Multiple sequence alignment - TraesCS5A01G175100

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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 TraesCS5A01G175100 chr5A 100.000 3792 0 0 1 3792 368134083 368130292 0.000000e+00 7003.0
1 TraesCS5A01G175100 chr5A 86.885 854 96 9 1 840 292145672 292146523 0.000000e+00 942.0
2 TraesCS5A01G175100 chr5A 88.619 782 70 10 1 769 458476329 458477104 0.000000e+00 933.0
3 TraesCS5A01G175100 chr5A 89.417 652 64 3 1 649 703379285 703379934 0.000000e+00 817.0
4 TraesCS5A01G175100 chr5A 87.368 665 78 6 1 663 611121148 611121808 0.000000e+00 758.0
5 TraesCS5A01G175100 chr5A 81.552 786 140 3 1125 1906 448291427 448292211 0.000000e+00 643.0
6 TraesCS5A01G175100 chr5D 97.584 1076 20 5 853 1927 281527174 281526104 0.000000e+00 1838.0
7 TraesCS5A01G175100 chr5D 96.087 869 33 1 1929 2796 281525985 281525117 0.000000e+00 1415.0
8 TraesCS5A01G175100 chr5D 92.596 959 70 1 948 1906 281684418 281683461 0.000000e+00 1376.0
9 TraesCS5A01G175100 chr5D 90.219 869 73 7 1936 2796 281683327 281682463 0.000000e+00 1123.0
10 TraesCS5A01G175100 chr5D 81.748 778 139 1 1132 1906 348161290 348162067 0.000000e+00 647.0
11 TraesCS5A01G175100 chr5D 93.443 183 12 0 2842 3024 281525135 281524953 4.830000e-69 272.0
12 TraesCS5A01G175100 chr5B 92.075 959 75 1 948 1906 319651325 319650368 0.000000e+00 1349.0
13 TraesCS5A01G175100 chr5B 90.080 877 73 8 1928 2796 319650245 319649375 0.000000e+00 1125.0
14 TraesCS5A01G175100 chr5B 81.491 778 141 1 1132 1906 408345055 408345832 1.490000e-178 636.0
15 TraesCS5A01G175100 chr5B 89.617 183 17 1 2842 3024 319649393 319649213 8.190000e-57 231.0
16 TraesCS5A01G175100 chr4D 86.765 816 88 11 1 806 482688457 482689262 0.000000e+00 891.0
17 TraesCS5A01G175100 chr4D 91.217 649 54 1 1 649 334201296 334200651 0.000000e+00 880.0
18 TraesCS5A01G175100 chr2D 91.217 649 46 5 1 649 538755962 538756599 0.000000e+00 872.0
19 TraesCS5A01G175100 chr2D 86.424 523 67 4 3027 3547 131775667 131775147 1.530000e-158 569.0
20 TraesCS5A01G175100 chr3A 84.765 873 98 12 1 838 670928015 670928887 0.000000e+00 843.0
21 TraesCS5A01G175100 chr3A 86.832 524 64 4 3024 3547 711256616 711257134 7.060000e-162 580.0
22 TraesCS5A01G175100 chr2B 84.834 844 110 14 1 838 514777396 514778227 0.000000e+00 833.0
23 TraesCS5A01G175100 chr2B 86.796 515 64 4 3023 3536 478847169 478847680 4.250000e-159 571.0
24 TraesCS5A01G175100 chr2B 86.719 512 65 3 3027 3536 636877577 636878087 1.980000e-157 566.0
25 TraesCS5A01G175100 chr6D 80.879 910 99 46 1 840 120665165 120666069 0.000000e+00 647.0
26 TraesCS5A01G175100 chr6D 81.988 161 25 1 684 840 86614106 86613946 2.380000e-27 134.0
27 TraesCS5A01G175100 chr2A 80.319 879 123 31 1 836 121950063 121949192 1.500000e-173 619.0
28 TraesCS5A01G175100 chr2A 85.932 526 71 3 3023 3547 2741744 2742267 3.310000e-155 558.0
29 TraesCS5A01G175100 chr2A 81.529 157 24 2 684 836 628580942 628581097 1.430000e-24 124.0
30 TraesCS5A01G175100 chr7A 86.948 521 65 3 3027 3545 142950385 142950904 1.960000e-162 582.0
31 TraesCS5A01G175100 chr7A 87.230 509 60 4 3040 3547 719360311 719360815 3.290000e-160 575.0
32 TraesCS5A01G175100 chr7A 94.262 122 5 1 3671 3790 182381014 182380893 6.470000e-43 185.0
33 TraesCS5A01G175100 chr1D 86.476 525 61 10 3026 3547 472292507 472291990 5.500000e-158 568.0
34 TraesCS5A01G175100 chr1D 89.831 59 0 3 2792 2844 483017403 483017461 1.890000e-08 71.3
35 TraesCS5A01G175100 chr6A 86.154 520 71 1 3023 3542 497996295 497996813 9.200000e-156 560.0
36 TraesCS5A01G175100 chr4A 78.959 884 138 30 1 842 16993970 16994847 3.310000e-155 558.0
37 TraesCS5A01G175100 chr4A 88.333 60 6 1 782 840 4775177 4775236 1.890000e-08 71.3
38 TraesCS5A01G175100 chrUn 78.024 901 130 38 1 836 146937127 146936230 4.370000e-139 505.0
39 TraesCS5A01G175100 chr7D 79.310 261 37 9 596 840 599718409 599718150 2.340000e-37 167.0
40 TraesCS5A01G175100 chr3B 92.683 41 1 2 684 722 480427814 480427774 1.470000e-04 58.4


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 TraesCS5A01G175100 chr5A 368130292 368134083 3791 True 7003.000000 7003 100.000000 1 3792 1 chr5A.!!$R1 3791
1 TraesCS5A01G175100 chr5A 292145672 292146523 851 False 942.000000 942 86.885000 1 840 1 chr5A.!!$F1 839
2 TraesCS5A01G175100 chr5A 458476329 458477104 775 False 933.000000 933 88.619000 1 769 1 chr5A.!!$F3 768
3 TraesCS5A01G175100 chr5A 703379285 703379934 649 False 817.000000 817 89.417000 1 649 1 chr5A.!!$F5 648
4 TraesCS5A01G175100 chr5A 611121148 611121808 660 False 758.000000 758 87.368000 1 663 1 chr5A.!!$F4 662
5 TraesCS5A01G175100 chr5A 448291427 448292211 784 False 643.000000 643 81.552000 1125 1906 1 chr5A.!!$F2 781
6 TraesCS5A01G175100 chr5D 281682463 281684418 1955 True 1249.500000 1376 91.407500 948 2796 2 chr5D.!!$R2 1848
7 TraesCS5A01G175100 chr5D 281524953 281527174 2221 True 1175.000000 1838 95.704667 853 3024 3 chr5D.!!$R1 2171
8 TraesCS5A01G175100 chr5D 348161290 348162067 777 False 647.000000 647 81.748000 1132 1906 1 chr5D.!!$F1 774
