Multiple sequence alignment - TraesCS1A01G397000

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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 TraesCS1A01G397000 chr1A 100.000 5843 0 0 1 5843 562913653 562907811 0.000000e+00 10791.0
1 TraesCS1A01G397000 chr1D 92.347 2731 123 37 26 2717 469807171 469804488 0.000000e+00 3807.0
2 TraesCS1A01G397000 chr1D 88.391 3239 211 60 2718 5843 469804401 469801215 0.000000e+00 3746.0
3 TraesCS1A01G397000 chr1D 74.206 252 49 10 1787 2022 469805813 469805562 2.240000e-14 91.6
4 TraesCS1A01G397000 chr1B 88.978 2749 205 49 1 2720 651279896 651277217 0.000000e+00 3308.0
5 TraesCS1A01G397000 chr1B 87.126 2004 153 40 3752 5707 651275799 651273853 0.000000e+00 2174.0
6 TraesCS1A01G397000 chr1B 89.023 1075 69 18 2718 3752 651277125 651276060 0.000000e+00 1286.0
7 TraesCS1A01G397000 chr1B 90.050 995 78 9 4280 5260 649680177 649679190 0.000000e+00 1269.0
8 TraesCS1A01G397000 chr1B 85.530 387 26 15 5462 5843 649676514 649676153 1.540000e-100 377.0


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 TraesCS1A01G397000 chr1A 562907811 562913653 5842 True 10791.0 10791 100.000000 1 5843 1 chr1A.!!$R1 5842
1 TraesCS1A01G397000 chr1D 469801215 469807171 5956 True 2548.2 3807 84.981333 26 5843 3 chr1D.!!$R1 5817
2 TraesCS1A01G397000 chr1B 651273853 651279896 6043 True 2256.0 3308 88.375667 1 5707 3 chr1B.!!$R2 5706
3 TraesCS1A01G397000 chr1B 649676153 649680177 4024 True 823.0 1269 87.790000 4280 5843 2 chr1B.!!$R1 1563

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
896 906 0.178955 TACAGGACCCTCGGTGAACA 60.179 55.000 0.00 0.0 35.25 3.18 F
1393 1409 0.036732 TTCGGCTGCCACTTCTGATT 59.963 50.000 20.29 0.0 0.00 2.57 F
1394 1410 0.036732 TCGGCTGCCACTTCTGATTT 59.963 50.000 20.29 0.0 0.00 2.17 F
1431 1447 1.001378 GCCGCTGTTTGTTCATTGAGT 60.001 47.619 0.00 0.0 0.00 3.41 F
1463 1479 1.069906 GTTCGTCGCTTCAAACATGCT 60.070 47.619 0.00 0.0 0.00 3.79 F
2584 2640 1.277273 CCTTGTCTGAGCATCCTGTCA 59.723 52.381 0.00 0.0 0.00 3.58 F
3772 4268 0.181114 AGCTGCTGTTGACCTGTTGA 59.819 50.000 0.00 0.0 0.00 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2521 2577 2.940410 GCCAGAATCCCATGCATTTTTG 59.060 45.455 0.00 0.0 0.00 2.44 R
3333 3547 0.743688 ATGGTTTGCGAAAGTGCACA 59.256 45.000 21.04 0.0 46.25 4.57 R
3360 3594 1.285962 AGCATAACAAGGCAGATGGGT 59.714 47.619 0.00 0.0 0.00 4.51 R
3364 3598 3.931907 TGGTAGCATAACAAGGCAGAT 57.068 42.857 0.00 0.0 33.65 2.90 R
3401 3635 4.961438 ATCCTTGTTGCAGAAAATTGGT 57.039 36.364 0.00 0.0 0.00 3.67 R
3846 4356 1.401552 CACATGCATACAACTTCGGGG 59.598 52.381 0.00 0.0 0.00 5.73 R
5493 8509 0.106918 TGCGGTGTTCTTGGTCCTTT 60.107 50.000 0.00 0.0 0.00 3.11 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
32 33 5.353956 TGCTATGTAAATGACGAGCAAATGT 59.646 36.000 0.00 0.00 43.18 2.71
33 34 6.128035 TGCTATGTAAATGACGAGCAAATGTT 60.128 34.615 0.00 0.00 43.18 2.71
91 93 2.460918 CGGAGTATGAACACATCGGAC 58.539 52.381 0.00 0.00 0.00 4.79
175 177 2.741211 GGAACGGCGTCCCAGAAC 60.741 66.667 11.54 0.00 0.00 3.01
613 615 1.737008 GGCGAACTTGACGAGGACC 60.737 63.158 0.00 0.00 0.00 4.46
766 774 4.344865 GCCAGCCACGGAAGGGAA 62.345 66.667 0.00 0.00 35.60 3.97
767 775 2.045926 CCAGCCACGGAAGGGAAG 60.046 66.667 0.00 0.00 35.60 3.46
768 776 2.045926 CAGCCACGGAAGGGAAGG 60.046 66.667 0.00 0.00 35.60 3.46
769 777 3.330720 AGCCACGGAAGGGAAGGG 61.331 66.667 0.00 0.00 35.60 3.95
774 782 1.074244 CCACGGAAGGGAAGGGTTTTA 59.926 52.381 0.00 0.00 35.60 1.52
793 803 1.988956 CCTGGGCTCTCTGCTCTGT 60.989 63.158 0.00 0.00 44.09 3.41
794 804 1.516892 CTGGGCTCTCTGCTCTGTC 59.483 63.158 0.00 0.00 44.09 3.51
795 805 1.958902 CTGGGCTCTCTGCTCTGTCC 61.959 65.000 0.00 0.00 44.09 4.02
796 806 1.685421 GGGCTCTCTGCTCTGTCCT 60.685 63.158 0.00 0.00 39.58 3.85
