Multiple sequence alignment - TraesCS1D01G113600

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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 TraesCS1D01G113600 chr1D 100.000 3302 0 0 1 3302 109968475 109971776 0.000000e+00 6098
1 TraesCS1D01G113600 chr1D 100.000 1534 0 0 3543 5076 109972017 109973550 0.000000e+00 2833
2 TraesCS1D01G113600 chr1A 97.018 2549 62 9 763 3302 113850448 113852991 0.000000e+00 4274
3 TraesCS1D01G113600 chr1A 94.629 875 15 5 4202 5076 113857943 113858785 0.000000e+00 1327
4 TraesCS1D01G113600 chr1A 95.098 306 13 2 3543 3848 113853012 113853315 9.880000e-132 481
5 TraesCS1D01G113600 chr1A 96.923 260 8 0 3945 4204 113857646 113857905 2.170000e-118 436
6 TraesCS1D01G113600 chr1A 96.341 82 3 0 3843 3924 113857572 113857653 8.860000e-28 135
7 TraesCS1D01G113600 chr1B 94.732 1044 45 5 875 1909 166579254 166580296 0.000000e+00 1615
8 TraesCS1D01G113600 chr1B 95.682 718 21 5 2587 3302 166589507 166590216 0.000000e+00 1146
9 TraesCS1D01G113600 chr1B 92.492 626 29 12 4465 5076 166591557 166592178 0.000000e+00 880
10 TraesCS1D01G113600 chr1B 90.950 674 24 6 3543 4204 166590420 166591068 0.000000e+00 872
11 TraesCS1D01G113600 chr1B 97.342 489 9 4 1908 2393 166580534 166581021 0.000000e+00 828
12 TraesCS1D01G113600 chr1B 90.813 283 15 5 4202 4482 166591106 166591379 8.030000e-98 368
13 TraesCS1D01G113600 chr1B 90.419 167 8 2 2403 2562 166589110 166589275 3.980000e-51 213
14 TraesCS1D01G113600 chr3D 95.374 735 23 2 1 726 508566228 508566960 0.000000e+00 1158
15 TraesCS1D01G113600 chr7D 92.789 735 41 4 1 726 58057619 58056888 0.000000e+00 1053
16 TraesCS1D01G113600 chr3A 91.576 736 49 7 1 726 730642492 730643224 0.000000e+00 1003
17 TraesCS1D01G113600 chr3A 78.069 611 117 16 1 603 501188652 501189253 2.230000e-98 370
18 TraesCS1D01G113600 chr7B 90.476 735 60 5 1 726 673395621 673396354 0.000000e+00 961
19 TraesCS1D01G113600 chr5A 90.082 736 59 8 1 726 227932836 227932105 0.000000e+00 942
20 TraesCS1D01G113600 chr2B 88.649 740 66 12 1 727 243354926 243355660 0.000000e+00 885
21 TraesCS1D01G113600 chr2B 92.105 532 33 1 208 730 751002235 751002766 0.000000e+00 741
22 TraesCS1D01G113600 chr2D 79.487 702 123 17 1 692 603123635 603124325 3.550000e-131 479
23 TraesCS1D01G113600 chr7A 93.061 245 17 0 4440 4684 149286593 149286837 4.830000e-95 359
24 TraesCS1D01G113600 chr7A 76.007 596 129 13 1 591 666167603 666167017 3.840000e-76 296
25 TraesCS1D01G113600 chr7A 96.203 79 3 0 4372 4450 149284921 149284999 4.120000e-26 130


