Multiple sequence alignment - TraesCS6A01G206700

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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 TraesCS6A01G206700 chr6A 100.000 1943 0 0 1 1943 364627197 364625255 0.000000e+00 3589.0
1 TraesCS6A01G206700 chr6A 100.000 582 0 0 2353 2934 364624845 364624264 0.000000e+00 1075.0
2 TraesCS6A01G206700 chr6D 92.516 1109 24 19 877 1942 254236244 254237336 0.000000e+00 1533.0
3 TraesCS6A01G206700 chr6D 88.310 864 80 10 1 856 254235275 254236125 0.000000e+00 1016.0
4 TraesCS6A01G206700 chr6D 94.776 536 14 2 2353 2881 254237409 254237937 0.000000e+00 822.0
5 TraesCS6A01G206700 chr6B 91.019 412 25 3 1532 1943 372307505 372307904 1.990000e-151 545.0
6 TraesCS6A01G206700 chr6B 86.081 467 43 10 1087 1536 372305272 372305733 1.580000e-132 483.0
7 TraesCS6A01G206700 chr6B 95.671 231 4 2 850 1079 372303668 372303893 1.660000e-97 366.0
8 TraesCS6A01G206700 chr6B 91.386 267 16 3 2392 2658 372309792 372310051 2.780000e-95 359.0
9 TraesCS6A01G206700 chr6B 87.241 290 28 4 565 854 372303119 372303399 3.650000e-84 322.0
10 TraesCS6A01G206700 chr6B 94.536 183 10 0 2699 2881 372316723 372316905 1.720000e-72 283.0
11 TraesCS6A01G206700 chr3A 87.333 150 16 2 486 634 12259496 12259349 5.030000e-38 169.0
12 TraesCS6A01G206700 chr3A 94.444 36 2 0 787 822 617409029 617409064 4.080000e-04 56.5
13 TraesCS6A01G206700 chr7D 95.455 44 0 2 780 821 626231934 626231977 5.250000e-08 69.4


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 TraesCS6A01G206700 chr6A 364624264 364627197 2933 True 2332.000000 3589 100.000000 1 2934 2 chr6A.!!$R1 2933
1 TraesCS6A01G206700 chr6D 254235275 254237937 2662 False 1123.666667 1533 91.867333 1 2881 3 chr6D.!!$F1 2880
2 TraesCS6A01G206700 chr6B 372303119 372310051 6932 False 415.000000 545 90.279600 565 2658 5 chr6B.!!$F2 2093

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
416 425 0.034767 ATCATCACCACCTGCACCTG 60.035 55.000 0.0 0.0 0.00 4.00 F
423 432 0.392193 CCACCTGCACCTGACATCTC 60.392 60.000 0.0 0.0 0.00 2.75 F
436 445 0.465705 ACATCTCGGCATCGTGGAAT 59.534 50.000 0.0 0.0 37.69 3.01 F
437 446 1.686587 ACATCTCGGCATCGTGGAATA 59.313 47.619 0.0 0.0 37.69 1.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1498 3292 0.595095 GGCTCTTGGTCAGCTTGTTG 59.405 55.0 0.0 0.0 37.05 3.33 R
1540 5110 0.753479 TCCTCAGCTCCACGATCTCC 60.753 60.0 0.0 0.0 0.00 3.71 R
1729 5299 0.861450 CGTAACCGTAGCCGTAACCG 60.861 60.0 0.0 0.0 0.00 4.44 R
