Multiple sequence alignment - TraesCS1D01G027700

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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 TraesCS1D01G027700 chr1D 100.000 2216 0 0 1 2216 11092352 11090137 0.000000e+00 4093.0
1 TraesCS1D01G027700 chr1D 98.954 1529 14 2 688 2216 11042950 11041424 0.000000e+00 2734.0
2 TraesCS1D01G027700 chr1D 93.927 1482 46 12 683 2125 11126237 11124761 0.000000e+00 2198.0
3 TraesCS1D01G027700 chr1D 98.503 334 4 1 1 334 11046836 11046504 2.450000e-164 588.0
4 TraesCS1D01G027700 chr1D 96.899 258 7 1 75 332 11129723 11129467 4.370000e-117 431.0
5 TraesCS1D01G027700 chr1D 76.471 629 87 32 683 1294 11202251 11201667 3.600000e-73 285.0
6 TraesCS1D01G027700 chr1D 84.300 293 18 16 331 606 363858755 363859036 6.070000e-66 261.0
7 TraesCS1D01G027700 chr1D 100.000 59 0 0 1 59 453707151 453707209 2.330000e-20 110.0
8 TraesCS1D01G027700 chr1A 92.059 1423 56 12 746 2125 22631680 22633088 0.000000e+00 1949.0
9 TraesCS1D01G027700 chr1A 85.031 648 52 24 683 1314 12680083 12680701 3.130000e-173 617.0
10 TraesCS1D01G027700 chr1A 93.333 300 18 2 1818 2116 12688659 12688957 2.020000e-120 442.0
11 TraesCS1D01G027700 chr1A 92.806 139 1 4 1686 1817 12686574 12686710 2.250000e-45 193.0
12 TraesCS1D01G027700 chr1A 96.825 63 2 0 683 745 22631511 22631573 3.010000e-19 106.0
13 TraesCS1D01G027700 chr1A 84.722 72 5 4 1417 1487 108106603 108106537 1.420000e-07 67.6
14 TraesCS1D01G027700 chr1B 89.987 1488 68 24 683 2125 16480846 16479395 0.000000e+00 1847.0
15 TraesCS1D01G027700 chr1B 87.035 833 51 24 1340 2125 16647074 16646252 0.000000e+00 887.0
16 TraesCS1D01G027700 chr1B 95.699 372 13 2 974 1342 16652557 16652186 1.460000e-166 595.0
17 TraesCS1D01G027700 chr1B 97.091 275 7 1 60 334 16654870 16654597 1.550000e-126 462.0
18 TraesCS1D01G027700 chr1B 91.971 274 13 4 683 947 16652824 16652551 2.080000e-100 375.0
19 TraesCS1D01G027700 chr1B 90.545 275 10 2 60 334 16482957 16482699 1.260000e-92 350.0
20 TraesCS1D01G027700 chr1B 81.156 398 26 21 329 685 256200096 256200485 7.800000e-70 274.0
21 TraesCS1D01G027700 chr1B 85.567 291 8 13 423 684 666837595 666837310 7.800000e-70 274.0
22 TraesCS1D01G027700 chr1B 88.710 124 14 0 561 684 26590899 26591022 3.810000e-33 152.0
23 TraesCS1D01G027700 chr7B 85.031 648 52 24 683 1314 192779604 192780222 3.130000e-173 617.0
24 TraesCS1D01G027700 chr7B 84.818 303 24 10 386 682 664088481 664088767 3.600000e-73 285.0
25 TraesCS1D01G027700 chr7B 92.806 139 1 4 1686 1817 192786095 192786231 2.250000e-45 193.0
26 TraesCS1D01G027700 chr7B 88.722 133 15 0 553 685 687819745 687819877 1.760000e-36 163.0