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 TraesCS1D01G113600 chr1D 109968475 109973550 5075 False 4465.500000 6098 100.000000 1 5076 2 chr1D.!!$F1 5075
1 TraesCS1D01G113600 chr1A 113850448 113853315 2867 False 2377.500000 4274 96.058000 763 3848 2 chr1A.!!$F1 3085
2 TraesCS1D01G113600 chr1A 113857572 113858785 1213 False 632.666667 1327 95.964333 3843 5076 3 chr1A.!!$F2 1233
3 TraesCS1D01G113600 chr1B 166579254 166581021 1767 False 1221.500000 1615 96.037000 875 2393 2 chr1B.!!$F1 1518
4 TraesCS1D01G113600 chr1B 166589110 166592178 3068 False 695.800000 1146 92.071200 2403 5076 5 chr1B.!!$F2 2673
5 TraesCS1D01G113600 chr3D 508566228 508566960 732 False 1158.000000 1158 95.374000 1 726 1 chr3D.!!$F1 725
6 TraesCS1D01G113600 chr7D 58056888 58057619 731 True 1053.000000 1053 92.789000 1 726 1 chr7D.!!$R1 725
7 TraesCS1D01G113600 chr3A 730642492 730643224 732 False 1003.000000 1003 91.576000 1 726 1 chr3A.!!$F2 725
8 TraesCS1D01G113600 chr3A 501188652 501189253 601 False 370.000000 370 78.069000 1 603 1 chr3A.!!$F1 602
9 TraesCS1D01G113600 chr7B 673395621 673396354 733 False 961.000000 961 90.476000 1 726 1 chr7B.!!$F1 725
10 TraesCS1D01G113600 chr5A 227932105 227932836 731 True 942.000000 942 90.082000 1 726 1 chr5A.!!$R1 725
11 TraesCS1D01G113600 chr2B 243354926 243355660 734 False 885.000000 885 88.649000 1 727 1 chr2B.!!$F1 726
12 TraesCS1D01G113600 chr2B 751002235 751002766 531 False 741.000000 741 92.105000 208 730 1 chr2B.!!$F2 522
13 TraesCS1D01G113600 chr2D 603123635 603124325 690 False 479.000000 479 79.487000 1 692 1 chr2D.!!$F1 691
14 TraesCS1D01G113600 chr7A 666167017 666167603 586 True 296.000000 296 76.007000 1 591 1 chr7A.!!$R1 590
15 TraesCS1D01G113600 chr7A 149284921 149286837 1916 False 244.500000 359 94.632000 4372 4684 2 chr7A.!!$F1 312

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
544 549 0.107654 CTCTTGAAACCCTAGCCCGG 60.108 60.000 0.00 0.00 0.00 5.73 F
733 756 0.759346 AACGAGAGGGAACTTGCAGT 59.241 50.000 0.00 0.00 44.43 4.40 F
734 757 0.759346 ACGAGAGGGAACTTGCAGTT 59.241 50.000 0.00 1.82 44.43 3.16 F
735 758 1.141053 ACGAGAGGGAACTTGCAGTTT 59.859 47.619 0.00 0.00 44.43 2.66 F
1346 1370 1.227089 CTGCTCCAGGGTTCGATCG 60.227 63.158 9.36 9.36 0.00 3.69 F
1366 1391 1.427895 TTGGGGATTTCGTGTGGGGA 61.428 55.000 0.00 0.00 0.00 4.81 F
3826 4328 0.521291 TGCAATCCAGCGTGCTTAAC 59.479 50.000 0.00 0.00 41.48 2.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1501 1526 0.685097 GTTGGAGGGTAGCAGTGTCA 59.315 55.000 0.00 0.0 0.00 3.58 R
1698 1730 3.118665 TGCGAAATCAGATGTCTCATGGA 60.119 43.478 0.00 0.0 0.00 3.41 R
