Multiple sequence alignment - TraesCS3D01G287300

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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 TraesCS3D01G287300 chr3D 100.000 2828 0 0 1 2828 396204162 396206989 0.000000e+00 5223
1 TraesCS3D01G287300 chr3D 92.376 1587 76 24 614 2187 395836975 395838529 0.000000e+00 2218
2 TraesCS3D01G287300 chr3D 92.014 1465 65 29 579 2031 395832566 395833990 0.000000e+00 2010
3 TraesCS3D01G287300 chr3D 91.532 496 35 6 1 492 61218812 61218320 0.000000e+00 676
4 TraesCS3D01G287300 chr3B 93.148 1620 81 15 579 2187 521475816 521477416 0.000000e+00 2350
5 TraesCS3D01G287300 chr3B 95.004 1361 56 8 716 2071 521687801 521689154 0.000000e+00 2126
6 TraesCS3D01G287300 chr3B 94.275 1345 53 10 579 1916 521609256 521610583 0.000000e+00 2036
7 TraesCS3D01G287300 chr3B 93.463 1285 62 14 607 1876 521216742 521218019 0.000000e+00 1888
8 TraesCS3D01G287300 chr3B 94.640 1082 45 8 617 1688 521404928 521406006 0.000000e+00 1664
9 TraesCS3D01G287300 chr3B 84.706 765 95 12 2076 2828 521692901 521693655 0.000000e+00 745
10 TraesCS3D01G287300 chr3B 87.215 571 47 21 1 553 192887175 192886613 6.650000e-176 627
11 TraesCS3D01G287300 chr3B 88.132 514 39 15 1678 2187 521413619 521414114 2.430000e-165 592
12 TraesCS3D01G287300 chr3B 89.189 148 14 2 579 725 521684946 521685092 1.730000e-42 183
13 TraesCS3D01G287300 chr3B 90.816 98 8 1 1916 2013 521610664 521610760 2.290000e-26 130
14 TraesCS3D01G287300 chr3A 90.892 1570 90 33 608 2156 515860821 515862358 0.000000e+00 2058
15 TraesCS3D01G287300 chr3A 85.010 507 69 7 2309 2810 515862804 515863308 2.510000e-140 508
16 TraesCS3D01G287300 chr2D 89.573 585 51 5 1 577 260849865 260849283 0.000000e+00 734
17 TraesCS3D01G287300 chr2D 88.396 586 56 9 1 577 483160107 483159525 0.000000e+00 695
18 TraesCS3D01G287300 chr4D 88.756 587 52 8 1 577 464683977 464684559 0.000000e+00 706
19 TraesCS3D01G287300 chr4B 87.368 570 49 18 1 553 142041446 142040883 1.430000e-177 632
20 TraesCS3D01G287300 chr1B 90.000 500 31 17 1 493 467901105 467901592 1.850000e-176 628
21 TraesCS3D01G287300 chr1D 89.537 497 42 8 1 492 356941684 356942175 3.090000e-174 621
22 TraesCS3D01G287300 chrUn 89.315 496 43 8 1 492 240149061 240149550 5.180000e-172 614


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 TraesCS3D01G287300 chr3D 396204162 396206989 2827 False 5223 5223 100.0000 1 2828 1 chr3D.!!$F1 2827
1 TraesCS3D01G287300 chr3D 395832566 395838529 5963 False 2114 2218 92.1950 579 2187 2 chr3D.!!$F2 1608
