Multiple sequence alignment - TraesCS3B01G324400

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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 TraesCS3B01G324400 chr3B 100.000 3092 0 0 1 3092 525244012 525240921 0.000000e+00 5710.0
1 TraesCS3B01G324400 chr3B 86.325 117 12 4 1519 1633 507286943 507287057 1.160000e-24 124.0
2 TraesCS3B01G324400 chr3D 89.161 2980 142 73 2 2867 399382050 399379138 0.000000e+00 3546.0
3 TraesCS3B01G324400 chr3D 95.631 206 9 0 2877 3082 399379089 399378884 6.390000e-87 331.0
4 TraesCS3B01G324400 chr3D 85.470 117 13 4 1519 1633 390042179 390042293 5.420000e-23 119.0
5 TraesCS3B01G324400 chr3A 88.132 2553 116 70 43 2461 518644276 518641777 0.000000e+00 2863.0
6 TraesCS3B01G324400 chr3A 88.753 409 31 9 945 1340 589913979 589914385 1.290000e-133 486.0
7 TraesCS3B01G324400 chr3A 90.190 316 22 3 2561 2867 518641778 518641463 1.340000e-108 403.0
8 TraesCS3B01G324400 chr3A 91.011 178 8 4 2923 3092 518641385 518641208 1.850000e-57 233.0
9 TraesCS3B01G324400 chr3A 87.179 117 11 4 1519 1633 510664230 510664344 2.500000e-26 130.0
10 TraesCS3B01G324400 chr1D 90.830 229 14 3 945 1166 405003486 405003714 1.800000e-77 300.0
11 TraesCS3B01G324400 chr1D 91.870 123 10 0 1520 1642 283617842 283617964 4.100000e-39 172.0
12 TraesCS3B01G324400 chr1D 94.737 57 3 0 1350 1406 481603266 481603322 4.250000e-14 89.8
13 TraesCS3B01G324400 chr4B 90.541 222 15 4 945 1161 616747014 616747234 3.900000e-74 289.0
14 TraesCS3B01G324400 chr1A 90.090 222 17 3 945 1161 278372184 278371963 1.820000e-72 283.0
15 TraesCS3B01G324400 chr1A 91.870 123 10 0 1520 1642 355343726 355343848 4.100000e-39 172.0
16 TraesCS3B01G324400 chr2A 95.312 128 6 0 972 1099 505417413 505417286 1.450000e-48 204.0
17 TraesCS3B01G324400 chr2A 88.406 69 8 0 1338 1406 686214686 686214618 1.980000e-12 84.2
18 TraesCS3B01G324400 chr7A 92.647 136 7 1 972 1104 68202953 68202818 3.150000e-45 193.0
19 TraesCS3B01G324400 chr1B 91.870 123 10 0 1520 1642 385296794 385296916 4.100000e-39 172.0
20 TraesCS3B01G324400 chr1B 96.552 58 2 0 1349 1406 670202744 670202801 2.540000e-16 97.1
21 TraesCS3B01G324400 chr2B 88.406 69 8 0 1338 1406 648653144 648653076 1.980000e-12 84.2


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 TraesCS3B01G324400 chr3B 525240921 525244012 3091 True 5710.000000 5710 100.000000 1 3092 1 chr3B.!!$R1 3091
1 TraesCS3B01G324400 chr3D 399378884 399382050 3166 True 1938.500000 3546 92.396000 2 3082 2 chr3D.!!$R1 3080
2 TraesCS3B01G324400 chr3A 518641208 518644276 3068 True 1166.333333 2863 89.777667 43 3092 3 chr3A.!!$R1 3049

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
248 258 0.107361 CAGGCAGGCACATCTCATCA 60.107 55.0 0.0 0.0 0.0 3.07 F
1677 1853 0.178990 GCCAACCCAACAAGTCCTCT 60.179 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 2060 0.106719 CGAAGCTCTCCTCCTCCTCT 60.107 60.0 0.0 0.0 0.00 3.69 R
