Multiple sequence alignment - TraesCS6A01G116100

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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 TraesCS6A01G116100 chr6A 100.000 2633 0 0 1 2633 85767972 85765340 0.000000e+00 4863.0
1 TraesCS6A01G116100 chr7A 98.049 769 15 0 1865 2633 171274471 171275239 0.000000e+00 1338.0
2 TraesCS6A01G116100 chr6D 87.320 1183 103 20 469 1624 68361424 68360262 0.000000e+00 1310.0
3 TraesCS6A01G116100 chr6D 85.000 340 34 9 1 333 68361899 68361570 1.950000e-86 329.0
4 TraesCS6A01G116100 chr4B 95.845 746 30 1 1889 2633 629783365 629782620 0.000000e+00 1205.0
5 TraesCS6A01G116100 chr6B 90.055 915 62 5 710 1624 143461862 143460977 0.000000e+00 1158.0
6 TraesCS6A01G116100 chr6B 84.320 338 38 9 1 333 143464184 143463857 1.520000e-82 316.0
7 TraesCS6A01G116100 chr6B 93.182 176 11 1 1707 1881 143460575 143460400 9.350000e-65 257.0
8 TraesCS6A01G116100 chr6B 93.506 77 5 0 1630 1706 143460706 143460630 5.960000e-22 115.0
9 TraesCS6A01G116100 chr2A 93.478 46 3 0 472 517 122017622 122017667 4.700000e-08 69.4
10 TraesCS6A01G116100 chr1D 97.059 34 1 0 417 450 391301085 391301052 1.020000e-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 TraesCS6A01G116100 chr6A 85765340 85767972 2632 True 4863.0 4863 100.00000 1 2633 1 chr6A.!!$R1 2632
1 TraesCS6A01G116100 chr7A 171274471 171275239 768 False 1338.0 1338 98.04900 1865 2633 1 chr7A.!!$F1 768
2 TraesCS6A01G116100 chr6D 68360262 68361899 1637 True 819.5 1310 86.16000 1 1624 2 chr6D.!!$R1 1623
3 TraesCS6A01G116100 chr4B 629782620 629783365 745 True 1205.0 1205 95.84500 1889 2633 1 chr4B.!!$R1 744
4 TraesCS6A01G116100 chr6B 143460400 143464184 3784 True 461.5 1158 90.26575 1 1881 4 chr6B.!!$R1 1880

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
952 2739 0.03563 AGCAGGGTCATCAGCAGTTC 60.036 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1804 3910 0.179048 CTCACAGGGCACTTCACACA 60.179 55.0 0.0 0.0 0.0 3.72 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
41 42 7.918562 TGTTTTCTAAAGACCAAAGCAACATAC 59.081 33.333 0.00 0.00 0.00 2.39
54 56 2.643551 CAACATACTCCTTGCCCGAAT 58.356 47.619 0.00 0.00 0.00 3.34
73 75 5.408299 CCGAATATGACGGCTAATGAAATCA 59.592 40.000 8.32 0.00 43.74 2.57
77 79 5.695851 ATGACGGCTAATGAAATCATTCC 57.304 39.130 11.69 7.65 44.67 3.01
88 90 5.156001 ATGAAATCATTCCGTACACACGCT 61.156 41.667 0.00 0.00 39.05 5.07
112 114 7.538678 GCTCAACTGTGATTATTTTTGTACTGG 59.461 37.037 0.00 0.00 31.85 4.00
171 177 3.845781 CCACTTGTCTGGCCATATACT 57.154 47.619 5.51 0.00 0.00 2.12
172 178 3.733337 CCACTTGTCTGGCCATATACTC 58.267 50.000 5.51 0.00 0.00 2.59
173 179 3.134623 CCACTTGTCTGGCCATATACTCA 59.865 47.826 5.51 0.00 0.00 3.41
174 180 4.122776 CACTTGTCTGGCCATATACTCAC 58.877 47.826 5.51 0.00 0.00 3.51
175 181 3.774766 ACTTGTCTGGCCATATACTCACA 59.225 43.478 5.51 0.00 0.00 3.58
176 182 4.410228 ACTTGTCTGGCCATATACTCACAT 59.590 41.667 5.51 0.00 0.00 3.21
258 266 4.143389 GGTCTTGATGTCTTTCACGTTACG 60.143 45.833 2.19 2.19 0.00 3.18
279 287 6.024552 ACGCAAACAAATATGAAGGACATT 57.975 33.333 0.00 0.00 40.07 2.71
297 305 5.296151 ACATTTCATATCGACAGACCCAT 57.704 39.130 0.00 0.00 0.00 4.00