27 TraesCS1D01G027700 chr7B 88.722 133 15 0 553 685 687855437 687855569 1.760000e-36 163.0
28 TraesCS1D01G027700 chr7B 84.328 134 19 2 553 684 178749115 178748982 1.790000e-26 130.0
29 TraesCS1D01G027700 chr7B 89.412 85 8 1 61 144 587636869 587636953 3.010000e-19 106.0
30 TraesCS1D01G027700 chr2B 85.031 648 52 24 683 1314 47190680 47190062 3.130000e-173 617.0
31 TraesCS1D01G027700 chr2B 84.367 371 25 14 329 684 763402539 763402891 1.270000e-87 333.0
32 TraesCS1D01G027700 chr2B 84.711 242 16 8 329 557 689311779 689311546 2.860000e-54 222.0
33 TraesCS1D01G027700 chr2B 92.806 139 1 4 1686 1817 47184189 47184053 2.250000e-45 193.0
34 TraesCS1D01G027700 chr2B 94.253 87 5 0 2125 2211 767463670 767463584 1.380000e-27 134.0
35 TraesCS1D01G027700 chr2B 82.979 141 22 1 547 685 420747560 420747700 2.310000e-25 126.0
36 TraesCS1D01G027700 chr2B 91.011 89 8 0 2128 2216 254280679 254280767 1.070000e-23 121.0
37 TraesCS1D01G027700 chrUn 96.364 275 9 1 60 334 356320179 356320452 3.360000e-123 451.0
38 TraesCS1D01G027700 chrUn 88.850 287 22 7 683 965 351922129 351921849 5.860000e-91 344.0
39 TraesCS1D01G027700 chrUn 85.329 334 37 6 985 1314 261624300 261624625 3.530000e-88 335.0
40 TraesCS1D01G027700 chr7A 86.898 374 27 12 329 684 163391545 163391914 1.230000e-107 399.0
41 TraesCS1D01G027700 chr7A 90.110 91 8 1 2126 2216 706517646 706517735 1.390000e-22 117.0
42 TraesCS1D01G027700 chr5D 85.864 382 19 16 329 684 417621422 417621050 7.470000e-100 374.0
43 TraesCS1D01G027700 chr5D 89.011 91 10 0 2126 2216 456815264 456815354 1.800000e-21 113.0
44 TraesCS1D01G027700 chr3A 84.156 385 29 10 329 684 10634225 10633844 5.860000e-91 344.0
45 TraesCS1D01G027700 chr4A 83.375 397 18 15 329 684 136608576 136608965 7.630000e-85 324.0
46 TraesCS1D01G027700 chr4A 90.361 83 8 0 2134 2216 723608537 723608455 2.330000e-20 110.0
47 TraesCS1D01G027700 chr2A 83.051 295 23 17 329 604 72326699 72326413 2.200000e-60 243.0
48 TraesCS1D01G027700 chr3B 88.462 130 14 1 556 685 692133175 692133303 2.950000e-34 156.0
49 TraesCS1D01G027700 chr3B 95.082 61 3 0 1 61 697146667 697146727 1.810000e-16 97.1
50 TraesCS1D01G027700 chr5B 87.786 131 14 1 554 684 540862616 540862744 3.810000e-33 152.0
51 TraesCS1D01G027700 chr2D 93.258 89 6 0 2128 2216 196853797 196853885 4.960000e-27 132.0
52 TraesCS1D01G027700 chr4D 90.217 92 9 0 2125 2216 467584516 467584607 1.070000e-23 121.0
53 TraesCS1D01G027700 chr3D 100.000 59 0 0 1 59 418218364 418218422 2.330000e-20 110.0
54 TraesCS1D01G027700 chr6A 87.778 90 9 2 2127 2216 614935160 614935247 1.080000e-18 104.0