797 807 1.675720 GGGCTCTCTGCTCTGTCCTC 61.676 65.000 0.00 0.00 39.58 3.71
798 808 0.684153 GGCTCTCTGCTCTGTCCTCT 60.684 60.000 0.00 0.00 42.39 3.69
799 809 0.457035 GCTCTCTGCTCTGTCCTCTG 59.543 60.000 0.00 0.00 38.95 3.35
800 810 1.954733 GCTCTCTGCTCTGTCCTCTGA 60.955 57.143 0.00 0.00 38.95 3.27
821 831 1.982958 GGAACTGTCCTTGGGTCCTAA 59.017 52.381 0.00 0.00 41.24 2.69
823 833 3.559384 GGAACTGTCCTTGGGTCCTAAAG 60.559 52.174 0.00 0.00 41.24 1.85
830 840 3.265995 TCCTTGGGTCCTAAAGGCTTAAG 59.734 47.826 15.47 0.00 42.35 1.85
831 841 3.265995 CCTTGGGTCCTAAAGGCTTAAGA 59.734 47.826 6.67 0.00 36.78 2.10
869 879 9.615660 AGTGTATAATCATAAATAGACCCCTGA 57.384 33.333 0.00 0.00 0.00 3.86
891 901 5.842328 TGATAATTTATACAGGACCCTCGGT 59.158 40.000 0.00 0.00 39.44 4.69
892 902 4.417426 AATTTATACAGGACCCTCGGTG 57.583 45.455 0.00 0.00 35.25 4.94
893 903 2.832643 TTATACAGGACCCTCGGTGA 57.167 50.000 0.00 0.00 35.25 4.02
895 905 1.192428 ATACAGGACCCTCGGTGAAC 58.808 55.000 0.00 0.00 35.25 3.18
896 906 0.178955 TACAGGACCCTCGGTGAACA 60.179 55.000 0.00 0.00 35.25 3.18
897 907 1.052124 ACAGGACCCTCGGTGAACAA 61.052 55.000 0.00 0.00 35.25 2.83
898 908 0.320771 CAGGACCCTCGGTGAACAAG 60.321 60.000 0.00 0.00 35.25 3.16
899 909 0.763223 AGGACCCTCGGTGAACAAGT 60.763 55.000 0.00 0.00 35.25 3.16
900 910 0.602905 GGACCCTCGGTGAACAAGTG 60.603 60.000 0.00 0.00 35.25 3.16
901 911 0.391597 GACCCTCGGTGAACAAGTGA 59.608 55.000 0.00 0.00 35.25 3.41
902 912 0.834612 ACCCTCGGTGAACAAGTGAA 59.165 50.000 0.00 0.00 32.98 3.18
925 935 6.044512 ACACACATTTGTTCTTACGAAGAC 57.955 37.500 0.00 0.00 37.23 3.01
948 958 2.238521 TCAGGGGTTGAACTGCAAATC 58.761 47.619 0.00 0.00 38.44 2.17
949 959 1.068333 CAGGGGTTGAACTGCAAATCG 60.068 52.381 0.00 0.00 38.44 3.34
950 960 1.202879 AGGGGTTGAACTGCAAATCGA 60.203 47.619 0.00 0.00 38.44 3.59
953 963 2.095718 GGGTTGAACTGCAAATCGAGAC 60.096 50.000 0.00 0.00 38.44 3.36
954 964 2.548057 GGTTGAACTGCAAATCGAGACA 59.452 45.455 0.00 0.00 38.44 3.41
956 966 2.832563 TGAACTGCAAATCGAGACACA 58.167 42.857 0.00 0.00 0.00 3.72
957 967 2.543848 TGAACTGCAAATCGAGACACAC 59.456 45.455 0.00 0.00 0.00 3.82
959 969 0.439985 CTGCAAATCGAGACACACCG 59.560 55.000 0.00 0.00 0.00 4.94
962 972 1.736645 AAATCGAGACACACCGCCG 60.737 57.895 0.00 0.00 0.00 6.46
963 973 2.149803 AAATCGAGACACACCGCCGA 62.150 55.000 0.00 0.00 0.00 5.54
964 974 2.149803 AATCGAGACACACCGCCGAA 62.150 55.000 0.00 0.00 32.84 4.30
966 976 3.112709 GAGACACACCGCCGAAGC 61.113 66.667 0.00 0.00 0.00 3.86
967 977 4.681978 AGACACACCGCCGAAGCC 62.682 66.667 0.00 0.00 34.57 4.35
968 978 4.980805 GACACACCGCCGAAGCCA 62.981 66.667 0.00 0.00 34.57 4.75
969 979 4.988598 ACACACCGCCGAAGCCAG 62.989 66.667 0.00 0.00 34.57 4.85
978 988 3.431725 CGAAGCCAGCGGAAACCC 61.432 66.667 0.00 0.00 0.00 4.11
979 989 2.034221 GAAGCCAGCGGAAACCCT 59.966 61.111 0.00 0.00 0.00 4.34
980 990 2.034221 AAGCCAGCGGAAACCCTC 59.966 61.111 0.00 0.00 0.00 4.30
981 991 3.569200 AAGCCAGCGGAAACCCTCC 62.569 63.158 0.00 0.00 41.40 4.30
1366 1382 1.372087 CCCATTTGGTGAGCTCTCGC 61.372 60.000 16.19 6.32 39.26 5.03
1393 1409 0.036732 TTCGGCTGCCACTTCTGATT 59.963 50.000 20.29 0.00 0.00 2.57
1394 1410 0.036732 TCGGCTGCCACTTCTGATTT 59.963 50.000 20.29 0.00 0.00 2.17
1395 1411 1.277842 TCGGCTGCCACTTCTGATTTA 59.722 47.619 20.29 0.00 0.00 1.40
1396 1412 2.092968 TCGGCTGCCACTTCTGATTTAT 60.093 45.455 20.29 0.00 0.00 1.40
1397 1413 2.684881 CGGCTGCCACTTCTGATTTATT 59.315 45.455 20.29 0.00 0.00 1.40
1406 1422 6.474751 GCCACTTCTGATTTATTTTCAGCATC 59.525 38.462 0.00 0.00 40.35 3.91
1431 1447 1.001378 GCCGCTGTTTGTTCATTGAGT 60.001 47.619 0.00 0.00 0.00 3.41
1457 1473 4.377022 GCTTATTCAGTTCGTCGCTTCAAA 60.377 41.667 0.00 0.00 0.00 2.69
1463 1479 1.069906 GTTCGTCGCTTCAAACATGCT 60.070 47.619 0.00 0.00 0.00 3.79
