Multiple sequence alignment - TraesCS2A01G297600

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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 TraesCS2A01G297600 chr2A 100.000 5475 0 0 1 5475 511528991 511534465 0.000000e+00 10111.0
1 TraesCS2A01G297600 chr2D 95.643 5394 163 37 111 5475 377311519 377316869 0.000000e+00 8593.0
2 TraesCS2A01G297600 chr2D 92.920 113 7 1 1 113 377311310 377311421 4.390000e-36 163.0
3 TraesCS2A01G297600 chr2B 96.311 4066 95 25 257 4307 448915625 448919650 0.000000e+00 6626.0
4 TraesCS2A01G297600 chr2B 86.024 1152 110 23 4354 5475 448920048 448921178 0.000000e+00 1188.0
5 TraesCS2A01G297600 chr2B 93.750 240 11 3 1 239 448915404 448915640 1.880000e-94 357.0
6 TraesCS2A01G297600 chr4B 89.720 107 11 0 1611 1717 648061788 648061894 2.660000e-28 137.0
7 TraesCS2A01G297600 chr4B 88.073 109 13 0 1609 1717 647763006 647762898 4.450000e-26 130.0
8 TraesCS2A01G297600 chr4D 87.826 115 14 0 1603 1717 503140659 503140773 9.570000e-28 135.0
9 TraesCS2A01G297600 chr5A 88.073 109 13 0 1609 1717 687366215 687366107 4.450000e-26 130.0
10 TraesCS2A01G297600 chr5A 84.615 65 10 0 1625 1689 390566116 390566052 1.270000e-06 65.8
11 TraesCS2A01G297600 chr3D 86.139 101 14 0 1603 1703 530415867 530415967 5.800000e-20 110.0
12 TraesCS2A01G297600 chr3A 87.778 90 11 0 1614 1703 664137502 664137591 7.500000e-19 106.0
13 TraesCS2A01G297600 chr7D 100.000 38 0 0 4695 4732 47379576 47379613 2.740000e-08 71.3


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 TraesCS2A01G297600 chr2A 511528991 511534465 5474 False 10111.000000 10111 100.000000 1 5475 1 chr2A.!!$F1 5474
1 TraesCS2A01G297600 chr2D 377311310 377316869 5559 False 4378.000000 8593 94.281500 1 5475 2 chr2D.!!$F1 5474
2 TraesCS2A01G297600 chr2B 448915404 448921178 5774 False 2723.666667 6626 92.028333 1 5475 3 chr2B.!!$F1 5474


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
969 1081 0.470268 ACCCCTAGTAGCTGCTAGCC 60.470 60.0 27.95 0.0 43.77 3.93 F
1983 2107 0.605589 ACAAGGTCAAGAGAGGCGAG 59.394 55.0 0.00 0.0 0.00 5.03 F
2751 2875 0.250234 AGCGCCTCTCAACAGCAATA 59.750 50.0 2.29 0.0 0.00 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2302 0.106819 GGCAGTAGTACCCTCTCCGA 60.107 60.0 0.00 0.0 0.00 4.55 R
3277 3409 0.111061 TGGTTTGCTGCAGATGGAGT 59.889 50.0 20.43 0.0 35.78 3.85 R
4712 5197 0.032416 ACACCCGGCCTCTACATAGT 60.032 55.0 0.00 0.0 0.00 2.12 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
