Multiple sequence alignment - TraesCS2D01G534300

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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 TraesCS2D01G534300 chr2D 100.000 3066 0 0 1 3066 618135562 618138627 0.000000e+00 5662.0
1 TraesCS2D01G534300 chr2D 81.030 427 37 17 1 386 618081734 618082157 1.790000e-77 300.0
2 TraesCS2D01G534300 chr2D 83.387 313 32 4 87 382 618129324 618129633 3.900000e-69 272.0
3 TraesCS2D01G534300 chr2D 80.478 251 28 12 1 230 588531191 588531441 4.060000e-39 172.0
4 TraesCS2D01G534300 chr2B 95.633 1351 47 6 1724 3066 754648792 754650138 0.000000e+00 2158.0
5 TraesCS2D01G534300 chr2B 88.222 866 52 21 886 1719 754620731 754621578 0.000000e+00 989.0
6 TraesCS2D01G534300 chr2B 84.433 758 59 18 1 716 754614216 754614956 0.000000e+00 691.0
7 TraesCS2D01G534300 chr2B 83.256 430 25 10 114 500 754637938 754638363 4.860000e-93 351.0
8 TraesCS2D01G534300 chr2B 85.809 303 25 11 1718 2005 754621735 754622034 3.840000e-79 305.0
9 TraesCS2D01G534300 chr2B 83.891 329 21 11 83 382 754551179 754551504 5.000000e-73 285.0
10 TraesCS2D01G534300 chr2B 88.372 172 10 3 799 970 754638577 754638738 6.710000e-47 198.0
11 TraesCS2D01G534300 chr2B 91.971 137 10 1 794 929 754648557 754648693 1.120000e-44 191.0
12 TraesCS2D01G534300 chr2B 97.183 71 1 1 719 788 754618311 754618381 5.370000e-23 119.0
13 TraesCS2D01G534300 chr2B 94.366 71 3 1 719 788 754639462 754639532 1.160000e-19 108.0
14 TraesCS2D01G534300 chr2B 92.958 71 4 1 719 788 754638418 754638488 5.410000e-18 102.0
15 TraesCS2D01G534300 chr2A 93.424 958 48 10 2120 3066 748905046 748905999 0.000000e+00 1406.0
16 TraesCS2D01G534300 chr2A 85.000 680 55 23 1006 1665 748901230 748901882 0.000000e+00 647.0
17 TraesCS2D01G534300 chr2A 92.835 321 18 3 794 1113 748866359 748866675 7.750000e-126 460.0
18 TraesCS2D01G534300 chr2A 84.536 485 33 12 56 504 748824845 748825323 2.810000e-120 442.0
19 TraesCS2D01G534300 chr2A 84.615 390 35 11 2 376 748893016 748893395 6.250000e-97 364.0
20 TraesCS2D01G534300 chr2A 90.071 282 15 6 1677 1945 748903689 748903970 1.350000e-93 353.0
21 TraesCS2D01G534300 chr2A 83.060 366 44 13 37 386 748700764 748701127 1.770000e-82 316.0
22 TraesCS2D01G534300 chr2A 80.702 399 52 16 1 386 748819738 748820124 1.390000e-73 287.0
23 TraesCS2D01G534300 chr2A 90.000 60 4 2 731 788 748866180 748866239 3.280000e-10 76.8
24 TraesCS2D01G534300 chr7A 88.889 72 7 1 1951 2022 591561640 591561570 1.510000e-13 87.9
25 TraesCS2D01G534300 chr5A 97.059 34 0 1 3024 3056 657242197 657242230 4.270000e-04 56.5


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 TraesCS2D01G534300 chr2D 618135562 618138627 3065 False 5662.0 5662 100.000000 1 3066 1 chr2D.!!$F4 3065
1 TraesCS2D01G534300 chr2B 754648557 754650138 1581 False 1174.5 2158 93.802000 794 3066 2 chr2B.!!$F4 2272
