Multiple sequence alignment - TraesCS3A01G036000

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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 TraesCS3A01G036000 chr3A 100.000 3057 0 0 1 3057 19897123 19894067 0.000000e+00 5646.0
1 TraesCS3A01G036000 chr3A 90.323 124 11 1 1277 1399 623223453 623223576 8.770000e-36 161.0
2 TraesCS3A01G036000 chr3D 91.071 3136 120 64 1 3054 16886689 16889746 0.000000e+00 4093.0
3 TraesCS3A01G036000 chr3D 89.683 126 12 1 1277 1401 480149365 480149490 3.150000e-35 159.0
4 TraesCS3A01G036000 chr3B 92.086 1630 54 33 726 2315 24261296 24262890 0.000000e+00 2226.0
5 TraesCS3A01G036000 chr3B 86.587 753 47 29 2340 3054 24262881 24263617 0.000000e+00 782.0
6 TraesCS3A01G036000 chr3B 86.567 670 40 20 1 651 24260307 24260945 0.000000e+00 693.0
7 TraesCS3A01G036000 chr3B 91.228 114 10 0 1286 1399 640667601 640667714 4.080000e-34 156.0
8 TraesCS3A01G036000 chr2D 92.121 165 5 1 2877 3041 85707604 85707448 3.070000e-55 226.0
9 TraesCS3A01G036000 chr2D 87.200 125 8 4 2770 2886 85707784 85707660 5.320000e-28 135.0
10 TraesCS3A01G036000 chr7D 82.292 96 12 5 1305 1396 265004811 265004717 9.090000e-11 78.7
11 TraesCS3A01G036000 chr7B 82.292 96 12 5 1305 1396 245211839 245211745 9.090000e-11 78.7
12 TraesCS3A01G036000 chr5D 77.692 130 21 7 1297 1424 436971850 436971973 4.230000e-09 73.1
13 TraesCS3A01G036000 chr5B 79.279 111 17 5 1260 1364 531187481 531187591 4.230000e-09 73.1


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 TraesCS3A01G036000 chr3A 19894067 19897123 3056 True 5646.000000 5646 100.000000 1 3057 1 chr3A.!!$R1 3056
1 TraesCS3A01G036000 chr3D 16886689 16889746 3057 False 4093.000000 4093 91.071000 1 3054 1 chr3D.!!$F1 3053
2 TraesCS3A01G036000 chr3B 24260307 24263617 3310 False 1233.666667 2226 88.413333 1 3054 3 chr3B.!!$F2 3053

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
296 304 0.027324 GACCGATCGACGACCACTAC 59.973 60.0 18.66 0.0 45.77 2.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2181 2542 0.178944 ATGATGGATGGGTGCATGGG 60.179 55.0 0.0 0.0 36.44 4.0 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
28 29 0.677731 TGTTAGCTCCTGCACATGGC 60.678 55.000 0.00 0.00 42.74 4.40
67 68 2.638480 ACATTACACATCGATGGGGG 57.362 50.000 30.17 19.80 34.87 5.40
69 70 0.110486 ATTACACATCGATGGGGGCC 59.890 55.000 30.17 0.00 34.87 5.80
92 96 4.635765 CGGGGCCATAATACACAAGATATG 59.364 45.833 4.39 0.00 0.00 1.78