34 35 4.698304 CAGTTATTATGGTGTTTGACCCGT 59.302 41.667 0.00 0.00 45.45 5.28
52 53 1.634702 GTTTCAGCGACTCTGCTAGG 58.365 55.000 0.00 0.00 45.23 3.02
124 225 7.237679 TCCCTTTGCTAAATATATCAGGCTACT 59.762 37.037 0.00 0.00 0.00 2.57
138 239 6.747414 TCAGGCTACTGTATGTATGGATTT 57.253 37.500 0.00 0.00 45.14 2.17
144 245 6.206829 GCTACTGTATGTATGGATTTTTCCCC 59.793 42.308 0.00 0.00 0.00 4.81
160 261 5.638530 TTTCCCCTTTGCCATTTTTACTT 57.361 34.783 0.00 0.00 0.00 2.24
222 324 8.461222 CCATCACAACTCACAAACATATGTATT 58.539 33.333 9.21 3.31 30.84 1.89
249 351 3.876914 TCAGCTTTCTCTTTCTCGCAAAA 59.123 39.130 0.00 0.00 0.00 2.44
251 353 4.674211 CAGCTTTCTCTTTCTCGCAAAAAG 59.326 41.667 0.00 0.00 35.49 2.27
253 355 5.066505 AGCTTTCTCTTTCTCGCAAAAAGAA 59.933 36.000 6.61 1.40 41.02 2.52
377 484 1.129998 GCATGTGTCATGTCTCTGTGC 59.870 52.381 10.68 0.58 0.00 4.57
379 486 3.853475 CATGTGTCATGTCTCTGTGCTA 58.147 45.455 0.00 0.00 0.00 3.49
479 590 1.001764 CCAGGCCAGTGAGCAATGA 60.002 57.895 5.01 0.00 0.00 2.57
513 624 2.837591 TGTCCAAATCCTTCCAGATCGA 59.162 45.455 0.00 0.00 0.00 3.59
577 688 3.182572 GTGACGCATAGAATTTAGCTCCG 59.817 47.826 0.00 0.00 0.00 4.63
620 731 6.764308 AGTGATGACATACAAAATTCTGGG 57.236 37.500 0.00 0.00 0.00 4.45
696 807 5.427157 AGACACTGTGGTAGAGATAGAGAGA 59.573 44.000 13.09 0.00 0.00 3.10
697 808 5.680619 ACACTGTGGTAGAGATAGAGAGAG 58.319 45.833 13.09 0.00 0.00 3.20
708 819 0.568192 TAGAGAGAGGGGGAATGGGG 59.432 60.000 0.00 0.00 0.00 4.96
771 882 4.202161 ACATGCATTCTCCTCTACTTACCG 60.202 45.833 0.00 0.00 0.00 4.02
921 1033 6.655078 ACAAGAAAGGCACAAATTCATACT 57.345 33.333 0.00 0.00 0.00 2.12
937 1049 3.067742 TCATACTCCGAAATCCGTTCCTC 59.932 47.826 0.00 0.00 36.31 3.71
958 1070 1.274242 CCTTCACCCCTAACCCCTAGT 60.274 57.143 0.00 0.00 0.00 2.57
959 1071 2.022722 CCTTCACCCCTAACCCCTAGTA 60.023 54.545 0.00 0.00 0.00 1.82
960 1072 3.306613 CTTCACCCCTAACCCCTAGTAG 58.693 54.545 0.00 0.00 0.00 2.57
961 1073 1.062658 TCACCCCTAACCCCTAGTAGC 60.063 57.143 0.00 0.00 0.00 3.58
962 1074 1.062352 CACCCCTAACCCCTAGTAGCT 60.062 57.143 0.00 0.00 0.00 3.32
963 1075 1.062352 ACCCCTAACCCCTAGTAGCTG 60.062 57.143 0.00 0.00 0.00 4.24
964 1076 1.049402 CCCTAACCCCTAGTAGCTGC 58.951 60.000 0.00 0.00 0.00 5.25
965 1077 1.413227 CCCTAACCCCTAGTAGCTGCT 60.413 57.143 9.94 9.94 0.00 4.24
966 1078 2.158355 CCCTAACCCCTAGTAGCTGCTA 60.158 54.545 11.31 11.31 0.00 3.49