2 TraesCS2D01G534300 chr2B 754614216 754622034 7818 False 526.0 989 88.911750 1 2005 4 chr2B.!!$F2 2004
3 TraesCS2D01G534300 chr2A 748901230 748905999 4769 False 802.0 1406 89.498333 1006 3066 3 chr2A.!!$F6 2060

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
745 4140 0.462581 CCACATCTATGCCGCACACT 60.463 55.0 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2442 11064 0.597637 GTGGACGGCGGATGTGATAG 60.598 60.0 13.24 0.0 0.0 2.08 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
22 23 1.600076 CAGGCAGCTGAGCACACTT 60.600 57.895 20.43 0.00 35.83 3.16
23 24 1.600076 AGGCAGCTGAGCACACTTG 60.600 57.895 20.43 0.00 35.83 3.16
53 59 2.061773 CATCGAACGAAGCACTCAGTT 58.938 47.619 0.12 0.00 0.00 3.16
60 66 0.871057 GAAGCACTCAGTTGAGCACC 59.129 55.000 8.99 0.00 45.79 5.01
79 85 4.561530 GCACCTCGATATCTGCAATCCTAA 60.562 45.833 9.21 0.00 0.00 2.69
121 127 4.452733 CGGGAAGGTGACGGCCTC 62.453 72.222 0.00 0.00 38.03 4.70
175 187 3.706373 GGTGGAGGCGCTCAAGGA 61.706 66.667 7.64 0.00 31.08 3.36
303 330 3.855853 GGAGGAGGAAGGCGAGGC 61.856 72.222 0.00 0.00 0.00 4.70
309 336 4.847444 GGAAGGCGAGGCAGGAGC 62.847 72.222 0.00 0.00 41.10 4.70
376 406 5.316987 ACCAAACAACTAGCTAGCTGATTT 58.683 37.500 26.87 19.40 0.00 2.17
377 407 5.182001 ACCAAACAACTAGCTAGCTGATTTG 59.818 40.000 26.87 26.09 0.00 2.32
379 409 6.310197 CAAACAACTAGCTAGCTGATTTGTC 58.690 40.000 26.87 0.00 0.00 3.18
381 411 5.738909 ACAACTAGCTAGCTGATTTGTCAT 58.261 37.500 26.87 8.60 0.00 3.06
382 412 5.814705 ACAACTAGCTAGCTGATTTGTCATC 59.185 40.000 26.87 0.00 0.00 2.92
383 413 5.604758 ACTAGCTAGCTGATTTGTCATCA 57.395 39.130 27.68 1.11 0.00 3.07
384 414 5.599732 ACTAGCTAGCTGATTTGTCATCAG 58.400 41.667 27.68 13.70 46.12 2.90
391 430 3.870419 GCTGATTTGTCATCAGTCCTCTC 59.130 47.826 12.33 0.00 45.38 3.20
398 437 3.766591 TGTCATCAGTCCTCTCTTCTTCC 59.233 47.826 0.00 0.00 0.00 3.46
404 443 6.833346 TCAGTCCTCTCTTCTTCCTAGATA 57.167 41.667 0.00 0.00 0.00 1.98
407 446 5.372661 AGTCCTCTCTTCTTCCTAGATAGCT 59.627 44.000 0.00 0.00 0.00 3.32
409 448 7.073215 AGTCCTCTCTTCTTCCTAGATAGCTAA 59.927 40.741 0.00 0.00 0.00 3.09
412 451 8.357402 CCTCTCTTCTTCCTAGATAGCTAAAAC 58.643 40.741 0.00 0.00 0.00 2.43
421 460 3.262420 AGATAGCTAAAACGGTGCACTG 58.738 45.455 24.22 24.22 0.00 3.66
437 476 2.191908 TGGCTGCACCAGTTCGTT 59.808 55.556 0.50 0.00 46.36 3.85
452 491 0.911769 TCGTTTGGCTGGATCTGGAT 59.088 50.000 0.00 0.00 0.00 3.41
458 497 1.848388 TGGCTGGATCTGGATGTGAAT 59.152 47.619 0.00 0.00 0.00 2.57
459 498 2.242965 TGGCTGGATCTGGATGTGAATT 59.757 45.455 0.00 0.00 0.00 2.17
460 499 2.621998 GGCTGGATCTGGATGTGAATTG 59.378 50.000 0.00 0.00 0.00 2.32
461 500 3.285484 GCTGGATCTGGATGTGAATTGT 58.715 45.455 0.00 0.00 0.00 2.71
463 502 4.520179 CTGGATCTGGATGTGAATTGTGA 58.480 43.478 0.00 0.00 0.00 3.58
466 505 4.701651 GGATCTGGATGTGAATTGTGAACA 59.298 41.667 0.00 0.00 0.00 3.18