2 TraesCS3D01G287300 chr3B 521475816 521477416 1600 False 2350 2350 93.1480 579 2187 1 chr3B.!!$F4 1608
3 TraesCS3D01G287300 chr3B 521216742 521218019 1277 False 1888 1888 93.4630 607 1876 1 chr3B.!!$F1 1269
4 TraesCS3D01G287300 chr3B 521404928 521406006 1078 False 1664 1664 94.6400 617 1688 1 chr3B.!!$F2 1071
5 TraesCS3D01G287300 chr3B 521609256 521610760 1504 False 1083 2036 92.5455 579 2013 2 chr3B.!!$F5 1434
6 TraesCS3D01G287300 chr3B 521684946 521693655 8709 False 1018 2126 89.6330 579 2828 3 chr3B.!!$F6 2249
7 TraesCS3D01G287300 chr3B 192886613 192887175 562 True 627 627 87.2150 1 553 1 chr3B.!!$R1 552
8 TraesCS3D01G287300 chr3A 515860821 515863308 2487 False 1283 2058 87.9510 608 2810 2 chr3A.!!$F1 2202
9 TraesCS3D01G287300 chr2D 260849283 260849865 582 True 734 734 89.5730 1 577 1 chr2D.!!$R1 576
10 TraesCS3D01G287300 chr2D 483159525 483160107 582 True 695 695 88.3960 1 577 1 chr2D.!!$R2 576
11 TraesCS3D01G287300 chr4D 464683977 464684559 582 False 706 706 88.7560 1 577 1 chr4D.!!$F1 576
12 TraesCS3D01G287300 chr4B 142040883 142041446 563 True 632 632 87.3680 1 553 1 chr4B.!!$R1 552

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
562 578 0.11358 TGGGCAAGGGTCCCTTTTAC 59.886 55.0 21.49 12.89 41.69 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2387 13704 0.524604 AAACACGCAAAGTTGTCCGC 60.525 50.0 0.0 0.0 0.0 5.54 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
124 125 2.034939 TCAATCGTCACTTGTGTACCGT 59.965 45.455 0.46 0.00 0.00 4.83
129 130 2.553086 GTCACTTGTGTACCGTTTGGA 58.447 47.619 0.46 0.00 39.21 3.53
145 146 3.686227 TTGGAAGGGTGAATATGGCAT 57.314 42.857 4.88 4.88 0.00 4.40
169 170 4.689345 GTCCAGTACCAACAATCACTGTAC 59.311 45.833 0.00 0.00 37.23 2.90
238 239 6.992715 AGTTTGGAAATATTGTATCTCCCTCG 59.007 38.462 1.52 0.00 0.00 4.63
360 363 3.938963 TCTGTTGTTTCTTTTGCTCTCGT 59.061 39.130 0.00 0.00 0.00 4.18
362 365 5.583061 TCTGTTGTTTCTTTTGCTCTCGTTA 59.417 36.000 0.00 0.00 0.00 3.18
390 393 3.538346 CGTGCGTGATAACGTGTTC 57.462 52.632 4.14 0.00 35.13 3.18
391 394 0.779408 CGTGCGTGATAACGTGTTCA 59.221 50.000 4.14 0.00 35.13 3.18
402 405 8.166066 CGTGATAACGTGTTCAGAATCAAAATA 58.834 33.333 0.00 0.00 0.00 1.40
403 406 9.820229 GTGATAACGTGTTCAGAATCAAAATAA 57.180 29.630 1.21 0.00 0.00 1.40
413 416 9.294030 GTTCAGAATCAAAATAAATCGATTGCT 57.706 29.630 12.25 0.00 0.00 3.91
446 449 7.534723 TGGTTACAGGACGCTTATATATCTT 57.465 36.000 0.00 0.00 0.00 2.40
497 511 1.289380 GGTTCCAGAGAGACGCGTT 59.711 57.895 15.53 2.89 0.00 4.84
507 522 0.596600 GAGACGCGTTGGTTGTCAGA 60.597 55.000 15.53 0.00 35.09 3.27
