Multiple sequence alignment - TraesCS3B01G243400

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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 TraesCS3B01G243400 chr3B 100.000 5615 0 0 1 5615 384884539 384890153 0.000000e+00 10370.0
1 TraesCS3B01G243400 chr3B 87.288 236 21 3 461 688 384728284 384728050 1.550000e-65 261.0
2 TraesCS3B01G243400 chr3D 95.567 4579 164 26 707 5265 291757238 291761797 0.000000e+00 7295.0
3 TraesCS3B01G243400 chr3D 89.452 493 38 12 22 504 485217205 485216717 1.340000e-170 610.0
4 TraesCS3B01G243400 chr3D 92.079 101 8 0 5448 5548 378244619 378244519 5.860000e-30 143.0
5 TraesCS3B01G243400 chr3A 94.648 2560 98 14 713 3241 384310689 384313240 0.000000e+00 3932.0
6 TraesCS3B01G243400 chr3A 93.957 2085 98 16 3391 5457 384313291 384315365 0.000000e+00 3127.0
7 TraesCS3B01G243400 chr3A 92.453 106 8 0 5510 5615 384315386 384315491 9.740000e-33 152.0
8 TraesCS3B01G243400 chr2B 88.525 671 51 10 37 688 765875149 765875812 0.000000e+00 789.0
9 TraesCS3B01G243400 chr2B 87.168 226 19 3 461 678 671243644 671243421 1.210000e-61 248.0
10 TraesCS3B01G243400 chr2B 93.617 94 4 1 2875 2968 745678111 745678020 7.590000e-29 139.0
11 TraesCS3B01G243400 chr5A 86.441 708 55 27 1 688 307611238 307611924 0.000000e+00 737.0
12 TraesCS3B01G243400 chr7D 85.897 702 64 22 1 685 637921628 637922311 0.000000e+00 715.0
13 TraesCS3B01G243400 chr7D 84.353 703 78 18 1 688 116834081 116833396 0.000000e+00 660.0
14 TraesCS3B01G243400 chr7D 94.102 373 16 3 1 373 637894630 637894996 3.800000e-156 562.0
15 TraesCS3B01G243400 chr7D 85.833 120 17 0 5430 5549 386719190 386719309 1.640000e-25 128.0
16 TraesCS3B01G243400 chr4D 85.965 684 63 19 1 663 450126698 450127369 0.000000e+00 701.0
17 TraesCS3B01G243400 chr4D 88.430 121 13 1 5432 5552 57875246 57875365 1.630000e-30 145.0
18 TraesCS3B01G243400 chr4D 86.441 118 16 0 5431 5548 96905114 96905231 4.570000e-26 130.0
19 TraesCS3B01G243400 chr5B 93.333 375 19 3 1 375 474268485 474268853 2.960000e-152 549.0
20 TraesCS3B01G243400 chr5B 87.047 193 25 0 1788 1980 576520153 576520345 9.470000e-53 219.0
21 TraesCS3B01G243400 chr5B 85.816 141 12 2 2005 2137 576520441 576520581 5.860000e-30 143.0
22 TraesCS3B01G243400 chr5B 100.000 32 0 0 2532 2563 576520121 576520152 6.080000e-05 60.2
23 TraesCS3B01G243400 chr2D 93.333 375 19 3 1 375 18335992 18336360 2.960000e-152 549.0
24 TraesCS3B01G243400 chr2D 79.025 472 71 15 245 694 651005880 651005415 1.180000e-76 298.0
25 TraesCS3B01G243400 chr2D 79.095 464 68 15 245 690 512050472 512050020 5.500000e-75 292.0
26 TraesCS3B01G243400 chr2D 84.411 263 25 6 440 687 512097024 512097285 1.560000e-60 244.0
27 TraesCS3B01G243400 chr2A 85.400 500 46 17 1 476 676023581 676023085 1.410000e-135 494.0