467 506 5.392380 GGATCTGGATGTGAATTGTGAACAC 60.392 44.000 0.00 0.00 35.45 3.32
468 507 4.459330 TCTGGATGTGAATTGTGAACACA 58.541 39.130 3.39 3.39 46.04 3.72
469 508 4.516321 TCTGGATGTGAATTGTGAACACAG 59.484 41.667 7.67 0.00 45.38 3.66
470 509 3.004629 TGGATGTGAATTGTGAACACAGC 59.995 43.478 7.67 0.00 45.38 4.40
471 510 4.227512 GATGTGAATTGTGAACACAGCA 57.772 40.909 0.00 5.67 45.88 4.41
472 511 4.801891 GATGTGAATTGTGAACACAGCAT 58.198 39.130 0.00 8.50 45.88 3.79
473 512 4.652421 TGTGAATTGTGAACACAGCATT 57.348 36.364 7.67 6.22 42.94 3.56
474 513 5.764487 TGTGAATTGTGAACACAGCATTA 57.236 34.783 7.67 0.00 42.94 1.90
475 514 6.330004 TGTGAATTGTGAACACAGCATTAT 57.670 33.333 7.67 0.00 42.94 1.28
498 537 1.144969 CCTTGTCGAGCTTGCGTAAA 58.855 50.000 0.00 0.00 0.00 2.01
516 558 3.800685 AACACGGTGCGCTGCAGTA 62.801 57.895 16.64 0.00 40.08 2.74
520 562 2.787249 GGTGCGCTGCAGTACATG 59.213 61.111 16.64 1.75 40.08 3.21
532 574 1.071471 GTACATGCCTCCATCCGGG 59.929 63.158 0.00 0.00 38.37 5.73
549 591 6.467677 CATCCGGGAGAAATTCAGTACATAT 58.532 40.000 0.00 0.00 0.00 1.78
550 592 7.310423 CCATCCGGGAGAAATTCAGTACATATA 60.310 40.741 0.00 0.00 40.01 0.86
551 593 6.989659 TCCGGGAGAAATTCAGTACATATAC 58.010 40.000 0.00 0.00 0.00 1.47
552 594 5.862323 CCGGGAGAAATTCAGTACATATACG 59.138 44.000 0.00 0.00 36.33 3.06
553 595 5.862323 CGGGAGAAATTCAGTACATATACGG 59.138 44.000 0.00 0.00 36.33 4.02
554 596 6.516194 CGGGAGAAATTCAGTACATATACGGT 60.516 42.308 0.00 0.00 36.33 4.83
556 598 6.581542 GGAGAAATTCAGTACATATACGGTCG 59.418 42.308 0.00 0.00 36.33 4.79
559 601 4.818534 TTCAGTACATATACGGTCGTCC 57.181 45.455 0.00 0.00 36.33 4.79
590 632 1.600916 GCCTTCGTATGGCCCATCC 60.601 63.158 0.00 0.00 44.32 3.51
591 633 2.056906 GCCTTCGTATGGCCCATCCT 62.057 60.000 0.00 0.00 44.32 3.24
595 637 2.051334 TCGTATGGCCCATCCTTTTG 57.949 50.000 0.00 0.00 35.26 2.44
598 640 2.159254 CGTATGGCCCATCCTTTTGTTG 60.159 50.000 0.00 0.00 35.26 3.33
601 643 1.415659 TGGCCCATCCTTTTGTTGTTG 59.584 47.619 0.00 0.00 35.26 3.33
615 657 6.382821 TTTGTTGTTGTTGAAATGTTCGTC 57.617 33.333 0.00 0.00 0.00 4.20
616 658 4.416620 TGTTGTTGTTGAAATGTTCGTCC 58.583 39.130 0.00 0.00 0.00 4.79
624 666 2.739913 TGAAATGTTCGTCCGGTTCATC 59.260 45.455 0.00 0.00 0.00 2.92
646 688 4.624024 TCCTTGTTACTATTTCGTTCTGCG 59.376 41.667 0.00 0.00 43.01 5.18
651 693 1.274167 ACTATTTCGTTCTGCGGTCCA 59.726 47.619 0.00 0.00 41.72 4.02
654 696 0.941542 TTTCGTTCTGCGGTCCAAAG 59.058 50.000 0.00 0.00 41.72 2.77
672 714 4.109766 CAAAGGGAAAACGAAAACTGTCC 58.890 43.478 0.00 0.00 0.00 4.02
686 728 2.025155 ACTGTCCGTTCTGCTATCGAT 58.975 47.619 2.16 2.16 0.00 3.59
687 729 2.033550 ACTGTCCGTTCTGCTATCGATC 59.966 50.000 0.00 0.00 0.00 3.69
688 730 1.002792 TGTCCGTTCTGCTATCGATCG 60.003 52.381 9.36 9.36 0.00 3.69
689 731 1.263484 GTCCGTTCTGCTATCGATCGA 59.737 52.381 21.86 21.86 0.00 3.59