517 532 1.279840 GTTGTCAGAACACAGGCGC 59.720 57.895 0.00 0.00 34.35 6.53
539 555 2.050985 GCCGTGCAACTGCTTGTC 60.051 61.111 2.95 0.00 44.20 3.18
542 558 2.534019 CGTGCAACTGCTTGTCCGT 61.534 57.895 2.95 0.00 42.66 4.69
553 569 2.976494 CTTGTCCGTTGGGCAAGGGT 62.976 60.000 19.87 0.00 44.36 4.34
554 570 2.671963 GTCCGTTGGGCAAGGGTC 60.672 66.667 0.00 0.00 44.36 4.46
555 571 3.961414 TCCGTTGGGCAAGGGTCC 61.961 66.667 0.00 0.00 44.36 4.46
557 573 3.966543 CGTTGGGCAAGGGTCCCT 61.967 66.667 3.85 3.85 44.23 4.20
558 574 2.526110 GTTGGGCAAGGGTCCCTT 59.474 61.111 18.29 18.29 45.88 3.95
559 575 1.152333 GTTGGGCAAGGGTCCCTTT 60.152 57.895 21.49 3.54 41.69 3.11
560 576 0.762842 GTTGGGCAAGGGTCCCTTTT 60.763 55.000 21.49 0.00 41.69 2.27
561 577 0.861155 TTGGGCAAGGGTCCCTTTTA 59.139 50.000 21.49 4.70 41.69 1.52
562 578 0.113580 TGGGCAAGGGTCCCTTTTAC 59.886 55.000 21.49 12.89 41.69 2.01
563 579 0.113580 GGGCAAGGGTCCCTTTTACA 59.886 55.000 21.49 0.00 41.69 2.41
564 580 1.545841 GGCAAGGGTCCCTTTTACAG 58.454 55.000 21.49 10.38 41.69 2.74
565 581 1.074889 GGCAAGGGTCCCTTTTACAGA 59.925 52.381 21.49 0.00 41.69 3.41
566 582 2.490168 GGCAAGGGTCCCTTTTACAGAA 60.490 50.000 21.49 0.00 41.69 3.02
567 583 3.431415 GCAAGGGTCCCTTTTACAGAAT 58.569 45.455 21.49 0.00 41.69 2.40
568 584 3.832490 GCAAGGGTCCCTTTTACAGAATT 59.168 43.478 21.49 0.00 41.69 2.17
569 585 5.014202 GCAAGGGTCCCTTTTACAGAATTA 58.986 41.667 21.49 0.00 41.69 1.40
570 586 5.479027 GCAAGGGTCCCTTTTACAGAATTAA 59.521 40.000 21.49 0.00 41.69 1.40
571 587 6.154534 GCAAGGGTCCCTTTTACAGAATTAAT 59.845 38.462 21.49 0.00 41.69 1.40
572 588 7.310423 GCAAGGGTCCCTTTTACAGAATTAATT 60.310 37.037 21.49 0.00 41.69 1.40
573 589 8.593679 CAAGGGTCCCTTTTACAGAATTAATTT 58.406 33.333 21.49 0.00 41.69 1.82
574 590 8.362464 AGGGTCCCTTTTACAGAATTAATTTC 57.638 34.615 3.85 0.00 34.31 2.17
575 591 7.953493 AGGGTCCCTTTTACAGAATTAATTTCA 59.047 33.333 3.85 0.00 36.75 2.69
576 592 8.590204 GGGTCCCTTTTACAGAATTAATTTCAA 58.410 33.333 0.00 0.00 36.75 2.69
601 617 2.812619 GGAGCCCCTCCGAATCCTG 61.813 68.421 0.00 0.00 41.08 3.86
602 618 2.770048 AGCCCCTCCGAATCCTGG 60.770 66.667 0.00 0.00 0.00 4.45
612 628 0.380733 CGAATCCTGGACGATCACGA 59.619 55.000 0.00 0.00 42.66 4.35
762 3502 3.196613 CGAGAGGGCGGCTAATTAC 57.803 57.895 9.56 0.00 0.00 1.89
763 3503 0.674534 CGAGAGGGCGGCTAATTACT 59.325 55.000 9.56 0.00 0.00 2.24
764 3504 1.603172 CGAGAGGGCGGCTAATTACTG 60.603 57.143 9.56 0.00 0.00 2.74
765 3505 1.687123 GAGAGGGCGGCTAATTACTGA 59.313 52.381 9.56 0.00 0.00 3.41
766 3506 1.413077 AGAGGGCGGCTAATTACTGAC 59.587 52.381 9.56 0.00 0.00 3.51