28 TraesCS3B01G243400 chr2A 84.496 129 16 3 5421 5548 410614811 410614936 2.120000e-24 124.0
29 TraesCS3B01G243400 chr6B 86.897 435 39 6 273 691 250588645 250589077 6.580000e-129 472.0
30 TraesCS3B01G243400 chr6B 88.889 108 12 0 5442 5549 644951232 644951339 3.530000e-27 134.0
31 TraesCS3B01G243400 chr5D 80.213 470 61 14 245 686 538211158 538211623 1.950000e-84 324.0
32 TraesCS3B01G243400 chr1D 78.112 466 75 14 245 690 208432576 208433034 2.580000e-68 270.0
33 TraesCS3B01G243400 chr1D 77.944 467 68 23 245 689 42811069 42811522 5.580000e-65 259.0
34 TraesCS3B01G243400 chr1B 93.069 101 7 0 5448 5548 10548578 10548478 1.260000e-31 148.0
35 TraesCS3B01G243400 chr1A 90.654 107 10 0 5443 5549 104854425 104854319 5.860000e-30 143.0
36 TraesCS3B01G243400 chr6A 84.211 133 19 2 5429 5561 17386598 17386468 1.640000e-25 128.0


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 TraesCS3B01G243400 chr3B 384884539 384890153 5614 False 10370.000000 10370 100.000 1 5615 1 chr3B.!!$F1 5614
1 TraesCS3B01G243400 chr3D 291757238 291761797 4559 False 7295.000000 7295 95.567 707 5265 1 chr3D.!!$F1 4558
2 TraesCS3B01G243400 chr3A 384310689 384315491 4802 False 2403.666667 3932 93.686 713 5615 3 chr3A.!!$F1 4902
3 TraesCS3B01G243400 chr2B 765875149 765875812 663 False 789.000000 789 88.525 37 688 1 chr2B.!!$F1 651
4 TraesCS3B01G243400 chr5A 307611238 307611924 686 False 737.000000 737 86.441 1 688 1 chr5A.!!$F1 687
5 TraesCS3B01G243400 chr7D 637921628 637922311 683 False 715.000000 715 85.897 1 685 1 chr7D.!!$F3 684
6 TraesCS3B01G243400 chr7D 116833396 116834081 685 True 660.000000 660 84.353 1 688 1 chr7D.!!$R1 687
7 TraesCS3B01G243400 chr4D 450126698 450127369 671 False 701.000000 701 85.965 1 663 1 chr4D.!!$F3 662

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
415 427 0.477597 AAGAATGAGGTGGGTGGGGA 60.478 55.000 0.00 0.00 0.00 4.81 F
494 514 0.745845 CATGTGTGGTGCCTAGCTCC 60.746 60.000 0.00 0.76 41.88 4.70 F
1360 1410 1.507140 ATCAAGACCCGGAATAGGCA 58.493 50.000 0.73 0.00 0.00 4.75 F
1989 2047 0.679321 TATCATTTGTGGGCGCTGCA 60.679 50.000 7.64 0.55 0.00 4.41 F
3566 3645 1.479730 TGCAGACTGAGCAGATGGTAG 59.520 52.381 6.65 0.00 37.02 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1509 0.110192 GGAAAACTACACGCTGCTGC 60.110 55.0 5.34 5.34 0.00 5.25 R
1751 1809 0.906066 TCATAACTGGGCGCCTACAA 59.094 50.0 28.56 9.01 0.00 2.41 R
3270 3338 0.179124 GACGCTCAAGCCCTGTCTAG 60.179 60.0 0.00 0.00 37.91 2.43 R
3729 3810 1.019805 GTACAAGGAAGCAGCGGTCC 61.020 60.0 9.61 9.61 0.00 4.46 R
4809 4896 0.729116 CCTCGCTCGCAATGTCATTT 59.271 50.0 0.00 0.00 0.00 2.32 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