690 732 1.944709 TCCGTTCTGCTATCGATCGAA 59.055 47.619 23.50 10.56 0.00 3.71
691 733 2.356695 TCCGTTCTGCTATCGATCGAAA 59.643 45.455 23.50 7.78 0.00 3.46
692 734 3.113322 CCGTTCTGCTATCGATCGAAAA 58.887 45.455 23.50 12.43 0.00 2.29
693 735 3.061139 CCGTTCTGCTATCGATCGAAAAC 60.061 47.826 23.50 14.17 0.00 2.43
716 758 2.428890 ACAGTCCGAATTTTGCAAACCA 59.571 40.909 12.39 0.00 0.00 3.67
717 759 3.069443 ACAGTCCGAATTTTGCAAACCAT 59.931 39.130 12.39 0.26 0.00 3.55
718 760 4.279671 ACAGTCCGAATTTTGCAAACCATA 59.720 37.500 12.39 0.00 0.00 2.74
719 761 4.621034 CAGTCCGAATTTTGCAAACCATAC 59.379 41.667 12.39 5.98 0.00 2.39
720 762 3.606346 GTCCGAATTTTGCAAACCATACG 59.394 43.478 12.39 12.71 0.00 3.06
745 4140 0.462581 CCACATCTATGCCGCACACT 60.463 55.000 0.00 0.00 0.00 3.55
788 4183 1.586123 CCACAAGCGAAACAAAAACCG 59.414 47.619 0.00 0.00 0.00 4.44
789 4184 2.520979 CACAAGCGAAACAAAAACCGA 58.479 42.857 0.00 0.00 0.00 4.69
790 4185 3.112580 CACAAGCGAAACAAAAACCGAT 58.887 40.909 0.00 0.00 0.00 4.18
791 4186 3.061271 CACAAGCGAAACAAAAACCGATG 60.061 43.478 0.00 0.00 0.00 3.84
792 4187 3.181495 ACAAGCGAAACAAAAACCGATGA 60.181 39.130 0.00 0.00 0.00 2.92
797 4314 2.741759 AACAAAAACCGATGATGCCC 57.258 45.000 0.00 0.00 0.00 5.36
844 4362 0.598065 AGAGAAAAACACCGGCATGC 59.402 50.000 9.90 9.90 0.00 4.06
870 4388 1.011968 TGCGACGAAGAACCAATCGG 61.012 55.000 0.00 0.00 43.11 4.18
891 6539 4.125703 GGTTCATCAGGCTCAGTAATCTG 58.874 47.826 0.00 0.00 42.54 2.90
931 6579 3.128465 GTACTACACGGCACTAGTCAC 57.872 52.381 0.00 0.00 0.00 3.67
973 6626 2.553247 GCCCTCTGCTCCCATATAAACC 60.553 54.545 0.00 0.00 36.87 3.27
985 6639 3.627237 CCATATAAACCCCAACCTGCAGT 60.627 47.826 13.81 0.00 0.00 4.40
986 6640 4.385865 CCATATAAACCCCAACCTGCAGTA 60.386 45.833 13.81 0.00 0.00 2.74
1023 6677 2.250939 CGTGGTTCAGAAGCGGCAA 61.251 57.895 7.83 0.00 0.00 4.52
1028 6682 1.098050 GTTCAGAAGCGGCAATCCAT 58.902 50.000 1.45 0.00 0.00 3.41
1031 6685 1.745087 TCAGAAGCGGCAATCCATTTC 59.255 47.619 1.45 0.00 0.00 2.17
1039 6693 1.672881 GGCAATCCATTTCCTCTGACG 59.327 52.381 0.00 0.00 0.00 4.35
1340 7006 4.335647 CCCCTGCTGGCTGTTCGT 62.336 66.667 3.63 0.00 0.00 3.85
1341 7007 2.281761 CCCTGCTGGCTGTTCGTT 60.282 61.111 3.63 0.00 0.00 3.85
1342 7008 2.328099 CCCTGCTGGCTGTTCGTTC 61.328 63.158 3.63 0.00 0.00 3.95
1343 7009 2.671177 CCTGCTGGCTGTTCGTTCG 61.671 63.158 0.00 0.00 0.00 3.95
1360 7026 3.436496 GTTCGTTCTCGAGTATCCAAGG 58.564 50.000 13.13 4.82 46.81 3.61
1365 7031 0.249073 CTCGAGTATCCAAGGCACGG 60.249 60.000 3.62 0.00 0.00 4.94
1396 7062 1.613317 TACGAGTGGGTGGCTGGATG 61.613 60.000 0.00 0.00 0.00 3.51
1398 7064 1.377725 GAGTGGGTGGCTGGATGTG 60.378 63.158 0.00 0.00 0.00 3.21
1410 7076 1.323271 TGGATGTGCTCTCCGTCTCC 61.323 60.000 0.00 0.00 35.41 3.71
1420 7086 2.106332 CCGTCTCCCCGTGTATGC 59.894 66.667 0.00 0.00 0.00 3.14
