Multiple sequence alignment - TraesCS2A01G324700

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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 TraesCS2A01G324700 chr2A 100.000 5613 0 0 1 5613 554736352 554741964 0.000000e+00 10366.0
1 TraesCS2A01G324700 chr2D 93.694 2664 106 25 685 3316 431681097 431678464 0.000000e+00 3932.0
2 TraesCS2A01G324700 chr2D 94.403 2287 93 13 3332 5613 431678478 431676222 0.000000e+00 3482.0
3 TraesCS2A01G324700 chr2B 93.949 1603 60 15 989 2564 510592111 510590519 0.000000e+00 2388.0
4 TraesCS2A01G324700 chr2B 94.457 1353 67 3 4262 5613 510588837 510587492 0.000000e+00 2076.0
5 TraesCS2A01G324700 chr2B 93.519 864 31 8 3332 4191 510589668 510588826 0.000000e+00 1262.0
6 TraesCS2A01G324700 chr2B 96.937 751 21 1 2566 3316 510590402 510589654 0.000000e+00 1258.0
7 TraesCS2A01G324700 chr2B 90.190 316 17 3 683 998 510592511 510592210 3.150000e-107 399.0
8 TraesCS2A01G324700 chr3D 85.239 691 88 10 1 681 577484037 577483351 0.000000e+00 699.0
9 TraesCS2A01G324700 chr3D 88.973 526 52 3 4 529 586515650 586515131 0.000000e+00 645.0
10 TraesCS2A01G324700 chr6A 84.241 698 86 17 1 687 15762500 15763184 0.000000e+00 658.0
11 TraesCS2A01G324700 chr6A 83.284 682 94 12 5 680 498945834 498946501 1.340000e-170 610.0
12 TraesCS2A01G324700 chr7B 81.264 886 95 39 1578 2445 599801242 599802074 0.000000e+00 651.0
13 TraesCS2A01G324700 chr7B 87.689 528 55 8 3 529 629543600 629544118 1.730000e-169 606.0
14 TraesCS2A01G324700 chr7B 87.311 528 60 5 1 527 464556711 464557232 1.040000e-166 597.0
15 TraesCS2A01G324700 chr5D 88.636 528 55 4 1 528 407360773 407360251 6.130000e-179 638.0
16 TraesCS2A01G324700 chr1D 88.145 523 58 3 1 522 240585749 240586268 2.220000e-173 619.0
17 TraesCS2A01G324700 chr5A 87.713 529 59 4 4 529 621997072 621996547 3.720000e-171 612.0
18 TraesCS2A01G324700 chr7D 84.146 656 61 18 1795 2446 553416843 553417459 3.740000e-166 595.0
19 TraesCS2A01G324700 chr7A 84.793 434 36 14 2012 2445 639271651 639272054 5.230000e-110 409.0
20 TraesCS2A01G324700 chr4A 92.308 52 3 1 4205 4256 97531533 97531583 7.800000e-09 73.1
21 TraesCS2A01G324700 chr4D 92.157 51 3 1 4204 4254 367719946 367719897 2.810000e-08 71.3
22 TraesCS2A01G324700 chr6B 90.566 53 4 1 4204 4256 538369703 538369754 1.010000e-07 69.4
23 TraesCS2A01G324700 chr6D 88.889 54 5 1 4204 4257 420893651 420893703 1.310000e-06 65.8


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 TraesCS2A01G324700 chr2A 554736352 554741964 5612 False 10366.0 10366 100.0000 1 5613 1 chr2A.!!$F1 5612
1 TraesCS2A01G324700 chr2D 431676222 431681097 4875 True 3707.0 3932 94.0485 685 5613 2 chr2D.!!$R1 4928
2 TraesCS2A01G324700 chr2B 510587492 510592511 5019 True 1476.6 2388 93.8104 683 5613 5 chr2B.!!$R1 4930
3 TraesCS2A01G324700 chr3D 577483351 577484037 686 True 699.0 699 85.2390 1 681 1 chr3D.!!$R1 680
4 TraesCS2A01G324700 chr3D 586515131 586515650 519 True 645.0 645 88.9730 4 529 1 chr3D.!!$R2 525