133 134 4.157840 GGTTCCACAATGACTACAAATCCC 59.842 45.833 0.00 0.00 0.00 3.85
244 245 2.690786 TGTGAACGAATTTACCGAGGG 58.309 47.619 0.00 0.00 0.00 4.30
248 249 4.393990 GTGAACGAATTTACCGAGGGAAAT 59.606 41.667 6.50 6.50 0.00 2.17
249 250 4.393680 TGAACGAATTTACCGAGGGAAATG 59.606 41.667 12.70 4.65 0.00 2.32
269 270 6.642733 AATGAAGGGATCAGAGGAGTTTAA 57.357 37.500 0.00 0.00 42.53 1.52
415 427 0.477597 AAGAATGAGGTGGGTGGGGA 60.478 55.000 0.00 0.00 0.00 4.81
419 431 3.339093 GAGGTGGGTGGGGAAGGG 61.339 72.222 0.00 0.00 0.00 3.95
422 434 2.612746 GTGGGTGGGGAAGGGCTA 60.613 66.667 0.00 0.00 0.00 3.93
494 514 0.745845 CATGTGTGGTGCCTAGCTCC 60.746 60.000 0.00 0.76 41.88 4.70
503 523 2.594882 CCTAGCTCCGAGGCGCTA 60.595 66.667 7.64 12.58 37.39 4.26
688 718 6.598850 ACAAGTCAAAATTGTCAAATTTGCCT 59.401 30.769 17.69 11.35 43.63 4.75
689 719 6.849588 AGTCAAAATTGTCAAATTTGCCTC 57.150 33.333 17.69 11.79 43.63 4.70
690 720 6.347696 AGTCAAAATTGTCAAATTTGCCTCA 58.652 32.000 17.69 9.36 43.63 3.86
691 721 6.258507 AGTCAAAATTGTCAAATTTGCCTCAC 59.741 34.615 17.69 12.09 43.63 3.51
692 722 6.258507 GTCAAAATTGTCAAATTTGCCTCACT 59.741 34.615 17.69 4.54 43.63 3.41
693 723 7.437862 GTCAAAATTGTCAAATTTGCCTCACTA 59.562 33.333 17.69 4.09 43.63 2.74
694 724 8.149647 TCAAAATTGTCAAATTTGCCTCACTAT 58.850 29.630 17.69 6.15 43.63 2.12
695 725 8.776470 CAAAATTGTCAAATTTGCCTCACTATT 58.224 29.630 13.54 11.25 43.63 1.73
696 726 9.995003 AAAATTGTCAAATTTGCCTCACTATTA 57.005 25.926 13.54 0.00 43.63 0.98
700 730 9.461312 TTGTCAAATTTGCCTCACTATTATACT 57.539 29.630 13.54 0.00 0.00 2.12
701 731 9.109393 TGTCAAATTTGCCTCACTATTATACTC 57.891 33.333 13.54 0.00 0.00 2.59
702 732 9.109393 GTCAAATTTGCCTCACTATTATACTCA 57.891 33.333 13.54 0.00 0.00 3.41
703 733 9.109393 TCAAATTTGCCTCACTATTATACTCAC 57.891 33.333 13.54 0.00 0.00 3.51
704 734 9.113838 CAAATTTGCCTCACTATTATACTCACT 57.886 33.333 5.01 0.00 0.00 3.41
705 735 8.894768 AATTTGCCTCACTATTATACTCACTC 57.105 34.615 0.00 0.00 0.00 3.51
1359 1409 2.495084 GAATCAAGACCCGGAATAGGC 58.505 52.381 0.73 0.00 0.00 3.93
1360 1410 1.507140 ATCAAGACCCGGAATAGGCA 58.493 50.000 0.73 0.00 0.00 4.75
1415 1466 3.458118 TGGTTATGGCTGTAGGTGCTAAT 59.542 43.478 0.00 0.00 0.00 1.73
1416 1467 4.656575 TGGTTATGGCTGTAGGTGCTAATA 59.343 41.667 0.00 0.00 0.00 0.98
1417 1468 5.131308 TGGTTATGGCTGTAGGTGCTAATAA 59.869 40.000 0.00 0.00 0.00 1.40
1425 1476 5.278022 GCTGTAGGTGCTAATAATTGCTTCC 60.278 44.000 0.00 0.00 0.00 3.46
1458 1509 3.728864 GCATCGACTGTAAATTGCCTGTG 60.729 47.826 0.00 0.00 0.00 3.66
1484 1535 3.067106 AGCGTGTAGTTTTCCACATCTG 58.933 45.455 0.00 0.00 0.00 2.90
1487 1538 4.772434 CGTGTAGTTTTCCACATCTGTTG 58.228 43.478 0.00 0.00 0.00 3.33
1496 1547 8.637986 AGTTTTCCACATCTGTTGCTAAATTTA 58.362 29.630 0.00 0.00 0.00 1.40
