Multiple sequence alignment - TraesCS1B01G242700

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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 TraesCS1B01G242700 chr1B 100.000 3225 0 0 1 3225 430619336 430616112 0.000000e+00 5956.0
1 TraesCS1B01G242700 chr1B 85.185 1404 151 33 918 2285 431032651 431034033 0.000000e+00 1387.0
2 TraesCS1B01G242700 chr1B 83.601 311 41 6 2789 3094 430884316 430884011 1.890000e-72 283.0
3 TraesCS1B01G242700 chr1B 79.048 315 31 20 2212 2523 430886974 430886692 1.980000e-42 183.0
4 TraesCS1B01G242700 chr1D 94.781 2491 101 14 754 3225 318498598 318496118 0.000000e+00 3853.0
5 TraesCS1B01G242700 chr1D 86.540 1419 137 29 897 2285 318722077 318723471 0.000000e+00 1513.0
6 TraesCS1B01G242700 chr1D 82.844 443 56 13 2789 3217 318560131 318559695 2.350000e-101 379.0
7 TraesCS1B01G242700 chr1A 92.295 1765 100 17 781 2523 399826827 399825077 0.000000e+00 2473.0
8 TraesCS1B01G242700 chr1A 85.824 1432 137 39 881 2285 405093041 405091649 0.000000e+00 1459.0
9 TraesCS1B01G242700 chr1A 82.118 727 101 21 6 715 579751676 579752390 2.140000e-166 595.0
10 TraesCS1B01G242700 chr1A 80.952 357 56 9 369 715 564571804 564572158 4.100000e-69 272.0
11 TraesCS1B01G242700 chr1A 83.824 204 31 2 2321 2523 405360129 405360331 3.280000e-45 193.0
12 TraesCS1B01G242700 chr2D 82.438 763 77 25 3 716 139739184 139739938 5.910000e-172 614.0
13 TraesCS1B01G242700 chr2D 74.009 454 93 17 4 444 42735993 42736434 9.260000e-36 161.0
14 TraesCS1B01G242700 chr3A 82.698 630 80 18 12 613 698728257 698727629 1.700000e-147 532.0
15 TraesCS1B01G242700 chr3A 86.058 416 47 4 5 419 648687644 648688049 1.370000e-118 436.0
16 TraesCS1B01G242700 chr7B 83.632 446 56 8 12 442 683290671 683290228 1.390000e-108 403.0
17 TraesCS1B01G242700 chr7B 82.254 355 45 12 368 715 717212550 717212207 1.130000e-74 291.0
18 TraesCS1B01G242700 chr3B 83.862 378 50 8 67 442 751836189 751835821 1.840000e-92 350.0
19 TraesCS1B01G242700 chr3B 85.401 137 12 6 313 443 781561324 781561190 5.610000e-28 135.0
20 TraesCS1B01G242700 chrUn 82.254 355 45 12 368 715 343657693 343658036 1.130000e-74 291.0
21 TraesCS1B01G242700 chr7A 81.728 301 48 7 431 727 715772963 715772666 8.940000e-61 244.0
22 TraesCS1B01G242700 chr7A 96.078 51 2 0 554 604 608682183 608682233 2.060000e-12 84.2
23 TraesCS1B01G242700 chr6B 80.183 328 60 4 392 716 294736525 294736200 1.160000e-59 241.0
24 TraesCS1B01G242700 chr6D 79.321 324 30 12 157 443 294438781 294438458 3.280000e-45 193.0