5 TraesCS2A01G324700 chr6A 15762500 15763184 684 False 658.0 658 84.2410 1 687 1 chr6A.!!$F1 686
6 TraesCS2A01G324700 chr6A 498945834 498946501 667 False 610.0 610 83.2840 5 680 1 chr6A.!!$F2 675
7 TraesCS2A01G324700 chr7B 599801242 599802074 832 False 651.0 651 81.2640 1578 2445 1 chr7B.!!$F2 867
8 TraesCS2A01G324700 chr7B 629543600 629544118 518 False 606.0 606 87.6890 3 529 1 chr7B.!!$F3 526
9 TraesCS2A01G324700 chr7B 464556711 464557232 521 False 597.0 597 87.3110 1 527 1 chr7B.!!$F1 526
10 TraesCS2A01G324700 chr5D 407360251 407360773 522 True 638.0 638 88.6360 1 528 1 chr5D.!!$R1 527
11 TraesCS2A01G324700 chr1D 240585749 240586268 519 False 619.0 619 88.1450 1 522 1 chr1D.!!$F1 521
12 TraesCS2A01G324700 chr5A 621996547 621997072 525 True 612.0 612 87.7130 4 529 1 chr5A.!!$R1 525
13 TraesCS2A01G324700 chr7D 553416843 553417459 616 False 595.0 595 84.1460 1795 2446 1 chr7D.!!$F1 651

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
941 962 0.036875 GGTCCCTGTTCCACTTCCAG 59.963 60.0 0.0 0.0 0.0 3.86 F
2665 2973 0.107165 GGTATTGGGGAGGTGTCTGC 60.107 60.0 0.0 0.0 0.0 4.26 F
3393 3701 0.028505 CAGCGGAATTTCATGGAGCG 59.971 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2880 3188 0.457851 CCCGAGAGTCTCCATCACAC 59.542 60.0 14.61 0.0 0.00 3.82 R
3875 4188 0.033228 CTGATGGCGAGAGATGACCC 59.967 60.0 0.00 0.0 0.00 4.46 R
5203 5516 0.687354 GGAGAGCCAGTGGTTCAAGA 59.313 55.0 25.84 0.0 35.33 3.02 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
97 98 5.674933 GGTCGAAAGATCAAATATGGGAC 57.325 43.478 0.00 0.00 45.19 4.46
98 99 5.368989 GGTCGAAAGATCAAATATGGGACT 58.631 41.667 0.00 0.00 45.19 3.85
103 104 8.428852 TCGAAAGATCAAATATGGGACTTCATA 58.571 33.333 0.00 0.00 32.69 2.15
139 140 5.708877 TCTTGCACAACATGATCATCAAA 57.291 34.783 4.86 0.00 0.00 2.69
154 155 2.479566 TCAAAAGCGAGCAGGAAGAT 57.520 45.000 0.00 0.00 0.00 2.40
197 198 1.361543 ACTACAGGCAGGGTCCTCTAA 59.638 52.381 0.00 0.00 33.25 2.10
228 229 0.811616 CATCAGCTACCGGCAACCTC 60.812 60.000 0.00 0.00 44.79 3.85
262 263 0.039074 GTATGCGTCAGGAGATCCGG 60.039 60.000 0.00 0.00 42.08 5.14
271 272 0.566176 AGGAGATCCGGGACCCATAA 59.434 55.000 12.15 0.00 42.08 1.90
307 308 0.987081 AGCAGGATCTGGTGGAGCAT 60.987 55.000 0.00 0.00 40.87 3.79
313 314 4.529769 CAGGATCTGGTGGAGCATCTATAA 59.470 45.833 0.00 0.00 33.73 0.98
477 484 6.071616 TGCTAAGAATTCAATACCAAACCACC 60.072 38.462 8.44 0.00 0.00 4.61
479 486 5.010708 AGAATTCAATACCAAACCACCCT 57.989 39.130 8.44 0.00 0.00 4.34
496 503 2.708861 ACCCTGAACCATGCCGAATATA 59.291 45.455 0.00 0.00 0.00 0.86
509 516 3.926616 CCGAATATAGGCCATTTCTCGT 58.073 45.455 5.01 0.00 0.00 4.18
551 558 6.913873 TTATTTATCTGACCGTAAAGTGGC 57.086 37.500 0.00 0.00 0.00 5.01
552 559 2.973694 TATCTGACCGTAAAGTGGCC 57.026 50.000 0.00 0.00 0.00 5.36
553 560 0.981183 ATCTGACCGTAAAGTGGCCA 59.019 50.000 0.00 0.00 0.00 5.36
554 561 0.981183 TCTGACCGTAAAGTGGCCAT 59.019 50.000 9.72 0.00 0.00 4.40
555 562 1.086696 CTGACCGTAAAGTGGCCATG 58.913 55.000 9.72 0.00 0.00 3.66