967 1079 3.158676 CCTAACCCCTAGTAGCTGCTAG 58.841 54.545 26.80 26.80 38.46 3.42
968 1080 1.415200 AACCCCTAGTAGCTGCTAGC 58.585 55.000 27.95 8.10 42.84 3.42
969 1081 0.470268 ACCCCTAGTAGCTGCTAGCC 60.470 60.000 27.95 0.00 43.77 3.93
970 1082 1.528292 CCCCTAGTAGCTGCTAGCCG 61.528 65.000 27.95 20.23 43.77 5.52
1014 1126 5.008019 ACTCATTCACCAATATAAAGCAGCG 59.992 40.000 0.00 0.00 0.00 5.18
1022 1134 1.095228 TATAAAGCAGCGCCACAGCC 61.095 55.000 2.29 0.00 38.01 4.85
1196 1320 3.840124 GCTAGGTAGCTATTGGTGGTT 57.160 47.619 1.35 0.00 45.62 3.67
1524 1648 4.514577 CCGCCGTCGCTCTCCAAT 62.515 66.667 0.00 0.00 0.00 3.16
1983 2107 0.605589 ACAAGGTCAAGAGAGGCGAG 59.394 55.000 0.00 0.00 0.00 5.03
2453 2577 4.745751 TACGTTTCCCAGGGCGCG 62.746 66.667 0.00 0.00 0.00 6.86
2534 2658 3.005791 TCTCTCTGACAATTCGTTGCTGA 59.994 43.478 0.00 0.00 0.00 4.26
2634 2758 0.668401 GCCTGCAATGTGGCTTTCAC 60.668 55.000 7.42 0.00 45.26 3.18
2751 2875 0.250234 AGCGCCTCTCAACAGCAATA 59.750 50.000 2.29 0.00 0.00 1.90
2752 2876 1.134280 AGCGCCTCTCAACAGCAATAT 60.134 47.619 2.29 0.00 0.00 1.28
2753 2877 2.103094 AGCGCCTCTCAACAGCAATATA 59.897 45.455 2.29 0.00 0.00 0.86
2754 2878 3.070018 GCGCCTCTCAACAGCAATATAT 58.930 45.455 0.00 0.00 0.00 0.86
2876 3008 7.865889 GTGGAATCTTATTCCGTTTGTTCTTTT 59.134 33.333 12.73 0.00 41.43 2.27
3096 3228 3.869272 CTCCAGCATTGCCGCGAC 61.869 66.667 8.23 0.00 36.85 5.19
3104 3236 3.675619 ATTGCCGCGACCAGGTACC 62.676 63.158 8.23 2.73 0.00 3.34
3144 3276 6.014755 ACTCGAGTGTCCAATCATCATCATAT 60.015 38.462 19.30 0.00 0.00 1.78
3147 3279 9.189156 TCGAGTGTCCAATCATCATCATATATA 57.811 33.333 0.00 0.00 0.00 0.86
3148 3280 9.807649 CGAGTGTCCAATCATCATCATATATAA 57.192 33.333 0.00 0.00 0.00 0.98
3162 3294 9.962809 TCATCATATATAAACCTTGATGATGCA 57.037 29.630 16.67 0.00 44.56 3.96
3223 3355 4.422073 TCTTCATCACTGACCTTTGTGT 57.578 40.909 0.00 0.00 35.82 3.72
3224 3356 4.780815 TCTTCATCACTGACCTTTGTGTT 58.219 39.130 0.00 0.00 35.82 3.32
3225 3357 5.924356 TCTTCATCACTGACCTTTGTGTTA 58.076 37.500 0.00 0.00 35.82 2.41
3226 3358 6.353323 TCTTCATCACTGACCTTTGTGTTAA 58.647 36.000 0.00 0.00 35.82 2.01
3602 3734 1.175983 AGATCGTCCCTGAGATCGCC 61.176 60.000 0.00 0.00 45.68 5.54
3729 3861 4.432741 GCAAGGAGAGGGTGGCCC 62.433 72.222 0.00 0.00 45.90 5.80
3791 3923 1.741770 GTCCATCAAACTCGGCGCT 60.742 57.895 7.64 0.00 0.00 5.92
3965 4097 0.179100 CCGATCAGTACTGCCAGGTG 60.179 60.000 18.45 4.48 0.00 4.00
4108 4240 1.651240 CCGCCAACCAAGCAGATGAG 61.651 60.000 0.00 0.00 0.00 2.90
