Multiple sequence alignment - TraesCS3A01G156800

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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 TraesCS3A01G156800 chr3A 100.000 3739 0 0 1 3739 153079264 153075526 0.000000e+00 6905.0
1 TraesCS3A01G156800 chr3D 91.151 3153 156 41 8 3112 136043419 136040342 0.000000e+00 4163.0
2 TraesCS3A01G156800 chr3D 93.121 596 26 11 3148 3739 136040344 136039760 0.000000e+00 859.0
3 TraesCS3A01G156800 chr3B 90.514 3131 158 54 38 3112 194328566 194325519 0.000000e+00 4008.0
4 TraesCS3A01G156800 chr3B 91.694 602 26 8 3148 3739 194325521 194324934 0.000000e+00 813.0
5 TraesCS3A01G156800 chr2D 79.452 146 23 4 190 328 593792021 593792166 3.070000e-16 97.1
6 TraesCS3A01G156800 chr4B 84.524 84 13 0 36 119 147097006 147096923 2.390000e-12 84.2
7 TraesCS3A01G156800 chr5A 73.604 197 52 0 1 197 7165428 7165232 4.000000e-10 76.8
8 TraesCS3A01G156800 chr4A 82.716 81 14 0 36 116 472358336 472358416 5.180000e-09 73.1
9 TraesCS3A01G156800 chr1B 86.792 53 5 2 130 182 308340442 308340392 1.450000e-04 58.4


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 TraesCS3A01G156800 chr3A 153075526 153079264 3738 True 6905.0 6905 100.000 1 3739 1 chr3A.!!$R1 3738
1 TraesCS3A01G156800 chr3D 136039760 136043419 3659 True 2511.0 4163 92.136 8 3739 2 chr3D.!!$R1 3731
2 TraesCS3A01G156800 chr3B 194324934 194328566 3632 True 2410.5 4008 91.104 38 3739 2 chr3B.!!$R1 3701

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
81 82 0.249120 TTCGAGATCAACGGGTGCAT 59.751 50.0 11.25 0.0 0.00 3.96 F
1052 1070 0.683973 CACTGCTGTCCAGAGGAAGT 59.316 55.0 0.00 0.0 44.64 3.01 F
2184 2232 0.249238 CTCGGGCATACTGCTGAGTC 60.249 60.0 0.00 0.0 44.28 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1131 1149 0.610687 AAGGAGAAGCCAAGGAGACG 59.389 55.0 0.0 0.0 40.02 4.18 R
2364 2414 0.933097 CCAAGATGAAGACGATGGCG 59.067 55.0 0.0 0.0 44.79 5.69 R
3179 3256 0.038744 TCCTACCGACTTCCCTCGTT 59.961 55.0 0.0 0.0 31.35 3.85 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
24 25 4.710375 GTCTACCTCCTGGAACAAGATGTA 59.290 45.833 0.00 0.00 38.70 2.29
55 56 5.489792 TGTGAACTTTCTAGAGATGCCTT 57.510 39.130 0.00 0.00 0.00 4.35
56 57 5.240891 TGTGAACTTTCTAGAGATGCCTTG 58.759 41.667 0.00 0.00 0.00 3.61
59 60 2.208431 CTTTCTAGAGATGCCTTGGCG 58.792 52.381 7.18 0.00 0.00 5.69
60 61 0.465705 TTCTAGAGATGCCTTGGCGG 59.534 55.000 7.18 0.00 0.00 6.13
81 82 0.249120 TTCGAGATCAACGGGTGCAT 59.751 50.000 11.25 0.00 0.00 3.96
99 100 6.202954 GGGTGCATGTATAACTACTCAATGAC 59.797 42.308 0.00 0.00 0.00 3.06
116 117 5.711506 TCAATGACCTTGTGAAGCATATGTT 59.288 36.000 4.29 0.00 36.20 2.71
121 122 5.503927 ACCTTGTGAAGCATATGTTGATCT 58.496 37.500 4.29 0.00 0.00 2.75