1421 7087 2.717044 CCGTCTCCCCGTGTATGCA 61.717 63.158 0.00 0.00 0.00 3.96
1422 7088 1.441729 CGTCTCCCCGTGTATGCAT 59.558 57.895 3.79 3.79 0.00 3.96
1423 7089 0.875908 CGTCTCCCCGTGTATGCATG 60.876 60.000 10.16 0.00 0.00 4.06
1424 7090 0.178068 GTCTCCCCGTGTATGCATGT 59.822 55.000 10.16 0.00 0.00 3.21
1425 7091 1.411246 GTCTCCCCGTGTATGCATGTA 59.589 52.381 10.16 0.00 0.00 2.29
1454 7120 6.856938 CGTAGAGGAGATGTAAAATTAGGACG 59.143 42.308 0.00 0.00 0.00 4.79
1460 7126 7.931948 AGGAGATGTAAAATTAGGACGGTAATG 59.068 37.037 0.00 0.00 0.00 1.90
1461 7127 7.307811 GGAGATGTAAAATTAGGACGGTAATGC 60.308 40.741 0.00 0.00 0.00 3.56
1462 7128 7.051623 AGATGTAAAATTAGGACGGTAATGCA 58.948 34.615 0.00 0.00 0.00 3.96
1529 7209 1.217882 CCCGTGATTCGCTTATGGTC 58.782 55.000 0.00 0.00 38.35 4.02
1554 7234 7.812191 TCAAACATGCTAATTGTAATGGTTGAC 59.188 33.333 18.19 0.00 39.76 3.18
1565 7245 0.762418 ATGGTTGACTGTTCGGGTGA 59.238 50.000 0.00 0.00 0.00 4.02
1568 7248 1.226746 GTTGACTGTTCGGGTGAAGG 58.773 55.000 0.00 0.00 33.98 3.46
1571 7251 0.966920 GACTGTTCGGGTGAAGGAGA 59.033 55.000 0.00 0.00 33.98 3.71
1631 7311 4.191544 CGAGCCAAACTGAAATGATAGGA 58.808 43.478 0.00 0.00 0.00 2.94
1647 7329 9.690913 AAATGATAGGAGAAAACATTCATGAGA 57.309 29.630 0.00 0.00 32.02 3.27
1788 9428 5.818136 ATCCACAAACACCAATCTATTCG 57.182 39.130 0.00 0.00 0.00 3.34
1790 9430 4.693566 TCCACAAACACCAATCTATTCGAC 59.306 41.667 0.00 0.00 0.00 4.20
2073 10694 5.679734 ACATAGATGAATAAAGCGCAAGG 57.320 39.130 11.47 0.00 38.28 3.61
2241 10863 6.042781 TCTCACTCTTCTGCTTACCCTAAAAA 59.957 38.462 0.00 0.00 0.00 1.94
2322 10944 6.767902 CCTATGTAAATAGCTTTGCAGGAAGA 59.232 38.462 2.23 0.00 39.78 2.87
2374 10996 7.390718 ACAACCCTTATTTCAGTCTACAACATC 59.609 37.037 0.00 0.00 0.00 3.06
2407 11029 2.283101 GCATGTCAGGGTGCCCAA 60.283 61.111 10.26 0.00 38.92 4.12
2442 11064 8.177663 CCGAATGGTGAAATAAGATATGTATGC 58.822 37.037 0.00 0.00 0.00 3.14
2542 11168 4.874396 CCTCCCCGTTAAGTAGCTTAAAAG 59.126 45.833 0.00 2.07 37.62 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 2.664518 TTCGATGCTGTGCGTGCA 60.665 55.556 0.79 0.79 44.95 4.57
23 24 2.202222 GTTCGATGCTGTGCGTGC 60.202 61.111 0.00 0.00 0.00 5.34
24 25 1.885814 TTCGTTCGATGCTGTGCGTG 61.886 55.000 0.00 0.00 0.00 5.34
25 26 1.617755 CTTCGTTCGATGCTGTGCGT 61.618 55.000 0.00 0.00 0.00 5.24
26 27 1.057822 CTTCGTTCGATGCTGTGCG 59.942 57.895 0.00 0.00 0.00 5.34
27 28 1.225854 GCTTCGTTCGATGCTGTGC 60.226 57.895 20.25 5.79 34.03 4.57
28 29 0.179240 GTGCTTCGTTCGATGCTGTG 60.179 55.000 24.97 4.12 36.61 3.66
53 59 1.402787 TGCAGATATCGAGGTGCTCA 58.597 50.000 13.83 0.00 36.84 4.26
60 66 6.146837 CCAACTTTAGGATTGCAGATATCGAG 59.853 42.308 0.00 0.00 0.00 4.04
79 85 0.674895 GCTCGCCATCTGACCAACTT 60.675 55.000 0.00 0.00 0.00 2.66
104 110 4.452733 GAGGCCGTCACCTTCCCG 62.453 72.222 0.00 0.00 41.32 5.14