1512 1537 5.986004 AAATACGCCTAGATTTGTAGTGC 57.014 39.130 0.00 0.00 0.00 4.40
1516 1541 2.281762 CGCCTAGATTTGTAGTGCGAAC 59.718 50.000 10.11 0.00 39.79 3.95
1545 1570 7.816640 TGCTAAAGTAAGGAATGCTTTGTTAG 58.183 34.615 0.00 0.50 42.88 2.34
1570 1595 3.619483 TGTTCCTATTCATGTTAACGGCG 59.381 43.478 4.80 4.80 0.00 6.46
1592 1617 2.534757 GCGCCAAGTTAGAATCGAGTAC 59.465 50.000 0.00 0.00 0.00 2.73
1636 1661 6.978659 TCCTCTGCATTTCAGTAGTAATTACG 59.021 38.462 9.91 0.00 43.32 3.18
1673 1698 2.104792 CTGGGATTAAGAAGATGCCCGA 59.895 50.000 0.00 0.00 38.42 5.14
1720 1745 4.637483 AATTCCAACAATATCGTGCCTG 57.363 40.909 0.00 0.00 0.00 4.85
1721 1746 3.342377 TTCCAACAATATCGTGCCTGA 57.658 42.857 0.00 0.00 0.00 3.86
1823 1863 4.201724 GCTTATTCAGTTCGTCGCTTCAAT 60.202 41.667 0.00 0.00 0.00 2.57
1857 1900 4.343814 TCAATTAGGTGATCCGTGCTATCA 59.656 41.667 0.00 0.00 39.05 2.15
1887 1930 7.019774 TCAAATATGACTTAATCTGTGCTGC 57.980 36.000 0.00 0.00 0.00 5.25
1891 1934 3.689347 TGACTTAATCTGTGCTGCCAAT 58.311 40.909 0.00 0.00 0.00 3.16
1902 1945 3.509184 TGTGCTGCCAATGCTAATGTAAA 59.491 39.130 0.00 0.00 38.71 2.01
1929 1972 9.832445 ATATGTTCTGTTCCTAATCGTGTTAAT 57.168 29.630 0.00 0.00 0.00 1.40
1991 2034 8.571336 AGGTATACTTTGCATTTCATCATTAGC 58.429 33.333 2.25 0.00 0.00 3.09
2071 2114 9.408648 ACTCATATTAAAAATTCCCTACCACAG 57.591 33.333 0.00 0.00 0.00 3.66
2079 2122 5.836024 AATTCCCTACCACAGTGAGTTAA 57.164 39.130 0.62 0.00 0.00 2.01
2182 2225 5.567423 GCCCATTGTTTATGAGACTGCTTTT 60.567 40.000 0.00 0.00 36.26 2.27
2186 2229 9.079833 CCATTGTTTATGAGACTGCTTTTATTG 57.920 33.333 0.00 0.00 36.26 1.90
2201 2249 6.148811 TGCTTTTATTGTAGTGGTGCTAAGAC 59.851 38.462 0.00 0.00 0.00 3.01
2205 2253 7.900782 TTATTGTAGTGGTGCTAAGACTTTC 57.099 36.000 0.00 0.00 0.00 2.62
2341 2389 3.679389 AGCACCAGATTTTGAGGTACAG 58.321 45.455 0.00 0.00 33.49 2.74
2352 2403 6.360370 TTTTGAGGTACAGATCTGCTACTT 57.640 37.500 22.83 18.12 0.00 2.24
2478 2532 3.848272 AGCGTTGGGTTTGATATTGTG 57.152 42.857 0.00 0.00 0.00 3.33
2521 2577 8.552083 AATTTTCTGGGAGCAATATTTTGTTC 57.448 30.769 4.52 4.52 41.02 3.18
2584 2640 1.277273 CCTTGTCTGAGCATCCTGTCA 59.723 52.381 0.00 0.00 0.00 3.58
2621 2677 8.193953 AGGAAAATGTGTTTGGATCAAATAGT 57.806 30.769 0.00 0.00 35.74 2.12
2818 2972 7.613411 CCCAGAGACTTTTTATGGAAGAAGATT 59.387 37.037 0.00 0.00 32.55 2.40
2866 3020 4.106029 TCTGTTCTATTGCTACCGTGTC 57.894 45.455 0.00 0.00 0.00 3.67
2965 3136 5.752955 GCAATTTCTGTTTCCAGTTGCTAAA 59.247 36.000 8.44 0.00 41.45 1.85
2974 3145 6.254589 TGTTTCCAGTTGCTAAATTTGTTTCG 59.745 34.615 0.00 0.00 0.00 3.46
2976 3147 6.621316 TCCAGTTGCTAAATTTGTTTCGTA 57.379 33.333 0.00 0.00 0.00 3.43
3116 3298 9.593134 CAAGTTTGCTGATAGATAGAGTAGTTT 57.407 33.333 0.00 0.00 0.00 2.66
3160 3373 7.630242 ATGAGGTGTAAACGAATTGATGATT 57.370 32.000 0.00 0.00 0.00 2.57
3163 3376 6.620678 AGGTGTAAACGAATTGATGATTTGG 58.379 36.000 0.00 0.00 34.01 3.28
3179 3392 6.139679 TGATTTGGTAGATTTTGGAGAGGT 57.860 37.500 0.00 0.00 0.00 3.85
3349 3563 6.869421 ATATTTATGTGCACTTTCGCAAAC 57.131 33.333 19.41 0.00 45.14 2.93
3360 3594 4.391830 CACTTTCGCAAACCATCTAGCTAA 59.608 41.667 0.00 0.00 0.00 3.09
3364 3598 2.679639 CGCAAACCATCTAGCTAACCCA 60.680 50.000 0.00 0.00 0.00 4.51
3401 3635 4.501571 GCTACCATTTTCTCCGCTGATCTA 60.502 45.833 0.00 0.00 0.00 1.98
3469 3703 1.952367 GCTATTCTGGCCACTGCTTGT 60.952 52.381 0.00 0.00 37.74 3.16
3482 3716 1.000607 CTGCTTGTTGCTGCATTCACT 60.001 47.619 1.84 0.00 43.37 3.41
3517 3751 2.455032 CTGCACTACATACTCTGTCGC 58.545 52.381 0.00 0.00 39.39 5.19
3584 3818 7.358066 CGATGATGTTATTTTCATTGGAGGAG 58.642 38.462 0.00 0.00 32.84 3.69
3617 3851 2.489938 TTCATTGGAGCAGTACCCAC 57.510 50.000 0.00 0.00 31.11 4.61
3637 3871 6.126185 ACCCACCCATAATGATTATATAGGGC 60.126 42.308 15.37 0.00 38.64 5.19
