Multiple sequence alignment - TraesCS4D01G136300

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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 TraesCS4D01G136300 chr4D 100.000 4025 0 0 1 4025 122276081 122272057 0.000000e+00 7433.0
1 TraesCS4D01G136300 chr4D 84.669 2146 261 39 992 3098 122287422 122285306 0.000000e+00 2078.0
2 TraesCS4D01G136300 chr4D 97.087 103 3 0 3248 3350 72678775 72678673 1.490000e-39 174.0
3 TraesCS4D01G136300 chr4D 95.181 83 2 1 3723 3803 48073558 48073640 3.260000e-26 130.0
4 TraesCS4D01G136300 chr4A 92.740 4036 195 61 14 4025 448091168 448095129 0.000000e+00 5740.0
5 TraesCS4D01G136300 chr4A 84.188 2106 262 44 992 3059 447791679 447793751 0.000000e+00 1978.0
6 TraesCS4D01G136300 chr4B 96.740 2761 76 7 513 3268 185911501 185908750 0.000000e+00 4588.0
7 TraesCS4D01G136300 chr4B 83.947 2118 269 45 992 3070 186592977 186590892 0.000000e+00 1962.0
8 TraesCS4D01G136300 chr4B 92.982 399 26 2 3324 3721 185908628 185908231 7.500000e-162 580.0
9 TraesCS4D01G136300 chr4B 95.671 231 10 0 3795 4025 185908247 185908017 4.910000e-99 372.0
10 TraesCS4D01G136300 chr4B 88.889 99 8 3 3723 3820 131711644 131711740 7.070000e-23 119.0
11 TraesCS4D01G136300 chr7D 98.113 106 2 0 3248 3353 60439692 60439587 6.870000e-43 185.0
12 TraesCS4D01G136300 chr7D 97.297 74 2 0 3723 3796 160552310 160552383 4.220000e-25 126.0
13 TraesCS4D01G136300 chr7A 99.029 103 1 0 3247 3349 222500873 222500975 6.870000e-43 185.0
14 TraesCS4D01G136300 chr7A 78.667 225 33 10 310 521 116191035 116190813 7.020000e-28 135.0
15 TraesCS4D01G136300 chr5A 89.262 149 12 4 3880 4025 671167577 671167724 2.470000e-42 183.0
16 TraesCS4D01G136300 chr5A 95.327 107 4 1 3248 3354 405160218 405160113 6.920000e-38 169.0
17 TraesCS4D01G136300 chr5A 79.545 220 33 12 308 521 401763835 401764048 3.240000e-31 147.0
18 TraesCS4D01G136300 chrUn 96.364 110 4 0 3246 3355 305213130 305213239 8.890000e-42 182.0
19 TraesCS4D01G136300 chr1D 94.690 113 3 3 3243 3354 472174540 472174430 5.350000e-39 172.0
20 TraesCS4D01G136300 chr5B 95.327 107 4 1 3248 3354 56123452 56123347 6.920000e-38 169.0
21 TraesCS4D01G136300 chr2D 93.103 116 7 1 3242 3356 13147724 13147609 6.920000e-38 169.0
22 TraesCS4D01G136300 chr2A 95.327 107 4 1 3248 3354 704122592 704122487 6.920000e-38 169.0
23 TraesCS4D01G136300 chr3A 78.189 243 39 13 310 542 722453601 722453363 4.190000e-30 143.0
24 TraesCS4D01G136300 chr3A 78.222 225 39 9 305 521 588838335 588838113 7.020000e-28 135.0
