Multiple sequence alignment - TraesCS3A01G215300

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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 TraesCS3A01G215300 chr3A 100.000 4454 0 0 1 4454 392798671 392803124 0.000000e+00 8226.0
1 TraesCS3A01G215300 chr3D 96.546 3474 97 8 934 4389 295140903 295144371 0.000000e+00 5729.0
2 TraesCS3A01G215300 chr3D 93.220 59 2 2 845 901 13815929 13815987 7.940000e-13 86.1
3 TraesCS3A01G215300 chr3D 91.525 59 3 2 845 901 7112335 7112393 3.690000e-11 80.5
4 TraesCS3A01G215300 chr3B 97.315 2011 54 0 1528 3538 389260682 389262692 0.000000e+00 3415.0
5 TraesCS3A01G215300 chr3B 97.033 910 25 2 3517 4426 389262740 389263647 0.000000e+00 1530.0
6 TraesCS3A01G215300 chr3B 92.433 859 45 9 1 843 2118340 2117486 0.000000e+00 1208.0
7 TraesCS3A01G215300 chr3B 93.439 442 15 5 919 1350 389260244 389260681 1.040000e-180 643.0
8 TraesCS3A01G215300 chr3B 97.222 36 1 0 4419 4454 18746176 18746211 1.340000e-05 62.1
9 TraesCS3A01G215300 chr3B 92.683 41 3 0 4414 4454 625336217 625336257 4.810000e-05 60.2
10 TraesCS3A01G215300 chr3B 100.000 30 0 0 4375 4404 389263663 389263692 6.220000e-04 56.5
11 TraesCS3A01G215300 chr7D 91.821 917 47 13 1 897 77440511 77441419 0.000000e+00 1253.0
12 TraesCS3A01G215300 chr7D 91.525 59 3 2 845 901 173609305 173609363 3.690000e-11 80.5
13 TraesCS3A01G215300 chr7D 97.297 37 0 1 4419 4454 47450455 47450491 1.340000e-05 62.1
14 TraesCS3A01G215300 chr5A 92.640 856 43 9 1 840 265554699 265555550 0.000000e+00 1214.0
15 TraesCS3A01G215300 chr4B 92.389 854 51 3 1 842 68086250 68087101 0.000000e+00 1205.0
16 TraesCS3A01G215300 chr4B 93.377 755 45 3 1 752 652894093 652894845 0.000000e+00 1112.0
17 TraesCS3A01G215300 chr4B 100.000 33 0 0 4422 4454 58761410 58761378 1.340000e-05 62.1
18 TraesCS3A01G215300 chr6B 91.967 859 49 10 2 843 179450828 179451683 0.000000e+00 1186.0
19 TraesCS3A01G215300 chr6B 92.336 809 45 7 1 793 554674088 554674895 0.000000e+00 1134.0
20 TraesCS3A01G215300 chr6B 100.000 36 0 0 4419 4454 85722312 85722347 2.880000e-07 67.6
21 TraesCS3A01G215300 chr5B 90.281 926 62 11 1 900 606902769 606903692 0.000000e+00 1186.0
22 TraesCS3A01G215300 chr5B 93.220 59 2 2 845 901 510452994 510452936 7.940000e-13 86.1
23 TraesCS3A01G215300 chr5B 100.000 34 0 0 4421 4454 584998444 584998477 3.720000e-06 63.9
24 TraesCS3A01G215300 chr7B 92.556 806 47 3 1 794 713432242 713433046 0.000000e+00 1144.0
25 TraesCS3A01G215300 chr1B 93.220 59 2 2 845 901 187202435 187202377 7.940000e-13 86.1
26 TraesCS3A01G215300 chr1B 100.000 33 0 0 4422 4454 651554671 651554639 1.340000e-05 62.1