303 311 2.757894 ATCGACAGACCCATAGACCT 57.242 50.000 0.00 0.00 0.00 3.85
322 330 4.744795 CCTGAGTGGTCTGCTTTATACT 57.255 45.455 0.00 0.00 0.00 2.12
323 331 4.688021 CCTGAGTGGTCTGCTTTATACTC 58.312 47.826 0.00 0.00 36.11 2.59
324 332 4.404073 CCTGAGTGGTCTGCTTTATACTCT 59.596 45.833 0.00 0.00 36.43 3.24
325 333 5.451242 CCTGAGTGGTCTGCTTTATACTCTC 60.451 48.000 0.00 0.00 36.43 3.20
326 334 5.265191 TGAGTGGTCTGCTTTATACTCTCT 58.735 41.667 0.00 0.00 36.43 3.10
327 335 5.358442 TGAGTGGTCTGCTTTATACTCTCTC 59.642 44.000 0.00 0.00 36.43 3.20
328 336 5.515106 AGTGGTCTGCTTTATACTCTCTCT 58.485 41.667 0.00 0.00 0.00 3.10
329 337 5.592688 AGTGGTCTGCTTTATACTCTCTCTC 59.407 44.000 0.00 0.00 0.00 3.20
330 338 5.592688 GTGGTCTGCTTTATACTCTCTCTCT 59.407 44.000 0.00 0.00 0.00 3.10
331 339 5.825679 TGGTCTGCTTTATACTCTCTCTCTC 59.174 44.000 0.00 0.00 0.00 3.20
332 340 6.062095 GGTCTGCTTTATACTCTCTCTCTCT 58.938 44.000 0.00 0.00 0.00 3.10
333 341 6.204882 GGTCTGCTTTATACTCTCTCTCTCTC 59.795 46.154 0.00 0.00 0.00 3.20
334 342 6.992715 GTCTGCTTTATACTCTCTCTCTCTCT 59.007 42.308 0.00 0.00 0.00 3.10
335 343 7.171678 GTCTGCTTTATACTCTCTCTCTCTCTC 59.828 44.444 0.00 0.00 0.00 3.20
336 344 7.071196 TCTGCTTTATACTCTCTCTCTCTCTCT 59.929 40.741 0.00 0.00 0.00 3.10
337 345 7.217200 TGCTTTATACTCTCTCTCTCTCTCTC 58.783 42.308 0.00 0.00 0.00 3.20
338 346 7.071196 TGCTTTATACTCTCTCTCTCTCTCTCT 59.929 40.741 0.00 0.00 0.00 3.10
339 347 7.600752 GCTTTATACTCTCTCTCTCTCTCTCTC 59.399 44.444 0.00 0.00 0.00 3.20
340 348 8.783660 TTTATACTCTCTCTCTCTCTCTCTCT 57.216 38.462 0.00 0.00 0.00 3.10
341 349 6.909550 ATACTCTCTCTCTCTCTCTCTCTC 57.090 45.833 0.00 0.00 0.00 3.20
342 350 4.877773 ACTCTCTCTCTCTCTCTCTCTCT 58.122 47.826 0.00 0.00 0.00 3.10
343 351 4.892934 ACTCTCTCTCTCTCTCTCTCTCTC 59.107 50.000 0.00 0.00 0.00 3.20
344 352 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
345 353 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
346 354 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
347 355 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
348 356 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
349 357 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
350 358 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
351 359 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
352 360 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
353 361 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
354 362 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
355 363 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
356 364 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
357 365 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
358 366 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
359 367 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
360 368 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
361 369 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
362 370 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
363 371 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
364 372 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