25 TraesCS4D01G136300 chr3A 93.976 83 3 2 3723 3805 457630666 457630586 1.520000e-24 124.0
26 TraesCS4D01G136300 chr3A 88.776 98 9 2 3723 3819 596803986 596803890 7.070000e-23 119.0
27 TraesCS4D01G136300 chr3B 97.368 76 2 0 3723 3798 400338457 400338382 3.260000e-26 130.0
28 TraesCS4D01G136300 chr6A 93.182 88 4 2 3723 3809 104306573 104306487 1.170000e-25 128.0
29 TraesCS4D01G136300 chr6A 81.443 97 11 7 447 539 582518090 582518183 5.580000e-09 73.1
30 TraesCS4D01G136300 chr2B 92.045 88 5 2 3723 3809 286979560 286979646 5.460000e-24 122.0
31 TraesCS4D01G136300 chr6B 77.273 220 24 16 310 519 544633501 544633298 5.500000e-19 106.0


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 TraesCS4D01G136300 chr4D 122272057 122276081 4024 True 7433.000000 7433 100.000 1 4025 1 chr4D.!!$R2 4024
1 TraesCS4D01G136300 chr4D 122285306 122287422 2116 True 2078.000000 2078 84.669 992 3098 1 chr4D.!!$R3 2106
2 TraesCS4D01G136300 chr4A 448091168 448095129 3961 False 5740.000000 5740 92.740 14 4025 1 chr4A.!!$F2 4011
3 TraesCS4D01G136300 chr4A 447791679 447793751 2072 False 1978.000000 1978 84.188 992 3059 1 chr4A.!!$F1 2067
4 TraesCS4D01G136300 chr4B 186590892 186592977 2085 True 1962.000000 1962 83.947 992 3070 1 chr4B.!!$R1 2078
5 TraesCS4D01G136300 chr4B 185908017 185911501 3484 True 1846.666667 4588 95.131 513 4025 3 chr4B.!!$R2 3512

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
993 1004 0.036577 AACACAGCCTAGCAGAGCAG 60.037 55.0 0.0 0.0 0.00 4.24 F
994 1005 0.902048 ACACAGCCTAGCAGAGCAGA 60.902 55.0 0.0 0.0 0.00 4.26 F
1140 1160 0.948623 CCTCGTTTGACGACATGGCA 60.949 55.0 0.0 0.0 46.73 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2222 1.000274 GCAAAGATGAACGCCACCTTT 60.000 47.619 0.00 0.0 0.00 3.11 R
2721 2795 3.182590 AAGCAGCAGACGCCCTTCA 62.183 57.895 0.00 0.0 39.83 3.02 R
3105 3186 5.769662 TGGCACCATGGAATTATAAGATCAC 59.230 40.000 21.47 0.0 0.00 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
21 22 0.174162 GATTGCAACCAGGATGCCAC 59.826 55.000 18.59 6.67 43.16 5.01
22 23 1.259840 ATTGCAACCAGGATGCCACC 61.260 55.000 18.59 0.00 43.16 4.61
26 27 2.971598 AACCAGGATGCCACCGAGG 61.972 63.158 0.00 0.00 41.84 4.63
28 29 2.187946 CAGGATGCCACCGAGGAC 59.812 66.667 0.00 0.00 41.22 3.85
32 33 1.305930 GGATGCCACCGAGGACAAAC 61.306 60.000 0.00 0.00 41.22 2.93
35 36 1.070786 GCCACCGAGGACAAACAGA 59.929 57.895 0.00 0.00 41.22 3.41
39 40 2.233922 CCACCGAGGACAAACAGACTAT 59.766 50.000 0.00 0.00 41.22 2.12
41 42 2.163815 ACCGAGGACAAACAGACTATCG 59.836 50.000 0.00 0.00 0.00 2.92
