Multiple sequence alignment - TraesCS3D01G004200

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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 TraesCS3D01G004200 chr3D 100.000 3251 0 0 1 3251 1742863 1746113 0.000000e+00 6004.0
1 TraesCS3D01G004200 chr3D 90.476 63 4 2 59 121 469168401 469168461 7.480000e-12 82.4
2 TraesCS3D01G004200 chr3B 92.806 1946 94 14 857 2789 4780504 4782416 0.000000e+00 2776.0
3 TraesCS3D01G004200 chr3B 92.754 1946 95 14 857 2789 3893578 3895490 0.000000e+00 2771.0
4 TraesCS3D01G004200 chr3B 89.401 434 34 4 2790 3220 3895851 3896275 1.330000e-148 536.0
5 TraesCS3D01G004200 chr3B 89.401 434 34 4 2790 3220 4782777 4783201 1.330000e-148 536.0
6 TraesCS3D01G004200 chr3B 81.027 448 59 20 172 602 412721415 412721853 1.870000e-87 333.0
7 TraesCS3D01G004200 chr3A 88.673 1960 125 46 860 2795 7280346 7278460 0.000000e+00 2300.0
8 TraesCS3D01G004200 chr3A 89.868 454 36 6 2790 3236 7277998 7277548 2.810000e-160 575.0
9 TraesCS3D01G004200 chr3A 77.335 728 117 32 59 770 550491114 550491809 1.410000e-103 387.0
10 TraesCS3D01G004200 chr3A 80.252 476 72 20 59 520 594347018 594346551 4.020000e-89 339.0
11 TraesCS3D01G004200 chr4A 82.311 978 132 23 1672 2634 669235705 669236656 0.000000e+00 809.0
12 TraesCS3D01G004200 chr4A 84.578 616 74 10 984 1595 669234991 669235589 2.790000e-165 592.0
13 TraesCS3D01G004200 chr7D 82.088 977 136 22 1672 2634 21008382 21007431 0.000000e+00 798.0
14 TraesCS3D01G004200 chr7D 83.389 602 74 16 993 1591 21009083 21008505 4.770000e-148 534.0
15 TraesCS3D01G004200 chr7D 80.000 545 82 17 148 678 123436588 123437119 8.510000e-101 377.0
16 TraesCS3D01G004200 chr7D 79.123 479 75 19 59 525 491867867 491868332 1.130000e-79 307.0
17 TraesCS3D01G004200 chr7D 81.618 272 25 16 2790 3061 21006996 21006750 5.500000e-48 202.0
18 TraesCS3D01G004200 chr7A 81.153 971 141 24 1670 2634 21359190 21358256 0.000000e+00 741.0
19 TraesCS3D01G004200 chr7A 83.887 602 77 11 998 1595 21359889 21359304 1.020000e-154 556.0
20 TraesCS3D01G004200 chr7A 81.364 440 61 19 155 580 126186613 126187045 4.020000e-89 339.0
21 TraesCS3D01G004200 chr7A 84.677 248 28 7 2920 3160 21355581 21355337 4.190000e-59 239.0
22 TraesCS3D01G004200 chr5D 79.584 529 86 21 59 575 290752726 290753244 3.080000e-95 359.0
23 TraesCS3D01G004200 chr5D 76.274 628 103 37 207 810 361575444 361576049 3.170000e-75 292.0
24 TraesCS3D01G004200 chr5D 77.672 421 67 22 169 580 482253688 482253286 7.010000e-57 231.0
25 TraesCS3D01G004200 chr1B 79.127 527 65 31 259 777 625771981 625772470 4.050000e-84 322.0
26 TraesCS3D01G004200 chr1B 80.556 432 64 17 107 525 34200578 34201002 6.770000e-82 315.0