767 3507 1.138266 GAGGGCGGCTAATTACTGACA 59.862 52.381 9.56 0.00 0.00 3.58
768 3508 1.768870 AGGGCGGCTAATTACTGACAT 59.231 47.619 9.56 0.00 0.00 3.06
769 3509 1.873591 GGGCGGCTAATTACTGACATG 59.126 52.381 9.56 0.00 0.00 3.21
770 3510 1.873591 GGCGGCTAATTACTGACATGG 59.126 52.381 0.00 0.00 0.00 3.66
771 3511 2.484770 GGCGGCTAATTACTGACATGGA 60.485 50.000 0.00 0.00 0.00 3.41
772 3512 3.403038 GCGGCTAATTACTGACATGGAT 58.597 45.455 0.00 0.00 0.00 3.41
773 3513 3.433615 GCGGCTAATTACTGACATGGATC 59.566 47.826 0.00 0.00 0.00 3.36
774 3514 3.675225 CGGCTAATTACTGACATGGATCG 59.325 47.826 0.00 0.00 0.00 3.69
775 3515 4.558697 CGGCTAATTACTGACATGGATCGA 60.559 45.833 0.00 0.00 0.00 3.59
776 3516 5.482908 GGCTAATTACTGACATGGATCGAT 58.517 41.667 0.00 0.00 0.00 3.59
892 8036 1.267121 CCAGTATATAGCCCCGCACT 58.733 55.000 0.00 0.00 0.00 4.40
1291 8459 3.303135 TCCTCAGCGACGCCAACT 61.303 61.111 17.79 0.00 0.00 3.16
1693 8864 4.166011 GCGACGGCAAGGACATGC 62.166 66.667 0.00 0.00 45.67 4.06
1803 8974 4.408821 GTCCAGGACGGCATGCCA 62.409 66.667 34.93 12.24 35.37 4.92
1849 9020 1.033746 CATCCGTCCCTGCTGCATTT 61.034 55.000 1.31 0.00 0.00 2.32
1894 9069 5.259632 ACCTTATCTTCTGATTTGCTTGCT 58.740 37.500 0.00 0.00 34.32 3.91
1895 9070 5.713861 ACCTTATCTTCTGATTTGCTTGCTT 59.286 36.000 0.00 0.00 34.32 3.91
1958 9216 5.123936 GTCGGTGGAAGCTAATTAAGGATT 58.876 41.667 0.00 0.00 0.00 3.01
1959 9217 5.236695 GTCGGTGGAAGCTAATTAAGGATTC 59.763 44.000 0.00 0.00 0.00 2.52
1991 9252 0.861837 CCAATGGCGAACTCGATAGC 59.138 55.000 2.69 0.00 43.02 2.97
2000 9261 4.396519 GCGAACTCGATAGCAGTAGTATC 58.603 47.826 2.69 0.00 43.02 2.24
2006 9267 5.699001 ACTCGATAGCAGTAGTATCTGACTG 59.301 44.000 0.00 0.00 44.88 3.51
2031 9292 4.003788 CGTGTCGTCCTTGGGCCT 62.004 66.667 4.53 0.00 0.00 5.19
2071 9344 5.751028 GCTCGCTGTATCCCATTTATCTATC 59.249 44.000 0.00 0.00 0.00 2.08
2079 13097 7.973944 TGTATCCCATTTATCTATCGATTGACG 59.026 37.037 11.76 0.00 44.09 4.35
2101 13119 7.441157 TGACGAAAAGAATACTTGAGTTGATGT 59.559 33.333 0.00 0.00 36.39 3.06
2106 13124 5.171476 AGAATACTTGAGTTGATGTGACGG 58.829 41.667 0.00 0.00 0.00 4.79
2161 13179 0.617535 TGCTGCCCTGCTACCTTCTA 60.618 55.000 0.00 0.00 0.00 2.10
2164 13182 1.765314 CTGCCCTGCTACCTTCTACAT 59.235 52.381 0.00 0.00 0.00 2.29
2166 13184 2.576191 TGCCCTGCTACCTTCTACATTT 59.424 45.455 0.00 0.00 0.00 2.32
2196 13215 9.974750 GGAATATTTTTCTTCTTTCGTAGACAG 57.025 33.333 0.00 0.00 35.31 3.51
2211 13274 5.302568 TCGTAGACAGAGTAAAAGTTCCCAA 59.697 40.000 0.00 0.00 0.00 4.12
2229 13294 6.713762 TCCCAATTGTATGCAAATAGAAGG 57.286 37.500 4.43 0.00 38.21 3.46