2732 2955 0.108520 GGGCACGAATACGGTTCAGA 60.109 55.0 0.0 0.0 44.46 3.27 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
36 37 1.643292 CACGGCGCATGAAGTATGG 59.357 57.895 10.83 0.00 37.26 2.74
101 108 4.137543 GGGTCAAAAACTGAGAGACATGT 58.862 43.478 0.00 0.00 33.60 3.21
112 119 3.507622 TGAGAGACATGTACAGAGTGGTG 59.492 47.826 8.32 0.00 0.00 4.17
116 123 2.299013 GACATGTACAGAGTGGTGGTGA 59.701 50.000 8.32 0.00 0.00 4.02
142 149 1.588139 CGTATCCTGGCCGTCGAAC 60.588 63.158 0.00 0.00 0.00 3.95
239 249 2.827642 GCTGGATCAGGCAGGCAC 60.828 66.667 0.00 0.00 31.21 5.01
240 250 2.672908 CTGGATCAGGCAGGCACA 59.327 61.111 0.00 0.00 0.00 4.57
241 251 1.226542 CTGGATCAGGCAGGCACAT 59.773 57.895 0.00 0.00 0.00 3.21
242 252 0.818445 CTGGATCAGGCAGGCACATC 60.818 60.000 0.00 0.00 0.00 3.06
243 253 1.276859 TGGATCAGGCAGGCACATCT 61.277 55.000 0.00 0.00 0.00 2.90
246 256 0.844660 ATCAGGCAGGCACATCTCAT 59.155 50.000 0.00 0.00 0.00 2.90
247 257 0.179702 TCAGGCAGGCACATCTCATC 59.820 55.000 0.00 0.00 0.00 2.92
248 258 0.107361 CAGGCAGGCACATCTCATCA 60.107 55.000 0.00 0.00 0.00 3.07
250 260 1.202782 AGGCAGGCACATCTCATCATC 60.203 52.381 0.00 0.00 0.00 2.92
289 325 4.034279 GCACATGCACAAAACAAAAGATGT 59.966 37.500 0.00 0.00 42.22 3.06
354 392 1.364171 CAGATCGGTTAGCGAGGGG 59.636 63.158 12.92 0.03 0.00 4.79
378 416 3.154473 ATCGCAGCCTCCGCCTAA 61.154 61.111 0.00 0.00 34.57 2.69
380 418 2.441822 ATCGCAGCCTCCGCCTAATC 62.442 60.000 0.00 0.00 34.57 1.75
381 419 2.825264 GCAGCCTCCGCCTAATCT 59.175 61.111 0.00 0.00 34.57 2.40
383 421 0.393077 GCAGCCTCCGCCTAATCTAA 59.607 55.000 0.00 0.00 34.57 2.10
384 422 1.002544 GCAGCCTCCGCCTAATCTAAT 59.997 52.381 0.00 0.00 34.57 1.73
385 423 2.933056 GCAGCCTCCGCCTAATCTAATC 60.933 54.545 0.00 0.00 34.57 1.75
386 424 1.546476 AGCCTCCGCCTAATCTAATCG 59.454 52.381 0.00 0.00 34.57 3.34
387 425 1.272769 GCCTCCGCCTAATCTAATCGT 59.727 52.381 0.00 0.00 0.00 3.73
388 426 2.671632 GCCTCCGCCTAATCTAATCGTC 60.672 54.545 0.00 0.00 0.00 4.20
389 427 2.094649 CCTCCGCCTAATCTAATCGTCC 60.095 54.545 0.00 0.00 0.00 4.79
390 428 1.538512 TCCGCCTAATCTAATCGTCCG 59.461 52.381 0.00 0.00 0.00 4.79
391 429 1.337821 CGCCTAATCTAATCGTCCGC 58.662 55.000 0.00 0.00 0.00 5.54
392 430 1.711206 GCCTAATCTAATCGTCCGCC 58.289 55.000 0.00 0.00 0.00 6.13
393 431 1.672145 GCCTAATCTAATCGTCCGCCC 60.672 57.143 0.00 0.00 0.00 6.13
394 432 1.893801 CCTAATCTAATCGTCCGCCCT 59.106 52.381 0.00 0.00 0.00 5.19
417 464 3.441290 AAGACGTCGCCCTCCTCG 61.441 66.667 10.46 0.00 0.00 4.63
455 511 3.706373 GCAACAGCGAGGGAGGGA 61.706 66.667 0.00 0.00 0.00 4.20
456 512 2.581354 CAACAGCGAGGGAGGGAG 59.419 66.667 0.00 0.00 0.00 4.30
457 513 1.984570 CAACAGCGAGGGAGGGAGA 60.985 63.158 0.00 0.00 0.00 3.71
485 541 0.546598 ATCCAATCCAGAACCCGGAC 59.453 55.000 0.73 0.00 34.69 4.79