2518 2803 5.711506 ACAATTCATGCTATCACAGGAAACA 59.288 36.000 0.00 0.0 42.85 2.83 R
2878 3376 9.535170 AACATAAATAGCCTCTAGTCTATAGCA 57.465 33.333 0.00 0.0 0.00 3.49 R
2995 3495 4.740902 AGGCTACCCAATTCAGAAACTTT 58.259 39.130 0.00 0.0 0.00 2.66 R
3835 4337 5.191722 TCCAGATAAGTTAAGCATGTTCCCT 59.808 40.000 0.00 0.0 0.00 4.20 R
4955 7341 2.271800 CGATGTGGAGCTCAAAGTACC 58.728 52.381 17.19 0.0 0.00 3.34 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
173 174 5.350365 TCGTATGGTTTCAGAATTACAGCAC 59.650 40.000 0.00 0.00 0.00 4.40
174 175 5.447279 CGTATGGTTTCAGAATTACAGCACC 60.447 44.000 0.00 0.00 0.00 5.01
261 265 7.272978 ACTGCACCGTATACAAATTATCTTCT 58.727 34.615 3.32 0.00 0.00 2.85
458 462 2.025887 GTCCCAACTCCTCCATCAATGT 60.026 50.000 0.00 0.00 0.00 2.71
544 549 0.107654 CTCTTGAAACCCTAGCCCGG 60.108 60.000 0.00 0.00 0.00 5.73
641 652 0.814010 CGCCCCGATCGAAGGAAAAT 60.814 55.000 23.43 0.00 0.00 1.82
730 753 2.011540 CCTAACGAGAGGGAACTTGC 57.988 55.000 0.00 0.00 44.43 4.01
731 754 1.275291 CCTAACGAGAGGGAACTTGCA 59.725 52.381 0.00 0.00 44.43 4.08
732 755 2.611518 CTAACGAGAGGGAACTTGCAG 58.388 52.381 0.00 0.00 44.43 4.41
733 756 0.759346 AACGAGAGGGAACTTGCAGT 59.241 50.000 0.00 0.00 44.43 4.40
734 757 0.759346 ACGAGAGGGAACTTGCAGTT 59.241 50.000 0.00 1.82 44.43 3.16
735 758 1.141053 ACGAGAGGGAACTTGCAGTTT 59.859 47.619 0.00 0.00 44.43 2.66
736 759 2.222027 CGAGAGGGAACTTGCAGTTTT 58.778 47.619 3.56 0.00 44.43 2.43
737 760 2.618709 CGAGAGGGAACTTGCAGTTTTT 59.381 45.455 3.56 0.00 44.43 1.94
760 783 5.432680 TCTTCCGTAGAGAAGAGGAGTAA 57.567 43.478 0.00 0.00 45.67 2.24
761 784 5.184711 TCTTCCGTAGAGAAGAGGAGTAAC 58.815 45.833 0.00 0.00 45.67 2.50
777 800 2.563179 AGTAACATGAGGAGTTGCGTCT 59.437 45.455 0.00 0.00 36.81 4.18
865 888 3.133362 ACTGAATATTTAACTCGGCCGGA 59.867 43.478 27.83 11.38 0.00 5.14
981 1004 2.439701 CCGTCTCCACTCCCGCTA 60.440 66.667 0.00 0.00 0.00 4.26
1172 1195 3.123804 GCGTAATCAGATCGAACCATGT 58.876 45.455 0.00 0.00 0.00 3.21
1336 1360 1.433534 GTTTCTCGGAACTGCTCCAG 58.566 55.000 0.00 0.00 45.74 3.86
1346 1370 1.227089 CTGCTCCAGGGTTCGATCG 60.227 63.158 9.36 9.36 0.00 3.69
1366 1391 1.427895 TTGGGGATTTCGTGTGGGGA 61.428 55.000 0.00 0.00 0.00 4.81
1425 1450 4.891727 CCGATCCCCAAGCCGACG 62.892 72.222 0.00 0.00 0.00 5.12
1655 1687 6.128200 GCACTGTGAATGAATGATGACTGTTA 60.128 38.462 12.86 0.00 0.00 2.41
1698 1730 8.929260 TTCTGCAGAATATTCATACATCCATT 57.071 30.769 25.16 0.00 0.00 3.16
1729 1761 2.998772 TCTGATTTCGCAAGTGCAAAC 58.001 42.857 3.87 0.00 42.21 2.93
1814 1846 9.650714 AATTGGTGATATACTACCACTACTACA 57.349 33.333 8.95 0.00 46.03 2.74