130 138 4.662145 GCATATAGCAACAAAGAAGCGTT 58.338 39.130 0.00 0.00 44.79 4.84
144 152 8.015658 ACAAAGAAGCGTTCACTTATTGTATTC 58.984 33.333 0.00 0.00 37.70 1.75
145 153 6.663944 AGAAGCGTTCACTTATTGTATTCC 57.336 37.500 1.58 0.00 0.00 3.01
200 208 5.849861 GCAAGCGTAAACTATTGCATTAC 57.150 39.130 11.83 0.00 45.66 1.89
234 242 9.722056 CATGTAAATTAAACTAGATGGTTGAGC 57.278 33.333 0.00 0.00 0.00 4.26
236 244 9.461312 TGTAAATTAAACTAGATGGTTGAGCAT 57.539 29.630 0.00 0.00 0.00 3.79
238 246 7.573968 AATTAAACTAGATGGTTGAGCATCC 57.426 36.000 16.97 0.00 0.00 3.51
239 247 4.851639 AAACTAGATGGTTGAGCATCCT 57.148 40.909 16.97 9.04 0.00 3.24
240 248 4.851639 AACTAGATGGTTGAGCATCCTT 57.148 40.909 16.97 5.21 0.00 3.36
241 249 4.414337 ACTAGATGGTTGAGCATCCTTC 57.586 45.455 16.97 4.54 0.00 3.46
242 250 2.725221 AGATGGTTGAGCATCCTTCC 57.275 50.000 16.97 0.00 0.00 3.46
243 251 2.203584 AGATGGTTGAGCATCCTTCCT 58.796 47.619 16.97 0.00 0.00 3.36
287 295 0.318275 GCTCCATGAGACCGATCGAC 60.318 60.000 18.66 10.37 0.00 4.20
296 304 0.027324 GACCGATCGACGACCACTAC 59.973 60.000 18.66 0.00 45.77 2.73
346 354 1.774856 AGTTGGCCACTTAGTTCTGGT 59.225 47.619 3.88 0.00 27.32 4.00
364 372 4.122776 CTGGTTATGGCTAGTGACACATC 58.877 47.826 8.59 0.00 31.68 3.06
477 499 5.276536 GCTGAATAAAAATGCTTTGATCGGC 60.277 40.000 0.00 0.00 31.76 5.54
484 506 3.692257 ATGCTTTGATCGGCTAGCTAT 57.308 42.857 15.72 8.75 34.77 2.97
485 507 4.808414 ATGCTTTGATCGGCTAGCTATA 57.192 40.909 15.72 0.33 34.77 1.31
486 508 4.808414 TGCTTTGATCGGCTAGCTATAT 57.192 40.909 15.72 5.70 34.77 0.86
487 509 5.914898 TGCTTTGATCGGCTAGCTATATA 57.085 39.130 15.72 0.00 34.77 0.86
488 510 6.471233 TGCTTTGATCGGCTAGCTATATAT 57.529 37.500 15.72 1.24 34.77 0.86
489 511 6.276091 TGCTTTGATCGGCTAGCTATATATG 58.724 40.000 15.72 0.88 34.77 1.78
490 512 6.127338 TGCTTTGATCGGCTAGCTATATATGT 60.127 38.462 15.72 0.00 34.77 2.29
491 513 6.199908 GCTTTGATCGGCTAGCTATATATGTG 59.800 42.308 15.72 0.23 0.00 3.21
492 514 5.188327 TGATCGGCTAGCTATATATGTGC 57.812 43.478 15.72 0.07 0.00 4.57
493 515 4.644685 TGATCGGCTAGCTATATATGTGCA 59.355 41.667 15.72 0.00 0.00 4.57
494 516 5.302823 TGATCGGCTAGCTATATATGTGCAT 59.697 40.000 15.72 0.00 0.00 3.96
535 561 1.275010 TCCTATCATGCGTGTGTGTGT 59.725 47.619 5.68 0.00 0.00 3.72
536 562 1.394572 CCTATCATGCGTGTGTGTGTG 59.605 52.381 5.68 0.00 0.00 3.82
537 563 2.068519 CTATCATGCGTGTGTGTGTGT 58.931 47.619 5.68 0.00 0.00 3.72
538 564 0.587768 ATCATGCGTGTGTGTGTGTG 59.412 50.000 5.68 0.00 0.00 3.82