27 TraesCS3A01G215300 chr7A 91.803 61 3 2 845 905 688024606 688024664 2.850000e-12 84.2
28 TraesCS3A01G215300 chr6D 89.231 65 6 1 845 909 270572614 270572677 3.690000e-11 80.5
29 TraesCS3A01G215300 chr4D 91.525 59 3 2 845 901 6920382 6920324 3.690000e-11 80.5
30 TraesCS3A01G215300 chr4D 91.525 59 3 2 845 901 248323086 248323028 3.690000e-11 80.5
31 TraesCS3A01G215300 chr1A 100.000 33 0 0 4422 4454 94502274 94502306 1.340000e-05 62.1
32 TraesCS3A01G215300 chr4A 100.000 32 0 0 4423 4454 2150369 2150338 4.810000e-05 60.2


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 TraesCS3A01G215300 chr3A 392798671 392803124 4453 False 8226.000 8226 100.00000 1 4454 1 chr3A.!!$F1 4453
1 TraesCS3A01G215300 chr3D 295140903 295144371 3468 False 5729.000 5729 96.54600 934 4389 1 chr3D.!!$F3 3455
2 TraesCS3A01G215300 chr3B 389260244 389263692 3448 False 1411.125 3415 96.94675 919 4426 4 chr3B.!!$F3 3507
3 TraesCS3A01G215300 chr3B 2117486 2118340 854 True 1208.000 1208 92.43300 1 843 1 chr3B.!!$R1 842
4 TraesCS3A01G215300 chr7D 77440511 77441419 908 False 1253.000 1253 91.82100 1 897 1 chr7D.!!$F2 896
5 TraesCS3A01G215300 chr5A 265554699 265555550 851 False 1214.000 1214 92.64000 1 840 1 chr5A.!!$F1 839
6 TraesCS3A01G215300 chr4B 68086250 68087101 851 False 1205.000 1205 92.38900 1 842 1 chr4B.!!$F1 841
7 TraesCS3A01G215300 chr4B 652894093 652894845 752 False 1112.000 1112 93.37700 1 752 1 chr4B.!!$F2 751
8 TraesCS3A01G215300 chr6B 179450828 179451683 855 False 1186.000 1186 91.96700 2 843 1 chr6B.!!$F2 841
9 TraesCS3A01G215300 chr6B 554674088 554674895 807 False 1134.000 1134 92.33600 1 793 1 chr6B.!!$F3 792
10 TraesCS3A01G215300 chr5B 606902769 606903692 923 False 1186.000 1186 90.28100 1 900 1 chr5B.!!$F2 899
11 TraesCS3A01G215300 chr7B 713432242 713433046 804 False 1144.000 1144 92.55600 1 794 1 chr7B.!!$F1 793

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
324 332 0.605589 AGGTAGGGCGCTGTGTTTTC 60.606 55.0 14.51 0.0 0.0 2.29 F
1635 1677 0.038251 CTGCTGAGACCGTGTTGCTA 60.038 55.0 0.00 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 1875 0.329596 GCCCTCTCTTGACCACCAAT 59.670 55.000 0.00 0.0 33.68 3.16 R
3483 3525 2.498481 CCATGGTGGCATTTCAGATTGT 59.502 45.455 2.57 0.0 0.00 2.71 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
54 55 2.676265 CCGGTAACCAGGGGAAGGG 61.676 68.421 0.00 0.00 0.00 3.95
92 93 3.680786 CACCGCCGTCTCCACTGA 61.681 66.667 0.00 0.00 0.00 3.41
197 198 2.233566 ATGGGTGAAGAGGCAGGCA 61.234 57.895 0.00 0.00 0.00 4.75
324 332 0.605589 AGGTAGGGCGCTGTGTTTTC 60.606 55.000 14.51 0.00 0.00 2.29
