Multiple sequence alignment - TraesCS5D01G175900

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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 TraesCS5D01G175900 chr5D 100.000 2549 0 0 1 2549 275988952 275986404 0.000000e+00 4708
1 TraesCS5D01G175900 chr5D 93.040 546 37 1 2004 2549 118066407 118066951 0.000000e+00 797
2 TraesCS5D01G175900 chr5D 92.870 547 36 3 2004 2549 521868964 521869508 0.000000e+00 791
3 TraesCS5D01G175900 chr5A 93.866 864 42 3 562 1416 364572324 364571463 0.000000e+00 1291
4 TraesCS5D01G175900 chr5A 92.295 597 29 9 1418 2004 364565092 364564503 0.000000e+00 832
5 TraesCS5D01G175900 chr2B 95.336 536 20 3 1 533 69363123 69363656 0.000000e+00 846
6 TraesCS5D01G175900 chr2B 91.304 207 17 1 326 532 564873667 564873872 5.370000e-72 281
7 TraesCS5D01G175900 chr2B 91.626 203 15 2 326 528 217716328 217716528 1.930000e-71 279
8 TraesCS5D01G175900 chr1B 94.766 535 22 5 1 532 627469016 627468485 0.000000e+00 828
9 TraesCS5D01G175900 chr4D 94.413 537 23 4 1 532 420964338 420963804 0.000000e+00 819
10 TraesCS5D01G175900 chr1D 93.566 544 34 1 2005 2547 202951223 202951766 0.000000e+00 809
11 TraesCS5D01G175900 chr1D 93.223 546 37 0 2004 2549 3553729 3554274 0.000000e+00 804
12 TraesCS5D01G175900 chr1D 93.530 541 25 5 1 532 460540335 460539796 0.000000e+00 797
13 TraesCS5D01G175900 chr1D 92.844 545 37 2 2005 2549 46358475 46359017 0.000000e+00 789
14 TraesCS5D01G175900 chr6D 93.211 545 36 1 2005 2549 363024926 363025469 0.000000e+00 800
15 TraesCS5D01G175900 chr6D 93.211 545 35 2 2006 2549 428548924 428549467 0.000000e+00 800
16 TraesCS5D01G175900 chr6D 93.053 547 36 2 2004 2549 346459525 346460070 0.000000e+00 798
17 TraesCS5D01G175900 chr7D 92.870 547 38 1 2004 2549 15394160 15394706 0.000000e+00 793
18 TraesCS5D01G175900 chr3D 93.396 212 12 2 326 536 437681609 437681819 1.900000e-81 313
19 TraesCS5D01G175900 chr7A 90.686 204 18 1 326 529 143098150 143097948 1.160000e-68 270
20 TraesCS5D01G175900 chr1A 90.338 207 19 1 326 532 499836935 499837140 1.160000e-68 270


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 TraesCS5D01G175900 chr5D 275986404 275988952 2548 True 4708 4708 100.000 1 2549 1 chr5D.!!$R1 2548
1 TraesCS5D01G175900 chr5D 118066407 118066951 544 False 797 797 93.040 2004 2549 1 chr5D.!!$F1 545
2 TraesCS5D01G175900 chr5D 521868964 521869508 544 False 791 791 92.870 2004 2549 1 chr5D.!!$F2 545
3 TraesCS5D01G175900 chr5A 364571463 364572324 861 True 1291 1291 93.866 562 1416 1 chr5A.!!$R2 854