55 TraesCS1D01G027700 chr6B 93.333 60 4 0 1 60 41324199 41324258 3.030000e-14 89.8
56 TraesCS1D01G027700 chr7D 91.935 62 5 0 1 62 180758243 180758304 1.090000e-13 87.9


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 TraesCS1D01G027700 chr1D 11090137 11092352 2215 True 4093.000000 4093 100.000000 1 2216 1 chr1D.!!$R1 2215
1 TraesCS1D01G027700 chr1D 11041424 11046836 5412 True 1661.000000 2734 98.728500 1 2216 2 chr1D.!!$R3 2215
2 TraesCS1D01G027700 chr1D 11124761 11129723 4962 True 1314.500000 2198 95.413000 75 2125 2 chr1D.!!$R4 2050
3 TraesCS1D01G027700 chr1D 11201667 11202251 584 True 285.000000 285 76.471000 683 1294 1 chr1D.!!$R2 611
4 TraesCS1D01G027700 chr1A 22631511 22633088 1577 False 1027.500000 1949 94.442000 683 2125 2 chr1A.!!$F3 1442
5 TraesCS1D01G027700 chr1A 12680083 12680701 618 False 617.000000 617 85.031000 683 1314 1 chr1A.!!$F1 631
6 TraesCS1D01G027700 chr1A 12686574 12688957 2383 False 317.500000 442 93.069500 1686 2116 2 chr1A.!!$F2 430
7 TraesCS1D01G027700 chr1B 16479395 16482957 3562 True 1098.500000 1847 90.266000 60 2125 2 chr1B.!!$R3 2065
8 TraesCS1D01G027700 chr1B 16646252 16647074 822 True 887.000000 887 87.035000 1340 2125 1 chr1B.!!$R1 785
9 TraesCS1D01G027700 chr1B 16652186 16654870 2684 True 477.333333 595 94.920333 60 1342 3 chr1B.!!$R4 1282
10 TraesCS1D01G027700 chr7B 192779604 192780222 618 False 617.000000 617 85.031000 683 1314 1 chr7B.!!$F1 631
11 TraesCS1D01G027700 chr2B 47190062 47190680 618 True 617.000000 617 85.031000 683 1314 1 chr2B.!!$R2 631

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
360 376 0.179161 CTCGGAGTAGTTCTGCACCG 60.179 60.0 16.9 16.9 41.39 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2157 9004 2.87655 GCCGGGTGTAATTGGTATCTTC 59.123 50.0 2.18 0.0 0.0 2.87 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 2.995258 TCGGATTAAAGAAAACGGACGG 59.005 45.455 0.00 0.00 0.00 4.79
178 179 5.768980 TCATTTTCTCCTCAACCTCATCT 57.231 39.130 0.00 0.00 0.00 2.90
334 350 1.493022 CCCCGTTCCCCTTTATGATGA 59.507 52.381 0.00 0.00 0.00 2.92
335 351 2.108250 CCCCGTTCCCCTTTATGATGAT 59.892 50.000 0.00 0.00 0.00 2.45
336 352 3.149196 CCCGTTCCCCTTTATGATGATG 58.851 50.000 0.00 0.00 0.00 3.07
337 353 3.181445 CCCGTTCCCCTTTATGATGATGA 60.181 47.826 0.00 0.00 0.00 2.92
338 354 4.067896 CCGTTCCCCTTTATGATGATGAG 58.932 47.826 0.00 0.00 0.00 2.90
339 355 4.067896 CGTTCCCCTTTATGATGATGAGG 58.932 47.826 0.00 0.00 0.00 3.86
340 356 4.202357 CGTTCCCCTTTATGATGATGAGGA 60.202 45.833 0.00 0.00 0.00 3.71
343 359 4.594920 TCCCCTTTATGATGATGAGGACTC 59.405 45.833 0.00 0.00 0.00 3.36
344 360 4.562347 CCCCTTTATGATGATGAGGACTCG 60.562 50.000 0.00 0.00 0.00 4.18