363 371 3.498777 TGAAAATAACATGCACCGACGAA 59.501 39.130 0.00 0.00 0.00 3.85
386 394 1.416772 AGCTAGCGGATCCCCTTAAAC 59.583 52.381 9.55 0.00 0.00 2.01
452 465 9.040939 ACGATTGATGACGTTGATAAATATTGA 57.959 29.630 0.00 0.00 39.75 2.57
542 555 3.444703 ACTACGCTCATAGGAAGCTTG 57.555 47.619 2.10 0.00 0.00 4.01
579 592 3.971245 AACAGTTTCTGCCCAAACAAA 57.029 38.095 9.57 0.00 38.53 2.83
583 596 4.020662 ACAGTTTCTGCCCAAACAAAGAAA 60.021 37.500 9.57 0.00 38.53 2.52
605 618 3.617263 AGAAAGTTATGGACGTGATTCGC 59.383 43.478 0.00 0.00 44.19 4.70
628 641 5.398416 GCAAGGAAACAAACGTTATGAAGAC 59.602 40.000 0.00 0.00 0.00 3.01
629 642 6.491394 CAAGGAAACAAACGTTATGAAGACA 58.509 36.000 0.00 0.00 0.00 3.41
633 646 7.647715 AGGAAACAAACGTTATGAAGACAAATG 59.352 33.333 0.00 0.00 0.00 2.32
757 778 1.588674 TTTCGTTGTGTGAGGCGAAT 58.411 45.000 0.00 0.00 41.85 3.34
768 789 5.221283 TGTGTGAGGCGAATATAAACCGATA 60.221 40.000 0.00 0.00 0.00 2.92
773 794 7.596248 GTGAGGCGAATATAAACCGATAAAGTA 59.404 37.037 0.00 0.00 0.00 2.24
778 799 7.605449 CGAATATAAACCGATAAAGTAGGGGA 58.395 38.462 0.00 0.00 0.00 4.81
782 803 3.409804 ACCGATAAAGTAGGGGAAGGA 57.590 47.619 0.00 0.00 0.00 3.36
861 891 2.553172 CCACGGACAAAAATAAACCCGA 59.447 45.455 0.00 0.00 40.10 5.14
865 895 4.097589 ACGGACAAAAATAAACCCGAAACA 59.902 37.500 0.00 0.00 40.10 2.83
880 910 3.005472 CCGAAACAGAGACTACCAACTGA 59.995 47.826 0.00 0.00 34.88 3.41
894 924 8.375493 ACTACCAACTGAGACATTAGGAATAA 57.625 34.615 0.00 0.00 0.00 1.40
895 925 8.478877 ACTACCAACTGAGACATTAGGAATAAG 58.521 37.037 0.00 0.00 0.00 1.73
896 926 7.496346 ACCAACTGAGACATTAGGAATAAGA 57.504 36.000 0.00 0.00 0.00 2.10
897 927 7.331791 ACCAACTGAGACATTAGGAATAAGAC 58.668 38.462 0.00 0.00 0.00 3.01
898 928 7.038302 ACCAACTGAGACATTAGGAATAAGACA 60.038 37.037 0.00 0.00 0.00 3.41
899 929 7.989741 CCAACTGAGACATTAGGAATAAGACAT 59.010 37.037 0.00 0.00 0.00 3.06
900 930 9.388506 CAACTGAGACATTAGGAATAAGACATT 57.611 33.333 0.00 0.00 0.00 2.71
903 933 9.703892 CTGAGACATTAGGAATAAGACATTAGG 57.296 37.037 0.00 0.00 0.00 2.69
904 934 9.434275 TGAGACATTAGGAATAAGACATTAGGA 57.566 33.333 0.00 0.00 0.00 2.94
919 949 8.324191 AGACATTAGGAATAGAGATTTGGTCA 57.676 34.615 0.00 0.00 0.00 4.02
920 950 8.772250 AGACATTAGGAATAGAGATTTGGTCAA 58.228 33.333 0.00 0.00 0.00 3.18
921 951 9.566432 GACATTAGGAATAGAGATTTGGTCAAT 57.434 33.333 0.00 0.00 0.00 2.57
922 952 9.927081 ACATTAGGAATAGAGATTTGGTCAATT 57.073 29.630 0.00 0.00 0.00 2.32
930 960 9.981460 AATAGAGATTTGGTCAATTTCTTAGGT 57.019 29.630 0.00 0.00 37.48 3.08
957 987 1.352156 CCTGTAAGCGTCTTCGTGGC 61.352 60.000 0.00 0.00 39.49 5.01