557 564 1.072489 TGACCGTAAAGTGGCCATGAA 59.928 47.619 9.72 0.00 0.00 2.57
558 565 2.290641 TGACCGTAAAGTGGCCATGAAT 60.291 45.455 9.72 0.00 0.00 2.57
559 566 2.091541 ACCGTAAAGTGGCCATGAATG 58.908 47.619 9.72 0.29 0.00 2.67
572 582 3.301794 CATGAATGGATCAAGGGGACA 57.698 47.619 0.00 0.00 42.54 4.02
574 584 4.220724 CATGAATGGATCAAGGGGACAAT 58.779 43.478 0.00 0.00 42.54 2.71
577 587 4.726317 TGAATGGATCAAGGGGACAATCTA 59.274 41.667 0.00 0.00 34.30 1.98
578 588 5.193527 TGAATGGATCAAGGGGACAATCTAA 59.806 40.000 0.00 0.00 34.30 2.10
579 589 5.732331 ATGGATCAAGGGGACAATCTAAA 57.268 39.130 0.00 0.00 0.00 1.85
580 590 5.116084 TGGATCAAGGGGACAATCTAAAG 57.884 43.478 0.00 0.00 0.00 1.85
595 605 1.895020 TAAAGGCGACGGCTGGATGT 61.895 55.000 25.70 5.62 38.81 3.06
600 610 1.153369 CGACGGCTGGATGTCCAAT 60.153 57.895 2.97 0.00 46.97 3.16
604 614 1.153086 GGCTGGATGTCCAATCGCT 60.153 57.895 2.97 0.00 46.97 4.93
606 616 0.179062 GCTGGATGTCCAATCGCTCT 60.179 55.000 2.97 0.00 46.97 4.09
631 642 2.202703 GTTGTATCGCCGGCTCGT 60.203 61.111 26.68 12.61 0.00 4.18
652 665 2.099405 CCCCAGCGGTGATTTTTATGT 58.901 47.619 17.83 0.00 0.00 2.29
655 668 3.181497 CCCAGCGGTGATTTTTATGTCTG 60.181 47.826 17.83 0.00 0.00 3.51
661 674 3.429410 GGTGATTTTTATGTCTGCTGGGC 60.429 47.826 0.00 0.00 0.00 5.36
666 683 0.323360 TTATGTCTGCTGGGCCAACC 60.323 55.000 8.04 1.75 40.81 3.77
681 698 1.756950 AACCGCGGGAGATGCTCTA 60.757 57.895 31.76 0.00 0.00 2.43
720 737 4.680237 TCACTTGTCGGCGGGCAG 62.680 66.667 7.21 2.59 0.00 4.85
756 773 2.345991 CCACCAACATCGTCCCGT 59.654 61.111 0.00 0.00 0.00 5.28
757 774 1.740296 CCACCAACATCGTCCCGTC 60.740 63.158 0.00 0.00 0.00 4.79
758 775 1.740296 CACCAACATCGTCCCGTCC 60.740 63.158 0.00 0.00 0.00 4.79
759 776 2.125269 CCAACATCGTCCCGTCCC 60.125 66.667 0.00 0.00 0.00 4.46
760 777 2.508439 CAACATCGTCCCGTCCCG 60.508 66.667 0.00 0.00 0.00 5.14
831 848 2.440247 CCCCACGAGGCCCAATTC 60.440 66.667 0.00 0.00 0.00 2.17
832 849 2.677228 CCCACGAGGCCCAATTCT 59.323 61.111 0.00 0.00 0.00 2.40
833 850 1.000896 CCCACGAGGCCCAATTCTT 60.001 57.895 0.00 0.00 0.00 2.52
849 866 6.127253 CCCAATTCTTGTTGAGCTTATCCATT 60.127 38.462 0.00 0.00 0.00 3.16
851 868 7.363181 CCAATTCTTGTTGAGCTTATCCATTCA 60.363 37.037 0.00 0.00 0.00 2.57
941 962 0.036875 GGTCCCTGTTCCACTTCCAG 59.963 60.000 0.00 0.00 0.00 3.86
1128 1257 2.496341 CGCGAGCTCATCTCCCAA 59.504 61.111 15.40 0.00 38.62 4.12
1259 1388 1.227383 CCATCCCCAAGTAGGTGGC 59.773 63.158 0.00 0.00 37.34 5.01
1314 1443 2.547211 CGTCGGTCCGAGATACTAATGT 59.453 50.000 15.95 0.00 36.23 2.71
1319 1448 4.497006 CGGTCCGAGATACTAATGTTCGTT 60.497 45.833 4.91 0.00 0.00 3.85
1320 1449 4.974888 GGTCCGAGATACTAATGTTCGTTC 59.025 45.833 0.00 0.00 0.00 3.95
1321 1450 4.669728 GTCCGAGATACTAATGTTCGTTCG 59.330 45.833 0.00 0.00 0.00 3.95
1322 1451 4.333649 TCCGAGATACTAATGTTCGTTCGT 59.666 41.667 0.00 0.00 0.00 3.85
1348 1477 0.906282 TGCTGTGCAGAGGATGGAGA 60.906 55.000 13.44 0.00 33.32 3.71
1519 1648 2.203494 GATGGGGATTTCCGGGCC 60.203 66.667 0.00 0.00 36.71 5.80