123 124 6.765036 ACCTTGTGAAGCATATGTTGATCTAG 59.235 38.462 4.29 0.00 0.00 2.43
125 126 7.171167 CCTTGTGAAGCATATGTTGATCTAGAG 59.829 40.741 4.29 0.00 0.00 2.43
287 291 6.757237 TGTGGTTGCATGTATTTGAGATTTT 58.243 32.000 0.00 0.00 0.00 1.82
292 304 8.437742 GGTTGCATGTATTTGAGATTTTGAAAG 58.562 33.333 0.00 0.00 0.00 2.62
293 305 8.981647 GTTGCATGTATTTGAGATTTTGAAAGT 58.018 29.630 0.00 0.00 0.00 2.66
294 306 8.523523 TGCATGTATTTGAGATTTTGAAAGTG 57.476 30.769 0.00 0.00 0.00 3.16
295 307 8.358895 TGCATGTATTTGAGATTTTGAAAGTGA 58.641 29.630 0.00 0.00 0.00 3.41
296 308 8.857216 GCATGTATTTGAGATTTTGAAAGTGAG 58.143 33.333 0.00 0.00 0.00 3.51
297 309 9.350357 CATGTATTTGAGATTTTGAAAGTGAGG 57.650 33.333 0.00 0.00 0.00 3.86
298 310 7.885297 TGTATTTGAGATTTTGAAAGTGAGGG 58.115 34.615 0.00 0.00 0.00 4.30
299 311 7.723616 TGTATTTGAGATTTTGAAAGTGAGGGA 59.276 33.333 0.00 0.00 0.00 4.20
396 409 8.948631 ATACATTGTTGTAGATGGTCTAAGTG 57.051 34.615 0.00 0.00 41.49 3.16
397 410 6.769512 ACATTGTTGTAGATGGTCTAAGTGT 58.230 36.000 0.00 0.00 33.16 3.55
412 425 5.924825 GTCTAAGTGTCTAACGTGTTGGAAT 59.075 40.000 0.08 0.00 31.87 3.01
420 433 6.201425 TGTCTAACGTGTTGGAATAGAACAAC 59.799 38.462 0.08 0.00 45.35 3.32
455 468 7.613801 TGTACTCCAACATGCATAGGTAAATTT 59.386 33.333 0.00 0.00 0.00 1.82
463 479 8.200364 ACATGCATAGGTAAATTTCATTTTGC 57.800 30.769 0.00 1.35 33.73 3.68
616 634 6.806739 CGGGAGGAATTTTTAATTCTTGACAC 59.193 38.462 10.85 3.05 0.00 3.67
622 640 9.065871 GGAATTTTTAATTCTTGACACATCTCG 57.934 33.333 10.85 0.00 0.00 4.04
637 655 8.260114 TGACACATCTCGCATCCATTTATATAT 58.740 33.333 0.00 0.00 0.00 0.86
720 738 6.036517 CAGATTACCAAAGTCATAGCACAGAC 59.963 42.308 0.00 0.00 35.02 3.51
743 761 3.417069 TCCCAACAACATGTCCTACAG 57.583 47.619 0.00 0.00 0.00 2.74
930 948 1.650314 GGCACCCACGTAATTTCCCG 61.650 60.000 0.00 0.00 0.00 5.14
1043 1061 1.023513 GCTGGTGATCACTGCTGTCC 61.024 60.000 24.50 7.53 0.00 4.02
1051 1069 0.972134 TCACTGCTGTCCAGAGGAAG 59.028 55.000 0.00 0.00 44.64 3.46
1052 1070 0.683973 CACTGCTGTCCAGAGGAAGT 59.316 55.000 0.00 0.00 44.64 3.01
1053 1071 1.071385 CACTGCTGTCCAGAGGAAGTT 59.929 52.381 0.00 0.00 44.64 2.66
1054 1072 1.346068 ACTGCTGTCCAGAGGAAGTTC 59.654 52.381 0.00 0.00 44.64 3.01
1068 1086 2.103263 GGAAGTTCCTACGCATCCATCT 59.897 50.000 15.09 0.00 32.53 2.90
1123 1141 3.596310 AGTTTCCGTTCCTTCTAGCTC 57.404 47.619 0.00 0.00 0.00 4.09
1131 1149 0.983378 TCCTTCTAGCTCCCCTTGCC 60.983 60.000 0.00 0.00 0.00 4.52
1240 1261 0.453793 AGAGGAAGATGACGAGCGTG 59.546 55.000 0.00 0.00 0.00 5.34
1360 1381 1.301677 GAGCTCCGGGTTCTTGCAAG 61.302 60.000 20.81 20.81 0.00 4.01
1405 1426 8.785101 CGTTACGAAATTTTGAAATGGTAGATG 58.215 33.333 12.54 0.00 0.00 2.90
1406 1427 9.834628 GTTACGAAATTTTGAAATGGTAGATGA 57.165 29.630 12.54 0.00 0.00 2.92