4 TraesCS5D01G175900 chr5A 364564503 364565092 589 True 832 832 92.295 1418 2004 1 chr5A.!!$R1 586
5 TraesCS5D01G175900 chr2B 69363123 69363656 533 False 846 846 95.336 1 533 1 chr2B.!!$F1 532
6 TraesCS5D01G175900 chr1B 627468485 627469016 531 True 828 828 94.766 1 532 1 chr1B.!!$R1 531
7 TraesCS5D01G175900 chr4D 420963804 420964338 534 True 819 819 94.413 1 532 1 chr4D.!!$R1 531
8 TraesCS5D01G175900 chr1D 202951223 202951766 543 False 809 809 93.566 2005 2547 1 chr1D.!!$F3 542
9 TraesCS5D01G175900 chr1D 3553729 3554274 545 False 804 804 93.223 2004 2549 1 chr1D.!!$F1 545
10 TraesCS5D01G175900 chr1D 460539796 460540335 539 True 797 797 93.530 1 532 1 chr1D.!!$R1 531
11 TraesCS5D01G175900 chr1D 46358475 46359017 542 False 789 789 92.844 2005 2549 1 chr1D.!!$F2 544
12 TraesCS5D01G175900 chr6D 363024926 363025469 543 False 800 800 93.211 2005 2549 1 chr6D.!!$F2 544
13 TraesCS5D01G175900 chr6D 428548924 428549467 543 False 800 800 93.211 2006 2549 1 chr6D.!!$F3 543
14 TraesCS5D01G175900 chr6D 346459525 346460070 545 False 798 798 93.053 2004 2549 1 chr6D.!!$F1 545
15 TraesCS5D01G175900 chr7D 15394160 15394706 546 False 793 793 92.870 2004 2549 1 chr7D.!!$F1 545

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
537 548 0.110599 CTATCGCCGCACTCGACTAG 60.111 60.0 0.0 0.0 38.88 2.57 F
1311 1331 0.038159 AGCTGTACGAAGTGCTCCAC 60.038 55.0 0.0 0.0 45.46 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1449 1469 1.066587 GTCCCTGCGGATCTCTTCG 59.933 63.158 0.0 0.0 41.4 3.79 R
2329 2360 2.306805 AGCACTGAAGATGGATTGGTGA 59.693 45.455 0.0 0.0 0.0 4.02 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
75 77 6.580963 TTTTGACGTGGATGAACATTTTTG 57.419 33.333 0.00 0.00 0.00 2.44
144 154 5.986501 TGAAAAATAGTAACGGGGCATTT 57.013 34.783 0.00 0.00 0.00 2.32
289 300 0.611200 CGGTGTATGTTCCTCCCACA 59.389 55.000 0.00 0.00 0.00 4.17
339 350 1.599071 CTGTGCATGCCGGTTATGTAG 59.401 52.381 16.68 12.08 0.00 2.74
433 444 2.963101 CCTTCTACGGTGATACATCCCA 59.037 50.000 0.00 0.00 0.00 4.37
435 446 1.951602 TCTACGGTGATACATCCCACG 59.048 52.381 0.00 0.00 34.30 4.94
441 452 1.598130 GATACATCCCACGCTGCCC 60.598 63.158 0.00 0.00 0.00 5.36
457 468 1.966762 CCCGCTGAAGGCAATTGTT 59.033 52.632 7.40 0.00 41.91 2.83
487 498 0.460284 GTCGATGTCCAGTTCGCCAT 60.460 55.000 0.00 0.00 35.39 4.40
533 544 3.023118 CTCTATCGCCGCACTCGA 58.977 61.111 0.00 0.00 40.45 4.04
534 545 1.369448 CTCTATCGCCGCACTCGAC 60.369 63.158 0.00 0.00 38.88 4.20