1588 1717 1.348036 GGTAGGCAGACTTCACCTTGT 59.652 52.381 0.00 0.00 34.92 3.16
1652 1802 5.255397 TGGAATCTTAGTGGAATGGTTGT 57.745 39.130 0.00 0.00 0.00 3.32
1763 1913 5.066375 TGAAGGAATCAATCAAGTAATGCCG 59.934 40.000 0.00 0.00 34.30 5.69
1764 1914 3.316308 AGGAATCAATCAAGTAATGCCGC 59.684 43.478 0.00 0.00 0.00 6.53
1767 1936 2.710377 TCAATCAAGTAATGCCGCACT 58.290 42.857 0.00 0.00 0.00 4.40
1788 1959 4.634443 ACTACTACAACGGCATGGATTTTC 59.366 41.667 0.00 0.00 0.00 2.29
1792 1963 3.913089 ACAACGGCATGGATTTTCTTTC 58.087 40.909 0.00 0.00 0.00 2.62
1793 1964 3.573967 ACAACGGCATGGATTTTCTTTCT 59.426 39.130 0.00 0.00 0.00 2.52
1804 1975 6.924111 TGGATTTTCTTTCTTTCTATGTGGC 58.076 36.000 0.00 0.00 0.00 5.01
1817 1996 3.772572 TCTATGTGGCAGTGGCTTACTTA 59.227 43.478 18.53 9.79 37.60 2.24
1818 1997 3.652057 ATGTGGCAGTGGCTTACTTAT 57.348 42.857 18.53 0.00 37.60 1.73
2165 2356 4.454161 GCCGCACCCTTCATTTTTATTTTT 59.546 37.500 0.00 0.00 0.00 1.94
2166 2357 5.639931 GCCGCACCCTTCATTTTTATTTTTA 59.360 36.000 0.00 0.00 0.00 1.52
2170 2361 9.753669 CGCACCCTTCATTTTTATTTTTATTTC 57.246 29.630 0.00 0.00 0.00 2.17
2316 2507 8.842358 AATAGTTAACGAATTCAAGGAAGTGA 57.158 30.769 6.22 0.00 0.00 3.41
2665 2973 0.107165 GGTATTGGGGAGGTGTCTGC 60.107 60.000 0.00 0.00 0.00 4.26
2689 2997 2.031870 TCATCGGACGTGATGGAGAAT 58.968 47.619 14.00 0.00 44.68 2.40
2880 3188 3.189287 GGTGTGAAGGTAGATGTGCAAAG 59.811 47.826 0.00 0.00 0.00 2.77
3151 3459 2.158842 AGAAGATTTCATGCCTCGGGAG 60.159 50.000 0.00 0.00 0.00 4.30
3226 3534 3.052944 TGGGAGAAATTTTCATCCCGGAT 60.053 43.478 25.40 0.00 43.88 4.18
3278 3586 4.402474 GCACCCTTTAGTTTGATTAGCCAT 59.598 41.667 0.00 0.00 0.00 4.40
3319 3627 9.995957 GTATCAGCTAATTTTCTCTCTTTTTCC 57.004 33.333 0.00 0.00 0.00 3.13
3320 3628 7.454260 TCAGCTAATTTTCTCTCTTTTTCCC 57.546 36.000 0.00 0.00 0.00 3.97
3321 3629 7.004086 TCAGCTAATTTTCTCTCTTTTTCCCA 58.996 34.615 0.00 0.00 0.00 4.37
3322 3630 7.040409 TCAGCTAATTTTCTCTCTTTTTCCCAC 60.040 37.037 0.00 0.00 0.00 4.61
3323 3631 6.777580 AGCTAATTTTCTCTCTTTTTCCCACA 59.222 34.615 0.00 0.00 0.00 4.17
3324 3632 7.287696 AGCTAATTTTCTCTCTTTTTCCCACAA 59.712 33.333 0.00 0.00 0.00 3.33
3325 3633 7.926018 GCTAATTTTCTCTCTTTTTCCCACAAA 59.074 33.333 0.00 0.00 0.00 2.83
3326 3634 9.816354 CTAATTTTCTCTCTTTTTCCCACAAAA 57.184 29.630 0.00 0.00 0.00 2.44
3393 3701 0.028505 CAGCGGAATTTCATGGAGCG 59.971 55.000 0.00 0.00 0.00 5.03
3433 3741 3.330701 AGGTGGTGTTTATGTCAGGTGAT 59.669 43.478 0.00 0.00 0.00 3.06
3547 3856 0.798776 CCAGGAGTGCACGATTTCAC 59.201 55.000 12.01 0.00 0.00 3.18
3563 3872 5.622856 CGATTTCACTGTTCTGAAAAAGCTC 59.377 40.000 0.00 0.00 42.14 4.09
3695 4004 3.315191 CACACCCCAATTTAGCTTATCCG 59.685 47.826 0.00 0.00 0.00 4.18
3787 4100 3.290710 ACCTGAACAATTTGTCTGCTGT 58.709 40.909 1.83 0.00 0.00 4.40
3875 4188 0.370958 CCACCGCCGTTAACATAACG 59.629 55.000 14.01 14.01 42.74 3.18
4007 4320 4.022935 ACTCATTTCTTCTTCGCAATTGCA 60.023 37.500 28.77 14.00 42.21 4.08
4023 4336 6.733725 CGCAATTGCATCTTATCTATTGTACG 59.266 38.462 28.77 3.27 42.21 3.67
