Multiple sequence alignment - TraesCS2D01G571400

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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 TraesCS2D01G571400 chr2D 100.000 3005 0 0 1 3005 637801110 637804114 0.000000e+00 5550.0
1 TraesCS2D01G571400 chr2B 92.968 1095 68 4 931 2016 796341178 796342272 0.000000e+00 1587.0
2 TraesCS2D01G571400 chr2B 84.504 897 137 2 1037 1932 796277424 796278319 0.000000e+00 885.0
3 TraesCS2D01G571400 chr2B 87.900 438 25 16 454 887 796340677 796341090 9.680000e-135 490.0
4 TraesCS2D01G571400 chr2B 85.135 518 30 28 2519 3005 796343112 796343613 1.250000e-133 486.0
5 TraesCS2D01G571400 chr2B 87.264 212 9 7 2014 2207 796342432 796342643 3.010000e-55 226.0
6 TraesCS2D01G571400 chr2B 94.253 87 5 0 2296 2382 796342886 796342972 1.880000e-27 134.0
7 TraesCS2D01G571400 chr2A 88.889 1296 71 24 1 1271 761543672 761542425 0.000000e+00 1528.0
8 TraesCS2D01G571400 chr2A 93.884 932 52 3 1262 2188 761541984 761541053 0.000000e+00 1400.0
9 TraesCS2D01G571400 chr2A 88.919 749 33 17 2302 3005 761540958 761540215 0.000000e+00 878.0
10 TraesCS2D01G571400 chr2A 82.323 594 61 31 1017 1594 14997657 14998222 2.710000e-130 475.0
11 TraesCS2D01G571400 chrUn 81.998 1161 183 15 941 2089 249446102 249447248 0.000000e+00 963.0
12 TraesCS2D01G571400 chrUn 79.316 585 93 14 940 1511 22708931 22708362 4.700000e-103 385.0
13 TraesCS2D01G571400 chr1D 82.968 957 131 16 1026 1969 342170284 342171221 0.000000e+00 835.0
14 TraesCS2D01G571400 chr1B 83.209 935 129 19 1052 1969 458081538 458082461 0.000000e+00 832.0
15 TraesCS2D01G571400 chr1B 82.781 935 124 21 1052 1969 458129707 458130621 0.000000e+00 800.0
16 TraesCS2D01G571400 chr1B 82.460 935 127 21 1052 1969 458263075 458263989 0.000000e+00 784.0
17 TraesCS2D01G571400 chr1A 82.225 962 139 16 1021 1969 441842018 441842960 0.000000e+00 800.0
18 TraesCS2D01G571400 chr5A 79.303 947 167 19 1022 1955 597280040 597279110 1.180000e-178 636.0
19 TraesCS2D01G571400 chr7A 87.251 251 22 9 2494 2737 663800511 663800264 8.200000e-71 278.0
20 TraesCS2D01G571400 chr4A 85.657 251 26 9 2494 2737 17735693 17735940 3.840000e-64 255.0
21 TraesCS2D01G571400 chr3A 77.419 217 43 5 210 422 713933736 713933522 1.130000e-24 124.0
22 TraesCS2D01G571400 chr3A 100.000 32 0 0 18 49 602890692 602890723 3.240000e-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 TraesCS2D01G571400 chr2D 637801110 637804114 3004 False 5550.000000 5550 100.000 1 3005 1 chr2D.!!$F1 3004
1 TraesCS2D01G571400 chr2B 796277424 796278319 895 False 885.000000 885 84.504 1037 1932 1 chr2B.!!$F1 895
2 TraesCS2D01G571400 chr2B 796340677 796343613 2936 False 584.600000 1587 89.504 454 3005 5 chr2B.!!$F2 2551