2366 5945 0.879090 CGGCTACAACCTTCCAAACC 59.121 55.0 0.0 0.0 0.00 3.27 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
18 19 2.840974 GCCGGACCATAATGGATCG 58.159 57.895 5.05 0.00 40.96 3.69
47 52 5.277538 GCATAAAATTAGACGAGAAGCCCAG 60.278 44.000 0.00 0.00 0.00 4.45
120 125 4.767255 GGGCCAGCCTCGACACAG 62.767 72.222 4.39 0.00 36.10 3.66
206 211 2.990479 GAGGCATCGGACCTTGGT 59.010 61.111 0.00 0.00 37.77 3.67
208 213 3.134127 GGCATCGGACCTTGGTGC 61.134 66.667 0.00 0.00 35.17 5.01
211 216 2.610859 ATCGGACCTTGGTGCCCT 60.611 61.111 5.74 0.00 0.00 5.19
239 244 2.126071 CCCGACGACAGCACGAAT 60.126 61.111 0.00 0.00 37.03 3.34
249 254 1.344438 ACAGCACGAATGAGGAAGACA 59.656 47.619 0.00 0.00 0.00 3.41
262 267 0.884704 GAAGACAAGGCCACAAGCGA 60.885 55.000 5.01 0.00 45.17 4.93
272 277 2.034221 ACAAGCGAAGGGGAAGGC 59.966 61.111 0.00 0.00 0.00 4.35
293 298 2.747855 GAGCCGGGCAACAAGGAG 60.748 66.667 23.09 0.00 38.06 3.69
310 315 1.001503 AGAGCTGACCAGGGAGGAG 59.998 63.158 0.00 0.00 41.22 3.69
322 331 0.565674 GGGAGGAGGGAGGAGAGATT 59.434 60.000 0.00 0.00 0.00 2.40
332 341 0.681564 AGGAGAGATTCAGCGACCGT 60.682 55.000 0.00 0.00 0.00 4.83
333 342 0.248702 GGAGAGATTCAGCGACCGTC 60.249 60.000 0.00 0.00 0.00 4.79
394 403 2.114625 ACGACCACGACCCAGAGA 59.885 61.111 0.00 0.00 42.66 3.10
416 425 0.034767 ATCATCACCACCTGCACCTG 60.035 55.000 0.00 0.00 0.00 4.00
423 432 0.392193 CCACCTGCACCTGACATCTC 60.392 60.000 0.00 0.00 0.00 2.75
428 437 1.153289 GCACCTGACATCTCGGCAT 60.153 57.895 0.00 0.00 0.00 4.40
436 445 0.465705 ACATCTCGGCATCGTGGAAT 59.534 50.000 0.00 0.00 37.69 3.01
437 446 1.686587 ACATCTCGGCATCGTGGAATA 59.313 47.619 0.00 0.00 37.69 1.75
439 448 2.438868 TCTCGGCATCGTGGAATATG 57.561 50.000 0.00 0.00 37.69 1.78
444 453 3.069016 TCGGCATCGTGGAATATGTAACT 59.931 43.478 0.00 0.00 37.69 2.24
451 460 4.707934 TCGTGGAATATGTAACTCACCTGA 59.292 41.667 0.00 0.00 0.00 3.86
453 462 6.548251 TCGTGGAATATGTAACTCACCTGATA 59.452 38.462 0.00 0.00 0.00 2.15
482 491 6.784031 AGTCAACCACTGAATTTCCTCTAAT 58.216 36.000 0.00 0.00 35.22 1.73
511 520 3.782656 TCTTTGGTCTTCCCCTGTAAC 57.217 47.619 0.00 0.00 0.00 2.50
512 521 2.374170 TCTTTGGTCTTCCCCTGTAACC 59.626 50.000 0.00 0.00 0.00 2.85
520 529 3.328343 TCTTCCCCTGTAACCGATGAAAA 59.672 43.478 0.00 0.00 0.00 2.29
521 530 3.791953 TCCCCTGTAACCGATGAAAAA 57.208 42.857 0.00 0.00 0.00 1.94
554 563 3.690628 TCGCTTCTGATGCATTCATTCAA 59.309 39.130 14.78 0.00 32.72 2.69