53 54 3.067461 ACAGACTATCGGACATGCTCTTC 59.933 47.826 0.00 0.00 0.00 2.87
59 60 1.153349 GGACATGCTCTTCCGGTCC 60.153 63.158 0.00 0.00 41.00 4.46
71 72 0.252057 TCCGGTCCTCCACATCTCAA 60.252 55.000 0.00 0.00 0.00 3.02
72 73 0.613260 CCGGTCCTCCACATCTCAAA 59.387 55.000 0.00 0.00 0.00 2.69
87 88 3.390135 TCTCAAACCATGTTCGAGTCAC 58.610 45.455 0.00 0.00 0.00 3.67
88 89 3.069586 TCTCAAACCATGTTCGAGTCACT 59.930 43.478 0.00 0.00 0.00 3.41
89 90 3.130633 TCAAACCATGTTCGAGTCACTG 58.869 45.455 0.00 0.00 0.00 3.66
90 91 2.872245 CAAACCATGTTCGAGTCACTGT 59.128 45.455 0.00 0.00 0.00 3.55
91 92 4.055360 CAAACCATGTTCGAGTCACTGTA 58.945 43.478 0.00 0.00 0.00 2.74
92 93 3.299340 ACCATGTTCGAGTCACTGTAC 57.701 47.619 0.00 0.00 0.00 2.90
100 101 4.126208 TCGAGTCACTGTACCAAACAAA 57.874 40.909 0.00 0.00 37.74 2.83
101 102 4.505808 TCGAGTCACTGTACCAAACAAAA 58.494 39.130 0.00 0.00 37.74 2.44
103 104 5.007234 TCGAGTCACTGTACCAAACAAAATG 59.993 40.000 0.00 0.00 37.74 2.32
108 109 5.124138 TCACTGTACCAAACAAAATGTCGTT 59.876 36.000 0.00 0.00 37.74 3.85
137 138 6.555463 AAAATCCTAGTCTGATTTACGGGA 57.445 37.500 6.05 0.00 40.57 5.14
140 141 4.800023 TCCTAGTCTGATTTACGGGATGA 58.200 43.478 0.00 0.00 0.00 2.92
187 188 2.730672 CTACGCCGCTGCAGTGAAC 61.731 63.158 28.54 17.99 37.32 3.18
192 193 2.227968 GCCGCTGCAGTGAACGTAAG 62.228 60.000 28.54 10.72 40.05 2.34
197 198 2.932614 GCTGCAGTGAACGTAAGATGAT 59.067 45.455 16.64 0.00 43.62 2.45
206 207 5.689514 GTGAACGTAAGATGATGATCCTCTG 59.310 44.000 0.92 0.00 43.62 3.35
236 237 9.283768 TGTGAGCTTAAAATCTTACATCTTTCA 57.716 29.630 0.00 0.00 0.00 2.69
248 249 9.807649 ATCTTACATCTTTCATTTTAACATGCC 57.192 29.630 0.00 0.00 0.00 4.40
257 259 6.211587 TCATTTTAACATGCCTTGGATCTG 57.788 37.500 0.00 0.00 0.00 2.90
273 275 4.823442 TGGATCTGGATGCAAATATGTGAC 59.177 41.667 0.00 0.00 36.19 3.67
274 276 4.217118 GGATCTGGATGCAAATATGTGACC 59.783 45.833 0.00 0.00 0.00 4.02
275 277 4.233632 TCTGGATGCAAATATGTGACCA 57.766 40.909 0.00 2.32 0.00 4.02
276 278 4.201657 TCTGGATGCAAATATGTGACCAG 58.798 43.478 19.40 19.40 40.15 4.00
279 281 3.554934 GATGCAAATATGTGACCAGGGA 58.445 45.455 0.00 0.00 0.00 4.20
282 284 3.088532 GCAAATATGTGACCAGGGACAA 58.911 45.455 0.00 0.00 0.00 3.18
345 348 8.980610 TGCATATCAAATTTGTTTGAAGTCAAG 58.019 29.630 17.47 0.00 43.28 3.02
346 349 8.981647 GCATATCAAATTTGTTTGAAGTCAAGT 58.018 29.630 17.47 0.00 43.28 3.16
351 354 8.816144 TCAAATTTGTTTGAAGTCAAGTTATGC 58.184 29.630 17.47 0.00 37.93 3.14
358 361 7.487829 TGTTTGAAGTCAAGTTATGCAAAGTTC 59.512 33.333 0.00 0.00 37.15 3.01