579 605 1.376424 CAAGCATGAGTCGCCCTGT 60.376 57.895 0.00 0.00 0.00 4.00
652 697 2.607750 ATATGGAGCCCGGCCGAT 60.608 61.111 30.73 13.86 0.00 4.18
719 764 0.178861 ACCACCACTGATCCCCTCTT 60.179 55.000 0.00 0.00 0.00 2.85
724 769 1.004891 ACTGATCCCCTCTTCCCCC 59.995 63.158 0.00 0.00 0.00 5.40
775 1090 7.218614 TCTATCTCTTCTAGCAGTGGTACTAC 58.781 42.308 0.19 0.19 0.00 2.73
940 1264 0.905337 ACTGGGAGGACTACTGTGCC 60.905 60.000 0.00 0.00 34.93 5.01
944 1268 1.261238 GGAGGACTACTGTGCCTGCT 61.261 60.000 9.33 0.00 37.20 4.24
947 1271 1.301677 GGACTACTGTGCCTGCTTGC 61.302 60.000 0.00 0.00 0.00 4.01
1056 1385 3.593442 TCTCCATCTCCTCTCTTCTCC 57.407 52.381 0.00 0.00 0.00 3.71
1057 1386 2.158682 TCTCCATCTCCTCTCTTCTCCG 60.159 54.545 0.00 0.00 0.00 4.63
1085 1428 3.033184 CTCTGCTCAATTCTCTCCTCCT 58.967 50.000 0.00 0.00 0.00 3.69
1086 1429 3.030291 TCTGCTCAATTCTCTCCTCCTC 58.970 50.000 0.00 0.00 0.00 3.71
1454 1804 4.865761 GCGCGCTGTACCATCGGA 62.866 66.667 26.67 0.00 0.00 4.55
1943 2297 1.675552 GGATGAATTACCCACCCACG 58.324 55.000 0.00 0.00 0.00 4.94
1944 2298 1.021968 GATGAATTACCCACCCACGC 58.978 55.000 0.00 0.00 0.00 5.34
1945 2299 0.329931 ATGAATTACCCACCCACGCA 59.670 50.000 0.00 0.00 0.00 5.24
1946 2300 0.606944 TGAATTACCCACCCACGCAC 60.607 55.000 0.00 0.00 0.00 5.34
1950 2304 1.829523 TTACCCACCCACGCACTACC 61.830 60.000 0.00 0.00 0.00 3.18
1975 2329 2.845752 TACCTGCATGCGTCCGAACC 62.846 60.000 14.09 0.00 0.00 3.62
1986 2340 1.439679 GTCCGAACCAAAGCTCGATT 58.560 50.000 0.00 0.00 37.23 3.34
2116 2477 1.601166 GCCTTGTAACCGAACCAACT 58.399 50.000 0.00 0.00 0.00 3.16
2117 2478 1.534163 GCCTTGTAACCGAACCAACTC 59.466 52.381 0.00 0.00 0.00 3.01
2118 2479 2.148768 CCTTGTAACCGAACCAACTCC 58.851 52.381 0.00 0.00 0.00 3.85
2146 2507 4.244425 ACGTTCTTGATATGATCCGAGG 57.756 45.455 0.00 0.00 0.00 4.63
2181 2542 4.679654 CGCCTTGTAAATTCTTGGTCAAAC 59.320 41.667 0.00 0.00 0.00 2.93
2186 2547 6.095432 TGTAAATTCTTGGTCAAACCCATG 57.905 37.500 0.00 0.00 37.50 3.66
2199 2560 1.230783 CCCATGCACCCATCCATCA 59.769 57.895 0.00 0.00 0.00 3.07
2200 2561 0.178944 CCCATGCACCCATCCATCAT 60.179 55.000 0.00 0.00 0.00 2.45
2201 2562 1.254026 CCATGCACCCATCCATCATC 58.746 55.000 0.00 0.00 0.00 2.92
2247 2612 7.959658 TGATCAATATCACCCATTTTCTTGT 57.040 32.000 0.00 0.00 37.20 3.16
2248 2613 8.365060 TGATCAATATCACCCATTTTCTTGTT 57.635 30.769 0.00 0.00 37.20 2.83
2249 2614 8.469200 TGATCAATATCACCCATTTTCTTGTTC 58.531 33.333 0.00 0.00 37.20 3.18