9 TraesCS5A01G175100 chr5B 319649213 319651325 2112 True 901.666667 1349 90.590667 948 3024 3 chr5B.!!$R1 2076
10 TraesCS5A01G175100 chr5B 408345055 408345832 777 False 636.000000 636 81.491000 1132 1906 1 chr5B.!!$F1 774
11 TraesCS5A01G175100 chr4D 482688457 482689262 805 False 891.000000 891 86.765000 1 806 1 chr4D.!!$F1 805
12 TraesCS5A01G175100 chr4D 334200651 334201296 645 True 880.000000 880 91.217000 1 649 1 chr4D.!!$R1 648
13 TraesCS5A01G175100 chr2D 538755962 538756599 637 False 872.000000 872 91.217000 1 649 1 chr2D.!!$F1 648
14 TraesCS5A01G175100 chr2D 131775147 131775667 520 True 569.000000 569 86.424000 3027 3547 1 chr2D.!!$R1 520
15 TraesCS5A01G175100 chr3A 670928015 670928887 872 False 843.000000 843 84.765000 1 838 1 chr3A.!!$F1 837
16 TraesCS5A01G175100 chr3A 711256616 711257134 518 False 580.000000 580 86.832000 3024 3547 1 chr3A.!!$F2 523
17 TraesCS5A01G175100 chr2B 514777396 514778227 831 False 833.000000 833 84.834000 1 838 1 chr2B.!!$F2 837
18 TraesCS5A01G175100 chr2B 478847169 478847680 511 False 571.000000 571 86.796000 3023 3536 1 chr2B.!!$F1 513
19 TraesCS5A01G175100 chr2B 636877577 636878087 510 False 566.000000 566 86.719000 3027 3536 1 chr2B.!!$F3 509
20 TraesCS5A01G175100 chr6D 120665165 120666069 904 False 647.000000 647 80.879000 1 840 1 chr6D.!!$F1 839
21 TraesCS5A01G175100 chr2A 121949192 121950063 871 True 619.000000 619 80.319000 1 836 1 chr2A.!!$R1 835
22 TraesCS5A01G175100 chr2A 2741744 2742267 523 False 558.000000 558 85.932000 3023 3547 1 chr2A.!!$F1 524
23 TraesCS5A01G175100 chr7A 142950385 142950904 519 False 582.000000 582 86.948000 3027 3545 1 chr7A.!!$F1 518
24 TraesCS5A01G175100 chr7A 719360311 719360815 504 False 575.000000 575 87.230000 3040 3547 1 chr7A.!!$F2 507
25 TraesCS5A01G175100 chr1D 472291990 472292507 517 True 568.000000 568 86.476000 3026 3547 1 chr1D.!!$R1 521
26 TraesCS5A01G175100 chr6A 497996295 497996813 518 False 560.000000 560 86.154000 3023 3542 1 chr6A.!!$F1 519
27 TraesCS5A01G175100 chr4A 16993970 16994847 877 False 558.000000 558 78.959000 1 842 1 chr4A.!!$F2 841
28 TraesCS5A01G175100 chrUn 146936230 146937127 897 True 505.000000 505 78.024000 1 836 1 chrUn.!!$R1 835

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
96 103 0.249447 CACCTTCGAGACTGTGCACA 60.249 55.000 20.37 20.37 0.00 4.57 F
498 529 0.249911 GGACATGTGGCTCGATACCC 60.250 60.000 1.15 0.00 0.00 3.69 F
792 942 0.806868 ATGATGGACGTGCTGCAAAG 59.193 50.000 8.99 4.18 0.00 2.77 F
1020 1170 1.815421 AGCCCATCGCATCGTGAAC 60.815 57.895 0.00 0.00 41.38 3.18 F
2525 2800 1.228245 GTTTGAGTGGAGGCTGCCA 60.228 57.895 22.65 2.36 35.02 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1741 1895 1.018148 CTCAGATGCTCGACGGTACT 58.982 55.0 0.00 0.0 0.00 2.73 R
2119 2394 0.031178 CTGCTTTGCACCAACCACTC 59.969 55.0 0.00 0.0 33.79 3.51 R
2402 2677 0.389948 GCATGAACTCGAACCGGTCT 60.390 55.0 8.04 0.0 0.00 3.85 R
2637 2912 0.782384 CTACGCAGACAACCAACGAC 59.218 55.0 0.00 0.0 0.00 4.34 R
3752 4034 0.108585 AGAACGCAAAGCCCAGAGAA 59.891 50.0 0.00 0.0 0.00 2.87 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
96 103 0.249447 CACCTTCGAGACTGTGCACA 60.249 55.000 20.37 20.37 0.00 4.57
101 108 1.301244 CGAGACTGTGCACAAGGCT 60.301 57.895 21.98 21.02 45.15 4.58
105 112 2.596631 CTGTGCACAAGGCTGCCT 60.597 61.111 21.98 17.22 45.15 4.75
108 115 4.898765 TGCACAAGGCTGCCTGCA 62.899 61.111 24.84 24.84 45.15 4.41
301 308 4.221422 GCGAGGCATGGCGGAGTA 62.221 66.667 14.30 0.00 0.00 2.59
333 340 1.300620 CTGAAGGACGTCGCCAACA 60.301 57.895 9.92 4.64 0.00 3.33
345 352 1.586541 GCCAACAAGCAAGCCTACC 59.413 57.895 0.00 0.00 0.00 3.18
438 469 2.348362 CAGTGCGATATCGTTGAAGCAA 59.652 45.455 24.99 0.36 42.22 3.91
459 490 1.135199 GTGGGCAGTCGATCTTTACGA 60.135 52.381 0.00 0.00 37.43 3.43
471 502 9.698309 AGTCGATCTTTACGAATAATGATCATT 57.302 29.630 23.75 23.75 44.60 2.57
498 529 0.249911 GGACATGTGGCTCGATACCC 60.250 60.000 1.15 0.00 0.00 3.69
503 534 2.042741 TGGCTCGATACCCCGGAA 60.043 61.111 0.73 0.00 0.00 4.30
522 553 2.073252 ACAGACCAGCGAGGATGATA 57.927 50.000 5.19 0.00 41.22 2.15
534 565 6.539103 CAGCGAGGATGATAATGATGATGATT 59.461 38.462 0.00 0.00 0.00 2.57
675 821 7.561021 TTAAATATGTATGCAATGTCCGTGT 57.439 32.000 0.00 0.00 0.00 4.49
682 828 1.338579 TGCAATGTCCGTGTGATAGCA 60.339 47.619 0.00 0.00 0.00 3.49
731 881 2.542595 AGCTACGCGCGCTAAATTTTAT 59.457 40.909 32.58 8.80 45.59 1.40
773 923 2.584970 CCGCCGCGCTAAATCAGA 60.585 61.111 7.42 0.00 0.00 3.27
792 942 0.806868 ATGATGGACGTGCTGCAAAG 59.193 50.000 8.99 4.18 0.00 2.77
806 956 4.097135 TGCTGCAAAGTACTTTTTAGCACA 59.903 37.500 32.28 25.34 40.69 4.57
842 992 4.708177 GGCTGTTGGAGATGCTCTTATAA 58.292 43.478 0.00 0.00 0.00 0.98
843 993 4.513318 GGCTGTTGGAGATGCTCTTATAAC 59.487 45.833 0.00 0.00 0.00 1.89
844 994 5.363939 GCTGTTGGAGATGCTCTTATAACT 58.636 41.667 0.00 0.00 0.00 2.24
845 995 6.463049 GGCTGTTGGAGATGCTCTTATAACTA 60.463 42.308 0.00 0.00 0.00 2.24