346 362 4.281941 CCTTTATGATGATGAGGACTCGGA 59.718 45.833 0.00 0.00 0.00 4.55
347 363 5.459536 TTTATGATGATGAGGACTCGGAG 57.540 43.478 2.83 2.83 0.00 4.63
348 364 2.443958 TGATGATGAGGACTCGGAGT 57.556 50.000 11.09 11.09 0.00 3.85
349 365 3.577805 TGATGATGAGGACTCGGAGTA 57.422 47.619 11.27 0.00 0.00 2.59
350 366 3.481453 TGATGATGAGGACTCGGAGTAG 58.519 50.000 11.27 0.00 0.00 2.57
352 368 3.367646 TGATGAGGACTCGGAGTAGTT 57.632 47.619 11.27 0.00 0.00 2.24
354 370 3.054287 TGATGAGGACTCGGAGTAGTTCT 60.054 47.826 11.27 6.57 38.07 3.01
355 371 2.712709 TGAGGACTCGGAGTAGTTCTG 58.287 52.381 11.27 0.00 35.34 3.02
357 373 1.174783 GGACTCGGAGTAGTTCTGCA 58.825 55.000 11.27 0.00 34.03 4.41
358 374 1.135344 GGACTCGGAGTAGTTCTGCAC 60.135 57.143 11.27 0.00 34.03 4.57
359 375 0.889306 ACTCGGAGTAGTTCTGCACC 59.111 55.000 9.33 0.00 34.03 5.01
360 376 0.179161 CTCGGAGTAGTTCTGCACCG 60.179 60.000 16.90 16.90 41.39 4.94
361 377 0.892358 TCGGAGTAGTTCTGCACCGT 60.892 55.000 20.40 0.00 40.93 4.83
362 378 0.806868 CGGAGTAGTTCTGCACCGTA 59.193 55.000 15.42 0.00 36.38 4.02
363 379 1.202154 CGGAGTAGTTCTGCACCGTAG 60.202 57.143 15.42 0.00 36.38 3.51
366 382 3.305881 GGAGTAGTTCTGCACCGTAGTTT 60.306 47.826 0.00 0.00 34.56 2.66
367 383 4.304939 GAGTAGTTCTGCACCGTAGTTTT 58.695 43.478 0.00 0.00 0.00 2.43
368 384 4.700700 AGTAGTTCTGCACCGTAGTTTTT 58.299 39.130 0.00 0.00 0.00 1.94
390 406 7.733402 TTTTTATCTAGTTGCACCGTAGTTT 57.267 32.000 0.00 0.00 0.00 2.66
392 408 8.830201 TTTTATCTAGTTGCACCGTAGTTTTA 57.170 30.769 0.00 0.00 0.00 1.52
394 410 8.638685 TTATCTAGTTGCACCGTAGTTTTATC 57.361 34.615 0.00 0.00 0.00 1.75
396 412 7.395190 TCTAGTTGCACCGTAGTTTTATCTA 57.605 36.000 0.00 0.00 0.00 1.98
397 413 7.478322 TCTAGTTGCACCGTAGTTTTATCTAG 58.522 38.462 0.00 0.00 0.00 2.43
398 414 6.034161 AGTTGCACCGTAGTTTTATCTAGT 57.966 37.500 0.00 0.00 0.00 2.57
399 415 6.461640 AGTTGCACCGTAGTTTTATCTAGTT 58.538 36.000 0.00 0.00 0.00 2.24
400 416 6.367969 AGTTGCACCGTAGTTTTATCTAGTTG 59.632 38.462 0.00 0.00 0.00 3.16
401 417 4.628333 TGCACCGTAGTTTTATCTAGTTGC 59.372 41.667 0.00 0.00 0.00 4.17
405 421 4.266976 CCGTAGTTTTATCTAGTTGCACCG 59.733 45.833 0.00 0.00 0.00 4.94
406 422 4.860907 CGTAGTTTTATCTAGTTGCACCGT 59.139 41.667 0.00 0.00 0.00 4.83
411 427 6.589139 AGTTTTATCTAGTTGCACCGTAGTTC 59.411 38.462 0.00 0.00 0.00 3.01
431 1679 9.472361 GTAGTTCGGTTTTATCTATGCTATGAA 57.528 33.333 0.00 0.00 0.00 2.57
432 1680 8.366671 AGTTCGGTTTTATCTATGCTATGAAC 57.633 34.615 0.00 0.00 0.00 3.18
435 1683 8.365399 TCGGTTTTATCTATGCTATGAACTTG 57.635 34.615 0.00 0.00 0.00 3.16