558 567 6.507929 CGCTTCTGATGCATTCATTCAAAATG 60.508 38.462 14.78 0.00 37.21 2.32
606 615 6.668283 TGGTCTATTAGAAGTAGAAGGTGCTT 59.332 38.462 0.00 0.00 33.04 3.91
615 624 6.881602 AGAAGTAGAAGGTGCTTTAATGGAAG 59.118 38.462 0.00 0.00 29.99 3.46
617 626 5.940470 AGTAGAAGGTGCTTTAATGGAAGTG 59.060 40.000 0.00 0.00 0.00 3.16
630 639 5.432885 AATGGAAGTGTTACCGACAAAAG 57.567 39.130 0.00 0.00 40.65 2.27
647 656 5.745227 ACAAAAGAGAGACAAAGTCTTCCA 58.255 37.500 0.70 0.00 43.53 3.53
656 665 2.689983 ACAAAGTCTTCCAGCCAAAGTG 59.310 45.455 0.00 0.00 0.00 3.16
702 711 3.098636 GCTTTTGTTTATCGGCGATGAC 58.901 45.455 31.08 26.33 0.00 3.06
704 713 4.033587 GCTTTTGTTTATCGGCGATGACTA 59.966 41.667 31.08 21.40 0.00 2.59
777 786 8.975410 ACATGACTTGTCATTTAAACATGATG 57.025 30.769 12.95 0.00 35.60 3.07
802 811 7.066284 TGTTATGTACTAGTACTTTCTCCGTCC 59.934 40.741 28.56 9.93 37.00 4.79
817 826 6.922247 TCTCCGTCCTATAATATAAGAGCG 57.078 41.667 0.00 0.00 0.00 5.03
868 1150 1.790755 GTGTCAGCACCGTTATGTCA 58.209 50.000 0.00 0.00 39.61 3.58
869 1151 2.346803 GTGTCAGCACCGTTATGTCAT 58.653 47.619 0.00 0.00 39.61 3.06
870 1152 3.517602 GTGTCAGCACCGTTATGTCATA 58.482 45.455 0.00 0.00 39.61 2.15
871 1153 3.306166 GTGTCAGCACCGTTATGTCATAC 59.694 47.826 0.00 0.00 39.61 2.39
872 1154 3.056465 TGTCAGCACCGTTATGTCATACA 60.056 43.478 0.00 0.00 0.00 2.29
1099 2848 4.632153 TCTTCTTCTTCTTCTTTGGGACG 58.368 43.478 0.00 0.00 0.00 4.79
1132 2881 8.874816 TCTATCGTCTTATCTCTCAATACATCG 58.125 37.037 0.00 0.00 0.00 3.84
1281 3075 3.510360 GGTACGTATATGCTGGGTCATCT 59.490 47.826 0.00 0.00 0.00 2.90
1498 3292 4.773117 GGCGACGACGTGGACTCC 62.773 72.222 14.57 0.00 41.98 3.85
1567 5137 3.115556 GAGCTGAGGACGCTCGAT 58.884 61.111 0.00 0.00 43.69 3.59
1735 5305 2.458610 GCAAGGCGGCTACGGTTAC 61.459 63.158 13.71 0.00 41.36 2.50
1744 5314 1.993369 GCTACGGTTACGGCTACGGT 61.993 60.000 0.00 0.00 46.48 4.83
1942 5521 1.595382 CATACAGTAGCAGGCGCCC 60.595 63.158 26.15 9.10 39.83 6.13
2395 5981 2.769893 GGTTGTAGCCGACCTTGTAAA 58.230 47.619 0.00 0.00 41.39 2.01
2431 7789 2.038952 CCTGTTGATGGTCTGAAGTGGA 59.961 50.000 0.00 0.00 0.00 4.02
2559 7917 1.339151 GGGCTGTTGAACCAGAGGTAG 60.339 57.143 0.00 0.00 33.12 3.18
2678 8036 1.000843 GCTTTGGCCGGACTTCAAATT 59.999 47.619 9.82 0.00 31.21 1.82
2679 8037 2.230266 GCTTTGGCCGGACTTCAAATTA 59.770 45.455 9.82 0.00 31.21 1.40
2798 8156 8.585881 TGGAACTATCCTAGATATTTAGCACAC 58.414 37.037 0.00 0.00 46.70 3.82