1407 1428 9.834628 TTACGAAATTTTGAAATGGTAGATGAC 57.165 29.630 12.54 0.00 0.00 3.06
1413 1438 6.662414 TTTGAAATGGTAGATGACGATGTC 57.338 37.500 0.00 0.00 32.45 3.06
1562 1587 7.032598 TCTCCTCCAGAAATTAAGGTGAAAT 57.967 36.000 0.00 0.00 30.64 2.17
1600 1627 9.598517 CGGTACCTAATTAGTATTGGTTTTGTA 57.401 33.333 10.90 0.29 31.75 2.41
1626 1653 4.137116 TGCTTAGCACATAACAGTAGGG 57.863 45.455 1.39 0.00 31.71 3.53
1651 1686 6.346896 AGTAGCCACCTTAATTAGTGCTAAC 58.653 40.000 0.00 0.00 32.48 2.34
1707 1742 8.517062 AAGGATAAGAAAACATCCAAGATCAG 57.483 34.615 0.00 0.00 42.78 2.90
1873 1910 3.452878 TCGGGTAATTTCTTAGGGTCCA 58.547 45.455 0.00 0.00 0.00 4.02
1877 1914 6.330778 TCGGGTAATTTCTTAGGGTCCATATT 59.669 38.462 0.00 0.00 0.00 1.28
1918 1955 6.054941 CCTTGCCTTTTGAACAAAATAACCT 58.945 36.000 12.11 0.00 39.29 3.50
1948 1985 9.686683 ATTATCCTGCTTTCACATAACTAAACT 57.313 29.630 0.00 0.00 0.00 2.66
1949 1986 9.515226 TTATCCTGCTTTCACATAACTAAACTT 57.485 29.630 0.00 0.00 0.00 2.66
1950 1987 7.817418 TCCTGCTTTCACATAACTAAACTTT 57.183 32.000 0.00 0.00 0.00 2.66
1951 1988 8.911918 TCCTGCTTTCACATAACTAAACTTTA 57.088 30.769 0.00 0.00 0.00 1.85
1952 1989 9.344772 TCCTGCTTTCACATAACTAAACTTTAA 57.655 29.630 0.00 0.00 0.00 1.52
1990 2027 8.911247 TTCTTAGAACAAAAAGAAGACAAAGC 57.089 30.769 0.00 0.00 36.93 3.51
2018 2059 8.498054 TGGAATCTTCTCACATATGTTTCTTC 57.502 34.615 5.37 3.17 0.00 2.87
2135 2176 9.927668 AACAGTAATTAATTAAGCTGCACAATT 57.072 25.926 18.75 13.58 0.00 2.32
2162 2210 1.210722 TGTTGCCACAGGTACACTCAA 59.789 47.619 0.00 0.00 0.00 3.02
2183 2231 0.684479 TCTCGGGCATACTGCTGAGT 60.684 55.000 15.99 0.00 44.28 3.41
2184 2232 0.249238 CTCGGGCATACTGCTGAGTC 60.249 60.000 0.00 0.00 44.28 3.36
2283 2333 7.596995 GCTAATGAAACTATCGAGCTAATCAGT 59.403 37.037 0.00 0.00 0.00 3.41
2307 2357 6.096846 GTGTTGGTTAATATGCAGATTTCCCT 59.903 38.462 12.49 0.00 0.00 4.20
2364 2414 4.026357 ACCACTCCCCTCTCCCCC 62.026 72.222 0.00 0.00 0.00 5.40
2429 2479 2.234296 CCAAGGAGGAGCCCAAGGT 61.234 63.158 0.00 0.00 41.22 3.50
2440 2490 4.148825 CCAAGGTCGAGCCCGAGG 62.149 72.222 11.73 4.45 46.52 4.63
2441 2491 3.382832 CAAGGTCGAGCCCGAGGT 61.383 66.667 11.73 0.00 46.52 3.85
2442 2492 3.069318 AAGGTCGAGCCCGAGGTC 61.069 66.667 11.73 0.00 46.52 3.85
2515 2565 0.618968 GGAGAAGAAGGAGGAGGCCA 60.619 60.000 5.01 0.00 0.00 5.36
2606 2662 2.973406 AGAAGAAAGAGGAGAAACCCGT 59.027 45.455 0.00 0.00 40.05 5.28
3062 3139 5.977171 TGATATGGTTGATTTTACCGTCG 57.023 39.130 0.00 0.00 38.55 5.12
3073 3150 1.705256 TTACCGTCGTTCACATCAGC 58.295 50.000 0.00 0.00 0.00 4.26
3112 3189 0.394216 TTTGCATGCATACGCCTCCT 60.394 50.000 23.37 0.00 37.32 3.69
3113 3190 0.815213 TTGCATGCATACGCCTCCTC 60.815 55.000 23.37 0.00 37.32 3.71
3114 3191 1.963338 GCATGCATACGCCTCCTCC 60.963 63.158 14.21 0.00 37.32 4.30