25 TraesCS1B01G242700 chr6D 84.559 136 19 2 583 716 294438164 294438029 2.020000e-27 134.0
26 TraesCS1B01G242700 chr7D 78.339 277 51 7 390 660 195261682 195261409 1.540000e-38 171.0


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 TraesCS1B01G242700 chr1B 430616112 430619336 3224 True 5956 5956 100.0000 1 3225 1 chr1B.!!$R1 3224
1 TraesCS1B01G242700 chr1B 431032651 431034033 1382 False 1387 1387 85.1850 918 2285 1 chr1B.!!$F1 1367
2 TraesCS1B01G242700 chr1B 430884011 430886974 2963 True 233 283 81.3245 2212 3094 2 chr1B.!!$R2 882
3 TraesCS1B01G242700 chr1D 318496118 318498598 2480 True 3853 3853 94.7810 754 3225 1 chr1D.!!$R1 2471
4 TraesCS1B01G242700 chr1D 318722077 318723471 1394 False 1513 1513 86.5400 897 2285 1 chr1D.!!$F1 1388
5 TraesCS1B01G242700 chr1A 399825077 399826827 1750 True 2473 2473 92.2950 781 2523 1 chr1A.!!$R1 1742
6 TraesCS1B01G242700 chr1A 405091649 405093041 1392 True 1459 1459 85.8240 881 2285 1 chr1A.!!$R2 1404
7 TraesCS1B01G242700 chr1A 579751676 579752390 714 False 595 595 82.1180 6 715 1 chr1A.!!$F3 709
8 TraesCS1B01G242700 chr2D 139739184 139739938 754 False 614 614 82.4380 3 716 1 chr2D.!!$F2 713
9 TraesCS1B01G242700 chr3A 698727629 698728257 628 True 532 532 82.6980 12 613 1 chr3A.!!$R1 601

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
168 171 0.244450 CATGCCGAGCCAACAACAAT 59.756 50.0 0.00 0.0 0.00 2.71 F
251 254 0.621609 CTTTGGTTACCCCGGGATGA 59.378 55.0 26.32 0.0 35.15 2.92 F
1872 1981 0.538287 ACCAAAGCCAAGCCAGAGAC 60.538 55.0 0.00 0.0 0.00 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1558 1665 0.168348 CTCGAGTCGAACACGGACAT 59.832 55.0 17.27 0.00 34.74 3.06 R
1909 2018 0.892755 GGGATAGTGACACACCGACA 59.107 55.0 8.59 0.00 34.49 4.35 R
3073 5356 0.804364 CATACTGTTGCATGCACGGT 59.196 50.0 26.73 26.73 0.00 4.83 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
40 41 2.020926 CACACGTGTGGCACAATGA 58.979 52.632 35.65 5.77 44.16 2.57
72 74 3.574074 GACCCTGTGTGGCATGCCT 62.574 63.158 35.53 14.60 36.94 4.75
93 96 4.101448 AGGCAGCCCACACGATCC 62.101 66.667 8.22 0.00 0.00 3.36
97 100 1.897423 CAGCCCACACGATCCTGTA 59.103 57.895 0.00 0.00 0.00 2.74
119 122 0.373716 GGCGAACATTAGAACTGCCG 59.626 55.000 0.00 0.00 0.00 5.69
157 160 2.741985 TTCGTGCCACATGCCGAG 60.742 61.111 0.00 0.00 41.44 4.63
168 171 0.244450 CATGCCGAGCCAACAACAAT 59.756 50.000 0.00 0.00 0.00 2.71
170 173 0.749649 TGCCGAGCCAACAACAATTT 59.250 45.000 0.00 0.00 0.00 1.82