2847 8205 7.251321 AGATAACAATCCTGGATAAGCTAGG 57.749 40.000 10.13 0.00 46.11 3.02
2881 8239 9.096160 GATATATCAGCAATCCAACTACATCTG 57.904 37.037 7.89 0.00 0.00 2.90
2882 8240 4.824479 TCAGCAATCCAACTACATCTGA 57.176 40.909 0.00 0.00 0.00 3.27
2883 8241 4.507710 TCAGCAATCCAACTACATCTGAC 58.492 43.478 0.00 0.00 0.00 3.51
2884 8242 3.624861 CAGCAATCCAACTACATCTGACC 59.375 47.826 0.00 0.00 0.00 4.02
2885 8243 3.521126 AGCAATCCAACTACATCTGACCT 59.479 43.478 0.00 0.00 0.00 3.85
2886 8244 4.018960 AGCAATCCAACTACATCTGACCTT 60.019 41.667 0.00 0.00 0.00 3.50
2887 8245 5.189736 AGCAATCCAACTACATCTGACCTTA 59.810 40.000 0.00 0.00 0.00 2.69
2888 8246 5.880332 GCAATCCAACTACATCTGACCTTAA 59.120 40.000 0.00 0.00 0.00 1.85
2889 8247 6.037610 GCAATCCAACTACATCTGACCTTAAG 59.962 42.308 0.00 0.00 0.00 1.85
2890 8248 6.875972 ATCCAACTACATCTGACCTTAAGT 57.124 37.500 0.97 0.00 0.00 2.24
2891 8249 7.973048 ATCCAACTACATCTGACCTTAAGTA 57.027 36.000 0.97 0.00 0.00 2.24
2892 8250 7.786046 TCCAACTACATCTGACCTTAAGTAA 57.214 36.000 0.97 0.00 0.00 2.24
2893 8251 8.197592 TCCAACTACATCTGACCTTAAGTAAA 57.802 34.615 0.97 0.00 0.00 2.01
2894 8252 8.311836 TCCAACTACATCTGACCTTAAGTAAAG 58.688 37.037 0.97 0.00 34.73 1.85
2895 8253 8.095169 CCAACTACATCTGACCTTAAGTAAAGT 58.905 37.037 0.97 0.00 32.89 2.66
2896 8254 9.490379 CAACTACATCTGACCTTAAGTAAAGTT 57.510 33.333 0.97 0.00 32.89 2.66
2897 8255 9.490379 AACTACATCTGACCTTAAGTAAAGTTG 57.510 33.333 0.97 3.98 32.89 3.16
2898 8256 8.648693 ACTACATCTGACCTTAAGTAAAGTTGT 58.351 33.333 0.97 8.90 33.23 3.32
2899 8257 7.964604 ACATCTGACCTTAAGTAAAGTTGTC 57.035 36.000 0.97 0.66 32.89 3.18
2900 8258 7.506114 ACATCTGACCTTAAGTAAAGTTGTCA 58.494 34.615 0.97 5.20 35.37 3.58
2901 8259 7.441458 ACATCTGACCTTAAGTAAAGTTGTCAC 59.559 37.037 0.97 0.00 33.83 3.67
2902 8260 7.120923 TCTGACCTTAAGTAAAGTTGTCACT 57.879 36.000 0.97 0.00 33.83 3.41
2903 8261 8.241497 TCTGACCTTAAGTAAAGTTGTCACTA 57.759 34.615 0.97 0.00 33.83 2.74
2904 8262 8.698210 TCTGACCTTAAGTAAAGTTGTCACTAA 58.302 33.333 0.97 0.00 33.83 2.24
2905 8263 9.321562 CTGACCTTAAGTAAAGTTGTCACTAAA 57.678 33.333 0.97 0.00 33.83 1.85
2906 8264 9.669887 TGACCTTAAGTAAAGTTGTCACTAAAA 57.330 29.630 0.97 0.00 33.83 1.52
2913 8271 8.843885 AGTAAAGTTGTCACTAAAATAGTCCC 57.156 34.615 0.00 0.00 36.76 4.46
2914 8272 8.434392 AGTAAAGTTGTCACTAAAATAGTCCCA 58.566 33.333 0.00 0.00 36.76 4.37
2915 8273 9.059260 GTAAAGTTGTCACTAAAATAGTCCCAA 57.941 33.333 0.00 0.00 36.76 4.12