3651 3885 8.627208 ATTATATAGGGCAATGAGTTTGAGTG 57.373 34.615 0.00 0.00 37.53 3.51
3679 3913 8.531146 ACATTTTATCCCTATTTCACTGTTTGG 58.469 33.333 0.00 0.00 0.00 3.28
3710 3944 2.341846 TGGATGATTAAACCCTCCGC 57.658 50.000 0.00 0.00 0.00 5.54
3723 3958 1.014352 CCTCCGCCCTTAATTTGTCG 58.986 55.000 0.00 0.00 0.00 4.35
3727 3962 2.496871 TCCGCCCTTAATTTGTCGTCTA 59.503 45.455 0.00 0.00 0.00 2.59
3728 3963 3.133362 TCCGCCCTTAATTTGTCGTCTAT 59.867 43.478 0.00 0.00 0.00 1.98
3741 3976 8.818141 ATTTGTCGTCTATATGGTTCATACAG 57.182 34.615 0.00 0.00 0.00 2.74
3746 3981 9.343103 GTCGTCTATATGGTTCATACAGTATTG 57.657 37.037 0.00 0.00 0.00 1.90
3772 4268 0.181114 AGCTGCTGTTGACCTGTTGA 59.819 50.000 0.00 0.00 0.00 3.18
3846 4356 1.141858 CCTAATTCCAGGAGCCAGGAC 59.858 57.143 0.00 0.00 38.00 3.85
3906 4419 6.990341 TGAGTTGGTGACATTATGATCTTG 57.010 37.500 0.00 0.00 42.32 3.02
3920 4433 9.836076 CATTATGATCTTGTATGCTAAACATGG 57.164 33.333 0.00 0.00 40.06 3.66
3934 4447 7.053498 TGCTAAACATGGATGTATGCTTAAGA 58.947 34.615 6.67 0.00 40.80 2.10
3945 4458 8.394121 GGATGTATGCTTAAGACTCTTTCAAAG 58.606 37.037 6.67 0.00 0.00 2.77
3969 4482 5.116180 CCGTTCAGCTTAACTTGATATCCA 58.884 41.667 9.02 0.00 0.00 3.41
3992 4505 7.126268 TCCATCTGTTCATCTGATTTCTCCTAA 59.874 37.037 0.00 0.00 33.48 2.69
3995 4508 5.431765 TGTTCATCTGATTTCTCCTAAGCC 58.568 41.667 0.00 0.00 0.00 4.35
4059 4572 8.362860 ACGAAGATGATGAAATACTGATTCAG 57.637 34.615 12.17 12.17 39.92 3.02
4237 4750 5.390356 GCAGAAGAAGAAGCTACAACATCAC 60.390 44.000 0.00 0.00 0.00 3.06
4295 4808 1.065854 AGCCTACACAGGAATCACAGC 60.066 52.381 0.00 0.00 45.91 4.40
4409 4922 0.689623 ACTCACCTTTCCAGCTCCAG 59.310 55.000 0.00 0.00 0.00 3.86
4461 4974 6.662755 TGCTTTGGTAGGTATGAAGATCAAT 58.337 36.000 0.00 0.00 0.00 2.57
4473 4986 9.064706 GGTATGAAGATCAATGAGTCAAATGAT 57.935 33.333 19.28 19.28 35.33 2.45
4508 5021 2.325082 GCACCACGTCCAAATCGCT 61.325 57.895 0.00 0.00 0.00 4.93
4559 5072 2.156917 TGCCTTGCTTTCAGAGACATG 58.843 47.619 0.00 0.00 0.00 3.21
4626 5139 1.269051 CGCCCAACTTTTGACTCCAAC 60.269 52.381 0.00 0.00 30.88 3.77
4702 5215 1.546923 CTGTGGATGATTTGCTTGCCA 59.453 47.619 0.00 0.00 0.00 4.92
4803 5316 1.134670 CCACCTTCTGGATCCTCGAAC 60.135 57.143 14.23 0.00 43.95 3.95
4823 5336 3.596214 ACGTATCGGCTGACTTTGATTT 58.404 40.909 0.00 0.00 0.00 2.17
4844 5357 4.322080 TGTGGTTTGACTCACTGTAGAG 57.678 45.455 5.93 5.93 41.44 2.43
5004 5518 0.703488 TGGAGGTCCATGGAAATGCA 59.297 50.000 18.20 16.38 42.01 3.96
5074 5588 2.220653 AGGCCTGTGTTATGTTGCAT 57.779 45.000 3.11 0.00 0.00 3.96
5120 5637 1.821136 GAAGGCTGGCTGCTGTTAAAT 59.179 47.619 16.14 0.00 42.39 1.40
5149 5666 2.161012 TGTCGATCTGTACCTTCGTGAC 59.839 50.000 8.45 2.85 34.60 3.67
5157 5674 2.816087 TGTACCTTCGTGACCTGTACTC 59.184 50.000 0.00 0.00 34.37 2.59
5158 5675 1.991121 ACCTTCGTGACCTGTACTCA 58.009 50.000 0.00 0.00 0.00 3.41
5219 5745 8.690840 GTTGATTTAACAGAGTAATGCAAACAC 58.309 33.333 0.00 0.00 39.16 3.32
5266 5793 5.698832 TGTATGTACTTTTCTGTTGCATGC 58.301 37.500 11.82 11.82 0.00 4.06
5273 5800 0.895100 TTCTGTTGCATGCCCACTCC 60.895 55.000 16.68 0.00 0.00 3.85
5276 5803 3.267233 TTGCATGCCCACTCCCCT 61.267 61.111 16.68 0.00 0.00 4.79
5280 5807 2.693864 ATGCCCACTCCCCTCCTG 60.694 66.667 0.00 0.00 0.00 3.86
5290 5817 4.412199 CCACTCCCCTCCTGATTACATTTA 59.588 45.833 0.00 0.00 0.00 1.40
5303 5830 8.362639 CCTGATTACATTTATTCTGGGGAAATG 58.637 37.037 5.30 5.30 43.23 2.32
5305 5832 9.265862 TGATTACATTTATTCTGGGGAAATGTT 57.734 29.630 15.13 1.70 46.49 2.71
5306 5833 9.533253 GATTACATTTATTCTGGGGAAATGTTG 57.467 33.333 15.13 0.00 46.49 3.33
5310 5837 9.438163 ACATTTATTCTGGGGAAATGTTGATAT 57.562 29.630 6.43 0.00 46.49 1.63
5311 5838 9.918630 CATTTATTCTGGGGAAATGTTGATATC 57.081 33.333 0.00 0.00 36.33 1.63
5312 5839 7.744087 TTATTCTGGGGAAATGTTGATATCG 57.256 36.000 0.00 0.00 34.90 2.92