4109 4241 1.651240 CGCCAACCAAGCAGATGAGG 61.651 60.000 0.00 0.00 0.00 3.86
4140 4272 1.021390 GGAGGAGCACACGGTTGATG 61.021 60.000 0.00 0.00 0.00 3.07
4166 4298 2.064762 CACAAAGAAGCTGAGACCTCG 58.935 52.381 0.00 0.00 0.00 4.63
4182 4314 1.656095 CCTCGTCGTCTTGCTTTGATC 59.344 52.381 0.00 0.00 0.00 2.92
4214 4346 0.741326 TAGAGAGTGAGCATGCGGAC 59.259 55.000 13.01 12.83 0.00 4.79
4543 5027 3.446161 TCATCTACTCTACGGTTTGGGTG 59.554 47.826 0.00 0.00 0.00 4.61
4587 5071 6.372381 TGACGTGTAAGCTGTATTCTAGTGTA 59.628 38.462 0.00 0.00 0.00 2.90
4641 5125 6.613233 CATAGTGTCGGTCCTATATGACTTC 58.387 44.000 7.91 1.27 35.54 3.01
4648 5132 7.068962 TGTCGGTCCTATATGACTTCATTGTTA 59.931 37.037 7.91 0.00 37.76 2.41
4650 5134 6.645415 CGGTCCTATATGACTTCATTGTTACC 59.355 42.308 7.91 0.02 37.76 2.85
4697 5182 5.954296 ATTCTCAGACTGTTGATGTTTGG 57.046 39.130 1.59 0.00 0.00 3.28
4712 5197 6.000840 TGATGTTTGGCTGTGTGTATCTTAA 58.999 36.000 0.00 0.00 0.00 1.85
4740 5225 0.479378 AGGCCGGGTGTTTCCTTTAA 59.521 50.000 2.18 0.00 36.25 1.52
4746 5231 3.759618 CCGGGTGTTTCCTTTAATGCTTA 59.240 43.478 0.00 0.00 36.25 3.09
4774 5260 2.169561 TCCTCACAATGCTATTACGCCA 59.830 45.455 0.00 0.00 0.00 5.69
4795 5281 4.038883 CCAATAAGTAGACTTACCCCTCCG 59.961 50.000 4.28 0.00 40.81 4.63
5127 5641 3.683937 GCGGTGCATGGCAACCTT 61.684 61.111 5.37 0.00 44.30 3.50
5206 5720 1.067250 GTGGTGGCGTGCATGTTTT 59.933 52.632 7.93 0.00 0.00 2.43
5207 5721 0.529555 GTGGTGGCGTGCATGTTTTT 60.530 50.000 7.93 0.00 0.00 1.94
5224 5738 0.035820 TTTCTACATCCGGTGGTGGC 60.036 55.000 0.00 0.00 0.00 5.01
5343 5858 1.425066 TGTTGTCTGCCCCTTTGATCT 59.575 47.619 0.00 0.00 0.00 2.75
5407 5922 2.668632 GGGATGTCCGGTGCTGAA 59.331 61.111 0.00 0.00 36.71 3.02
5416 5931 1.733041 CGGTGCTGAACGACGACAT 60.733 57.895 0.00 0.00 0.00 3.06
5428 5943 1.007011 CGACGACATTTGCGCTCTAAG 60.007 52.381 9.73 0.00 0.00 2.18
5435 5950 3.257393 CATTTGCGCTCTAAGTCTGTCT 58.743 45.455 9.73 0.00 0.00 3.41
5444 5959 4.219725 GCTCTAAGTCTGTCTGGTTCTTCT 59.780 45.833 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 6.725246 TCTACTTGCAAAACTTAGAGCAAAC 58.275 36.000 0.00 0.00 45.18 2.93
124 225 6.127196 GCAAAGGGGAAAAATCCATACATACA 60.127 38.462 0.00 0.00 0.00 2.29
138 239 5.372373 CAAGTAAAAATGGCAAAGGGGAAA 58.628 37.500 0.00 0.00 0.00 3.13
144 245 6.701400 ACAACTAGCAAGTAAAAATGGCAAAG 59.299 34.615 0.00 0.00 33.75 2.77
160 261 6.350110 GGCCATGAATCTTTTTACAACTAGCA 60.350 38.462 0.00 0.00 0.00 3.49