3115 3192 1.302033 CATGCATACGCCTCCTCCC 60.302 63.158 0.00 0.00 37.32 4.30
3116 3193 1.766059 ATGCATACGCCTCCTCCCA 60.766 57.895 0.00 0.00 37.32 4.37
3117 3194 1.344953 ATGCATACGCCTCCTCCCAA 61.345 55.000 0.00 0.00 37.32 4.12
3118 3195 1.227674 GCATACGCCTCCTCCCAAG 60.228 63.158 0.00 0.00 0.00 3.61
3119 3196 1.972660 GCATACGCCTCCTCCCAAGT 61.973 60.000 0.00 0.00 0.00 3.16
3120 3197 0.179073 CATACGCCTCCTCCCAAGTG 60.179 60.000 0.00 0.00 0.00 3.16
3121 3198 1.338136 ATACGCCTCCTCCCAAGTGG 61.338 60.000 0.00 0.00 0.00 4.00
3122 3199 2.449967 TACGCCTCCTCCCAAGTGGA 62.450 60.000 0.00 0.00 42.41 4.02
3134 3211 5.525454 TCCCAAGTGGAGTACTAACTAGA 57.475 43.478 10.33 6.36 39.18 2.43
3135 3212 5.895807 TCCCAAGTGGAGTACTAACTAGAA 58.104 41.667 10.33 0.00 39.18 2.10
3136 3213 6.317312 TCCCAAGTGGAGTACTAACTAGAAA 58.683 40.000 10.33 0.00 39.18 2.52
3137 3214 6.210185 TCCCAAGTGGAGTACTAACTAGAAAC 59.790 42.308 10.33 0.00 39.18 2.78
3138 3215 6.396450 CCAAGTGGAGTACTAACTAGAAACC 58.604 44.000 10.33 0.00 39.18 3.27
3139 3216 6.210984 CCAAGTGGAGTACTAACTAGAAACCT 59.789 42.308 10.33 0.00 39.18 3.50
3140 3217 7.314393 CAAGTGGAGTACTAACTAGAAACCTC 58.686 42.308 10.33 0.00 39.18 3.85
3141 3218 5.647225 AGTGGAGTACTAACTAGAAACCTCG 59.353 44.000 8.58 0.00 38.04 4.63
3142 3219 5.645497 GTGGAGTACTAACTAGAAACCTCGA 59.355 44.000 0.00 0.00 35.56 4.04
3143 3220 6.318396 GTGGAGTACTAACTAGAAACCTCGAT 59.682 42.308 0.00 0.00 35.56 3.59
3144 3221 6.541641 TGGAGTACTAACTAGAAACCTCGATC 59.458 42.308 0.00 0.00 35.56 3.69
3145 3222 6.541641 GGAGTACTAACTAGAAACCTCGATCA 59.458 42.308 0.00 0.00 35.56 2.92
3146 3223 7.229106 GGAGTACTAACTAGAAACCTCGATCAT 59.771 40.741 0.00 0.00 35.56 2.45
3147 3224 8.522542 AGTACTAACTAGAAACCTCGATCATT 57.477 34.615 0.00 0.00 32.84 2.57
3148 3225 8.623030 AGTACTAACTAGAAACCTCGATCATTC 58.377 37.037 0.00 0.00 32.84 2.67
3149 3226 6.807789 ACTAACTAGAAACCTCGATCATTCC 58.192 40.000 0.00 0.00 0.00 3.01
3247 3324 0.794473 GCACGAAACCTAGAAACCGG 59.206 55.000 0.00 0.00 0.00 5.28
3261 3338 2.068834 AACCGGTCGATGGAGATAGT 57.931 50.000 8.04 0.00 0.00 2.12
3305 3383 6.882656 ACTGACATTGCACATACTTATCTCT 58.117 36.000 0.00 0.00 0.00 3.10
3306 3384 6.983307 ACTGACATTGCACATACTTATCTCTC 59.017 38.462 0.00 0.00 0.00 3.20
3405 3483 3.175240 CGACACGCCTCTTGCTCG 61.175 66.667 0.00 0.00 38.05 5.03
3412 3490 2.507992 CCTCTTGCTCGTCAGCCG 60.508 66.667 0.00 0.00 46.26 5.52
3413 3491 2.507992 CTCTTGCTCGTCAGCCGG 60.508 66.667 0.00 0.00 46.26 6.13
3414 3492 2.989253 TCTTGCTCGTCAGCCGGA 60.989 61.111 5.05 0.00 46.26 5.14
3415 3493 2.811317 CTTGCTCGTCAGCCGGAC 60.811 66.667 5.05 0.00 46.26 4.79
3416 3494 4.373116 TTGCTCGTCAGCCGGACC 62.373 66.667 5.05 0.00 46.26 4.46
3547 3632 1.809619 CCACTGATGGGTACACGCG 60.810 63.158 3.53 3.53 43.04 6.01