2250 2615 8.599624 ATCAATATCACCCATTTTCTTGTTCT 57.400 30.769 0.00 0.00 0.00 3.01
2251 2616 8.421249 TCAATATCACCCATTTTCTTGTTCTT 57.579 30.769 0.00 0.00 0.00 2.52
2252 2617 8.306038 TCAATATCACCCATTTTCTTGTTCTTG 58.694 33.333 0.00 0.00 0.00 3.02
2272 2637 6.314018 TCTTGTTGATGTGTTAATCGCAATC 58.686 36.000 0.00 0.00 40.08 2.67
2309 2678 4.221342 CGAGGACATGTGTTTGATTTGTG 58.779 43.478 1.15 0.00 0.00 3.33
2318 2690 4.892345 TGTGTTTGATTTGTGAAGGATCCA 59.108 37.500 15.82 0.00 0.00 3.41
2361 2733 5.560966 TTGTGAAGGAGAGTTCAAACAAC 57.439 39.130 0.00 0.00 38.17 3.32
2429 2802 5.181245 GTGTATTCTAAACGGGCATGCATAT 59.819 40.000 21.36 0.00 0.00 1.78
2498 2871 0.391661 CACCATGAGTCAGTTCCCCG 60.392 60.000 0.00 0.00 0.00 5.73
2519 2892 3.119388 CGCTTGTTCCATTTCCATCATGT 60.119 43.478 0.00 0.00 0.00 3.21
2555 2928 6.939730 ACTTTGTTTGCCCCCTTTTAATTATG 59.060 34.615 0.00 0.00 0.00 1.90
2598 2972 3.483421 TCTCCTATTTCAGCATGCATGG 58.517 45.455 27.34 12.41 34.76 3.66
2599 2973 1.958579 TCCTATTTCAGCATGCATGGC 59.041 47.619 27.34 18.86 34.76 4.40
2600 2974 1.684450 CCTATTTCAGCATGCATGGCA 59.316 47.619 27.34 0.00 44.86 4.92
2601 2975 2.545113 CCTATTTCAGCATGCATGGCAC 60.545 50.000 27.34 11.50 43.04 5.01
2602 2976 0.899019 ATTTCAGCATGCATGGCACA 59.101 45.000 27.34 8.08 43.04 4.57
2604 2978 0.896479 TTCAGCATGCATGGCACACT 60.896 50.000 27.34 12.91 43.04 3.55
2645 3020 6.010219 ACCAATTAGCACCAGTAACAATCTT 58.990 36.000 0.00 0.00 0.00 2.40
2650 3025 7.667043 TTAGCACCAGTAACAATCTTACTTG 57.333 36.000 0.00 0.00 33.30 3.16
2667 3042 7.556844 TCTTACTTGCTCTAGAATTAACCCAG 58.443 38.462 0.00 0.00 0.00 4.45
2713 3099 2.352421 CGACAGTTACCCATATAGGCCG 60.352 54.545 0.00 0.00 35.39 6.13
2714 3100 1.975680 ACAGTTACCCATATAGGCCGG 59.024 52.381 0.00 0.00 35.39 6.13
2717 3103 0.474079 TTACCCATATAGGCCGGCCA 60.474 55.000 45.13 31.09 38.92 5.36
2718 3104 0.252974 TACCCATATAGGCCGGCCAT 60.253 55.000 45.13 34.50 38.92 4.40
2719 3105 0.252974 ACCCATATAGGCCGGCCATA 60.253 55.000 45.13 35.33 38.92 2.74
2727 3113 0.689745 AGGCCGGCCATAACTACTCA 60.690 55.000 45.13 0.00 38.92 3.41
2729 3115 0.532196 GCCGGCCATAACTACTCACC 60.532 60.000 18.11 0.00 0.00 4.02
2731 3117 1.416401 CCGGCCATAACTACTCACCAT 59.584 52.381 2.24 0.00 0.00 3.55
2732 3118 2.548067 CCGGCCATAACTACTCACCATC 60.548 54.545 2.24 0.00 0.00 3.51
2741 3127 2.692557 ACTACTCACCATCAGCTAGCAG 59.307 50.000 18.83 9.54 0.00 4.24
2742 3128 0.829333 ACTCACCATCAGCTAGCAGG 59.171 55.000 18.83 14.92 0.00 4.85
