Multiple sequence alignment - TraesCS5B01G358900

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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 TraesCS5B01G358900 chr5B 100.000 2732 0 0 490 3221 538726897 538724166 0.000000e+00 5046.0
1 TraesCS5B01G358900 chr5B 100.000 357 0 0 1 357 538727386 538727030 0.000000e+00 660.0
2 TraesCS5B01G358900 chr5B 97.479 357 9 0 1 357 427656862 427657218 7.640000e-171 610.0
3 TraesCS5B01G358900 chr5B 96.639 357 12 0 1 357 419840716 419841072 7.690000e-166 593.0
4 TraesCS5B01G358900 chr5B 92.233 309 24 0 493 801 427657271 427657579 3.810000e-119 438.0
5 TraesCS5B01G358900 chr5B 90.446 314 27 3 490 801 427651471 427651159 8.320000e-111 411.0
6 TraesCS5B01G358900 chr5D 94.202 2363 104 15 883 3221 442506129 442503776 0.000000e+00 3574.0
7 TraesCS5B01G358900 chr5D 97.458 354 9 0 4 357 239949195 239948842 3.550000e-169 604.0
8 TraesCS5B01G358900 chr5D 85.668 307 37 4 506 807 534059228 534058924 1.870000e-82 316.0
9 TraesCS5B01G358900 chr5D 83.660 306 41 6 507 805 340330793 340331096 2.450000e-71 279.0
10 TraesCS5B01G358900 chr5A 94.401 2054 78 14 891 2918 558693854 558691812 0.000000e+00 3121.0
11 TraesCS5B01G358900 chr5A 90.265 226 15 3 2914 3136 558691782 558691561 4.070000e-74 289.0
12 TraesCS5B01G358900 chr4B 97.207 358 9 1 1 357 457047468 457047825 3.550000e-169 604.0
13 TraesCS5B01G358900 chr4B 96.919 357 11 0 1 357 581852001 581852357 1.650000e-167 599.0
14 TraesCS5B01G358900 chr4B 96.919 357 11 0 1 357 609385266 609385622 1.650000e-167 599.0
15 TraesCS5B01G358900 chr4B 96.359 357 13 0 1 357 68858826 68858470 3.580000e-164 588.0
16 TraesCS5B01G358900 chr4B 92.038 314 23 2 490 801 457047872 457048185 1.060000e-119 440.0
17 TraesCS5B01G358900 chr4B 91.318 311 27 0 491 801 474326701 474326391 2.970000e-115 425.0
18 TraesCS5B01G358900 chr1D 96.639 357 12 0 1 357 223442339 223441983 7.690000e-166 593.0
19 TraesCS5B01G358900 chr1D 84.146 246 32 4 567 806 76926358 76926602 6.950000e-57 231.0
20 TraesCS5B01G358900 chr6B 96.359 357 13 0 1 357 624871434 624871078 3.580000e-164 588.0
21 TraesCS5B01G358900 chr6B 91.987 312 24 1 490 801 369528120 369527810 1.370000e-118 436.0
22 TraesCS5B01G358900 chr2B 93.939 297 17 1 506 802 152571799 152571504 6.340000e-122 448.0
23 TraesCS5B01G358900 chr4A 91.401 314 24 3 490 801 697744729 697744417 8.260000e-116 427.0