4197 4510 6.403636 GCTTACATTTGTTGAGACTGTATGGG 60.404 42.308 0.00 0.00 0.00 4.00
4201 4514 1.696884 TGTTGAGACTGTATGGGTGCA 59.303 47.619 0.00 0.00 0.00 4.57
4228 4541 2.917933 TCATTCTGGTTAATGGAGCCG 58.082 47.619 0.00 0.00 37.44 5.52
4290 4603 9.036671 GTTGAGCCTAGTTTACTTCATATTCTC 57.963 37.037 0.00 0.00 0.00 2.87
4307 4620 8.939929 TCATATTCTCACAGAAACAGTCATTTC 58.060 33.333 0.00 0.00 37.82 2.17
4477 4790 1.618837 GGGGCGTATTCATCTGCTAGA 59.381 52.381 0.00 0.00 0.00 2.43
4761 5074 6.478344 AGCTTCAGAAATAATTACTCTGCTCG 59.522 38.462 16.53 10.61 37.17 5.03
4765 5078 3.454371 AATAATTACTCTGCTCGCCGT 57.546 42.857 0.00 0.00 0.00 5.68
4794 5107 7.617041 AGAAGTATGTTCTTTCTTACCATGC 57.383 36.000 0.00 0.00 0.00 4.06
4817 5130 0.247379 GTCGTGTTTTCGTGTGCGTT 60.247 50.000 0.00 0.00 39.49 4.84
4848 5161 4.449743 GTGTTTTCTGTGTCGTTATGGCTA 59.550 41.667 0.00 0.00 0.00 3.93
5013 5326 7.661968 TCTGAACTCTGAAGGATATTATTCCG 58.338 38.462 0.05 0.00 40.94 4.30
5059 5372 3.869272 CGGCGCCTTTGCAGCTAG 61.869 66.667 26.68 0.00 37.25 3.42
5060 5373 2.747855 GGCGCCTTTGCAGCTAGT 60.748 61.111 22.15 0.00 37.25 2.57
5061 5374 1.449601 GGCGCCTTTGCAGCTAGTA 60.450 57.895 22.15 0.00 37.25 1.82
5203 5516 2.236223 CTCCTCGTGCTGCTCACCAT 62.236 60.000 0.00 0.00 42.69 3.55
5319 5638 4.119363 AGAGCATGCCACGGCCAT 62.119 61.111 15.66 0.00 41.09 4.40
5320 5639 3.589881 GAGCATGCCACGGCCATC 61.590 66.667 15.66 0.00 41.09 3.51
5414 5733 1.731613 GGACATGTCGTCGTCGCAA 60.732 57.895 19.33 0.00 46.42 4.85
5525 5844 2.043248 TACTCCCAGGCCTCCGTC 60.043 66.667 0.00 0.00 0.00 4.79
5526 5845 3.674050 TACTCCCAGGCCTCCGTCC 62.674 68.421 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 7.595875 TGCAAGATGACACAACAAATTATGAAG 59.404 33.333 0.00 0.00 0.00 3.02
98 99 7.381948 GTGCAAGATGACACAACAAATTATGAA 59.618 33.333 0.00 0.00 36.77 2.57
103 104 5.008619 TGTGCAAGATGACACAACAAATT 57.991 34.783 0.00 0.00 43.48 1.82
139 140 0.177604 CTGGATCTTCCTGCTCGCTT 59.822 55.000 0.00 0.00 37.46 4.68
154 155 4.698201 TGGTTCAGTGTCAAATACTGGA 57.302 40.909 5.42 0.00 44.33 3.86
197 198 3.430929 GGTAGCTGATGATCAACTTCGGT 60.431 47.826 3.43 0.00 33.36 4.69
262 263 3.213206 TGATGATGCACTTATGGGTCC 57.787 47.619 0.00 0.00 0.00 4.46
271 272 0.809385 GCTGCAGTTGATGATGCACT 59.191 50.000 16.64 0.00 46.97 4.40
307 308 3.005472 CGTCGCCCTTGATCCTTTATAGA 59.995 47.826 0.00 0.00 0.00 1.98
313 314 2.125106 GCGTCGCCCTTGATCCTT 60.125 61.111 5.75 0.00 0.00 3.36
454 461 6.663523 AGGGTGGTTTGGTATTGAATTCTTAG 59.336 38.462 7.05 0.00 0.00 2.18
470 477 0.831711 GGCATGGTTCAGGGTGGTTT 60.832 55.000 0.00 0.00 0.00 3.27
477 484 3.338249 CCTATATTCGGCATGGTTCAGG 58.662 50.000 0.00 0.00 0.00 3.86
479 486 2.778299 GCCTATATTCGGCATGGTTCA 58.222 47.619 10.02 0.00 46.77 3.18
496 503 2.351835 CGATATCGACGAGAAATGGCCT 60.352 50.000 20.50 0.00 43.02 5.19
501 508 1.067776 GGCCCGATATCGACGAGAAAT 60.068 52.381 26.32 0.00 43.02 2.17
502 509 0.313043 GGCCCGATATCGACGAGAAA 59.687 55.000 26.32 0.00 43.02 2.52