535 546 1.777030 CTCTATCGCCGCACTCGACT 61.777 60.000 0.00 0.00 38.88 4.18
536 547 0.531311 TCTATCGCCGCACTCGACTA 60.531 55.000 0.00 0.00 38.88 2.59
537 548 0.110599 CTATCGCCGCACTCGACTAG 60.111 60.000 0.00 0.00 38.88 2.57
538 549 0.812811 TATCGCCGCACTCGACTAGT 60.813 55.000 0.00 0.00 38.88 2.57
545 556 4.845811 ACTCGACTAGTGCCCTGT 57.154 55.556 0.00 0.00 36.93 4.00
546 557 3.053146 ACTCGACTAGTGCCCTGTT 57.947 52.632 0.00 0.00 36.93 3.16
547 558 1.339097 ACTCGACTAGTGCCCTGTTT 58.661 50.000 0.00 0.00 36.93 2.83
548 559 1.692519 ACTCGACTAGTGCCCTGTTTT 59.307 47.619 0.00 0.00 36.93 2.43
549 560 2.288886 ACTCGACTAGTGCCCTGTTTTC 60.289 50.000 0.00 0.00 36.93 2.29
550 561 1.968493 TCGACTAGTGCCCTGTTTTCT 59.032 47.619 0.00 0.00 0.00 2.52
551 562 3.159472 TCGACTAGTGCCCTGTTTTCTA 58.841 45.455 0.00 0.00 0.00 2.10
552 563 3.057033 TCGACTAGTGCCCTGTTTTCTAC 60.057 47.826 0.00 0.00 0.00 2.59
553 564 3.056749 CGACTAGTGCCCTGTTTTCTACT 60.057 47.826 0.00 0.00 0.00 2.57
554 565 4.157289 CGACTAGTGCCCTGTTTTCTACTA 59.843 45.833 0.00 0.00 0.00 1.82
555 566 5.652518 GACTAGTGCCCTGTTTTCTACTAG 58.347 45.833 0.00 0.00 41.88 2.57
556 567 3.336138 AGTGCCCTGTTTTCTACTAGC 57.664 47.619 0.00 0.00 0.00 3.42
557 568 2.000447 GTGCCCTGTTTTCTACTAGCG 59.000 52.381 0.00 0.00 0.00 4.26
558 569 1.066430 TGCCCTGTTTTCTACTAGCGG 60.066 52.381 0.00 0.00 0.00 5.52
559 570 1.066358 GCCCTGTTTTCTACTAGCGGT 60.066 52.381 0.00 0.00 0.00 5.68
560 571 2.167075 GCCCTGTTTTCTACTAGCGGTA 59.833 50.000 0.00 0.00 0.00 4.02
575 586 1.001158 GCGGTAGTAGCATCACTCTCC 60.001 57.143 0.00 0.00 34.19 3.71
589 600 1.006878 ACTCTCCCACCTACTGTACCC 59.993 57.143 0.00 0.00 0.00 3.69
590 601 0.337428 TCTCCCACCTACTGTACCCC 59.663 60.000 0.00 0.00 0.00 4.95
597 608 0.611714 CCTACTGTACCCCGCAAAGT 59.388 55.000 0.00 0.00 0.00 2.66
598 609 1.674817 CCTACTGTACCCCGCAAAGTG 60.675 57.143 0.00 0.00 0.00 3.16
700 711 9.888878 CTGTCCAATTAAATGTGAGCTATATTG 57.111 33.333 0.00 0.00 0.00 1.90
748 759 1.455248 TTTCCCCATTTCTTACCGCG 58.545 50.000 0.00 0.00 0.00 6.46
754 765 2.032924 CCCATTTCTTACCGCGGATTTC 59.967 50.000 35.90 0.00 0.00 2.17
769 780 4.917998 GCGGATTTCAGAACTTTCCTTTTC 59.082 41.667 5.02 0.00 0.00 2.29
776 787 2.033424 AGAACTTTCCTTTTCTGCGCAC 59.967 45.455 5.66 0.00 30.65 5.34
777 788 0.307760 ACTTTCCTTTTCTGCGCACG 59.692 50.000 5.66 2.75 0.00 5.34
778 789 0.998727 CTTTCCTTTTCTGCGCACGC 60.999 55.000 5.66 8.33 42.35 5.34
804 815 0.736053 GCTCACTCTCTCACCTACCG 59.264 60.000 0.00 0.00 0.00 4.02
822 833 1.078759 CGTCTACCGAGCAAAGCAGG 61.079 60.000 0.00 0.00 39.56 4.85