846 996 6.644592 GCTGTTGGAGATGCTCTTATAACTAG 59.355 42.308 0.00 0.00 0.00 2.57
847 997 6.516718 TGTTGGAGATGCTCTTATAACTAGC 58.483 40.000 7.75 7.75 36.77 3.42
863 1013 5.508280 AACTAGCAAGGTGGGTAATTACA 57.492 39.130 17.16 0.00 0.00 2.41
872 1022 7.201705 GCAAGGTGGGTAATTACAATCTACTTC 60.202 40.741 17.16 0.00 0.00 3.01
874 1024 7.565680 AGGTGGGTAATTACAATCTACTTCTG 58.434 38.462 17.16 0.00 0.00 3.02
994 1144 4.081761 GTCGTACTGCGTTCAATCAATTG 58.918 43.478 0.00 0.00 42.13 2.32
1015 1165 2.711311 CAACAGCCCATCGCATCG 59.289 61.111 0.00 0.00 41.38 3.84
1020 1170 1.815421 AGCCCATCGCATCGTGAAC 60.815 57.895 0.00 0.00 41.38 3.18
1021 1171 1.815421 GCCCATCGCATCGTGAACT 60.815 57.895 0.00 0.00 37.47 3.01
1098 1249 2.288825 CGCCTCTTGTGTCCTCTACAAA 60.289 50.000 0.00 0.00 40.63 2.83
1099 1250 3.067833 GCCTCTTGTGTCCTCTACAAAC 58.932 50.000 0.00 0.00 40.63 2.93
1116 1267 3.136626 ACAAACTCTTCCTTGTAGGCAGT 59.863 43.478 0.00 0.00 34.04 4.40
1908 2062 5.705609 TCAAGTCCTTTCTTTTGGTATGC 57.294 39.130 0.00 0.00 0.00 3.14
1915 2069 5.833131 TCCTTTCTTTTGGTATGCTTGACTT 59.167 36.000 0.00 0.00 0.00 3.01
1926 2196 5.121454 GGTATGCTTGACTTCTGAACTGAAG 59.879 44.000 16.04 16.04 46.33 3.02
1958 2232 4.193826 TCTTTGAAGATCCGAGGAAGTG 57.806 45.455 0.00 0.00 0.00 3.16
2126 2401 2.753029 GAGCTGCAGGGAGTGGTT 59.247 61.111 17.12 0.00 0.00 3.67
2402 2677 1.304052 CATGGACTTCCGGGGCAAA 60.304 57.895 0.00 0.00 39.43 3.68
2525 2800 1.228245 GTTTGAGTGGAGGCTGCCA 60.228 57.895 22.65 2.36 35.02 4.92
2582 2857 4.742012 ACCGGTATAGGATGTCTCTCAAT 58.258 43.478 4.49 0.00 34.73 2.57
2618 2893 2.749839 GCCGTGCCACTGCCATTA 60.750 61.111 0.00 0.00 36.33 1.90
2637 2912 6.432936 CCATTATTCTCGTGATGGATTGTTG 58.567 40.000 0.00 0.00 41.20 3.33
2640 2915 2.606108 TCTCGTGATGGATTGTTGTCG 58.394 47.619 0.00 0.00 0.00 4.35
2663 2938 2.823747 TGGTTGTCTGCGTAGATGTAGT 59.176 45.455 6.47 0.00 34.94 2.73
2678 2953 0.706729 GTAGTACGCGTGCACTGTTC 59.293 55.000 28.70 10.97 0.00 3.18
2712 2987 2.351738 GGTATCAGCAGTTTGTGTTGGC 60.352 50.000 0.00 0.00 37.93 4.52
2827 3107 9.693739 TGAAATAACCACATGTATTCCATTAGT 57.306 29.630 0.00 0.00 0.00 2.24
2831 3111 9.998106 ATAACCACATGTATTCCATTAGTAGAC 57.002 33.333 0.00 0.00 0.00 2.59
2832 3112 7.432148 ACCACATGTATTCCATTAGTAGACA 57.568 36.000 0.00 0.00 0.00 3.41
2833 3113 7.857456 ACCACATGTATTCCATTAGTAGACAA 58.143 34.615 0.00 0.00 0.00 3.18
2834 3114 8.325787 ACCACATGTATTCCATTAGTAGACAAA 58.674 33.333 0.00 0.00 0.00 2.83
2835 3115 8.612619 CCACATGTATTCCATTAGTAGACAAAC 58.387 37.037 0.00 0.00 0.00 2.93
2836 3116 9.383519 CACATGTATTCCATTAGTAGACAAACT 57.616 33.333 0.00 0.00 0.00 2.66
2837 3117 9.959721 ACATGTATTCCATTAGTAGACAAACTT 57.040 29.630 0.00 0.00 0.00 2.66
2916 3196 1.068748 GTGGTGTCGTCGCTCTAAAGA 60.069 52.381 0.00 0.00 0.00 2.52
2969 3249 4.112634 AGAACAATTGTGGGCTTTCCTA 57.887 40.909 12.82 0.00 36.20 2.94
2996 3276 2.128535 TGGAAGTTGAAGGTGGTACCA 58.871 47.619 11.60 11.60 41.95 3.25
3019 3299 1.003223 GGTACGCTTGTTGTGTTGGAC 60.003 52.381 0.00 0.00 40.30 4.02
3024 3304 1.135228 GCTTGTTGTGTTGGACGGTTT 60.135 47.619 0.00 0.00 0.00 3.27
3025 3305 2.525055 CTTGTTGTGTTGGACGGTTTG 58.475 47.619 0.00 0.00 0.00 2.93
3202 3482 1.079127 CATCGGAGCCGGACAAACT 60.079 57.895 5.05 0.00 40.25 2.66
3264 3544 0.981183 ATAGGACCAACGCACCAGAA 59.019 50.000 0.00 0.00 0.00 3.02
3322 3602 5.765182 CAGAAGGATCAAACCTGTAAACACT 59.235 40.000 0.00 0.00 40.49 3.55
3334 3614 6.343703 ACCTGTAAACACTTAAACGAAGACT 58.656 36.000 0.00 0.00 38.65 3.24
3379 3659 0.179161 CACCGAAGACTAGCACCGAG 60.179 60.000 0.00 0.00 0.00 4.63
3412 3692 2.900546 AGATCCGACAGAGACAAACCTT 59.099 45.455 0.00 0.00 0.00 3.50
3427 3707 1.002134 CCTTCACACGCCCTCCAAT 60.002 57.895 0.00 0.00 0.00 3.16
3428 3708 0.251916 CCTTCACACGCCCTCCAATA 59.748 55.000 0.00 0.00 0.00 1.90
3450 3730 0.753262 GCTAGACACACCATCGGGAT 59.247 55.000 0.00 0.00 38.05 3.85
3478 3758 6.239829 GGATAGAATGTGGGAGACATCATTCT 60.240 42.308 18.54 18.54 45.12 2.40
3499 3779 1.557099 ACTAAGAGACATCACCGCCA 58.443 50.000 0.00 0.00 0.00 5.69
3532 3812 2.989840 CAACCAAGACGCTGACTCTAAG 59.010 50.000 0.00 0.00 0.00 2.18
3538 3820 5.223382 CAAGACGCTGACTCTAAGAAGAAA 58.777 41.667 0.00 0.00 0.00 2.52
3547 3829 4.811908 ACTCTAAGAAGAAAGAGAACGGC 58.188 43.478 6.36 0.00 41.51 5.68
3548 3830 4.281182 ACTCTAAGAAGAAAGAGAACGGCA 59.719 41.667 6.36 0.00 41.51 5.69
3549 3831 4.810790 TCTAAGAAGAAAGAGAACGGCAG 58.189 43.478 0.00 0.00 0.00 4.85
3550 3832 3.477210 AAGAAGAAAGAGAACGGCAGT 57.523 42.857 0.00 0.00 0.00 4.40
3551 3833 2.760374 AGAAGAAAGAGAACGGCAGTG 58.240 47.619 0.00 0.00 0.00 3.66
3552 3834 1.801178 GAAGAAAGAGAACGGCAGTGG 59.199 52.381 0.00 0.00 0.00 4.00
3553 3835 0.603975 AGAAAGAGAACGGCAGTGGC 60.604 55.000 6.62 6.62 40.13 5.01
3603 3885 4.848685 CCCCCTAATGGTCGAACG 57.151 61.111 0.00 0.00 0.00 3.95
3604 3886 2.204748 CCCCCTAATGGTCGAACGA 58.795 57.895 0.00 0.00 0.00 3.85
3605 3887 0.756903 CCCCCTAATGGTCGAACGAT 59.243 55.000 0.00 0.00 0.00 3.73
3606 3888 1.965643 CCCCCTAATGGTCGAACGATA 59.034 52.381 0.00 0.00 0.00 2.92