365 373 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
366 374 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
367 375 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
368 376 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
369 377 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
370 378 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
371 379 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
372 380 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
373 381 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
374 382 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
385 393 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
386 394 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
389 397 5.462240 TCTCTCTCTCTCTCTCTCTCTCAT 58.538 45.833 0.00 0.00 0.00 2.90
463 2061 1.824230 TGTTTATGGGCACTTGCATCC 59.176 47.619 3.15 0.00 44.36 3.51
466 2064 0.747644 TATGGGCACTTGCATCCACG 60.748 55.000 3.15 0.00 44.36 4.94
467 2065 3.443045 GGGCACTTGCATCCACGG 61.443 66.667 3.15 0.00 44.36 4.94
477 2138 5.006358 CACTTGCATCCACGGTACTAAATAC 59.994 44.000 0.00 0.00 0.00 1.89
479 2140 4.435425 TGCATCCACGGTACTAAATACAC 58.565 43.478 0.00 0.00 35.23 2.90
587 2249 8.349983 TCAAAGTTTATGGAGCTTGACTTTTAC 58.650 33.333 0.00 0.00 35.75 2.01
588 2250 6.481954 AGTTTATGGAGCTTGACTTTTACG 57.518 37.500 0.00 0.00 0.00 3.18
596 2258 6.080406 GGAGCTTGACTTTTACGAAAATCTG 58.920 40.000 0.00 0.00 0.00 2.90
606 2268 1.333619 ACGAAAATCTGTGTGCACCAC 59.666 47.619 15.69 12.94 44.78 4.16
638 2300 4.226761 CGTTGTGAGCAAAAATCTTACCC 58.773 43.478 0.00 0.00 36.22 3.69
641 2303 4.138290 TGTGAGCAAAAATCTTACCCGAA 58.862 39.130 0.00 0.00 0.00 4.30
651 2314 7.940178 AAAATCTTACCCGAAACAACAATTC 57.060 32.000 0.00 0.00 0.00 2.17
653 2316 5.682943 TCTTACCCGAAACAACAATTCAG 57.317 39.130 0.00 0.00 0.00 3.02
656 2319 6.425721 TCTTACCCGAAACAACAATTCAGTAG 59.574 38.462 0.00 0.00 0.00 2.57
657 2320 3.252458 ACCCGAAACAACAATTCAGTAGC 59.748 43.478 0.00 0.00 0.00 3.58
670 2336 4.380843 TTCAGTAGCATTTCCCCTTCAA 57.619 40.909 0.00 0.00 0.00 2.69
704 2463 6.949352 AAATGTCTCAAACCTGGCTATATG 57.051 37.500 0.00 0.00 0.00 1.78
705 2464 3.808728 TGTCTCAAACCTGGCTATATGC 58.191 45.455 0.00 0.00 41.94 3.14
707 2466 4.653801 TGTCTCAAACCTGGCTATATGCTA 59.346 41.667 0.00 0.00 42.39 3.49
708 2467 4.991687 GTCTCAAACCTGGCTATATGCTAC 59.008 45.833 0.00 0.00 42.39 3.58
709 2468 4.901849 TCTCAAACCTGGCTATATGCTACT 59.098 41.667 0.00 0.00 42.39 2.57
710 2469 5.366768 TCTCAAACCTGGCTATATGCTACTT 59.633 40.000 0.00 0.00 42.39 2.24
711 2470 6.553476 TCTCAAACCTGGCTATATGCTACTTA 59.447 38.462 0.00 0.00 42.39 2.24
712 2471 7.070696 TCTCAAACCTGGCTATATGCTACTTAA 59.929 37.037 0.00 0.00 42.39 1.85
737 2496 6.159398 ACTGGAGATCAAAGTTCTAATCCCAT 59.841 38.462 0.00 0.00 0.00 4.00
784 2543 6.223852 TGTTTTTGTTTTCTGGTAGCACAAA 58.776 32.000 4.16 4.16 35.94 2.83
790 2549 4.566545 TTTCTGGTAGCACAAACATGTG 57.433 40.909 0.00 4.64 42.32 3.21
798 2557 2.410785 CACAAACATGTGCACCTGAG 57.589 50.000 26.20 17.24 32.72 3.35
813 2572 2.026449 ACCTGAGAATTCTCTTGGCCAG 60.026 50.000 30.40 21.86 43.25 4.85