2916 8274 8.706322 AAAGTTGTCACTAAAATAGTCCCAAT 57.294 30.769 0.00 0.00 36.76 3.16
2917 8275 8.706322 AAGTTGTCACTAAAATAGTCCCAATT 57.294 30.769 0.00 0.00 36.76 2.32
2918 8276 8.110860 AGTTGTCACTAAAATAGTCCCAATTG 57.889 34.615 0.00 0.00 36.76 2.32
2919 8277 7.942341 AGTTGTCACTAAAATAGTCCCAATTGA 59.058 33.333 7.12 0.00 36.76 2.57
2920 8278 7.681939 TGTCACTAAAATAGTCCCAATTGAC 57.318 36.000 7.12 0.00 36.76 3.18
2921 8279 7.227873 TGTCACTAAAATAGTCCCAATTGACA 58.772 34.615 7.12 0.00 36.76 3.58
2922 8280 7.174253 TGTCACTAAAATAGTCCCAATTGACAC 59.826 37.037 7.12 2.76 36.76 3.67
2923 8281 7.174253 GTCACTAAAATAGTCCCAATTGACACA 59.826 37.037 7.12 0.00 36.76 3.72
2924 8282 7.390440 TCACTAAAATAGTCCCAATTGACACAG 59.610 37.037 7.12 0.00 36.76 3.66
2925 8283 5.391312 AAAATAGTCCCAATTGACACAGC 57.609 39.130 7.12 0.00 37.73 4.40
2926 8284 2.093306 TAGTCCCAATTGACACAGCG 57.907 50.000 7.12 0.00 37.73 5.18
2927 8285 1.210155 GTCCCAATTGACACAGCGC 59.790 57.895 7.12 0.00 35.29 5.92
2928 8286 1.073025 TCCCAATTGACACAGCGCT 59.927 52.632 2.64 2.64 0.00 5.92
2929 8287 0.323302 TCCCAATTGACACAGCGCTA 59.677 50.000 10.99 0.00 0.00 4.26
2930 8288 1.065491 TCCCAATTGACACAGCGCTAT 60.065 47.619 10.99 0.00 0.00 2.97
2931 8289 1.331756 CCCAATTGACACAGCGCTATC 59.668 52.381 10.99 9.22 0.00 2.08
2932 8290 2.009051 CCAATTGACACAGCGCTATCA 58.991 47.619 10.99 12.09 0.00 2.15
2933 8291 2.223112 CCAATTGACACAGCGCTATCAC 60.223 50.000 10.99 3.01 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 5.277538 GCTGGGCTTCTCGTCTAATTTTATG 60.278 44.000 0.00 0.00 0.00 1.90
56 61 1.668101 GGCTAGTGGGTCGGACTCTG 61.668 65.000 9.80 0.00 0.00 3.35
101 106 4.767255 GTGTCGAGGCTGGCCCTG 62.767 72.222 8.11 1.23 46.60 4.45
116 121 0.467384 CCCTAGGGTCAGATGCTGTG 59.533 60.000 20.88 0.00 32.61 3.66
184 189 3.515286 GGTCCGATGCCTCGTCGA 61.515 66.667 10.54 0.00 44.49 4.20
229 234 1.344438 TGTCTTCCTCATTCGTGCTGT 59.656 47.619 0.00 0.00 0.00 4.40
232 237 1.734465 CCTTGTCTTCCTCATTCGTGC 59.266 52.381 0.00 0.00 0.00 5.34
237 242 1.425066 TGTGGCCTTGTCTTCCTCATT 59.575 47.619 3.32 0.00 0.00 2.57
239 244 0.843309 TTGTGGCCTTGTCTTCCTCA 59.157 50.000 3.32 0.00 0.00 3.86
249 254 2.282462 CCCTTCGCTTGTGGCCTT 60.282 61.111 3.32 0.00 37.74 4.35
262 267 4.083862 GCTCGTCGCCTTCCCCTT 62.084 66.667 0.00 0.00 0.00 3.95
279 284 2.747855 GCTCTCCTTGTTGCCCGG 60.748 66.667 0.00 0.00 0.00 5.73
281 286 0.957888 GTCAGCTCTCCTTGTTGCCC 60.958 60.000 0.00 0.00 0.00 5.36