3607 3889 2.288640 CCCCCTAATGGTCGAACGATAC 60.289 54.545 0.00 0.00 0.00 2.24
3608 3890 2.626743 CCCCTAATGGTCGAACGATACT 59.373 50.000 0.00 0.00 0.00 2.12
3609 3891 3.822735 CCCCTAATGGTCGAACGATACTA 59.177 47.826 0.00 0.00 0.00 1.82
3610 3892 4.461781 CCCCTAATGGTCGAACGATACTAT 59.538 45.833 0.00 0.00 0.00 2.12
3611 3893 5.399858 CCCTAATGGTCGAACGATACTATG 58.600 45.833 0.00 0.00 0.00 2.23
3612 3894 5.048224 CCCTAATGGTCGAACGATACTATGT 60.048 44.000 0.00 0.00 0.00 2.29
3613 3895 6.149973 CCCTAATGGTCGAACGATACTATGTA 59.850 42.308 0.00 0.00 0.00 2.29
3614 3896 7.308770 CCCTAATGGTCGAACGATACTATGTAA 60.309 40.741 0.00 0.00 0.00 2.41
3615 3897 8.242053 CCTAATGGTCGAACGATACTATGTAAT 58.758 37.037 0.00 0.00 0.00 1.89
3616 3898 9.622004 CTAATGGTCGAACGATACTATGTAATT 57.378 33.333 0.00 0.00 0.00 1.40
3618 3900 9.622004 AATGGTCGAACGATACTATGTAATTAG 57.378 33.333 0.00 0.00 0.00 1.73
3619 3901 7.080099 TGGTCGAACGATACTATGTAATTAGC 58.920 38.462 0.00 0.00 0.00 3.09
3620 3902 6.248001 GGTCGAACGATACTATGTAATTAGCG 59.752 42.308 0.00 0.00 0.00 4.26
3621 3903 7.011773 GTCGAACGATACTATGTAATTAGCGA 58.988 38.462 0.00 0.00 0.00 4.93
3622 3904 7.691463 GTCGAACGATACTATGTAATTAGCGAT 59.309 37.037 0.00 0.00 0.00 4.58
3623 3905 8.872845 TCGAACGATACTATGTAATTAGCGATA 58.127 33.333 0.00 0.00 0.00 2.92
3624 3906 8.931972 CGAACGATACTATGTAATTAGCGATAC 58.068 37.037 0.00 0.00 0.00 2.24
3625 3907 8.817677 AACGATACTATGTAATTAGCGATACG 57.182 34.615 0.00 0.00 0.00 3.06
3626 3908 8.189709 ACGATACTATGTAATTAGCGATACGA 57.810 34.615 0.00 0.00 0.00 3.43
3627 3909 8.659491 ACGATACTATGTAATTAGCGATACGAA 58.341 33.333 0.00 0.00 0.00 3.85
3628 3910 8.931972 CGATACTATGTAATTAGCGATACGAAC 58.068 37.037 0.00 0.00 0.00 3.95
3629 3911 8.817677 ATACTATGTAATTAGCGATACGAACG 57.182 34.615 0.00 0.00 0.00 3.95
3644 3926 3.329743 CGAACGCTCGTATTCCTTAGA 57.670 47.619 0.00 0.00 40.33 2.10
3645 3927 3.034562 CGAACGCTCGTATTCCTTAGAC 58.965 50.000 0.00 0.00 40.33 2.59
3646 3928 3.242673 CGAACGCTCGTATTCCTTAGACT 60.243 47.826 0.00 0.00 40.33 3.24
3647 3929 4.670347 GAACGCTCGTATTCCTTAGACTT 58.330 43.478 0.00 0.00 0.00 3.01
3648 3930 5.503031 CGAACGCTCGTATTCCTTAGACTTA 60.503 44.000 0.00 0.00 40.33 2.24
3649 3931 6.388435 AACGCTCGTATTCCTTAGACTTAT 57.612 37.500 0.00 0.00 0.00 1.73
3650 3932 7.502120 AACGCTCGTATTCCTTAGACTTATA 57.498 36.000 0.00 0.00 0.00 0.98
3651 3933 6.896969 ACGCTCGTATTCCTTAGACTTATAC 58.103 40.000 0.00 0.00 0.00 1.47
3652 3934 6.014293 CGCTCGTATTCCTTAGACTTATACG 58.986 44.000 0.00 0.00 43.08 3.06
3653 3935 6.347240 CGCTCGTATTCCTTAGACTTATACGT 60.347 42.308 0.00 0.00 42.60 3.57
3654 3936 7.358830 GCTCGTATTCCTTAGACTTATACGTT 58.641 38.462 0.00 0.00 42.60 3.99
3655 3937 7.859875 GCTCGTATTCCTTAGACTTATACGTTT 59.140 37.037 0.00 0.00 42.60 3.60
3656 3938 9.379811 CTCGTATTCCTTAGACTTATACGTTTC 57.620 37.037 0.00 0.00 42.60 2.78
3657 3939 9.113838 TCGTATTCCTTAGACTTATACGTTTCT 57.886 33.333 0.00 0.00 42.60 2.52
3658 3940 9.167239 CGTATTCCTTAGACTTATACGTTTCTG 57.833 37.037 0.00 0.00 39.22 3.02
3659 3941 9.460906 GTATTCCTTAGACTTATACGTTTCTGG 57.539 37.037 0.00 0.00 0.00 3.86
3660 3942 5.899299 TCCTTAGACTTATACGTTTCTGGC 58.101 41.667 0.00 0.00 0.00 4.85
3661 3943 5.048507 CCTTAGACTTATACGTTTCTGGCC 58.951 45.833 0.00 0.00 0.00 5.36
3662 3944 3.538634 AGACTTATACGTTTCTGGCCC 57.461 47.619 0.00 0.00 0.00 5.80
3663 3945 2.169978 AGACTTATACGTTTCTGGCCCC 59.830 50.000 0.00 0.00 0.00 5.80
3664 3946 1.211212 ACTTATACGTTTCTGGCCCCC 59.789 52.381 0.00 0.00 0.00 5.40
3679 3961 3.309582 CCCCCTATGTCACAGCGT 58.690 61.111 0.00 0.00 0.00 5.07
3680 3962 1.153369 CCCCCTATGTCACAGCGTG 60.153 63.158 2.79 2.79 34.45 5.34
3681 3963 1.613317 CCCCCTATGTCACAGCGTGA 61.613 60.000 7.20 7.20 40.50 4.35
3682 3964 0.249120 CCCCTATGTCACAGCGTGAA 59.751 55.000 11.92 5.05 44.49 3.18
3683 3965 1.134401 CCCCTATGTCACAGCGTGAAT 60.134 52.381 11.92 10.38 44.49 2.57
3684 3966 2.632377 CCCTATGTCACAGCGTGAATT 58.368 47.619 11.92 6.46 44.49 2.17
3685 3967 3.009723 CCCTATGTCACAGCGTGAATTT 58.990 45.455 11.92 4.51 44.49 1.82
3686 3968 3.181507 CCCTATGTCACAGCGTGAATTTG 60.182 47.826 11.92 5.33 44.49 2.32
3687 3969 3.436704 CCTATGTCACAGCGTGAATTTGT 59.563 43.478 11.92 0.00 44.49 2.83
3688 3970 4.629634 CCTATGTCACAGCGTGAATTTGTA 59.370 41.667 11.92 2.96 44.49 2.41
3689 3971 5.121611 CCTATGTCACAGCGTGAATTTGTAA 59.878 40.000 11.92 0.00 44.49 2.41
3690 3972 4.884458 TGTCACAGCGTGAATTTGTAAA 57.116 36.364 11.92 0.00 44.49 2.01
3691 3973 5.236655 TGTCACAGCGTGAATTTGTAAAA 57.763 34.783 11.92 0.00 44.49 1.52
3692 3974 5.641709 TGTCACAGCGTGAATTTGTAAAAA 58.358 33.333 11.92 0.00 44.49 1.94
3710 3992 4.341366 AAAAAGAGAAAAGGCCCATGTG 57.659 40.909 0.00 0.00 0.00 3.21
3711 3993 2.978156 AAGAGAAAAGGCCCATGTGA 57.022 45.000 0.00 0.00 0.00 3.58
3712 3994 2.978156 AGAGAAAAGGCCCATGTGAA 57.022 45.000 0.00 0.00 0.00 3.18
3713 3995 2.800250 AGAGAAAAGGCCCATGTGAAG 58.200 47.619 0.00 0.00 0.00 3.02
3714 3996 1.203287 GAGAAAAGGCCCATGTGAAGC 59.797 52.381 0.00 0.00 0.00 3.86
3718 4000 3.070576 GGCCCATGTGAAGCCCAC 61.071 66.667 0.00 0.29 45.88 4.61