3 TraesCS2D01G571400 chr2A 761540215 761543672 3457 True 1268.666667 1528 90.564 1 3005 3 chr2A.!!$R1 3004
4 TraesCS2D01G571400 chr2A 14997657 14998222 565 False 475.000000 475 82.323 1017 1594 1 chr2A.!!$F1 577
5 TraesCS2D01G571400 chrUn 249446102 249447248 1146 False 963.000000 963 81.998 941 2089 1 chrUn.!!$F1 1148
6 TraesCS2D01G571400 chrUn 22708362 22708931 569 True 385.000000 385 79.316 940 1511 1 chrUn.!!$R1 571
7 TraesCS2D01G571400 chr1D 342170284 342171221 937 False 835.000000 835 82.968 1026 1969 1 chr1D.!!$F1 943
8 TraesCS2D01G571400 chr1B 458081538 458082461 923 False 832.000000 832 83.209 1052 1969 1 chr1B.!!$F1 917
9 TraesCS2D01G571400 chr1B 458129707 458130621 914 False 800.000000 800 82.781 1052 1969 1 chr1B.!!$F2 917
10 TraesCS2D01G571400 chr1B 458263075 458263989 914 False 784.000000 784 82.460 1052 1969 1 chr1B.!!$F3 917
11 TraesCS2D01G571400 chr1A 441842018 441842960 942 False 800.000000 800 82.225 1021 1969 1 chr1A.!!$F1 948
12 TraesCS2D01G571400 chr5A 597279110 597280040 930 True 636.000000 636 79.303 1022 1955 1 chr5A.!!$R1 933

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
888 903 0.040958 CTTGAACCAACGAGCAGCAC 60.041 55.0 0.0 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2216 2957 0.031178 GCTGTTTGCTTGTGACCAGG 59.969 55.0 0.0 0.0 38.95 4.45 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
85 86 4.825085 GGGAACATCACTTACCACTGAAAA 59.175 41.667 0.00 0.00 0.00 2.29
128 129 7.307632 CCTGAAATAAATCTAGGAATGTGCGAG 60.308 40.741 0.00 0.00 0.00 5.03
129 130 5.931441 AATAAATCTAGGAATGTGCGAGC 57.069 39.130 0.00 0.00 0.00 5.03
130 131 2.988010 AATCTAGGAATGTGCGAGCA 57.012 45.000 0.00 0.00 0.00 4.26
131 132 2.231215 ATCTAGGAATGTGCGAGCAC 57.769 50.000 20.14 20.14 46.33 4.40
132 133 0.175760 TCTAGGAATGTGCGAGCACC 59.824 55.000 23.31 9.72 45.63 5.01
133 134 0.176680 CTAGGAATGTGCGAGCACCT 59.823 55.000 23.31 16.00 45.63 4.00
134 135 0.175760 TAGGAATGTGCGAGCACCTC 59.824 55.000 23.31 18.68 45.63 3.85
147 148 0.810031 GCACCTCGCACCGATAACAT 60.810 55.000 0.00 0.00 41.79 2.71
212 213 7.768807 AATTAATAAAGCAGTACCAACACCA 57.231 32.000 0.00 0.00 0.00 4.17
221 222 0.250124 TACCAACACCAGCCAACTCG 60.250 55.000 0.00 0.00 0.00 4.18
237 239 1.226746 CTCGAAACTCCACACCAACC 58.773 55.000 0.00 0.00 0.00 3.77
250 252 2.342650 CCAACCTGCCCACAATCCG 61.343 63.158 0.00 0.00 0.00 4.18
339 341 0.953471 CGTCATCGCCCCTTGTCAAA 60.953 55.000 0.00 0.00 0.00 2.69
353 355 5.299279 CCCTTGTCAAAGACTTAAGCTTTCA 59.701 40.000 16.86 12.35 35.19 2.69
358 360 4.821805 TCAAAGACTTAAGCTTTCACCCAG 59.178 41.667 16.86 8.98 33.56 4.45
361 363 3.648545 AGACTTAAGCTTTCACCCAGAGT 59.351 43.478 3.20 0.00 0.00 3.24