283 288 0.250467 TGGTCAGCTCTCCTTGTTGC 60.250 55.000 5.46 0.00 0.00 4.17
285 290 0.689623 CCTGGTCAGCTCTCCTTGTT 59.310 55.000 5.46 0.00 0.00 2.83
293 298 2.063378 CCTCCTCCCTGGTCAGCTC 61.063 68.421 0.00 0.00 37.07 4.09
310 315 0.387565 GTCGCTGAATCTCTCCTCCC 59.612 60.000 0.00 0.00 0.00 4.30
364 373 4.295119 GTCGTGTGGTGGCCTCGT 62.295 66.667 3.32 0.00 0.00 4.18
394 403 1.409241 GGTGCAGGTGGTGATGATCAT 60.409 52.381 8.25 8.25 0.00 2.45
416 425 0.179111 TTCCACGATGCCGAGATGTC 60.179 55.000 0.00 0.00 39.50 3.06
423 432 3.390135 AGTTACATATTCCACGATGCCG 58.610 45.455 0.00 0.00 42.50 5.69
428 437 4.707934 TCAGGTGAGTTACATATTCCACGA 59.292 41.667 0.00 0.00 0.00 4.35
436 445 7.563556 TGACTTGGATATCAGGTGAGTTACATA 59.436 37.037 4.83 0.00 35.72 2.29
437 446 6.384015 TGACTTGGATATCAGGTGAGTTACAT 59.616 38.462 4.83 0.00 35.72 2.29
439 448 6.222038 TGACTTGGATATCAGGTGAGTTAC 57.778 41.667 4.83 0.00 35.72 2.50
444 453 3.843619 TGGTTGACTTGGATATCAGGTGA 59.156 43.478 4.83 0.00 35.72 4.02
451 460 6.378280 GGAAATTCAGTGGTTGACTTGGATAT 59.622 38.462 0.00 0.00 34.94 1.63
453 462 4.524328 GGAAATTCAGTGGTTGACTTGGAT 59.476 41.667 0.00 0.00 34.94 3.41
482 491 3.560025 GGGAAGACCAAAGATCTTGCTCA 60.560 47.826 9.17 0.00 42.41 4.26
534 543 6.533723 TCATTTTGAATGAATGCATCAGAAGC 59.466 34.615 0.00 0.00 42.53 3.86
537 546 8.474831 AGAATCATTTTGAATGAATGCATCAGA 58.525 29.630 0.00 0.00 42.53 3.27
540 549 9.314321 AGAAGAATCATTTTGAATGAATGCATC 57.686 29.630 0.00 0.00 35.10 3.91
558 567 9.995003 ACCATGAACAATAGATAGAGAAGAATC 57.005 33.333 0.00 0.00 0.00 2.52
606 615 6.766944 TCTTTTGTCGGTAACACTTCCATTAA 59.233 34.615 0.00 0.00 37.70 1.40
615 624 4.365723 TGTCTCTCTTTTGTCGGTAACAC 58.634 43.478 0.00 0.00 37.70 3.32
617 626 5.522824 ACTTTGTCTCTCTTTTGTCGGTAAC 59.477 40.000 0.00 0.00 0.00 2.50
630 639 2.694213 GGCTGGAAGACTTTGTCTCTC 58.306 52.381 0.42 2.14 42.59 3.20
656 665 5.449999 CCCAAGTTCGAATATTTAAGTGGCC 60.450 44.000 0.00 0.00 0.00 5.36
777 786 7.281999 AGGACGGAGAAAGTACTAGTACATAAC 59.718 40.741 29.87 18.79 38.48 1.89
790 799 8.741841 GCTCTTATATTATAGGACGGAGAAAGT 58.258 37.037 0.00 0.00 0.00 2.66
792 801 7.392673 ACGCTCTTATATTATAGGACGGAGAAA 59.607 37.037 15.28 0.00 0.00 2.52
793 802 6.883217 ACGCTCTTATATTATAGGACGGAGAA 59.117 38.462 15.28 0.00 0.00 2.87
794 803 6.413052 ACGCTCTTATATTATAGGACGGAGA 58.587 40.000 15.28 3.34 0.00 3.71
797 806 8.530269 AAAAACGCTCTTATATTATAGGACGG 57.470 34.615 15.28 5.50 0.00 4.79