1499 1550 5.703592 TCCACATCTGTTGCTAAATTTACGT 59.296 36.000 0.00 0.00 0.00 3.57
1554 1607 4.143094 GCTTCTCGAGTTTGTTGGTATGTC 60.143 45.833 13.13 0.00 0.00 3.06
1595 1648 4.110482 CTGGTCGTATACTTGTACTTGCC 58.890 47.826 0.56 0.00 0.00 4.52
1651 1704 5.628797 TCTCCCATGTAACATAGATGCAA 57.371 39.130 0.00 0.00 0.00 4.08
1682 1735 3.555956 CGGCTTACCAGTTGATACATCAC 59.444 47.826 0.00 0.00 33.79 3.06
1748 1806 6.274579 TGTTCTTGTTGCCATATATTGCATG 58.725 36.000 11.91 4.43 37.33 4.06
1751 1809 3.574749 TGTTGCCATATATTGCATGGGT 58.425 40.909 11.91 0.00 42.79 4.51
1764 1822 4.028490 TGGGTTGTAGGCGCCCAG 62.028 66.667 26.15 0.00 46.59 4.45
1792 1850 3.848975 ACTGGAAGGAAGACCATCTCATT 59.151 43.478 0.00 0.00 39.30 2.57
1813 1871 9.429359 CTCATTAGTAGATAGGCCAGTAAATTG 57.571 37.037 5.01 0.00 0.00 2.32
1821 1879 6.493458 AGATAGGCCAGTAAATTGTTTTGTGT 59.507 34.615 5.01 0.00 0.00 3.72
1829 1887 9.319143 CCAGTAAATTGTTTTGTGTAATTCCAA 57.681 29.630 0.00 0.00 0.00 3.53
1943 2001 6.326375 CCAGATATTCTAATAGCAGACGGAC 58.674 44.000 1.27 0.00 29.96 4.79
1984 2042 4.539870 GATTCACATATCATTTGTGGGCG 58.460 43.478 8.21 0.00 43.67 6.13
1985 2043 1.675483 TCACATATCATTTGTGGGCGC 59.325 47.619 8.21 0.00 43.67 6.53
1989 2047 0.679321 TATCATTTGTGGGCGCTGCA 60.679 50.000 7.64 0.55 0.00 4.41
2116 2179 9.185680 ACTGTGTTTTCCTGTATTTTATATCCC 57.814 33.333 0.00 0.00 0.00 3.85
2153 2216 6.399639 AACCTTCGAATGAAAAAGGCTTTA 57.600 33.333 13.77 0.00 42.76 1.85
2294 2360 6.917217 ACATCGTAGTAGGTTAGTGTCTAC 57.083 41.667 0.00 0.00 36.89 2.59
2309 2375 8.475639 GTTAGTGTCTACCATTCAGGATTAGAA 58.524 37.037 0.00 0.00 41.22 2.10
2348 2414 9.871238 ACTATACTTGTCAACAATAACTACAGG 57.129 33.333 0.00 0.00 35.02 4.00
2502 2568 2.559698 TCTGCAAGAAATGGTTCCGA 57.440 45.000 0.00 0.00 42.31 4.55
2940 3006 6.093495 TGACTAAGTTGTTAATACATGCTGCC 59.907 38.462 0.00 0.00 33.44 4.85
3144 3210 1.679680 GTGCCATCACAGATTCCCATG 59.320 52.381 0.00 0.00 42.66 3.66
3187 3253 4.748892 TCTTGTGCTGTCTACTGATAAGC 58.251 43.478 0.00 0.00 36.15 3.09
3270 3338 3.071479 TCGGCAAGTCATGGTTTACTTC 58.929 45.455 0.00 0.00 33.72 3.01
3301 3369 2.046283 TGAGCGTCACAACTCTTACG 57.954 50.000 0.00 0.00 38.34 3.18
3346 3415 3.758554 ACTCAAAGCGAATTGGTGCTAAT 59.241 39.130 0.00 0.00 41.46 1.73
3352 3421 7.328249 TCAAAGCGAATTGGTGCTAATTAAAAG 59.672 33.333 0.00 0.00 41.46 2.27
3375 3444 7.486802 AGAAAATGAAAGAAAGCAATTGGTG 57.513 32.000 11.56 0.00 0.00 4.17
3472 3543 6.707161 AGCAAACTGTATGCAAACAAATGAAT 59.293 30.769 0.00 0.00 46.22 2.57
3566 3645 1.479730 TGCAGACTGAGCAGATGGTAG 59.520 52.381 6.65 0.00 37.02 3.18
3714 3795 5.484644 AGGCATCTAATCATGATCTAGCAGT 59.515 40.000 9.06 0.00 0.00 4.40
3729 3810 6.223138 TCTAGCAGTGTTAAAATGTTGACG 57.777 37.500 0.00 0.00 0.00 4.35