5322 5849 5.643379 AATGTTGATATCGGCAAGTTTGT 57.357 34.783 0.00 0.00 0.00 2.83
5325 5852 4.517075 TGTTGATATCGGCAAGTTTGTTGA 59.483 37.500 0.00 0.00 0.00 3.18
5331 5858 2.159310 TCGGCAAGTTTGTTGAGTTTGG 60.159 45.455 0.00 0.00 0.00 3.28
5350 5893 3.738982 TGGTCACTGATTTGTACACCTG 58.261 45.455 0.00 0.00 0.00 4.00
5357 5900 4.080863 ACTGATTTGTACACCTGATCCCTC 60.081 45.833 0.00 0.00 0.00 4.30
5371 5914 1.153469 CCCTCTTGAGCTCGAAGGC 60.153 63.158 18.68 0.00 0.00 4.35
5372 5915 1.612395 CCCTCTTGAGCTCGAAGGCT 61.612 60.000 18.68 0.00 46.11 4.58
5386 5929 2.871022 CGAAGGCTTCAGATGGATTCAG 59.129 50.000 25.66 2.31 0.00 3.02
5396 5940 7.041916 GCTTCAGATGGATTCAGATAACTCAAG 60.042 40.741 0.00 0.00 0.00 3.02
5400 5944 4.183865 TGGATTCAGATAACTCAAGTGCG 58.816 43.478 0.00 0.00 0.00 5.34
5418 5962 1.963338 GAAGCCTGCAACAGTCGCT 60.963 57.895 0.00 0.00 32.10 4.93
5425 5969 1.206072 GCAACAGTCGCTGCTTCTG 59.794 57.895 15.57 15.57 34.37 3.02
5428 5972 1.070309 CAACAGTCGCTGCTTCTGAAC 60.070 52.381 21.23 2.27 34.37 3.18
5430 5974 0.510359 CAGTCGCTGCTTCTGAACAC 59.490 55.000 13.07 0.00 0.00 3.32
5455 6002 2.241176 TGTCTGGTTCAGTTGTTTCCCT 59.759 45.455 0.00 0.00 32.61 4.20
5456 6003 3.288092 GTCTGGTTCAGTTGTTTCCCTT 58.712 45.455 0.00 0.00 32.61 3.95
5467 8483 5.183713 CAGTTGTTTCCCTTTATGATCTGCA 59.816 40.000 0.00 0.00 0.00 4.41
5483 8499 3.282021 TCTGCAAAGGATCAAGCATACC 58.718 45.455 0.00 0.00 36.28 2.73
5484 8500 3.018856 CTGCAAAGGATCAAGCATACCA 58.981 45.455 0.00 0.00 36.28 3.25
5485 8501 2.754552 TGCAAAGGATCAAGCATACCAC 59.245 45.455 0.00 0.00 31.05 4.16
5493 8509 0.327924 CAAGCATACCACCCACCTCA 59.672 55.000 0.00 0.00 0.00 3.86
5520 8536 1.267806 CAAGAACACCGCAATTCAGCT 59.732 47.619 0.00 0.00 0.00 4.24
5602 8628 4.145436 TCCCTCGCCATGGAGAAA 57.855 55.556 19.39 5.30 36.08 2.52
5603 8629 1.602237 TCCCTCGCCATGGAGAAAC 59.398 57.895 19.39 0.00 36.08 2.78
5604 8630 1.452108 CCCTCGCCATGGAGAAACC 60.452 63.158 19.39 0.00 36.08 3.27
5667 8694 4.141846 TGGTATCTTCTGCTTGATCTGGAC 60.142 45.833 0.00 0.00 0.00 4.02
5724 8751 6.070897 TCGTTTTGATTGACATCACATGTT 57.929 33.333 0.00 0.00 45.03 2.71
5790 8821 2.280797 TGTCCAGGTTCGTGCTGC 60.281 61.111 0.00 0.00 0.00 5.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.233789 GCCAAACATTTGCTCGTCATTTA 58.766 39.130 0.00 0.00 36.86 1.40
32 33 7.147312 CAGTGAGATTTATTCTTGTTGCCAAA 58.853 34.615 0.00 0.00 33.74 3.28
33 34 6.680810 CAGTGAGATTTATTCTTGTTGCCAA 58.319 36.000 0.00 0.00 33.74 4.52
46 47 1.813753 GCCGCGGCAGTGAGATTTA 60.814 57.895 43.55 0.00 41.49 1.40
76 78 2.357952 CGAGGAGTCCGATGTGTTCATA 59.642 50.000 2.76 0.00 34.06 2.15
78 80 0.526211 CGAGGAGTCCGATGTGTTCA 59.474 55.000 2.76 0.00 0.00 3.18
91 93 1.728672 GGAGTACGCCTTCGAGGAG 59.271 63.158 8.60 0.00 41.31 3.69
129 131 1.605058 CCCCGTGATCGAGAAGGTGT 61.605 60.000 0.00 0.00 39.71 4.16
613 615 1.608717 CGGTCTGGAACTCCTCCCTG 61.609 65.000 0.00 0.00 44.69 4.45
765 773 1.354705 GAGAGCCCAGGTAAAACCCTT 59.645 52.381 0.00 0.00 39.75 3.95
766 774 0.992695 GAGAGCCCAGGTAAAACCCT 59.007 55.000 0.00 0.00 39.75 4.34
767 775 0.992695 AGAGAGCCCAGGTAAAACCC 59.007 55.000 0.00 0.00 39.75 4.11
768 776 1.950954 GCAGAGAGCCCAGGTAAAACC 60.951 57.143 0.00 0.00 36.28 3.27
769 777 1.454201 GCAGAGAGCCCAGGTAAAAC 58.546 55.000 0.00 0.00 37.23 2.43
812 822 2.238898 GCTCTTAAGCCTTTAGGACCCA 59.761 50.000 0.00 0.00 43.10 4.51
813 823 2.920524 GCTCTTAAGCCTTTAGGACCC 58.079 52.381 0.00 0.00 43.10 4.46
830 840 2.674796 ATACACTTTCACGAGGGCTC 57.325 50.000 0.00 0.00 0.00 4.70
831 841 4.161565 TGATTATACACTTTCACGAGGGCT 59.838 41.667 0.00 0.00 0.00 5.19
860 870 6.272558 GGTCCTGTATAAATTATCAGGGGTCT 59.727 42.308 20.75 0.00 45.07 3.85
861 871 6.473758 GGTCCTGTATAAATTATCAGGGGTC 58.526 44.000 20.75 14.89 45.07 4.46
862 872 5.312443 GGGTCCTGTATAAATTATCAGGGGT 59.688 44.000 20.75 0.00 45.07 4.95