1344 1386 1.374125 CGACGGAATGCCACACAGA 60.374 57.895 0.00 0.00 0.00 3.41
1381 1423 1.289380 GCCCTCTTATCCGCCTACG 59.711 63.158 0.00 0.00 39.67 3.51
1416 1458 2.422231 CGAGGAGGCTCTGGACCTG 61.422 68.421 15.23 0.00 37.77 4.00
1421 1463 1.528129 GAGGCTCTGGACCTGTTTTG 58.472 55.000 7.40 0.00 37.77 2.44
1435 1477 4.097892 ACCTGTTTTGTCAGATGAACCAAC 59.902 41.667 0.00 0.00 37.61 3.77
1440 1482 9.447596 CTGTTTTGTCAGATGAACCAACAAGGT 62.448 40.741 0.00 0.00 44.59 3.50
1560 1602 3.446442 AAGTTGCAAGGTCTGGATGAT 57.554 42.857 0.00 0.00 0.00 2.45
1572 1614 0.468226 TGGATGATCCCTACGTTGGC 59.532 55.000 10.83 0.00 35.03 4.52
1594 1636 1.459592 CGTCCCTTGTTCAAGCTTACG 59.540 52.381 0.00 10.93 0.00 3.18
1598 1640 1.732259 CCTTGTTCAAGCTTACGCGAT 59.268 47.619 15.93 0.00 42.32 4.58
1601 1643 1.337354 TGTTCAAGCTTACGCGATCCA 60.337 47.619 15.93 0.00 42.32 3.41
1626 1668 2.433318 GTGGACGCTGCTGAGACC 60.433 66.667 8.60 8.60 0.00 3.85
1630 1672 3.559657 GACGCTGCTGAGACCGTGT 62.560 63.158 0.48 0.00 33.63 4.49
1635 1677 0.038251 CTGCTGAGACCGTGTTGCTA 60.038 55.000 0.00 0.00 0.00 3.49
1644 1686 2.690778 CGTGTTGCTAGGCTTGCCC 61.691 63.158 18.00 9.28 0.00 5.36
1657 1699 3.793775 TTGCCCGAACGAAGCGACA 62.794 57.895 0.00 0.00 0.00 4.35
1718 1760 1.675714 CGACTACAGAAAGGCCATGCA 60.676 52.381 5.01 0.00 0.00 3.96
1737 1779 5.132897 TGCATGTTTTCCATAAGTTGTCC 57.867 39.130 0.00 0.00 30.71 4.02
1768 1810 7.436933 TGGTGATGAGATAAGCAAGTATACTG 58.563 38.462 6.06 2.23 0.00 2.74
1782 1824 6.628398 GCAAGTATACTGTGCCTACTCTTCTT 60.628 42.308 20.40 0.00 31.94 2.52
1812 1854 3.320611 TGTGGAACTCGGTCTTGCAAAG 61.321 50.000 0.00 0.00 41.76 2.77
1818 1860 0.468226 TCGGTCTTGCAAAGTCTGGT 59.532 50.000 0.00 0.00 46.34 4.00
1833 1875 0.035725 CTGGTCAGGCTCTTCATGCA 60.036 55.000 0.00 0.00 0.00 3.96
1875 1917 2.093783 GGAAACCGATAACGTGCTGAAG 59.906 50.000 0.00 0.00 37.88 3.02
2055 2097 3.584406 AGATGTCAGACATGGGAGTCAAA 59.416 43.478 21.26 0.00 39.27 2.69
2129 2171 1.208642 GCAAACCTTTGTCGCTGTGC 61.209 55.000 0.00 0.00 40.24 4.57
2151 2193 3.820689 TCATGCGTATGTTGTGAAAAGC 58.179 40.909 13.39 0.00 35.73 3.51
2379 2421 6.892658 TCAGCCAACAAATACACTTATGTT 57.107 33.333 0.00 0.00 40.48 2.71
2423 2465 5.363562 AGCTTGATGAACCTGATGTATGA 57.636 39.130 0.00 0.00 0.00 2.15
2673 2715 5.246883 AGAAAACAAAAGGCCTAATGATGCT 59.753 36.000 21.20 11.88 0.00 3.79
3066 3108 5.521906 TGCTGAGTAGTGTCTATGGAATC 57.478 43.478 0.00 0.00 0.00 2.52
3255 3297 5.157940 AGAGAGCAGCAGAAAGATTGTTA 57.842 39.130 0.00 0.00 0.00 2.41
3476 3518 4.909305 AGAATTTGTTACAACGTGCATTCG 59.091 37.500 11.41 0.00 0.00 3.34
3483 3525 1.228003 AACGTGCATTCGGTTCCCA 60.228 52.632 1.59 0.00 34.94 4.37