27 TraesCS3D01G004200 chr6D 94.340 53 3 0 60 112 18031470 18031418 7.480000e-12 82.4
28 TraesCS3D01G004200 chr6D 94.340 53 3 0 60 112 18151673 18151621 7.480000e-12 82.4
29 TraesCS3D01G004200 chr6B 79.000 100 14 6 60 156 540211363 540211268 9.740000e-06 62.1


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 TraesCS3D01G004200 chr3D 1742863 1746113 3250 False 6004.000000 6004 100.0000 1 3251 1 chr3D.!!$F1 3250
1 TraesCS3D01G004200 chr3B 4780504 4783201 2697 False 1656.000000 2776 91.1035 857 3220 2 chr3B.!!$F3 2363
2 TraesCS3D01G004200 chr3B 3893578 3896275 2697 False 1653.500000 2771 91.0775 857 3220 2 chr3B.!!$F2 2363
3 TraesCS3D01G004200 chr3A 7277548 7280346 2798 True 1437.500000 2300 89.2705 860 3236 2 chr3A.!!$R2 2376
4 TraesCS3D01G004200 chr3A 550491114 550491809 695 False 387.000000 387 77.3350 59 770 1 chr3A.!!$F1 711
5 TraesCS3D01G004200 chr4A 669234991 669236656 1665 False 700.500000 809 83.4445 984 2634 2 chr4A.!!$F1 1650
6 TraesCS3D01G004200 chr7D 21006750 21009083 2333 True 511.333333 798 82.3650 993 3061 3 chr7D.!!$R1 2068
7 TraesCS3D01G004200 chr7D 123436588 123437119 531 False 377.000000 377 80.0000 148 678 1 chr7D.!!$F1 530
8 TraesCS3D01G004200 chr7A 21355337 21359889 4552 True 512.000000 741 83.2390 998 3160 3 chr7A.!!$R1 2162
9 TraesCS3D01G004200 chr5D 290752726 290753244 518 False 359.000000 359 79.5840 59 575 1 chr5D.!!$F1 516
10 TraesCS3D01G004200 chr5D 361575444 361576049 605 False 292.000000 292 76.2740 207 810 1 chr5D.!!$F2 603

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
842 918 0.109342 CCGGCCCATCTTGCTTATCT 59.891 55.0 0.0 0.0 0.00 1.98 F
858 934 0.820871 ATCTCCTTCAGCGAGGTGTC 59.179 55.0 2.1 0.0 38.04 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2031 2204 0.037303 CCTCCCATGTGAACAGCAGT 59.963 55.0 0.0 0.0 0.0 4.40 R
2384 2564 0.250770 ACGGGAGAAAAGAACAGCCC 60.251 55.0 0.0 0.0 0.0 5.19 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
26 27 9.968743 CTCGTCTTTTATTGTTTTCCTATACAC 57.031 33.333 0.00 0.00 0.00 2.90
382 392 7.903995 TCCAAATGCTTGATTACCATTTTTC 57.096 32.000 0.00 0.00 37.14 2.29
644 695 7.043458 CGTGATAAACATTTTTCTTTGCACACT 60.043 33.333 0.00 0.00 0.00 3.55
663 714 8.725148 TGCACACTTTTAACATTTTTCAAATGT 58.275 25.926 8.71 8.71 42.19 2.71
805 881 6.790232 AAAATGAGAAAAAGGAGGTTGTGA 57.210 33.333 0.00 0.00 0.00 3.58
815 891 4.081050 GGTTGTGACCTCCCTTGC 57.919 61.111 0.00 0.00 42.99 4.01
816 892 1.456287 GGTTGTGACCTCCCTTGCT 59.544 57.895 0.00 0.00 42.99 3.91
817 893 0.606673 GGTTGTGACCTCCCTTGCTC 60.607 60.000 0.00 0.00 42.99 4.26
818 894 0.398318 GTTGTGACCTCCCTTGCTCT 59.602 55.000 0.00 0.00 0.00 4.09