3711 3799 1.257750 TGCTGGGCTCTGTCACGTAT 61.258 55.000 0.00 0.00 0.00 3.06
3712 3800 0.744874 GCTGGGCTCTGTCACGTATA 59.255 55.000 0.00 0.00 0.00 1.47
3736 3824 3.457263 TACGAGCCATGGCAGCGA 61.457 61.111 40.39 27.39 44.88 4.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.254093 TCTTGTTCCAGGAGGTAGACA 57.746 47.619 0.00 0.00 35.89 3.41
1 2 3.515901 ACATCTTGTTCCAGGAGGTAGAC 59.484 47.826 0.00 0.00 33.11 2.59
2 3 3.791320 ACATCTTGTTCCAGGAGGTAGA 58.209 45.455 0.00 0.00 33.11 2.59
3 4 5.269505 CTACATCTTGTTCCAGGAGGTAG 57.730 47.826 11.84 11.84 43.89 3.18
5 6 3.772025 CTCTACATCTTGTTCCAGGAGGT 59.228 47.826 0.00 0.00 38.05 3.85
6 7 3.431486 GCTCTACATCTTGTTCCAGGAGG 60.431 52.174 0.00 0.00 0.00 4.30
7 8 3.196469 TGCTCTACATCTTGTTCCAGGAG 59.804 47.826 0.00 0.00 0.00 3.69
8 9 3.173151 TGCTCTACATCTTGTTCCAGGA 58.827 45.455 0.00 0.00 0.00 3.86
9 10 3.616956 TGCTCTACATCTTGTTCCAGG 57.383 47.619 0.00 0.00 0.00 4.45
10 11 7.187244 CAATATGCTCTACATCTTGTTCCAG 57.813 40.000 0.00 0.00 37.81 3.86
16 17 7.783090 AGTTCACAATATGCTCTACATCTTG 57.217 36.000 3.17 3.17 44.40 3.02
24 25 8.072321 TCTCTAGAAAGTTCACAATATGCTCT 57.928 34.615 0.00 0.00 0.00 4.09
55 56 1.447838 GTTGATCTCGAAGCCGCCA 60.448 57.895 0.00 0.00 35.37 5.69
56 57 2.517450 CGTTGATCTCGAAGCCGCC 61.517 63.158 5.24 0.00 35.37 6.13
59 60 1.084370 CACCCGTTGATCTCGAAGCC 61.084 60.000 11.24 0.00 0.00 4.35
60 61 1.696832 GCACCCGTTGATCTCGAAGC 61.697 60.000 11.24 8.54 0.00 3.86
81 82 8.129496 TCACAAGGTCATTGAGTAGTTATACA 57.871 34.615 3.86 0.00 41.83 2.29
99 100 6.988580 TCTAGATCAACATATGCTTCACAAGG 59.011 38.462 1.58 0.00 0.00 3.61
287 291 3.084039 GCAATCACATCCCTCACTTTCA 58.916 45.455 0.00 0.00 0.00 2.69
292 304 0.729116 CGTGCAATCACATCCCTCAC 59.271 55.000 0.00 0.00 43.28 3.51
293 305 0.392863 CCGTGCAATCACATCCCTCA 60.393 55.000 0.00 0.00 43.28 3.86
294 306 1.718757 GCCGTGCAATCACATCCCTC 61.719 60.000 0.00 0.00 43.28 4.30
295 307 1.750399 GCCGTGCAATCACATCCCT 60.750 57.895 0.00 0.00 43.28 4.20
296 308 1.594194 TTGCCGTGCAATCACATCCC 61.594 55.000 7.15 0.00 43.99 3.85
297 309 1.882311 TTGCCGTGCAATCACATCC 59.118 52.632 7.15 0.00 43.99 3.51
359 372 9.537192 TCTACAACAATGTATAAATCTTACCCG 57.463 33.333 0.00 0.00 41.09 5.28
390 403 7.310664 TCTATTCCAACACGTTAGACACTTAG 58.689 38.462 0.00 0.00 0.00 2.18
391 404 7.218228 TCTATTCCAACACGTTAGACACTTA 57.782 36.000 0.00 0.00 0.00 2.24
392 405 6.092955 TCTATTCCAACACGTTAGACACTT 57.907 37.500 0.00 0.00 0.00 3.16
393 406 5.717078 TCTATTCCAACACGTTAGACACT 57.283 39.130 0.00 0.00 0.00 3.55
394 407 5.693104 TGTTCTATTCCAACACGTTAGACAC 59.307 40.000 0.00 0.00 0.00 3.67
395 408 5.845103 TGTTCTATTCCAACACGTTAGACA 58.155 37.500 0.00 0.00 0.00 3.41
396 409 6.423001 AGTTGTTCTATTCCAACACGTTAGAC 59.577 38.462 5.45 0.00 42.62 2.59