510 573 1.259507 GACTGCACGAAACGCTAAACA 59.740 47.619 0.00 0.00 0.00 2.83
566 637 6.611642 ACACATCCATTCCATACAGTAGTAGT 59.388 38.462 0.00 0.00 32.86 2.73
567 638 7.783119 ACACATCCATTCCATACAGTAGTAGTA 59.217 37.037 0.00 0.00 32.86 1.82
568 639 8.082852 CACATCCATTCCATACAGTAGTAGTAC 58.917 40.741 0.00 0.00 32.86 2.73
569 640 6.872628 TCCATTCCATACAGTAGTAGTACG 57.127 41.667 2.04 0.91 33.97 3.67
570 641 5.240183 TCCATTCCATACAGTAGTAGTACGC 59.760 44.000 2.04 0.00 33.97 4.42
628 699 4.760047 GTCCGTCCACCAGCGCAT 62.760 66.667 11.47 0.00 0.00 4.73
630 701 2.890474 CCGTCCACCAGCGCATAC 60.890 66.667 11.47 0.00 0.00 2.39
631 702 3.254654 CGTCCACCAGCGCATACG 61.255 66.667 11.47 5.99 44.07 3.06
641 712 3.304613 CGCATACGCACGCACATA 58.695 55.556 0.00 0.00 38.40 2.29
642 713 1.852648 CGCATACGCACGCACATAT 59.147 52.632 0.00 0.00 38.40 1.78
643 714 1.056869 CGCATACGCACGCACATATA 58.943 50.000 0.00 0.00 38.40 0.86
644 715 1.201661 CGCATACGCACGCACATATAC 60.202 52.381 0.00 0.00 38.40 1.47
645 716 1.790043 GCATACGCACGCACATATACA 59.210 47.619 0.00 0.00 38.36 2.29
696 767 1.243342 TTGAAAGCTGCACCCATCCG 61.243 55.000 1.02 0.00 0.00 4.18
701 772 4.489771 CTGCACCCATCCGTCCCC 62.490 72.222 0.00 0.00 0.00 4.81
703 774 3.809013 GCACCCATCCGTCCCCAT 61.809 66.667 0.00 0.00 0.00 4.00
704 775 3.006677 CACCCATCCGTCCCCATT 58.993 61.111 0.00 0.00 0.00 3.16
706 777 1.037030 CACCCATCCGTCCCCATTTG 61.037 60.000 0.00 0.00 0.00 2.32
707 778 2.127232 CCCATCCGTCCCCATTTGC 61.127 63.158 0.00 0.00 0.00 3.68
708 779 1.076777 CCATCCGTCCCCATTTGCT 60.077 57.895 0.00 0.00 0.00 3.91
716 787 3.814268 CCCATTTGCTCGCCACCG 61.814 66.667 0.00 0.00 0.00 4.94
731 802 2.044352 CCGTTTCCACCATCCCCC 60.044 66.667 0.00 0.00 0.00 5.40
751 822 1.381327 ATCCATCACTCGACCCGGT 60.381 57.895 0.00 0.00 0.00 5.28
768 843 3.135530 CCCGGTCCTGTACTACTACTACT 59.864 52.174 0.00 0.00 0.00 2.57
770 845 4.047822 CGGTCCTGTACTACTACTACTCG 58.952 52.174 0.00 0.00 0.00 4.18
775 850 4.057432 CTGTACTACTACTACTCGCCTCC 58.943 52.174 0.00 0.00 0.00 4.30
776 851 3.452264 TGTACTACTACTACTCGCCTCCA 59.548 47.826 0.00 0.00 0.00 3.86
783 858 2.575455 CTACTCGCCTCCACCCCTCT 62.575 65.000 0.00 0.00 0.00 3.69
787 862 2.285743 GCCTCCACCCCTCTTCCT 60.286 66.667 0.00 0.00 0.00 3.36
794 878 0.615850 CACCCCTCTTCCTTCCTGAC 59.384 60.000 0.00 0.00 0.00 3.51
803 890 4.223953 TCTTCCTTCCTGACAGTACACTT 58.776 43.478 0.93 0.00 0.00 3.16
804 891 4.281182 TCTTCCTTCCTGACAGTACACTTC 59.719 45.833 0.93 0.00 0.00 3.01
809 896 2.691526 TCCTGACAGTACACTTCGTTGT 59.308 45.455 0.93 0.00 0.00 3.32
812 899 1.525619 GACAGTACACTTCGTTGTGGC 59.474 52.381 13.17 7.15 41.84 5.01
817 904 2.972505 ACTTCGTTGTGGCAGCCG 60.973 61.111 7.03 0.00 0.00 5.52
828 915 1.228063 GGCAGCCGGTGATCATCAT 60.228 57.895 6.80 0.00 0.00 2.45
895 987 2.418628 CGCTTTGAGCTTTTTATCCGGA 59.581 45.455 6.61 6.61 39.60 5.14