2750 3136 2.047844 AGCTAGCAGGCACACACG 60.048 61.111 18.83 0.00 34.17 4.49
2752 3138 1.080093 GCTAGCAGGCACACACGTA 60.080 57.895 10.63 0.00 0.00 3.57
2753 3139 1.352156 GCTAGCAGGCACACACGTAC 61.352 60.000 10.63 0.00 0.00 3.67
2755 3141 0.606096 TAGCAGGCACACACGTACAT 59.394 50.000 0.00 0.00 0.00 2.29
2756 3142 0.950555 AGCAGGCACACACGTACATG 60.951 55.000 0.00 0.00 0.00 3.21
2795 3187 7.718272 TTACCTGCATATTTTACGGATACAC 57.282 36.000 0.00 0.00 0.00 2.90
2856 3255 1.449423 CATGGGTGATTGGACGCGA 60.449 57.895 15.93 0.00 0.00 5.87
2897 3296 1.160137 GAGTGCACCACCAAAGCTAG 58.840 55.000 14.63 0.00 34.49 3.42
2898 3297 0.890996 AGTGCACCACCAAAGCTAGC 60.891 55.000 14.63 6.62 34.49 3.42
2899 3298 1.965930 TGCACCACCAAAGCTAGCG 60.966 57.895 9.55 0.00 0.00 4.26
2900 3299 1.966451 GCACCACCAAAGCTAGCGT 60.966 57.895 9.55 2.32 0.00 5.07
2901 3300 1.868997 CACCACCAAAGCTAGCGTG 59.131 57.895 9.55 11.07 0.00 5.34
2902 3301 1.966451 ACCACCAAAGCTAGCGTGC 60.966 57.895 9.55 0.00 0.00 5.34
2903 3302 2.476051 CACCAAAGCTAGCGTGCG 59.524 61.111 9.55 8.38 38.13 5.34
2904 3303 2.030562 ACCAAAGCTAGCGTGCGT 59.969 55.556 9.55 8.95 38.13 5.24
3054 3470 4.320456 ACTGCTCACCGCACCCTG 62.320 66.667 0.00 0.00 45.47 4.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 6.739331 ATGTAGAAAGAGATAACAGAGGGG 57.261 41.667 0.00 0.00 0.00 4.79
67 68 0.466555 TTGTGTATTATGGCCCCGGC 60.467 55.000 0.00 0.00 41.06 6.13
69 70 2.631160 TCTTGTGTATTATGGCCCCG 57.369 50.000 0.00 0.00 0.00 5.73
126 134 4.852609 ACGGAATACAATAAGTGAACGC 57.147 40.909 0.00 0.00 0.00 4.84
128 136 5.123344 AGGCAACGGAATACAATAAGTGAAC 59.877 40.000 0.00 0.00 46.39 3.18
130 138 4.839121 AGGCAACGGAATACAATAAGTGA 58.161 39.130 0.00 0.00 46.39 3.41
145 153 4.680237 TGTGGAGGCGAGGCAACG 62.680 66.667 0.00 0.08 46.39 4.10
225 233 2.357569 GGAAGGAAGGATGCTCAACCAT 60.358 50.000 7.53 0.00 0.00 3.55
228 236 2.797177 AGGAAGGAAGGATGCTCAAC 57.203 50.000 0.00 0.00 0.00 3.18
230 238 1.561542 GGAAGGAAGGAAGGATGCTCA 59.438 52.381 0.00 0.00 0.00 4.26
231 239 1.843206 AGGAAGGAAGGAAGGATGCTC 59.157 52.381 0.00 0.00 0.00 4.26
232 240 1.978361 AGGAAGGAAGGAAGGATGCT 58.022 50.000 0.00 0.00 0.00 3.79
233 241 2.649190 GAAGGAAGGAAGGAAGGATGC 58.351 52.381 0.00 0.00 0.00 3.91
234 242 2.849318 AGGAAGGAAGGAAGGAAGGATG 59.151 50.000 0.00 0.00 0.00 3.51
236 244 2.743131 AGGAAGGAAGGAAGGAAGGA 57.257 50.000 0.00 0.00 0.00 3.36
238 246 2.916269 AGGAAGGAAGGAAGGAAGGAAG 59.084 50.000 0.00 0.00 0.00 3.46