303 330 2.433994 GCTCCTCCTCCTGCTCCTG 61.434 68.421 0.00 0.00 0.00 3.86
329 359 3.513912 CCCAGTTACTGAGGTACATGACA 59.486 47.826 14.66 0.00 32.44 3.58
356 386 5.997746 TGACAAATCAGCTAGCTAGTTGTTT 59.002 36.000 29.65 25.43 36.17 2.83
376 406 3.766591 GGAAGAAGAGAGGACTGATGACA 59.233 47.826 0.00 0.00 0.00 3.58
377 407 4.023291 AGGAAGAAGAGAGGACTGATGAC 58.977 47.826 0.00 0.00 0.00 3.06
379 409 5.445069 TCTAGGAAGAAGAGAGGACTGATG 58.555 45.833 0.00 0.00 0.00 3.07
381 411 5.725551 ATCTAGGAAGAAGAGAGGACTGA 57.274 43.478 0.00 0.00 34.73 3.41
382 412 5.473504 GCTATCTAGGAAGAAGAGAGGACTG 59.526 48.000 0.00 0.00 33.78 3.51
383 413 5.372661 AGCTATCTAGGAAGAAGAGAGGACT 59.627 44.000 0.00 0.00 33.78 3.85
384 414 5.631119 AGCTATCTAGGAAGAAGAGAGGAC 58.369 45.833 0.00 0.00 33.78 3.85
391 430 6.697892 CACCGTTTTAGCTATCTAGGAAGAAG 59.302 42.308 11.30 0.00 34.73 2.85
398 437 4.504461 CAGTGCACCGTTTTAGCTATCTAG 59.496 45.833 14.63 0.00 0.00 2.43
404 443 1.515521 GCCAGTGCACCGTTTTAGCT 61.516 55.000 14.63 0.00 37.47 3.32
407 446 2.326222 CAGCCAGTGCACCGTTTTA 58.674 52.632 14.63 0.00 41.13 1.52
421 460 1.008538 CAAACGAACTGGTGCAGCC 60.009 57.895 14.36 5.89 34.37 4.85
437 476 1.288188 TCACATCCAGATCCAGCCAA 58.712 50.000 0.00 0.00 0.00 4.52
452 491 4.652421 AATGCTGTGTTCACAATTCACA 57.348 36.364 7.07 0.00 39.31 3.58
478 517 0.315886 TTACGCAAGCTCGACAAGGA 59.684 50.000 1.33 0.00 45.62 3.36
480 519 2.033236 TGTTTTACGCAAGCTCGACAAG 60.033 45.455 1.33 0.00 45.62 3.16
483 522 1.717429 CGTGTTTTACGCAAGCTCGAC 60.717 52.381 1.33 0.00 46.92 4.20
498 537 3.800685 TACTGCAGCGCACCGTGTT 62.801 57.895 15.27 0.00 33.79 3.32
516 558 2.366837 TCCCGGATGGAGGCATGT 60.367 61.111 0.73 0.00 38.61 3.21
532 574 7.137426 ACGACCGTATATGTACTGAATTTCTC 58.863 38.462 0.00 0.00 0.00 2.87
535 577 6.211515 GGACGACCGTATATGTACTGAATTT 58.788 40.000 0.00 0.00 0.00 1.82
537 579 5.368256 GGACGACCGTATATGTACTGAAT 57.632 43.478 0.00 0.00 0.00 2.57
552 594 1.997606 CACCTGTAAATTCGGACGACC 59.002 52.381 0.00 0.00 0.00 4.79
553 595 1.392510 GCACCTGTAAATTCGGACGAC 59.607 52.381 0.00 0.00 0.00 4.34
554 596 1.673626 GGCACCTGTAAATTCGGACGA 60.674 52.381 0.00 0.00 0.00 4.20
556 598 2.109425 AGGCACCTGTAAATTCGGAC 57.891 50.000 0.00 0.00 0.00 4.79
559 601 2.073816 ACGAAGGCACCTGTAAATTCG 58.926 47.619 4.99 4.99 43.67 3.34
584 626 4.399004 TCAACAACAACAAAAGGATGGG 57.601 40.909 0.00 0.00 0.00 4.00
585 627 6.315891 ACATTTCAACAACAACAAAAGGATGG 59.684 34.615 0.00 0.00 0.00 3.51
590 632 6.816377 ACGAACATTTCAACAACAACAAAAG 58.184 32.000 0.00 0.00 0.00 2.27
591 633 6.128795 GGACGAACATTTCAACAACAACAAAA 60.129 34.615 0.00 0.00 0.00 2.44
595 637 3.480668 CGGACGAACATTTCAACAACAAC 59.519 43.478 0.00 0.00 0.00 3.32
598 640 2.032426 ACCGGACGAACATTTCAACAAC 59.968 45.455 9.46 0.00 0.00 3.32
601 643 2.288458 TGAACCGGACGAACATTTCAAC 59.712 45.455 9.46 0.00 0.00 3.18