437 1685 8.612619 CGGTTTTATCTATGCTATGAACTTGTT 58.387 33.333 0.00 0.00 0.00 2.83
533 3543 9.499585 TTTTGTGTTCAAAATGCAACAAATATG 57.500 25.926 9.23 0.00 45.03 1.78
534 3544 7.187244 TGTGTTCAAAATGCAACAAATATGG 57.813 32.000 0.00 0.00 34.33 2.74
536 3546 7.042187 TGTGTTCAAAATGCAACAAATATGGAC 60.042 33.333 0.00 0.00 34.33 4.02
537 3547 6.988580 TGTTCAAAATGCAACAAATATGGACA 59.011 30.769 0.00 0.00 29.43 4.02
539 3549 7.598189 TCAAAATGCAACAAATATGGACATG 57.402 32.000 0.00 0.00 0.00 3.21
541 3551 6.971527 AAATGCAACAAATATGGACATGTG 57.028 33.333 1.15 0.00 0.00 3.21
542 3552 3.847542 TGCAACAAATATGGACATGTGC 58.152 40.909 10.90 10.90 0.00 4.57
543 3553 2.853594 GCAACAAATATGGACATGTGCG 59.146 45.455 13.03 0.00 0.00 5.34
544 3554 3.437428 CAACAAATATGGACATGTGCGG 58.563 45.455 13.03 0.77 0.00 5.69
546 3556 2.945008 ACAAATATGGACATGTGCGGAG 59.055 45.455 13.03 2.17 0.00 4.63
576 3586 2.318360 CGCGCGCGCTGTATTTTA 59.682 55.556 45.97 0.00 39.32 1.52
577 3587 1.714366 CGCGCGCGCTGTATTTTAG 60.714 57.895 45.97 27.04 39.32 1.85
578 3588 1.998772 GCGCGCGCTGTATTTTAGC 60.999 57.895 44.38 17.67 38.26 3.09
583 3593 4.589967 GCTGTATTTTAGCGCGGC 57.410 55.556 8.83 0.00 0.00 6.53
584 3594 2.014594 GCTGTATTTTAGCGCGGCT 58.985 52.632 8.83 8.38 43.41 5.52
585 3595 0.316196 GCTGTATTTTAGCGCGGCTG 60.316 55.000 8.83 0.00 40.10 4.85
586 3596 0.316196 CTGTATTTTAGCGCGGCTGC 60.316 55.000 8.83 7.70 40.10 5.25
588 3598 0.316196 GTATTTTAGCGCGGCTGCTG 60.316 55.000 22.96 10.42 46.70 4.41
589 3599 1.436195 TATTTTAGCGCGGCTGCTGG 61.436 55.000 22.96 1.40 46.70 4.85
591 3601 4.819761 TTAGCGCGGCTGCTGGAG 62.820 66.667 22.96 0.14 46.70 3.86
624 3634 2.480555 GCGCCAAACCTGACGATG 59.519 61.111 0.00 0.00 0.00 3.84
625 3635 3.039202 GCGCCAAACCTGACGATGG 62.039 63.158 0.00 0.00 36.00 3.51
626 3636 2.398554 CGCCAAACCTGACGATGGG 61.399 63.158 0.00 0.00 33.45 4.00
627 3637 2.700773 GCCAAACCTGACGATGGGC 61.701 63.158 0.00 0.00 33.45 5.36
629 3639 2.746277 AAACCTGACGATGGGCGC 60.746 61.111 0.00 0.00 46.04 6.53
644 3654 4.450955 CGCGCCGCAAACTATTTT 57.549 50.000 10.75 0.00 0.00 1.82
645 3655 2.719454 CGCGCCGCAAACTATTTTT 58.281 47.368 10.75 0.00 0.00 1.94
659 3669 2.249896 TTTTTAGCGCGCCACGTG 59.750 55.556 30.33 9.08 46.11 4.49
660 3670 2.535788 TTTTTAGCGCGCCACGTGT 61.536 52.632 30.33 11.01 46.11 4.49
661 3671 2.049475 TTTTTAGCGCGCCACGTGTT 62.049 50.000 30.33 10.14 46.11 3.32
662 3672 2.432841 TTTTAGCGCGCCACGTGTTC 62.433 55.000 30.33 4.87 46.11 3.18
672 3682 4.903010 ACGTGTTCCGCGGCTGTT 62.903 61.111 23.51 0.00 41.96 3.16
673 3683 4.368808 CGTGTTCCGCGGCTGTTG 62.369 66.667 23.51 6.16 33.47 3.33
674 3684 4.025401 GTGTTCCGCGGCTGTTGG 62.025 66.667 23.51 0.00 0.00 3.77