239 247 3.005529 AGGAAGGAAGGAAGGAAGGAA 57.994 47.619 0.00 0.00 0.00 3.36
240 248 2.743131 AGGAAGGAAGGAAGGAAGGA 57.257 50.000 0.00 0.00 0.00 3.36
241 249 2.025793 GGAAGGAAGGAAGGAAGGAAGG 60.026 54.545 0.00 0.00 0.00 3.46
242 250 2.916269 AGGAAGGAAGGAAGGAAGGAAG 59.084 50.000 0.00 0.00 0.00 3.46
243 251 3.005529 AGGAAGGAAGGAAGGAAGGAA 57.994 47.619 0.00 0.00 0.00 3.36
287 295 3.617263 GCCATTCTAAACTGTAGTGGTCG 59.383 47.826 0.00 0.00 0.00 4.79
296 304 0.394352 AGGGGCGCCATTCTAAACTG 60.394 55.000 30.85 0.00 0.00 3.16
346 354 4.758688 CACTGATGTGTCACTAGCCATAA 58.241 43.478 4.27 0.00 39.24 1.90
413 425 9.304731 GATCAGAGTACTATATACGACACCTAG 57.695 40.741 0.00 0.00 0.00 3.02
414 426 8.810041 TGATCAGAGTACTATATACGACACCTA 58.190 37.037 0.00 0.00 0.00 3.08
415 427 7.677892 TGATCAGAGTACTATATACGACACCT 58.322 38.462 0.00 0.00 0.00 4.00
416 428 7.902387 TGATCAGAGTACTATATACGACACC 57.098 40.000 0.00 0.00 0.00 4.16
417 429 9.373603 AGATGATCAGAGTACTATATACGACAC 57.626 37.037 0.09 0.00 0.00 3.67
420 432 9.752961 GCTAGATGATCAGAGTACTATATACGA 57.247 37.037 0.09 0.00 0.00 3.43
421 433 9.758651 AGCTAGATGATCAGAGTACTATATACG 57.241 37.037 0.09 0.00 0.00 3.06
485 507 7.976175 CGGCCGAGATATATTATATGCACATAT 59.024 37.037 24.07 8.16 37.69 1.78
486 508 7.312899 CGGCCGAGATATATTATATGCACATA 58.687 38.462 24.07 0.00 0.00 2.29
487 509 6.159293 CGGCCGAGATATATTATATGCACAT 58.841 40.000 24.07 0.00 0.00 3.21
488 510 5.508994 CCGGCCGAGATATATTATATGCACA 60.509 44.000 30.73 0.00 0.00 4.57
489 511 4.923871 CCGGCCGAGATATATTATATGCAC 59.076 45.833 30.73 0.00 0.00 4.57
490 512 4.830600 TCCGGCCGAGATATATTATATGCA 59.169 41.667 30.73 0.00 0.00 3.96
491 513 5.047943 ACTCCGGCCGAGATATATTATATGC 60.048 44.000 30.73 0.00 41.63 3.14
492 514 6.349445 GGACTCCGGCCGAGATATATTATATG 60.349 46.154 30.73 4.00 41.63 1.78
493 515 5.711036 GGACTCCGGCCGAGATATATTATAT 59.289 44.000 30.73 1.81 41.63 0.86
494 516 5.068636 GGACTCCGGCCGAGATATATTATA 58.931 45.833 30.73 0.00 41.63 0.98
535 561 0.867086 TACGATCGTCGACACACACA 59.133 50.000 26.48 0.00 43.74 3.72
536 562 1.954437 TTACGATCGTCGACACACAC 58.046 50.000 26.48 1.05 43.74 3.82
537 563 2.905959 ATTACGATCGTCGACACACA 57.094 45.000 26.48 0.63 43.74 3.72
538 564 4.028187 GGTTTATTACGATCGTCGACACAC 60.028 45.833 26.48 14.82 43.74 3.82
579 605 0.542938 CTGGACTGGACTGGACTGGA 60.543 60.000 0.00 0.00 0.00 3.86
652 697 4.211164 CGTTGTTGAGTTCTAGATTGTGCA 59.789 41.667 0.00 0.00 0.00 4.57
724 769 2.806945 AGGTGTGAGAGAGAGAGAGG 57.193 55.000 0.00 0.00 0.00 3.69