376 378 1.600916 GAGTGACCCACAACAGCCC 60.601 63.158 0.00 0.00 36.74 5.19
567 575 4.550076 ACACTAGTAGGAGTACACGACT 57.450 45.455 1.45 2.21 42.90 4.18
586 594 4.334759 CGACTCCAAATTTGAGCAGATCAT 59.665 41.667 19.86 0.00 37.89 2.45
642 651 3.924114 TCCTGTTGTCTTCTTGGTTGA 57.076 42.857 0.00 0.00 0.00 3.18
661 670 4.639078 TGAGATCAAATCCCAACAGTGA 57.361 40.909 0.00 0.00 0.00 3.41
664 673 3.753272 AGATCAAATCCCAACAGTGAACG 59.247 43.478 0.00 0.00 0.00 3.95
705 714 4.233632 TGAAGATATGCCACATGGTTCA 57.766 40.909 0.00 0.00 37.57 3.18
706 715 4.598022 TGAAGATATGCCACATGGTTCAA 58.402 39.130 0.00 0.00 37.57 2.69
707 716 4.398988 TGAAGATATGCCACATGGTTCAAC 59.601 41.667 0.00 0.00 37.57 3.18
708 717 2.945008 AGATATGCCACATGGTTCAACG 59.055 45.455 0.00 0.00 37.57 4.10
709 718 2.481289 TATGCCACATGGTTCAACGA 57.519 45.000 0.00 0.00 37.57 3.85
710 719 1.614996 ATGCCACATGGTTCAACGAA 58.385 45.000 0.00 0.00 37.57 3.85
711 720 0.950836 TGCCACATGGTTCAACGAAG 59.049 50.000 0.00 0.00 37.57 3.79
712 721 1.234821 GCCACATGGTTCAACGAAGA 58.765 50.000 0.00 0.00 37.57 2.87
713 722 1.812571 GCCACATGGTTCAACGAAGAT 59.187 47.619 0.00 0.00 37.57 2.40
714 723 3.006940 GCCACATGGTTCAACGAAGATA 58.993 45.455 0.00 0.00 37.57 1.98
715 724 3.627577 GCCACATGGTTCAACGAAGATAT 59.372 43.478 0.00 0.00 37.57 1.63
716 725 4.496341 GCCACATGGTTCAACGAAGATATG 60.496 45.833 0.00 0.00 37.57 1.78
717 726 4.496341 CCACATGGTTCAACGAAGATATGC 60.496 45.833 0.00 0.00 0.00 3.14
718 727 3.627577 ACATGGTTCAACGAAGATATGCC 59.372 43.478 0.00 0.00 0.00 4.40
719 728 3.342377 TGGTTCAACGAAGATATGCCA 57.658 42.857 0.00 0.00 0.00 4.92
720 729 3.006940 TGGTTCAACGAAGATATGCCAC 58.993 45.455 0.00 0.00 0.00 5.01
721 730 3.006940 GGTTCAACGAAGATATGCCACA 58.993 45.455 0.00 0.00 0.00 4.17
722 731 3.627577 GGTTCAACGAAGATATGCCACAT 59.372 43.478 0.00 0.00 0.00 3.21
723 732 4.496341 GGTTCAACGAAGATATGCCACATG 60.496 45.833 0.00 0.00 0.00 3.21
724 733 3.205338 TCAACGAAGATATGCCACATGG 58.795 45.455 0.00 0.00 38.53 3.66
725 734 2.945008 CAACGAAGATATGCCACATGGT 59.055 45.455 0.00 0.00 37.57 3.55
726 735 3.281727 ACGAAGATATGCCACATGGTT 57.718 42.857 0.00 0.00 37.57 3.67
727 736 3.206150 ACGAAGATATGCCACATGGTTC 58.794 45.455 0.00 0.00 37.57 3.62
761 770 8.623903 TGAACTAATTTATCAATCAGATGTGGC 58.376 33.333 0.00 0.00 37.57 5.01
763 772 9.851686 AACTAATTTATCAATCAGATGTGGCTA 57.148 29.630 0.00 0.00 37.57 3.93
770 779 3.845781 ATCAGATGTGGCTAATCGGTT 57.154 42.857 0.00 0.00 0.00 4.44
779 788 2.685897 TGGCTAATCGGTTATTGTTGGC 59.314 45.455 0.00 0.00 0.00 4.52
851 861 4.030913 TGAAGATGATAAGGGGAACTCGT 58.969 43.478 0.00 0.00 0.00 4.18
852 862 4.141937 TGAAGATGATAAGGGGAACTCGTG 60.142 45.833 0.00 0.00 0.00 4.35