3585 3695 0.453390 GCAGGCTGATACAAAGTGCC 59.547 55.000 20.86 0.00 43.52 5.01
3815 3925 4.503910 CAGAAAATCCACCGACATAGTCA 58.496 43.478 0.00 0.00 32.09 3.41
3922 4033 2.094700 TCTTGCCTGTAACGTGAGCTAG 60.095 50.000 0.00 0.00 0.00 3.42
3948 4059 4.243793 TGGTTACGGATCAATTTGGGAT 57.756 40.909 0.00 0.00 0.00 3.85
3977 4088 0.692476 CTGATGGTGACCCACTTCCA 59.308 55.000 0.00 0.00 45.65 3.53
3984 4095 3.527253 TGGTGACCCACTTCCATTGATAT 59.473 43.478 0.00 0.00 35.17 1.63
4000 4111 6.015772 CCATTGATATTGGATTGCTCATGTCA 60.016 38.462 0.00 0.00 36.26 3.58
4033 4144 1.803453 ATTGGGACCCCTGTGCATGT 61.803 55.000 8.45 0.00 33.90 3.21
4142 4253 0.599728 GGGATCGCTGCTGATGAGAC 60.600 60.000 10.76 0.00 0.00 3.36
4153 4264 1.010795 TGATGAGACTCCAGAGGGGA 58.989 55.000 0.00 0.00 45.89 4.81
4234 4345 1.070758 CCCTTCCCATCACCGATGTAG 59.929 57.143 3.47 0.00 38.28 2.74
4398 4518 9.571810 TTCAGCACACACAATATTTTATCAATC 57.428 29.630 0.00 0.00 0.00 2.67
4426 4546 8.607441 TTGACAATACATCATGCCTAATACTC 57.393 34.615 0.00 0.00 0.00 2.59
4428 4548 7.016563 TGACAATACATCATGCCTAATACTCCT 59.983 37.037 0.00 0.00 0.00 3.69
4429 4549 7.749666 ACAATACATCATGCCTAATACTCCTT 58.250 34.615 0.00 0.00 0.00 3.36
4430 4550 7.880195 ACAATACATCATGCCTAATACTCCTTC 59.120 37.037 0.00 0.00 0.00 3.46
4431 4551 5.234466 ACATCATGCCTAATACTCCTTCC 57.766 43.478 0.00 0.00 0.00 3.46
4432 4552 4.248859 CATCATGCCTAATACTCCTTCCG 58.751 47.826 0.00 0.00 0.00 4.30
4434 4554 3.709653 TCATGCCTAATACTCCTTCCGTT 59.290 43.478 0.00 0.00 0.00 4.44
4435 4555 3.814005 TGCCTAATACTCCTTCCGTTC 57.186 47.619 0.00 0.00 0.00 3.95
4436 4556 2.433239 TGCCTAATACTCCTTCCGTTCC 59.567 50.000 0.00 0.00 0.00 3.62
4439 4559 4.624604 GCCTAATACTCCTTCCGTTCCAAA 60.625 45.833 0.00 0.00 0.00 3.28
4440 4560 5.493809 CCTAATACTCCTTCCGTTCCAAAA 58.506 41.667 0.00 0.00 0.00 2.44
4441 4561 6.120220 CCTAATACTCCTTCCGTTCCAAAAT 58.880 40.000 0.00 0.00 0.00 1.82
4444 4564 4.903045 ACTCCTTCCGTTCCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
4445 4565 5.437191 ACTCCTTCCGTTCCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
4446 4566 5.186198 ACTCCTTCCGTTCCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
4449 4569 4.335594 CCTTCCGTTCCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
4453 4573 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 2.797177 AAATCTTCTCCCACTCTGCC 57.203 50.000 0.00 0.00 0.00 4.85
92 93 2.508928 CGGCGGGGACACCATATT 59.491 61.111 0.00 0.00 40.22 1.28
151 152 0.390860 CCTCCTCTTCACCATAGCCG 59.609 60.000 0.00 0.00 0.00 5.52
184 185 2.033141 GCACTGCCTGCCTCTTCA 59.967 61.111 0.00 0.00 40.42 3.02