2257 13323 0.178924 AGGGGCAACAAATTGGAGCT 60.179 50.000 10.72 0.00 36.23 4.09
2265 13331 5.229423 GCAACAAATTGGAGCTAAATCACA 58.771 37.500 0.00 0.00 36.23 3.58
2276 13342 5.869344 GGAGCTAAATCACAAATTTGTTCCC 59.131 40.000 21.10 8.09 39.91 3.97
2277 13343 6.418057 AGCTAAATCACAAATTTGTTCCCA 57.582 33.333 21.10 6.32 39.91 4.37
2299 13614 5.634859 CCACCAACACATCTTTTTGAATAGC 59.365 40.000 0.00 0.00 0.00 2.97
2310 13625 9.727627 CATCTTTTTGAATAGCTTGGATTACTC 57.272 33.333 0.00 0.00 0.00 2.59
2314 13629 4.693283 TGAATAGCTTGGATTACTCACCG 58.307 43.478 0.00 0.00 0.00 4.94
2322 13637 1.665679 GGATTACTCACCGCATGTGTG 59.334 52.381 5.38 8.22 45.61 3.82
2325 13640 0.037697 TACTCACCGCATGTGTGACC 60.038 55.000 13.93 0.00 45.61 4.02
2326 13641 2.031919 TCACCGCATGTGTGACCC 59.968 61.111 13.93 0.00 45.61 4.46
2327 13642 2.032528 CACCGCATGTGTGACCCT 59.967 61.111 10.84 0.00 40.26 4.34
2357 13673 3.693085 CCAACACATCTAGCAGCAATCTT 59.307 43.478 0.00 0.00 0.00 2.40
2387 13704 0.725686 CTGAAGCTGCTTGTCATCGG 59.274 55.000 21.25 6.16 0.00 4.18
2415 13732 4.320608 ACTTTGCGTGTTTGATTCCATT 57.679 36.364 0.00 0.00 0.00 3.16
2417 13734 2.610219 TGCGTGTTTGATTCCATTCG 57.390 45.000 0.00 0.00 0.00 3.34
2419 13736 3.067833 TGCGTGTTTGATTCCATTCGTA 58.932 40.909 0.00 0.00 0.00 3.43
2421 13738 4.023963 TGCGTGTTTGATTCCATTCGTAAA 60.024 37.500 0.00 0.00 0.00 2.01
2423 13740 5.399892 GCGTGTTTGATTCCATTCGTAAAAA 59.600 36.000 0.00 0.00 0.00 1.94
2466 13783 3.181524 CCGCAATATCTGACGAACGTTTT 60.182 43.478 0.46 0.00 0.00 2.43
2487 13804 5.342361 TTTTAGGAGGGGTTGGTATTTGT 57.658 39.130 0.00 0.00 0.00 2.83
2491 13808 3.336694 AGGAGGGGTTGGTATTTGTGAAT 59.663 43.478 0.00 0.00 0.00 2.57
2500 13817 7.597369 GGGTTGGTATTTGTGAATGTTTTAGAC 59.403 37.037 0.00 0.00 0.00 2.59
2501 13818 8.138712 GGTTGGTATTTGTGAATGTTTTAGACA 58.861 33.333 0.00 0.00 43.71 3.41
2557 13875 7.789026 TCTTCAGAGATGCATGAGATTTTCTA 58.211 34.615 2.46 0.00 0.00 2.10
2559 13877 8.434733 TTCAGAGATGCATGAGATTTTCTAAG 57.565 34.615 2.46 0.00 0.00 2.18
2560 13878 6.990939 TCAGAGATGCATGAGATTTTCTAAGG 59.009 38.462 2.46 0.00 0.00 2.69
2659 13981 0.832135 TCCTCTCCCAGCTGACGTTT 60.832 55.000 17.39 0.00 0.00 3.60
2680 14003 2.218603 GCCGGTTATCATTTCCGTGAT 58.781 47.619 1.90 0.00 42.30 3.06
2734 14057 4.520492 GTGGTCACAAATTGATGAACCTCT 59.480 41.667 0.00 0.00 36.32 3.69
2742 14065 2.865119 TGATGAACCTCTGTGCACAT 57.135 45.000 22.00 4.45 31.02 3.21
2743 14066 3.144657 TGATGAACCTCTGTGCACATT 57.855 42.857 22.00 11.90 31.02 2.71
2788 14111 6.707161 ACTTGCCACGTCTTTGTTTACTATTA 59.293 34.615 0.00 0.00 0.00 0.98