853 863 3.643237 AGATGATAAGGGGAACTCGTGA 58.357 45.455 0.00 0.00 0.00 4.35
854 864 3.385111 AGATGATAAGGGGAACTCGTGAC 59.615 47.826 0.00 0.00 0.00 3.67
855 865 2.531771 TGATAAGGGGAACTCGTGACA 58.468 47.619 0.00 0.00 0.00 3.58
858 868 1.056660 AAGGGGAACTCGTGACATGT 58.943 50.000 0.00 0.00 0.00 3.21
887 902 0.463654 ACTTGAACCAACGAGCAGCA 60.464 50.000 0.00 0.00 0.00 4.41
888 903 0.040958 CTTGAACCAACGAGCAGCAC 60.041 55.000 0.00 0.00 0.00 4.40
892 907 4.374702 CCAACGAGCAGCACGCAC 62.375 66.667 12.54 0.00 46.13 5.34
893 908 4.374702 CAACGAGCAGCACGCACC 62.375 66.667 12.54 0.00 46.13 5.01
895 910 4.609018 ACGAGCAGCACGCACCTT 62.609 61.111 12.54 0.00 46.13 3.50
896 911 3.349006 CGAGCAGCACGCACCTTT 61.349 61.111 0.00 0.00 46.13 3.11
900 932 2.970974 GCAGCACGCACCTTTCTCC 61.971 63.158 0.00 0.00 41.79 3.71
914 946 2.940994 TTCTCCACCGATTTTCCACA 57.059 45.000 0.00 0.00 0.00 4.17
928 960 7.201723 CCGATTTTCCACACATAGAATTGATCA 60.202 37.037 0.00 0.00 0.00 2.92
931 963 8.578448 TTTTCCACACATAGAATTGATCATGA 57.422 30.769 0.00 0.00 0.00 3.07
932 964 7.558161 TTCCACACATAGAATTGATCATGAC 57.442 36.000 0.00 0.00 0.00 3.06
933 965 6.057533 TCCACACATAGAATTGATCATGACC 58.942 40.000 0.00 0.00 0.00 4.02
935 967 6.017357 CCACACATAGAATTGATCATGACCAG 60.017 42.308 0.00 0.00 0.00 4.00
957 1016 6.393990 CAGAGATCTATAAATAGCGGCACTT 58.606 40.000 1.45 0.00 0.00 3.16
978 1037 2.084546 GGTTGGCGCCATAATCTATCC 58.915 52.381 33.25 17.37 0.00 2.59
990 1055 3.864789 AATCTATCCGGCACCAAGATT 57.135 42.857 0.00 3.76 33.23 2.40
995 1060 0.107214 TCCGGCACCAAGATTGATCC 60.107 55.000 0.00 0.00 0.00 3.36
1000 1065 1.678728 GCACCAAGATTGATCCGACCA 60.679 52.381 0.00 0.00 0.00 4.02
1007 1072 2.909006 AGATTGATCCGACCATGCCTAT 59.091 45.455 0.00 0.00 0.00 2.57
1024 1093 3.831911 GCCTATACTGAGAATGAGAGCCT 59.168 47.826 0.00 0.00 0.00 4.58
1171 1249 2.124507 TTACTGTGGCAGCACCTCCC 62.125 60.000 0.00 0.00 40.22 4.30
1554 2102 3.303189 CCATCGTCAGAGTGGCCT 58.697 61.111 3.32 0.00 0.00 5.19
1668 2216 0.550914 TGCTCAACAACCCAGACCTT 59.449 50.000 0.00 0.00 0.00 3.50
1725 2273 1.003839 GTGGTTCTGGATGACGCCA 60.004 57.895 0.00 0.00 36.30 5.69
1840 2388 3.436359 CGTCATCACCAACATCATCAACA 59.564 43.478 0.00 0.00 0.00 3.33
1842 2390 4.011698 TCATCACCAACATCATCAACAGG 58.988 43.478 0.00 0.00 0.00 4.00
1891 2439 2.047655 GTGTTGCCGACCGGATCA 60.048 61.111 9.46 4.78 37.50 2.92
1995 2543 1.067354 GGGCTTTTGATCCAGCAAGTG 60.067 52.381 10.00 0.00 37.81 3.16
2159 2884 1.983224 CTCCACCCGATCACAGGTT 59.017 57.895 0.00 0.00 32.72 3.50
2165 2890 3.370527 CCACCCGATCACAGGTTCTTTAT 60.371 47.826 0.00 0.00 32.72 1.40
2198 2939 5.130975 TGTCTTCCCATGTATGCATAACTCT 59.869 40.000 8.28 0.00 33.30 3.24