819 895 1.140312 TTGTGACCTCCCTTGCTCTT 58.860 50.000 0.00 0.00 0.00 2.85
820 896 1.140312 TGTGACCTCCCTTGCTCTTT 58.860 50.000 0.00 0.00 0.00 2.52
821 897 1.202806 TGTGACCTCCCTTGCTCTTTG 60.203 52.381 0.00 0.00 0.00 2.77
822 898 0.401738 TGACCTCCCTTGCTCTTTGG 59.598 55.000 0.00 0.00 0.00 3.28
823 899 0.962855 GACCTCCCTTGCTCTTTGGC 60.963 60.000 0.00 0.00 0.00 4.52
824 900 1.680314 CCTCCCTTGCTCTTTGGCC 60.680 63.158 0.00 0.00 0.00 5.36
825 901 2.034066 TCCCTTGCTCTTTGGCCG 59.966 61.111 0.00 0.00 0.00 6.13
826 902 3.064324 CCCTTGCTCTTTGGCCGG 61.064 66.667 0.00 0.00 0.00 6.13
827 903 3.752339 CCTTGCTCTTTGGCCGGC 61.752 66.667 21.18 21.18 0.00 6.13
828 904 3.752339 CTTGCTCTTTGGCCGGCC 61.752 66.667 39.40 39.40 0.00 6.13
832 908 2.830370 CTCTTTGGCCGGCCCATC 60.830 66.667 41.75 18.68 44.89 3.51
833 909 3.338250 TCTTTGGCCGGCCCATCT 61.338 61.111 41.75 0.00 44.89 2.90
834 910 2.362889 CTTTGGCCGGCCCATCTT 60.363 61.111 41.75 0.00 44.89 2.40
835 911 2.679642 TTTGGCCGGCCCATCTTG 60.680 61.111 41.75 0.00 44.89 3.02
839 915 2.124320 GCCGGCCCATCTTGCTTA 60.124 61.111 18.11 0.00 0.00 3.09
840 916 1.529244 GCCGGCCCATCTTGCTTAT 60.529 57.895 18.11 0.00 0.00 1.73
841 917 1.518903 GCCGGCCCATCTTGCTTATC 61.519 60.000 18.11 0.00 0.00 1.75
842 918 0.109342 CCGGCCCATCTTGCTTATCT 59.891 55.000 0.00 0.00 0.00 1.98
843 919 1.517242 CGGCCCATCTTGCTTATCTC 58.483 55.000 0.00 0.00 0.00 2.75
844 920 1.879796 CGGCCCATCTTGCTTATCTCC 60.880 57.143 0.00 0.00 0.00 3.71
845 921 1.423161 GGCCCATCTTGCTTATCTCCT 59.577 52.381 0.00 0.00 0.00 3.69
846 922 2.158549 GGCCCATCTTGCTTATCTCCTT 60.159 50.000 0.00 0.00 0.00 3.36
847 923 3.145286 GCCCATCTTGCTTATCTCCTTC 58.855 50.000 0.00 0.00 0.00 3.46
848 924 3.434167 GCCCATCTTGCTTATCTCCTTCA 60.434 47.826 0.00 0.00 0.00 3.02
849 925 4.387598 CCCATCTTGCTTATCTCCTTCAG 58.612 47.826 0.00 0.00 0.00 3.02
850 926 3.814283 CCATCTTGCTTATCTCCTTCAGC 59.186 47.826 0.00 0.00 0.00 4.26
851 927 3.170791 TCTTGCTTATCTCCTTCAGCG 57.829 47.619 0.00 0.00 34.82 5.18
852 928 2.760650 TCTTGCTTATCTCCTTCAGCGA 59.239 45.455 0.00 0.00 34.82 4.93
853 929 2.879002 TGCTTATCTCCTTCAGCGAG 57.121 50.000 0.00 0.00 34.82 5.03
854 930 1.410517 TGCTTATCTCCTTCAGCGAGG 59.589 52.381 0.00 0.00 38.20 4.63
855 931 1.410882 GCTTATCTCCTTCAGCGAGGT 59.589 52.381 4.16 0.00 38.04 3.85
856 932 2.801342 GCTTATCTCCTTCAGCGAGGTG 60.801 54.545 4.16 0.00 38.04 4.00
857 933 2.145397 TATCTCCTTCAGCGAGGTGT 57.855 50.000 2.10 0.00 38.04 4.16
858 934 0.820871 ATCTCCTTCAGCGAGGTGTC 59.179 55.000 2.10 0.00 38.04 3.67
881 957 3.561120 TAGGCCCAACGCAACCCTG 62.561 63.158 0.00 0.00 40.31 4.45
892 968 0.823356 GCAACCCTGCTGAAGTTCCA 60.823 55.000 0.00 0.00 45.74 3.53