359 362 5.747565 TGAAGTCAAGTTATGCAAAGTTCG 58.252 37.500 0.00 0.00 0.00 3.95
361 364 5.344207 AGTCAAGTTATGCAAAGTTCGAC 57.656 39.130 0.00 6.97 0.00 4.20
369 372 6.983890 AGTTATGCAAAGTTCGACCAAATTTT 59.016 30.769 0.00 0.00 29.75 1.82
370 373 8.138712 AGTTATGCAAAGTTCGACCAAATTTTA 58.861 29.630 0.00 0.00 29.75 1.52
373 378 7.171447 TGCAAAGTTCGACCAAATTTTATTG 57.829 32.000 0.00 0.00 29.75 1.90
375 380 7.492669 TGCAAAGTTCGACCAAATTTTATTGAA 59.507 29.630 0.00 0.00 29.75 2.69
570 576 2.504175 CCTAGCTTGCTTAGGGTTGGTA 59.496 50.000 0.00 0.00 35.13 3.25
602 613 3.887716 AGCTCAGCTCATTTTGTTCTTGT 59.112 39.130 0.00 0.00 30.62 3.16
810 821 5.334414 GGAGTTGCAGTTGAGTATTTGACTG 60.334 44.000 0.00 0.00 39.06 3.51
929 940 5.471456 CAGAGCTTCACAGTGGAGTAAATTT 59.529 40.000 10.78 0.00 0.00 1.82
941 952 9.057089 CAGTGGAGTAAATTTCACTTCTTTAGT 57.943 33.333 7.36 0.00 38.27 2.24
993 1004 0.036577 AACACAGCCTAGCAGAGCAG 60.037 55.000 0.00 0.00 0.00 4.24
994 1005 0.902048 ACACAGCCTAGCAGAGCAGA 60.902 55.000 0.00 0.00 0.00 4.26
1140 1160 0.948623 CCTCGTTTGACGACATGGCA 60.949 55.000 0.00 0.00 46.73 4.92
1804 1875 1.427020 GTTCAGCAGCTTCGCATCC 59.573 57.895 0.00 0.00 0.00 3.51
1845 1916 2.011122 AGAACAGACGGAAGAAGGGA 57.989 50.000 0.00 0.00 0.00 4.20
1929 2003 2.267006 CAGGCGCTGTCCACAGAT 59.733 61.111 7.64 0.00 46.59 2.90
2004 2078 2.403378 GGGTAATGCGGCGCAAAGA 61.403 57.895 39.46 23.26 43.62 2.52
2595 2669 1.817099 CAGGAAGATGCGCCCAGAC 60.817 63.158 4.18 0.00 0.00 3.51
3041 3115 6.127786 GCAACCTAGCTTCTTTTCTCAATCAT 60.128 38.462 0.00 0.00 0.00 2.45
3046 3121 9.823647 CCTAGCTTCTTTTCTCAATCATACTTA 57.176 33.333 0.00 0.00 0.00 2.24
3105 3186 6.992063 AGTTAGCACTTATCTCACCATTTG 57.008 37.500 0.00 0.00 0.00 2.32
3257 3338 2.972713 GTCTTGGCATATACTCCCTCCA 59.027 50.000 0.00 0.00 0.00 3.86
3268 3397 7.337942 GCATATACTCCCTCCATTCCAAAATAG 59.662 40.741 0.00 0.00 0.00 1.73
3269 3398 8.605947 CATATACTCCCTCCATTCCAAAATAGA 58.394 37.037 0.00 0.00 0.00 1.98
3273 3402 5.694995 TCCCTCCATTCCAAAATAGATGAC 58.305 41.667 0.00 0.00 0.00 3.06
3280 3409 7.890127 TCCATTCCAAAATAGATGACTCAACTT 59.110 33.333 0.00 0.00 0.00 2.66
3282 3411 9.350357 CATTCCAAAATAGATGACTCAACTTTG 57.650 33.333 0.00 0.00 0.00 2.77
3285 3414 8.999431 TCCAAAATAGATGACTCAACTTTGTAC 58.001 33.333 0.00 0.00 0.00 2.90
3319 3448 9.716531 AGTACAAAGTTAGTATAAAGTTGGGTC 57.283 33.333 0.00 0.00 0.00 4.46
3320 3449 9.492973 GTACAAAGTTAGTATAAAGTTGGGTCA 57.507 33.333 0.00 0.00 0.00 4.02