181 184 3.258722 ACAACAATTTCTCACCCCCAT 57.741 42.857 0.00 0.00 0.00 4.00
251 254 0.621609 CTTTGGTTACCCCGGGATGA 59.378 55.000 26.32 0.00 35.15 2.92
315 343 2.670592 GGGGGTTTCGTTCGGGTG 60.671 66.667 0.00 0.00 0.00 4.61
347 375 4.699637 TGCCATGTCTAATTAACGGTAGG 58.300 43.478 0.00 0.00 0.00 3.18
350 378 5.667466 CCATGTCTAATTAACGGTAGGTGT 58.333 41.667 0.00 0.00 0.00 4.16
376 404 4.690748 CGTGTGATCAAACCATAGTTGTCT 59.309 41.667 10.52 0.00 35.97 3.41
419 494 4.213270 CACGTGTGGTCAAATCATAGTTGT 59.787 41.667 7.58 0.00 0.00 3.32
428 503 5.796935 GTCAAATCATAGTTGTCATGTGTGC 59.203 40.000 0.00 0.00 0.00 4.57
448 523 5.943416 TGTGCTTAACTAGTTGCCACATATT 59.057 36.000 22.76 0.00 0.00 1.28
456 531 3.495331 AGTTGCCACATATTCACACCAA 58.505 40.909 0.00 0.00 0.00 3.67
474 550 4.876107 CACCAATAGTTGTGTCTATCACCC 59.124 45.833 0.00 0.00 45.61 4.61
486 562 2.279502 TATCACCCTGTGAGCGTCGC 62.280 60.000 9.80 9.80 46.04 5.19
591 667 2.325583 AATGATAACGCCCACACGAT 57.674 45.000 0.00 0.00 36.70 3.73
605 681 1.202710 ACACGATGTTGGGTGCTTACA 60.203 47.619 0.00 0.00 37.68 2.41
610 686 0.897863 TGTTGGGTGCTTACATGGCC 60.898 55.000 0.00 0.00 0.00 5.36
639 715 3.493002 CCAGATGGCAACTGCTTCAAAAA 60.493 43.478 18.36 0.00 41.70 1.94
641 717 4.753107 CAGATGGCAACTGCTTCAAAAATT 59.247 37.500 12.00 0.00 41.70 1.82
661 737 1.083489 GTGCAAATGGATCGAACGGA 58.917 50.000 0.00 0.00 0.00 4.69
675 751 2.666344 CGAACGGAATCGAGTGTGTGTA 60.666 50.000 0.00 0.00 45.48 2.90
690 767 5.245301 AGTGTGTGTAGGCTGTTGATAAGTA 59.755 40.000 0.00 0.00 0.00 2.24
701 778 5.872617 GCTGTTGATAAGTACCACACATGTA 59.127 40.000 0.00 0.00 0.00 2.29
710 787 6.001449 AGTACCACACATGTAGGCATTATT 57.999 37.500 14.64 0.00 31.99 1.40
716 793 9.415008 ACCACACATGTAGGCATTATTATTTAA 57.585 29.630 14.64 0.00 31.99 1.52
751 828 7.827701 TCTACTCTAACCATTATTAGGCATCG 58.172 38.462 0.00 0.00 33.65 3.84
752 829 6.420913 ACTCTAACCATTATTAGGCATCGT 57.579 37.500 0.00 0.00 33.65 3.73
760 837 5.186021 CCATTATTAGGCATCGTCTAGGTCT 59.814 44.000 0.00 0.00 0.00 3.85
762 839 3.292492 TTAGGCATCGTCTAGGTCTCA 57.708 47.619 0.00 0.00 0.00 3.27
763 840 1.686355 AGGCATCGTCTAGGTCTCAG 58.314 55.000 0.00 0.00 0.00 3.35
767 844 3.380637 GGCATCGTCTAGGTCTCAGTTAA 59.619 47.826 0.00 0.00 0.00 2.01
769 846 5.038033 GCATCGTCTAGGTCTCAGTTAAAG 58.962 45.833 0.00 0.00 0.00 1.85
779 856 5.845065 AGGTCTCAGTTAAAGGAGTAAACCT 59.155 40.000 9.17 9.17 42.69 3.50
799 876 7.868792 AACCTAGGTTTTTACTCCTCTAACT 57.131 36.000 21.96 0.00 34.22 2.24