831 2590 4.032703 CCAGTTGGCAATTGCTATACAC 57.967 45.455 28.42 17.97 41.70 2.90
866 2625 4.074970 AGATCACCTTTACTTTGTGGCTG 58.925 43.478 0.00 0.00 0.00 4.85
902 2688 4.202121 TGGACTATGAGACATCGGCTTTAC 60.202 45.833 0.00 0.00 0.00 2.01
945 2732 2.046988 CGCACAGCAGGGTCATCA 60.047 61.111 0.00 0.00 0.00 3.07
946 2733 2.104859 CGCACAGCAGGGTCATCAG 61.105 63.158 0.00 0.00 0.00 2.90
947 2734 2.404995 GCACAGCAGGGTCATCAGC 61.405 63.158 0.00 0.00 0.00 4.26
948 2735 1.002990 CACAGCAGGGTCATCAGCA 60.003 57.895 0.00 0.00 0.00 4.41
949 2736 1.025113 CACAGCAGGGTCATCAGCAG 61.025 60.000 0.00 0.00 0.00 4.24
950 2737 1.298993 CAGCAGGGTCATCAGCAGT 59.701 57.895 0.00 0.00 0.00 4.40
951 2738 0.322277 CAGCAGGGTCATCAGCAGTT 60.322 55.000 0.00 0.00 0.00 3.16
952 2739 0.035630 AGCAGGGTCATCAGCAGTTC 60.036 55.000 0.00 0.00 0.00 3.01
975 2762 2.288666 CACACCTACACAAGCAACTGT 58.711 47.619 0.00 0.00 0.00 3.55
993 2780 2.334946 TGCCGTTCATCCTTGCAGC 61.335 57.895 0.00 0.00 0.00 5.25
1042 2829 2.407428 CGTCTGGCCGTCTCAGCTA 61.407 63.158 0.00 0.00 32.63 3.32
1094 2881 1.450312 CCCAAGCAAGGCTCCTACG 60.450 63.158 0.00 0.00 38.25 3.51
1095 2882 1.450312 CCAAGCAAGGCTCCTACGG 60.450 63.158 0.00 0.00 38.25 4.02
1323 3110 2.124860 GTGGGGCGTGGTGGTATC 60.125 66.667 0.00 0.00 0.00 2.24
1389 3176 4.746309 GTGCATGCAGGGGCTGGA 62.746 66.667 23.41 0.00 41.91 3.86
1399 3186 4.106925 GGGCTGGAGCTGGAGGTG 62.107 72.222 0.00 0.00 41.70 4.00
1400 3187 4.106925 GGCTGGAGCTGGAGGTGG 62.107 72.222 0.00 0.00 41.70 4.61
1401 3188 3.325753 GCTGGAGCTGGAGGTGGT 61.326 66.667 0.00 0.00 38.21 4.16
1402 3189 2.667418 CTGGAGCTGGAGGTGGTG 59.333 66.667 0.00 0.00 0.00 4.17
1403 3190 2.122413 TGGAGCTGGAGGTGGTGT 60.122 61.111 0.00 0.00 0.00 4.16
1485 3272 2.531942 GGAGGTGGAAGTGGGGGT 60.532 66.667 0.00 0.00 0.00 4.95
1489 3276 0.840722 AGGTGGAAGTGGGGGTAGTG 60.841 60.000 0.00 0.00 0.00 2.74
1493 3280 3.325201 GAAGTGGGGGTAGTGGCGG 62.325 68.421 0.00 0.00 0.00 6.13
1499 3286 4.338710 GGGTAGTGGCGGTGGCAA 62.339 66.667 0.00 0.00 40.46 4.52
1540 3327 2.339556 GGCCGTGCTGGTAATGCAA 61.340 57.895 0.00 0.00 42.41 4.08
1592 3379 1.318158 GGTTCTACCGGAAGCGGAGA 61.318 60.000 9.46 0.00 41.59 3.71
1624 3411 2.682494 GGTCGGCCAGTGGAGGTA 60.682 66.667 15.20 0.00 34.09 3.08
1625 3412 2.577593 GTCGGCCAGTGGAGGTAC 59.422 66.667 15.20 0.69 0.00 3.34
1649 3701 4.319177 GCTTAAGACGGAGCAATGGATAT 58.681 43.478 6.67 0.00 38.73 1.63
1650 3702 4.153117 GCTTAAGACGGAGCAATGGATATG 59.847 45.833 6.67 0.00 38.73 1.78
1721 3827 5.422012 TGTGTAAGGAGATGAAGATACTGCA 59.578 40.000 0.00 0.00 0.00 4.41
1738 3844 1.351430 GCACATAAGCTCGTCGCACA 61.351 55.000 0.00 0.00 42.61 4.57
1761 3867 2.485814 GGTCTGGTTGAGTCAGAAATGC 59.514 50.000 0.00 0.00 42.13 3.56
1788 3894 6.176183 GTGATATGGCTATTGCATAGGAAGT 58.824 40.000 0.66 0.00 41.91 3.01
1804 3910 0.181824 AAGTTACACGTTGGGCCAGT 59.818 50.000 6.23 3.50 0.00 4.00
1809 3916 2.515991 ACGTTGGGCCAGTGTGTG 60.516 61.111 6.23 0.00 0.00 3.82
1811 3918 1.821759 CGTTGGGCCAGTGTGTGAA 60.822 57.895 6.23 0.00 0.00 3.18
1815 3922 2.555547 GGGCCAGTGTGTGAAGTGC 61.556 63.158 4.39 0.00 0.00 4.40
1817 3924 2.555547 GCCAGTGTGTGAAGTGCCC 61.556 63.158 0.00 0.00 0.00 5.36