3725 4007 3.876300 GTGAAGCCCACACTAGCG 58.124 61.111 2.33 0.00 45.03 4.26
3726 4008 1.741770 GTGAAGCCCACACTAGCGG 60.742 63.158 2.33 0.00 45.03 5.52
3727 4009 2.820037 GAAGCCCACACTAGCGGC 60.820 66.667 0.00 0.00 43.35 6.53
3728 4010 4.410400 AAGCCCACACTAGCGGCC 62.410 66.667 0.00 0.00 44.13 6.13
3731 4013 4.473520 CCCACACTAGCGGCCAGG 62.474 72.222 2.24 0.00 0.00 4.45
3732 4014 3.706373 CCACACTAGCGGCCAGGT 61.706 66.667 2.24 3.81 0.00 4.00
3733 4015 2.347490 CACACTAGCGGCCAGGTT 59.653 61.111 2.24 0.00 0.00 3.50
3734 4016 1.302511 CACACTAGCGGCCAGGTTT 60.303 57.895 2.24 0.00 0.00 3.27
3735 4017 1.003718 ACACTAGCGGCCAGGTTTC 60.004 57.895 2.24 0.00 0.00 2.78
3736 4018 2.100631 CACTAGCGGCCAGGTTTCG 61.101 63.158 2.24 0.00 0.00 3.46
3741 4023 2.577059 CGGCCAGGTTTCGCTCTA 59.423 61.111 2.24 0.00 0.00 2.43
3742 4024 1.519455 CGGCCAGGTTTCGCTCTAG 60.519 63.158 2.24 0.00 0.00 2.43
3743 4025 1.597461 GGCCAGGTTTCGCTCTAGT 59.403 57.895 0.00 0.00 0.00 2.57
3744 4026 0.460459 GGCCAGGTTTCGCTCTAGTC 60.460 60.000 0.00 0.00 0.00 2.59
3745 4027 0.460459 GCCAGGTTTCGCTCTAGTCC 60.460 60.000 0.00 0.00 0.00 3.85
3746 4028 0.175989 CCAGGTTTCGCTCTAGTCCC 59.824 60.000 0.00 0.00 0.00 4.46
3747 4029 0.895530 CAGGTTTCGCTCTAGTCCCA 59.104 55.000 0.00 0.00 0.00 4.37
3748 4030 1.482593 CAGGTTTCGCTCTAGTCCCAT 59.517 52.381 0.00 0.00 0.00 4.00
3749 4031 2.693591 CAGGTTTCGCTCTAGTCCCATA 59.306 50.000 0.00 0.00 0.00 2.74
3750 4032 2.959707 AGGTTTCGCTCTAGTCCCATAG 59.040 50.000 0.00 0.00 0.00 2.23
3751 4033 2.694109 GGTTTCGCTCTAGTCCCATAGT 59.306 50.000 0.00 0.00 0.00 2.12
3752 4034 3.132467 GGTTTCGCTCTAGTCCCATAGTT 59.868 47.826 0.00 0.00 0.00 2.24
3753 4035 4.382793 GGTTTCGCTCTAGTCCCATAGTTT 60.383 45.833 0.00 0.00 0.00 2.66
3754 4036 4.650754 TTCGCTCTAGTCCCATAGTTTC 57.349 45.455 0.00 0.00 0.00 2.78
3755 4037 3.899726 TCGCTCTAGTCCCATAGTTTCT 58.100 45.455 0.00 0.00 0.00 2.52
3756 4038 3.884091 TCGCTCTAGTCCCATAGTTTCTC 59.116 47.826 0.00 0.00 0.00 2.87
3757 4039 3.886505 CGCTCTAGTCCCATAGTTTCTCT 59.113 47.826 0.00 0.00 0.00 3.10
3758 4040 4.261405 CGCTCTAGTCCCATAGTTTCTCTG 60.261 50.000 0.00 0.00 0.00 3.35
3759 4041 4.038642 GCTCTAGTCCCATAGTTTCTCTGG 59.961 50.000 0.00 0.00 0.00 3.86
3760 4042 4.547671 TCTAGTCCCATAGTTTCTCTGGG 58.452 47.826 12.22 12.22 45.71 4.45
3761 4043 1.840635 AGTCCCATAGTTTCTCTGGGC 59.159 52.381 13.24 9.57 44.50 5.36
3762 4044 1.840635 GTCCCATAGTTTCTCTGGGCT 59.159 52.381 13.24 0.00 44.50 5.19
3763 4045 2.239907 GTCCCATAGTTTCTCTGGGCTT 59.760 50.000 13.24 0.00 44.50 4.35
3764 4046 2.919602 TCCCATAGTTTCTCTGGGCTTT 59.080 45.455 13.24 0.00 44.50 3.51
3765 4047 3.019564 CCCATAGTTTCTCTGGGCTTTG 58.980 50.000 7.17 0.00 40.23 2.77
3766 4048 2.424956 CCATAGTTTCTCTGGGCTTTGC 59.575 50.000 0.00 0.00 0.00 3.68
3767 4049 1.808411 TAGTTTCTCTGGGCTTTGCG 58.192 50.000 0.00 0.00 0.00 4.85
3768 4050 0.179018 AGTTTCTCTGGGCTTTGCGT 60.179 50.000 0.00 0.00 0.00 5.24
3769 4051 0.668535 GTTTCTCTGGGCTTTGCGTT 59.331 50.000 0.00 0.00 0.00 4.84
3770 4052 0.951558 TTTCTCTGGGCTTTGCGTTC 59.048 50.000 0.00 0.00 0.00 3.95
3771 4053 0.108585 TTCTCTGGGCTTTGCGTTCT 59.891 50.000 0.00 0.00 0.00 3.01
3772 4054 0.320771 TCTCTGGGCTTTGCGTTCTC 60.321 55.000 0.00 0.00 0.00 2.87
3773 4055 1.630244 CTCTGGGCTTTGCGTTCTCG 61.630 60.000 0.00 0.00 40.37 4.04
3785 4067 1.858091 CGTTCTCGCATGATTAGCCT 58.142 50.000 0.00 0.00 0.00 4.58
3786 4068 1.524355 CGTTCTCGCATGATTAGCCTG 59.476 52.381 0.00 0.00 0.00 4.85
3787 4069 2.555199 GTTCTCGCATGATTAGCCTGT 58.445 47.619 0.00 0.00 0.00 4.00
3788 4070 3.717707 GTTCTCGCATGATTAGCCTGTA 58.282 45.455 0.00 0.00 0.00 2.74
3789 4071 3.371102 TCTCGCATGATTAGCCTGTAC 57.629 47.619 0.00 0.00 0.00 2.90
3790 4072 2.054363 CTCGCATGATTAGCCTGTACG 58.946 52.381 0.00 0.00 0.00 3.67
3791 4073 1.407618 TCGCATGATTAGCCTGTACGT 59.592 47.619 0.00 0.00 0.00 3.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
96 103 2.358737 GTACGTGCAGGCAGCCTT 60.359 61.111 12.86 0.00 44.83 4.35
204 211 0.745486 TCCGTGATAAGACGAGGCGA 60.745 55.000 0.00 0.00 42.10 5.54
316 323 0.878523 CTTGTTGGCGACGTCCTTCA 60.879 55.000 10.58 2.96 0.00 3.02
318 325 2.251642 GCTTGTTGGCGACGTCCTT 61.252 57.895 10.58 0.00 0.00 3.36
438 469 1.135083 CGTAAAGATCGACTGCCCACT 60.135 52.381 0.00 0.00 0.00 4.00
459 490 6.434302 TGTCCTCCCAACAATGATCATTATT 58.566 36.000 20.32 13.37 0.00 1.40
471 502 1.074775 GCCACATGTCCTCCCAACA 59.925 57.895 0.00 0.00 0.00 3.33
498 529 2.125912 CTCGCTGGTCTGTTCCGG 60.126 66.667 0.00 0.00 36.96 5.14
503 534 2.073252 TATCATCCTCGCTGGTCTGT 57.927 50.000 0.00 0.00 37.07 3.41
522 553 5.512060 CCCAGTCGTCCTAATCATCATCATT 60.512 44.000 0.00 0.00 0.00 2.57
534 565 0.917533 AGCTACTCCCAGTCGTCCTA 59.082 55.000 0.00 0.00 0.00 2.94
682 828 1.154225 GTGCTAAAATGCAGCGCGT 60.154 52.632 8.43 0.00 44.20 6.01
731 881 3.921767 CTGGCTTCAGCAGACGCGA 62.922 63.158 15.93 0.00 45.49 5.87
773 923 0.806868 CTTTGCAGCACGTCCATCAT 59.193 50.000 0.00 0.00 0.00 2.45
792 942 1.528161 ACGCGGTGTGCTAAAAAGTAC 59.472 47.619 12.47 0.00 43.27 2.73