2518 2803 7.363530 GGAGTTTCTGTTTCCAAAAACCTAAGT 60.364 37.037 0.00 0.00 43.44 2.24
2879 3377 2.758009 CCTTGTTGGAAGGCACATTTG 58.242 47.619 0.00 0.00 38.35 2.32
2880 3378 3.124319 CCTTGTTGGAAGGCACATTTGC 61.124 50.000 0.00 0.00 42.98 3.68
2881 3379 5.370737 CCTTGTTGGAAGGCACATTTGCT 62.371 47.826 3.47 0.00 43.16 3.91
2882 3380 6.064478 CCTTGTTGGAAGGCACATTTGCTA 62.064 45.833 3.47 0.00 43.16 3.49
2883 3381 7.304933 CCTTGTTGGAAGGCACATTTGCTAT 62.305 44.000 3.47 0.00 43.16 2.97
2947 3445 9.628500 AACATTAAGTGTAAGTTTTCCTCTCTT 57.372 29.630 0.00 0.00 41.14 2.85
3570 4072 3.189080 TGTTTCATCGTGCAATCTTCCAG 59.811 43.478 0.00 0.00 0.00 3.86
3761 4263 2.299582 TGCCATGTTCTTGGTGAAATGG 59.700 45.455 6.60 0.00 41.22 3.16
3775 4277 8.429237 TTGGTGAAATGGAAGTAACCAATATT 57.571 30.769 1.07 0.00 41.49 1.28
3817 4319 2.012673 CTACTGTCCTTGCAATCCAGC 58.987 52.381 15.92 0.00 0.00 4.85
3818 4320 0.957395 ACTGTCCTTGCAATCCAGCG 60.957 55.000 15.92 0.00 37.31 5.18
3819 4321 0.957395 CTGTCCTTGCAATCCAGCGT 60.957 55.000 0.00 0.00 37.31 5.07
3820 4322 1.236616 TGTCCTTGCAATCCAGCGTG 61.237 55.000 0.00 0.00 37.31 5.34
3821 4323 2.180017 CCTTGCAATCCAGCGTGC 59.820 61.111 0.00 0.00 41.29 5.34
3822 4324 2.338015 CCTTGCAATCCAGCGTGCT 61.338 57.895 0.00 0.00 41.48 4.40
3823 4325 1.582968 CTTGCAATCCAGCGTGCTT 59.417 52.632 0.00 0.00 41.48 3.91
3824 4326 0.804364 CTTGCAATCCAGCGTGCTTA 59.196 50.000 0.00 0.00 41.48 3.09
3825 4327 1.199789 CTTGCAATCCAGCGTGCTTAA 59.800 47.619 0.00 0.00 41.48 1.85
3826 4328 0.521291 TGCAATCCAGCGTGCTTAAC 59.479 50.000 0.00 0.00 41.48 2.01
3827 4329 0.804989 GCAATCCAGCGTGCTTAACT 59.195 50.000 0.00 0.00 37.78 2.24
3828 4330 1.200020 GCAATCCAGCGTGCTTAACTT 59.800 47.619 0.00 0.00 37.78 2.66
3829 4331 2.351738 GCAATCCAGCGTGCTTAACTTT 60.352 45.455 0.00 0.00 37.78 2.66
3830 4332 3.857010 GCAATCCAGCGTGCTTAACTTTT 60.857 43.478 0.00 0.00 37.78 2.27
3831 4333 4.298332 CAATCCAGCGTGCTTAACTTTTT 58.702 39.130 0.00 0.00 0.00 1.94
3884 4387 5.686397 CACCGCTTTAGTCATAGTTAGCTAC 59.314 44.000 0.00 0.00 0.00 3.58
3967 4473 5.453621 GCCTTTCATGCCCATCATTCAAATA 60.454 40.000 0.00 0.00 31.79 1.40
4018 4525 5.240623 CACCATTCTGCTTTGTAGGTTTGTA 59.759 40.000 0.00 0.00 0.00 2.41
4104 4611 1.140852 CGAGGGGCTGTTGGATTATCA 59.859 52.381 0.00 0.00 0.00 2.15
4204 4718 2.901192 TCTGAAGAACCGGTGAACCATA 59.099 45.455 8.52 0.00 35.14 2.74
4243 4797 8.907885 AGAGATGAATTATAGGTTTTTCCTTGC 58.092 33.333 0.00 0.00 45.67 4.01
4450 5004 2.929641 TGCTTCATCTGTGAAACACCA 58.070 42.857 0.00 0.00 45.67 4.17
4542 6893 5.362556 ACTGAAATGTACATCACTTGCAC 57.637 39.130 9.23 0.00 0.00 4.57