863 873 5.551977 AGGGTCCTGTATAAATTATCAGGGG 59.448 44.000 20.75 8.63 45.07 4.79
869 879 5.842328 TCACCGAGGGTCCTGTATAAATTAT 59.158 40.000 0.00 0.00 31.02 1.28
870 880 5.210430 TCACCGAGGGTCCTGTATAAATTA 58.790 41.667 0.00 0.00 31.02 1.40
877 887 0.178955 TGTTCACCGAGGGTCCTGTA 60.179 55.000 0.00 0.00 31.02 2.74
879 889 0.320771 CTTGTTCACCGAGGGTCCTG 60.321 60.000 0.00 0.00 31.02 3.86
882 892 0.391597 TCACTTGTTCACCGAGGGTC 59.608 55.000 0.00 0.00 31.02 4.46
884 894 1.226746 GTTCACTTGTTCACCGAGGG 58.773 55.000 0.00 0.00 0.00 4.30
887 897 2.004017 GTGTGTTCACTTGTTCACCGA 58.996 47.619 4.59 0.00 40.98 4.69
888 898 1.735018 TGTGTGTTCACTTGTTCACCG 59.265 47.619 4.59 0.00 44.14 4.94
889 899 4.370364 AATGTGTGTTCACTTGTTCACC 57.630 40.909 4.59 0.00 44.14 4.02
891 901 5.384063 ACAAATGTGTGTTCACTTGTTCA 57.616 34.783 4.59 0.00 44.14 3.18
919 929 3.195825 AGTTCAACCCCTGATAGTCTTCG 59.804 47.826 0.00 0.00 32.78 3.79
925 935 2.787473 TGCAGTTCAACCCCTGATAG 57.213 50.000 0.00 0.00 32.78 2.08
948 958 2.805353 CTTCGGCGGTGTGTCTCG 60.805 66.667 7.21 0.00 0.00 4.04
949 959 3.112709 GCTTCGGCGGTGTGTCTC 61.113 66.667 7.21 0.00 0.00 3.36
950 960 4.681978 GGCTTCGGCGGTGTGTCT 62.682 66.667 7.21 0.00 42.91 3.41
959 969 4.103103 GTTTCCGCTGGCTTCGGC 62.103 66.667 12.04 0.00 46.05 5.54
962 972 2.034221 AGGGTTTCCGCTGGCTTC 59.966 61.111 0.00 0.00 38.33 3.86
963 973 2.034221 GAGGGTTTCCGCTGGCTT 59.966 61.111 0.00 0.00 38.33 4.35
964 974 4.035102 GGAGGGTTTCCGCTGGCT 62.035 66.667 0.00 0.00 35.91 4.75
971 981 3.009714 AGCGGAGGGAGGGTTTCC 61.010 66.667 0.00 0.00 46.00 3.13
972 982 2.269241 CAGCGGAGGGAGGGTTTC 59.731 66.667 0.00 0.00 0.00 2.78
973 983 4.035102 GCAGCGGAGGGAGGGTTT 62.035 66.667 0.00 0.00 0.00 3.27
995 1005 1.072159 GCCTTGGGATCCATCGGAG 59.928 63.158 15.23 3.28 34.05 4.63
996 1006 2.807107 CGCCTTGGGATCCATCGGA 61.807 63.158 15.23 0.00 35.55 4.55
1406 1422 1.919918 TGAACAAACAGCGGCAAAAG 58.080 45.000 1.45 0.00 0.00 2.27
1431 1447 4.106029 AGCGACGAACTGAATAAGCTTA 57.894 40.909 8.99 8.99 0.00 3.09
1457 1473 2.162208 CGCACAATTGACCTAAGCATGT 59.838 45.455 13.59 0.00 0.00 3.21
1463 1479 3.627395 AGGATCGCACAATTGACCTAA 57.373 42.857 13.59 0.00 0.00 2.69
1512 1537 5.917541 TTCCTTACTTTAGCAAGTGTTCG 57.082 39.130 0.00 0.00 43.54 3.95
1516 1541 5.886960 AGCATTCCTTACTTTAGCAAGTG 57.113 39.130 0.00 0.00 43.54 3.16
1545 1570 5.798434 GCCGTTAACATGAATAGGAACAAAC 59.202 40.000 6.39 0.00 0.00 2.93
1570 1595 0.931005 CTCGATTCTAACTTGGCGCC 59.069 55.000 22.73 22.73 0.00 6.53
1592 1617 3.446161 AGGATGCCTTGTGATGTTTGATG 59.554 43.478 0.00 0.00 0.00 3.07
1636 1661 1.339151 CCCAGTCCTAACAAGAGCACC 60.339 57.143 0.00 0.00 0.00 5.01
1673 1698 5.706833 TCAACACTGCACATAATCAATCTGT 59.293 36.000 0.00 0.00 0.00 3.41
1720 1745 6.472686 ACTATGAAACAGAGGGTGAGTATC 57.527 41.667 0.00 0.00 0.00 2.24
1721 1746 6.875972 AACTATGAAACAGAGGGTGAGTAT 57.124 37.500 0.00 0.00 0.00 2.12
1823 1863 7.054124 GGATCACCTAATTGACCTAAACATGA 58.946 38.462 0.00 0.00 0.00 3.07
1891 1934 9.461312 AGGAACAGAACATATTTTACATTAGCA 57.539 29.630 0.00 0.00 0.00 3.49
1902 1945 9.661563 TTAACACGATTAGGAACAGAACATATT 57.338 29.630 0.00 0.00 0.00 1.28
1929 1972 3.311871 GCACTCGATTCTAAGTCTCGGTA 59.688 47.826 0.00 0.00 33.38 4.02
1991 2034 7.062749 TCCAGCCCTTATAATAACACAGTAG 57.937 40.000 0.00 0.00 0.00 2.57
2079 2122 9.100554 CATATCAATTTTGCCAACATTATGTGT 57.899 29.630 0.00 0.00 44.84 3.72
2120 2163 3.474806 GTGCTATGTTCAGCGCGT 58.525 55.556 8.43 0.00 44.88 6.01
2182 2225 6.999950 TGAAAGTCTTAGCACCACTACAATA 58.000 36.000 0.00 0.00 0.00 1.90
2186 2229 6.803154 AAATGAAAGTCTTAGCACCACTAC 57.197 37.500 0.00 0.00 0.00 2.73
2341 2389 8.545229 AACATGATATAGCAAAGTAGCAGATC 57.455 34.615 0.00 0.00 36.85 2.75
2521 2577 2.940410 GCCAGAATCCCATGCATTTTTG 59.060 45.455 0.00 0.00 0.00 2.44