2823 14146 6.600032 CCGTCATAGGCAGTTATAGAGAGTAT 59.400 42.308 0.00 0.00 0.00 2.12
2824 14147 7.769507 CCGTCATAGGCAGTTATAGAGAGTATA 59.230 40.741 0.00 0.00 0.00 1.47
2825 14148 8.605746 CGTCATAGGCAGTTATAGAGAGTATAC 58.394 40.741 0.00 0.00 0.00 1.47
2826 14149 8.605746 GTCATAGGCAGTTATAGAGAGTATACG 58.394 40.741 0.00 0.00 0.00 3.06
2827 14150 8.319881 TCATAGGCAGTTATAGAGAGTATACGT 58.680 37.037 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.584253 ATCGAGATATCCGTAAGAATGGG 57.416 43.478 11.65 0.00 43.02 4.00
124 125 3.464720 TGCCATATTCACCCTTCCAAA 57.535 42.857 0.00 0.00 0.00 3.28
129 130 2.244510 TGGACATGCCATATTCACCCTT 59.755 45.455 4.93 0.00 43.33 3.95
145 146 3.135712 ACAGTGATTGTTGGTACTGGACA 59.864 43.478 0.00 0.00 43.56 4.02
238 239 2.981898 GTGGTACCACAACTCCATACC 58.018 52.381 35.21 7.53 45.53 2.73
360 363 1.267533 TCACGCACGTAGAACAGCTAA 59.732 47.619 0.00 0.00 0.00 3.09
362 365 0.243907 ATCACGCACGTAGAACAGCT 59.756 50.000 0.00 0.00 0.00 4.24
402 405 4.816385 ACCATCGTCAATAGCAATCGATTT 59.184 37.500 8.21 0.00 38.82 2.17
403 406 4.380531 ACCATCGTCAATAGCAATCGATT 58.619 39.130 4.39 4.39 38.82 3.34
413 416 3.735820 GCGTCCTGTAACCATCGTCAATA 60.736 47.826 0.00 0.00 0.00 1.90
414 417 2.888594 CGTCCTGTAACCATCGTCAAT 58.111 47.619 0.00 0.00 0.00 2.57
416 419 0.108992 GCGTCCTGTAACCATCGTCA 60.109 55.000 0.00 0.00 0.00 4.35
417 420 0.172803 AGCGTCCTGTAACCATCGTC 59.827 55.000 0.00 0.00 0.00 4.20
418 421 0.606604 AAGCGTCCTGTAACCATCGT 59.393 50.000 0.00 0.00 0.00 3.73
446 449 1.370609 GATCGTCGTGTCTCTCCAGA 58.629 55.000 0.00 0.00 0.00 3.86
497 511 0.813610 CGCCTGTGTTCTGACAACCA 60.814 55.000 0.00 0.00 37.57 3.67
524 539 2.047151 AACGGACAAGCAGTTGCACG 62.047 55.000 6.90 5.47 45.16 5.34
526 541 1.723608 CCAACGGACAAGCAGTTGCA 61.724 55.000 6.90 0.00 46.88 4.08
536 552 3.485346 GACCCTTGCCCAACGGACA 62.485 63.158 3.56 0.00 0.00 4.02
561 577 8.139989 GCTCCTGCATATTGAAATTAATTCTGT 58.860 33.333 0.10 0.00 37.78 3.41
562 578 7.597743 GGCTCCTGCATATTGAAATTAATTCTG 59.402 37.037 0.10 0.00 41.91 3.02
563 579 7.256083 GGGCTCCTGCATATTGAAATTAATTCT 60.256 37.037 0.10 0.00 41.91 2.40
564 580 6.870439 GGGCTCCTGCATATTGAAATTAATTC 59.130 38.462 0.10 0.00 41.91 2.17
565 581 6.239686 GGGGCTCCTGCATATTGAAATTAATT 60.240 38.462 0.00 0.00 41.91 1.40
566 582 5.246883 GGGGCTCCTGCATATTGAAATTAAT 59.753 40.000 0.00 0.00 41.91 1.40
567 583 4.588528 GGGGCTCCTGCATATTGAAATTAA 59.411 41.667 0.00 0.00 41.91 1.40
568 584 4.140947 AGGGGCTCCTGCATATTGAAATTA 60.141 41.667 2.82 0.00 42.98 1.40
569 585 2.967887 GGGGCTCCTGCATATTGAAATT 59.032 45.455 0.00 0.00 41.91 1.82