900 976 1.134220 TGCTGAAGTTCCACCTCGTTT 60.134 47.619 0.00 0.00 0.00 3.60
1290 1391 3.839432 GACCCCCTCTTCGGCTCG 61.839 72.222 0.00 0.00 0.00 5.03
1579 1683 1.375396 CCTGTTCGACGGAATGCCA 60.375 57.895 0.00 0.00 34.05 4.92
1594 1698 2.047844 CCACAGAGGGCAGTCGTG 60.048 66.667 0.00 0.00 0.00 4.35
1595 1699 2.574018 CCACAGAGGGCAGTCGTGA 61.574 63.158 10.41 0.00 0.00 4.35
1596 1700 1.080230 CACAGAGGGCAGTCGTGAG 60.080 63.158 0.00 0.00 0.00 3.51
1597 1701 1.228583 ACAGAGGGCAGTCGTGAGA 60.229 57.895 0.00 0.00 38.16 3.27
1607 1711 2.264480 TCGTGAGACCGCCAATGG 59.736 61.111 0.00 0.00 33.31 3.16
1609 1713 2.390599 CGTGAGACCGCCAATGGTG 61.391 63.158 5.73 5.73 44.01 4.17
1610 1714 2.359850 TGAGACCGCCAATGGTGC 60.360 61.111 7.43 0.00 44.01 5.01
1611 1715 3.134127 GAGACCGCCAATGGTGCC 61.134 66.667 7.43 1.32 44.01 5.01
1679 1852 3.853330 CGGTGGAAGTGATGCGCG 61.853 66.667 0.00 0.00 0.00 6.86
1866 2039 1.471119 CGTCTGCCTACTACCCTTCA 58.529 55.000 0.00 0.00 0.00 3.02
1940 2113 8.746623 GAAGAATTCATCGAGCCACAGTTTGG 62.747 46.154 8.44 0.00 46.83 3.28
2025 2198 2.443255 CAATCCTTGGGGTGGCTATACT 59.557 50.000 0.00 0.00 0.00 2.12
2142 2315 3.287222 GCCAGGGTTAATGACAGCAATA 58.713 45.455 0.00 0.00 0.00 1.90
2327 2501 4.265073 AGTGATGGCTCTTGGTAATGTTC 58.735 43.478 0.00 0.00 0.00 3.18
2344 2519 4.801330 TGTTCCATCTGTCGAACACTAT 57.199 40.909 0.00 0.00 42.52 2.12
2381 2556 6.240894 TCTTCAGATTGTAATGCAAACCTCT 58.759 36.000 0.00 0.00 40.91 3.69
2384 2564 5.645067 TCAGATTGTAATGCAAACCTCTCTG 59.355 40.000 5.61 5.61 40.91 3.35
2421 2601 1.594862 CGTGGCTTCTGTAATGCTAGC 59.405 52.381 8.10 8.10 0.00 3.42
2422 2602 2.739932 CGTGGCTTCTGTAATGCTAGCT 60.740 50.000 17.23 0.00 32.58 3.32
2423 2603 3.490933 CGTGGCTTCTGTAATGCTAGCTA 60.491 47.826 17.23 2.58 32.58 3.32
2424 2604 4.054671 GTGGCTTCTGTAATGCTAGCTAG 58.945 47.826 16.84 16.84 32.58 3.42
2425 2605 3.706594 TGGCTTCTGTAATGCTAGCTAGT 59.293 43.478 21.62 5.14 32.58 2.57
2445 2625 8.478877 AGCTAGTGTTGCTAGTATTGAATTACT 58.521 33.333 0.00 0.00 46.81 2.24
2462 2642 8.969121 TGAATTACTTCATGTTGCTTTATGTG 57.031 30.769 0.00 0.00 36.46 3.21
2464 2644 8.970691 AATTACTTCATGTTGCTTTATGTGAC 57.029 30.769 0.00 0.00 0.00 3.67
2513 2693 4.481368 TGTCTGTAGTGGAAGTTTGTGT 57.519 40.909 0.00 0.00 0.00 3.72
2635 2831 8.560355 ACCCTATTTATTTTGGCATTTCAAAC 57.440 30.769 0.00 0.00 36.49 2.93
2682 2878 5.312079 ACTCTCTCCCAGTTTGAATGAAAG 58.688 41.667 0.00 0.00 0.00 2.62
2705 2901 5.841783 AGAGTCTTAACCTTGAACTCTTCCT 59.158 40.000 0.00 0.00 29.93 3.36
2724 2920 4.136796 TCCTCAGTTCACATTTCAACCTG 58.863 43.478 0.00 0.00 0.00 4.00
2758 2955 2.307496 TCCGGTTTAGGACCTGTACA 57.693 50.000 3.53 0.00 46.92 2.90