906 917 7.321271 CGCGCTACCTATAATTTCATTTCAAAG 59.679 37.037 5.56 0.00 0.00 2.77
950 970 2.091885 CGGTACCTACCTACCCACCTAA 60.092 54.545 10.90 0.00 44.25 2.69
953 973 2.013777 ACCTACCTACCCACCTAACCT 58.986 52.381 0.00 0.00 0.00 3.50
964 984 4.140782 ACCCACCTAACCTCTTTCCATTTT 60.141 41.667 0.00 0.00 0.00 1.82
965 985 4.838423 CCCACCTAACCTCTTTCCATTTTT 59.162 41.667 0.00 0.00 0.00 1.94
966 986 6.014012 CCCACCTAACCTCTTTCCATTTTTA 58.986 40.000 0.00 0.00 0.00 1.52
984 1004 7.758076 CCATTTTTATTTCGAAAGGTAGGGTTC 59.242 37.037 16.80 0.00 0.00 3.62
1061 1081 0.467384 CACGGAGGGCTGAAGATCAT 59.533 55.000 0.00 0.00 0.00 2.45
1142 1162 8.660373 GTCAAAGGTCATCAGTAAAAGTATCTG 58.340 37.037 0.00 0.00 0.00 2.90
1205 1225 2.358247 GGCGGTCAACATGGTCGT 60.358 61.111 0.00 0.00 0.00 4.34
1207 1227 2.677003 GCGGTCAACATGGTCGTGG 61.677 63.158 0.00 0.00 0.00 4.94
1262 1282 3.047877 GACGCACGGGTGGGAAAG 61.048 66.667 20.75 0.00 45.10 2.62
1268 1288 1.263356 CACGGGTGGGAAAGAGAGTA 58.737 55.000 0.00 0.00 0.00 2.59
1311 1331 0.038159 AGCTGTACGAAGTGCTCCAC 60.038 55.000 0.00 0.00 45.46 4.02
1380 1400 1.349627 CGTCGCCAACATGATCAGC 59.650 57.895 0.00 0.00 0.00 4.26
1498 1518 3.079960 TCGATATGACGGCTGAAGAAC 57.920 47.619 0.00 0.00 0.00 3.01
1501 1521 2.672961 TATGACGGCTGAAGAACAGG 57.327 50.000 0.00 0.00 45.82 4.00
1507 1527 1.869690 GCTGAAGAACAGGCCGAAC 59.130 57.895 0.00 0.00 45.82 3.95
1513 1533 2.048127 AACAGGCCGAACTCGAGC 60.048 61.111 13.61 0.00 43.02 5.03
1514 1534 2.493907 GAACAGGCCGAACTCGAGCT 62.494 60.000 13.61 0.00 43.02 4.09
1516 1536 3.816524 AGGCCGAACTCGAGCTCG 61.817 66.667 30.03 30.03 43.02 5.03
1517 1537 4.117661 GGCCGAACTCGAGCTCGT 62.118 66.667 33.33 16.80 43.02 4.18
1518 1538 2.758089 GGCCGAACTCGAGCTCGTA 61.758 63.158 33.33 19.74 43.02 3.43
1519 1539 1.355916 GCCGAACTCGAGCTCGTAT 59.644 57.895 33.33 20.74 43.02 3.06
1522 1542 1.331138 CCGAACTCGAGCTCGTATTCT 59.669 52.381 32.29 19.41 43.02 2.40
1528 1552 3.242478 ACTCGAGCTCGTATTCTTCTTCG 60.242 47.826 33.33 6.41 40.80 3.79
1563 1587 3.680642 TTTTGATCGATGCTGCTTAGC 57.319 42.857 0.54 0.00 0.00 3.09
1579 1603 6.358974 TGCTTAGCTCTGCCATTACATATA 57.641 37.500 5.60 0.00 0.00 0.86
1580 1604 6.950842 TGCTTAGCTCTGCCATTACATATAT 58.049 36.000 5.60 0.00 0.00 0.86
1581 1605 6.820152 TGCTTAGCTCTGCCATTACATATATG 59.180 38.462 11.29 11.29 0.00 1.78
1582 1606 6.820656 GCTTAGCTCTGCCATTACATATATGT 59.179 38.462 21.57 21.57 44.48 2.29
1583 1607 7.981789 GCTTAGCTCTGCCATTACATATATGTA 59.018 37.037 19.51 19.51 41.97 2.29
