.001048 TCGTCCGAAATGACTTGACGT 60.001 47.619 9.74 0.00 46.41 4.34
3044 3524 6.270815 TCTTATACTTCCTTCGTCCGAAATG 58.729 40.000 3.52 0.00 33.34 2.32
3048 3528 6.994496 TCTTATCTTATACTTCCTTCGTCCGA 59.006 38.462 0.00 0.00 0.00 4.55
3094 3578 0.179000 AAGATCTAGCCGCACCCTTG 59.821 55.000 0.00 0.00 0.00 3.61
3102 3586 4.452795 TCTCAATCGACTAAGATCTAGCCG 59.547 45.833 0.00 0.00 0.00 5.52
3132 3616 4.258702 TCTGTCACTTGACTAAGGCTTC 57.741 45.455 1.30 0.00 44.99 3.86
3136 3620 9.653287 TTTATATGTTCTGTCACTTGACTAAGG 57.347 33.333 10.63 0.00 44.99 2.69
3140 3624 9.778741 TCTTTTTATATGTTCTGTCACTTGACT 57.221 29.630 10.63 0.00 44.99 3.41
3208 3692 9.578439 TCAATGCTATATTCATGAGATCTTACG 57.422 33.333 0.00 0.00 0.00 3.18
3220 3704 6.920210 CGAAGTCTCAGTCAATGCTATATTCA 59.080 38.462 0.00 0.00 0.00 2.57
3228 3712 5.591643 TTTAACGAAGTCTCAGTCAATGC 57.408 39.130 0.00 0.00 45.00 3.56
3255 3739 6.484643 GCAGGATTGCTAAATCTCAGTTGATA 59.515 38.462 0.00 0.00 46.95 2.15
3256 3740 5.298777 GCAGGATTGCTAAATCTCAGTTGAT 59.701 40.000 0.00 0.00 46.95 2.57
3301 3897 6.014499 ACCGATCCTATAAACCGAATCAGAAT 60.014 38.462 0.00 0.00 0.00 2.40
3310 3906 2.750948 CCACACCGATCCTATAAACCG 58.249 52.381 0.00 0.00 0.00 4.44
3319 3915 2.187946 CAGAGGCCACACCGATCC 59.812 66.667 5.01 0.00 46.52 3.36
3323 3919 2.357517 GACACAGAGGCCACACCG 60.358 66.667 5.01 0.00 46.52 4.94
3331 3927 2.366916 AGTCAAACTGAGGACACAGAGG 59.633 50.000 3.79 0.00 40.63 3.69
3334 3930 4.058817 GGTTAGTCAAACTGAGGACACAG 58.941 47.826 0.00 0.00 42.78 3.66
3336 3932 4.338379 AGGTTAGTCAAACTGAGGACAC 57.662 45.455 0.00 0.00 38.23 3.67
3337 3933 4.897076 TGTAGGTTAGTCAAACTGAGGACA 59.103 41.667 0.00 0.00 38.23 4.02
3343 3939 6.861065 AACACATGTAGGTTAGTCAAACTG 57.139 37.500 0.00 0.00 38.23 3.16
3417 4013 7.650504 TGTTATATGCTACCGAAACTATGTGTC 59.349 37.037 0.00 0.00 0.00 3.67
3464 4060 4.428845 GGGTGTCCTAGGTCGTCA 57.571 61.111 9.08 1.88 0.00 4.35


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

AutoCloner maintained by Alex Coulton.