1826 3933 0.819259 GTGAAGTGCCCTGTGAGCAA 60.819 55.000 0.00 0.00 43.02 3.91
1969 4076 1.904865 CACAAGCCATGGTGCCAGT 60.905 57.895 14.67 2.67 0.00 4.00
2069 4176 3.006728 CCACCCTACCGGCTCCAA 61.007 66.667 0.00 0.00 33.26 3.53
2247 4354 3.279116 GCCATTATGAGCGCGGCA 61.279 61.111 8.83 11.47 42.50 5.69
2594 4701 0.533755 AGAACTGTGAGCTGCGCTTT 60.534 50.000 9.73 0.00 39.88 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 1.502231 CGTCATATTCGGGCAAGGAG 58.498 55.000 0.00 0.00 0.00 3.69
54 56 5.408299 CGGAATGATTTCATTAGCCGTCATA 59.592 40.000 18.29 0.00 45.72 2.15
62 64 6.410845 CGTGTGTACGGAATGATTTCATTAG 58.589 40.000 5.80 6.31 43.91 1.73
77 79 3.173931 ATCACAGTTGAGCGTGTGTACG 61.174 50.000 2.63 0.00 43.80 3.67
88 90 8.458573 ACCAGTACAAAAATAATCACAGTTGA 57.541 30.769 0.00 0.00 35.73 3.18
122 124 6.968904 CAGCGCTGAATATACACAAAATCTTT 59.031 34.615 33.66 0.00 0.00 2.52
166 172 9.571810 GCACAAATGATCAAAAATGTGAGTATA 57.428 29.630 25.17 0.00 40.32 1.47
168 174 6.581919 CGCACAAATGATCAAAAATGTGAGTA 59.418 34.615 25.17 0.00 40.32 2.59
169 175 5.403166 CGCACAAATGATCAAAAATGTGAGT 59.597 36.000 25.17 5.23 40.32 3.41
170 176 5.666913 GCGCACAAATGATCAAAAATGTGAG 60.667 40.000 25.17 23.28 40.32 3.51
171 177 4.150274 GCGCACAAATGATCAAAAATGTGA 59.850 37.500 25.17 0.00 40.32 3.58
172 178 4.387936 GCGCACAAATGATCAAAAATGTG 58.612 39.130 20.34 20.34 40.72 3.21
173 179 3.432933 GGCGCACAAATGATCAAAAATGT 59.567 39.130 10.83 0.00 0.00 2.71
174 180 3.432592 TGGCGCACAAATGATCAAAAATG 59.567 39.130 10.83 0.00 0.00 2.32
175 181 3.661944 TGGCGCACAAATGATCAAAAAT 58.338 36.364 10.83 0.00 0.00 1.82
176 182 3.103447 TGGCGCACAAATGATCAAAAA 57.897 38.095 10.83 0.00 0.00 1.94
258 266 7.887996 TGAAATGTCCTTCATATTTGTTTGC 57.112 32.000 0.00 0.00 35.48 3.68
279 287 4.523173 GGTCTATGGGTCTGTCGATATGAA 59.477 45.833 0.00 0.00 0.00 2.57
303 311 5.265191 AGAGAGTATAAAGCAGACCACTCA 58.735 41.667 9.51 0.00 35.87 3.41
321 329 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
322 330 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
323 331 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
324 332 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
325 333 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
326 334 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
327 335 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
328 336 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
329 337 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
330 338 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
331 339 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
332 340 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
333 341 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
334 342 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
335 343 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
336 344 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
337 345 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
338 346 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
339 347 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