570 586 2.178544 AGGGGCTCCTGCATATTGAAAT 59.821 45.455 2.82 0.00 42.98 2.17
571 587 1.570501 AGGGGCTCCTGCATATTGAAA 59.429 47.619 2.82 0.00 42.98 2.69
572 588 1.143684 GAGGGGCTCCTGCATATTGAA 59.856 52.381 11.93 0.00 45.05 2.69
573 589 0.767375 GAGGGGCTCCTGCATATTGA 59.233 55.000 11.93 0.00 45.05 2.57
574 590 3.336122 GAGGGGCTCCTGCATATTG 57.664 57.895 11.93 0.00 45.05 1.90
595 611 0.460311 GGTCGTGATCGTCCAGGATT 59.540 55.000 0.00 0.00 42.84 3.01
601 617 1.445582 GGTGTGGTCGTGATCGTCC 60.446 63.158 0.00 0.00 43.41 4.79
602 618 1.007336 GTGGTGTGGTCGTGATCGTC 61.007 60.000 0.00 0.00 38.33 4.20
612 628 2.426023 GGCTTCTCGTGGTGTGGT 59.574 61.111 0.00 0.00 0.00 4.16
744 3480 0.674534 AGTAATTAGCCGCCCTCTCG 59.325 55.000 0.00 0.00 0.00 4.04
747 3487 1.138266 TGTCAGTAATTAGCCGCCCTC 59.862 52.381 0.00 0.00 0.00 4.30
762 3502 2.521105 TGCAGATCGATCCATGTCAG 57.479 50.000 21.66 4.87 0.00 3.51
763 3503 2.554142 GTTGCAGATCGATCCATGTCA 58.446 47.619 21.66 12.97 0.00 3.58
764 3504 1.524355 CGTTGCAGATCGATCCATGTC 59.476 52.381 21.66 10.84 0.00 3.06
765 3505 1.575244 CGTTGCAGATCGATCCATGT 58.425 50.000 21.66 0.00 0.00 3.21
766 3506 0.234106 GCGTTGCAGATCGATCCATG 59.766 55.000 21.66 15.13 0.00 3.66
767 3507 1.217585 CGCGTTGCAGATCGATCCAT 61.218 55.000 21.66 1.12 0.00 3.41
768 3508 1.878069 CGCGTTGCAGATCGATCCA 60.878 57.895 21.66 10.83 0.00 3.41
769 3509 2.923854 CGCGTTGCAGATCGATCC 59.076 61.111 21.66 8.20 0.00 3.36
770 3510 2.243810 GCGCGTTGCAGATCGATC 59.756 61.111 17.91 17.91 45.45 3.69
866 3624 1.623542 GGCTATATACTGGCCCGGGG 61.624 65.000 25.28 9.31 45.51 5.73
892 8036 3.319198 GGAAGGGTGTGGAGGCGA 61.319 66.667 0.00 0.00 0.00 5.54
1222 8390 2.507547 GATGGCGGCGACAACGTA 60.508 61.111 23.82 0.00 41.98 3.57
1291 8459 1.153568 CGGCCTCGATGAAGAAGCA 60.154 57.895 0.00 0.00 39.00 3.91
1529 8700 2.353607 CGTCGCCGAGGTAGATGC 60.354 66.667 0.00 0.00 35.63 3.91
1849 9020 6.273730 AGGTATCGATCCCCAAATTAATGGTA 59.726 38.462 0.00 0.00 38.91 3.25
1894 9069 6.294361 ACTACTACACACCAGCATATCAAA 57.706 37.500 0.00 0.00 0.00 2.69
1895 9070 5.932619 ACTACTACACACCAGCATATCAA 57.067 39.130 0.00 0.00 0.00 2.57
1958 9216 3.583276 ATTGGCGCTCGAACACCGA 62.583 57.895 7.64 0.00 46.35 4.69
1959 9217 3.118454 ATTGGCGCTCGAACACCG 61.118 61.111 7.64 0.00 40.25 4.94
1991 9252 5.230936 CGCACAAATCAGTCAGATACTACTG 59.769 44.000 0.00 0.00 43.63 2.74
2000 9261 1.136529 CGACACGCACAAATCAGTCAG 60.137 52.381 0.00 0.00 0.00 3.51
2006 9267 0.865769 AAGGACGACACGCACAAATC 59.134 50.000 0.00 0.00 0.00 2.17