675 3685 4.243008 TGTTCCGCGGCTGTTGGA 62.243 61.111 23.51 0.00 0.00 3.53
676 3686 3.423154 GTTCCGCGGCTGTTGGAG 61.423 66.667 23.51 0.00 32.39 3.86
677 3687 3.621805 TTCCGCGGCTGTTGGAGA 61.622 61.111 23.51 0.00 32.39 3.71
680 3690 3.869272 CGCGGCTGTTGGAGATGC 61.869 66.667 0.00 0.00 0.00 3.91
681 3691 2.437359 GCGGCTGTTGGAGATGCT 60.437 61.111 0.00 0.00 0.00 3.79
1043 5876 2.059541 CGGTGGAAAGAAGACTTCGTC 58.940 52.381 9.53 10.67 35.05 4.20
1479 6323 1.997791 ACCGGGGGTAATCCTTCTTTT 59.002 47.619 6.32 0.00 32.11 2.27
1480 6324 2.380932 ACCGGGGGTAATCCTTCTTTTT 59.619 45.455 6.32 0.00 32.11 1.94
1648 6519 7.048629 TCACAGCTCAATTTTAATCACCAAA 57.951 32.000 0.00 0.00 0.00 3.28
2002 8847 1.250328 CCAGCATTGCCTTGAGTCAA 58.750 50.000 5.25 5.25 0.00 3.18
2178 9025 2.632987 AGATACCAATTACACCCGGC 57.367 50.000 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.738314 ACCGTCCGTTTTCTTTAATCCG 59.262 45.455 0.00 0.00 0.00 4.18
24 25 5.995897 ACAGTACCCTTAAATCAACACAGAC 59.004 40.000 0.00 0.00 0.00 3.51
178 179 2.685017 AGCGAGGGATGCCACTCA 60.685 61.111 5.86 0.00 33.36 3.41
300 316 1.299648 CGGGGCATCCAGAGTCAAA 59.700 57.895 0.00 0.00 34.36 2.69
334 350 3.283751 CAGAACTACTCCGAGTCCTCAT 58.716 50.000 3.74 0.00 0.00 2.90
335 351 2.712709 CAGAACTACTCCGAGTCCTCA 58.287 52.381 3.74 0.00 0.00 3.86
336 352 1.402613 GCAGAACTACTCCGAGTCCTC 59.597 57.143 3.74 0.63 0.00 3.71
337 353 1.271982 TGCAGAACTACTCCGAGTCCT 60.272 52.381 3.74 0.00 0.00 3.85
338 354 1.135344 GTGCAGAACTACTCCGAGTCC 60.135 57.143 3.74 0.00 0.00 3.85
339 355 1.135344 GGTGCAGAACTACTCCGAGTC 60.135 57.143 3.74 0.00 0.00 3.36
340 356 0.889306 GGTGCAGAACTACTCCGAGT 59.111 55.000 6.25 6.25 0.00 4.18
343 359 0.806868 TACGGTGCAGAACTACTCCG 59.193 55.000 12.13 12.13 38.78 4.63
344 360 1.817447 ACTACGGTGCAGAACTACTCC 59.183 52.381 0.00 0.00 0.00 3.85
346 362 4.332428 AAAACTACGGTGCAGAACTACT 57.668 40.909 0.00 0.00 0.00 2.57
366 382 7.733402 AAACTACGGTGCAACTAGATAAAAA 57.267 32.000 13.15 0.00 36.74 1.94
367 383 7.733402 AAAACTACGGTGCAACTAGATAAAA 57.267 32.000 13.15 0.00 36.74 1.52
368 384 9.090692 GATAAAACTACGGTGCAACTAGATAAA 57.909 33.333 13.15 0.50 36.74 1.40
370 386 8.004087 AGATAAAACTACGGTGCAACTAGATA 57.996 34.615 13.15 5.83 36.74 1.98
371 387 6.875076 AGATAAAACTACGGTGCAACTAGAT 58.125 36.000 13.15 1.45 36.74 1.98
372 388 6.276832 AGATAAAACTACGGTGCAACTAGA 57.723 37.500 13.15 0.00 36.74 2.43
374 390 7.161773 ACTAGATAAAACTACGGTGCAACTA 57.838 36.000 0.00 0.00 36.74 2.24
375 391 6.034161 ACTAGATAAAACTACGGTGCAACT 57.966 37.500 0.00 0.00 36.74 3.16
376 392 6.531439 CAACTAGATAAAACTACGGTGCAAC 58.469 40.000 0.00 0.00 0.00 4.17