24 TraesCS5B01G358900 chr7B 90.735 313 29 0 491 803 556752934 556753246 4.970000e-113 418.0
25 TraesCS5B01G358900 chr3B 90.064 312 29 2 491 801 699670215 699670525 1.390000e-108 403.0
26 TraesCS5B01G358900 chr7D 84.918 305 40 3 506 805 626741741 626741438 1.450000e-78 303.0
27 TraesCS5B01G358900 chr7D 82.965 317 45 6 506 815 426547040 426547354 8.800000e-71 278.0
28 TraesCS5B01G358900 chr2D 84.641 306 41 3 505 805 542722019 542722323 1.880000e-77 300.0
29 TraesCS5B01G358900 chr2D 83.388 307 45 4 504 805 50053858 50053553 2.450000e-71 279.0
30 TraesCS5B01G358900 chr2D 84.112 107 8 6 2232 2333 633305081 633304979 9.510000e-16 95.3
31 TraesCS5B01G358900 chr3D 84.466 309 41 4 505 807 134009522 134009215 6.760000e-77 298.0
32 TraesCS5B01G358900 chr4D 85.425 247 30 3 567 808 67318443 67318688 5.330000e-63 252.0


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 TraesCS5B01G358900 chr5B 538724166 538727386 3220 True 2853 5046 100.0000 1 3221 2 chr5B.!!$R2 3220
1 TraesCS5B01G358900 chr5B 427656862 427657579 717 False 524 610 94.8560 1 801 2 chr5B.!!$F2 800
2 TraesCS5B01G358900 chr5D 442503776 442506129 2353 True 3574 3574 94.2020 883 3221 1 chr5D.!!$R2 2338
3 TraesCS5B01G358900 chr5A 558691561 558693854 2293 True 1705 3121 92.3330 891 3136 2 chr5A.!!$R1 2245
4 TraesCS5B01G358900 chr4B 457047468 457048185 717 False 522 604 94.6225 1 801 2 chr4B.!!$F3 800

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
834 835 0.306533 TCGTTGCAAAGGAAGCGAAC 59.693 50.0 12.54 0.0 37.84 3.95 F
836 837 0.383949 GTTGCAAAGGAAGCGAACCA 59.616 50.0 0.00 0.0 33.85 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2074 0.982852 ATGGCACCGATCCTTCCTGA 60.983 55.000 0.0 0.0 0.0 3.86 R
2805 2847 1.283793 CCAAACTTCAGTGGCAGCG 59.716 57.895 0.0 0.0 0.0 5.18 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
152 153 4.341806 TGGCAAACAAACATCTCACATCTT 59.658 37.500 0.00 0.00 0.00 2.40
250 251 3.609853 TGGATCAAAACAAGAGGATCGG 58.390 45.455 0.00 0.00 42.67 4.18
276 277 4.706616 AGATTACCTTGAGGGAGGGTTTA 58.293 43.478 1.54 0.00 41.31 2.01
332 333 3.766051 GCAAGATTTGGGAGAGGATTTGT 59.234 43.478 0.00 0.00 0.00 2.83
586 587 1.003959 TAGGCGCTGCACATTGTGA 60.004 52.632 20.77 5.05 35.23 3.58
613 614 3.276091 CACCGAGGCGTTGCACAA 61.276 61.111 0.00 0.00 0.00 3.33