2789 3019 4.319190 CCGTTTGACTGAATTTAACGCTGA 60.319 41.667 0.00 0.00 39.96 4.26
2791 3021 5.281376 CGTTTGACTGAATTTAACGCTGATG 59.719 40.000 0.00 0.00 35.76 3.07
2795 3025 6.734137 TGACTGAATTTAACGCTGATGTTTT 58.266 32.000 0.00 0.00 33.32 2.43
2923 3647 9.587772 TCAATTTCTGTGAGCTACTAATCTTAC 57.412 33.333 0.00 0.00 0.00 2.34
3070 5821 4.302455 CAGGGATGTTCTGCTATCGTTAG 58.698 47.826 0.00 0.00 0.00 2.34
3076 5827 1.006102 CTGCTATCGTTAGGCCCGG 60.006 63.158 0.00 0.00 0.00 5.73
3077 5828 2.342648 GCTATCGTTAGGCCCGGG 59.657 66.667 19.09 19.09 0.00 5.73
3171 5927 3.676291 TGGGCCAAATTACTTGCTTTC 57.324 42.857 2.13 0.00 33.27 2.62
3183 5939 8.621532 AATTACTTGCTTTCACTCTGTTATGA 57.378 30.769 0.00 0.00 0.00 2.15
3198 5957 3.521531 TGTTATGACAGGGATGGCTGTTA 59.478 43.478 0.00 0.00 33.50 2.41
3233 5992 4.518249 GGATAAGCTAGCTGTTTGGTTCT 58.482 43.478 20.16 0.95 0.00 3.01
3236 5995 6.037281 GGATAAGCTAGCTGTTTGGTTCTAAC 59.963 42.308 20.16 2.11 0.00 2.34
3237 5996 4.625607 AGCTAGCTGTTTGGTTCTAACT 57.374 40.909 18.57 0.00 0.00 2.24
3238 5997 4.974399 AGCTAGCTGTTTGGTTCTAACTT 58.026 39.130 18.57 0.00 0.00 2.66
3239 5998 6.110411 AGCTAGCTGTTTGGTTCTAACTTA 57.890 37.500 18.57 0.00 0.00 2.24
3240 5999 6.531021 AGCTAGCTGTTTGGTTCTAACTTAA 58.469 36.000 18.57 0.00 0.00 1.85
3241 6000 6.427242 AGCTAGCTGTTTGGTTCTAACTTAAC 59.573 38.462 18.57 0.00 0.00 2.01
3242 6001 6.427242 GCTAGCTGTTTGGTTCTAACTTAACT 59.573 38.462 7.70 0.00 0.00 2.24
3243 6002 6.862711 AGCTGTTTGGTTCTAACTTAACTC 57.137 37.500 0.00 4.97 0.00 3.01
3244 6003 5.465724 AGCTGTTTGGTTCTAACTTAACTCG 59.534 40.000 0.00 0.00 0.00 4.18
3245 6004 5.662211 TGTTTGGTTCTAACTTAACTCGC 57.338 39.130 10.00 0.00 0.00 5.03
3246 6005 5.362263 TGTTTGGTTCTAACTTAACTCGCT 58.638 37.500 10.00 0.00 0.00 4.93
3247 6006 6.514947 TGTTTGGTTCTAACTTAACTCGCTA 58.485 36.000 10.00 0.00 0.00 4.26
3248 6007 7.156673 TGTTTGGTTCTAACTTAACTCGCTAT 58.843 34.615 10.00 0.00 0.00 2.97
3249 6008 7.117236 TGTTTGGTTCTAACTTAACTCGCTATG 59.883 37.037 10.00 0.00 0.00 2.23
3250 6009 5.107133 TGGTTCTAACTTAACTCGCTATGC 58.893 41.667 0.00 0.00 0.00 3.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
340 350 9.757859 GCATTTGGAAAATGTTAAATGTGTATG 57.242 29.630 12.82 0.00 40.70 2.39
445 458 9.173939 GCTGACTATGTATTAAAACAATGATGC 57.826 33.333 0.00 0.00 32.02 3.91
618 669 7.043458 AGTGTGCAAAGAAAAATGTTTATCACG 60.043 33.333 0.00 0.00 0.00 4.35
633 684 8.539770 TGAAAAATGTTAAAAGTGTGCAAAGA 57.460 26.923 0.00 0.00 0.00 2.52
634 685 9.604626 TTTGAAAAATGTTAAAAGTGTGCAAAG 57.395 25.926 0.00 0.00 0.00 2.77
638 689 9.553418 AACATTTGAAAAATGTTAAAAGTGTGC 57.447 25.926 22.92 0.00 45.80 4.57