812 962 2.124529 TCCAACAGCCGTGCAACA 60.125 55.556 0.00 0.00 35.74 3.33
842 992 5.508280 TTGTAATTACCCACCTTGCTAGT 57.492 39.130 13.01 0.00 0.00 2.57
843 993 6.357367 AGATTGTAATTACCCACCTTGCTAG 58.643 40.000 13.01 0.00 0.00 3.42
844 994 6.321821 AGATTGTAATTACCCACCTTGCTA 57.678 37.500 13.01 0.00 0.00 3.49
845 995 5.193099 AGATTGTAATTACCCACCTTGCT 57.807 39.130 13.01 0.00 0.00 3.91
846 996 6.120220 AGTAGATTGTAATTACCCACCTTGC 58.880 40.000 13.01 0.00 0.00 4.01
847 997 8.047310 AGAAGTAGATTGTAATTACCCACCTTG 58.953 37.037 13.01 0.00 0.00 3.61
848 998 8.047310 CAGAAGTAGATTGTAATTACCCACCTT 58.953 37.037 13.01 7.41 0.00 3.50
849 999 7.182206 ACAGAAGTAGATTGTAATTACCCACCT 59.818 37.037 13.01 7.44 0.00 4.00
850 1000 7.336396 ACAGAAGTAGATTGTAATTACCCACC 58.664 38.462 13.01 0.54 0.00 4.61
851 1001 8.788325 AACAGAAGTAGATTGTAATTACCCAC 57.212 34.615 13.01 4.40 0.00 4.61
881 1031 9.656323 ATCCAGAAGTAGATAGTAAACCATGTA 57.344 33.333 0.00 0.00 0.00 2.29
882 1032 7.973048 TCCAGAAGTAGATAGTAAACCATGT 57.027 36.000 0.00 0.00 0.00 3.21
883 1033 7.875041 CCATCCAGAAGTAGATAGTAAACCATG 59.125 40.741 0.00 0.00 0.00 3.66
884 1034 7.789831 TCCATCCAGAAGTAGATAGTAAACCAT 59.210 37.037 0.00 0.00 0.00 3.55
931 1081 9.424319 CAACTGCGATAGTAAAATCTATATGGT 57.576 33.333 0.00 0.00 39.18 3.55
1015 1165 3.602390 TTTCGCTTGCTACAAGTTCAC 57.398 42.857 8.95 0.00 0.00 3.18
1020 1170 3.829886 TCCATTTTCGCTTGCTACAAG 57.170 42.857 2.95 2.95 0.00 3.16
1021 1171 3.611530 GCTTCCATTTTCGCTTGCTACAA 60.612 43.478 0.00 0.00 0.00 2.41
1098 1249 4.417437 TCTTACTGCCTACAAGGAAGAGT 58.583 43.478 8.00 3.49 44.42 3.24
1099 1250 4.464597 ACTCTTACTGCCTACAAGGAAGAG 59.535 45.833 19.31 19.31 44.42 2.85
1116 1267 2.125673 GGCAGCCGCGAACTCTTA 60.126 61.111 8.23 0.00 39.92 2.10
1741 1895 1.018148 CTCAGATGCTCGACGGTACT 58.982 55.000 0.00 0.00 0.00 2.73
1908 2062 9.050601 AGTTTATTCTTCAGTTCAGAAGTCAAG 57.949 33.333 0.00 0.00 44.18 3.02
1915 2069 9.784531 AAAGATCAGTTTATTCTTCAGTTCAGA 57.215 29.630 0.00 0.00 0.00 3.27
1958 2232 3.181506 GCTCGGATTTCTCATTTGTGTCC 60.182 47.826 0.00 0.00 0.00 4.02
2119 2394 0.031178 CTGCTTTGCACCAACCACTC 59.969 55.000 0.00 0.00 33.79 3.51
2126 2401 0.676466 CGGGATACTGCTTTGCACCA 60.676 55.000 0.00 0.00 33.79 4.17
2344 2619 2.268920 GCATGAACTCCTCGGGCA 59.731 61.111 0.00 0.00 0.00 5.36
2402 2677 0.389948 GCATGAACTCGAACCGGTCT 60.390 55.000 8.04 0.00 0.00 3.85
2525 2800 3.790437 CACGGCTGCATCCCCTCT 61.790 66.667 0.00 0.00 0.00 3.69
2618 2893 3.618594 CGACAACAATCCATCACGAGAAT 59.381 43.478 0.00 0.00 0.00 2.40
2637 2912 0.782384 CTACGCAGACAACCAACGAC 59.218 55.000 0.00 0.00 0.00 4.34
2640 2915 2.413837 ACATCTACGCAGACAACCAAC 58.586 47.619 0.00 0.00 32.25 3.77
2663 2938 1.146957 AAACGAACAGTGCACGCGTA 61.147 50.000 22.90 0.00 34.46 4.42
2712 2987 2.766313 TGAACGTCTCCCTTGTTCATG 58.234 47.619 3.12 0.00 44.97 3.07
2801 3081 9.693739 ACTAATGGAATACATGTGGTTATTTCA 57.306 29.630 9.11 5.55 40.44 2.69
2805 3085 9.998106 GTCTACTAATGGAATACATGTGGTTAT 57.002 33.333 9.11 0.00 40.44 1.89
2806 3086 8.983789 TGTCTACTAATGGAATACATGTGGTTA 58.016 33.333 9.11 0.00 40.44 2.85
2807 3087 7.857456 TGTCTACTAATGGAATACATGTGGTT 58.143 34.615 9.11 3.10 40.44 3.67
2808 3088 7.432148 TGTCTACTAATGGAATACATGTGGT 57.568 36.000 9.11 0.00 40.44 4.16
2809 3089 8.612619 GTTTGTCTACTAATGGAATACATGTGG 58.387 37.037 9.11 0.00 40.44 4.17
2810 3090 9.383519 AGTTTGTCTACTAATGGAATACATGTG 57.616 33.333 9.11 0.00 40.44 3.21
2811 3091 9.959721 AAGTTTGTCTACTAATGGAATACATGT 57.040 29.630 2.69 2.69 40.44 3.21
2837 3117 9.469097 ACCCAAAGCACTTGTACATTTATAATA 57.531 29.630 0.00 0.00 32.65 0.98
2838 3118 8.361169 ACCCAAAGCACTTGTACATTTATAAT 57.639 30.769 0.00 0.00 32.65 1.28
2839 3119 7.768807 ACCCAAAGCACTTGTACATTTATAA 57.231 32.000 0.00 0.00 32.65 0.98
2840 3120 8.865420 TTACCCAAAGCACTTGTACATTTATA 57.135 30.769 0.00 0.00 32.65 0.98
2841 3121 7.768807 TTACCCAAAGCACTTGTACATTTAT 57.231 32.000 0.00 0.00 32.65 1.40
2842 3122 7.285858 AGTTTACCCAAAGCACTTGTACATTTA 59.714 33.333 0.00 0.00 32.65 1.40
2843 3123 6.097696 AGTTTACCCAAAGCACTTGTACATTT 59.902 34.615 0.00 0.00 32.65 2.32
2844 3124 5.596772 AGTTTACCCAAAGCACTTGTACATT 59.403 36.000 0.00 0.00 32.65 2.71
2845 3125 5.137551 AGTTTACCCAAAGCACTTGTACAT 58.862 37.500 0.00 0.00 32.65 2.29
2846 3126 4.528920 AGTTTACCCAAAGCACTTGTACA 58.471 39.130 0.00 0.00 32.65 2.90
2847 3127 6.428771 TGATAGTTTACCCAAAGCACTTGTAC 59.571 38.462 0.00 0.00 32.65 2.90
2848 3128 6.535540 TGATAGTTTACCCAAAGCACTTGTA 58.464 36.000 0.00 0.00 32.65 2.41
2849 3129 5.381757 TGATAGTTTACCCAAAGCACTTGT 58.618 37.500 0.00 0.00 32.65 3.16
2850 3130 5.957842 TGATAGTTTACCCAAAGCACTTG 57.042 39.130 0.00 0.00 34.52 3.16
2851 3131 5.048013 GCTTGATAGTTTACCCAAAGCACTT 60.048 40.000 0.00 0.00 0.00 3.16
2852 3132 4.459337 GCTTGATAGTTTACCCAAAGCACT 59.541 41.667 0.00 0.00 0.00 4.40
2853 3133 4.217550 TGCTTGATAGTTTACCCAAAGCAC 59.782 41.667 3.24 0.00 0.00 4.40
2854 3134 4.402829 TGCTTGATAGTTTACCCAAAGCA 58.597 39.130 3.24 3.24 0.00 3.91