3322 3451 9.227777 ACAAAGTTAGTATAAAGTTGGGTCATC 57.772 33.333 0.00 0.00 0.00 2.92
3371 3518 1.488390 AATTGGATGCTTCGGCCATT 58.512 45.000 2.24 0.00 40.91 3.16
3395 3542 4.442073 GTGTTGCTGCAGATTTTGTAACAG 59.558 41.667 20.43 0.00 0.00 3.16
3411 3558 4.400884 TGTAACAGCACACCACAAAATCTT 59.599 37.500 0.00 0.00 0.00 2.40
3417 3564 3.320826 GCACACCACAAAATCTTTAGGGT 59.679 43.478 0.00 0.00 0.00 4.34
3467 3614 1.035139 ACTTGCTTTTGAGCCTGTGG 58.965 50.000 0.00 0.00 0.00 4.17
3468 3615 1.321474 CTTGCTTTTGAGCCTGTGGA 58.679 50.000 0.00 0.00 0.00 4.02
3501 3648 4.397417 AGATATGTGTTGAAGCCTCAAAGC 59.603 41.667 0.00 0.00 43.18 3.51
3504 3651 0.670162 TGTTGAAGCCTCAAAGCTGC 59.330 50.000 0.00 0.00 44.11 5.25
3607 3754 2.442212 TGAAGTTTGCACCGACGATA 57.558 45.000 0.00 0.00 0.00 2.92
3730 3877 1.334160 TCGGGCAAGCCGATCTTATA 58.666 50.000 4.80 0.00 36.85 0.98
3752 3899 1.139256 GTTTCAGCTCTAGCCTACCCC 59.861 57.143 0.00 0.00 43.38 4.95
3786 3933 4.803613 GGACTAAAGGCTTTGTTGTTGTTG 59.196 41.667 22.32 0.00 0.00 3.33
3787 3934 5.400066 ACTAAAGGCTTTGTTGTTGTTGT 57.600 34.783 22.32 0.00 0.00 3.32
3789 3936 5.637387 ACTAAAGGCTTTGTTGTTGTTGTTG 59.363 36.000 22.32 0.00 0.00 3.33
3790 3937 3.676291 AGGCTTTGTTGTTGTTGTTGT 57.324 38.095 0.00 0.00 0.00 3.32
3791 3938 4.001618 AGGCTTTGTTGTTGTTGTTGTT 57.998 36.364 0.00 0.00 0.00 2.83
3792 3939 4.384940 AGGCTTTGTTGTTGTTGTTGTTT 58.615 34.783 0.00 0.00 0.00 2.83
3793 3940 4.213059 AGGCTTTGTTGTTGTTGTTGTTTG 59.787 37.500 0.00 0.00 0.00 2.93
3997 4144 2.507407 TACATGGCCAGAGAAAACCC 57.493 50.000 13.05 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.679559 GGCATCCTGGTTGCAATCCC 61.680 60.000 26.21 2.89 41.95 3.85
1 2 0.971959 TGGCATCCTGGTTGCAATCC 60.972 55.000 26.21 9.04 41.95 3.01
4 5 1.907807 GGTGGCATCCTGGTTGCAA 60.908 57.895 26.21 16.12 41.95 4.08
5 6 2.283101 GGTGGCATCCTGGTTGCA 60.283 61.111 26.21 12.97 41.95 4.08
6 7 3.443045 CGGTGGCATCCTGGTTGC 61.443 66.667 19.19 19.19 39.41 4.17
7 8 1.746615 CTCGGTGGCATCCTGGTTG 60.747 63.158 0.22 0.22 0.00 3.77
8 9 2.671070 CTCGGTGGCATCCTGGTT 59.329 61.111 0.00 0.00 0.00 3.67
9 10 3.402681 CCTCGGTGGCATCCTGGT 61.403 66.667 0.00 0.00 0.00 4.00
10 11 3.083349 TCCTCGGTGGCATCCTGG 61.083 66.667 0.00 0.00 35.26 4.45
11 12 2.184020 TTGTCCTCGGTGGCATCCTG 62.184 60.000 0.00 0.00 35.26 3.86
12 13 1.488705 TTTGTCCTCGGTGGCATCCT 61.489 55.000 0.00 0.00 35.26 3.24
15 16 0.606401 CTGTTTGTCCTCGGTGGCAT 60.606 55.000 0.00 0.00 35.26 4.40
21 22 2.479730 CCGATAGTCTGTTTGTCCTCGG 60.480 54.545 0.00 0.00 38.51 4.63
22 23 2.422479 TCCGATAGTCTGTTTGTCCTCG 59.578 50.000 0.00 0.00 0.00 4.63