197 198 4.251246 TTTTTGGCCACGAGCACT 57.749 50.000 3.88 0.00 46.50 4.40
324 332 2.859165 TCACAAGCAACTCCCCTAAG 57.141 50.000 0.00 0.00 0.00 2.18
355 363 1.712977 CCGCTAGCTACTTCGTCGGT 61.713 60.000 13.93 0.00 0.00 4.69
356 364 1.009900 CCGCTAGCTACTTCGTCGG 60.010 63.158 13.93 0.00 0.00 4.79
363 371 0.188834 AAGGGGATCCGCTAGCTACT 59.811 55.000 29.84 11.93 38.30 2.57
369 377 3.109151 TCTTGTTTAAGGGGATCCGCTA 58.891 45.455 29.84 14.17 38.30 4.26
386 394 0.525668 AATCCGCTCGCTACGTCTTG 60.526 55.000 0.00 0.00 0.00 3.02
450 463 8.995027 ATAGTAAATTAGGCCAACATTCATCA 57.005 30.769 5.01 0.00 0.00 3.07
452 465 8.995027 TGATAGTAAATTAGGCCAACATTCAT 57.005 30.769 5.01 0.00 0.00 2.57
517 530 6.896021 AGCTTCCTATGAGCGTAGTAATAA 57.104 37.500 0.00 0.00 44.71 1.40
542 555 4.508662 ACTGTTTGGTAGCAGAGATTAGC 58.491 43.478 0.00 0.00 36.62 3.09
579 592 6.090898 CGAATCACGTCCATAACTTTCTTTCT 59.909 38.462 0.00 0.00 37.22 2.52
583 596 3.617263 GCGAATCACGTCCATAACTTTCT 59.383 43.478 0.00 0.00 44.60 2.52
605 618 6.491394 TGTCTTCATAACGTTTGTTTCCTTG 58.509 36.000 5.91 0.00 39.54 3.61
757 778 7.075148 TCCTTCCCCTACTTTATCGGTTTATA 58.925 38.462 0.00 0.00 0.00 0.98
768 789 2.617840 TCGTCTCCTTCCCCTACTTT 57.382 50.000 0.00 0.00 0.00 2.66
843 865 4.608951 TGTTTCGGGTTTATTTTTGTCCG 58.391 39.130 0.00 0.00 38.92 4.79
861 891 4.649674 TGTCTCAGTTGGTAGTCTCTGTTT 59.350 41.667 0.00 0.00 0.00 2.83
865 895 5.654650 CCTAATGTCTCAGTTGGTAGTCTCT 59.345 44.000 0.00 0.00 0.00 3.10
894 924 8.324191 TGACCAAATCTCTATTCCTAATGTCT 57.676 34.615 0.00 0.00 0.00 3.41
895 925 8.964476 TTGACCAAATCTCTATTCCTAATGTC 57.036 34.615 0.00 0.00 0.00 3.06
896 926 9.927081 AATTGACCAAATCTCTATTCCTAATGT 57.073 29.630 0.00 0.00 0.00 2.71
904 934 9.981460 ACCTAAGAAATTGACCAAATCTCTATT 57.019 29.630 0.00 0.00 0.00 1.73
907 937 9.232473 GTTACCTAAGAAATTGACCAAATCTCT 57.768 33.333 0.00 0.00 0.00 3.10
908 938 9.232473 AGTTACCTAAGAAATTGACCAAATCTC 57.768 33.333 0.00 0.00 0.00 2.75
909 939 9.588096 AAGTTACCTAAGAAATTGACCAAATCT 57.412 29.630 0.00 0.00 0.00 2.40
911 941 9.981114 CAAAGTTACCTAAGAAATTGACCAAAT 57.019 29.630 0.00 0.00 0.00 2.32
912 942 7.923878 GCAAAGTTACCTAAGAAATTGACCAAA 59.076 33.333 0.00 0.00 0.00 3.28
913 943 7.430441 GCAAAGTTACCTAAGAAATTGACCAA 58.570 34.615 0.00 0.00 0.00 3.67
914 944 6.015772 GGCAAAGTTACCTAAGAAATTGACCA 60.016 38.462 0.00 0.00 0.00 4.02
915 945 6.208797 AGGCAAAGTTACCTAAGAAATTGACC 59.791 38.462 0.00 0.00 33.38 4.02
916 946 7.084486 CAGGCAAAGTTACCTAAGAAATTGAC 58.916 38.462 0.00 0.00 33.38 3.18
917 947 6.775629 ACAGGCAAAGTTACCTAAGAAATTGA 59.224 34.615 0.00 0.00 33.38 2.57