2855 3135 5.582689 ATGCTTGATAGTTTACCCAAAGC 57.417 39.130 0.00 0.00 0.00 3.51
2916 3196 1.168714 GCTTCCAACATCGCTCCTTT 58.831 50.000 0.00 0.00 0.00 3.11
2925 3205 4.832248 TCTAACGATGAAGCTTCCAACAT 58.168 39.130 23.42 10.90 0.00 2.71
2943 3223 5.010617 GGAAAGCCCACAATTGTTCTTCTAA 59.989 40.000 8.77 0.00 34.14 2.10
2944 3224 4.522789 GGAAAGCCCACAATTGTTCTTCTA 59.477 41.667 8.77 0.00 34.14 2.10
2969 3249 3.834231 CCACCTTCAACTTCCAATTCCAT 59.166 43.478 0.00 0.00 0.00 3.41
2996 3276 2.098443 CCAACACAACAAGCGTACCTTT 59.902 45.455 0.00 0.00 0.00 3.11
3090 3370 9.627395 CATGGACACGGTTGTAATTTTTATTAA 57.373 29.630 0.00 0.00 35.47 1.40
3108 3388 0.107654 GCTAGGTGGTCCATGGACAC 60.108 60.000 38.83 31.90 46.20 3.67
3142 3422 2.347490 GCCTTCGGCTCACTCCAA 59.653 61.111 0.00 0.00 46.69 3.53
3166 3446 0.039764 TGAGGGAGAGGTGATGACGT 59.960 55.000 0.00 0.00 0.00 4.34
3202 3482 9.871238 GACTTCCTGATTATCTACTACAACAAA 57.129 33.333 0.00 0.00 0.00 2.83
3221 3501 1.215647 CTTAGCACGGCGACTTCCT 59.784 57.895 16.62 4.34 0.00 3.36
3264 3544 0.392706 TCATCGGCGATGGTTGCTAT 59.607 50.000 39.82 9.05 40.15 2.97
3322 3602 4.849926 CGATCTTCGTCAGTCTTCGTTTAA 59.150 41.667 0.00 0.00 34.72 1.52
3334 3614 3.819564 ATTTGGATCCGATCTTCGTCA 57.180 42.857 7.39 0.00 38.40 4.35
3384 3664 0.387202 CTCTGTCGGATCTTGCGGAT 59.613 55.000 0.00 0.00 37.37 4.18
3412 3692 2.016604 GCATTATTGGAGGGCGTGTGA 61.017 52.381 0.00 0.00 0.00 3.58
3427 3707 2.102420 CCCGATGGTGTGTCTAGCATTA 59.898 50.000 0.00 0.00 38.76 1.90
3428 3708 1.134401 CCCGATGGTGTGTCTAGCATT 60.134 52.381 0.00 0.00 38.76 3.56
3450 3730 2.293519 TGTCTCCCACATTCTATCCCCA 60.294 50.000 0.00 0.00 0.00 4.96
3478 3758 3.093814 TGGCGGTGATGTCTCTTAGTAA 58.906 45.455 0.00 0.00 0.00 2.24
3499 3779 2.927201 CTTGGTTGGGGCTGTGTGGT 62.927 60.000 0.00 0.00 0.00 4.16
3532 3812 1.801178 CCACTGCCGTTCTCTTTCTTC 59.199 52.381 0.00 0.00 0.00 2.87
3538 3820 4.379243 CCGCCACTGCCGTTCTCT 62.379 66.667 0.00 0.00 0.00 3.10
3586 3868 0.756903 ATCGTTCGACCATTAGGGGG 59.243 55.000 0.00 0.00 42.91 5.40
3587 3869 2.626743 AGTATCGTTCGACCATTAGGGG 59.373 50.000 0.00 0.00 42.91 4.79
3588 3870 5.048224 ACATAGTATCGTTCGACCATTAGGG 60.048 44.000 0.00 0.00 44.81 3.53
3589 3871 6.010294 ACATAGTATCGTTCGACCATTAGG 57.990 41.667 0.00 0.00 42.21 2.69
3590 3872 9.622004 AATTACATAGTATCGTTCGACCATTAG 57.378 33.333 0.00 0.00 0.00 1.73
3592 3874 9.622004 CTAATTACATAGTATCGTTCGACCATT 57.378 33.333 0.00 0.00 0.00 3.16
3593 3875 7.754027 GCTAATTACATAGTATCGTTCGACCAT 59.246 37.037 0.00 0.00 0.00 3.55
3594 3876 7.080099 GCTAATTACATAGTATCGTTCGACCA 58.920 38.462 0.00 0.00 0.00 4.02
3595 3877 6.248001 CGCTAATTACATAGTATCGTTCGACC 59.752 42.308 0.00 0.00 0.00 4.79
3596 3878 7.011773 TCGCTAATTACATAGTATCGTTCGAC 58.988 38.462 0.00 0.00 0.00 4.20
3597 3879 7.120789 TCGCTAATTACATAGTATCGTTCGA 57.879 36.000 0.00 0.00 0.00 3.71
3598 3880 7.950108 ATCGCTAATTACATAGTATCGTTCG 57.050 36.000 0.00 0.00 0.00 3.95
3599 3881 8.931972 CGTATCGCTAATTACATAGTATCGTTC 58.068 37.037 0.00 0.00 0.00 3.95
3600 3882 8.659491 TCGTATCGCTAATTACATAGTATCGTT 58.341 33.333 0.00 0.00 0.00 3.85
3601 3883 8.189709 TCGTATCGCTAATTACATAGTATCGT 57.810 34.615 0.00 0.00 0.00 3.73
3602 3884 8.931972 GTTCGTATCGCTAATTACATAGTATCG 58.068 37.037 0.00 0.00 0.00 2.92
3603 3885 8.931972 CGTTCGTATCGCTAATTACATAGTATC 58.068 37.037 0.00 0.00 0.00 2.24
3604 3886 8.817677 CGTTCGTATCGCTAATTACATAGTAT 57.182 34.615 0.00 0.00 0.00 2.12
3625 3907 4.290104 AGTCTAAGGAATACGAGCGTTC 57.710 45.455 0.00 0.00 0.00 3.95
3626 3908 4.715527 AAGTCTAAGGAATACGAGCGTT 57.284 40.909 0.00 0.00 0.00 4.84
3627 3909 6.347240 CGTATAAGTCTAAGGAATACGAGCGT 60.347 42.308 7.24 0.00 44.97 5.07
3628 3910 6.014293 CGTATAAGTCTAAGGAATACGAGCG 58.986 44.000 7.24 0.00 44.97 5.03
3629 3911 6.896969 ACGTATAAGTCTAAGGAATACGAGC 58.103 40.000 17.13 0.00 44.97 5.03
3630 3912 9.379811 GAAACGTATAAGTCTAAGGAATACGAG 57.620 37.037 17.13 0.00 44.97 4.18
3631 3913 9.113838 AGAAACGTATAAGTCTAAGGAATACGA 57.886 33.333 17.13 0.00 44.97 3.43
3632 3914 9.167239 CAGAAACGTATAAGTCTAAGGAATACG 57.833 37.037 10.61 10.61 46.58 3.06
3633 3915 9.460906 CCAGAAACGTATAAGTCTAAGGAATAC 57.539 37.037 0.00 0.00 0.00 1.89
3634 3916 8.139989 GCCAGAAACGTATAAGTCTAAGGAATA 58.860 37.037 0.00 0.00 0.00 1.75
3635 3917 6.985059 GCCAGAAACGTATAAGTCTAAGGAAT 59.015 38.462 0.00 0.00 0.00 3.01
3636 3918 6.335777 GCCAGAAACGTATAAGTCTAAGGAA 58.664 40.000 0.00 0.00 0.00 3.36
3637 3919 5.163478 GGCCAGAAACGTATAAGTCTAAGGA 60.163 44.000 0.00 0.00 0.00 3.36
3638 3920 5.048507 GGCCAGAAACGTATAAGTCTAAGG 58.951 45.833 0.00 0.00 0.00 2.69
3639 3921 5.048507 GGGCCAGAAACGTATAAGTCTAAG 58.951 45.833 4.39 0.00 0.00 2.18
3640 3922 4.141869 GGGGCCAGAAACGTATAAGTCTAA 60.142 45.833 4.39 0.00 0.00 2.10
3641 3923 3.385755 GGGGCCAGAAACGTATAAGTCTA 59.614 47.826 4.39 0.00 0.00 2.59
3642 3924 2.169978 GGGGCCAGAAACGTATAAGTCT 59.830 50.000 4.39 0.00 0.00 3.24
3643 3925 2.558378 GGGGCCAGAAACGTATAAGTC 58.442 52.381 4.39 0.00 0.00 3.01
3644 3926 1.211212 GGGGGCCAGAAACGTATAAGT 59.789 52.381 4.39 0.00 0.00 2.24