222 324 5.105752 GCGAGAAAGAGAAAGCTGAGATTA 58.894 41.667 0.00 0.00 0.00 1.75
223 325 3.932089 GCGAGAAAGAGAAAGCTGAGATT 59.068 43.478 0.00 0.00 0.00 2.40
224 326 3.056250 TGCGAGAAAGAGAAAGCTGAGAT 60.056 43.478 0.00 0.00 0.00 2.75
228 330 3.885484 TTTGCGAGAAAGAGAAAGCTG 57.115 42.857 0.00 0.00 0.00 4.24
253 355 6.387465 GCTTTTATAGAAAGCCGAGGTTTTT 58.613 36.000 11.39 0.20 45.01 1.94
261 363 8.408416 GAGCATCAAAGCTTTTATAGAAAGCCG 61.408 40.741 9.53 8.65 46.75 5.52
262 364 6.694844 GAGCATCAAAGCTTTTATAGAAAGCC 59.305 38.462 9.53 4.16 46.75 4.35
302 408 5.144359 GTTGGCGTCACAATTAACTTACAG 58.856 41.667 0.00 0.00 32.24 2.74
415 522 7.254084 GCAAGAGTTTAAACATCAACTTTGTGG 60.254 37.037 20.06 6.90 33.22 4.17
479 590 5.363580 AGGATTTGGACAAGTGACAAATGTT 59.636 36.000 17.12 7.64 42.84 2.71
513 624 8.798859 AACTGACAAGCATAAGATTTATCACT 57.201 30.769 0.00 0.00 0.00 3.41
577 688 4.154918 CACTTGCCTCTAAAGAATGACCAC 59.845 45.833 0.00 0.00 0.00 4.16
708 819 3.443925 GGCGCCTCAGCTTTTCCC 61.444 66.667 22.15 0.00 36.60 3.97
771 882 3.801114 AGAAAAAGGTGTTGTTGGCTC 57.199 42.857 0.00 0.00 0.00 4.70
921 1033 0.616679 AGGGAGGAACGGATTTCGGA 60.617 55.000 0.00 0.00 44.45 4.55
937 1049 0.045162 TAGGGGTTAGGGGTGAAGGG 59.955 60.000 0.00 0.00 0.00 3.95
958 1070 3.540751 CAGGCCGGCTAGCAGCTA 61.541 66.667 28.56 1.13 41.99 3.32
961 1073 4.906792 GAGCAGGCCGGCTAGCAG 62.907 72.222 33.65 13.09 45.99 4.24
963 1075 3.976701 TTTGAGCAGGCCGGCTAGC 62.977 63.158 31.05 28.42 45.99 3.42
964 1076 1.372087 CTTTTGAGCAGGCCGGCTAG 61.372 60.000 31.05 19.87 45.99 3.42
965 1077 1.377202 CTTTTGAGCAGGCCGGCTA 60.377 57.895 31.05 13.77 45.99 3.93
967 1079 2.048603 ATCTTTTGAGCAGGCCGGC 61.049 57.895 21.36 21.36 0.00 6.13
968 1080 0.677731 TCATCTTTTGAGCAGGCCGG 60.678 55.000 0.00 0.00 0.00 6.13
969 1081 1.135575 GTTCATCTTTTGAGCAGGCCG 60.136 52.381 0.00 0.00 35.76 6.13
970 1082 1.888512 TGTTCATCTTTTGAGCAGGCC 59.111 47.619 0.00 0.00 40.23 5.19
1014 1126 3.982241 GCAAGTGGTGGCTGTGGC 61.982 66.667 0.00 0.00 37.82 5.01
1022 1134 1.512996 CCACTGCAGAGCAAGTGGTG 61.513 60.000 23.35 5.26 44.58 4.17
1196 1320 4.147449 CGGCCCTCATGTCGAGCA 62.147 66.667 0.00 0.00 40.78 4.26
1572 1696 1.662608 CTGCTGGCTATCGACGGAT 59.337 57.895 0.00 0.00 36.65 4.18
1746 1870 4.114997 GGATTGGCGTTGGTGGCG 62.115 66.667 0.00 0.00 37.19 5.69
1756 1880 1.676968 GGTTTTGGTGGGGATTGGC 59.323 57.895 0.00 0.00 0.00 4.52
2175 2299 0.179936 AGTAGTACCCTCTCCGACCG 59.820 60.000 0.00 0.00 0.00 4.79