529 536 5.104859 TGGCCACTTTACGGTCAGATAAATA 60.105 40.000 0.00 0.00 31.74 1.40
530 537 4.196971 GGCCACTTTACGGTCAGATAAAT 58.803 43.478 0.00 0.00 0.00 1.40
531 538 3.008157 TGGCCACTTTACGGTCAGATAAA 59.992 43.478 0.00 0.00 31.74 1.40
532 539 2.568062 TGGCCACTTTACGGTCAGATAA 59.432 45.455 0.00 0.00 31.74 1.75
533 540 2.181125 TGGCCACTTTACGGTCAGATA 58.819 47.619 0.00 0.00 31.74 1.98
535 542 0.981183 ATGGCCACTTTACGGTCAGA 59.019 50.000 8.16 0.00 42.54 3.27
536 543 1.086696 CATGGCCACTTTACGGTCAG 58.913 55.000 8.16 0.00 42.54 3.51
539 546 2.091541 CATTCATGGCCACTTTACGGT 58.908 47.619 8.16 0.00 0.00 4.83
540 547 1.405105 CCATTCATGGCCACTTTACGG 59.595 52.381 8.16 0.06 41.75 4.02
552 559 3.301794 TGTCCCCTTGATCCATTCATG 57.698 47.619 0.00 0.00 33.34 3.07
553 560 4.169461 AGATTGTCCCCTTGATCCATTCAT 59.831 41.667 0.00 0.00 33.34 2.57
554 561 3.528905 AGATTGTCCCCTTGATCCATTCA 59.471 43.478 0.00 0.00 0.00 2.57
555 562 4.176120 AGATTGTCCCCTTGATCCATTC 57.824 45.455 0.00 0.00 0.00 2.67
557 564 5.399497 CCTTTAGATTGTCCCCTTGATCCAT 60.399 44.000 0.00 0.00 0.00 3.41
558 565 4.079787 CCTTTAGATTGTCCCCTTGATCCA 60.080 45.833 0.00 0.00 0.00 3.41
559 566 4.464947 CCTTTAGATTGTCCCCTTGATCC 58.535 47.826 0.00 0.00 0.00 3.36
560 567 3.885901 GCCTTTAGATTGTCCCCTTGATC 59.114 47.826 0.00 0.00 0.00 2.92
561 568 3.685550 CGCCTTTAGATTGTCCCCTTGAT 60.686 47.826 0.00 0.00 0.00 2.57
562 569 2.355716 CGCCTTTAGATTGTCCCCTTGA 60.356 50.000 0.00 0.00 0.00 3.02
564 571 1.913419 TCGCCTTTAGATTGTCCCCTT 59.087 47.619 0.00 0.00 0.00 3.95
565 572 1.209747 GTCGCCTTTAGATTGTCCCCT 59.790 52.381 0.00 0.00 0.00 4.79
570 580 0.249398 AGCCGTCGCCTTTAGATTGT 59.751 50.000 0.00 0.00 34.57 2.71
572 582 0.462047 CCAGCCGTCGCCTTTAGATT 60.462 55.000 0.00 0.00 34.57 2.40
574 584 1.327690 ATCCAGCCGTCGCCTTTAGA 61.328 55.000 0.00 0.00 34.57 2.10
577 587 2.436646 CATCCAGCCGTCGCCTTT 60.437 61.111 0.00 0.00 34.57 3.11
578 588 3.665675 GACATCCAGCCGTCGCCTT 62.666 63.158 0.00 0.00 34.57 4.35
579 589 4.148825 GACATCCAGCCGTCGCCT 62.149 66.667 0.00 0.00 34.57 5.52
604 614 0.248907 GCGATACAACTGGCGCTAGA 60.249 55.000 28.72 4.87 45.41 2.43
606 616 4.412933 GCGATACAACTGGCGCTA 57.587 55.556 7.64 0.00 45.41 4.26
613 624 2.104331 CGAGCCGGCGATACAACT 59.896 61.111 23.20 0.00 0.00 3.16
614 625 2.202703 ACGAGCCGGCGATACAAC 60.203 61.111 23.20 6.83 34.83 3.32
631 642 2.291282 ACATAAAAATCACCGCTGGGGA 60.291 45.455 18.53 2.00 40.55 4.81
638 649 3.181497 CCCAGCAGACATAAAAATCACCG 60.181 47.826 0.00 0.00 0.00 4.94
641 652 2.760092 GGCCCAGCAGACATAAAAATCA 59.240 45.455 0.00 0.00 0.00 2.57
661 674 4.473520 AGCATCTCCCGCGGTTGG 62.474 66.667 26.12 13.50 0.00 3.77
681 698 1.201424 GGTAGAACCTCCCGGTGATT 58.799 55.000 0.00 0.00 44.73 2.57
694 711 0.242825 CCGACAAGTGAGCGGTAGAA 59.757 55.000 0.00 0.00 40.17 2.10
831 848 6.976925 GGAATTGAATGGATAAGCTCAACAAG 59.023 38.462 0.00 0.00 31.00 3.16
832 849 6.664816 AGGAATTGAATGGATAAGCTCAACAA 59.335 34.615 0.00 0.00 31.00 2.83
833 850 6.189859 AGGAATTGAATGGATAAGCTCAACA 58.810 36.000 0.00 0.00 31.00 3.33