26 27 3.307242 GCATGTCCGATAGTCTGTTTGTC 59.693 47.826 0.00 0.00 0.00 3.18
28 29 3.525537 AGCATGTCCGATAGTCTGTTTG 58.474 45.455 0.00 0.00 0.00 2.93
32 33 3.551863 GGAAGAGCATGTCCGATAGTCTG 60.552 52.174 0.00 0.00 0.00 3.51
41 42 1.153349 GGACCGGAAGAGCATGTCC 60.153 63.158 9.46 0.00 38.78 4.02
53 54 0.613260 TTTGAGATGTGGAGGACCGG 59.387 55.000 0.00 0.00 39.42 5.28
59 60 3.125829 CGAACATGGTTTGAGATGTGGAG 59.874 47.826 0.00 0.00 33.03 3.86
71 72 2.910688 ACAGTGACTCGAACATGGTT 57.089 45.000 0.00 0.00 0.00 3.67
72 73 2.029290 GGTACAGTGACTCGAACATGGT 60.029 50.000 0.00 0.00 0.00 3.55
87 88 5.574082 TCAACGACATTTTGTTTGGTACAG 58.426 37.500 0.00 0.00 42.39 2.74
88 89 5.562506 TCAACGACATTTTGTTTGGTACA 57.437 34.783 0.00 0.00 34.12 2.90
89 90 9.828852 TTATATCAACGACATTTTGTTTGGTAC 57.171 29.630 0.00 0.00 0.00 3.34
91 92 9.751542 TTTTATATCAACGACATTTTGTTTGGT 57.248 25.926 0.00 0.00 0.00 3.67
101 102 9.698309 CAGACTAGGATTTTATATCAACGACAT 57.302 33.333 0.00 0.00 0.00 3.06
103 104 9.915629 ATCAGACTAGGATTTTATATCAACGAC 57.084 33.333 0.00 0.00 0.00 4.34
134 135 2.441001 AGAGTGGTCAATGGATCATCCC 59.559 50.000 0.00 0.00 36.34 3.85
137 138 3.118112 GGACAGAGTGGTCAATGGATCAT 60.118 47.826 0.00 0.00 36.34 2.45
140 141 2.026822 GTGGACAGAGTGGTCAATGGAT 60.027 50.000 0.00 0.00 39.59 3.41
185 186 4.343526 AGCAGAGGATCATCATCTTACGTT 59.656 41.667 10.44 0.00 35.04 3.99
187 188 4.517952 AGCAGAGGATCATCATCTTACG 57.482 45.455 10.44 0.00 35.04 3.18
189 190 6.053650 CACAAAGCAGAGGATCATCATCTTA 58.946 40.000 10.44 0.00 35.04 2.10
192 193 4.449131 TCACAAAGCAGAGGATCATCATC 58.551 43.478 10.44 0.51 37.82 2.92
225 226 9.421806 CAAGGCATGTTAAAATGAAAGATGTAA 57.578 29.630 9.96 0.00 31.94 2.41
226 227 8.034215 CCAAGGCATGTTAAAATGAAAGATGTA 58.966 33.333 9.96 0.00 31.94 2.29
228 229 7.098477 TCCAAGGCATGTTAAAATGAAAGATG 58.902 34.615 9.96 1.11 32.35 2.90
236 237 5.271598 TCCAGATCCAAGGCATGTTAAAAT 58.728 37.500 0.00 0.00 0.00 1.82
244 245 0.554305 TGCATCCAGATCCAAGGCAT 59.446 50.000 0.00 0.00 0.00 4.40
248 249 5.533528 TCACATATTTGCATCCAGATCCAAG 59.466 40.000 0.00 0.00 0.00 3.61
257 259 2.624838 CCCTGGTCACATATTTGCATCC 59.375 50.000 0.00 0.00 0.00 3.51
273 275 0.324552 TGGCCATTGATTGTCCCTGG 60.325 55.000 0.00 0.00 0.00 4.45
274 276 1.684983 GATGGCCATTGATTGTCCCTG 59.315 52.381 21.84 0.00 0.00 4.45
275 277 1.288633 TGATGGCCATTGATTGTCCCT 59.711 47.619 21.84 0.00 0.00 4.20
276 278 1.684983 CTGATGGCCATTGATTGTCCC 59.315 52.381 21.84 3.83 0.00 4.46
279 281 3.090210 TGACTGATGGCCATTGATTGT 57.910 42.857 21.84 13.89 0.00 2.71