621 622 2.477176 GCGTTGCACAACTGGGTGA 61.477 57.895 11.44 0.00 41.32 4.02
626 627 3.133365 GCACAACTGGGTGAGGGGT 62.133 63.158 6.00 0.00 41.32 4.95
632 633 3.537506 TGGGTGAGGGGTCCAGGA 61.538 66.667 0.00 0.00 0.00 3.86
658 659 2.899838 GTGGACTGGCGTGCAACA 60.900 61.111 5.42 0.00 43.33 3.33
660 661 2.591715 GGACTGGCGTGCAACACT 60.592 61.111 0.00 0.00 35.74 3.55
662 663 1.887242 GACTGGCGTGCAACACTCA 60.887 57.895 0.00 0.00 35.74 3.41
672 673 1.140852 TGCAACACTCACTTGCTAGGT 59.859 47.619 0.00 0.00 43.76 3.08
721 722 1.669760 CGGGCGCTACACAAAAGGA 60.670 57.895 7.64 0.00 0.00 3.36
791 792 8.030692 TGATTTCATCCACAGATCAAAATTGTC 58.969 33.333 0.00 0.00 30.45 3.18
801 802 6.205270 ACAGATCAAAATTGTCAAATTTGCCC 59.795 34.615 17.69 12.54 43.63 5.36
802 803 6.205076 CAGATCAAAATTGTCAAATTTGCCCA 59.795 34.615 17.69 9.45 43.63 5.36
803 804 6.771749 AGATCAAAATTGTCAAATTTGCCCAA 59.228 30.769 17.69 18.99 43.63 4.12
804 805 6.764308 TCAAAATTGTCAAATTTGCCCAAA 57.236 29.167 17.69 10.44 43.63 3.28
805 806 7.161773 TCAAAATTGTCAAATTTGCCCAAAA 57.838 28.000 17.69 5.61 43.63 2.44
806 807 7.779073 TCAAAATTGTCAAATTTGCCCAAAAT 58.221 26.923 17.69 12.85 43.63 1.82
807 808 7.919621 TCAAAATTGTCAAATTTGCCCAAAATC 59.080 29.630 17.69 4.44 43.63 2.17
808 809 5.610235 ATTGTCAAATTTGCCCAAAATCG 57.390 34.783 19.97 0.00 37.51 3.34
809 810 4.327982 TGTCAAATTTGCCCAAAATCGA 57.672 36.364 13.54 0.00 37.51 3.59
810 811 4.892433 TGTCAAATTTGCCCAAAATCGAT 58.108 34.783 13.54 0.00 37.51 3.59
811 812 5.303971 TGTCAAATTTGCCCAAAATCGATT 58.696 33.333 13.54 4.39 37.51 3.34
812 813 6.459066 TGTCAAATTTGCCCAAAATCGATTA 58.541 32.000 11.83 0.00 37.51 1.75
813 814 6.367422 TGTCAAATTTGCCCAAAATCGATTAC 59.633 34.615 11.83 1.15 37.51 1.89
814 815 6.589907 GTCAAATTTGCCCAAAATCGATTACT 59.410 34.615 11.83 0.00 37.51 2.24
815 816 7.117667 GTCAAATTTGCCCAAAATCGATTACTT 59.882 33.333 11.83 0.00 37.51 2.24
816 817 7.330700 TCAAATTTGCCCAAAATCGATTACTTC 59.669 33.333 11.83 1.14 37.51 3.01
817 818 5.339990 ATTTGCCCAAAATCGATTACTTCG 58.660 37.500 11.83 0.00 40.37 3.79
818 819 5.105917 ATTTGCCCAAAATCGATTACTTCGT 60.106 36.000 11.83 0.00 40.14 3.85
819 820 6.571537 ATTTGCCCAAAATCGATTACTTCGTT 60.572 34.615 11.83 0.00 40.14 3.85
820 821 8.521380 ATTTGCCCAAAATCGATTACTTCGTTG 61.521 37.037 11.83 10.64 40.14 4.10
832 833 2.696566 TTCGTTGCAAAGGAAGCGA 58.303 47.368 12.54 7.95 44.73 4.93