377 393 5.121142 GCAACTAGATAAAACTACGGTGCAA 59.879 40.000 0.00 0.00 35.92 4.08
378 394 4.628333 GCAACTAGATAAAACTACGGTGCA 59.372 41.667 0.00 0.00 35.92 4.57
379 395 4.628333 TGCAACTAGATAAAACTACGGTGC 59.372 41.667 0.00 0.00 36.15 5.01
380 396 5.063060 GGTGCAACTAGATAAAACTACGGTG 59.937 44.000 0.00 0.00 36.74 4.94
381 397 5.173664 GGTGCAACTAGATAAAACTACGGT 58.826 41.667 0.00 0.00 36.74 4.83
382 398 4.266976 CGGTGCAACTAGATAAAACTACGG 59.733 45.833 0.00 0.00 36.74 4.02
383 399 4.860907 ACGGTGCAACTAGATAAAACTACG 59.139 41.667 0.00 0.00 36.74 3.51
384 400 7.031975 ACTACGGTGCAACTAGATAAAACTAC 58.968 38.462 13.15 0.00 36.74 2.73
386 402 6.034161 ACTACGGTGCAACTAGATAAAACT 57.966 37.500 13.15 0.00 36.74 2.66
387 403 6.453396 CGAACTACGGTGCAACTAGATAAAAC 60.453 42.308 13.15 0.00 38.46 2.43
390 406 4.665212 CGAACTACGGTGCAACTAGATAA 58.335 43.478 13.15 0.00 38.46 1.75
392 408 3.146618 CGAACTACGGTGCAACTAGAT 57.853 47.619 13.15 3.69 38.46 1.98
405 421 9.472361 TTCATAGCATAGATAAAACCGAACTAC 57.528 33.333 0.00 0.00 0.00 2.73
406 422 9.472361 GTTCATAGCATAGATAAAACCGAACTA 57.528 33.333 0.00 0.00 0.00 2.24
411 427 8.142994 ACAAGTTCATAGCATAGATAAAACCG 57.857 34.615 0.00 0.00 0.00 4.44
509 3519 7.496920 TCCATATTTGTTGCATTTTGAACACAA 59.503 29.630 0.00 0.00 31.85 3.33
512 3522 6.988580 TGTCCATATTTGTTGCATTTTGAACA 59.011 30.769 0.00 0.00 0.00 3.18
513 3523 7.418840 TGTCCATATTTGTTGCATTTTGAAC 57.581 32.000 0.00 0.00 0.00 3.18
516 3526 7.237871 CACATGTCCATATTTGTTGCATTTTG 58.762 34.615 0.00 0.00 0.00 2.44
518 3528 5.352016 GCACATGTCCATATTTGTTGCATTT 59.648 36.000 0.00 0.00 0.00 2.32
522 3532 2.853594 CGCACATGTCCATATTTGTTGC 59.146 45.455 0.00 0.00 0.00 4.17
524 3534 3.351740 TCCGCACATGTCCATATTTGTT 58.648 40.909 0.00 0.00 0.00 2.83
525 3535 2.945008 CTCCGCACATGTCCATATTTGT 59.055 45.455 0.00 0.00 0.00 2.83
526 3536 2.287188 GCTCCGCACATGTCCATATTTG 60.287 50.000 0.00 0.00 0.00 2.32
530 3540 1.068588 GTAGCTCCGCACATGTCCATA 59.931 52.381 0.00 0.00 0.00 2.74
531 3541 0.179073 GTAGCTCCGCACATGTCCAT 60.179 55.000 0.00 0.00 0.00 3.41
532 3542 1.218047 GTAGCTCCGCACATGTCCA 59.782 57.895 0.00 0.00 0.00 4.02
533 3543 0.807667 CTGTAGCTCCGCACATGTCC 60.808 60.000 0.00 0.00 0.00 4.02
534 3544 0.807667 CCTGTAGCTCCGCACATGTC 60.808 60.000 0.00 0.00 0.00 3.06
536 3546 0.529337 CTCCTGTAGCTCCGCACATG 60.529 60.000 0.00 0.00 0.00 3.21
537 3547 1.819229 CTCCTGTAGCTCCGCACAT 59.181 57.895 0.00 0.00 0.00 3.21
560 3570 1.998772 GCTAAAATACAGCGCGCGC 60.999 57.895 45.10 45.10 42.33 6.86
561 3571 4.173659 GCTAAAATACAGCGCGCG 57.826 55.556 28.44 28.44 0.00 6.86
566 3576 0.316196 CAGCCGCGCTAAAATACAGC 60.316 55.000 5.56 0.00 36.40 4.40