4820 7206 9.072375 TCATTTTAATTGTAACTGACATGTCCA 57.928 29.630 22.85 10.29 38.07 4.02
4821 7207 9.859427 CATTTTAATTGTAACTGACATGTCCAT 57.141 29.630 22.85 11.28 38.07 3.41
4825 7211 9.733556 TTAATTGTAACTGACATGTCCATTACT 57.266 29.630 30.20 20.98 38.07 2.24
4826 7212 8.635765 AATTGTAACTGACATGTCCATTACTT 57.364 30.769 30.20 21.78 38.07 2.24
4827 7213 7.433708 TTGTAACTGACATGTCCATTACTTG 57.566 36.000 30.20 14.33 38.07 3.16
4828 7214 6.530120 TGTAACTGACATGTCCATTACTTGT 58.470 36.000 30.20 14.76 46.15 3.16
4829 7215 7.672240 TGTAACTGACATGTCCATTACTTGTA 58.328 34.615 30.20 18.28 44.19 2.41
4830 7216 8.151596 TGTAACTGACATGTCCATTACTTGTAA 58.848 33.333 30.20 18.04 44.19 2.41
4955 7341 1.000717 ACGAAATTTTCACGCCCTTGG 60.001 47.619 9.66 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
261 265 6.059484 CCAGGAAGTTTAGTTCAAACCACTA 58.941 40.000 0.22 0.00 46.55 2.74
458 462 0.605319 GGAACCAGACGATGTGGCAA 60.605 55.000 0.00 0.00 38.83 4.52
544 549 2.626780 GGCCCGCCACTTTTCTGAC 61.627 63.158 0.00 0.00 35.81 3.51
641 652 1.068588 CTCCGCCAATAATCCTCGACA 59.931 52.381 0.00 0.00 0.00 4.35
738 761 5.184711 GTTACTCCTCTTCTCTACGGAAGA 58.815 45.833 6.73 6.73 46.22 2.87
739 762 4.942483 TGTTACTCCTCTTCTCTACGGAAG 59.058 45.833 0.00 0.00 42.72 3.46
740 763 4.914983 TGTTACTCCTCTTCTCTACGGAA 58.085 43.478 0.00 0.00 0.00 4.30
741 764 4.564782 TGTTACTCCTCTTCTCTACGGA 57.435 45.455 0.00 0.00 0.00 4.69
742 765 4.882427 TCATGTTACTCCTCTTCTCTACGG 59.118 45.833 0.00 0.00 0.00 4.02
743 766 5.008217 CCTCATGTTACTCCTCTTCTCTACG 59.992 48.000 0.00 0.00 0.00 3.51
744 767 6.123651 TCCTCATGTTACTCCTCTTCTCTAC 58.876 44.000 0.00 0.00 0.00 2.59
745 768 6.069323 ACTCCTCATGTTACTCCTCTTCTCTA 60.069 42.308 0.00 0.00 0.00 2.43
746 769 5.199982 TCCTCATGTTACTCCTCTTCTCT 57.800 43.478 0.00 0.00 0.00 3.10
747 770 4.953579 ACTCCTCATGTTACTCCTCTTCTC 59.046 45.833 0.00 0.00 0.00 2.87
748 771 4.941713 ACTCCTCATGTTACTCCTCTTCT 58.058 43.478 0.00 0.00 0.00 2.85
749 772 5.415221 CAACTCCTCATGTTACTCCTCTTC 58.585 45.833 0.00 0.00 0.00 2.87
750 773 4.323104 GCAACTCCTCATGTTACTCCTCTT 60.323 45.833 0.00 0.00 0.00 2.85
751 774 3.196685 GCAACTCCTCATGTTACTCCTCT 59.803 47.826 0.00 0.00 0.00 3.69
752 775 3.526534 GCAACTCCTCATGTTACTCCTC 58.473 50.000 0.00 0.00 0.00 3.71
753 776 2.093973 CGCAACTCCTCATGTTACTCCT 60.094 50.000 0.00 0.00 0.00 3.69
754 777 2.271800 CGCAACTCCTCATGTTACTCC 58.728 52.381 0.00 0.00 0.00 3.85
755 778 2.924290 GACGCAACTCCTCATGTTACTC 59.076 50.000 0.00 0.00 0.00 2.59
756 779 2.563179 AGACGCAACTCCTCATGTTACT 59.437 45.455 0.00 0.00 0.00 2.24
757 780 2.960819 AGACGCAACTCCTCATGTTAC 58.039 47.619 0.00 0.00 0.00 2.50