1623 1647 7.898636 TCCTAAAATGGTGGATACTGGATTTTT 59.101 33.333 0.00 0.00 37.61 1.94
1690 1714 3.135167 CCCTTGGGAATTTCATGGAATGG 59.865 47.826 0.00 0.00 46.73 3.16
1745 1769 2.128035 CTTTATGCTAGGGCTTCGACG 58.872 52.381 0.00 0.00 39.59 5.12
1782 1806 5.291858 TGCTTATGTACTTCGAATTCTGCAG 59.708 40.000 7.63 7.63 0.00 4.41
1807 1831 4.457257 AGCAACATACTTTCTTGGAGAAGC 59.543 41.667 0.00 0.00 35.37 3.86
1823 1847 9.750125 CTTGGAGAAGCAGTAAAAAGTAAAAAT 57.250 29.630 0.00 0.00 0.00 1.82
1839 1863 8.962884 AAGTAAAAATTTCTGCCACAAAGAAT 57.037 26.923 0.00 0.00 33.79 2.40
1857 1881 3.193479 AGAATGGTTTGCGATTCTTTCCC 59.807 43.478 0.00 0.00 44.23 3.97
1877 1901 4.407621 TCCCAGCTACTATTCGAATTGGAA 59.592 41.667 20.79 5.30 0.00 3.53
2030 2060 0.423544 AGAAATGGAGGAGGACCCCT 59.576 55.000 1.40 1.40 39.77 4.79
2037 2067 4.741239 GGAGGACCCCTGGCCTCA 62.741 72.222 16.00 0.00 43.12 3.86
2038 2068 2.367512 GAGGACCCCTGGCCTCAT 60.368 66.667 9.61 0.00 41.91 2.90
2071 2101 4.108699 TGCATGCAGCCACTTTATTAAC 57.891 40.909 18.46 0.00 44.83 2.01
2157 2187 4.135306 CTGTCGCTACTCCTATCCAGTTA 58.865 47.826 0.00 0.00 0.00 2.24
2199 2229 2.916934 TGGGCCTAATACCAAACAGACT 59.083 45.455 4.53 0.00 32.89 3.24
2202 2232 4.566907 GGGCCTAATACCAAACAGACTTCA 60.567 45.833 0.84 0.00 0.00 3.02
2259 2290 2.897350 GACGCCTGCCTGGTATGC 60.897 66.667 2.08 2.08 38.35 3.14
2312 2343 2.494445 CGCCTGCCGTGTATGAGA 59.506 61.111 0.00 0.00 0.00 3.27
2510 2543 2.512286 CGACGTGCCAGATGCCAT 60.512 61.111 0.00 0.00 40.16 4.40
2512 2545 1.746615 GACGTGCCAGATGCCATGT 60.747 57.895 0.00 0.00 40.16 3.21
2520 2553 0.463295 CAGATGCCATGTCGCTCCTT 60.463 55.000 0.00 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 212 7.040755 TGCTTAAAAGAAGCTAGCAACACATTA 60.041 33.333 18.83 6.18 43.38 1.90
305 316 2.556257 TGCACAGCTAAGTTCGTTTGA 58.444 42.857 0.00 0.00 0.00 2.69
339 350 2.562298 TGACTTTGGGATGTTCCATTGC 59.438 45.455 0.00 0.00 38.64 3.56
379 390 1.002624 GGAAACAGCCCCGTCATCA 60.003 57.895 0.00 0.00 0.00 3.07
487 498 2.351244 CGCCTGCTCCTGGTAGTGA 61.351 63.158 0.00 0.00 0.00 3.41
533 544 4.081586 GCTAGTAGAAAACAGGGCACTAGT 60.082 45.833 0.00 0.00 38.36 2.57
534 545 4.434520 GCTAGTAGAAAACAGGGCACTAG 58.565 47.826 0.00 0.00 38.85 2.57
535 546 3.119245 CGCTAGTAGAAAACAGGGCACTA 60.119 47.826 0.00 0.00 0.00 2.74
536 547 2.353803 CGCTAGTAGAAAACAGGGCACT 60.354 50.000 0.00 0.00 0.00 4.40
537 548 2.000447 CGCTAGTAGAAAACAGGGCAC 59.000 52.381 0.00 0.00 0.00 5.01
538 549 1.066430 CCGCTAGTAGAAAACAGGGCA 60.066 52.381 0.00 0.00 0.00 5.36