397 410 6.518493 AGTTGTTCTATTCCAACACGTTAGA 58.482 36.000 5.45 0.00 42.62 2.10
455 468 8.425577 TTTCACCTAAAAATTTCGCAAAATGA 57.574 26.923 0.00 0.00 35.27 2.57
463 479 9.626045 AGCTTCTATTTTCACCTAAAAATTTCG 57.374 29.630 0.00 0.00 40.37 3.46
637 655 8.149647 TGAGACGGTTAATAGTTCACCTTTTTA 58.850 33.333 0.00 0.00 0.00 1.52
643 661 6.592607 TGATTTGAGACGGTTAATAGTTCACC 59.407 38.462 0.00 0.00 0.00 4.02
644 662 7.591006 TGATTTGAGACGGTTAATAGTTCAC 57.409 36.000 0.00 0.00 0.00 3.18
646 664 9.490663 CAAATGATTTGAGACGGTTAATAGTTC 57.509 33.333 12.37 0.00 43.26 3.01
694 712 6.048732 TGTGCTATGACTTTGGTAATCTGA 57.951 37.500 0.00 0.00 0.00 3.27
720 738 2.113860 AGGACATGTTGTTGGGATCG 57.886 50.000 0.00 0.00 0.00 3.69
1043 1061 2.482142 GGATGCGTAGGAACTTCCTCTG 60.482 54.545 13.99 8.93 45.66 3.35
1051 1069 3.385577 GAAGAGATGGATGCGTAGGAAC 58.614 50.000 0.00 0.00 0.00 3.62
1052 1070 2.365617 GGAAGAGATGGATGCGTAGGAA 59.634 50.000 0.00 0.00 0.00 3.36
1053 1071 1.964223 GGAAGAGATGGATGCGTAGGA 59.036 52.381 0.00 0.00 0.00 2.94
1054 1072 1.336332 CGGAAGAGATGGATGCGTAGG 60.336 57.143 0.00 0.00 0.00 3.18
1123 1141 2.045926 CAAGGAGACGGCAAGGGG 60.046 66.667 0.00 0.00 0.00 4.79
1131 1149 0.610687 AAGGAGAAGCCAAGGAGACG 59.389 55.000 0.00 0.00 40.02 4.18
1179 1197 6.959639 ACTCCAACACAAGAACACAATTAT 57.040 33.333 0.00 0.00 0.00 1.28
1182 1200 4.821805 CCTACTCCAACACAAGAACACAAT 59.178 41.667 0.00 0.00 0.00 2.71
1185 1206 2.548480 GCCTACTCCAACACAAGAACAC 59.452 50.000 0.00 0.00 0.00 3.32
1193 1214 0.731855 GACGACGCCTACTCCAACAC 60.732 60.000 0.00 0.00 0.00 3.32
1240 1261 1.271434 GGGAGAACCTTGGTCTTCCAC 60.271 57.143 18.17 8.76 44.22 4.02
1360 1381 5.448926 AACGCACAAATTTCACAAGAAAC 57.551 34.783 0.00 0.00 45.79 2.78
1405 1426 5.591643 ACAAAACACATGTAGACATCGTC 57.408 39.130 0.00 0.00 33.61 4.20
1406 1427 6.198687 CAAACAAAACACATGTAGACATCGT 58.801 36.000 0.00 0.00 33.61 3.73
1407 1428 5.115472 GCAAACAAAACACATGTAGACATCG 59.885 40.000 0.00 0.00 33.61 3.84
1413 1438 6.309980 TCAACAAGCAAACAAAACACATGTAG 59.690 34.615 0.00 0.00 0.00 2.74
1562 1587 9.287373 ACTAATTAGGTACCGAAACAAAAATCA 57.713 29.630 16.73 0.00 0.00 2.57
1600 1627 4.335416 ACTGTTATGTGCTAAGCAACCAT 58.665 39.130 0.00 0.00 41.47 3.55
1626 1653 5.024785 AGCACTAATTAAGGTGGCTACTC 57.975 43.478 0.00 0.00 34.41 2.59
1651 1686 5.527582 GCCCTACAACAAGATAACAGTATGG 59.472 44.000 0.00 0.00 43.62 2.74
1707 1742 1.149148 GACGGCAACTGAGTTCTTCC 58.851 55.000 0.00 0.00 0.00 3.46
1854 1891 8.777578 AAAATATGGACCCTAAGAAATTACCC 57.222 34.615 0.00 0.00 0.00 3.69
1918 1955 8.579850 AGTTATGTGAAAGCAGGATAATGAAA 57.420 30.769 0.00 0.00 0.00 2.69
1967 2004 8.687824 TTGCTTTGTCTTCTTTTTGTTCTAAG 57.312 30.769 0.00 0.00 0.00 2.18