3745 3826 3.121030 CGGACCGCTGCTTCCTTG 61.121 66.667 0.00 0.00 0.00 3.61
3772 3853 8.521170 ACTAACATGTCTAGCTGAACTGTATA 57.479 34.615 0.00 0.00 0.00 1.47
3844 3925 8.773645 TGTTGTCATAGAATGTTTCTTACACAG 58.226 33.333 0.00 0.00 40.19 3.66
3854 3935 8.682936 AATGTTTCTTACACAGAGAAGTTGAT 57.317 30.769 0.00 0.00 40.19 2.57
4126 4210 6.424812 CAGAAAATTTCGAGGGCTCAAAATTT 59.575 34.615 9.85 9.85 34.02 1.82
4136 4220 6.018016 CGAGGGCTCAAAATTTGTTTTTCATT 60.018 34.615 5.56 0.00 35.31 2.57
4447 4533 9.265901 TCTGTTTAGATTCTTGAACAAGAGAAG 57.734 33.333 15.23 7.50 46.80 2.85
4456 4542 7.430992 TCTTGAACAAGAGAAGAATGACATG 57.569 36.000 12.40 0.00 42.06 3.21
4461 4547 5.732633 ACAAGAGAAGAATGACATGGAGAG 58.267 41.667 0.00 0.00 0.00 3.20
4542 4628 2.714808 ACTTCCCCCTGTTTACCTCTT 58.285 47.619 0.00 0.00 0.00 2.85
4543 4629 3.061369 ACTTCCCCCTGTTTACCTCTTT 58.939 45.455 0.00 0.00 0.00 2.52
4567 4653 6.396459 GTTGAAAACTATCTTCTCCAGTCG 57.604 41.667 0.00 0.00 45.32 4.18
4629 4715 6.655003 CAGGTGTTTAATCTCAGAGGCTAAAA 59.345 38.462 0.00 0.00 0.00 1.52
4809 4896 5.193124 TCTCTCTGTAGAACCACCATAGGTA 59.807 44.000 0.00 0.00 42.25 3.08
5130 5220 2.290367 TCAACATTCCTTCACAACGCTG 59.710 45.455 0.00 0.00 0.00 5.18
5134 5224 0.944386 TTCCTTCACAACGCTGCTTC 59.056 50.000 0.00 0.00 0.00 3.86
5144 5234 1.137513 ACGCTGCTTCAAGTTCGTAC 58.862 50.000 0.00 0.00 0.00 3.67
5220 5310 5.018809 ACCAGGAATTGCAATTCTATGTGT 58.981 37.500 37.77 30.06 43.33 3.72
5221 5311 5.105635 ACCAGGAATTGCAATTCTATGTGTG 60.106 40.000 37.77 26.94 43.33 3.82
5227 5317 5.868043 TTGCAATTCTATGTGTGACTCAG 57.132 39.130 0.00 0.00 0.00 3.35
5251 5341 8.706035 CAGGCTCTTCAATGTATTTTTCTTTTG 58.294 33.333 0.00 0.00 0.00 2.44
5401 5492 3.193267 GTGCACAATATCAAGAGGGCAAA 59.807 43.478 13.17 0.00 0.00 3.68
5406 5497 6.183360 GCACAATATCAAGAGGGCAAATACTT 60.183 38.462 0.00 0.00 0.00 2.24
5416 5507 4.850680 AGGGCAAATACTTGATTTCCGTA 58.149 39.130 0.00 0.00 35.45 4.02
5429 5520 8.194769 ACTTGATTTCCGTAAAACAACTGAAAT 58.805 29.630 6.21 6.21 42.41 2.17
5457 5548 7.238710 ACCCTCTTTGTCCATAAATACTTGTT 58.761 34.615 0.00 0.00 0.00 2.83
5459 5550 7.362920 CCCTCTTTGTCCATAAATACTTGTTGG 60.363 40.741 0.00 0.00 0.00 3.77
5460 5551 7.393234 CCTCTTTGTCCATAAATACTTGTTGGA 59.607 37.037 0.00 0.00 0.00 3.53
5461 5552 8.335532 TCTTTGTCCATAAATACTTGTTGGAG 57.664 34.615 0.00 0.00 0.00 3.86
5462 5553 8.160765 TCTTTGTCCATAAATACTTGTTGGAGA 58.839 33.333 0.00 0.00 0.00 3.71
5463 5554 8.698973 TTTGTCCATAAATACTTGTTGGAGAA 57.301 30.769 0.00 0.00 0.00 2.87
5464 5555 8.698973 TTGTCCATAAATACTTGTTGGAGAAA 57.301 30.769 0.00 0.00 0.00 2.52
5465 5556 8.877864 TGTCCATAAATACTTGTTGGAGAAAT 57.122 30.769 0.00 0.00 0.00 2.17
5466 5557 8.739039 TGTCCATAAATACTTGTTGGAGAAATG 58.261 33.333 0.00 0.00 0.00 2.32