2200 2941 6.647067 GTCTTCCCATGTATGCATAACTCTAC 59.353 42.308 8.28 0.00 33.30 2.59
2207 2948 7.600375 CCATGTATGCATAACTCTACCAAGTAG 59.400 40.741 8.28 0.00 34.32 2.57
2208 2949 7.050970 TGTATGCATAACTCTACCAAGTAGG 57.949 40.000 8.28 0.00 45.67 3.18
2209 2950 7.290248 ATGTATGCATAACTCTACCAAGTAGGT 59.710 37.037 8.28 0.00 43.30 3.08
2258 3121 8.967218 CAGCGAAAATTTCAGAGAATTAAACAA 58.033 29.630 6.53 0.00 0.00 2.83
2259 3122 9.528018 AGCGAAAATTTCAGAGAATTAAACAAA 57.472 25.926 6.53 0.00 0.00 2.83
2382 3296 7.337942 AGTTTGATAGAAATTAGCACAAGAGGG 59.662 37.037 0.00 0.00 0.00 4.30
2383 3297 5.684704 TGATAGAAATTAGCACAAGAGGGG 58.315 41.667 0.00 0.00 0.00 4.79
2384 3298 3.372440 AGAAATTAGCACAAGAGGGGG 57.628 47.619 0.00 0.00 0.00 5.40
2438 3352 5.750067 CAGCTCAAAAACATTAAAGCACAGT 59.250 36.000 0.00 0.00 32.25 3.55
2446 3360 4.148838 ACATTAAAGCACAGTTAAGGCCA 58.851 39.130 5.01 0.00 0.00 5.36
2456 3370 0.386113 GTTAAGGCCAACCAAACGCA 59.614 50.000 5.01 0.00 39.06 5.24
2457 3371 1.000394 GTTAAGGCCAACCAAACGCAT 60.000 47.619 5.01 0.00 39.06 4.73
2466 3381 2.036958 ACCAAACGCATAGCAGCATA 57.963 45.000 0.00 0.00 0.00 3.14
2474 3389 3.499918 ACGCATAGCAGCATAAGGAAATC 59.500 43.478 0.00 0.00 0.00 2.17
2486 3401 2.503895 AGGAAATCTGCAGGACTTGG 57.496 50.000 15.13 0.00 0.00 3.61
2546 3505 5.902613 ACAATCCGATCAACAACATCATT 57.097 34.783 0.00 0.00 0.00 2.57
2554 3513 8.951243 TCCGATCAACAACATCATTTAACATAA 58.049 29.630 0.00 0.00 0.00 1.90
2568 3527 8.119845 TCATTTAACATAACAATCCGATCAACG 58.880 33.333 0.00 0.00 42.18 4.10
2571 3530 3.550275 ACATAACAATCCGATCAACGACG 59.450 43.478 0.00 0.00 45.77 5.12
2696 3656 4.007644 GCAGCAAACCCAAGGCCC 62.008 66.667 0.00 0.00 0.00 5.80
2777 3762 0.823356 GTTGTGGCTTCAGGGAGCAA 60.823 55.000 1.39 0.00 44.49 3.91
2883 3869 4.201980 GCTGCATGCTCAAAAGTGATATCA 60.202 41.667 20.33 0.00 38.95 2.15
2907 3897 3.438087 CAGAAGAGCTAACCAATGGTGTG 59.562 47.826 5.34 2.88 35.34 3.82
2950 3940 6.092396 TCGACGAGATAGATAAGCCTGATTAC 59.908 42.308 0.00 0.00 0.00 1.89
2954 3944 5.715070 AGATAGATAAGCCTGATTACGCAC 58.285 41.667 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.735471 TCTCAAGACTCATCGCCTCG 59.265 55.000 0.00 0.00 0.00 4.63
43 44 6.773200 TGTTCCCAACAACAATAACTCACATA 59.227 34.615 0.00 0.00 38.72 2.29
46 47 5.508200 TGTTCCCAACAACAATAACTCAC 57.492 39.130 0.00 0.00 38.72 3.51
128 129 0.810031 ATGTTATCGGTGCGAGGTGC 60.810 55.000 0.00 0.00 39.91 5.01
129 130 2.502213 TATGTTATCGGTGCGAGGTG 57.498 50.000 0.00 0.00 39.91 4.00
130 131 2.891580 AGATATGTTATCGGTGCGAGGT 59.108 45.455 0.00 0.00 39.91 3.85
131 132 3.577649 AGATATGTTATCGGTGCGAGG 57.422 47.619 0.00 0.00 39.91 4.63