786 862 3.551846 GGTCACAACCTCCTTTTTCTCA 58.448 45.455 0.00 0.00 42.80 3.27
800 876 1.140312 AAGAGCAAGGGAGGTCACAA 58.860 50.000 0.00 0.00 38.44 3.33
805 881 1.075659 GCCAAAGAGCAAGGGAGGT 59.924 57.895 0.00 0.00 0.00 3.85
810 886 3.752339 GCCGGCCAAAGAGCAAGG 61.752 66.667 18.11 0.00 35.82 3.61
811 887 3.752339 GGCCGGCCAAAGAGCAAG 61.752 66.667 40.73 0.00 35.81 4.01
815 891 2.830370 GATGGGCCGGCCAAAGAG 60.830 66.667 44.46 0.00 37.98 2.85
816 892 2.917897 AAGATGGGCCGGCCAAAGA 61.918 57.895 44.46 26.10 37.98 2.52
817 893 2.362889 AAGATGGGCCGGCCAAAG 60.363 61.111 44.46 0.00 37.98 2.77
818 894 2.679642 CAAGATGGGCCGGCCAAA 60.680 61.111 44.46 32.79 37.98 3.28
821 897 2.983725 ATAAGCAAGATGGGCCGGCC 62.984 60.000 38.57 38.57 0.00 6.13
822 898 1.518903 GATAAGCAAGATGGGCCGGC 61.519 60.000 21.18 21.18 0.00 6.13
823 899 0.109342 AGATAAGCAAGATGGGCCGG 59.891 55.000 0.00 0.00 0.00 6.13
824 900 1.517242 GAGATAAGCAAGATGGGCCG 58.483 55.000 0.00 0.00 0.00 6.13
825 901 1.423161 AGGAGATAAGCAAGATGGGCC 59.577 52.381 0.00 0.00 0.00 5.80
826 902 2.947127 AGGAGATAAGCAAGATGGGC 57.053 50.000 0.00 0.00 0.00 5.36
827 903 4.387598 CTGAAGGAGATAAGCAAGATGGG 58.612 47.826 0.00 0.00 0.00 4.00
828 904 3.814283 GCTGAAGGAGATAAGCAAGATGG 59.186 47.826 0.00 0.00 35.69 3.51
829 905 3.493877 CGCTGAAGGAGATAAGCAAGATG 59.506 47.826 0.00 0.00 35.33 2.90
830 906 3.386078 TCGCTGAAGGAGATAAGCAAGAT 59.614 43.478 0.00 0.00 35.33 2.40
831 907 2.760650 TCGCTGAAGGAGATAAGCAAGA 59.239 45.455 0.00 0.00 35.33 3.02
832 908 3.122297 CTCGCTGAAGGAGATAAGCAAG 58.878 50.000 0.00 0.00 35.33 4.01
833 909 2.159043 CCTCGCTGAAGGAGATAAGCAA 60.159 50.000 0.00 0.00 38.87 3.91
834 910 1.410517 CCTCGCTGAAGGAGATAAGCA 59.589 52.381 0.00 0.00 38.87 3.91
835 911 1.410882 ACCTCGCTGAAGGAGATAAGC 59.589 52.381 3.90 0.00 38.87 3.09
836 912 2.428890 ACACCTCGCTGAAGGAGATAAG 59.571 50.000 3.90 0.00 38.87 1.73
837 913 2.427453 GACACCTCGCTGAAGGAGATAA 59.573 50.000 3.90 0.00 38.87 1.75
838 914 2.025155 GACACCTCGCTGAAGGAGATA 58.975 52.381 3.90 0.00 38.87 1.98
839 915 0.820871 GACACCTCGCTGAAGGAGAT 59.179 55.000 3.90 0.00 38.87 2.75
840 916 1.251527 GGACACCTCGCTGAAGGAGA 61.252 60.000 3.90 0.00 38.87 3.71
841 917 1.216710 GGACACCTCGCTGAAGGAG 59.783 63.158 3.90 0.00 38.87 3.69
842 918 0.039180 TAGGACACCTCGCTGAAGGA 59.961 55.000 3.90 0.00 38.87 3.36
843 919 0.457851 CTAGGACACCTCGCTGAAGG 59.542 60.000 0.00 0.00 42.55 3.46
844 920 1.178276 ACTAGGACACCTCGCTGAAG 58.822 55.000 0.00 0.00 34.61 3.02
845 921 2.366533 CTACTAGGACACCTCGCTGAA 58.633 52.381 0.00 0.00 34.61 3.02
846 922 1.408405 CCTACTAGGACACCTCGCTGA 60.408 57.143 0.00 0.00 37.67 4.26