2178 2302 0.106819 GGCAGTAGTACCCTCTCCGA 60.107 60.000 0.00 0.00 0.00 4.55
2453 2577 3.562973 CAGGGACATTCACATACTGATGC 59.437 47.826 0.00 0.00 36.43 3.91
2454 2578 4.774124 ACAGGGACATTCACATACTGATG 58.226 43.478 0.00 0.00 39.16 3.07
2751 2875 7.008021 AGTTGGGCAAACAAATTGAAGATAT 57.992 32.000 7.64 0.00 41.85 1.63
2752 2876 6.418057 AGTTGGGCAAACAAATTGAAGATA 57.582 33.333 7.64 0.00 41.85 1.98
2753 2877 5.294734 AGTTGGGCAAACAAATTGAAGAT 57.705 34.783 7.64 0.00 41.85 2.40
2754 2878 4.751767 AGTTGGGCAAACAAATTGAAGA 57.248 36.364 7.64 0.00 41.85 2.87
3104 3236 4.691685 CACTCGAGTACTAGCTAGGGTATG 59.308 50.000 24.35 11.23 0.00 2.39
3105 3237 4.347583 ACACTCGAGTACTAGCTAGGGTAT 59.652 45.833 24.35 6.28 0.00 2.73
3110 3242 3.794717 TGGACACTCGAGTACTAGCTAG 58.205 50.000 19.57 19.44 0.00 3.42
3111 3243 3.900966 TGGACACTCGAGTACTAGCTA 57.099 47.619 19.57 1.17 0.00 3.32
3112 3244 2.783609 TGGACACTCGAGTACTAGCT 57.216 50.000 19.57 0.00 0.00 3.32
3113 3245 3.377485 TGATTGGACACTCGAGTACTAGC 59.623 47.826 19.57 11.56 0.00 3.42
3114 3246 5.297029 TGATGATTGGACACTCGAGTACTAG 59.703 44.000 19.57 8.51 0.00 2.57
3144 3276 9.812347 AAGGAATATGCATCATCAAGGTTTATA 57.188 29.630 0.19 0.00 0.00 0.98
3147 3279 8.537728 TTAAGGAATATGCATCATCAAGGTTT 57.462 30.769 0.19 0.00 0.00 3.27
3148 3280 8.716674 ATTAAGGAATATGCATCATCAAGGTT 57.283 30.769 0.19 0.00 0.00 3.50
3149 3281 8.716674 AATTAAGGAATATGCATCATCAAGGT 57.283 30.769 0.19 0.00 0.00 3.50
3164 3296 9.640952 TTGGATCGGAGAAATTAATTAAGGAAT 57.359 29.630 0.01 0.00 43.58 3.01
3165 3297 9.640952 ATTGGATCGGAGAAATTAATTAAGGAA 57.359 29.630 0.01 0.00 43.58 3.36
3166 3298 9.284968 GATTGGATCGGAGAAATTAATTAAGGA 57.715 33.333 0.01 0.00 43.58 3.36
3167 3299 9.289782 AGATTGGATCGGAGAAATTAATTAAGG 57.710 33.333 0.01 0.00 43.58 2.69
3176 3308 8.752005 TCAAAATAAGATTGGATCGGAGAAAT 57.248 30.769 0.00 0.00 43.58 2.17
3179 3311 7.739825 AGATCAAAATAAGATTGGATCGGAGA 58.260 34.615 0.00 0.00 45.75 3.71
3195 3327 7.232127 ACAAAGGTCAGTGATGAAGATCAAAAT 59.768 33.333 0.00 0.00 40.39 1.82
3277 3409 0.111061 TGGTTTGCTGCAGATGGAGT 59.889 50.000 20.43 0.00 35.78 3.85
3401 3533 2.892425 GGATGCTTGCCGTCGAGG 60.892 66.667 0.00 0.00 44.97 4.63
3791 3923 2.488355 GATGCGGACGTCGAGGAA 59.512 61.111 12.85 0.00 42.43 3.36
4108 4240 3.787001 CCTCCTTGGTCTCCGGCC 61.787 72.222 0.00 0.00 0.00 6.13
4109 4241 2.683933 TCCTCCTTGGTCTCCGGC 60.684 66.667 0.00 0.00 37.07 6.13