340 348 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
341 349 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
342 350 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
343 351 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
344 352 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
345 353 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
346 354 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
347 355 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
348 356 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
349 357 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
350 358 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
351 359 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
352 360 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
353 361 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
354 362 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
355 363 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
356 364 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
357 365 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
358 366 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
359 367 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
360 368 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
361 369 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
362 370 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
363 371 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
364 372 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
365 373 4.892345 TGAGAGAGAGAGAGAGAGAGAGAG 59.108 50.000 0.00 0.00 0.00 3.20
366 374 4.871822 TGAGAGAGAGAGAGAGAGAGAGA 58.128 47.826 0.00 0.00 0.00 3.10
367 375 5.804944 ATGAGAGAGAGAGAGAGAGAGAG 57.195 47.826 0.00 0.00 0.00 3.20
368 376 7.290948 ACATTATGAGAGAGAGAGAGAGAGAGA 59.709 40.741 0.00 0.00 0.00 3.10
369 377 7.448420 ACATTATGAGAGAGAGAGAGAGAGAG 58.552 42.308 0.00 0.00 0.00 3.20
370 378 7.379059 ACATTATGAGAGAGAGAGAGAGAGA 57.621 40.000 0.00 0.00 0.00 3.10
371 379 8.370940 ACTACATTATGAGAGAGAGAGAGAGAG 58.629 40.741 0.00 0.00 0.00 3.20
372 380 8.150296 CACTACATTATGAGAGAGAGAGAGAGA 58.850 40.741 0.00 0.00 0.00 3.10
373 381 7.933577 ACACTACATTATGAGAGAGAGAGAGAG 59.066 40.741 0.00 0.00 0.00 3.20
374 382 7.714813 CACACTACATTATGAGAGAGAGAGAGA 59.285 40.741 0.00 0.00 0.00 3.10
434 1976 3.900601 AGTGCCCATAAACATGGTCAAAA 59.099 39.130 0.00 0.00 40.06 2.44
450 2048 2.813226 TACCGTGGATGCAAGTGCCC 62.813 60.000 0.00 0.00 41.18 5.36
463 2061 9.692749 ATCTAATGATGTGTATTTAGTACCGTG 57.307 33.333 0.00 0.00 32.03 4.94
517 2178 6.597832 AATATCTGCATCTGGAGTACCTAC 57.402 41.667 0.00 0.00 37.04 3.18
571 2233 5.763204 AGATTTTCGTAAAAGTCAAGCTCCA 59.237 36.000 0.00 0.00 34.49 3.86
573 2235 6.575201 CACAGATTTTCGTAAAAGTCAAGCTC 59.425 38.462 0.00 0.00 34.49 4.09
606 2268 1.805943 TGCTCACAACGTTCCATGATG 59.194 47.619 0.00 0.00 0.00 3.07
609 2271 2.772568 TTTGCTCACAACGTTCCATG 57.227 45.000 0.00 0.00 34.87 3.66
618 2280 4.138290 TCGGGTAAGATTTTTGCTCACAA 58.862 39.130 0.00 0.00 0.00 3.33
619 2281 3.745799 TCGGGTAAGATTTTTGCTCACA 58.254 40.909 0.00 0.00 0.00 3.58