833 834 1.018148 TTCGTTGCAAAGGAAGCGAA 58.982 45.000 14.10 14.10 44.73 4.70
834 835 0.306533 TCGTTGCAAAGGAAGCGAAC 59.693 50.000 12.54 0.00 37.84 3.95
835 836 0.660300 CGTTGCAAAGGAAGCGAACC 60.660 55.000 0.00 0.00 32.44 3.62
836 837 0.383949 GTTGCAAAGGAAGCGAACCA 59.616 50.000 0.00 0.00 33.85 3.67
837 838 1.107114 TTGCAAAGGAAGCGAACCAA 58.893 45.000 0.00 0.00 33.85 3.67
838 839 1.327303 TGCAAAGGAAGCGAACCAAT 58.673 45.000 0.00 0.00 33.85 3.16
839 840 1.686052 TGCAAAGGAAGCGAACCAATT 59.314 42.857 0.00 0.00 33.85 2.32
840 841 2.102252 TGCAAAGGAAGCGAACCAATTT 59.898 40.909 0.00 0.00 33.85 1.82
841 842 3.130633 GCAAAGGAAGCGAACCAATTTT 58.869 40.909 0.00 0.00 0.00 1.82
842 843 3.559655 GCAAAGGAAGCGAACCAATTTTT 59.440 39.130 0.00 0.00 0.00 1.94
873 874 8.084590 TCTTTTTGAGAAAGTATTCGTCTTCC 57.915 34.615 0.00 0.00 40.63 3.46
874 875 7.931948 TCTTTTTGAGAAAGTATTCGTCTTCCT 59.068 33.333 0.00 0.00 40.63 3.36
875 876 7.653767 TTTTGAGAAAGTATTCGTCTTCCTC 57.346 36.000 0.00 0.00 40.63 3.71
876 877 4.982999 TGAGAAAGTATTCGTCTTCCTCG 58.017 43.478 0.00 0.00 40.63 4.63
877 878 4.698780 TGAGAAAGTATTCGTCTTCCTCGA 59.301 41.667 0.00 0.00 40.63 4.04
878 879 5.357314 TGAGAAAGTATTCGTCTTCCTCGAT 59.643 40.000 0.00 0.00 40.63 3.59
879 880 6.127703 TGAGAAAGTATTCGTCTTCCTCGATT 60.128 38.462 0.00 0.00 40.63 3.34
880 881 6.267070 AGAAAGTATTCGTCTTCCTCGATTC 58.733 40.000 0.00 0.00 40.63 2.52
881 882 5.578005 AAGTATTCGTCTTCCTCGATTCA 57.422 39.130 0.00 0.00 37.18 2.57
919 920 0.846870 AACCCTCCTTCCCCTTCCTG 60.847 60.000 0.00 0.00 0.00 3.86
958 965 2.929724 TCCTTCCCCCAAATATCCACAA 59.070 45.455 0.00 0.00 0.00 3.33
1716 1729 0.387202 CCATCTCCAAGCTCGTCGAT 59.613 55.000 0.00 0.00 0.00 3.59
1740 1753 4.147449 TATGCTGACGCTGCCGCT 62.147 61.111 0.00 0.00 38.22 5.52
1782 1795 2.047443 GGTCGACTCCCTCTTCGCT 61.047 63.158 16.46 0.00 35.15 4.93
2028 2041 1.089920 CAGCTACTGATTTGGCGCTT 58.910 50.000 7.64 0.00 32.44 4.68
2061 2074 2.896801 CGCGCTTGACAAGGCTGTT 61.897 57.895 16.80 0.00 35.30 3.16
2079 2092 1.198094 TTCAGGAAGGATCGGTGCCA 61.198 55.000 0.00 0.00 0.00 4.92
2085 2098 0.469917 AAGGATCGGTGCCATTCGAT 59.530 50.000 5.76 5.76 46.96 3.59
2166 2179 1.683917 ACCAAGGTTAACAATGCGCAA 59.316 42.857 17.11 0.00 0.00 4.85
2181 2194 3.730761 CAACAGCAGGCGCAGGTC 61.731 66.667 10.83 0.00 42.27 3.85