132 133 7.582435 AAAATAGATATGTTATCGGTGCGAG 57.418 36.000 0.00 0.00 39.91 5.03
133 134 8.517056 TCTAAAATAGATATGTTATCGGTGCGA 58.483 33.333 0.00 0.00 41.13 5.10
134 135 8.683550 TCTAAAATAGATATGTTATCGGTGCG 57.316 34.615 0.00 0.00 0.00 5.34
206 207 1.021968 GTTTCGAGTTGGCTGGTGTT 58.978 50.000 0.00 0.00 0.00 3.32
212 213 0.468226 TGTGGAGTTTCGAGTTGGCT 59.532 50.000 0.00 0.00 0.00 4.75
221 222 0.668535 GCAGGTTGGTGTGGAGTTTC 59.331 55.000 0.00 0.00 0.00 2.78
237 239 0.107017 AATCTCCGGATTGTGGGCAG 60.107 55.000 3.57 0.00 40.30 4.85
250 252 4.202070 CGAAGAGTTCTCCCACTAATCTCC 60.202 50.000 0.00 0.00 0.00 3.71
296 298 2.736682 GACGAAACCATGGGCGTCG 61.737 63.158 28.64 26.48 42.71 5.12
339 341 3.648545 ACTCTGGGTGAAAGCTTAAGTCT 59.351 43.478 0.00 0.00 0.00 3.24
353 355 0.986019 TGTTGTGGGTCACTCTGGGT 60.986 55.000 0.00 0.00 35.11 4.51
358 360 1.600916 GGGCTGTTGTGGGTCACTC 60.601 63.158 0.00 0.00 35.11 3.51
361 363 3.099841 TGGGGCTGTTGTGGGTCA 61.100 61.111 0.00 0.00 0.00 4.02
376 378 0.320771 CGTCTTCCAAGGTCTGGTGG 60.321 60.000 0.00 0.00 46.51 4.61
434 436 0.396811 ACACAAGGGTCACAGGTAGC 59.603 55.000 0.00 0.00 0.00 3.58
438 440 4.280436 TGTATTACACAAGGGTCACAGG 57.720 45.455 0.00 0.00 32.95 4.00
567 575 9.412460 AGTTATAATGATCTGCTCAAATTTGGA 57.588 29.630 17.90 7.73 37.44 3.53
586 594 9.802039 ATGTTGTCCTGTTCCTAAAAGTTATAA 57.198 29.630 0.00 0.00 0.00 0.98
642 651 3.753272 CGTTCACTGTTGGGATTTGATCT 59.247 43.478 0.00 0.00 0.00 2.75
664 673 3.745975 TCATTGAACCATGTGACGAAGAC 59.254 43.478 0.00 0.00 0.00 3.01
705 714 3.281727 ACCATGTGGCATATCTTCGTT 57.718 42.857 0.00 0.00 39.32 3.85
706 715 3.206150 GAACCATGTGGCATATCTTCGT 58.794 45.455 0.00 0.00 39.32 3.85
707 716 3.205338 TGAACCATGTGGCATATCTTCG 58.795 45.455 0.00 0.00 39.32 3.79
708 717 4.823442 TGATGAACCATGTGGCATATCTTC 59.177 41.667 0.00 0.00 39.32 2.87
709 718 4.795469 TGATGAACCATGTGGCATATCTT 58.205 39.130 0.00 0.00 39.32 2.40
710 719 4.141321 ACTGATGAACCATGTGGCATATCT 60.141 41.667 0.00 0.00 39.32 1.98
711 720 4.139786 ACTGATGAACCATGTGGCATATC 58.860 43.478 0.00 1.68 39.32 1.63
712 721 4.174704 ACTGATGAACCATGTGGCATAT 57.825 40.909 0.00 0.00 39.32 1.78
713 722 3.650281 ACTGATGAACCATGTGGCATA 57.350 42.857 0.00 0.00 39.32 3.14
714 723 2.519771 ACTGATGAACCATGTGGCAT 57.480 45.000 0.00 0.00 39.32 4.40
715 724 3.054508 TCATACTGATGAACCATGTGGCA 60.055 43.478 0.00 0.00 39.20 4.92
716 725 3.544684 TCATACTGATGAACCATGTGGC 58.455 45.455 0.00 0.00 39.20 5.01
745 754 5.012046 ACCGATTAGCCACATCTGATTGATA 59.988 40.000 0.00 0.00 33.36 2.15
756 765 3.692101 CCAACAATAACCGATTAGCCACA 59.308 43.478 0.00 0.00 0.00 4.17
761 770 6.861065 ATGTAGCCAACAATAACCGATTAG 57.139 37.500 0.00 0.00 42.70 1.73