621 2283 4.580995 TGTTTCGGGTAAGATTTTTGCTCA 59.419 37.500 0.00 0.00 0.00 4.26
638 2300 6.088085 GGAAATGCTACTGAATTGTTGTTTCG 59.912 38.462 0.00 0.00 0.00 3.46
641 2303 5.279456 GGGGAAATGCTACTGAATTGTTGTT 60.279 40.000 0.00 0.00 0.00 2.83
651 2314 3.633986 GGATTGAAGGGGAAATGCTACTG 59.366 47.826 0.00 0.00 0.00 2.74
653 2316 3.631250 TGGATTGAAGGGGAAATGCTAC 58.369 45.455 0.00 0.00 0.00 3.58
656 2319 1.137675 GCTGGATTGAAGGGGAAATGC 59.862 52.381 0.00 0.00 0.00 3.56
657 2320 1.758862 GGCTGGATTGAAGGGGAAATG 59.241 52.381 0.00 0.00 0.00 2.32
701 2368 8.079211 ACTTTGATCTCCAGTTAAGTAGCATA 57.921 34.615 0.00 0.00 0.00 3.14
704 2463 7.100409 AGAACTTTGATCTCCAGTTAAGTAGC 58.900 38.462 0.00 0.00 30.71 3.58
707 2466 9.660180 GATTAGAACTTTGATCTCCAGTTAAGT 57.340 33.333 0.00 0.00 30.71 2.24
708 2467 9.103861 GGATTAGAACTTTGATCTCCAGTTAAG 57.896 37.037 0.00 0.00 30.71 1.85
709 2468 8.047310 GGGATTAGAACTTTGATCTCCAGTTAA 58.953 37.037 0.00 0.00 30.71 2.01
710 2469 7.182026 TGGGATTAGAACTTTGATCTCCAGTTA 59.818 37.037 0.00 0.00 30.71 2.24
711 2470 6.012508 TGGGATTAGAACTTTGATCTCCAGTT 60.013 38.462 4.91 4.91 33.32 3.16
712 2471 5.488919 TGGGATTAGAACTTTGATCTCCAGT 59.511 40.000 0.00 0.00 0.00 4.00
737 2496 5.557576 AGCTTAAGCCACATGATCATCTA 57.442 39.130 23.71 0.00 43.38 1.98
784 2543 3.008813 AGAGAATTCTCAGGTGCACATGT 59.991 43.478 31.79 11.25 45.21 3.21
790 2549 1.742268 GCCAAGAGAATTCTCAGGTGC 59.258 52.381 31.19 24.75 45.21 5.01
794 2553 3.347077 ACTGGCCAAGAGAATTCTCAG 57.653 47.619 31.79 23.78 45.21 3.35
813 2572 3.694072 TGAGGTGTATAGCAATTGCCAAC 59.306 43.478 26.45 18.95 43.38 3.77
831 2590 3.843422 AGGTGATCTGATCCTAGTGAGG 58.157 50.000 14.71 0.00 45.35 3.86
881 2667 5.189659 AGTAAAGCCGATGTCTCATAGTC 57.810 43.478 0.00 0.00 0.00 2.59
882 2668 5.105310 ACAAGTAAAGCCGATGTCTCATAGT 60.105 40.000 0.00 0.00 0.00 2.12
883 2669 5.352284 ACAAGTAAAGCCGATGTCTCATAG 58.648 41.667 0.00 0.00 0.00 2.23
884 2670 5.339008 ACAAGTAAAGCCGATGTCTCATA 57.661 39.130 0.00 0.00 0.00 2.15
885 2671 4.207891 ACAAGTAAAGCCGATGTCTCAT 57.792 40.909 0.00 0.00 0.00 2.90
886 2672 3.678056 ACAAGTAAAGCCGATGTCTCA 57.322 42.857 0.00 0.00 0.00 3.27
902 2688 6.742718 CAGTGCGTGGATTTTTATAGAACAAG 59.257 38.462 0.00 0.00 0.00 3.16
934 2721 0.321919 TGAACTGCTGATGACCCTGC 60.322 55.000 0.00 0.00 0.00 4.85
945 2732 0.758734 TGTAGGTGTGCTGAACTGCT 59.241 50.000 5.42 0.00 0.00 4.24
946 2733 0.868406 GTGTAGGTGTGCTGAACTGC 59.132 55.000 0.00 0.00 0.00 4.40
947 2734 2.238942 TGTGTAGGTGTGCTGAACTG 57.761 50.000 0.00 0.00 0.00 3.16
948 2735 2.838736 CTTGTGTAGGTGTGCTGAACT 58.161 47.619 0.00 0.00 0.00 3.01
949 2736 1.264288 GCTTGTGTAGGTGTGCTGAAC 59.736 52.381 0.00 0.00 0.00 3.18
950 2737 1.134250 TGCTTGTGTAGGTGTGCTGAA 60.134 47.619 0.00 0.00 0.00 3.02
951 2738 0.467804 TGCTTGTGTAGGTGTGCTGA 59.532 50.000 0.00 0.00 0.00 4.26
952 2739 1.002468 GTTGCTTGTGTAGGTGTGCTG 60.002 52.381 0.00 0.00 0.00 4.41
975 2762 2.334946 GCTGCAAGGATGAACGGCA 61.335 57.895 0.00 0.00 0.00 5.69
993 2780 4.247380 GGAGCGGCCATGGAGGAG 62.247 72.222 18.40 3.75 41.22 3.69
1042 2829 0.798776 GAAACGCACAGCAGCACTAT 59.201 50.000 0.00 0.00 0.00 2.12