809 886 8.906238 TTTTACTCCTCTAACTGGTTATAGGT 57.094 34.615 18.16 8.19 39.24 3.08
813 890 6.551601 ACTCCTCTAACTGGTTATAGGTGATG 59.448 42.308 22.15 14.42 39.24 3.07
814 891 5.839063 TCCTCTAACTGGTTATAGGTGATGG 59.161 44.000 18.16 6.74 39.24 3.51
815 892 5.012148 CCTCTAACTGGTTATAGGTGATGGG 59.988 48.000 13.45 0.00 35.73 4.00
833 910 2.647299 TGGGTTAGAAATGCCCTGAGAA 59.353 45.455 0.00 0.00 42.77 2.87
834 911 3.282885 GGGTTAGAAATGCCCTGAGAAG 58.717 50.000 0.00 0.00 39.31 2.85
835 912 3.308473 GGGTTAGAAATGCCCTGAGAAGT 60.308 47.826 0.00 0.00 39.31 3.01
879 959 1.114722 CCATTTGCACACCACACCCT 61.115 55.000 0.00 0.00 0.00 4.34
913 993 7.706179 CCGTTGCCAAATTAATAAACTCATCAT 59.294 33.333 0.00 0.00 0.00 2.45
923 1003 8.839947 TTAATAAACTCATCATCATTTGCACG 57.160 30.769 0.00 0.00 0.00 5.34
960 1041 2.092914 GCCAATATTATCTCCCCCTCCG 60.093 54.545 0.00 0.00 0.00 4.63
976 1058 2.092049 CCTCCGCCCTTTTATAAACCCT 60.092 50.000 0.00 0.00 0.00 4.34
1046 1139 5.962031 TCTTCCCCATTCTTAGTTGCTACTA 59.038 40.000 3.76 3.76 35.78 1.82
1047 1140 5.609533 TCCCCATTCTTAGTTGCTACTAC 57.390 43.478 7.56 0.00 36.61 2.73
1048 1141 4.407945 TCCCCATTCTTAGTTGCTACTACC 59.592 45.833 7.56 0.00 36.61 3.18
1056 1149 5.421374 TCTTAGTTGCTACTACCTTTCCCTC 59.579 44.000 7.56 0.00 36.61 4.30
1060 1153 3.105283 TGCTACTACCTTTCCCTCTTCC 58.895 50.000 0.00 0.00 0.00 3.46
1071 1164 1.437573 CCTCTTCCTCGCGTGCATA 59.562 57.895 5.77 0.00 0.00 3.14
1326 1433 0.670546 CGGTGGAGACGAGCAAACAT 60.671 55.000 0.00 0.00 0.00 2.71
1442 1549 2.413765 GAAGCGAGGGCCGTCTAG 59.586 66.667 22.38 9.67 41.24 2.43
1488 1595 1.078637 ATCGACCGACTCGTCTCCA 60.079 57.895 0.00 0.00 43.45 3.86
1558 1665 3.943137 ATCCCGTCTTCCCTGCCCA 62.943 63.158 0.00 0.00 0.00 5.36
1575 1682 1.071019 CCATGTCCGTGTTCGACTCG 61.071 60.000 0.00 0.00 39.71 4.18
1719 1826 1.142185 CGTGGCTGCATCTACACTCG 61.142 60.000 4.89 0.00 0.00 4.18
1829 1938 2.982130 GGTGTGAGGCGGATCTGT 59.018 61.111 2.89 0.00 0.00 3.41
1871 1980 1.003580 CTACCAAAGCCAAGCCAGAGA 59.996 52.381 0.00 0.00 0.00 3.10
1872 1981 0.538287 ACCAAAGCCAAGCCAGAGAC 60.538 55.000 0.00 0.00 0.00 3.36
1876 1985 2.437359 GCCAAGCCAGAGACGCAT 60.437 61.111 0.00 0.00 0.00 4.73
1909 2018 2.728383 CGACACGCGTCTTTCGGT 60.728 61.111 20.99 11.26 40.23 4.69
1921 2030 0.528901 CTTTCGGTGTCGGTGTGTCA 60.529 55.000 0.00 0.00 36.95 3.58
2344 2492 1.736032 CGCTTGGGAAGGTAGAAGTCG 60.736 57.143 0.00 0.00 0.00 4.18
2399 2547 5.686159 ATCAAGAAACAAGCAGACTCAAG 57.314 39.130 0.00 0.00 0.00 3.02