758 781 3.258372 AGAAGACGCAACTCCTCATGTTA 59.742 43.478 0.00 0.00 0.00 2.41
759 782 2.037772 AGAAGACGCAACTCCTCATGTT 59.962 45.455 0.00 0.00 0.00 2.71
760 783 1.620819 AGAAGACGCAACTCCTCATGT 59.379 47.619 0.00 0.00 0.00 3.21
761 784 2.266554 GAGAAGACGCAACTCCTCATG 58.733 52.381 0.00 0.00 0.00 3.07
865 888 0.700564 ATGCAATGATATCGGCCCCT 59.299 50.000 0.00 0.00 0.00 4.79
1038 1061 1.228190 GGAGGAGGAGTAGGAGGAGT 58.772 60.000 0.00 0.00 0.00 3.85
1336 1360 0.107361 AATCCCCAACGATCGAACCC 60.107 55.000 24.34 0.00 0.00 4.11
1346 1370 1.248101 CCCCACACGAAATCCCCAAC 61.248 60.000 0.00 0.00 0.00 3.77
1366 1391 4.440250 CGAGAGAACCAAATCACCGATACT 60.440 45.833 0.00 0.00 0.00 2.12
1501 1526 0.685097 GTTGGAGGGTAGCAGTGTCA 59.315 55.000 0.00 0.00 0.00 3.58
1698 1730 3.118665 TGCGAAATCAGATGTCTCATGGA 60.119 43.478 0.00 0.00 0.00 3.41
2001 2273 8.456471 ACAGATCATTCACAAAACACAGATATG 58.544 33.333 0.00 0.00 31.79 1.78
2518 2803 5.711506 ACAATTCATGCTATCACAGGAAACA 59.288 36.000 0.00 0.00 42.85 2.83
2878 3376 9.535170 AACATAAATAGCCTCTAGTCTATAGCA 57.465 33.333 0.00 0.00 0.00 3.49
2883 3381 9.742144 CCTAGAACATAAATAGCCTCTAGTCTA 57.258 37.037 0.00 0.00 33.53 2.59
2995 3495 4.740902 AGGCTACCCAATTCAGAAACTTT 58.259 39.130 0.00 0.00 0.00 2.66
3828 4330 7.833285 AAGTTAAGCATGTTCCCTAGAAAAA 57.167 32.000 0.00 0.00 32.58 1.94
3829 4331 9.174166 GATAAGTTAAGCATGTTCCCTAGAAAA 57.826 33.333 0.00 0.00 32.58 2.29
3830 4332 8.548877 AGATAAGTTAAGCATGTTCCCTAGAAA 58.451 33.333 0.00 0.00 32.58 2.52
3831 4333 7.987458 CAGATAAGTTAAGCATGTTCCCTAGAA 59.013 37.037 0.00 0.00 0.00 2.10
3832 4334 7.419057 CCAGATAAGTTAAGCATGTTCCCTAGA 60.419 40.741 0.00 0.00 0.00 2.43
3833 4335 6.708054 CCAGATAAGTTAAGCATGTTCCCTAG 59.292 42.308 0.00 0.00 0.00 3.02
3834 4336 6.385759 TCCAGATAAGTTAAGCATGTTCCCTA 59.614 38.462 0.00 0.00 0.00 3.53
3835 4337 5.191722 TCCAGATAAGTTAAGCATGTTCCCT 59.808 40.000 0.00 0.00 0.00 4.20
3836 4338 5.297029 GTCCAGATAAGTTAAGCATGTTCCC 59.703 44.000 0.00 0.00 0.00 3.97
3837 4339 5.880332 TGTCCAGATAAGTTAAGCATGTTCC 59.120 40.000 0.00 0.00 0.00 3.62
3838 4340 6.183360 GGTGTCCAGATAAGTTAAGCATGTTC 60.183 42.308 0.00 0.00 0.00 3.18
3839 4341 5.648092 GGTGTCCAGATAAGTTAAGCATGTT 59.352 40.000 0.00 0.00 0.00 2.71
3840 4342 5.186198 GGTGTCCAGATAAGTTAAGCATGT 58.814 41.667 0.00 0.00 0.00 3.21
3884 4387 2.036086 GCACGCACAAAACTAAACAACG 60.036 45.455 0.00 0.00 0.00 4.10
4018 4525 2.735762 GCTATCAGAAACCGCTTCTCGT 60.736 50.000 0.00 0.00 42.84 4.18
4149 4656 0.603707 CACGCTCCCAAGAAAGCTCA 60.604 55.000 0.00 0.00 36.35 4.26
4150 4657 1.301677 CCACGCTCCCAAGAAAGCTC 61.302 60.000 0.00 0.00 36.35 4.09