539 550 1.066358 ACCGCTAGTAGAAAACAGGGC 60.066 52.381 0.00 0.00 0.00 5.19
550 561 4.063689 GAGTGATGCTACTACCGCTAGTA 58.936 47.826 0.00 0.00 34.79 1.82
551 562 2.879646 GAGTGATGCTACTACCGCTAGT 59.120 50.000 0.00 0.00 37.04 2.57
552 563 3.142951 AGAGTGATGCTACTACCGCTAG 58.857 50.000 0.00 0.00 0.00 3.42
553 564 3.139850 GAGAGTGATGCTACTACCGCTA 58.860 50.000 0.00 0.00 0.00 4.26
554 565 1.950909 GAGAGTGATGCTACTACCGCT 59.049 52.381 0.00 0.00 0.00 5.52
555 566 1.001158 GGAGAGTGATGCTACTACCGC 60.001 57.143 0.00 0.00 0.00 5.68
556 567 1.609555 GGGAGAGTGATGCTACTACCG 59.390 57.143 0.00 0.00 31.95 4.02
557 568 2.362717 GTGGGAGAGTGATGCTACTACC 59.637 54.545 0.00 0.00 0.00 3.18
558 569 2.362717 GGTGGGAGAGTGATGCTACTAC 59.637 54.545 0.00 0.00 0.00 2.73
559 570 2.245028 AGGTGGGAGAGTGATGCTACTA 59.755 50.000 0.00 0.00 0.00 1.82
560 571 1.007721 AGGTGGGAGAGTGATGCTACT 59.992 52.381 0.00 0.00 0.00 2.57
565 576 2.461695 ACAGTAGGTGGGAGAGTGATG 58.538 52.381 0.00 0.00 0.00 3.07
575 586 1.546589 TTGCGGGGTACAGTAGGTGG 61.547 60.000 0.00 0.00 0.00 4.61
597 608 4.336280 AGTATATACTCATCGCAGGCTCA 58.664 43.478 9.71 0.00 0.00 4.26
598 609 4.974368 AGTATATACTCATCGCAGGCTC 57.026 45.455 9.71 0.00 0.00 4.70
778 789 1.226547 GAGAGAGTGAGCGCTTCCG 60.227 63.158 13.26 0.00 37.57 4.30
784 795 0.736053 GGTAGGTGAGAGAGTGAGCG 59.264 60.000 0.00 0.00 0.00 5.03
804 815 1.362406 GCCTGCTTTGCTCGGTAGAC 61.362 60.000 0.00 0.00 0.00 2.59
906 917 2.818274 GATCGTGTGAACGGGGGC 60.818 66.667 0.00 0.00 0.00 5.80
950 970 8.088365 CCTTTCGAAATAAAAATGGAAAGAGGT 58.912 33.333 11.70 0.00 41.59 3.85
964 984 4.020307 ACGGAACCCTACCTTTCGAAATAA 60.020 41.667 11.70 0.00 0.00 1.40
965 985 3.515104 ACGGAACCCTACCTTTCGAAATA 59.485 43.478 11.70 0.91 0.00 1.40
966 986 2.303890 ACGGAACCCTACCTTTCGAAAT 59.696 45.455 11.70 0.00 0.00 2.17
974 994 3.387947 CCGCACGGAACCCTACCT 61.388 66.667 2.01 0.00 37.50 3.08
1037 1057 4.704103 TCAGCCCTCCGTGCTCCT 62.704 66.667 0.00 0.00 36.81 3.69
1050 1070 1.859703 CTGACGAGCATGATCTTCAGC 59.140 52.381 27.70 6.51 38.33 4.26
1142 1162 4.849329 CGTCGGTGAGGTAGCCGC 62.849 72.222 0.00 0.00 46.79 6.53
1158 1178 4.829518 TCGAGCGTGATGTCGGCG 62.830 66.667 0.00 0.00 36.81 6.46
1197 1217 0.246360 TGCAGTACTCCACGACCATG 59.754 55.000 0.00 0.00 0.00 3.66
1205 1225 0.037326 CTTCCGCTTGCAGTACTCCA 60.037 55.000 0.00 0.00 0.00 3.86
1207 1227 1.362406 GCCTTCCGCTTGCAGTACTC 61.362 60.000 0.00 0.00 0.00 2.59
1236 1256 2.024868 CCCGTGCGTCATTTCGACA 61.025 57.895 0.00 0.00 45.70 4.35
1318 1338 2.107141 CTCGATCTCGGGGTTGCC 59.893 66.667 0.00 0.00 40.29 4.52