830 839 7.306283 GCTGACACGACTCATATTTTCAGTATC 60.306 40.741 0.00 0.00 33.30 2.24
831 840 6.477033 GCTGACACGACTCATATTTTCAGTAT 59.523 38.462 0.00 0.00 33.30 2.12
833 842 4.627467 GCTGACACGACTCATATTTTCAGT 59.373 41.667 0.00 0.00 33.30 3.41
868 1150 7.704578 ACACACTTCTAGACATGTACTGTAT 57.295 36.000 0.00 0.00 38.54 2.29
869 1151 7.148523 CGTACACACTTCTAGACATGTACTGTA 60.149 40.741 21.20 12.66 40.01 2.74
870 1152 6.348295 CGTACACACTTCTAGACATGTACTGT 60.348 42.308 21.20 13.32 40.01 3.55
871 1153 6.022208 CGTACACACTTCTAGACATGTACTG 58.978 44.000 21.20 15.22 40.01 2.74
872 1154 5.123502 CCGTACACACTTCTAGACATGTACT 59.876 44.000 21.20 0.37 40.01 2.73
1099 2848 9.737427 TTGAGAGATAAGACGATAGACAAAATC 57.263 33.333 0.00 0.00 41.38 2.17
1257 3041 0.963962 ACCCAGCATATACGTACCGG 59.036 55.000 0.00 0.00 0.00 5.28
1498 3292 0.595095 GGCTCTTGGTCAGCTTGTTG 59.405 55.000 0.00 0.00 37.05 3.33
1540 5110 0.753479 TCCTCAGCTCCACGATCTCC 60.753 60.000 0.00 0.00 0.00 3.71
1688 5258 4.980805 CGACGGGTGGTGGTGGTG 62.981 72.222 0.00 0.00 0.00 4.17
1729 5299 0.861450 CGTAACCGTAGCCGTAACCG 60.861 60.000 0.00 0.00 0.00 4.44
1732 5302 1.138671 GCCGTAACCGTAGCCGTAA 59.861 57.895 0.00 0.00 0.00 3.18
1735 5305 2.581409 CTGCCGTAACCGTAGCCG 60.581 66.667 0.00 0.00 0.00 5.52
1744 5314 1.138883 CGAGTAGCTGCTGCCGTAA 59.861 57.895 9.82 0.00 40.80 3.18
2359 5938 2.621526 ACAACCTTCCAAACCGATGAAC 59.378 45.455 0.00 0.00 0.00 3.18
2366 5945 0.879090 CGGCTACAACCTTCCAAACC 59.121 55.000 0.00 0.00 0.00 3.27
2395 5981 1.221840 CAGGGCGACAACCAGCTAT 59.778 57.895 0.00 0.00 0.00 2.97
2447 7805 9.649167 ACTGAAGTAGCAACGTAATTAGTAATT 57.351 29.630 12.61 12.61 34.90 1.40
2448 7806 9.649167 AACTGAAGTAGCAACGTAATTAGTAAT 57.351 29.630 0.00 0.00 0.00 1.89
2449 7807 9.480053 AAACTGAAGTAGCAACGTAATTAGTAA 57.520 29.630 0.00 0.00 0.00 2.24
2450 7808 8.918658 CAAACTGAAGTAGCAACGTAATTAGTA 58.081 33.333 0.00 0.00 0.00 1.82
2451 7809 7.440255 ACAAACTGAAGTAGCAACGTAATTAGT 59.560 33.333 0.00 0.00 0.00 2.24
2452 7810 7.740346 CACAAACTGAAGTAGCAACGTAATTAG 59.260 37.037 0.00 0.00 0.00 1.73
2453 7811 7.225145 ACACAAACTGAAGTAGCAACGTAATTA 59.775 33.333 0.00 0.00 0.00 1.40
2559 7917 4.442706 TCTTGTGATTCTCCGCCTAATTC 58.557 43.478 0.00 0.00 0.00 2.17
2585 7943 4.201930 CCGATTGGTGAGTACTGAGTAGTC 60.202 50.000 18.27 18.27 38.52 2.59
2678 8036 1.681780 GCTACTGCTGGGTTGCCAATA 60.682 52.381 0.00 0.00 33.26 1.90
2679 8037 0.967380 GCTACTGCTGGGTTGCCAAT 60.967 55.000 0.00 0.00 33.26 3.16