927 1036 1.221021 GGGCCGGGACTTCTGTTAG 59.779 63.158 2.18 0.00 0.00 2.34
928 1037 1.449778 GGCCGGGACTTCTGTTAGC 60.450 63.158 2.18 0.00 0.00 3.09
930 1039 1.221021 CCGGGACTTCTGTTAGCCC 59.779 63.158 0.00 0.00 35.40 5.19
931 1040 1.550130 CCGGGACTTCTGTTAGCCCA 61.550 60.000 0.00 0.00 38.75 5.36
932 1041 0.323629 CGGGACTTCTGTTAGCCCAA 59.676 55.000 0.00 0.00 38.75 4.12
934 1043 1.613520 GGGACTTCTGTTAGCCCAACC 60.614 57.143 0.00 0.00 38.68 3.77
935 1044 1.613520 GGACTTCTGTTAGCCCAACCC 60.614 57.143 0.00 0.00 36.20 4.11
952 1066 1.360551 CCAGATAGCTCCGTCCGTG 59.639 63.158 0.00 0.00 0.00 4.94
1472 1636 4.976116 GCGGCAATTAAATCATCAGTTACC 59.024 41.667 0.00 0.00 0.00 2.85
1505 1671 4.391830 GGCTCGTCTGATTTGTGTGAATTA 59.608 41.667 0.00 0.00 0.00 1.40
1677 1853 0.178990 GCCAACCCAACAAGTCCTCT 60.179 55.000 0.00 0.00 0.00 3.69
1780 1977 3.494336 CTGAAGCGCCGGAGCAAG 61.494 66.667 32.12 21.00 39.83 4.01
1781 1978 3.939837 CTGAAGCGCCGGAGCAAGA 62.940 63.158 32.12 13.45 39.83 3.02
1782 1979 2.512515 GAAGCGCCGGAGCAAGAT 60.513 61.111 32.12 14.85 39.83 2.40
1788 1985 1.221840 GCCGGAGCAAGATCAGGAA 59.778 57.895 5.05 0.00 36.74 3.36
1916 2113 3.687102 CCAGTACCCGACGTGGCA 61.687 66.667 0.00 0.00 35.87 4.92
2135 2340 2.436542 CCCGTTTTCCCCCTTTCTTTTT 59.563 45.455 0.00 0.00 0.00 1.94
2188 2395 4.380841 TTTGGAGGTGTAGTACATAGCG 57.619 45.455 6.21 0.00 0.00 4.26
2221 2428 2.859165 AGGGATTTCGCTGTTCAAGA 57.141 45.000 0.00 0.00 37.77 3.02
2244 2451 4.412207 GTGGCTTTCCGCTTATTTTACTG 58.588 43.478 0.00 0.00 39.75 2.74
2245 2452 4.076394 TGGCTTTCCGCTTATTTTACTGT 58.924 39.130 0.00 0.00 39.13 3.55
2261 2468 4.093952 GTCTCGGTTCCGTCGCGA 62.094 66.667 3.71 3.71 0.00 5.87
2336 2543 0.454600 GAGCAGTTCCGGTCACGATA 59.545 55.000 0.00 0.00 44.60 2.92
2340 2547 1.068125 CAGTTCCGGTCACGATACACA 60.068 52.381 0.00 0.00 44.60 3.72
2351 2558 3.052745 CACGATACACATCCGATTCCAG 58.947 50.000 0.00 0.00 0.00 3.86
2386 2594 1.412343 AGGTTGCATTTTCAGGCGTTT 59.588 42.857 0.00 0.00 0.00 3.60
2388 2596 2.611751 GGTTGCATTTTCAGGCGTTTTT 59.388 40.909 0.00 0.00 0.00 1.94
2603 2821 0.455972 CGGCTTGGTAATTTGGTGCG 60.456 55.000 0.00 0.00 0.00 5.34
2724 2947 1.062587 GTGCGATGTCTTGAATTCGGG 59.937 52.381 0.04 0.00 32.45 5.14
2732 2955 3.706594 TGTCTTGAATTCGGGCTCTATCT 59.293 43.478 0.04 0.00 0.00 1.98
2736 2959 3.566351 TGAATTCGGGCTCTATCTCTGA 58.434 45.455 0.04 0.00 0.00 3.27
2794 3018 2.612212 CGGTCGTGATATTTTTGGGAGG 59.388 50.000 0.00 0.00 0.00 4.30
2864 3093 1.332997 GGCATGAAAAGATCGAGCCAG 59.667 52.381 0.00 0.00 45.16 4.85
2867 3096 3.461061 CATGAAAAGATCGAGCCAGCTA 58.539 45.455 0.00 0.00 0.00 3.32
2869 3098 1.864082 GAAAAGATCGAGCCAGCTAGC 59.136 52.381 6.62 6.62 0.00 3.42
2872 3101 0.673437 AGATCGAGCCAGCTAGCTTC 59.327 55.000 16.46 9.80 45.15 3.86
2873 3102 0.673437 GATCGAGCCAGCTAGCTTCT 59.327 55.000 16.46 15.17 45.15 2.85