615 657 5.006358 CGAAATAGTAACAAGGATGAACCGG 59.994 44.000 0.00 0.00 44.74 5.28
616 658 5.579511 ACGAAATAGTAACAAGGATGAACCG 59.420 40.000 0.00 0.00 44.74 4.44
646 688 3.131577 AGTTTTCGTTTTCCCTTTGGACC 59.868 43.478 0.00 0.00 41.57 4.46
651 693 3.181494 CGGACAGTTTTCGTTTTCCCTTT 60.181 43.478 0.00 0.00 0.00 3.11
654 696 1.672363 ACGGACAGTTTTCGTTTTCCC 59.328 47.619 0.00 0.00 32.95 3.97
672 714 4.090828 GTTTTCGATCGATAGCAGAACG 57.909 45.455 20.18 0.00 35.64 3.95
687 729 3.515071 AAATTCGGACTGTCGTTTTCG 57.485 42.857 1.07 0.00 45.64 3.46
688 730 3.420904 GCAAAATTCGGACTGTCGTTTTC 59.579 43.478 1.07 0.00 0.00 2.29
689 731 3.181495 TGCAAAATTCGGACTGTCGTTTT 60.181 39.130 1.07 4.33 0.00 2.43
690 732 2.356382 TGCAAAATTCGGACTGTCGTTT 59.644 40.909 1.07 0.00 0.00 3.60
691 733 1.944024 TGCAAAATTCGGACTGTCGTT 59.056 42.857 1.07 0.00 0.00 3.85
692 734 1.588674 TGCAAAATTCGGACTGTCGT 58.411 45.000 1.07 0.00 0.00 4.34
693 735 2.679355 TTGCAAAATTCGGACTGTCG 57.321 45.000 0.00 0.00 0.00 4.35
716 758 4.569943 GGCATAGATGTGGACATTCGTAT 58.430 43.478 0.00 0.00 36.57 3.06
717 759 3.552068 CGGCATAGATGTGGACATTCGTA 60.552 47.826 0.00 0.00 36.57 3.43
718 760 2.803133 CGGCATAGATGTGGACATTCGT 60.803 50.000 0.00 0.00 36.57 3.85
719 761 1.794701 CGGCATAGATGTGGACATTCG 59.205 52.381 0.00 0.00 36.57 3.34
720 762 1.532868 GCGGCATAGATGTGGACATTC 59.467 52.381 0.00 0.00 36.57 2.67
745 4140 2.093869 GCACACAGGTAACGGGAATCTA 60.094 50.000 0.00 0.00 46.39 1.98
788 4183 1.601759 CCGTCCATGGGGCATCATC 60.602 63.158 13.02 0.00 0.00 2.92
789 4184 2.517414 CCGTCCATGGGGCATCAT 59.483 61.111 13.02 0.00 0.00 2.45
797 4314 1.891919 CGGTATTGGCCGTCCATGG 60.892 63.158 4.97 4.97 46.11 3.66
817 4334 0.942252 GTGTTTTTCTCTTCCGGCGT 59.058 50.000 6.01 0.00 0.00 5.68
844 4362 1.513373 TTCTTCGTCGCATCGTCGG 60.513 57.895 6.10 0.00 38.67 4.79
870 4388 5.016051 TCAGATTACTGAGCCTGATGAAC 57.984 43.478 0.00 0.00 46.55 3.18
891 6539 0.608130 GGTTGGGCTCCAAAACCATC 59.392 55.000 14.36 0.00 45.73 3.51
925 6573 2.270257 CCGTGGACCGTGGTGACTA 61.270 63.158 0.00 0.00 33.66 2.59
929 6577 4.697756 ATGCCGTGGACCGTGGTG 62.698 66.667 0.00 0.00 33.66 4.17
930 6578 4.697756 CATGCCGTGGACCGTGGT 62.698 66.667 0.00 0.00 33.66 4.16
931 6579 4.697756 ACATGCCGTGGACCGTGG 62.698 66.667 0.00 0.00 33.66 4.94
957 6610 3.222603 GTTGGGGTTTATATGGGAGCAG 58.777 50.000 0.00 0.00 0.00 4.24
965 6618 4.688874 GCTACTGCAGGTTGGGGTTTATAT 60.689 45.833 19.93 0.00 39.41 0.86
973 6626 2.436646 CGGCTACTGCAGGTTGGG 60.437 66.667 19.93 4.10 41.91 4.12
985 6639 1.610967 TGGTGATGGTGGTCGGCTA 60.611 57.895 0.00 0.00 0.00 3.93
986 6640 2.927856 TGGTGATGGTGGTCGGCT 60.928 61.111 0.00 0.00 0.00 5.52
1023 6677 4.010349 GGAAAACGTCAGAGGAAATGGAT 58.990 43.478 0.00 0.00 0.00 3.41
1028 6682 3.830744 TGAGGAAAACGTCAGAGGAAA 57.169 42.857 0.00 0.00 0.00 3.13
1031 6685 3.879932 GTTTGAGGAAAACGTCAGAGG 57.120 47.619 0.00 0.00 38.92 3.69