2762 8120 7.496346 TCTAGGATAGTTCCACTTGTCATTT 57.504 36.000 0.00 0.00 45.30 2.32
2778 8136 9.244292 CTACTGGTGTGCTAAATATCTAGGATA 57.756 37.037 0.00 0.00 0.00 2.59
2858 8216 6.933521 GTCAGATGTAGTTGGATTGCTGATAT 59.066 38.462 0.00 0.00 34.19 1.63
2887 8245 9.281371 GGGACTATTTTAGTGACAACTTTACTT 57.719 33.333 0.00 0.00 39.59 2.24
2888 8246 8.434392 TGGGACTATTTTAGTGACAACTTTACT 58.566 33.333 0.00 0.00 39.59 2.24
2889 8247 8.611654 TGGGACTATTTTAGTGACAACTTTAC 57.388 34.615 0.00 0.00 39.59 2.01
2890 8248 9.802039 ATTGGGACTATTTTAGTGACAACTTTA 57.198 29.630 0.00 0.00 39.59 1.85
2891 8249 8.706322 ATTGGGACTATTTTAGTGACAACTTT 57.294 30.769 0.00 0.00 39.59 2.66
2892 8250 8.576442 CAATTGGGACTATTTTAGTGACAACTT 58.424 33.333 0.00 0.00 39.59 2.66
2893 8251 7.942341 TCAATTGGGACTATTTTAGTGACAACT 59.058 33.333 5.42 0.00 39.59 3.16
2894 8252 8.021396 GTCAATTGGGACTATTTTAGTGACAAC 58.979 37.037 5.42 0.00 39.59 3.32
2895 8253 7.721842 TGTCAATTGGGACTATTTTAGTGACAA 59.278 33.333 5.42 0.00 39.59 3.18
2896 8254 7.174253 GTGTCAATTGGGACTATTTTAGTGACA 59.826 37.037 5.42 0.00 39.59 3.58
2897 8255 7.174253 TGTGTCAATTGGGACTATTTTAGTGAC 59.826 37.037 5.42 0.00 39.59 3.67
2898 8256 7.227873 TGTGTCAATTGGGACTATTTTAGTGA 58.772 34.615 5.42 0.00 39.59 3.41
2899 8257 7.447374 TGTGTCAATTGGGACTATTTTAGTG 57.553 36.000 5.42 0.00 39.59 2.74
2900 8258 6.151144 GCTGTGTCAATTGGGACTATTTTAGT 59.849 38.462 5.42 0.00 42.86 2.24
2901 8259 6.555315 GCTGTGTCAATTGGGACTATTTTAG 58.445 40.000 5.42 0.00 38.61 1.85
2902 8260 5.123186 CGCTGTGTCAATTGGGACTATTTTA 59.877 40.000 5.42 0.00 38.61 1.52
2903 8261 4.082787 CGCTGTGTCAATTGGGACTATTTT 60.083 41.667 5.42 0.00 38.61 1.82
2904 8262 3.440173 CGCTGTGTCAATTGGGACTATTT 59.560 43.478 5.42 0.00 38.61 1.40
2905 8263 3.009723 CGCTGTGTCAATTGGGACTATT 58.990 45.455 5.42 0.00 38.61 1.73
2906 8264 2.632377 CGCTGTGTCAATTGGGACTAT 58.368 47.619 5.42 0.00 38.61 2.12
2907 8265 1.943968 GCGCTGTGTCAATTGGGACTA 60.944 52.381 5.42 0.00 38.61 2.59
2908 8266 1.237285 GCGCTGTGTCAATTGGGACT 61.237 55.000 5.42 0.00 38.61 3.85
2909 8267 1.210155 GCGCTGTGTCAATTGGGAC 59.790 57.895 5.42 3.33 38.29 4.46
2910 8268 0.323302 TAGCGCTGTGTCAATTGGGA 59.677 50.000 22.90 0.00 0.00 4.37
2911 8269 1.331756 GATAGCGCTGTGTCAATTGGG 59.668 52.381 22.90 0.00 0.00 4.12
2912 8270 2.009051 TGATAGCGCTGTGTCAATTGG 58.991 47.619 22.90 0.00 0.00 3.16
2913 8271 3.043635 GTGATAGCGCTGTGTCAATTG 57.956 47.619 22.90 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.