849 866 3.130633 CGTCATCGCCAATAGGAATTGA 58.869 45.455 0.00 0.00 44.50 2.57
851 868 3.393800 CTCGTCATCGCCAATAGGAATT 58.606 45.455 0.00 0.00 36.29 2.17
941 962 2.126031 GGGGTCGTCGAACTGCTC 60.126 66.667 10.65 0.00 0.00 4.26
987 1008 2.094659 CGACATTGCGCCTCGAAGT 61.095 57.895 4.18 0.00 0.00 3.01
1120 1249 4.209866 GGGCGGGCATTGGGAGAT 62.210 66.667 3.27 0.00 0.00 2.75
1221 1350 2.341101 GCCGAGGGAGAAGACGTGA 61.341 63.158 0.00 0.00 0.00 4.35
1314 1443 0.865111 CAGCAACCATCACGAACGAA 59.135 50.000 0.14 0.00 0.00 3.85
1319 1448 1.227793 TGCACAGCAACCATCACGA 60.228 52.632 0.00 0.00 34.76 4.35
1320 1449 1.208358 CTGCACAGCAACCATCACG 59.792 57.895 0.00 0.00 38.41 4.35
1321 1450 0.520404 CTCTGCACAGCAACCATCAC 59.480 55.000 0.00 0.00 38.41 3.06
1322 1451 0.607217 CCTCTGCACAGCAACCATCA 60.607 55.000 0.00 0.00 38.41 3.07
1348 1477 0.250467 ACTTGAACAGCGACAGCCAT 60.250 50.000 0.00 0.00 46.67 4.40
1507 1636 4.129148 AGGCTGGCCCGGAAATCC 62.129 66.667 0.73 0.00 39.21 3.01
1519 1648 2.352805 GGACACCCTTGGAGGCTG 59.647 66.667 0.00 0.00 32.73 4.85
1532 1661 0.614697 TGGAGCTCATTCTCGGGACA 60.615 55.000 17.19 0.00 33.98 4.02
1588 1717 5.067674 GCCAAGCACCATAACATTCATAAGA 59.932 40.000 0.00 0.00 0.00 2.10
1652 1802 3.713003 TCAGGATCACCTAGCAAAGAGA 58.287 45.455 0.00 0.00 45.94 3.10
1689 1839 1.006086 CGAATACCGCATCAACAGCA 58.994 50.000 0.00 0.00 0.00 4.41
1763 1913 1.006832 CCATGCCGTTGTAGTAGTGC 58.993 55.000 0.00 0.00 0.00 4.40
1764 1914 2.665649 TCCATGCCGTTGTAGTAGTG 57.334 50.000 0.00 0.00 0.00 2.74
1767 1936 4.839121 AGAAAATCCATGCCGTTGTAGTA 58.161 39.130 0.00 0.00 0.00 1.82
1788 1959 3.119708 GCCACTGCCACATAGAAAGAAAG 60.120 47.826 0.00 0.00 0.00 2.62
1792 1963 2.119801 AGCCACTGCCACATAGAAAG 57.880 50.000 0.00 0.00 38.69 2.62
1793 1964 2.584835 AAGCCACTGCCACATAGAAA 57.415 45.000 0.00 0.00 38.69 2.52
1804 1975 8.085296 CCTACAGAAGATATAAGTAAGCCACTG 58.915 40.741 0.00 0.00 37.63 3.66
1866 2045 6.954102 TGCTTATATATACCTCCTTGCTCTCA 59.046 38.462 0.00 0.00 0.00 3.27
1889 2068 6.745116 AGGTGATAAAAGTGTAAAAACCTGC 58.255 36.000 0.00 0.00 34.30 4.85
1924 2107 6.065976 AGATATGTCCAAGATCAACAACCA 57.934 37.500 0.00 0.00 0.00 3.67
2165 2356 7.265599 TGAAGGAGGTGTATTTCAGGAAATA 57.734 36.000 9.75 9.75 40.99 1.40
2166 2357 6.139679 TGAAGGAGGTGTATTTCAGGAAAT 57.860 37.500 11.59 11.59 42.95 2.17
2170 2361 5.945784 TCAAATGAAGGAGGTGTATTTCAGG 59.054 40.000 0.00 0.00 33.53 3.86
2172 2363 9.699410 ATTATCAAATGAAGGAGGTGTATTTCA 57.301 29.630 0.00 0.00 34.42 2.69
2564 2757 7.715249 TCAGCAAAAGATGACCCTTACATATAC 59.285 37.037 0.00 0.00 0.00 1.47
2569 2877 4.326826 CTCAGCAAAAGATGACCCTTACA 58.673 43.478 0.00 0.00 0.00 2.41
2574 2882 1.538047 TGCTCAGCAAAAGATGACCC 58.462 50.000 0.00 0.00 34.76 4.46
2608 2916 3.504863 TGCGTAGACGTACCTGAAATTC 58.495 45.455 3.73 0.00 42.22 2.17
2689 2997 6.430616 CGGGGTAAACTAGTTTTGGATTGTAA 59.569 38.462 25.07 1.96 34.23 2.41
2880 3188 0.457851 CCCGAGAGTCTCCATCACAC 59.542 60.000 14.61 0.00 0.00 3.82