2874 3103 0.388659 ATCGAGCCAGCTAGCTTCTG 59.611 55.000 16.46 7.93 45.15 3.02
2892 3160 2.950309 TCTGCGAATGAGTACTACTCCC 59.050 50.000 12.79 2.99 44.44 4.30
2909 3177 6.773685 ACTACTCCCTCTGTCTCATAATACAC 59.226 42.308 0.00 0.00 0.00 2.90
2916 3184 4.822350 TCTGTCTCATAATACACGAGGGAG 59.178 45.833 0.00 0.00 0.00 4.30
2950 3221 2.522638 GGCGTTGTATTCGAGCCGG 61.523 63.158 0.00 0.00 38.28 6.13
2983 3254 0.254747 GGGAACCGATGGATGGTGAA 59.745 55.000 0.00 0.00 40.86 3.18
3005 3279 2.180276 AGGTAGATTCGTGGTGCTCTT 58.820 47.619 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.923204 GTGCAGATGCTCTAGTGAACG 59.077 52.381 6.35 0.00 42.66 3.95
7 8 2.104928 CGCCGTGCAGATGCTCTA 59.895 61.111 6.35 0.00 42.66 2.43
20 21 1.821241 CGACCATACTTCATGCGCCG 61.821 60.000 4.18 0.00 32.84 6.46
29 30 3.118775 TGCTTGCTACATCGACCATACTT 60.119 43.478 0.00 0.00 0.00 2.24
36 37 3.109619 GAGTACTGCTTGCTACATCGAC 58.890 50.000 0.00 0.00 0.00 4.20
101 108 1.550524 GATGCTCACCACCACTCTGTA 59.449 52.381 0.00 0.00 0.00 2.74
112 119 0.669077 AGGATACGTCGATGCTCACC 59.331 55.000 4.06 3.76 46.39 4.02
116 123 1.364171 GCCAGGATACGTCGATGCT 59.636 57.895 4.06 0.00 46.39 3.79
142 149 4.100653 TCCAACTGGAGCATCAGATTCTAG 59.899 45.833 12.34 0.00 39.78 2.43
239 249 2.414426 CGGAGCGAGAGATGATGAGATG 60.414 54.545 0.00 0.00 0.00 2.90
240 250 1.811965 CGGAGCGAGAGATGATGAGAT 59.188 52.381 0.00 0.00 0.00 2.75
241 251 1.233919 CGGAGCGAGAGATGATGAGA 58.766 55.000 0.00 0.00 0.00 3.27
242 252 0.240678 CCGGAGCGAGAGATGATGAG 59.759 60.000 0.00 0.00 0.00 2.90
243 253 1.800283 GCCGGAGCGAGAGATGATGA 61.800 60.000 5.05 0.00 0.00 2.92
246 256 2.124109 AGCCGGAGCGAGAGATGA 60.124 61.111 5.05 0.00 46.67 2.92
247 257 2.334653 GAGCCGGAGCGAGAGATG 59.665 66.667 5.05 0.00 46.67 2.90
248 258 2.909965 GGAGCCGGAGCGAGAGAT 60.910 66.667 5.05 0.00 46.67 2.75
319 357 4.256090 GGCCAATCATGTCCGCGC 62.256 66.667 0.00 0.00 0.00 6.86
375 413 2.927014 GCAGGGCGGACGATTAGATTAG 60.927 54.545 0.00 0.00 0.00 1.73
376 414 1.000506 GCAGGGCGGACGATTAGATTA 59.999 52.381 0.00 0.00 0.00 1.75
378 416 1.367840 GCAGGGCGGACGATTAGAT 59.632 57.895 0.00 0.00 0.00 1.98
380 418 2.280186 GGCAGGGCGGACGATTAG 60.280 66.667 0.00 0.00 0.00 1.73
381 419 3.857038 GGGCAGGGCGGACGATTA 61.857 66.667 0.00 0.00 0.00 1.75
391 429 4.760047 CGACGTCTTGGGGCAGGG 62.760 72.222 14.70 0.00 0.00 4.45
417 464 2.442519 TATAGGAGGAGGGCCGGAGC 62.443 65.000 5.05 0.00 39.96 4.70
418 465 0.612453 GTATAGGAGGAGGGCCGGAG 60.612 65.000 5.05 0.00 39.96 4.63
419 466 1.463824 GTATAGGAGGAGGGCCGGA 59.536 63.158 5.05 0.00 39.96 5.14
420 467 1.977544 CGTATAGGAGGAGGGCCGG 60.978 68.421 0.00 0.00 39.96 6.13
423 470 0.033642 GTTGCGTATAGGAGGAGGGC 59.966 60.000 0.00 0.00 0.00 5.19
424 471 1.341531 CTGTTGCGTATAGGAGGAGGG 59.658 57.143 0.00 0.00 0.00 4.30
453 509 1.272212 GATTGGATCGCTCTCCTCTCC 59.728 57.143 3.43 0.00 36.20 3.71