2584 2640 9.108284 CAAACACATTTTCCTTCCATAAACTTT 57.892 29.630 0.00 0.00 0.00 2.66
2674 2734 4.093743 GGGTCCACCAATCCAAATAAAGT 58.906 43.478 0.00 0.00 39.85 2.66
2675 2735 4.352893 AGGGTCCACCAATCCAAATAAAG 58.647 43.478 0.00 0.00 43.89 1.85
2818 2972 3.461085 AGTACCAGATCCTCGGGTAGTAA 59.539 47.826 10.79 0.00 45.44 2.24
2965 3136 7.754851 AGGAAAGTACCAATACGAAACAAAT 57.245 32.000 0.00 0.00 36.33 2.32
2974 3145 6.489022 ACCAACTGAAAGGAAAGTACCAATAC 59.511 38.462 0.00 0.00 39.30 1.89
2976 3147 5.454966 ACCAACTGAAAGGAAAGTACCAAT 58.545 37.500 0.00 0.00 39.30 3.16
3090 3270 9.593134 AAACTACTCTATCTATCAGCAAACTTG 57.407 33.333 0.00 0.00 0.00 3.16
3160 3373 3.913799 TGGACCTCTCCAAAATCTACCAA 59.086 43.478 0.00 0.00 44.26 3.67
3205 3418 9.817809 GTGTACAGATTGGATTAGAGTTTATCA 57.182 33.333 0.00 0.00 0.00 2.15
3212 3425 6.796426 TCTTCGTGTACAGATTGGATTAGAG 58.204 40.000 0.00 0.00 0.00 2.43
3333 3547 0.743688 ATGGTTTGCGAAAGTGCACA 59.256 45.000 21.04 0.00 46.25 4.57
3349 3563 2.289945 GGCAGATGGGTTAGCTAGATGG 60.290 54.545 0.00 0.00 0.00 3.51
3360 3594 1.285962 AGCATAACAAGGCAGATGGGT 59.714 47.619 0.00 0.00 0.00 4.51
3364 3598 3.931907 TGGTAGCATAACAAGGCAGAT 57.068 42.857 0.00 0.00 33.65 2.90
3401 3635 4.961438 ATCCTTGTTGCAGAAAATTGGT 57.039 36.364 0.00 0.00 0.00 3.67
3469 3703 2.009051 CCGTGATAGTGAATGCAGCAA 58.991 47.619 0.00 0.00 0.00 3.91
3482 3716 1.742831 GTGCAGGAAATTGCCGTGATA 59.257 47.619 0.00 0.00 43.43 2.15
3559 3793 7.263100 TCCTCCAATGAAAATAACATCATCG 57.737 36.000 0.00 0.00 35.29 3.84
3584 3818 2.794350 CCAATGAAAGGAACAAACGTGC 59.206 45.455 0.00 0.00 0.00 5.34
3597 3831 2.554344 GGTGGGTACTGCTCCAATGAAA 60.554 50.000 0.00 0.00 34.47 2.69
3617 3851 9.293404 CTCATTGCCCTATATAATCATTATGGG 57.707 37.037 6.85 6.85 32.29 4.00
3637 3871 7.756722 GGATAAAATGTCCACTCAAACTCATTG 59.243 37.037 0.00 0.00 36.74 2.82
3651 3885 7.881775 ACAGTGAAATAGGGATAAAATGTCC 57.118 36.000 0.00 0.00 34.92 4.02
3679 3913 6.199393 GTTTAATCATCCAAGTGTAATCGGC 58.801 40.000 0.00 0.00 0.00 5.54
3710 3944 7.713507 TGAACCATATAGACGACAAATTAAGGG 59.286 37.037 0.00 0.00 0.00 3.95
3741 3976 6.457528 GGTCAACAGCAGCTTTATCTCAATAC 60.458 42.308 0.00 0.00 0.00 1.89
3746 3981 3.373439 CAGGTCAACAGCAGCTTTATCTC 59.627 47.826 0.00 0.00 0.00 2.75
3846 4356 1.401552 CACATGCATACAACTTCGGGG 59.598 52.381 0.00 0.00 0.00 5.73
3850 4360 5.505173 AATAGGCACATGCATACAACTTC 57.495 39.130 0.00 0.00 40.26 3.01
3851 4361 5.920193 AAATAGGCACATGCATACAACTT 57.080 34.783 0.00 0.00 40.26 2.66
3899 4412 7.056006 ACATCCATGTTTAGCATACAAGATCA 58.944 34.615 0.00 0.00 37.90 2.92
3906 4419 6.808008 AGCATACATCCATGTTTAGCATAC 57.192 37.500 0.00 0.00 41.97 2.39
3920 4433 7.907563 GCTTTGAAAGAGTCTTAAGCATACATC 59.092 37.037 24.45 10.06 40.92 3.06
3934 4447 1.604278 GCTGAACGGCTTTGAAAGAGT 59.396 47.619 9.48 4.94 0.00 3.24
3945 4458 4.024809 GGATATCAAGTTAAGCTGAACGGC 60.025 45.833 8.36 0.00 34.36 5.68
3957 4470 7.799081 TCAGATGAACAGATGGATATCAAGTT 58.201 34.615 4.83 1.60 36.88 2.66
3969 4482 6.991531 GCTTAGGAGAAATCAGATGAACAGAT 59.008 38.462 0.00 0.00 0.00 2.90
3992 4505 4.137543 GGGAATAACAAGATGAATCGGCT 58.862 43.478 0.00 0.00 0.00 5.52
3995 4508 5.409826 GCCTAGGGAATAACAAGATGAATCG 59.590 44.000 11.72 0.00 0.00 3.34
4237 4750 5.463724 GCATAGGTCGAGGAATAACTTTGAG 59.536 44.000 0.00 0.00 0.00 3.02
4295 4808 1.474077 GCCCTGCATTTGGAACAGTAG 59.526 52.381 1.50 0.00 42.39 2.57
4362 4875 7.386025 CCATCGAGTGAATTAAGAAGCATATCA 59.614 37.037 0.00 0.00 0.00 2.15
4409 4922 4.246458 ACTTCCAAACGACTCATCTAAGC 58.754 43.478 0.00 0.00 0.00 3.09
4461 4974 6.455647 AGACGTGACTTTATCATTTGACTCA 58.544 36.000 0.00 0.00 40.28 3.41
4473 4986 2.352421 GGTGCTGCTAGACGTGACTTTA 60.352 50.000 0.00 0.00 0.00 1.85
4508 5021 2.106338 TCATCAACAGGAGAAAGTGCCA 59.894 45.455 0.00 0.00 0.00 4.92