1094 2881 2.307686 TCCAGTGTGGTTTTATCCTCCC 59.692 50.000 0.00 0.00 39.03 4.30
1095 2882 3.713826 TCCAGTGTGGTTTTATCCTCC 57.286 47.619 0.00 0.00 39.03 4.30
1101 2888 3.146066 GCTGTCATCCAGTGTGGTTTTA 58.854 45.455 0.00 0.00 43.55 1.52
1106 2893 1.162698 CTTGCTGTCATCCAGTGTGG 58.837 55.000 0.00 0.00 43.55 4.17
1108 2895 1.606480 CGACTTGCTGTCATCCAGTGT 60.606 52.381 10.17 0.00 45.60 3.55
1177 2964 1.303074 CGCCATGGCCTATGCTGAT 60.303 57.895 30.79 0.00 37.98 2.90
1179 2966 2.981909 CCGCCATGGCCTATGCTG 60.982 66.667 30.79 14.53 37.98 4.41
1289 3076 2.325082 ACGTCAATGCCAACGCCTC 61.325 57.895 0.00 0.00 42.47 4.70
1290 3077 2.281484 ACGTCAATGCCAACGCCT 60.281 55.556 0.00 0.00 42.47 5.52
1323 3110 4.969196 CCGCCGATCCCCACATCG 62.969 72.222 0.00 0.00 44.45 3.84
1385 3172 2.177594 GACACCACCTCCAGCTCCAG 62.178 65.000 0.00 0.00 0.00 3.86
1389 3176 3.314331 CCGACACCACCTCCAGCT 61.314 66.667 0.00 0.00 0.00 4.24
1398 3185 2.632136 GAACACCGACACCGACACCA 62.632 60.000 0.00 0.00 38.22 4.17
1399 3186 1.952635 GAACACCGACACCGACACC 60.953 63.158 0.00 0.00 38.22 4.16
1400 3187 1.227031 TGAACACCGACACCGACAC 60.227 57.895 0.00 0.00 38.22 3.67
1401 3188 1.227031 GTGAACACCGACACCGACA 60.227 57.895 0.00 0.00 38.22 4.35
1402 3189 0.599204 ATGTGAACACCGACACCGAC 60.599 55.000 2.46 0.00 38.22 4.79
1403 3190 0.319211 GATGTGAACACCGACACCGA 60.319 55.000 2.46 0.00 38.22 4.69
1485 3272 2.345991 GAGTTGCCACCGCCACTA 59.654 61.111 0.00 0.00 40.88 2.74
1493 3280 2.978010 CACCACCGGAGTTGCCAC 60.978 66.667 9.46 0.00 35.94 5.01
1499 3286 1.911766 CCACTACCACCACCGGAGT 60.912 63.158 9.46 1.17 0.00 3.85
1592 3379 0.903454 CGACCCAACTCCACTACCCT 60.903 60.000 0.00 0.00 0.00 4.34
1649 3701 4.283978 AGTTCATCAACAATTTCCATGCCA 59.716 37.500 0.00 0.00 34.60 4.92
1650 3702 4.824289 AGTTCATCAACAATTTCCATGCC 58.176 39.130 0.00 0.00 34.60 4.40
1682 3734 7.067615 TCTCCTTACACATACAACATCTCTCTC 59.932 40.741 0.00 0.00 0.00 3.20
1691 3743 9.250624 GTATCTTCATCTCCTTACACATACAAC 57.749 37.037 0.00 0.00 0.00 3.32
1698 3750 5.751028 GTGCAGTATCTTCATCTCCTTACAC 59.249 44.000 0.00 0.00 0.00 2.90
1738 3844 4.330250 CATTTCTGACTCAACCAGACCAT 58.670 43.478 0.00 0.00 40.05 3.55
1761 3867 4.330894 CCTATGCAATAGCCATATCACACG 59.669 45.833 0.00 0.00 45.64 4.49
1788 3894 0.816018 CACACTGGCCCAACGTGTAA 60.816 55.000 8.30 0.00 39.66 2.41
1804 3910 0.179048 CTCACAGGGCACTTCACACA 60.179 55.000 0.00 0.00 0.00 3.72
1809 3916 1.068055 CATTTGCTCACAGGGCACTTC 60.068 52.381 0.00 0.00 39.55 3.01
1811 3918 0.896940 CCATTTGCTCACAGGGCACT 60.897 55.000 0.00 0.00 39.55 4.40
1826 3933 3.820557 ACAACTGTAACTGTGAGCCATT 58.179 40.909 0.00 0.00 0.00 3.16
1946 4053 1.904865 CACCATGGCTTGTGGCTGT 60.905 57.895 13.04 0.00 40.49 4.40
1969 4076 3.625897 CAGGGGATGCGCGGGATA 61.626 66.667 8.83 0.00 0.00 2.59
2064 4171 1.858739 TTGGGGGACGGGATTTGGAG 61.859 60.000 0.00 0.00 0.00 3.86
2069 4176 4.419921 GCGTTGGGGGACGGGATT 62.420 66.667 0.00 0.00 42.98 3.01
2105 4212 2.675423 GGGGCAAAGGACGAACCC 60.675 66.667 0.00 0.00 40.05 4.11
2225 4332 1.072159 GCGCTCATAATGGCCCTCT 59.928 57.895 0.00 0.00 0.00 3.69
2247 4354 1.693640 CATCTGCAAAGGAGGGGGT 59.306 57.895 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.