2415 2568 1.070134 TCAAGACCCAAGTGGAAGTCG 59.930 52.381 0.00 0.00 37.39 4.18
2429 2582 3.635373 TGGAAGTCGCTGTAATAGTAGGG 59.365 47.826 0.00 0.00 0.00 3.53
2493 2646 2.940410 TGACTTGGGTCGTTCAAAGTTC 59.060 45.455 2.98 0.00 44.83 3.01
2601 2805 1.195448 CGCGCAGATGCTTAATTAGGG 59.805 52.381 8.75 0.00 39.32 3.53
2646 2850 5.048846 TGGGGAAAATAGAGGATTGCTAC 57.951 43.478 0.00 0.00 0.00 3.58
2647 2851 4.726825 TGGGGAAAATAGAGGATTGCTACT 59.273 41.667 0.00 0.00 0.00 2.57
2663 2867 2.775890 CTACTATCTGCCTGCCCATTG 58.224 52.381 0.00 0.00 0.00 2.82
2758 2966 7.917505 AGAGCTCAGACTTTGTGTAAAATTTTG 59.082 33.333 17.77 0.00 0.00 2.44
2833 5111 5.923733 ATCCATAGGATGACGATTCCTAC 57.076 43.478 12.65 0.00 46.07 3.18
2848 5126 6.532657 ACGATTCCTACGAAAATCACGTAAAT 59.467 34.615 0.00 0.00 43.72 1.40
2852 5130 8.929827 TTCCTACGAAAATCACGTAAATATCA 57.070 30.769 0.00 0.00 43.72 2.15
2874 5153 8.985315 ATCATATGAATCAAAGTAGCTTTCCA 57.015 30.769 9.99 0.00 30.60 3.53
2963 5242 1.489230 ACGAAACCACTGACCTTTCCT 59.511 47.619 0.00 0.00 0.00 3.36
2979 5262 5.171476 CCTTTCCTCACATGTACAGTACAG 58.829 45.833 18.30 12.51 42.77 2.74
3073 5356 1.613925 GTCCACTGAGTCACTGCACTA 59.386 52.381 0.00 0.00 0.00 2.74
3186 5477 2.281484 GTTTCGTGCTGCCCCAGA 60.281 61.111 0.00 0.00 32.44 3.86
3197 5488 2.836360 CCCCAGACCCATGCATGC 60.836 66.667 21.69 11.82 0.00 4.06
3198 5489 2.043752 CCCAGACCCATGCATGCA 60.044 61.111 25.04 25.04 0.00 3.96
3199 5490 1.456892 CCCAGACCCATGCATGCAT 60.457 57.895 27.46 27.46 37.08 3.96
3200 5491 0.178984 CCCAGACCCATGCATGCATA 60.179 55.000 31.73 6.51 34.91 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.694910 GTGGTAGTTATCGGTGTCCAATATG 59.305 44.000 0.00 0.00 0.00 1.78
2 3 4.710865 TGTGGTAGTTATCGGTGTCCAATA 59.289 41.667 0.00 0.00 0.00 1.90
3 4 3.516300 TGTGGTAGTTATCGGTGTCCAAT 59.484 43.478 0.00 0.00 0.00 3.16
4 5 2.898612 TGTGGTAGTTATCGGTGTCCAA 59.101 45.455 0.00 0.00 0.00 3.53
40 41 1.072505 GGGTCATGTGGTCGGTGTT 59.927 57.895 0.00 0.00 0.00 3.32
72 74 4.393155 CGTGTGGGCTGCCTGCTA 62.393 66.667 19.68 0.00 42.39 3.49
91 94 3.035363 TCTAATGTTCGCCCATACAGGA 58.965 45.455 0.00 0.00 41.22 3.86
93 96 4.271049 CAGTTCTAATGTTCGCCCATACAG 59.729 45.833 0.00 0.00 0.00 2.74
97 100 2.017049 GCAGTTCTAATGTTCGCCCAT 58.983 47.619 0.00 0.00 0.00 4.00
119 122 1.859427 TAGCTGTGTCCGGACGTGTC 61.859 60.000 28.70 18.45 0.00 3.67
132 135 0.321671 ATGTGGCACGAAGTAGCTGT 59.678 50.000 13.77 0.00 41.61 4.40
157 160 2.547855 GGGGTGAGAAATTGTTGTTGGC 60.548 50.000 0.00 0.00 0.00 4.52