847 923 1.025812 CCTACTAGGACACCTCGCTG 58.974 60.000 0.00 0.00 37.67 5.18
848 924 0.752376 GCCTACTAGGACACCTCGCT 60.752 60.000 6.26 0.00 37.67 4.93
849 925 1.734748 GCCTACTAGGACACCTCGC 59.265 63.158 6.26 0.00 37.67 5.03
850 926 2.416901 GGCCTACTAGGACACCTCG 58.583 63.158 6.26 0.00 45.15 4.63
856 932 1.143401 GCGTTGGGCCTACTAGGAC 59.857 63.158 15.95 2.33 45.05 3.85
857 933 0.905809 TTGCGTTGGGCCTACTAGGA 60.906 55.000 15.95 0.00 42.61 2.94
858 934 0.743345 GTTGCGTTGGGCCTACTAGG 60.743 60.000 15.95 0.00 42.61 3.02
881 957 1.264288 CAAACGAGGTGGAACTTCAGC 59.736 52.381 0.00 0.00 44.15 4.26
889 965 2.281484 GGCTGCAAACGAGGTGGA 60.281 61.111 0.50 0.00 0.00 4.02
1017 1108 2.364186 TGGATCTGGCAGCGGAGA 60.364 61.111 10.34 0.00 0.00 3.71
1531 1632 2.286523 CGAAGTCCTGGCAGGAGGT 61.287 63.158 35.81 25.63 46.90 3.85
1579 1683 1.228583 TCTCACGACTGCCCTCTGT 60.229 57.895 0.00 0.00 0.00 3.41
1590 1694 2.264480 CCATTGGCGGTCTCACGA 59.736 61.111 0.00 0.00 35.47 4.35
1591 1695 2.047274 ACCATTGGCGGTCTCACG 60.047 61.111 1.54 0.00 32.11 4.35
1592 1696 2.690778 GCACCATTGGCGGTCTCAC 61.691 63.158 1.54 0.00 37.07 3.51
1593 1697 2.359850 GCACCATTGGCGGTCTCA 60.360 61.111 1.54 0.00 37.07 3.27
1594 1698 3.134127 GGCACCATTGGCGGTCTC 61.134 66.667 1.54 0.00 37.07 3.36
1600 1704 3.281359 GAACACCGGCACCATTGGC 62.281 63.158 0.00 0.00 44.96 4.52
1601 1705 1.603455 AGAACACCGGCACCATTGG 60.603 57.895 0.00 0.00 0.00 3.16
1602 1706 0.888736 TCAGAACACCGGCACCATTG 60.889 55.000 0.00 0.00 0.00 2.82
1603 1707 0.606401 CTCAGAACACCGGCACCATT 60.606 55.000 0.00 0.00 0.00 3.16
1604 1708 1.003355 CTCAGAACACCGGCACCAT 60.003 57.895 0.00 0.00 0.00 3.55
1605 1709 2.425592 CTCAGAACACCGGCACCA 59.574 61.111 0.00 0.00 0.00 4.17
1606 1710 1.961277 CACTCAGAACACCGGCACC 60.961 63.158 0.00 0.00 0.00 5.01
1607 1711 1.069090 TCACTCAGAACACCGGCAC 59.931 57.895 0.00 0.00 0.00 5.01
1608 1712 1.069090 GTCACTCAGAACACCGGCA 59.931 57.895 0.00 0.00 0.00 5.69
1609 1713 1.668151 GGTCACTCAGAACACCGGC 60.668 63.158 0.00 0.00 32.78 6.13
1610 1714 1.004918 GGGTCACTCAGAACACCGG 60.005 63.158 0.00 0.00 34.85 5.28
1611 1715 1.004918 GGGGTCACTCAGAACACCG 60.005 63.158 0.00 0.00 34.85 4.94
1612 1716 1.004918 CGGGGTCACTCAGAACACC 60.005 63.158 0.00 0.00 31.95 4.16
1613 1717 1.004918 CCGGGGTCACTCAGAACAC 60.005 63.158 0.00 0.00 34.85 3.32
1614 1718 1.458777 ACCGGGGTCACTCAGAACA 60.459 57.895 6.32 0.00 34.85 3.18
1615 1719 1.004918 CACCGGGGTCACTCAGAAC 60.005 63.158 6.32 0.00 0.00 3.01
1616 1720 1.152419 TCACCGGGGTCACTCAGAA 60.152 57.895 2.12 0.00 0.00 3.02
1668 1835 1.448540 CTCTTCCCGCGCATCACTT 60.449 57.895 8.75 0.00 0.00 3.16
1679 1852 2.026822 TCTTGTTCAGCATCCTCTTCCC 60.027 50.000 0.00 0.00 0.00 3.97