918 948 6.981722 ACAGGCAAAGTTACCTAAGAAATTG 58.018 36.000 0.00 0.00 33.38 2.32
919 949 8.700439 TTACAGGCAAAGTTACCTAAGAAATT 57.300 30.769 0.00 0.00 33.38 1.82
920 950 7.094334 GCTTACAGGCAAAGTTACCTAAGAAAT 60.094 37.037 9.86 0.00 33.38 2.17
921 951 6.206048 GCTTACAGGCAAAGTTACCTAAGAAA 59.794 38.462 9.86 0.00 33.38 2.52
922 952 5.704053 GCTTACAGGCAAAGTTACCTAAGAA 59.296 40.000 9.86 1.11 33.38 2.52
923 953 5.243207 GCTTACAGGCAAAGTTACCTAAGA 58.757 41.667 9.86 0.00 33.38 2.10
924 954 4.092968 CGCTTACAGGCAAAGTTACCTAAG 59.907 45.833 0.00 1.37 33.38 2.18
925 955 3.998341 CGCTTACAGGCAAAGTTACCTAA 59.002 43.478 0.00 0.00 33.38 2.69
926 956 3.007182 ACGCTTACAGGCAAAGTTACCTA 59.993 43.478 0.00 0.00 33.38 3.08
927 957 2.224450 ACGCTTACAGGCAAAGTTACCT 60.224 45.455 0.00 0.00 36.45 3.08
928 958 2.148768 ACGCTTACAGGCAAAGTTACC 58.851 47.619 0.00 0.00 0.00 2.85
929 959 3.064931 AGACGCTTACAGGCAAAGTTAC 58.935 45.455 0.00 0.00 0.00 2.50
930 960 3.396260 AGACGCTTACAGGCAAAGTTA 57.604 42.857 0.00 0.00 0.00 2.24
931 961 2.256117 AGACGCTTACAGGCAAAGTT 57.744 45.000 0.00 0.00 0.00 2.66
932 962 2.143925 GAAGACGCTTACAGGCAAAGT 58.856 47.619 0.00 0.00 0.00 2.66
944 974 3.616721 AGTGGCCACGAAGACGCT 61.617 61.111 29.68 7.25 43.96 5.07
957 987 1.270907 AAGAGTAGAGTGGGCAGTGG 58.729 55.000 0.00 0.00 0.00 4.00
1091 1121 2.705826 GAGAAGAATGCGCTGCGG 59.294 61.111 24.61 5.63 0.00 5.69
1095 1125 0.107459 GGGAAGGAGAAGAATGCGCT 60.107 55.000 9.73 0.00 0.00 5.92
1416 1458 5.043248 CCTTGTTGGTTCATCTGACAAAAC 58.957 41.667 0.00 0.00 30.72 2.43
1440 1482 1.375013 GAACCCGTTAGGCGCAAGA 60.375 57.895 10.83 0.00 40.58 3.02
1445 1487 3.484547 GCGTGAACCCGTTAGGCG 61.485 66.667 0.00 0.00 40.58 5.52
1560 1602 2.345760 GGACGAGCCAACGTAGGGA 61.346 63.158 10.18 0.00 46.52 4.20
1572 1614 1.884235 AAGCTTGAACAAGGGACGAG 58.116 50.000 14.95 0.00 38.80 4.18
1594 1636 2.111878 CACCTCCCCATGGATCGC 59.888 66.667 15.22 0.00 40.80 4.58
1598 1640 2.687200 CGTCCACCTCCCCATGGA 60.687 66.667 15.22 0.00 42.88 3.41
1601 1643 3.402681 CAGCGTCCACCTCCCCAT 61.403 66.667 0.00 0.00 0.00 4.00
1608 1650 2.433318 GTCTCAGCAGCGTCCACC 60.433 66.667 0.00 0.00 0.00 4.61
1626 1668 2.690778 GGGCAAGCCTAGCAACACG 61.691 63.158 11.40 0.00 36.10 4.49
1630 1672 1.674322 GTTCGGGCAAGCCTAGCAA 60.674 57.895 11.40 0.00 36.10 3.91
1635 1677 2.358737 CTTCGTTCGGGCAAGCCT 60.359 61.111 11.40 0.00 36.10 4.58
1644 1686 0.992072 ATGACATGTCGCTTCGTTCG 59.008 50.000 20.54 0.00 0.00 3.95
1657 1699 2.092592 TGAGCAGAGCATTCCATGACAT 60.093 45.455 0.00 0.00 0.00 3.06
1718 1760 6.834168 ATTCGGACAACTTATGGAAAACAT 57.166 33.333 0.00 0.00 43.68 2.71