168 171 2.978946 GCGGGATGGGGGTGAGAAA 61.979 63.158 0.00 0.00 0.00 2.52
170 173 4.731853 TGCGGGATGGGGGTGAGA 62.732 66.667 0.00 0.00 0.00 3.27
347 375 1.937223 TGGTTTGATCACACGTGACAC 59.063 47.619 25.01 10.79 43.11 3.67
350 378 4.265904 ACTATGGTTTGATCACACGTGA 57.734 40.909 25.01 0.00 44.59 4.35
376 404 4.212425 CGTGGCAACTAGTTAATCACACAA 59.788 41.667 23.05 0.00 37.61 3.33
410 438 6.230472 AGTTAAGCACACATGACAACTATGA 58.770 36.000 0.00 0.00 0.00 2.15
419 494 3.751175 GGCAACTAGTTAAGCACACATGA 59.249 43.478 17.00 0.00 0.00 3.07
428 503 7.414098 GGTGTGAATATGTGGCAACTAGTTAAG 60.414 40.741 8.04 0.00 37.61 1.85
486 562 0.179189 GAAATTGCTCTTCGCCCACG 60.179 55.000 0.00 0.00 42.01 4.94
501 577 1.508632 CCCGAACGTGTGAGTGAAAT 58.491 50.000 0.00 0.00 0.00 2.17
506 582 3.553437 CTCGCCCGAACGTGTGAGT 62.553 63.158 10.88 0.00 35.04 3.41
560 636 4.390603 GGCGTTATCATTTAGTGTCACACA 59.609 41.667 11.40 0.00 36.74 3.72
591 667 0.897863 GGCCATGTAAGCACCCAACA 60.898 55.000 0.00 0.00 0.00 3.33
610 686 1.379044 GTTGCCATCTGGGTGGAGG 60.379 63.158 3.79 0.00 42.02 4.30
639 715 2.159393 CCGTTCGATCCATTTGCACAAT 60.159 45.455 0.00 0.00 0.00 2.71
641 717 0.801872 CCGTTCGATCCATTTGCACA 59.198 50.000 0.00 0.00 0.00 4.57
661 737 1.618837 ACAGCCTACACACACTCGATT 59.381 47.619 0.00 0.00 0.00 3.34
670 746 4.528987 TGGTACTTATCAACAGCCTACACA 59.471 41.667 0.00 0.00 0.00 3.72
675 751 3.326588 TGTGTGGTACTTATCAACAGCCT 59.673 43.478 0.00 0.00 0.00 4.58
690 767 7.896383 AAATAATAATGCCTACATGTGTGGT 57.104 32.000 9.11 0.00 36.36 4.16
725 802 8.304596 CGATGCCTAATAATGGTTAGAGTAGAA 58.695 37.037 0.00 0.00 34.34 2.10
726 803 7.450634 ACGATGCCTAATAATGGTTAGAGTAGA 59.549 37.037 0.00 0.00 34.34 2.59
727 804 7.603651 ACGATGCCTAATAATGGTTAGAGTAG 58.396 38.462 0.00 0.00 34.34 2.57
728 805 7.450634 AGACGATGCCTAATAATGGTTAGAGTA 59.549 37.037 0.00 0.00 34.34 2.59
729 806 6.267928 AGACGATGCCTAATAATGGTTAGAGT 59.732 38.462 0.00 0.00 34.34 3.24
730 807 6.692486 AGACGATGCCTAATAATGGTTAGAG 58.308 40.000 0.00 0.00 34.34 2.43
731 808 6.665992 AGACGATGCCTAATAATGGTTAGA 57.334 37.500 0.00 0.00 34.34 2.10
732 809 7.036220 CCTAGACGATGCCTAATAATGGTTAG 58.964 42.308 0.00 0.00 0.00 2.34
733 810 6.495872 ACCTAGACGATGCCTAATAATGGTTA 59.504 38.462 0.00 0.00 0.00 2.85
734 811 5.307196 ACCTAGACGATGCCTAATAATGGTT 59.693 40.000 0.00 0.00 0.00 3.67
735 812 4.838986 ACCTAGACGATGCCTAATAATGGT 59.161 41.667 0.00 0.00 0.00 3.55
736 813 5.186021 AGACCTAGACGATGCCTAATAATGG 59.814 44.000 0.00 0.00 0.00 3.16