4559 5072 4.712476 ACCATCATTCTGGACAGATAAGC 58.288 43.478 2.42 0.00 39.73 3.09
4626 5139 4.726021 GCATATCTGAAGTCAACGTTGCTG 60.726 45.833 23.47 12.76 0.00 4.41
4683 5196 1.630223 TGGCAAGCAAATCATCCACA 58.370 45.000 0.00 0.00 0.00 4.17
4702 5215 0.111253 CTCAGGCAGAAAGGGGTGTT 59.889 55.000 0.00 0.00 0.00 3.32
4803 5316 3.370978 ACAAATCAAAGTCAGCCGATACG 59.629 43.478 0.00 0.00 0.00 3.06
4823 5336 3.069586 CCTCTACAGTGAGTCAAACCACA 59.930 47.826 0.00 0.00 35.84 4.17
4844 5357 4.922103 ACGATCGAAAGTGTTTCTTCTACC 59.078 41.667 24.34 0.00 37.52 3.18
4890 5403 0.539669 ACAAAAGCACAGTAGGCCCC 60.540 55.000 0.00 0.00 0.00 5.80
4891 5404 1.269723 GAACAAAAGCACAGTAGGCCC 59.730 52.381 0.00 0.00 0.00 5.80
5038 5552 0.732880 CCTAGCACCGAACTGACACG 60.733 60.000 0.00 0.00 0.00 4.49
5074 5588 6.183361 TGGACTCATGATCAGTATGGCAATAA 60.183 38.462 0.09 0.00 36.16 1.40
5120 5637 5.230323 AGGTACAGATCGACAGCTATAGA 57.770 43.478 3.21 0.00 0.00 1.98
5149 5666 4.887748 ACAAAGATGTGACTGAGTACAGG 58.112 43.478 0.00 0.00 42.35 4.00
5157 5674 5.388475 GCAACGTACTACAAAGATGTGACTG 60.388 44.000 0.00 0.00 40.84 3.51
5158 5675 4.684703 GCAACGTACTACAAAGATGTGACT 59.315 41.667 0.00 0.00 40.84 3.41
5266 5793 1.132500 GTAATCAGGAGGGGAGTGGG 58.868 60.000 0.00 0.00 0.00 4.61
5273 5800 6.006449 CCCAGAATAAATGTAATCAGGAGGG 58.994 44.000 0.00 0.00 0.00 4.30
5276 5803 6.840090 TCCCCAGAATAAATGTAATCAGGA 57.160 37.500 0.00 0.00 0.00 3.86
5290 5817 5.072741 CCGATATCAACATTTCCCCAGAAT 58.927 41.667 3.12 0.00 0.00 2.40
5303 5830 5.041951 TCAACAAACTTGCCGATATCAAC 57.958 39.130 3.12 0.00 0.00 3.18
5305 5832 4.323417 ACTCAACAAACTTGCCGATATCA 58.677 39.130 3.12 0.00 0.00 2.15
5306 5833 4.946784 ACTCAACAAACTTGCCGATATC 57.053 40.909 0.00 0.00 0.00 1.63
5310 5837 2.159310 CCAAACTCAACAAACTTGCCGA 60.159 45.455 0.00 0.00 0.00 5.54
5311 5838 2.192624 CCAAACTCAACAAACTTGCCG 58.807 47.619 0.00 0.00 0.00 5.69
5312 5839 3.186909 GACCAAACTCAACAAACTTGCC 58.813 45.455 0.00 0.00 0.00 4.52
5322 5849 5.883115 TGTACAAATCAGTGACCAAACTCAA 59.117 36.000 0.00 0.00 0.00 3.02
5325 5852 4.578928 GGTGTACAAATCAGTGACCAAACT 59.421 41.667 0.00 0.00 0.00 2.66
5331 5858 4.631813 GGATCAGGTGTACAAATCAGTGAC 59.368 45.833 0.00 0.00 0.00 3.67
5350 5893 1.068434 CCTTCGAGCTCAAGAGGGATC 59.932 57.143 20.66 0.00 35.88 3.36
5357 5900 1.067283 TCTGAAGCCTTCGAGCTCAAG 60.067 52.381 15.40 15.21 44.11 3.02
5371 5914 7.986320 ACTTGAGTTATCTGAATCCATCTGAAG 59.014 37.037 0.00 0.00 39.17 3.02
5372 5915 7.767659 CACTTGAGTTATCTGAATCCATCTGAA 59.232 37.037 0.00 0.00 39.17 3.02
5386 5929 2.349886 CAGGCTTCGCACTTGAGTTATC 59.650 50.000 0.00 0.00 0.00 1.75
5396 5940 2.253452 CTGTTGCAGGCTTCGCAC 59.747 61.111 0.00 0.00 39.59 5.34
5400 5944 1.963338 AGCGACTGTTGCAGGCTTC 60.963 57.895 21.37 0.00 37.36 3.86
5408 5952 1.070309 GTTCAGAAGCAGCGACTGTTG 60.070 52.381 17.15 0.00 33.43 3.33
5418 5962 2.880268 CAGACAATGGTGTTCAGAAGCA 59.120 45.455 0.00 0.00 38.41 3.91
5467 8483 2.311542 TGGGTGGTATGCTTGATCCTTT 59.688 45.455 0.00 0.00 0.00 3.11
5477 8493 1.463674 CTTTGAGGTGGGTGGTATGC 58.536 55.000 0.00 0.00 0.00 3.14
5483 8499 0.184933 TTGGTCCTTTGAGGTGGGTG 59.815 55.000 0.00 0.00 36.53 4.61
5484 8500 0.478507 CTTGGTCCTTTGAGGTGGGT 59.521 55.000 0.00 0.00 36.53 4.51
5485 8501 0.771127 TCTTGGTCCTTTGAGGTGGG 59.229 55.000 0.00 0.00 36.53 4.61
5493 8509 0.106918 TGCGGTGTTCTTGGTCCTTT 60.107 50.000 0.00 0.00 0.00 3.11
5520 8536 4.041567 TGGCACTTTAGAGTCCTTGAATCA 59.958 41.667 0.00 0.00 32.54 2.57
5667 8694 1.227205 GGATGAGCGCACCTCTCTG 60.227 63.158 11.47 0.00 41.35 3.35
5724 8751 1.476085 CAAAACAACTGGGCAGACACA 59.524 47.619 0.00 0.00 0.00 3.72
5790 8821 4.717233 AGATAGATGATAGGCTTCAGCG 57.283 45.455 0.00 0.00 43.26 5.18


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

AutoCloner maintained by Alex Coulton.