2260 2273 7.966812 AGGTCAGTATACATGCTTTATGATCA 58.033 34.615 5.50 0.00 39.21 2.92
2341 2355 5.519927 TCGATGTGTGTGCTTACTGAATATG 59.480 40.000 0.00 0.00 0.00 1.78
2348 2362 6.368791 TGTGTGCTTACTGAATATGAACAGAC 59.631 38.462 0.00 0.00 37.54 3.51
2426 2440 3.916359 TGTGTAGGGTTGTTGAACTCA 57.084 42.857 0.00 0.00 34.65 3.41
2495 2510 5.241064 TGTCTGTCTTGGTAAGTCTCTACAC 59.759 44.000 0.00 0.00 0.00 2.90
2498 2513 6.654161 TCTGTCTTGGTAAGTCTCTACACTAC 59.346 42.308 0.00 0.00 0.00 2.73
2540 2563 8.592809 TCCATGTTTGTTTAGATAGGCAAAAAT 58.407 29.630 0.00 0.00 33.43 1.82
2552 2583 7.059156 AGATAGGCAAAAATACATTCAGAGCT 58.941 34.615 0.00 0.00 0.00 4.09
2707 2743 2.553602 TGGCACTGCTGTGAACTTATTG 59.446 45.455 25.94 0.00 46.55 1.90
2721 2757 7.331934 TGTGAACTTATTGCACTCTTGATACTC 59.668 37.037 0.00 0.00 33.83 2.59
2735 2771 5.892119 TCTTGATACTCGGAACTGGAATAGT 59.108 40.000 0.00 0.00 42.89 2.12
2760 2796 2.037772 CCTAGCTGTGATATCCGGCTTT 59.962 50.000 23.89 10.53 41.74 3.51
2852 2894 3.902881 TTGGCTTGATGTTGGTGTTTT 57.097 38.095 0.00 0.00 0.00 2.43
2862 2904 0.459489 TTGGTGTTTTGAGGCTGTGC 59.541 50.000 0.00 0.00 0.00 4.57
2894 2936 2.663119 GCCGACTGTTTCATTGCAATTC 59.337 45.455 9.83 1.95 0.00 2.17
2945 3020 5.291971 ACAATGTTTCTTGAATTGCAGACC 58.708 37.500 0.00 0.00 35.20 3.85
3089 3165 8.474831 GGAAAAGCTATTTAAAAGCCTATTCCA 58.525 33.333 23.99 0.00 41.44 3.53
3103 3179 2.729028 ATTCCAATCTTACCACCCCG 57.271 50.000 0.00 0.00 0.00 5.73
3118 3196 4.264487 ACCACCCCGAAATTACCCTTTTAT 60.264 41.667 0.00 0.00 0.00 1.40
3121 3199 5.067283 CACCCCGAAATTACCCTTTTATGAG 59.933 44.000 0.00 0.00 0.00 2.90
3136 3214 4.940468 TTATGAGATCCCATGCCATGAT 57.060 40.909 6.18 0.00 0.00 2.45
3138 3216 1.074889 TGAGATCCCATGCCATGATGG 59.925 52.381 7.21 7.21 42.45 3.51
3181 3259 5.745312 TGTATGTCCATAGATGTGATCCC 57.255 43.478 0.00 0.00 0.00 3.85
3187 3265 4.999950 GTCCATAGATGTGATCCCAACATC 59.000 45.833 14.01 14.01 40.19 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
152 153 6.417258 TGTTTGGATCTAGAGATTTGCATGA 58.583 36.000 0.00 0.00 34.37 3.07
243 244 4.547671 TCAAGGTAATCTTCTCCGATCCT 58.452 43.478 0.00 0.00 32.41 3.24
250 251 3.389656 CCCTCCCTCAAGGTAATCTTCTC 59.610 52.174 0.00 0.00 36.75 2.87
276 277 5.982890 ATTTGTCCATGGATTTCGAAGTT 57.017 34.783 19.62 0.00 0.00 2.66
332 333 1.862138 TCCCACTCTCTCCCCCTCA 60.862 63.158 0.00 0.00 0.00 3.86