454 510 1.272212 GGATTGGATCGCTCTCCTCTC 59.728 57.143 3.43 0.91 36.20 3.20
455 511 1.337118 GGATTGGATCGCTCTCCTCT 58.663 55.000 3.43 0.00 36.20 3.69
456 512 1.000731 CTGGATTGGATCGCTCTCCTC 59.999 57.143 3.43 0.00 36.20 3.71
457 513 1.047002 CTGGATTGGATCGCTCTCCT 58.953 55.000 3.43 0.00 36.20 3.69
485 541 4.072088 GTTTCGTGCAGTCCCGCG 62.072 66.667 0.00 0.00 39.87 6.46
496 559 3.687200 CCTGTTTTGTTTAGCGTTTCGT 58.313 40.909 0.00 0.00 0.00 3.85
541 604 5.957771 ACTACTGTATGGAATGGATGTGT 57.042 39.130 0.00 0.00 0.00 3.72
542 605 7.055667 ACTACTACTGTATGGAATGGATGTG 57.944 40.000 0.00 0.00 0.00 3.21
628 699 2.877335 TGTTGTATATGTGCGTGCGTA 58.123 42.857 0.00 0.00 0.00 4.42
630 701 2.796976 TTGTTGTATATGTGCGTGCG 57.203 45.000 0.00 0.00 0.00 5.34
631 702 2.837878 CGTTTGTTGTATATGTGCGTGC 59.162 45.455 0.00 0.00 0.00 5.34
632 703 2.837878 GCGTTTGTTGTATATGTGCGTG 59.162 45.455 0.00 0.00 0.00 5.34
633 704 2.473212 CGCGTTTGTTGTATATGTGCGT 60.473 45.455 0.00 0.00 38.39 5.24
634 705 2.090667 CGCGTTTGTTGTATATGTGCG 58.909 47.619 0.00 0.00 36.96 5.34
635 706 1.837747 GCGCGTTTGTTGTATATGTGC 59.162 47.619 8.43 0.00 0.00 4.57
636 707 2.837878 GTGCGCGTTTGTTGTATATGTG 59.162 45.455 8.43 0.00 0.00 3.21
637 708 2.473212 CGTGCGCGTTTGTTGTATATGT 60.473 45.455 12.43 0.00 0.00 2.29
638 709 2.090667 CGTGCGCGTTTGTTGTATATG 58.909 47.619 12.43 0.00 0.00 1.78
639 710 2.429213 CGTGCGCGTTTGTTGTATAT 57.571 45.000 12.43 0.00 0.00 0.86
640 711 3.931105 CGTGCGCGTTTGTTGTATA 57.069 47.368 12.43 0.00 0.00 1.47
641 712 4.810278 CGTGCGCGTTTGTTGTAT 57.190 50.000 12.43 0.00 0.00 2.29
696 767 2.361104 TGGCGAGCAAATGGGGAC 60.361 61.111 0.00 0.00 0.00 4.46
700 771 2.141122 AAACGGTGGCGAGCAAATGG 62.141 55.000 0.00 0.00 0.00 3.16
701 772 0.729140 GAAACGGTGGCGAGCAAATG 60.729 55.000 0.00 0.00 0.00 2.32
702 773 1.579429 GAAACGGTGGCGAGCAAAT 59.421 52.632 0.00 0.00 0.00 2.32
703 774 2.548295 GGAAACGGTGGCGAGCAAA 61.548 57.895 0.00 0.00 0.00 3.68
704 775 2.975799 GGAAACGGTGGCGAGCAA 60.976 61.111 0.00 0.00 0.00 3.91
706 777 3.723348 GTGGAAACGGTGGCGAGC 61.723 66.667 0.00 0.00 0.00 5.03
707 778 3.047877 GGTGGAAACGGTGGCGAG 61.048 66.667 0.00 0.00 0.00 5.03
708 779 3.185299 ATGGTGGAAACGGTGGCGA 62.185 57.895 0.00 0.00 0.00 5.54
731 802 1.068083 CGGGTCGAGTGATGGATGG 59.932 63.158 0.00 0.00 0.00 3.51
732 803 1.068083 CCGGGTCGAGTGATGGATG 59.932 63.158 0.00 0.00 0.00 3.51
733 804 1.381327 ACCGGGTCGAGTGATGGAT 60.381 57.895 6.32 0.00 0.00 3.41
734 805 2.036731 ACCGGGTCGAGTGATGGA 59.963 61.111 6.32 0.00 0.00 3.41
751 822 3.708631 AGGCGAGTAGTAGTAGTACAGGA 59.291 47.826 15.89 0.00 0.00 3.86
768 843 2.683933 GAAGAGGGGTGGAGGCGA 60.684 66.667 0.00 0.00 0.00 5.54
770 845 1.916206 GAAGGAAGAGGGGTGGAGGC 61.916 65.000 0.00 0.00 0.00 4.70
775 850 0.615850 GTCAGGAAGGAAGAGGGGTG 59.384 60.000 0.00 0.00 0.00 4.61
776 851 0.193574 TGTCAGGAAGGAAGAGGGGT 59.806 55.000 0.00 0.00 0.00 4.95