737 814 6.071896 TGAGACCTAGACGATGCCTAATAATG 60.072 42.308 0.00 0.00 0.00 1.90
738 815 6.010850 TGAGACCTAGACGATGCCTAATAAT 58.989 40.000 0.00 0.00 0.00 1.28
739 816 5.382616 TGAGACCTAGACGATGCCTAATAA 58.617 41.667 0.00 0.00 0.00 1.40
740 817 4.981812 TGAGACCTAGACGATGCCTAATA 58.018 43.478 0.00 0.00 0.00 0.98
741 818 3.823873 CTGAGACCTAGACGATGCCTAAT 59.176 47.826 0.00 0.00 0.00 1.73
742 819 3.215151 CTGAGACCTAGACGATGCCTAA 58.785 50.000 0.00 0.00 0.00 2.69
743 820 2.172930 ACTGAGACCTAGACGATGCCTA 59.827 50.000 0.00 0.00 0.00 3.93
744 821 1.064314 ACTGAGACCTAGACGATGCCT 60.064 52.381 0.00 0.00 0.00 4.75
745 822 1.394618 ACTGAGACCTAGACGATGCC 58.605 55.000 0.00 0.00 0.00 4.40
746 823 4.634184 TTAACTGAGACCTAGACGATGC 57.366 45.455 0.00 0.00 0.00 3.91
747 824 5.357314 TCCTTTAACTGAGACCTAGACGATG 59.643 44.000 0.00 0.00 0.00 3.84
748 825 5.507637 TCCTTTAACTGAGACCTAGACGAT 58.492 41.667 0.00 0.00 0.00 3.73
749 826 4.914983 TCCTTTAACTGAGACCTAGACGA 58.085 43.478 0.00 0.00 0.00 4.20
750 827 4.701171 ACTCCTTTAACTGAGACCTAGACG 59.299 45.833 7.29 0.00 32.84 4.18
751 828 7.700022 TTACTCCTTTAACTGAGACCTAGAC 57.300 40.000 7.29 0.00 32.84 2.59
752 829 7.178097 GGTTTACTCCTTTAACTGAGACCTAGA 59.822 40.741 7.29 0.00 32.84 2.43
760 837 7.622502 AACCTAGGTTTACTCCTTTAACTGA 57.377 36.000 21.96 0.00 38.86 3.41
779 856 7.622502 AACCAGTTAGAGGAGTAAAAACCTA 57.377 36.000 0.00 0.00 36.57 3.08
799 876 6.894735 TTTCTAACCCATCACCTATAACCA 57.105 37.500 0.00 0.00 0.00 3.67
809 886 2.580322 TCAGGGCATTTCTAACCCATCA 59.420 45.455 0.00 0.00 46.88 3.07
813 890 3.282885 CTTCTCAGGGCATTTCTAACCC 58.717 50.000 0.00 0.00 44.62 4.11
814 891 3.956744 ACTTCTCAGGGCATTTCTAACC 58.043 45.455 0.00 0.00 0.00 2.85
815 892 6.879458 TCTTAACTTCTCAGGGCATTTCTAAC 59.121 38.462 0.00 0.00 0.00 2.34
833 910 4.842380 TGTAACCTAGGTTGGCTCTTAACT 59.158 41.667 33.19 8.39 38.92 2.24
834 911 5.156608 TGTAACCTAGGTTGGCTCTTAAC 57.843 43.478 33.19 21.58 38.92 2.01
835 912 5.072058 TGTTGTAACCTAGGTTGGCTCTTAA 59.928 40.000 33.19 11.15 38.92 1.85
879 959 5.769484 TTAATTTGGCAACGGTTTGACTA 57.231 34.783 0.00 0.00 41.96 2.59
913 993 1.609555 GGGTTTGGTACGTGCAAATGA 59.390 47.619 5.86 0.00 0.00 2.57
923 1003 0.111639 TGGCTCTTGGGGTTTGGTAC 59.888 55.000 0.00 0.00 0.00 3.34
960 1041 4.037565 CGAATGGAGGGTTTATAAAAGGGC 59.962 45.833 0.00 0.00 0.00 5.19
976 1058 0.984230 AGGAAAGTGGAGCGAATGGA 59.016 50.000 0.00 0.00 0.00 3.41