282 284 3.377253 ACTTGACTGATGGCCATTGAT 57.623 42.857 21.84 8.06 0.00 2.57
326 329 8.602328 TGCATAACTTGACTTCAAACAAATTTG 58.398 29.630 16.67 16.67 45.67 2.32
345 348 6.763303 AAATTTGGTCGAACTTTGCATAAC 57.237 33.333 0.33 0.00 0.00 1.89
346 349 9.482627 AATAAAATTTGGTCGAACTTTGCATAA 57.517 25.926 0.33 0.00 0.00 1.90
521 527 4.757149 CACTCTGTTTCCTTTTAGACCCTG 59.243 45.833 0.00 0.00 0.00 4.45
523 529 4.755629 GTCACTCTGTTTCCTTTTAGACCC 59.244 45.833 0.00 0.00 0.00 4.46
526 532 5.057149 GCAGTCACTCTGTTTCCTTTTAGA 58.943 41.667 0.00 0.00 45.23 2.10
570 576 0.752054 GAGCTGAGCTGAGCAGGTAT 59.248 55.000 27.28 5.68 43.44 2.73
602 613 7.558444 ACTTATTAATTAATTGAACAGGGCGGA 59.442 33.333 15.64 0.00 0.00 5.54
631 642 3.498774 AGATTTCTGTTGTGGAGCACT 57.501 42.857 0.00 0.00 35.11 4.40
670 681 2.205307 AGCGAACAATAGTACGGAGC 57.795 50.000 0.00 0.00 0.00 4.70
671 682 3.729716 GCTAAGCGAACAATAGTACGGAG 59.270 47.826 0.00 0.00 0.00 4.63
993 1004 3.512516 GTGGCGGCCATTGCTCTC 61.513 66.667 26.68 6.37 35.28 3.20
1140 1160 2.808315 CGCGAGATGTAGGGCAGT 59.192 61.111 0.00 0.00 0.00 4.40
1239 1262 3.131478 TCGACGAGGATCTGCGCA 61.131 61.111 10.98 10.98 0.00 6.09
1456 1515 2.668185 TTTTGGGCTTCCTCGTCGCA 62.668 55.000 0.00 0.00 0.00 5.10
1674 1736 3.731728 GCCCTGCCCATGTCTGGA 61.732 66.667 8.93 0.00 46.37 3.86
1719 1787 2.755876 TCTCGTGCGCCATCCTCT 60.756 61.111 4.18 0.00 0.00 3.69
1845 1916 3.692406 GAGTCCCGTCTTGGCCGT 61.692 66.667 0.00 0.00 35.87 5.68
1929 2003 4.745751 CTTGCGGTCCGGCGGTTA 62.746 66.667 27.32 4.04 35.06 2.85
1990 2064 2.562912 CAGTCTTTGCGCCGCATT 59.437 55.556 14.63 0.00 38.76 3.56
2148 2222 1.000274 GCAAAGATGAACGCCACCTTT 60.000 47.619 0.00 0.00 0.00 3.11
2595 2669 3.565063 TCATAATGCCATGGATGAACACG 59.435 43.478 18.40 0.00 0.00 4.49
2721 2795 3.182590 AAGCAGCAGACGCCCTTCA 62.183 57.895 0.00 0.00 39.83 3.02
3105 3186 5.769662 TGGCACCATGGAATTATAAGATCAC 59.230 40.000 21.47 0.00 0.00 3.06
3138 3219 8.204836 ACTACTTGGCATAGTAGAAGTAATTGG 58.795 37.037 28.00 8.73 46.88 3.16
3257 3338 9.082313 ACAAAGTTGAGTCATCTATTTTGGAAT 57.918 29.630 14.35 0.00 40.00 3.01
3294 3423 9.492973 TGACCCAACTTTATACTAACTTTGTAC 57.507 33.333 0.00 0.00 0.00 2.90
3296 3425 9.227777 GATGACCCAACTTTATACTAACTTTGT 57.772 33.333 0.00 0.00 0.00 2.83
3297 3426 9.449719 AGATGACCCAACTTTATACTAACTTTG 57.550 33.333 0.00 0.00 0.00 2.77
3304 3433 9.408648 CCAAAATAGATGACCCAACTTTATACT 57.591 33.333 0.00 0.00 0.00 2.12
3305 3434 9.403583 TCCAAAATAGATGACCCAACTTTATAC 57.596 33.333 0.00 0.00 0.00 1.47