2031 9292 2.751436 GCTTCGCCATTGCCAGGA 60.751 61.111 0.00 0.00 0.00 3.86
2071 9344 7.050281 ACTCAAGTATTCTTTTCGTCAATCG 57.950 36.000 0.00 0.00 41.41 3.34
2079 13097 7.742089 CGTCACATCAACTCAAGTATTCTTTTC 59.258 37.037 0.00 0.00 0.00 2.29
2090 13108 3.181470 TGACTTCCGTCACATCAACTCAA 60.181 43.478 0.00 0.00 44.85 3.02
2106 13124 1.004927 CGATCGGCCGAAATTGACTTC 60.005 52.381 34.66 20.92 0.00 3.01
2184 13202 6.365518 GGGAACTTTTACTCTGTCTACGAAAG 59.634 42.308 0.00 0.00 0.00 2.62
2196 13215 6.919721 TGCATACAATTGGGAACTTTTACTC 58.080 36.000 10.83 0.00 0.00 2.59
2211 13274 7.615365 TCCAAGTTCCTTCTATTTGCATACAAT 59.385 33.333 0.00 0.00 35.21 2.71
2229 13294 1.408969 TTGTTGCCCCTTCCAAGTTC 58.591 50.000 0.00 0.00 0.00 3.01
2257 13323 6.485830 TGGTGGGAACAAATTTGTGATTTA 57.514 33.333 23.93 7.83 46.06 1.40
2265 13331 4.408596 AGATGTGTTGGTGGGAACAAATTT 59.591 37.500 0.00 0.00 46.06 1.82
2276 13342 6.449698 AGCTATTCAAAAAGATGTGTTGGTG 58.550 36.000 0.00 0.00 0.00 4.17
2277 13343 6.655078 AGCTATTCAAAAAGATGTGTTGGT 57.345 33.333 0.00 0.00 0.00 3.67
2299 13614 2.632377 ACATGCGGTGAGTAATCCAAG 58.368 47.619 0.00 0.00 0.00 3.61
2314 13629 0.537143 TGGAACAGGGTCACACATGC 60.537 55.000 0.00 0.00 0.00 4.06
2327 13642 2.875672 GCTAGATGTGTTGGCTGGAACA 60.876 50.000 0.00 0.00 33.36 3.18
2357 13673 2.301296 AGCAGCTTCAGAAAGACTAGCA 59.699 45.455 0.00 0.00 33.90 3.49
2387 13704 0.524604 AAACACGCAAAGTTGTCCGC 60.525 50.000 0.00 0.00 0.00 5.54
2421 13738 7.171848 GCGGTCCCAAATTTACAAGTTAATTTT 59.828 33.333 7.06 0.00 31.80 1.82
2423 13740 6.160684 GCGGTCCCAAATTTACAAGTTAATT 58.839 36.000 0.00 0.00 0.00 1.40
2424 13741 5.244178 TGCGGTCCCAAATTTACAAGTTAAT 59.756 36.000 0.00 0.00 0.00 1.40
2427 13744 2.959707 TGCGGTCCCAAATTTACAAGTT 59.040 40.909 0.00 0.00 0.00 2.66
2431 13748 5.067153 CAGATATTGCGGTCCCAAATTTACA 59.933 40.000 0.00 0.00 0.00 2.41
2432 13749 5.298276 TCAGATATTGCGGTCCCAAATTTAC 59.702 40.000 0.00 0.00 0.00 2.01
2466 13783 4.354387 TCACAAATACCAACCCCTCCTAAA 59.646 41.667 0.00 0.00 0.00 1.85
2584 13902 6.650120 TGGTAAGAGATGACAAATTCTACCC 58.350 40.000 0.00 0.00 0.00 3.69
2585 13903 8.561738 TTTGGTAAGAGATGACAAATTCTACC 57.438 34.615 0.00 0.00 0.00 3.18
2596 13916 6.945435 TGGCAACTTTATTTGGTAAGAGATGA 59.055 34.615 0.00 0.00 37.61 2.92
2734 14057 5.009911 GGATATATGCCTTCAAATGTGCACA 59.990 40.000 24.08 24.08 36.41 4.57
2742 14065 6.665992 AGTACGAGGATATATGCCTTCAAA 57.334 37.500 0.00 0.00 35.44 2.69
2743 14066 6.455647 CAAGTACGAGGATATATGCCTTCAA 58.544 40.000 0.00 0.00 35.44 2.69


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

AutoCloner maintained by Alex Coulton.