3040 3348 9.529325 GTACATAGCTCATACTGTTCACAAATA 57.471 33.333 0.00 0.00 0.00 1.40
3041 3349 8.040727 TGTACATAGCTCATACTGTTCACAAAT 58.959 33.333 0.00 0.00 0.00 2.32
3042 3350 7.382898 TGTACATAGCTCATACTGTTCACAAA 58.617 34.615 0.00 0.00 0.00 2.83
3151 3459 3.557207 CAGAGTTTGCAGTGTTGGC 57.443 52.632 0.00 0.00 0.00 4.52
3244 3552 7.669722 TCAAACTAAAGGGTGCAGAATAATCTT 59.330 33.333 0.00 0.00 32.03 2.40
3253 3561 4.142381 GGCTAATCAAACTAAAGGGTGCAG 60.142 45.833 0.00 0.00 0.00 4.41
3295 3603 7.671398 TGGGAAAAAGAGAGAAAATTAGCTGAT 59.329 33.333 0.00 0.00 0.00 2.90
3341 3649 7.308229 GCTTGCTCTTTACATCAGAAAGAAAGA 60.308 37.037 11.20 0.00 41.24 2.52
3342 3650 6.800892 GCTTGCTCTTTACATCAGAAAGAAAG 59.199 38.462 0.06 3.30 41.24 2.62
3343 3651 6.262944 TGCTTGCTCTTTACATCAGAAAGAAA 59.737 34.615 0.06 0.00 41.24 2.52
3344 3652 5.764686 TGCTTGCTCTTTACATCAGAAAGAA 59.235 36.000 0.06 0.00 41.24 2.52
3345 3653 5.308014 TGCTTGCTCTTTACATCAGAAAGA 58.692 37.500 0.00 0.00 39.92 2.52
3393 3701 1.044611 CTCCACTTAGAGCCCTAGCC 58.955 60.000 0.00 0.00 41.25 3.93
3433 3741 6.806249 CACCTGAAGAAAATGCGCTATAAAAA 59.194 34.615 9.73 0.00 0.00 1.94
3547 3856 4.802876 AGAACGAGCTTTTTCAGAACAG 57.197 40.909 10.06 0.00 0.00 3.16
3563 3872 0.738975 TCGAGCCATCTGGTAGAACG 59.261 55.000 0.00 0.00 37.57 3.95
3678 3987 4.401202 ACAAACCGGATAAGCTAAATTGGG 59.599 41.667 9.46 0.00 0.00 4.12
3695 4004 5.758296 TCAAATAGATAGCATCGGACAAACC 59.242 40.000 0.00 0.00 0.00 3.27
3705 4014 9.988815 AATTAGTCTTCGTCAAATAGATAGCAT 57.011 29.630 0.00 0.00 0.00 3.79
3787 4100 4.421058 CTGACAATTGAATACTCCGACGA 58.579 43.478 13.59 0.00 0.00 4.20
3875 4188 0.033228 CTGATGGCGAGAGATGACCC 59.967 60.000 0.00 0.00 0.00 4.46
4007 4320 9.303116 AGATCTTGACCGTACAATAGATAAGAT 57.697 33.333 0.00 0.00 35.69 2.40
4023 4336 7.387643 ACAGAAGGTTAACTAAGATCTTGACC 58.612 38.462 18.47 15.71 0.00 4.02
4197 4510 3.665745 ACCAGAATGAAACCAATGCAC 57.334 42.857 0.00 0.00 39.69 4.57
4201 4514 6.351286 GCTCCATTAACCAGAATGAAACCAAT 60.351 38.462 0.00 0.00 39.69 3.16
4257 4570 6.560253 AGTAAACTAGGCTCAACAAATGTG 57.440 37.500 0.00 0.00 0.00 3.21
4307 4620 4.792087 ACCGTAAACCTGGTGCAG 57.208 55.556 0.00 0.00 37.02 4.41
4345 4658 1.242076 ACATGTTGAGCAGTCCAAGC 58.758 50.000 0.00 0.00 0.00 4.01
4761 5074 8.421673 AGAAAGAACATACTTCTAAATACGGC 57.578 34.615 0.00 0.00 0.00 5.68
4794 5107 2.128274 CACGAAAACACGACGCGG 60.128 61.111 12.47 0.00 37.03 6.46
4817 5130 1.537638 ACACAGAAAACACACACGCAA 59.462 42.857 0.00 0.00 0.00 4.85
4994 5307 6.998802 AGAACCGGAATAATATCCTTCAGAG 58.001 40.000 9.46 0.00 37.34 3.35
5009 5322 1.204941 GAAGCTGCTCTAGAACCGGAA 59.795 52.381 9.46 0.00 0.00 4.30
5013 5326 2.223479 CGAGAGAAGCTGCTCTAGAACC 60.223 54.545 24.93 10.60 44.92 3.62
5203 5516 0.687354 GGAGAGCCAGTGGTTCAAGA 59.313 55.000 25.84 0.00 35.33 3.02
5333 5652 2.504026 GCATCGTCTGCGTCGTCA 60.504 61.111 0.00 0.00 41.97 4.35
5341 5660 3.071459 GCCGTCAACGCATCGTCTG 62.071 63.158 0.00 0.00 39.99 3.51


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

AutoCloner maintained by Alex Coulton.