613 614 2.203998 CTGGACCCCTCACCCAGT 60.204 66.667 0.00 0.00 41.81 4.00
621 622 4.270153 TGGCAGTCCTGGACCCCT 62.270 66.667 25.52 8.17 32.18 4.79
626 627 3.625897 CACCGTGGCAGTCCTGGA 61.626 66.667 0.00 0.00 34.17 3.86
632 633 3.941188 CCAGTCCACCGTGGCAGT 61.941 66.667 13.19 2.41 37.47 4.40
721 722 5.255397 TGAAACTATTTCACACCCCTGAT 57.745 39.130 0.00 0.00 44.21 2.90
772 773 8.995220 CAAATTTGACAATTTTGATCTGTGGAT 58.005 29.630 22.40 0.00 40.09 3.41
780 781 6.956202 TTGGGCAAATTTGACAATTTTGAT 57.044 29.167 27.56 2.32 40.09 2.57
791 792 6.966435 AGTAATCGATTTTGGGCAAATTTG 57.034 33.333 17.19 14.03 35.02 2.32
808 809 4.159120 GCTTCCTTTGCAACGAAGTAATC 58.841 43.478 25.40 12.72 45.00 1.75
809 810 3.364964 CGCTTCCTTTGCAACGAAGTAAT 60.365 43.478 25.40 0.00 45.00 1.89
810 811 2.032377 CGCTTCCTTTGCAACGAAGTAA 60.032 45.455 25.40 6.06 45.00 2.24
811 812 1.529438 CGCTTCCTTTGCAACGAAGTA 59.471 47.619 25.40 2.42 45.00 2.24
813 814 0.586319 TCGCTTCCTTTGCAACGAAG 59.414 50.000 22.68 22.68 36.82 3.79
814 815 1.018148 TTCGCTTCCTTTGCAACGAA 58.982 45.000 14.10 14.10 37.21 3.85
815 816 0.306533 GTTCGCTTCCTTTGCAACGA 59.693 50.000 4.19 3.94 0.00 3.85
816 817 0.660300 GGTTCGCTTCCTTTGCAACG 60.660 55.000 0.00 0.00 0.00 4.10
817 818 0.383949 TGGTTCGCTTCCTTTGCAAC 59.616 50.000 0.00 0.00 0.00 4.17
818 819 1.107114 TTGGTTCGCTTCCTTTGCAA 58.893 45.000 0.00 0.00 0.00 4.08
819 820 1.327303 ATTGGTTCGCTTCCTTTGCA 58.673 45.000 0.00 0.00 0.00 4.08
820 821 2.438868 AATTGGTTCGCTTCCTTTGC 57.561 45.000 0.00 0.00 0.00 3.68
847 848 8.557029 GGAAGACGAATACTTTCTCAAAAAGAA 58.443 33.333 4.64 0.00 42.35 2.52
848 849 7.931948 AGGAAGACGAATACTTTCTCAAAAAGA 59.068 33.333 4.64 0.00 28.16 2.52
849 850 8.089115 AGGAAGACGAATACTTTCTCAAAAAG 57.911 34.615 0.00 0.00 28.16 2.27
850 851 7.095774 CGAGGAAGACGAATACTTTCTCAAAAA 60.096 37.037 13.86 0.00 45.26 1.94
851 852 6.365247 CGAGGAAGACGAATACTTTCTCAAAA 59.635 38.462 13.86 0.00 45.26 2.44
852 853 5.862323 CGAGGAAGACGAATACTTTCTCAAA 59.138 40.000 13.86 0.00 45.26 2.69
853 854 5.182570 TCGAGGAAGACGAATACTTTCTCAA 59.817 40.000 13.86 0.00 45.26 3.02
854 855 4.698780 TCGAGGAAGACGAATACTTTCTCA 59.301 41.667 13.86 2.19 45.26 3.27
855 856 5.232610 TCGAGGAAGACGAATACTTTCTC 57.767 43.478 0.00 0.00 42.99 2.87
856 857 5.838531 ATCGAGGAAGACGAATACTTTCT 57.161 39.130 0.00 0.00 42.80 2.52