783 858 3.005472 CGAAGTGTACTGTCAGGAAGGAA 59.995 47.826 4.53 0.00 0.00 3.36
787 862 3.131577 ACAACGAAGTGTACTGTCAGGAA 59.868 43.478 4.53 0.00 45.00 3.36
794 878 1.526887 CTGCCACAACGAAGTGTACTG 59.473 52.381 10.20 4.09 45.00 2.74
809 896 1.986632 ATGATGATCACCGGCTGCCA 61.987 55.000 20.29 0.00 0.00 4.92
812 899 1.957668 TTGATGATGATCACCGGCTG 58.042 50.000 0.00 0.00 38.38 4.85
817 904 2.360165 GTGGGCTTTGATGATGATCACC 59.640 50.000 0.00 0.00 38.38 4.02
828 915 4.283467 AGCGTATATATCTGTGGGCTTTGA 59.717 41.667 0.00 0.00 0.00 2.69
861 953 2.197605 AAAGCGAAACCAACCCCGG 61.198 57.895 0.00 0.00 0.00 5.73
862 954 1.007849 CAAAGCGAAACCAACCCCG 60.008 57.895 0.00 0.00 0.00 5.73
927 1036 1.149401 GGAGCTATCTGGGTTGGGC 59.851 63.158 0.00 0.00 0.00 5.36
928 1037 1.338136 ACGGAGCTATCTGGGTTGGG 61.338 60.000 0.00 0.00 35.99 4.12
930 1039 0.105039 GGACGGAGCTATCTGGGTTG 59.895 60.000 0.00 0.00 35.99 3.77
931 1040 1.392710 CGGACGGAGCTATCTGGGTT 61.393 60.000 0.00 0.00 35.99 4.11
932 1041 1.828660 CGGACGGAGCTATCTGGGT 60.829 63.158 0.00 0.00 35.99 4.51
934 1043 1.360551 CACGGACGGAGCTATCTGG 59.639 63.158 6.04 0.00 35.99 3.86
935 1044 0.029567 GACACGGACGGAGCTATCTG 59.970 60.000 0.00 0.00 37.86 2.90
1399 1548 2.888594 TCTACGCGTAGTACTTACCGT 58.111 47.619 37.32 9.91 40.14 4.83
1472 1636 4.640789 ATCAGACGAGCCTACTTACTTG 57.359 45.455 0.00 0.00 0.00 3.16
1505 1671 2.029073 CCCTGAACACGCGACAGT 59.971 61.111 15.93 5.29 0.00 3.55
1662 1838 2.058675 CGGAGAGGACTTGTTGGGT 58.941 57.895 0.00 0.00 0.00 4.51
1763 1960 3.494336 CTTGCTCCGGCGCTTCAG 61.494 66.667 18.73 7.19 42.25 3.02
1764 1961 3.315142 ATCTTGCTCCGGCGCTTCA 62.315 57.895 18.73 0.86 42.25 3.02
1765 1962 2.512515 ATCTTGCTCCGGCGCTTC 60.513 61.111 18.73 0.00 42.25 3.86
1766 1963 2.512515 GATCTTGCTCCGGCGCTT 60.513 61.111 18.73 0.00 42.25 4.68
1767 1964 3.729965 CTGATCTTGCTCCGGCGCT 62.730 63.158 18.73 0.00 42.25 5.92
1768 1965 3.267860 CTGATCTTGCTCCGGCGC 61.268 66.667 10.14 10.14 42.25 6.53
1769 1966 2.578163 TTCCTGATCTTGCTCCGGCG 62.578 60.000 0.00 0.00 42.25 6.46
1770 1967 0.813210 CTTCCTGATCTTGCTCCGGC 60.813 60.000 0.00 0.00 39.26 6.13
1771 1968 0.826715 TCTTCCTGATCTTGCTCCGG 59.173 55.000 0.00 0.00 0.00 5.14
1772 1969 1.202510 CCTCTTCCTGATCTTGCTCCG 60.203 57.143 0.00 0.00 0.00 4.63
1773 1970 2.102925 CTCCTCTTCCTGATCTTGCTCC 59.897 54.545 0.00 0.00 0.00 4.70
1774 1971 2.483538 GCTCCTCTTCCTGATCTTGCTC 60.484 54.545 0.00 0.00 0.00 4.26
1775 1972 1.485895 GCTCCTCTTCCTGATCTTGCT 59.514 52.381 0.00 0.00 0.00 3.91
1776 1973 1.209019 TGCTCCTCTTCCTGATCTTGC 59.791 52.381 0.00 0.00 0.00 4.01
1777 1974 3.134262 TCATGCTCCTCTTCCTGATCTTG 59.866 47.826 0.00 0.00 0.00 3.02
1778 1975 3.382278 TCATGCTCCTCTTCCTGATCTT 58.618 45.455 0.00 0.00 0.00 2.40
1779 1976 2.967201 CTCATGCTCCTCTTCCTGATCT 59.033 50.000 0.00 0.00 0.00 2.75
1780 1977 2.548493 GCTCATGCTCCTCTTCCTGATC 60.548 54.545 0.00 0.00 36.03 2.92