3645 3927 1.963172 GGGGGCCAGAAACGTATAAG 58.037 55.000 4.39 0.00 0.00 1.73
3662 3944 1.153369 CACGCTGTGACATAGGGGG 60.153 63.158 18.35 12.01 35.23 5.40
3663 3945 0.249120 TTCACGCTGTGACATAGGGG 59.751 55.000 18.35 9.05 42.60 4.79
3664 3946 2.315925 ATTCACGCTGTGACATAGGG 57.684 50.000 13.67 13.67 42.60 3.53
3665 3947 3.436704 ACAAATTCACGCTGTGACATAGG 59.563 43.478 10.26 3.97 42.60 2.57
3666 3948 4.668576 ACAAATTCACGCTGTGACATAG 57.331 40.909 10.26 0.00 42.60 2.23
3667 3949 6.546972 TTTACAAATTCACGCTGTGACATA 57.453 33.333 10.26 0.00 42.60 2.29
3668 3950 5.431420 TTTACAAATTCACGCTGTGACAT 57.569 34.783 10.26 5.97 42.60 3.06
3669 3951 4.884458 TTTACAAATTCACGCTGTGACA 57.116 36.364 10.26 0.00 42.60 3.58
3689 3971 3.966665 TCACATGGGCCTTTTCTCTTTTT 59.033 39.130 4.53 0.00 0.00 1.94
3690 3972 3.575805 TCACATGGGCCTTTTCTCTTTT 58.424 40.909 4.53 0.00 0.00 2.27
3691 3973 3.243359 TCACATGGGCCTTTTCTCTTT 57.757 42.857 4.53 0.00 0.00 2.52
3692 3974 2.978156 TCACATGGGCCTTTTCTCTT 57.022 45.000 4.53 0.00 0.00 2.85
3693 3975 2.800250 CTTCACATGGGCCTTTTCTCT 58.200 47.619 4.53 0.00 0.00 3.10
3694 3976 1.203287 GCTTCACATGGGCCTTTTCTC 59.797 52.381 4.53 0.00 0.00 2.87
3695 3977 1.260544 GCTTCACATGGGCCTTTTCT 58.739 50.000 4.53 0.00 0.00 2.52
3696 3978 0.247460 GGCTTCACATGGGCCTTTTC 59.753 55.000 4.53 0.00 42.31 2.29
3697 3979 1.194121 GGGCTTCACATGGGCCTTTT 61.194 55.000 4.53 0.00 44.70 2.27
3698 3980 1.610379 GGGCTTCACATGGGCCTTT 60.610 57.895 4.53 0.00 44.70 3.11
3699 3981 2.037847 GGGCTTCACATGGGCCTT 59.962 61.111 4.53 0.00 44.70 4.35
3700 3982 3.267233 TGGGCTTCACATGGGCCT 61.267 61.111 4.53 0.00 46.53 5.19
3701 3983 3.070576 GTGGGCTTCACATGGGCC 61.071 66.667 0.00 0.00 45.39 5.80
3708 3990 1.741770 CCGCTAGTGTGGGCTTCAC 60.742 63.158 1.99 4.24 46.23 3.18
3709 3991 2.662596 CCGCTAGTGTGGGCTTCA 59.337 61.111 1.99 0.00 40.05 3.02
3710 3992 2.820037 GCCGCTAGTGTGGGCTTC 60.820 66.667 1.99 0.00 43.74 3.86
3714 3996 4.473520 CCTGGCCGCTAGTGTGGG 62.474 72.222 0.00 0.00 43.74 4.61
3715 3997 2.748058 AAACCTGGCCGCTAGTGTGG 62.748 60.000 0.00 1.93 46.17 4.17
3716 3998 1.298859 GAAACCTGGCCGCTAGTGTG 61.299 60.000 0.00 0.00 0.00 3.82
3717 3999 1.003718 GAAACCTGGCCGCTAGTGT 60.004 57.895 0.00 0.00 0.00 3.55
3718 4000 2.100631 CGAAACCTGGCCGCTAGTG 61.101 63.158 0.00 0.00 0.00 2.74
3719 4001 2.264794 CGAAACCTGGCCGCTAGT 59.735 61.111 0.00 0.00 0.00 2.57
3720 4002 3.195698 GCGAAACCTGGCCGCTAG 61.196 66.667 17.52 0.00 44.83 3.42
3724 4006 1.519455 CTAGAGCGAAACCTGGCCG 60.519 63.158 0.00 0.00 0.00 6.13
3725 4007 0.460459 GACTAGAGCGAAACCTGGCC 60.460 60.000 0.00 0.00 0.00 5.36
3726 4008 0.460459 GGACTAGAGCGAAACCTGGC 60.460 60.000 0.00 0.00 0.00 4.85
3727 4009 0.175989 GGGACTAGAGCGAAACCTGG 59.824 60.000 0.00 0.00 0.00 4.45
3728 4010 0.895530 TGGGACTAGAGCGAAACCTG 59.104 55.000 0.00 0.00 0.00 4.00
3729 4011 1.867363 ATGGGACTAGAGCGAAACCT 58.133 50.000 0.00 0.00 0.00 3.50
3730 4012 2.694109 ACTATGGGACTAGAGCGAAACC 59.306 50.000 0.00 0.00 0.00 3.27
3731 4013 4.388378 AACTATGGGACTAGAGCGAAAC 57.612 45.455 0.00 0.00 0.00 2.78
3732 4014 4.710375 AGAAACTATGGGACTAGAGCGAAA 59.290 41.667 0.00 0.00 0.00 3.46
3733 4015 4.279145 AGAAACTATGGGACTAGAGCGAA 58.721 43.478 0.00 0.00 0.00 4.70
3734 4016 3.884091 GAGAAACTATGGGACTAGAGCGA 59.116 47.826 0.00 0.00 0.00 4.93
3735 4017 3.886505 AGAGAAACTATGGGACTAGAGCG 59.113 47.826 0.00 0.00 0.00 5.03
3736 4018 4.038642 CCAGAGAAACTATGGGACTAGAGC 59.961 50.000 0.00 0.00 38.99 4.09
3737 4019 5.782893 CCAGAGAAACTATGGGACTAGAG 57.217 47.826 0.00 0.00 38.99 2.43
3745 4027 2.424956 GCAAAGCCCAGAGAAACTATGG 59.575 50.000 5.57 5.57 41.97 2.74
3746 4028 2.096496 CGCAAAGCCCAGAGAAACTATG 59.904 50.000 0.00 0.00 0.00 2.23
3747 4029 2.290323 ACGCAAAGCCCAGAGAAACTAT 60.290 45.455 0.00 0.00 0.00 2.12
3748 4030 1.071699 ACGCAAAGCCCAGAGAAACTA 59.928 47.619 0.00 0.00 0.00 2.24
3749 4031 0.179018 ACGCAAAGCCCAGAGAAACT 60.179 50.000 0.00 0.00 0.00 2.66
3750 4032 0.668535 AACGCAAAGCCCAGAGAAAC 59.331 50.000 0.00 0.00 0.00 2.78
3751 4033 0.951558 GAACGCAAAGCCCAGAGAAA 59.048 50.000 0.00 0.00 0.00 2.52
3752 4034 0.108585 AGAACGCAAAGCCCAGAGAA 59.891 50.000 0.00 0.00 0.00 2.87
3753 4035 0.320771 GAGAACGCAAAGCCCAGAGA 60.321 55.000 0.00 0.00 0.00 3.10
3754 4036 1.630244 CGAGAACGCAAAGCCCAGAG 61.630 60.000 0.00 0.00 0.00 3.35
3755 4037 1.667830 CGAGAACGCAAAGCCCAGA 60.668 57.895 0.00 0.00 0.00 3.86
3756 4038 2.863153 CGAGAACGCAAAGCCCAG 59.137 61.111 0.00 0.00 0.00 4.45
3766 4048 1.524355 CAGGCTAATCATGCGAGAACG 59.476 52.381 0.00 0.00 42.93 3.95
3767 4049 2.555199 ACAGGCTAATCATGCGAGAAC 58.445 47.619 0.00 0.00 0.00 3.01
3768 4050 2.988010 ACAGGCTAATCATGCGAGAA 57.012 45.000 0.00 0.00 0.00 2.87
3769 4051 2.287608 CGTACAGGCTAATCATGCGAGA 60.288 50.000 0.00 0.00 0.00 4.04
3770 4052 2.054363 CGTACAGGCTAATCATGCGAG 58.946 52.381 0.00 0.00 0.00 5.03
3771 4053 1.407618 ACGTACAGGCTAATCATGCGA 59.592 47.619 0.00 0.00 0.00 5.10
3772 4054 1.852942 ACGTACAGGCTAATCATGCG 58.147 50.000 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.