1333 1353 2.716017 CCAGGTCCACGAGCTCCTC 61.716 68.421 8.47 0.00 38.40 3.71
1369 1389 1.660560 GCCTTGCCGCTGATCATGTT 61.661 55.000 0.00 0.00 0.00 2.71
1449 1469 1.066587 GTCCCTGCGGATCTCTTCG 59.933 63.158 0.00 0.00 41.40 3.79
1498 1518 2.202676 GAGCTCGAGTTCGGCCTG 60.203 66.667 13.75 0.00 40.29 4.85
1507 1527 3.284914 CGAAGAAGAATACGAGCTCGAG 58.715 50.000 40.58 15.25 43.02 4.04
1513 1533 2.190325 ACGGCGAAGAAGAATACGAG 57.810 50.000 16.62 0.00 0.00 4.18
1514 1534 2.642139 AACGGCGAAGAAGAATACGA 57.358 45.000 16.62 0.00 0.00 3.43
1516 1536 6.817270 TGTAATAACGGCGAAGAAGAATAC 57.183 37.500 16.62 6.24 0.00 1.89
1517 1537 7.431249 AGATGTAATAACGGCGAAGAAGAATA 58.569 34.615 16.62 0.00 0.00 1.75
1518 1538 6.281405 AGATGTAATAACGGCGAAGAAGAAT 58.719 36.000 16.62 0.00 0.00 2.40
1519 1539 5.657474 AGATGTAATAACGGCGAAGAAGAA 58.343 37.500 16.62 0.00 0.00 2.52
1522 1542 6.730960 AAAAGATGTAATAACGGCGAAGAA 57.269 33.333 16.62 0.00 0.00 2.52
1528 1552 6.711579 TCGATCAAAAAGATGTAATAACGGC 58.288 36.000 0.00 0.00 37.00 5.68
1716 1740 6.013554 AGCCCTAGCATAAAGGAACAAATA 57.986 37.500 0.00 0.00 43.56 1.40
1782 1806 4.579869 TCTCCAAGAAAGTATGTTGCTCC 58.420 43.478 0.00 0.00 0.00 4.70
1797 1821 9.750125 ATTTTTACTTTTTACTGCTTCTCCAAG 57.250 29.630 0.00 0.00 0.00 3.61
1807 1831 9.092876 TGTGGCAGAAATTTTTACTTTTTACTG 57.907 29.630 0.00 0.00 0.00 2.74
1823 1847 4.440880 CAAACCATTCTTTGTGGCAGAAA 58.559 39.130 9.62 9.62 40.49 2.52
1824 1848 3.740764 GCAAACCATTCTTTGTGGCAGAA 60.741 43.478 0.00 0.00 40.49 3.02
1839 1863 1.988293 TGGGAAAGAATCGCAAACCA 58.012 45.000 0.00 0.00 46.81 3.67
1857 1881 5.692204 ACGATTCCAATTCGAATAGTAGCTG 59.308 40.000 11.83 4.68 36.64 4.24
1950 1980 7.490000 CATGGTATATCTTTATAGACCCGGAC 58.510 42.308 0.73 0.00 45.60 4.79
2071 2101 7.441157 TGACTTTGTAAGGTCTTGTGTGAATAG 59.559 37.037 8.11 0.00 34.01 1.73
2157 2187 4.285517 CCAGACTATCAGCATCCCTACATT 59.714 45.833 0.00 0.00 0.00 2.71
2199 2229 4.098914 AGATGTTAGGTTTGGCTGTGAA 57.901 40.909 0.00 0.00 0.00 3.18
2202 2232 5.246307 GTCTTAGATGTTAGGTTTGGCTGT 58.754 41.667 0.00 0.00 0.00 4.40
2252 2283 4.418328 GGTGGGTGCCGCATACCA 62.418 66.667 13.89 13.89 40.03 3.25
2304 2335 2.494445 CTGCGGCGGTCTCATACA 59.506 61.111 9.78 0.00 0.00 2.29
2329 2360 2.306805 AGCACTGAAGATGGATTGGTGA 59.693 45.455 0.00 0.00 0.00 4.02
2468 2501 4.147449 CGGGTCTCAGCGGCATGA 62.147 66.667 1.45 2.37 0.00 3.07
2520 2553 2.659244 GGTGGTGTTTCGCGTCGA 60.659 61.111 5.77 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.