857 858 6.034591 TGAATCGAGGAAGACGAATACTTTC 58.965 40.000 0.00 0.00 42.80 2.62
858 859 5.962433 TGAATCGAGGAAGACGAATACTTT 58.038 37.500 0.00 0.00 42.80 2.66
859 860 5.578005 TGAATCGAGGAAGACGAATACTT 57.422 39.130 0.00 0.00 42.80 2.24
860 861 5.776173 ATGAATCGAGGAAGACGAATACT 57.224 39.130 0.00 0.00 42.80 2.12
861 862 5.977725 TGAATGAATCGAGGAAGACGAATAC 59.022 40.000 0.00 0.00 42.80 1.89
862 863 6.144078 TGAATGAATCGAGGAAGACGAATA 57.856 37.500 0.00 0.00 42.80 1.75
863 864 5.011090 TGAATGAATCGAGGAAGACGAAT 57.989 39.130 0.00 0.00 42.80 3.34
864 865 4.450082 TGAATGAATCGAGGAAGACGAA 57.550 40.909 0.00 0.00 42.80 3.85
865 866 4.655762 ATGAATGAATCGAGGAAGACGA 57.344 40.909 0.00 0.00 43.65 4.20
866 867 4.551603 GCAATGAATGAATCGAGGAAGACG 60.552 45.833 0.00 0.00 0.00 4.18
867 868 4.333649 TGCAATGAATGAATCGAGGAAGAC 59.666 41.667 0.00 0.00 0.00 3.01
868 869 4.516323 TGCAATGAATGAATCGAGGAAGA 58.484 39.130 0.00 0.00 0.00 2.87
869 870 4.888038 TGCAATGAATGAATCGAGGAAG 57.112 40.909 0.00 0.00 0.00 3.46
870 871 5.393352 CCTTTGCAATGAATGAATCGAGGAA 60.393 40.000 13.58 0.00 0.00 3.36
871 872 4.096833 CCTTTGCAATGAATGAATCGAGGA 59.903 41.667 13.58 0.00 0.00 3.71
872 873 4.096833 TCCTTTGCAATGAATGAATCGAGG 59.903 41.667 13.58 6.49 0.00 4.63
873 874 5.239359 TCCTTTGCAATGAATGAATCGAG 57.761 39.130 13.58 0.00 0.00 4.04
874 875 5.641783 TTCCTTTGCAATGAATGAATCGA 57.358 34.783 13.58 0.00 0.00 3.59
875 876 4.266976 GCTTCCTTTGCAATGAATGAATCG 59.733 41.667 13.58 2.69 0.00 3.34
876 877 4.266976 CGCTTCCTTTGCAATGAATGAATC 59.733 41.667 13.58 4.36 0.00 2.52
877 878 4.082081 TCGCTTCCTTTGCAATGAATGAAT 60.082 37.500 13.58 0.00 0.00 2.57
878 879 3.255395 TCGCTTCCTTTGCAATGAATGAA 59.745 39.130 13.58 7.82 0.00 2.57
879 880 2.819019 TCGCTTCCTTTGCAATGAATGA 59.181 40.909 13.58 10.65 0.00 2.57
880 881 3.220507 TCGCTTCCTTTGCAATGAATG 57.779 42.857 13.58 8.85 0.00 2.67
881 882 3.578688 GTTCGCTTCCTTTGCAATGAAT 58.421 40.909 13.58 0.00 0.00 2.57
919 920 1.670380 GGAGGAAGAAGAGTGCACGAC 60.670 57.143 12.01 10.03 0.00 4.34
958 965 1.149101 TTTGGTCCTCCTGCCTTCTT 58.851 50.000 0.00 0.00 34.23 2.52
1260 1273 2.746277 GGCAGGTTGTAGGTGGCG 60.746 66.667 0.00 0.00 0.00 5.69
1602 1615 2.445845 TATGGGCGAGGGACAGGG 60.446 66.667 0.00 0.00 0.00 4.45
1866 1879 1.191489 TCACCACATCCTGAAGCCGA 61.191 55.000 0.00 0.00 0.00 5.54