763 772 6.151985 TGAAATGTAGCCAACAATAACCGATT 59.848 34.615 0.00 0.00 42.70 3.34
854 864 3.438087 GGTTCAAGTCTGGACATGACATG 59.562 47.826 14.02 14.02 38.55 3.21
855 865 3.072915 TGGTTCAAGTCTGGACATGACAT 59.927 43.478 0.00 0.00 38.55 3.06
858 868 3.476552 GTTGGTTCAAGTCTGGACATGA 58.523 45.455 0.00 4.81 37.27 3.07
872 887 2.551270 CGTGCTGCTCGTTGGTTC 59.449 61.111 15.22 0.00 0.00 3.62
887 902 1.827399 ATCGGTGGAGAAAGGTGCGT 61.827 55.000 0.00 0.00 0.00 5.24
888 903 0.673644 AATCGGTGGAGAAAGGTGCG 60.674 55.000 0.00 0.00 0.00 5.34
892 907 2.488153 GTGGAAAATCGGTGGAGAAAGG 59.512 50.000 0.00 0.00 0.00 3.11
893 908 3.058224 GTGTGGAAAATCGGTGGAGAAAG 60.058 47.826 0.00 0.00 0.00 2.62
895 910 2.158740 TGTGTGGAAAATCGGTGGAGAA 60.159 45.455 0.00 0.00 0.00 2.87
896 911 1.418264 TGTGTGGAAAATCGGTGGAGA 59.582 47.619 0.00 0.00 0.00 3.71
900 932 5.818136 ATTCTATGTGTGGAAAATCGGTG 57.182 39.130 0.00 0.00 0.00 4.94
914 946 7.370905 TCTCTGGTCATGATCAATTCTATGT 57.629 36.000 10.49 0.00 0.00 2.29
928 960 6.406400 GCCGCTATTTATAGATCTCTGGTCAT 60.406 42.308 0.00 0.00 32.05 3.06
931 963 4.772624 TGCCGCTATTTATAGATCTCTGGT 59.227 41.667 0.00 0.00 32.05 4.00
932 964 5.105554 AGTGCCGCTATTTATAGATCTCTGG 60.106 44.000 0.00 0.00 32.05 3.86
933 965 5.960113 AGTGCCGCTATTTATAGATCTCTG 58.040 41.667 0.00 0.00 32.05 3.35
935 967 5.578727 CCAAGTGCCGCTATTTATAGATCTC 59.421 44.000 0.00 0.00 32.05 2.75
957 1016 2.552155 GGATAGATTATGGCGCCAACCA 60.552 50.000 36.33 20.76 45.82 3.67
978 1037 0.461870 TCGGATCAATCTTGGTGCCG 60.462 55.000 0.00 0.00 37.63 5.69
990 1055 2.562738 CAGTATAGGCATGGTCGGATCA 59.437 50.000 0.00 0.00 0.00 2.92
995 1060 4.021981 TCATTCTCAGTATAGGCATGGTCG 60.022 45.833 0.00 0.00 0.00 4.79
1000 1065 4.222588 GGCTCTCATTCTCAGTATAGGCAT 59.777 45.833 0.00 0.00 0.00 4.40
1007 1072 2.302260 CCGAGGCTCTCATTCTCAGTA 58.698 52.381 13.50 0.00 0.00 2.74
1301 1837 2.719979 CGGCATCTGAGCATTGGC 59.280 61.111 0.00 0.00 41.61 4.52
1309 1845 4.467084 GAACCCGCCGGCATCTGA 62.467 66.667 28.98 0.00 0.00 3.27
1515 2063 2.967397 CAGTAGTCGGGCGGTGAA 59.033 61.111 0.00 0.00 0.00 3.18
1643 2191 1.352622 TGGGTTGTTGAGCAGGTCCT 61.353 55.000 0.00 0.00 0.00 3.85
1731 2279 1.228154 GTGGGAGGACGGCTTGTTT 60.228 57.895 0.00 0.00 0.00 2.83
1743 2291 2.509336 GTGATCACGGCGTGGGAG 60.509 66.667 36.30 14.46 33.87 4.30
1891 2439 0.818296 CAGTAGCGCTGGTAGAACCT 59.182 55.000 22.90 0.00 41.42 3.50
1995 2543 4.733565 CGTAGTATGTTGTTACTGCGTC 57.266 45.455 12.07 0.00 46.50 5.19
2118 2829 1.298339 GCTCACACACAACGGCAAC 60.298 57.895 0.00 0.00 0.00 4.17
2159 2884 7.831691 TGGGAAGACATGTTTTCAATAAAGA 57.168 32.000 25.39 3.60 0.00 2.52
2208 2949 2.500098 TGCTTGTGACCAGGTATAGGAC 59.500 50.000 0.00 0.00 0.00 3.85