1737 1779 5.739752 TGCTTATCTCATCACCAAATTCG 57.260 39.130 0.00 0.00 0.00 3.34
1768 1810 5.177696 CACAACACTTAAGAAGAGTAGGCAC 59.822 44.000 10.09 0.00 31.90 5.01
1782 1824 2.168936 ACCGAGTTCCACACAACACTTA 59.831 45.455 0.00 0.00 0.00 2.24
1812 1854 2.011046 GCATGAAGAGCCTGACCAGAC 61.011 57.143 0.00 0.00 0.00 3.51
1818 1860 1.005097 ACCAATGCATGAAGAGCCTGA 59.995 47.619 0.00 0.00 0.00 3.86
1833 1875 0.329596 GCCCTCTCTTGACCACCAAT 59.670 55.000 0.00 0.00 33.68 3.16
1875 1917 5.446473 CGAGTACATCTCAACAAGGCAATTC 60.446 44.000 0.00 0.00 42.88 2.17
2055 2097 4.642885 CCCACGAATGTATATTGGTTTGGT 59.357 41.667 0.00 0.00 33.64 3.67
2129 2171 3.848019 GCTTTTCACAACATACGCATGAG 59.152 43.478 1.75 0.00 35.96 2.90
2370 2412 5.630680 GCATCTCAAAACACCAACATAAGTG 59.369 40.000 0.00 0.00 39.93 3.16
2379 2421 1.337703 GTGCAGCATCTCAAAACACCA 59.662 47.619 0.00 0.00 0.00 4.17
2423 2465 2.156917 CACATGCATGAACCTGAGTGT 58.843 47.619 32.75 4.95 0.00 3.55
2673 2715 5.853936 ACACTCAATGAAACTGCTAGTGTA 58.146 37.500 0.00 0.00 42.99 2.90
3129 3171 5.536260 TGATTGATAAGAGATTCAGCCTCG 58.464 41.667 0.00 0.00 35.88 4.63
3255 3297 5.723887 AGAAACATCCTGTGGATCTAACTCT 59.276 40.000 0.00 0.00 40.98 3.24
3483 3525 2.498481 CCATGGTGGCATTTCAGATTGT 59.502 45.455 2.57 0.00 0.00 2.71
3609 3719 4.218200 CAGGTGTGGCATTTTCAGTAATCA 59.782 41.667 0.00 0.00 0.00 2.57
3754 3864 5.039920 TCAAACTGCAGGATAGCATATGT 57.960 39.130 19.93 0.00 44.68 2.29
3912 4023 3.252701 CGTAACCATATCCTAGCTCACGT 59.747 47.826 0.00 0.00 0.00 4.49
3922 4033 5.183140 CCCAAATTGATCCGTAACCATATCC 59.817 44.000 0.00 0.00 0.00 2.59
3948 4059 2.358300 GGTCACCATCAGACTCTCCCTA 60.358 54.545 0.00 0.00 36.29 3.53
3977 4088 6.548251 TGTGACATGAGCAATCCAATATCAAT 59.452 34.615 0.00 0.00 0.00 2.57
3984 4095 4.281435 ACAAATGTGACATGAGCAATCCAA 59.719 37.500 0.00 0.00 0.00 3.53
4033 4144 2.771089 GTGAACAAGCTGATCACCTCA 58.229 47.619 13.19 0.00 42.20 3.86
4153 4264 7.293073 ACTATGTCATGCCAAAGGAGAATTAT 58.707 34.615 0.00 0.00 0.00 1.28
4234 4345 2.294233 TGCCAAGAACAAGCACTTCATC 59.706 45.455 0.00 0.00 0.00 2.92
4309 4420 2.493278 CCTTGCCACCCATGAACTAAAG 59.507 50.000 0.00 0.00 0.00 1.85
4398 4518 4.621068 AGGCATGATGTATTGTCAAACG 57.379 40.909 0.00 0.00 0.00 3.60
4426 4546 4.335594 GGTCATCTATTTTGGAACGGAAGG 59.664 45.833 0.00 0.00 0.00 3.46
4428 4548 4.263550 TGGGTCATCTATTTTGGAACGGAA 60.264 41.667 0.00 0.00 0.00 4.30
4429 4549 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
4430 4550 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
4431 4551 4.981794 GTTGGGTCATCTATTTTGGAACG 58.018 43.478 0.00 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.