1974 1987 4.363990 CTGGACAGCACGTCGGCT 62.364 66.667 0.00 0.00 46.42 5.52
2028 2041 1.807226 CGCGTAGATGGTGTCCTCA 59.193 57.895 0.00 0.00 0.00 3.86
2061 2074 0.982852 ATGGCACCGATCCTTCCTGA 60.983 55.000 0.00 0.00 0.00 3.86
2079 2092 2.300437 GCTCCTAAGGTAGCCATCGAAT 59.700 50.000 0.00 0.00 32.40 3.34
2085 2098 1.956629 GCACGCTCCTAAGGTAGCCA 61.957 60.000 0.00 0.00 35.22 4.75
2175 2188 2.280457 GCCATCCTAGCGACCTGC 60.280 66.667 0.00 0.00 46.98 4.85
2193 2206 4.323477 TACTGTGGTGCCCGTGCC 62.323 66.667 0.00 0.00 36.33 5.01
2341 2355 2.148916 TGTGACACATCCGTCTGTTC 57.851 50.000 3.56 0.00 36.82 3.18
2472 2486 5.474189 AGTGTAGAGACTTACCAAGACAGAC 59.526 44.000 0.00 0.00 0.00 3.51
2495 2510 6.765036 ACATGGAAGCTTCATTCATACTGTAG 59.235 38.462 27.02 10.83 0.00 2.74
2498 2513 6.446781 AACATGGAAGCTTCATTCATACTG 57.553 37.500 27.02 13.41 0.00 2.74
2540 2563 4.690748 GCAACACACTAAGCTCTGAATGTA 59.309 41.667 0.00 0.00 0.00 2.29
2542 2565 3.750130 AGCAACACACTAAGCTCTGAATG 59.250 43.478 0.00 0.00 30.05 2.67
2544 2567 3.133691 CAGCAACACACTAAGCTCTGAA 58.866 45.455 0.00 0.00 34.61 3.02
2552 2583 5.535783 TGTACCTAGTACAGCAACACACTAA 59.464 40.000 3.51 0.00 42.99 2.24
2707 2743 3.182967 CAGTTCCGAGTATCAAGAGTGC 58.817 50.000 0.00 0.00 33.17 4.40
2735 2771 3.157881 CCGGATATCACAGCTAGGAGAA 58.842 50.000 0.00 0.00 0.00 2.87
2805 2847 1.283793 CCAAACTTCAGTGGCAGCG 59.716 57.895 0.00 0.00 0.00 5.18
2852 2894 1.079612 CAGATCACGCACAGCCTCA 60.080 57.895 0.00 0.00 0.00 3.86
2862 2904 0.109086 ACAGTCGGCTTCAGATCACG 60.109 55.000 0.00 0.00 0.00 4.35
2894 2936 3.277142 AATAAACCCCAAGCCTAGACG 57.723 47.619 0.00 0.00 0.00 4.18
2945 3020 8.218338 ACATAATCTACTTCAGCAAATTCAGG 57.782 34.615 0.00 0.00 0.00 3.86
3044 3120 2.447429 TCCACATAACACCCCAAAAGGA 59.553 45.455 0.00 0.00 38.24 3.36
3089 3165 4.529897 GGTAATTTCGGGGTGGTAAGATT 58.470 43.478 0.00 0.00 0.00 2.40
3103 3179 8.579863 CATGGGATCTCATAAAAGGGTAATTTC 58.420 37.037 8.02 0.00 0.00 2.17
3118 3196 1.074889 CCATCATGGCATGGGATCTCA 59.925 52.381 26.15 0.00 39.95 3.27
3136 3214 7.712264 CAAATCTCTTTGTTACAATTTGCCA 57.288 32.000 0.00 0.00 37.54 4.92
3164 3242 4.422073 TGTTGGGATCACATCTATGGAC 57.578 45.455 0.00 0.00 0.00 4.02
3181 3259 2.586425 AGTTGGAACCCTGTGATGTTG 58.414 47.619 0.00 0.00 0.00 3.33
3187 3265 1.956477 CTTGGAAGTTGGAACCCTGTG 59.044 52.381 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.