1866 2039 3.958860 GCACTCCACCCAGGCAGT 61.959 66.667 0.00 0.00 37.29 4.40
2025 2198 1.067364 CATGTGAACAGCAGTGGCAAA 59.933 47.619 0.00 0.00 44.61 3.68
2031 2204 0.037303 CCTCCCATGTGAACAGCAGT 59.963 55.000 0.00 0.00 0.00 4.40
2142 2315 3.307691 CCCAATCCAGCATATCATACGGT 60.308 47.826 0.00 0.00 0.00 4.83
2172 2345 1.985159 AGAAACACATCCCAGCCACTA 59.015 47.619 0.00 0.00 0.00 2.74
2229 2402 5.007385 ACTACGAATCCACACCTAATGAC 57.993 43.478 0.00 0.00 0.00 3.06
2327 2501 8.697846 TTTTACTTATAGTGTTCGACAGATGG 57.302 34.615 0.00 0.00 0.00 3.51
2369 2544 0.407139 AGCCCAGAGAGGTTTGCATT 59.593 50.000 0.00 0.00 34.66 3.56
2381 2556 1.073923 GGGAGAAAAGAACAGCCCAGA 59.926 52.381 0.00 0.00 35.63 3.86
2384 2564 0.250770 ACGGGAGAAAAGAACAGCCC 60.251 55.000 0.00 0.00 0.00 5.19
2423 2603 9.672673 ATGAAGTAATTCAATACTAGCAACACT 57.327 29.630 9.98 0.00 35.09 3.55
2424 2604 9.708222 CATGAAGTAATTCAATACTAGCAACAC 57.292 33.333 9.98 0.00 35.09 3.32
2425 2605 9.448438 ACATGAAGTAATTCAATACTAGCAACA 57.552 29.630 9.98 0.00 35.09 3.33
2513 2693 4.773674 ACCATTGAAATTTCAGCCATGAGA 59.226 37.500 23.74 9.35 38.61 3.27
2550 2732 8.164070 AGAAATATAGGGGGTGTATTCATGTTC 58.836 37.037 0.00 0.00 0.00 3.18
2635 2831 0.310854 GGTTGAAACCGTTGCCTCAG 59.689 55.000 0.00 0.00 39.66 3.35
2678 2874 7.171848 GGAAGAGTTCAAGGTTAAGACTCTTTC 59.828 40.741 15.62 11.41 41.38 2.62
2682 2878 6.104146 AGGAAGAGTTCAAGGTTAAGACTC 57.896 41.667 0.00 0.00 0.00 3.36
2705 2901 4.163441 TCCAGGTTGAAATGTGAACTGA 57.837 40.909 0.00 0.00 0.00 3.41
2724 2920 1.026718 CCGGACCATTGCAGAGTTCC 61.027 60.000 0.00 0.00 0.00 3.62
2758 2955 5.705609 AATTCAGTCAAACGGCATTAAGT 57.294 34.783 0.00 0.00 0.00 2.24
2821 3536 5.597182 AGTACAGTCACTTGTTTCAGGAGTA 59.403 40.000 0.00 0.00 32.56 2.59
2918 3642 3.185880 AGAGCACCTTACAGGGTAAGA 57.814 47.619 15.71 0.00 40.58 2.10
2923 3647 2.166664 GTCAGTAGAGCACCTTACAGGG 59.833 54.545 0.00 0.00 40.58 4.45
3061 5811 1.271656 CTTACCCGGGCCTAACGATAG 59.728 57.143 24.08 0.54 46.19 2.08
3064 5815 2.724273 GCTTACCCGGGCCTAACGA 61.724 63.158 24.08 0.00 0.00 3.85
3070 5821 3.162154 AGCTAGCTTACCCGGGCC 61.162 66.667 24.08 6.67 0.00 5.80
3076 5827 3.408634 TGAACCAAACAGCTAGCTTACC 58.591 45.455 16.46 0.00 0.00 2.85
3077 5828 5.008712 ACTTTGAACCAAACAGCTAGCTTAC 59.991 40.000 16.46 1.31 0.00 2.34
3143 5899 6.013812 AGCAAGTAATTTGGCCCAATTTAAGA 60.014 34.615 19.06 0.00 37.26 2.10
3192 5948 2.750712 TCCGGGCTTAACATTTAACAGC 59.249 45.455 0.00 0.00 0.00 4.40
3198 5957 3.898482 AGCTTATCCGGGCTTAACATTT 58.102 40.909 0.00 0.00 34.96 2.32


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

AutoCloner maintained by Alex Coulton.