1781 1978 1.417145 GCTCATGCTCCTCTTCCTGAT 59.583 52.381 0.00 0.00 36.03 2.90
1782 1979 0.829333 GCTCATGCTCCTCTTCCTGA 59.171 55.000 0.00 0.00 36.03 3.86
1788 1985 0.178533 GCTTCTGCTCATGCTCCTCT 59.821 55.000 0.00 0.00 40.48 3.69
1863 2060 0.106719 CGAAGCTCTCCTCCTCCTCT 60.107 60.000 0.00 0.00 0.00 3.69
2147 2353 5.939296 CCAAATTACTCCGGGTAAAACTACA 59.061 40.000 16.29 0.00 42.74 2.74
2188 2395 4.274459 CGAAATCCCTTTGATCTGATCCAC 59.726 45.833 14.71 0.00 31.61 4.02
2244 2451 3.392595 ATCGCGACGGAACCGAGAC 62.393 63.158 12.93 9.40 42.83 3.36
2245 2452 3.104602 GATCGCGACGGAACCGAGA 62.105 63.158 12.93 12.60 42.83 4.04
2336 2543 0.249120 TTCGCTGGAATCGGATGTGT 59.751 50.000 0.00 0.00 0.00 3.72
2340 2547 1.017387 GCTTTTCGCTGGAATCGGAT 58.983 50.000 0.00 0.00 35.14 4.18
2351 2558 0.317854 AACCTTTCGCTGCTTTTCGC 60.318 50.000 0.00 0.00 39.77 4.70
2407 2615 5.254115 AGGAGTATGTGTATATCTGCGCTA 58.746 41.667 9.73 0.00 0.00 4.26
2416 2633 2.156917 CGGGCGAGGAGTATGTGTATA 58.843 52.381 0.00 0.00 0.00 1.47
2418 2635 1.105167 CCGGGCGAGGAGTATGTGTA 61.105 60.000 0.00 0.00 0.00 2.90
2559 2777 4.431131 CCGGCAAGGATGGTGGCT 62.431 66.667 0.00 0.00 45.00 4.75
2654 2873 1.298339 CGCAAATTTCCCGCGGATC 60.298 57.895 30.73 4.82 45.08 3.36
2659 2881 2.809174 GGCACGCAAATTTCCCGC 60.809 61.111 7.47 0.00 0.00 6.13
2697 2920 1.800586 TCAAGACATCGCACTCAAAGC 59.199 47.619 0.00 0.00 0.00 3.51
2724 2947 4.023878 ACGAATACGGTTCAGAGATAGAGC 60.024 45.833 0.00 0.00 44.46 4.09
2732 2955 0.108520 GGGCACGAATACGGTTCAGA 60.109 55.000 0.00 0.00 44.46 3.27
2736 2959 0.390735 GACAGGGCACGAATACGGTT 60.391 55.000 0.00 0.00 44.46 4.44
2766 2989 2.660258 AATATCACGACCGGGCAGGC 62.660 60.000 8.76 0.00 46.52 4.85
2794 3018 3.773119 TGTCTGGTTGTAGGTAGATTCCC 59.227 47.826 0.00 0.00 0.00 3.97
2864 3093 1.933247 ACTCATTCGCAGAAGCTAGC 58.067 50.000 6.62 6.62 45.90 3.42
2867 3096 3.697045 AGTAGTACTCATTCGCAGAAGCT 59.303 43.478 0.00 0.00 45.90 3.74
2869 3098 4.498345 GGGAGTAGTACTCATTCGCAGAAG 60.498 50.000 27.41 0.00 46.79 2.85
2870 3099 3.380637 GGGAGTAGTACTCATTCGCAGAA 59.619 47.826 27.41 0.00 46.79 3.02
2872 3101 2.952978 AGGGAGTAGTACTCATTCGCAG 59.047 50.000 27.41 0.00 46.79 5.18
2873 3102 2.950309 GAGGGAGTAGTACTCATTCGCA 59.050 50.000 27.41 0.00 46.79 5.10
2874 3103 3.003897 CAGAGGGAGTAGTACTCATTCGC 59.996 52.174 27.41 18.17 46.79 4.70
2892 3160 4.822350 TCCCTCGTGTATTATGAGACAGAG 59.178 45.833 0.00 0.00 43.79 3.35
2909 3177 0.591741 GATTCGCACGTACTCCCTCG 60.592 60.000 0.00 0.00 0.00 4.63
2916 3184 1.713830 GCCAAGGATTCGCACGTAC 59.286 57.895 0.00 0.00 0.00 3.67
2983 3254 3.567397 AGAGCACCACGAATCTACCTAT 58.433 45.455 0.00 0.00 0.00 2.57
3005 3279 0.324943 GTCCTTTGGAGTGCTAGGCA 59.675 55.000 0.00 0.00 30.58 4.75


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

AutoCloner maintained by Alex Coulton.