734 1044 5.428457 AGAGATAGAGAGAGAAGGTGTGAGA 59.572 44.000 0.00 0.00 0.00 3.27
736 1046 5.708736 AGAGATAGAGAGAGAAGGTGTGA 57.291 43.478 0.00 0.00 0.00 3.58
775 1090 5.410924 TGTACAGATGCAAAGCAGTAGTAG 58.589 41.667 0.00 0.00 43.65 2.57
783 1098 2.704572 AGGACTGTACAGATGCAAAGC 58.295 47.619 29.30 7.37 0.00 3.51
1027 1355 0.885596 GGAGATGGAGATGCTGCTGC 60.886 60.000 8.89 8.89 40.20 5.25
1056 1385 2.426738 AGAATTGAGCAGAGAGGAGACG 59.573 50.000 0.00 0.00 0.00 4.18
1057 1386 3.701040 AGAGAATTGAGCAGAGAGGAGAC 59.299 47.826 0.00 0.00 0.00 3.36
1085 1428 2.099263 GGCTTGTCATGCTCGTACTAGA 59.901 50.000 10.26 0.00 0.00 2.43
1086 1429 2.464865 GGCTTGTCATGCTCGTACTAG 58.535 52.381 10.26 0.00 0.00 2.57
1444 1794 4.944372 CCGCCGCTCCGATGGTAC 62.944 72.222 0.00 0.00 0.00 3.34
1943 2297 1.822990 TGCAGGTACTAGTGGTAGTGC 59.177 52.381 5.39 11.90 39.96 4.40
1944 2298 3.738281 GCATGCAGGTACTAGTGGTAGTG 60.738 52.174 14.21 0.00 39.96 2.74
1945 2299 2.431057 GCATGCAGGTACTAGTGGTAGT 59.569 50.000 14.21 0.00 42.49 2.73
1946 2300 2.543861 CGCATGCAGGTACTAGTGGTAG 60.544 54.545 19.57 0.00 36.02 3.18
1950 2304 1.560923 GACGCATGCAGGTACTAGTG 58.439 55.000 19.57 0.00 36.02 2.74
2021 2379 6.616774 ACTTTACTTACTACCGCTAGCTAG 57.383 41.667 16.84 16.84 0.00 3.42
2116 2477 1.843368 ATCAAGAACGTACGGGAGGA 58.157 50.000 21.06 10.47 0.00 3.71
2117 2478 3.317149 TCATATCAAGAACGTACGGGAGG 59.683 47.826 21.06 5.09 0.00 4.30
2118 2479 4.563337 TCATATCAAGAACGTACGGGAG 57.437 45.455 21.06 4.74 0.00 4.30
2146 2507 0.525668 ACAAGGCGTCATCGATCGAC 60.526 55.000 22.06 7.72 39.71 4.20
2181 2542 0.178944 ATGATGGATGGGTGCATGGG 60.179 55.000 0.00 0.00 36.44 4.00
2186 2547 1.075050 AGATGGATGATGGATGGGTGC 59.925 52.381 0.00 0.00 0.00 5.01
2247 2612 5.681337 TGCGATTAACACATCAACAAGAA 57.319 34.783 0.00 0.00 0.00 2.52
2248 2613 5.681337 TTGCGATTAACACATCAACAAGA 57.319 34.783 0.00 0.00 0.00 3.02
2249 2614 5.225743 CGATTGCGATTAACACATCAACAAG 59.774 40.000 0.00 0.00 40.82 3.16
2250 2615 5.085390 CGATTGCGATTAACACATCAACAA 58.915 37.500 0.00 0.00 40.82 2.83
2251 2616 4.436718 CCGATTGCGATTAACACATCAACA 60.437 41.667 0.00 0.00 40.82 3.33
2252 2617 4.028383 CCGATTGCGATTAACACATCAAC 58.972 43.478 0.00 0.00 40.82 3.18
2336 2708 6.773976 TGTTTGAACTCTCCTTCACAATTT 57.226 33.333 0.00 0.00 29.62 1.82
2337 2709 6.405842 GGTTGTTTGAACTCTCCTTCACAATT 60.406 38.462 0.00 0.00 29.62 2.32
2338 2710 5.067805 GGTTGTTTGAACTCTCCTTCACAAT 59.932 40.000 0.00 0.00 29.62 2.71