5467 5558 8.190784 GTCCATAAATACTTGTTGGAGAAATGG 58.809 37.037 0.00 0.00 0.00 3.16
5468 5559 8.112822 TCCATAAATACTTGTTGGAGAAATGGA 58.887 33.333 0.00 0.00 36.53 3.41
5469 5560 8.917088 CCATAAATACTTGTTGGAGAAATGGAT 58.083 33.333 0.00 0.00 32.54 3.41
5477 5568 8.096414 ACTTGTTGGAGAAATGGATAAAAATGG 58.904 33.333 0.00 0.00 0.00 3.16
5478 5569 7.789202 TGTTGGAGAAATGGATAAAAATGGA 57.211 32.000 0.00 0.00 0.00 3.41
5479 5570 8.378115 TGTTGGAGAAATGGATAAAAATGGAT 57.622 30.769 0.00 0.00 0.00 3.41
5480 5571 9.486123 TGTTGGAGAAATGGATAAAAATGGATA 57.514 29.630 0.00 0.00 0.00 2.59
5533 5624 9.877178 ACATCTATTTCTTCGACAAGTATTTCT 57.123 29.630 0.00 0.00 0.00 2.52
5560 5651 8.865090 AGACGGAGAGAGTATGATTGATTATTT 58.135 33.333 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
133 134 8.592105 AAATTGAAATAGTGTGGTGTGATTTG 57.408 30.769 0.00 0.00 0.00 2.32
171 172 3.512724 CCCTTGATTTGCTTGGACTTGAT 59.487 43.478 0.00 0.00 0.00 2.57
176 177 2.029020 GGAACCCTTGATTTGCTTGGAC 60.029 50.000 0.00 0.00 0.00 4.02
201 202 6.925165 ACATTTGTCTCATTTAGCCAAGTTTG 59.075 34.615 0.00 0.00 0.00 2.93
244 245 4.769345 ACTCCTCTGATCCCTTCATTTC 57.231 45.455 0.00 0.00 32.72 2.17
248 249 5.094387 AGTTAAACTCCTCTGATCCCTTCA 58.906 41.667 0.00 0.00 0.00 3.02
249 250 5.685520 AGTTAAACTCCTCTGATCCCTTC 57.314 43.478 0.00 0.00 0.00 3.46
269 270 3.393426 TCCCTAATCCCTCGTACAAGT 57.607 47.619 0.00 0.00 0.00 3.16
432 446 3.339253 TGCACTGTGACTTAGATGCAT 57.661 42.857 12.86 0.00 38.11 3.96
528 556 1.435515 GCGTTGCACCTTTGTCCAA 59.564 52.632 0.00 0.00 0.00 3.53
588 616 1.550869 CCTTTTTGAGGGGTGCCTGAT 60.551 52.381 0.00 0.00 42.26 2.90
696 726 8.532819 CCTCCAAGTTACTTTTAGAGTGAGTAT 58.467 37.037 12.58 0.00 39.48 2.12
697 727 7.727186 TCCTCCAAGTTACTTTTAGAGTGAGTA 59.273 37.037 12.58 0.00 39.48 2.59
698 728 6.553852 TCCTCCAAGTTACTTTTAGAGTGAGT 59.446 38.462 12.58 0.00 39.48 3.41
699 729 6.994221 TCCTCCAAGTTACTTTTAGAGTGAG 58.006 40.000 12.58 4.52 39.48 3.51
700 730 6.989155 TCCTCCAAGTTACTTTTAGAGTGA 57.011 37.500 12.58 8.51 39.48 3.41
701 731 9.372369 CTTATCCTCCAAGTTACTTTTAGAGTG 57.628 37.037 12.58 7.01 39.48 3.51
702 732 9.322769 TCTTATCCTCCAAGTTACTTTTAGAGT 57.677 33.333 12.58 0.00 42.55 3.24
1359 1409 0.670162 CAAGTGCAGGGGTTCAGTTG 59.330 55.000 0.00 0.00 37.31 3.16
1360 1410 0.468029 CCAAGTGCAGGGGTTCAGTT 60.468 55.000 0.00 0.00 0.00 3.16
1365 1416 1.357272 TACCACCAAGTGCAGGGGTT 61.357 55.000 2.55 0.00 33.53 4.11
1415 1466 4.881920 GCTTTTGGAACTGGAAGCAATTA 58.118 39.130 2.37 0.00 42.94 1.40
1416 1467 3.732212 GCTTTTGGAACTGGAAGCAATT 58.268 40.909 2.37 0.00 42.94 2.32
1417 1468 3.391506 GCTTTTGGAACTGGAAGCAAT 57.608 42.857 2.37 0.00 42.94 3.56
1425 1476 2.549754 ACAGTCGATGCTTTTGGAACTG 59.450 45.455 0.00 0.00 0.00 3.16