1989 2026 6.630444 ACATATGTGAGAAGATTCCATTGC 57.370 37.500 7.78 0.00 0.00 3.56
1990 2027 8.900781 AGAAACATATGTGAGAAGATTCCATTG 58.099 33.333 9.63 0.00 0.00 2.82
2018 2059 1.619654 TGCATGGGAACTTCTGTTGG 58.380 50.000 0.00 0.00 36.39 3.77
2127 2168 4.548991 GGCAACAATGAAAAATTGTGCA 57.451 36.364 18.38 0.00 40.94 4.57
2183 2231 7.347508 GTTCTTTATTCTAGAACGCACAAGA 57.652 36.000 7.48 8.15 41.28 3.02
2256 2306 6.868864 TGATTAGCTCGATAGTTTCATTAGCC 59.131 38.462 0.00 0.00 37.40 3.93
2283 2333 6.096705 CAGGGAAATCTGCATATTAACCAACA 59.903 38.462 15.50 0.00 0.00 3.33
2307 2357 2.752358 CTCACCAGCTTGGCTCCA 59.248 61.111 2.50 0.00 42.67 3.86
2364 2414 0.933097 CCAAGATGAAGACGATGGCG 59.067 55.000 0.00 0.00 44.79 5.69
2484 2534 1.984570 CTTCTCCTCCTCCACGGCA 60.985 63.158 0.00 0.00 0.00 5.69
2490 2540 1.289530 TCCTCCTTCTTCTCCTCCTCC 59.710 57.143 0.00 0.00 0.00 4.30
2491 2541 2.666317 CTCCTCCTTCTTCTCCTCCTC 58.334 57.143 0.00 0.00 0.00 3.71
2492 2542 1.290732 CCTCCTCCTTCTTCTCCTCCT 59.709 57.143 0.00 0.00 0.00 3.69
2565 2615 2.363795 TCCACTACCTCAGCGGGG 60.364 66.667 0.00 0.00 36.97 5.73
2669 2725 1.246737 GGCTTGGGTTGCTCTTGGAG 61.247 60.000 0.00 0.00 0.00 3.86
2988 3045 3.149196 GGAAGAATGCACAAGTTCCTGA 58.851 45.455 10.36 0.00 34.89 3.86
3062 3139 3.435327 TGTTAATCCACGCTGATGTGAAC 59.565 43.478 2.53 0.79 42.55 3.18
3073 3150 3.848272 AGCCATTGTTGTTAATCCACG 57.152 42.857 0.00 0.00 0.00 4.94
3112 3189 5.525454 TCTAGTTAGTACTCCACTTGGGA 57.475 43.478 11.83 6.88 45.89 4.37
3113 3190 6.396450 GTTTCTAGTTAGTACTCCACTTGGG 58.604 44.000 11.83 5.16 38.80 4.12
3114 3191 6.210984 AGGTTTCTAGTTAGTACTCCACTTGG 59.789 42.308 11.83 7.03 38.80 3.61
3115 3192 7.229581 AGGTTTCTAGTTAGTACTCCACTTG 57.770 40.000 11.83 10.37 38.80 3.16
3116 3193 6.150809 CGAGGTTTCTAGTTAGTACTCCACTT 59.849 42.308 11.83 0.00 38.80 3.16
3117 3194 5.647225 CGAGGTTTCTAGTTAGTACTCCACT 59.353 44.000 0.00 5.74 41.62 4.00
3118 3195 5.645497 TCGAGGTTTCTAGTTAGTACTCCAC 59.355 44.000 0.00 0.00 35.78 4.02
3119 3196 5.809001 TCGAGGTTTCTAGTTAGTACTCCA 58.191 41.667 0.00 0.00 35.78 3.86
3120 3197 6.541641 TGATCGAGGTTTCTAGTTAGTACTCC 59.458 42.308 0.00 0.00 35.78 3.85
3121 3198 7.551035 TGATCGAGGTTTCTAGTTAGTACTC 57.449 40.000 0.00 0.00 35.78 2.59
3122 3199 8.522542 AATGATCGAGGTTTCTAGTTAGTACT 57.477 34.615 0.00 0.00 38.44 2.73
3123 3200 7.861872 GGAATGATCGAGGTTTCTAGTTAGTAC 59.138 40.741 0.00 0.00 0.00 2.73
3124 3201 7.255035 CGGAATGATCGAGGTTTCTAGTTAGTA 60.255 40.741 0.00 0.00 0.00 1.82
3125 3202 6.459848 CGGAATGATCGAGGTTTCTAGTTAGT 60.460 42.308 0.00 0.00 0.00 2.24
3126 3203 5.915758 CGGAATGATCGAGGTTTCTAGTTAG 59.084 44.000 0.00 0.00 0.00 2.34
3127 3204 5.221185 CCGGAATGATCGAGGTTTCTAGTTA 60.221 44.000 0.00 0.00 0.00 2.24
3128 3205 4.441634 CCGGAATGATCGAGGTTTCTAGTT 60.442 45.833 0.00 0.00 0.00 2.24