4243 4797 7.970384 TCAGTTTGCTAAATGTTCCGTTATAG 58.030 34.615 8.12 0.00 31.55 1.31
4360 4914 7.040961 GGTGCCTGTTTTTACTTACACATTCTA 60.041 37.037 0.00 0.00 0.00 2.10
4361 4915 6.238925 GGTGCCTGTTTTTACTTACACATTCT 60.239 38.462 0.00 0.00 0.00 2.40
4362 4916 5.918576 GGTGCCTGTTTTTACTTACACATTC 59.081 40.000 0.00 0.00 0.00 2.67
4363 4917 5.506649 CGGTGCCTGTTTTTACTTACACATT 60.507 40.000 0.00 0.00 0.00 2.71
4450 5004 4.042187 ACAGCTACAGTTCAAGGAGGAATT 59.958 41.667 0.00 0.00 0.00 2.17
4542 6893 7.361457 TCAGATTTACCTTGGACCATAGTAG 57.639 40.000 0.00 0.00 0.00 2.57
4728 7081 9.015367 TCTACCATGAAACTAGATAGCAGATAC 57.985 37.037 0.00 0.00 0.00 2.24
4809 7195 6.873605 TCAGTTACAAGTAATGGACATGTCAG 59.126 38.462 26.47 8.32 39.20 3.51
4810 7196 6.764379 TCAGTTACAAGTAATGGACATGTCA 58.236 36.000 26.47 13.45 39.20 3.58
4811 7197 7.667043 TTCAGTTACAAGTAATGGACATGTC 57.333 36.000 17.91 17.91 39.20 3.06
4812 7198 8.514594 CATTTCAGTTACAAGTAATGGACATGT 58.485 33.333 0.00 0.00 42.47 3.21
4813 7199 8.514594 ACATTTCAGTTACAAGTAATGGACATG 58.485 33.333 14.52 14.52 31.71 3.21
4814 7200 8.635765 ACATTTCAGTTACAAGTAATGGACAT 57.364 30.769 10.12 0.00 29.95 3.06
4815 7201 7.174253 GGACATTTCAGTTACAAGTAATGGACA 59.826 37.037 10.12 0.00 29.95 4.02
4816 7202 7.174253 TGGACATTTCAGTTACAAGTAATGGAC 59.826 37.037 10.12 5.20 29.95 4.02
4817 7203 7.227873 TGGACATTTCAGTTACAAGTAATGGA 58.772 34.615 10.12 0.00 29.95 3.41
4818 7204 7.447374 TGGACATTTCAGTTACAAGTAATGG 57.553 36.000 10.12 0.00 29.95 3.16
4819 7205 9.345517 CAATGGACATTTCAGTTACAAGTAATG 57.654 33.333 0.00 0.00 0.00 1.90
4820 7206 8.028938 GCAATGGACATTTCAGTTACAAGTAAT 58.971 33.333 0.00 0.00 0.00 1.89
4821 7207 7.230510 AGCAATGGACATTTCAGTTACAAGTAA 59.769 33.333 0.00 0.00 0.00 2.24
4822 7208 6.714810 AGCAATGGACATTTCAGTTACAAGTA 59.285 34.615 0.00 0.00 0.00 2.24
4823 7209 5.536161 AGCAATGGACATTTCAGTTACAAGT 59.464 36.000 0.00 0.00 0.00 3.16
4824 7210 6.017400 AGCAATGGACATTTCAGTTACAAG 57.983 37.500 0.00 0.00 0.00 3.16
4825 7211 6.040278 TGAAGCAATGGACATTTCAGTTACAA 59.960 34.615 0.00 0.00 0.00 2.41
4826 7212 5.534278 TGAAGCAATGGACATTTCAGTTACA 59.466 36.000 0.00 0.00 0.00 2.41
4827 7213 6.012658 TGAAGCAATGGACATTTCAGTTAC 57.987 37.500 0.00 0.00 0.00 2.50
4828 7214 6.839124 ATGAAGCAATGGACATTTCAGTTA 57.161 33.333 0.00 0.00 0.00 2.24
4829 7215 5.733620 ATGAAGCAATGGACATTTCAGTT 57.266 34.783 0.00 0.00 0.00 3.16
4830 7216 5.733620 AATGAAGCAATGGACATTTCAGT 57.266 34.783 0.00 0.00 30.31 3.41
4955 7341 2.271800 CGATGTGGAGCTCAAAGTACC 58.728 52.381 17.19 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.