4140 4272 4.332268 GGTCTCAGCTTCTTTGTGATCATC 59.668 45.833 0.00 0.00 0.00 2.92
4166 4298 3.494626 TGTTCAGATCAAAGCAAGACGAC 59.505 43.478 0.00 0.00 0.00 4.34
4182 4314 5.519566 GCTCACTCTCTATGTTGATGTTCAG 59.480 44.000 0.00 0.00 0.00 3.02
4214 4346 2.163390 CAGGCAGACATCACGCTCG 61.163 63.158 0.00 0.00 0.00 5.03
4244 4376 0.462225 TGAAAAACAGCGTCCGGTCA 60.462 50.000 0.00 0.00 0.00 4.02
4671 5155 7.707893 CCAAACATCAACAGTCTGAGAATTTTT 59.292 33.333 6.91 0.17 0.00 1.94
4672 5156 7.205297 CCAAACATCAACAGTCTGAGAATTTT 58.795 34.615 6.91 5.45 0.00 1.82
4673 5157 6.736794 GCCAAACATCAACAGTCTGAGAATTT 60.737 38.462 6.91 6.80 0.00 1.82
4674 5158 5.278660 GCCAAACATCAACAGTCTGAGAATT 60.279 40.000 6.91 1.40 0.00 2.17
4675 5159 4.217118 GCCAAACATCAACAGTCTGAGAAT 59.783 41.667 6.91 0.00 0.00 2.40
4677 5161 3.141398 GCCAAACATCAACAGTCTGAGA 58.859 45.455 6.91 4.56 0.00 3.27
4682 5167 2.358898 ACACAGCCAAACATCAACAGTC 59.641 45.455 0.00 0.00 0.00 3.51
4697 5182 7.863375 CCTCTACATAGTTAAGATACACACAGC 59.137 40.741 0.00 0.00 0.00 4.40
4712 5197 0.032416 ACACCCGGCCTCTACATAGT 60.032 55.000 0.00 0.00 0.00 2.12
4740 5225 5.300286 GCATTGTGAGGAAAGGTATAAGCAT 59.700 40.000 0.00 0.00 0.00 3.79
4746 5231 6.706270 CGTAATAGCATTGTGAGGAAAGGTAT 59.294 38.462 0.00 0.00 0.00 2.73
4774 5260 5.134725 TCGGAGGGGTAAGTCTACTTATT 57.865 43.478 5.90 0.00 40.20 1.40
4795 5281 6.320164 TGATCCTTAGTCTAGCTTCTCAGTTC 59.680 42.308 0.00 0.00 0.00 3.01
5001 5515 3.498397 AGTCATGTCGTGATTTTGGTGAC 59.502 43.478 0.00 0.00 39.48 3.67
5201 5715 3.142951 CACCACCGGATGTAGAAAAACA 58.857 45.455 9.46 0.00 0.00 2.83
5206 5720 1.600107 GCCACCACCGGATGTAGAA 59.400 57.895 9.46 0.00 0.00 2.10
5207 5721 2.363975 GGCCACCACCGGATGTAGA 61.364 63.158 9.46 0.00 0.00 2.59
5224 5738 4.553678 TCCACAACCTAACCCTAGATAGG 58.446 47.826 12.18 12.18 43.59 2.57
5311 5825 3.431346 GGCAGACAACATCATAGCTGAGA 60.431 47.826 0.00 0.00 34.12 3.27
5374 5889 2.660206 CCCGATGTTGGTCCACGA 59.340 61.111 0.00 0.00 0.00 4.35
5407 5922 0.109458 TAGAGCGCAAATGTCGTCGT 60.109 50.000 11.47 0.00 0.00 4.34
5416 5931 2.610479 CCAGACAGACTTAGAGCGCAAA 60.610 50.000 11.47 0.00 0.00 3.68
5428 5943 2.147150 GGCAAGAAGAACCAGACAGAC 58.853 52.381 0.00 0.00 0.00 3.51
5435 5950 1.494721 AGAACCAGGCAAGAAGAACCA 59.505 47.619 0.00 0.00 0.00 3.67
5444 5959 0.036388 GATGTCCGAGAACCAGGCAA 60.036 55.000 0.00 0.00 0.00 4.52



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

AutoCloner maintained by Alex Coulton.