3129 3206 3.068307 CCGGAATGATCGAGGTTTCTAGT 59.932 47.826 0.00 0.00 0.00 2.57
3130 3207 3.068307 ACCGGAATGATCGAGGTTTCTAG 59.932 47.826 9.46 0.00 34.78 2.43
3131 3208 3.028850 ACCGGAATGATCGAGGTTTCTA 58.971 45.455 9.46 0.00 34.78 2.10
3132 3209 1.831736 ACCGGAATGATCGAGGTTTCT 59.168 47.619 9.46 0.00 34.78 2.52
3133 3210 2.202566 GACCGGAATGATCGAGGTTTC 58.797 52.381 9.46 0.00 37.38 2.78
3134 3211 1.553248 TGACCGGAATGATCGAGGTTT 59.447 47.619 9.46 0.00 37.38 3.27
3135 3212 1.191535 TGACCGGAATGATCGAGGTT 58.808 50.000 9.46 0.00 37.38 3.50
3136 3213 1.137086 CTTGACCGGAATGATCGAGGT 59.863 52.381 9.46 0.00 39.15 3.85
3137 3214 1.137086 ACTTGACCGGAATGATCGAGG 59.863 52.381 9.46 0.00 0.00 4.63
3138 3215 2.586258 ACTTGACCGGAATGATCGAG 57.414 50.000 9.46 6.58 0.00 4.04
3139 3216 3.259064 GAAACTTGACCGGAATGATCGA 58.741 45.455 9.46 0.00 0.00 3.59
3140 3217 3.000041 TGAAACTTGACCGGAATGATCG 59.000 45.455 9.46 0.00 0.00 3.69
3141 3218 3.751175 TGTGAAACTTGACCGGAATGATC 59.249 43.478 9.46 0.00 38.04 2.92
3142 3219 3.750371 TGTGAAACTTGACCGGAATGAT 58.250 40.909 9.46 0.00 38.04 2.45
3143 3220 3.201353 TGTGAAACTTGACCGGAATGA 57.799 42.857 9.46 0.00 38.04 2.57
3144 3221 3.563808 TCTTGTGAAACTTGACCGGAATG 59.436 43.478 9.46 0.33 38.04 2.67
3145 3222 3.815809 TCTTGTGAAACTTGACCGGAAT 58.184 40.909 9.46 0.00 38.04 3.01
3146 3223 3.269538 TCTTGTGAAACTTGACCGGAA 57.730 42.857 9.46 0.00 38.04 4.30
3147 3224 2.992124 TCTTGTGAAACTTGACCGGA 57.008 45.000 9.46 0.00 38.04 5.14
3148 3225 2.878406 ACATCTTGTGAAACTTGACCGG 59.122 45.455 0.00 0.00 38.04 5.28
3170 3247 4.261114 CCGACTTCCCTCGTTCTTATCTAC 60.261 50.000 0.00 0.00 31.35 2.59
3171 3248 3.881688 CCGACTTCCCTCGTTCTTATCTA 59.118 47.826 0.00 0.00 31.35 1.98
3179 3256 0.038744 TCCTACCGACTTCCCTCGTT 59.961 55.000 0.00 0.00 31.35 3.85
3247 3324 4.985409 CCAAAGCTAACTATCTCCATCGAC 59.015 45.833 0.00 0.00 0.00 4.20
3261 3338 9.596308 TGTCAGTATAGTATATCCCAAAGCTAA 57.404 33.333 0.00 0.00 0.00 3.09
3305 3383 2.833943 TCACTGATCTGGCTAAGCAAGA 59.166 45.455 4.49 0.00 43.29 3.02
3306 3384 3.257469 TCACTGATCTGGCTAAGCAAG 57.743 47.619 4.49 0.00 0.00 4.01
3331 3409 1.086696 CGACCGGCACTGATTGATTT 58.913 50.000 0.00 0.00 0.00 2.17
3412 3490 3.332706 AGATCGAGATCTCCGGTCC 57.667 57.895 17.13 2.62 44.37 4.46
3547 3632 4.182339 GACTGAAACGTCTCCTTTATCCC 58.818 47.826 0.00 0.00 0.00 3.85
3654 3742 0.321298 TACCGGACAAAGGCAGAAGC 60.321 55.000 9.46 0.00 41.10 3.86
3670 3758 2.433664 CGACCAAGCCACGGTACC 60.434 66.667 0.16 0.16 36.69 3.34
3715 3803 1.435925 CTGCCATGGCTCGTACGTA 59.564 57.895 35.53 13.44 42.51 3.57
3719 3807 3.430565 CTCGCTGCCATGGCTCGTA 62.431 63.158 34.04 24.74 42.51 3.43


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

AutoCloner maintained by Alex Coulton.