1341 7007 1.404391 GCCTTGGATACTCGAGAACGA 59.596 52.381 21.68 4.24 46.56 3.85
1342 7008 1.134367 TGCCTTGGATACTCGAGAACG 59.866 52.381 21.68 0.00 41.26 3.95
1343 7009 2.541556 GTGCCTTGGATACTCGAGAAC 58.458 52.381 21.68 9.41 37.61 3.01
1360 7026 1.067416 TATGCTCCGATCACCGTGC 59.933 57.895 0.00 0.00 36.72 5.34
1365 7031 1.600663 CCACTCGTATGCTCCGATCAC 60.601 57.143 0.00 0.00 33.27 3.06
1396 7062 3.827898 CGGGGAGACGGAGAGCAC 61.828 72.222 0.00 0.00 0.00 4.40
1398 7064 3.827898 CACGGGGAGACGGAGAGC 61.828 72.222 0.00 0.00 38.39 4.09
1410 7076 2.417239 ACGTTTTACATGCATACACGGG 59.583 45.455 0.00 0.00 0.00 5.28
1420 7086 8.697846 TTTACATCTCCTCTACGTTTTACATG 57.302 34.615 0.00 0.00 0.00 3.21
1421 7087 9.886132 ATTTTACATCTCCTCTACGTTTTACAT 57.114 29.630 0.00 0.00 0.00 2.29
1422 7088 9.715121 AATTTTACATCTCCTCTACGTTTTACA 57.285 29.630 0.00 0.00 0.00 2.41
1425 7091 9.379791 CCTAATTTTACATCTCCTCTACGTTTT 57.620 33.333 0.00 0.00 0.00 2.43
1461 7127 3.501062 AGAACAAGTGTGCATCAGTGATG 59.499 43.478 25.91 25.91 42.37 3.07
1462 7128 3.748083 AGAACAAGTGTGCATCAGTGAT 58.252 40.909 0.00 0.00 0.00 3.06
1529 7209 7.814107 AGTCAACCATTACAATTAGCATGTTTG 59.186 33.333 0.00 0.00 32.27 2.93
1554 7234 1.618837 TCTTCTCCTTCACCCGAACAG 59.381 52.381 0.00 0.00 0.00 3.16
1565 7245 5.803552 CAGAATCCTCTGTTTCTTCTCCTT 58.196 41.667 0.00 0.00 43.64 3.36
1595 7275 1.295792 GGCTCGTTTCACTGACACAA 58.704 50.000 0.00 0.00 0.00 3.33
1631 7311 5.624159 TGTCAGGTCTCATGAATGTTTTCT 58.376 37.500 0.00 0.00 32.78 2.52
1647 7329 6.119536 TCTTATGTTCACAAAGTTGTCAGGT 58.880 36.000 0.00 0.00 39.91 4.00
2241 10863 9.732130 AGTTGAGCTCTTTTGTTCTATTAAGAT 57.268 29.630 16.19 0.00 0.00 2.40
2258 10880 2.734276 ACGGAAAGAGAGTTGAGCTC 57.266 50.000 6.82 6.82 44.45 4.09
2322 10944 1.952621 TAGTTAGCAAGCTGAGGGGT 58.047 50.000 4.53 0.00 0.00 4.95
2374 10996 3.316283 ACATGCAAAACAATGCTTACGG 58.684 40.909 0.00 0.00 46.54 4.02
2407 11029 5.982890 ATTTCACCATTCGGAAGTCATTT 57.017 34.783 0.00 0.00 35.59 2.32
2440 11062 1.067416 GACGGCGGATGTGATAGCA 59.933 57.895 13.24 0.00 0.00 3.49
2442 11064 0.597637 GTGGACGGCGGATGTGATAG 60.598 60.000 13.24 0.00 0.00 2.08
2542 11168 4.159135 ACCATTGTCTCTTGATCAATTGGC 59.841 41.667 8.96 7.01 30.74 4.52
2543 11169 5.888105 GACCATTGTCTCTTGATCAATTGG 58.112 41.667 8.96 9.68 38.53 3.16
2679 11306 7.570132 TCTCTGGGTATTTATTCGGAATCAAA 58.430 34.615 6.49 7.07 0.00 2.69
2689 11316 6.668133 TTCCCCTTTCTCTGGGTATTTATT 57.332 37.500 0.00 0.00 43.09 1.40
2701 11328 0.684479 GCCCACCATTCCCCTTTCTC 60.684 60.000 0.00 0.00 0.00 2.87
2712 11339 1.431243 TCCTTTTTGTAGGCCCACCAT 59.569 47.619 0.00 0.00 39.06 3.55
2713 11340 0.854218 TCCTTTTTGTAGGCCCACCA 59.146 50.000 0.00 0.00 39.06 4.17
3006 11633 5.776173 AGGTAAACATCTATCCTCGTCTG 57.224 43.478 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.