567 3577 0.316196 GCAGCCGCGCTAAAATACAG 60.316 55.000 5.56 0.00 36.40 2.74
568 3578 0.742990 AGCAGCCGCGCTAAAATACA 60.743 50.000 5.56 0.00 45.49 2.29
570 3580 1.436195 CCAGCAGCCGCGCTAAAATA 61.436 55.000 5.56 0.00 45.49 1.40
571 3581 2.764314 CCAGCAGCCGCGCTAAAAT 61.764 57.895 5.56 0.00 45.49 1.82
572 3582 3.430862 CCAGCAGCCGCGCTAAAA 61.431 61.111 5.56 0.00 45.49 1.52
573 3583 4.386951 TCCAGCAGCCGCGCTAAA 62.387 61.111 5.56 0.00 45.49 1.85
611 3621 3.039202 GCGCCCATCGTCAGGTTTG 62.039 63.158 0.00 0.00 41.07 2.93
612 3622 2.746277 GCGCCCATCGTCAGGTTT 60.746 61.111 0.00 0.00 41.07 3.27
627 3637 2.719454 AAAAATAGTTTGCGGCGCG 58.281 47.368 28.09 0.00 0.00 6.86
642 3652 2.049475 AACACGTGGCGCGCTAAAAA 62.049 50.000 32.29 8.97 46.11 1.94
643 3653 2.432841 GAACACGTGGCGCGCTAAAA 62.433 55.000 32.29 11.71 46.11 1.52
644 3654 2.945615 GAACACGTGGCGCGCTAAA 61.946 57.895 32.29 14.50 46.11 1.85
645 3655 3.408020 GAACACGTGGCGCGCTAA 61.408 61.111 32.29 17.34 46.11 3.09
655 3665 4.903010 AACAGCCGCGGAACACGT 62.903 61.111 33.48 14.52 46.52 4.49
657 3667 4.025401 CCAACAGCCGCGGAACAC 62.025 66.667 33.48 11.55 0.00 3.32
658 3668 4.243008 TCCAACAGCCGCGGAACA 62.243 61.111 33.48 0.56 0.00 3.18
659 3669 3.423154 CTCCAACAGCCGCGGAAC 61.423 66.667 33.48 12.91 0.00 3.62
660 3670 2.954684 ATCTCCAACAGCCGCGGAA 61.955 57.895 33.48 2.93 0.00 4.30
661 3671 3.390521 ATCTCCAACAGCCGCGGA 61.391 61.111 33.48 4.09 0.00 5.54
662 3672 3.197790 CATCTCCAACAGCCGCGG 61.198 66.667 24.05 24.05 0.00 6.46
663 3673 3.869272 GCATCTCCAACAGCCGCG 61.869 66.667 0.00 0.00 0.00 6.46
664 3674 2.437359 AGCATCTCCAACAGCCGC 60.437 61.111 0.00 0.00 0.00 6.53
665 3675 3.805267 GAGCATCTCCAACAGCCG 58.195 61.111 0.00 0.00 0.00 5.52
676 3686 5.047660 CCATGGTACCTTCTAGTAGAGCATC 60.048 48.000 14.36 0.00 0.00 3.91
677 3687 4.835615 CCATGGTACCTTCTAGTAGAGCAT 59.164 45.833 14.36 0.00 0.00 3.79
680 3690 4.585162 CACCCATGGTACCTTCTAGTAGAG 59.415 50.000 14.36 0.00 32.11 2.43
681 3691 4.543689 CACCCATGGTACCTTCTAGTAGA 58.456 47.826 14.36 0.00 32.11 2.59
808 5610 4.033358 GCCGATGATATTCGATGATTGACC 59.967 45.833 0.00 0.00 41.62 4.02
978 5808 5.339008 TCTTCGTAGCACTGGTTGATAAT 57.661 39.130 0.00 0.00 0.00 1.28
1648 6519 6.216456 AGAGGAAAGGTATTTCTGTCCAGAAT 59.784 38.462 10.34 4.45 45.78 2.40
2002 8847 8.846423 TTAAGACTATCTTTCTCCATCTTCCT 57.154 34.615 0.00 0.00 37.89 3.36
2157 9004 2.876550 GCCGGGTGTAATTGGTATCTTC 59.123 50.000 2.18 0.00 0.00 2.87
2178 9025 7.066284 CCTTTGAACATCTTGTTGGTATAGAGG 59.934 40.741 0.00 0.00 41.28 3.69


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

AutoCloner maintained by Alex Coulton.