2209 2950 2.827755 TGCTTGTGACCAGGTATAGGA 58.172 47.619 0.00 0.00 0.00 2.94
2213 2954 3.149196 CTGTTTGCTTGTGACCAGGTAT 58.851 45.455 0.00 0.00 0.00 2.73
2214 2955 2.571212 CTGTTTGCTTGTGACCAGGTA 58.429 47.619 0.00 0.00 0.00 3.08
2215 2956 1.392589 CTGTTTGCTTGTGACCAGGT 58.607 50.000 0.00 0.00 0.00 4.00
2216 2957 0.031178 GCTGTTTGCTTGTGACCAGG 59.969 55.000 0.00 0.00 38.95 4.45
2217 2958 0.317269 CGCTGTTTGCTTGTGACCAG 60.317 55.000 0.00 0.00 40.11 4.00
2218 2959 0.746204 TCGCTGTTTGCTTGTGACCA 60.746 50.000 0.00 0.00 40.11 4.02
2292 3194 4.270008 ACTGCTGTCAGGTACAAGTTTTT 58.730 39.130 1.14 0.00 44.54 1.94
2293 3195 3.886123 ACTGCTGTCAGGTACAAGTTTT 58.114 40.909 1.14 0.00 44.54 2.43
2294 3196 3.560636 ACTGCTGTCAGGTACAAGTTT 57.439 42.857 1.14 0.00 44.54 2.66
2295 3197 4.141801 TGTTACTGCTGTCAGGTACAAGTT 60.142 41.667 0.00 0.00 44.54 2.66
2296 3198 3.386726 TGTTACTGCTGTCAGGTACAAGT 59.613 43.478 0.00 0.00 44.54 3.16
2297 3199 3.990092 TGTTACTGCTGTCAGGTACAAG 58.010 45.455 0.00 0.00 44.54 3.16
2298 3200 3.386726 ACTGTTACTGCTGTCAGGTACAA 59.613 43.478 14.31 0.00 44.54 2.41
2299 3201 2.963101 ACTGTTACTGCTGTCAGGTACA 59.037 45.455 14.31 6.45 44.54 2.90
2300 3202 3.662247 ACTGTTACTGCTGTCAGGTAC 57.338 47.619 14.31 0.00 44.54 3.34
2382 3296 1.756430 GATTTCCTGTGAAGGCTCCC 58.244 55.000 0.00 0.00 0.00 4.30
2383 3297 1.066143 TCGATTTCCTGTGAAGGCTCC 60.066 52.381 0.00 0.00 0.00 4.70
2384 3298 2.275318 CTCGATTTCCTGTGAAGGCTC 58.725 52.381 0.00 0.00 0.00 4.70
2438 3352 1.333177 ATGCGTTTGGTTGGCCTTAA 58.667 45.000 3.32 0.00 35.27 1.85
2446 3360 1.176527 ATGCTGCTATGCGTTTGGTT 58.823 45.000 0.00 0.00 35.36 3.67
2466 3381 2.800250 CCAAGTCCTGCAGATTTCCTT 58.200 47.619 17.39 6.40 0.00 3.36
2474 3389 3.940209 TTATTTTGCCAAGTCCTGCAG 57.060 42.857 6.78 6.78 38.95 4.41
2486 3401 9.651913 TTCCATTGGAACTTCTTATTATTTTGC 57.348 29.630 14.24 0.00 36.71 3.68
2546 3505 6.237622 CGTCGTTGATCGGATTGTTATGTTAA 60.238 38.462 0.00 0.00 40.32 2.01
2554 3513 0.389296 TGCGTCGTTGATCGGATTGT 60.389 50.000 0.00 0.00 40.32 2.71
2568 3527 7.962934 TTGCAATTGTACTTAATAATGCGTC 57.037 32.000 7.40 0.00 0.00 5.19
2696 3656 3.295228 CTTCCGCGTTGCCAGAACG 62.295 63.158 4.92 3.61 45.56 3.95
2705 3665 1.332686 GTTCTTGTTTCCTTCCGCGTT 59.667 47.619 4.92 0.00 0.00 4.84
2777 3762 4.421131 ACTAGTGACAAGGACAAGGAGAT 58.579 43.478 0.00 0.00 0.00 2.75
2866 3851 7.333323 TCTTCTGATGATATCACTTTTGAGCA 58.667 34.615 7.78 0.00 34.35 4.26
2883 3869 4.018960 ACACCATTGGTTAGCTCTTCTGAT 60.019 41.667 5.34 0.00 31.02 2.90
2907 3897 1.316651 GATCTGCCCTTGATGGAAGC 58.683 55.000 0.00 0.00 38.35 3.86


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

AutoCloner maintained by Alex Coulton.