1458 1509 0.110192 GGAAAACTACACGCTGCTGC 60.110 55.000 5.34 5.34 0.00 5.25
1509 1560 6.779860 AGCTTCTACTGGTTAAAGAAATGGA 58.220 36.000 0.00 0.00 0.00 3.41
1519 1570 4.333690 ACTCGAGAAGCTTCTACTGGTTA 58.666 43.478 28.53 8.45 37.73 2.85
1554 1607 2.962421 CAGACCCCTCTCTAGGCTTAAG 59.038 54.545 0.00 0.00 42.14 1.85
1595 1648 9.755804 TTATATTTCAGATACTTCACAGCTCTG 57.244 33.333 0.00 0.00 35.67 3.35
1632 1685 5.532032 TCACATTGCATCTATGTTACATGGG 59.468 40.000 8.26 1.26 34.11 4.00
1651 1704 4.100963 TCAACTGGTAAGCCGATATCACAT 59.899 41.667 3.12 0.00 37.67 3.21
1682 1735 7.966753 CCATCAATGACACTACTGAAAATCTTG 59.033 37.037 0.00 0.00 0.00 3.02
1748 1806 2.187896 TAACTGGGCGCCTACAACCC 62.188 60.000 28.56 8.18 44.52 4.11
1751 1809 0.906066 TCATAACTGGGCGCCTACAA 59.094 50.000 28.56 9.01 0.00 2.41
1764 1822 4.553330 TGGTCTTCCTTCCAGTCATAAC 57.447 45.455 0.00 0.00 34.23 1.89
1792 1850 9.391006 CAAAACAATTTACTGGCCTATCTACTA 57.609 33.333 3.32 0.00 0.00 1.82
1829 1887 8.768955 GCTCACGATATCTTTCTGAATTACAAT 58.231 33.333 0.34 0.00 0.00 2.71
1943 2001 3.290948 TCGGGTGGATTAATTCCCTTG 57.709 47.619 16.68 7.37 44.77 3.61
1984 2042 3.190337 CAAGTGCTTTCCTTGCAGC 57.810 52.632 0.00 0.00 41.41 5.25
2046 2109 2.363306 TCCAAAAGGCTTGAAGCAGA 57.637 45.000 19.89 2.64 44.75 4.26
2153 2216 4.353788 TGGCATTATCTATAAAGTGGGGCT 59.646 41.667 0.00 0.00 0.00 5.19
2294 2360 7.340232 TGGAAACTGAATTCTAATCCTGAATGG 59.660 37.037 7.05 0.00 34.74 3.16
2309 2375 7.450074 TGACAAGTATAGTGTGGAAACTGAAT 58.550 34.615 0.00 0.00 0.00 2.57
2348 2414 2.156098 TCGGTAGCATGGTTTTGGTTC 58.844 47.619 1.12 0.00 0.00 3.62
2500 2566 4.737054 AGCATGGAAGCAAAGTTAAATCG 58.263 39.130 0.00 0.00 36.85 3.34
2502 2568 5.934043 GGAAAGCATGGAAGCAAAGTTAAAT 59.066 36.000 0.00 0.00 36.85 1.40
2822 2888 8.706322 ACAAAATGTACAGGACTCCTTATTTT 57.294 30.769 0.33 4.52 0.00 1.82
2940 3006 5.350365 CCATCCATTGCTTCAAAGTTCATTG 59.650 40.000 0.00 0.00 0.00 2.82
3144 3210 6.951256 AGAACAGCAGAAAACTTTCAAAAC 57.049 33.333 5.07 0.00 39.61 2.43
3270 3338 0.179124 GACGCTCAAGCCCTGTCTAG 60.179 60.000 0.00 0.00 37.91 2.43
3327 3396 6.942886 TTTAATTAGCACCAATTCGCTTTG 57.057 33.333 0.00 0.00 39.70 2.77
3328 3397 7.375053 TCTTTTAATTAGCACCAATTCGCTTT 58.625 30.769 0.00 0.00 39.70 3.51
3439 3510 3.569277 TGCATACAGTTTGCTCAATGTGT 59.431 39.130 15.91 2.27 40.77 3.72
3440 3511 4.163458 TGCATACAGTTTGCTCAATGTG 57.837 40.909 15.91 0.00 40.77 3.21
3442 3513 4.983538 TGTTTGCATACAGTTTGCTCAATG 59.016 37.500 15.91 0.00 40.77 2.82
3532 3611 3.087031 AGTCTGCATTGGGAAACATGAG 58.913 45.455 0.00 0.00 0.00 2.90
3566 3645 5.465056 GCATATCTCTGCTCCAAACTAAGTC 59.535 44.000 0.00 0.00 39.12 3.01
3618 3697 4.039488 TCCAAGTTGCAGCAATCATTCTTT 59.961 37.500 11.96 0.00 0.00 2.52