1046 1139 1.889530 CGCGAGGAAGAGGGAAAGGT 61.890 60.000 0.00 0.00 0.00 3.50
1047 1140 1.153549 CGCGAGGAAGAGGGAAAGG 60.154 63.158 0.00 0.00 0.00 3.11
1048 1141 0.737715 CACGCGAGGAAGAGGGAAAG 60.738 60.000 15.93 0.00 0.00 2.62
1056 1149 2.582959 GAGTATGCACGCGAGGAAG 58.417 57.895 15.93 0.00 0.00 3.46
1071 1164 3.063084 GGAGCACGAGGGACGAGT 61.063 66.667 0.00 0.00 45.77 4.18
1115 1212 1.363744 GACGTCCTTCCAAGCAGATG 58.636 55.000 3.51 0.00 0.00 2.90
1149 1249 7.820386 ACCGAACCTTTCTTGTTTTACAAATTT 59.180 29.630 0.00 0.00 37.69 1.82
1169 1269 4.025647 GTGCATAAATAGCAGAGACCGAAC 60.026 45.833 0.00 0.00 43.63 3.95
1558 1665 0.168348 CTCGAGTCGAACACGGACAT 59.832 55.000 17.27 0.00 34.74 3.06
1605 1712 4.687215 ATGCACACCGCGCAGTCT 62.687 61.111 8.75 0.00 46.97 3.24
1768 1875 2.342648 GTCGTTCTTGGGCTCGGT 59.657 61.111 0.00 0.00 0.00 4.69
1871 1980 1.632046 CTTCCGCCGTTTACATGCGT 61.632 55.000 11.25 0.00 46.44 5.24
1876 1985 2.739287 CGCCTTCCGCCGTTTACA 60.739 61.111 0.00 0.00 0.00 2.41
1909 2018 0.892755 GGGATAGTGACACACCGACA 59.107 55.000 8.59 0.00 34.49 4.35
1921 2030 3.571590 CAGGAGTCAGCTAAGGGATAGT 58.428 50.000 0.00 0.00 33.87 2.12
2325 2472 1.549170 TCGACTTCTACCTTCCCAAGC 59.451 52.381 0.00 0.00 0.00 4.01
2328 2475 3.835978 TCAATTCGACTTCTACCTTCCCA 59.164 43.478 0.00 0.00 0.00 4.37
2344 2492 5.463724 CCTACATTCTAGGCGAGTTCAATTC 59.536 44.000 0.00 0.00 0.00 2.17
2399 2547 0.951040 CAGCGACTTCCACTTGGGTC 60.951 60.000 0.00 0.00 38.11 4.46
2415 2568 4.674281 AGCAGTTCCCTACTATTACAGC 57.326 45.455 0.00 0.00 34.56 4.40
2429 2582 5.444745 GCATGTCGTAGTAGAAAAGCAGTTC 60.445 44.000 0.00 0.00 0.00 3.01
2646 2850 0.475475 TCCAATGGGCAGGCAGATAG 59.525 55.000 0.00 0.00 0.00 2.08
2647 2851 0.925558 TTCCAATGGGCAGGCAGATA 59.074 50.000 0.00 0.00 0.00 1.98
2758 2966 8.661345 AGGAATTTCCCCTAGTCTATTTCATAC 58.339 37.037 11.92 0.00 37.19 2.39
2773 2981 7.686859 GCCTTGATTTGTATTAGGAATTTCCCC 60.687 40.741 11.92 0.00 37.19 4.81
2852 5130 7.284034 CCACTGGAAAGCTACTTTGATTCATAT 59.716 37.037 0.00 0.00 33.49 1.78
2874 5153 2.122768 GGGAGGATCTGATGTTCCACT 58.877 52.381 15.18 0.00 35.14 4.00
2963 5242 3.765511 GGTACCCTGTACTGTACATGTGA 59.234 47.826 19.99 5.83 39.23 3.58
2979 5262 1.670083 GTGCGTCCAGTTGGTACCC 60.670 63.158 10.07 0.00 36.34 3.69
3073 5356 0.804364 CATACTGTTGCATGCACGGT 59.196 50.000 26.73 26.73 0.00 4.83
3186 5477 4.311520 AGATATGTATGCATGCATGGGT 57.688 40.909 37.43 25.06 37.82 4.51


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

AutoCloner maintained by Alex Coulton.