2343 2715 5.576447 TTTGGTTGTTTGAACTCTCCTTC 57.424 39.130 0.00 0.00 0.00 3.46
2369 2742 4.443913 TGCATGTGAACATCCTTGATTG 57.556 40.909 0.00 0.00 33.61 2.67
2429 2802 5.278414 CGCCTTGATTATAAATGGATGTGCA 60.278 40.000 0.00 0.00 0.00 4.57
2519 2892 5.011227 GGGGCAAACAAAGTTTATTAGGTGA 59.989 40.000 0.00 0.00 0.00 4.02
2602 2976 5.432680 TGGTCAGCACTAGTAGTAGTAGT 57.567 43.478 9.94 11.28 37.40 2.73
2604 2978 7.013083 GCTAATTGGTCAGCACTAGTAGTAGTA 59.987 40.741 9.94 0.00 37.40 1.82
2619 2993 4.359434 TGTTACTGGTGCTAATTGGTCA 57.641 40.909 0.00 0.00 0.00 4.02
2645 3020 5.962031 TCCTGGGTTAATTCTAGAGCAAGTA 59.038 40.000 0.00 0.00 0.00 2.24
2650 3025 5.454045 CCTTCTCCTGGGTTAATTCTAGAGC 60.454 48.000 0.00 0.00 0.00 4.09
2685 3062 0.317160 TGGGTAACTGTCGACTGCAG 59.683 55.000 20.88 13.48 39.67 4.41
2713 3099 3.733337 CTGATGGTGAGTAGTTATGGCC 58.267 50.000 0.00 0.00 0.00 5.36
2714 3100 3.134458 GCTGATGGTGAGTAGTTATGGC 58.866 50.000 0.00 0.00 0.00 4.40
2717 3103 4.895889 TGCTAGCTGATGGTGAGTAGTTAT 59.104 41.667 17.23 0.00 0.00 1.89
2718 3104 4.278310 TGCTAGCTGATGGTGAGTAGTTA 58.722 43.478 17.23 0.00 0.00 2.24
2719 3105 3.099905 TGCTAGCTGATGGTGAGTAGTT 58.900 45.455 17.23 0.00 0.00 2.24
2727 3113 1.222936 GTGCCTGCTAGCTGATGGT 59.777 57.895 21.96 0.00 0.00 3.55
2729 3115 0.392060 TGTGTGCCTGCTAGCTGATG 60.392 55.000 21.96 8.17 0.00 3.07
2731 3117 1.004560 GTGTGTGCCTGCTAGCTGA 60.005 57.895 21.96 1.01 0.00 4.26
2732 3118 2.385875 CGTGTGTGCCTGCTAGCTG 61.386 63.158 17.23 15.65 0.00 4.24
2741 3127 1.458064 GTGTACATGTACGTGTGTGCC 59.542 52.381 27.33 14.17 38.85 5.01
2742 3128 2.128821 TGTGTACATGTACGTGTGTGC 58.871 47.619 27.33 17.86 38.85 4.57
2755 3141 5.649831 TGCAGGTAAATATTGCATGTGTACA 59.350 36.000 0.00 0.00 42.41 2.90
2756 3142 6.130298 TGCAGGTAAATATTGCATGTGTAC 57.870 37.500 0.00 0.00 42.41 2.90
2768 3154 9.999660 TGTATCCGTAAAATATGCAGGTAAATA 57.000 29.630 0.00 0.00 0.00 1.40
2788 3174 1.528586 GCTCGTGATGCATGTGTATCC 59.471 52.381 2.46 0.00 36.50 2.59
2791 3177 0.805711 CCGCTCGTGATGCATGTGTA 60.806 55.000 2.46 0.00 0.00 2.90
2792 3178 2.102438 CCGCTCGTGATGCATGTGT 61.102 57.895 2.46 0.00 0.00 3.72
2795 3187 3.945434 GCCCGCTCGTGATGCATG 61.945 66.667 2.46 0.00 0.00 4.06
2989 3394 3.605749 TTTGGCCGGGAGCGAAGAG 62.606 63.158 2.18 0.00 45.17 2.85
2990 3395 3.632080 TTTGGCCGGGAGCGAAGA 61.632 61.111 2.18 0.00 45.17 2.87


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

AutoCloner maintained by Alex Coulton.