3714 3795 2.031857 GCGGTCCGTCAACATTTTAACA 60.032 45.455 13.94 0.00 0.00 2.41
3729 3810 1.019805 GTACAAGGAAGCAGCGGTCC 61.020 60.000 9.61 9.61 0.00 4.46
3745 3826 6.622549 ACAGTTCAGCTAGACATGTTAGTAC 58.377 40.000 0.00 0.00 0.00 2.73
3844 3925 3.378427 GGCCATGTGGTTATCAACTTCTC 59.622 47.826 0.00 0.00 37.57 2.87
3854 3935 1.487300 TACGCTAGGCCATGTGGTTA 58.513 50.000 5.01 0.00 37.57 2.85
3945 4026 5.931294 TCACTCGATCTATAGACAGGACTT 58.069 41.667 4.10 0.00 0.00 3.01
4136 4220 4.215399 GCCAGCAAGTCAGTTTATTACACA 59.785 41.667 0.00 0.00 0.00 3.72
4302 4386 9.646522 AACAATTAGATAAGCCAGGTCAAATAT 57.353 29.630 0.00 0.00 0.00 1.28
4447 4533 6.578023 ACTACTTAAGCTCTCCATGTCATTC 58.422 40.000 1.29 0.00 0.00 2.67
4456 4542 6.193514 AGTTCGTTACTACTTAAGCTCTCC 57.806 41.667 1.29 0.00 34.56 3.71
4514 4600 1.815757 ACAGGGGGAAGTAACTGTGT 58.184 50.000 0.00 0.00 42.14 3.72
4518 4604 3.586174 GAGGTAAACAGGGGGAAGTAACT 59.414 47.826 0.00 0.00 0.00 2.24
4542 4628 6.423905 CGACTGGAGAAGATAGTTTTCAACAA 59.576 38.462 0.00 0.00 0.00 2.83
4543 4629 5.926542 CGACTGGAGAAGATAGTTTTCAACA 59.073 40.000 0.00 0.00 0.00 3.33
4594 4680 5.561679 AGATTAAACACCTGAAGGAAGGAC 58.438 41.667 2.62 0.00 40.02 3.85
4809 4896 0.729116 CCTCGCTCGCAATGTCATTT 59.271 50.000 0.00 0.00 0.00 2.32
5004 5092 4.851010 ACAGCTTGCAAAAATCAAAATGC 58.149 34.783 0.00 0.00 39.22 3.56
5130 5220 5.539207 CATTACTTCGTACGAACTTGAAGC 58.461 41.667 26.00 0.00 41.11 3.86
5134 5224 5.275788 GCTAGCATTACTTCGTACGAACTTG 60.276 44.000 26.00 19.80 0.00 3.16
5144 5234 4.864916 AACACATGCTAGCATTACTTCG 57.135 40.909 27.59 17.03 33.90 3.79
5158 5248 3.614092 ACTCCTCTATGCCAAACACATG 58.386 45.455 0.00 0.00 0.00 3.21
5220 5310 5.426689 AATACATTGAAGAGCCTGAGTCA 57.573 39.130 0.00 0.00 0.00 3.41
5221 5311 6.749923 AAAATACATTGAAGAGCCTGAGTC 57.250 37.500 0.00 0.00 0.00 3.36
5227 5317 8.593492 ACAAAAGAAAAATACATTGAAGAGCC 57.407 30.769 0.00 0.00 0.00 4.70
5401 5492 8.385898 TCAGTTGTTTTACGGAAATCAAGTAT 57.614 30.769 19.22 7.02 36.45 2.12
5416 5507 9.143155 ACAAAGAGGGTATATTTCAGTTGTTTT 57.857 29.630 0.00 0.00 0.00 2.43
5434 5525 7.393234 TCCAACAAGTATTTATGGACAAAGAGG 59.607 37.037 1.81 0.00 35.33 3.69
5507 5598 9.877178 AGAAATACTTGTCGAAGAAATAGATGT 57.123 29.630 0.00 0.00 39.69 3.06
5512 5603 9.499585 CGTCTAGAAATACTTGTCGAAGAAATA 57.500 33.333 0.00 0.00 39.69 1.40
5515 5606 6.149973 TCCGTCTAGAAATACTTGTCGAAGAA 59.850 38.462 0.00 0.00 39.69 2.52
5519 5610 5.181009 TCTCCGTCTAGAAATACTTGTCGA 58.819 41.667 0.00 0.00 35.86 4.20
5533 5624 9.521841 AATAATCAATCATACTCTCTCCGTCTA 57.478 33.333 0.00 0.00 0.00 2.59
5534 5625 8.415950 AATAATCAATCATACTCTCTCCGTCT 57.584 34.615 0.00 0.00 0.00 4.18
5584 5675 3.627395 AAGGGTCGAAGTGCATATCAA 57.373 42.857 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.