3307 3436 8.749354 GTTCCAAAATAGATGACCCAACTTTAT 58.251 33.333 0.00 0.00 0.00 1.40
3309 3438 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
3311 3440 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
3312 3441 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
3313 3442 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
3315 3444 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
3316 3445 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
3317 3446 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
3319 3448 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
3320 3449 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
3321 3450 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
3322 3451 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
3328 3475 3.897657 AGATATACTCCCTCCGTTCCA 57.102 47.619 0.00 0.00 0.00 3.53
3364 3511 2.431260 GCAGCAACACAATGGCCG 60.431 61.111 0.00 0.00 0.00 6.13
3371 3518 4.142293 TGTTACAAAATCTGCAGCAACACA 60.142 37.500 9.47 0.82 0.00 3.72
3395 3542 3.320826 ACCCTAAAGATTTTGTGGTGTGC 59.679 43.478 0.00 0.00 0.00 4.57
3411 3558 9.967451 TTGACTGACATATTCATAAAACCCTAA 57.033 29.630 0.00 0.00 32.17 2.69
3467 3614 7.201565 GCTTCAACACATATCTGGTTACTCTTC 60.202 40.741 0.00 0.00 0.00 2.87
3468 3615 6.595716 GCTTCAACACATATCTGGTTACTCTT 59.404 38.462 0.00 0.00 0.00 2.85
3565 3712 2.747446 GTTATGTGTGGTCAAGCCGATT 59.253 45.455 0.00 0.00 41.21 3.34
3568 3715 1.518325 TGTTATGTGTGGTCAAGCCG 58.482 50.000 0.00 0.00 41.21 5.52
3607 3754 3.766051 GGTGCCCATCTTTCTCAGAAATT 59.234 43.478 0.00 0.00 34.16 1.82
3730 3877 2.112190 GGTAGGCTAGAGCTGAAACCT 58.888 52.381 0.00 0.00 41.70 3.50
3752 3899 3.636764 AGCCTTTAGTCCCAAACAAGTTG 59.363 43.478 0.00 0.00 36.94 3.16
3786 3933 5.176774 GCTTGCCCAAAGTTATACAAACAAC 59.823 40.000 0.00 0.00 38.25 3.32
3787 3934 5.069781 AGCTTGCCCAAAGTTATACAAACAA 59.930 36.000 0.00 0.00 38.25 2.83
3789 3936 5.134202 AGCTTGCCCAAAGTTATACAAAC 57.866 39.130 0.00 0.00 38.25 2.93
3790 3937 4.083003 CGAGCTTGCCCAAAGTTATACAAA 60.083 41.667 0.00 0.00 38.25 2.83
3791 3938 3.438781 CGAGCTTGCCCAAAGTTATACAA 59.561 43.478 0.00 0.00 38.25 2.41
3792 3939 3.006940 CGAGCTTGCCCAAAGTTATACA 58.993 45.455 0.00 0.00 38.25 2.29
3793 3940 2.354821 CCGAGCTTGCCCAAAGTTATAC 59.645 50.000 0.00 0.00 38.25 1.47
3874 4021 8.911918 AAATGTAACACAACTGGAGTAACATA 57.088 30.769 0.00 0.00 0.00 2.29
3997 4144 4.096532 TCACTCAGTATTCCTTGCTACTCG 59.903 45.833 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.