Multiple sequence alignment - TraesCS3B01G510000

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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 TraesCS3B01G510000 chr3B 100.000 2978 0 0 1 2978 753965633 753962656 0.000000e+00 5500.0
1 TraesCS3B01G510000 chr3B 79.582 1053 163 28 954 1967 752809645 752808606 0.000000e+00 706.0
2 TraesCS3B01G510000 chr3B 86.441 295 38 2 1969 2263 752808546 752808254 3.700000e-84 322.0
3 TraesCS3B01G510000 chr3B 87.204 211 26 1 965 1175 752178781 752178572 3.840000e-59 239.0
4 TraesCS3B01G510000 chr3B 81.270 315 33 7 2680 2978 752807277 752806973 6.420000e-57 231.0
5 TraesCS3B01G510000 chr3B 74.477 478 94 23 993 1453 753916223 753916689 6.560000e-42 182.0
6 TraesCS3B01G510000 chr3B 82.653 196 32 2 981 1175 752122936 752122742 3.950000e-39 172.0
7 TraesCS3B01G510000 chr3B 87.324 142 17 1 1031 1172 754879576 754879716 8.540000e-36 161.0
8 TraesCS3B01G510000 chr3B 85.149 101 15 0 2680 2780 752118026 752117926 1.460000e-18 104.0
9 TraesCS3B01G510000 chr3B 81.982 111 19 1 2680 2789 752130054 752129944 3.160000e-15 93.5
10 TraesCS3B01G510000 chr3A 85.824 1044 96 19 957 1967 700025623 700024599 0.000000e+00 1061.0
11 TraesCS3B01G510000 chr3A 87.944 788 46 21 1 750 700033705 700032929 0.000000e+00 883.0
12 TraesCS3B01G510000 chr3A 87.737 791 48 18 1 749 700037821 700037038 0.000000e+00 878.0
13 TraesCS3B01G510000 chr3A 87.421 795 48 23 1 750 700042070 700041283 0.000000e+00 867.0
14 TraesCS3B01G510000 chr3A 93.392 227 15 0 1969 2195 700024539 700024313 1.320000e-88 337.0
15 TraesCS3B01G510000 chr3A 87.273 55 6 1 441 494 702494927 702494981 8.910000e-06 62.1
16 TraesCS3B01G510000 chr3D 80.504 1031 167 22 954 1955 565258607 565259632 0.000000e+00 760.0
17 TraesCS3B01G510000 chr3D 83.105 657 83 15 965 1594 565162750 565163405 9.260000e-160 573.0
18 TraesCS3B01G510000 chr3D 88.152 211 24 1 965 1175 564513353 564513144 1.770000e-62 250.0
19 TraesCS3B01G510000 chr3D 89.560 182 17 2 992 1172 564905433 564905253 2.310000e-56 230.0
20 TraesCS3B01G510000 chr3D 84.459 148 14 5 2840 2978 565165468 565165615 1.440000e-28 137.0
21 TraesCS3B01G510000 chr3D 95.833 48 1 1 257 304 131717814 131717768 3.180000e-10 76.8
22 TraesCS3B01G510000 chr3D 100.000 28 0 0 2753 2780 567048728 567048701 5.000000e-03 52.8
23 TraesCS3B01G510000 chrUn 86.620 142 18 1 1031 1172 279459076 279458936 3.970000e-34 156.0
24 TraesCS3B01G510000 chr2D 92.982 57 2 2 247 303 608292718 608292772 6.840000e-12 82.4
25 TraesCS3B01G510000 chr2B 95.833 48 2 0 257 304 108073425 108073378 8.850000e-11 78.7
26 TraesCS3B01G510000 chr2B 88.000 50 6 0 46 95 523261248 523261297 3.210000e-05 60.2
27 TraesCS3B01G510000 chr1B 91.379 58 3 2 247 304 619497382 619497437 8.850000e-11 78.7
28 TraesCS3B01G510000 chr1B 86.765 68 5 4 246 310 561914548 561914482 4.120000e-09 73.1
29 TraesCS3B01G510000 chr6D 95.833 48 1 1 257 304 54706676 54706630 3.180000e-10 76.8
30 TraesCS3B01G510000 chr4D 82.927 82 10 3 416 494 503566848 503566768 1.480000e-08 71.3
31 TraesCS3B01G510000 chr4D 82.667 75 9 3 416 487 503566646 503566573 2.480000e-06 63.9
32 TraesCS3B01G510000 chr7D 89.796 49 3 1 441 487 392619158 392619110 8.910000e-06 62.1
33 TraesCS3B01G510000 chr2A 85.965 57 6 1 441 495 295207905 295207961 3.210000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G510000 chr3B 753962656 753965633 2977 True 5500.000000 5500 100.000000 1 2978 1 chr3B.!!$R5 2977
1 TraesCS3B01G510000 chr3B 752806973 752809645 2672 True 419.666667 706 82.431000 954 2978 3 chr3B.!!$R6 2024
2 TraesCS3B01G510000 chr3A 700032929 700042070 9141 True 876.000000 883 87.700667 1 750 3 chr3A.!!$R2 749
3 TraesCS3B01G510000 chr3A 700024313 700025623 1310 True 699.000000 1061 89.608000 957 2195 2 chr3A.!!$R1 1238
4 TraesCS3B01G510000 chr3D 565258607 565259632 1025 False 760.000000 760 80.504000 954 1955 1 chr3D.!!$F1 1001
5 TraesCS3B01G510000 chr3D 565162750 565165615 2865 False 355.000000 573 83.782000 965 2978 2 chr3D.!!$F2 2013

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
447 4698 0.035534 ACATGCACATACGGCCAAGA 60.036 50.0 2.24 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2067 8448 0.673956 TTTATAAGCGCCGGCACACA 60.674 50.0 28.98 9.03 43.41 3.72 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
22 23 3.577805 ACCTTTTTCCCCATATCCGAG 57.422 47.619 0.00 0.00 0.00 4.63
26 27 3.857157 TTTTCCCCATATCCGAGAAGG 57.143 47.619 0.00 0.00 42.97 3.46
54 55 3.451141 TGCTTCTTGCCGAAACAAATT 57.549 38.095 0.00 0.00 42.00 1.82
64 65 2.403259 CGAAACAAATTTGTGCCTCCC 58.597 47.619 23.93 9.05 41.31 4.30
65 66 2.766313 GAAACAAATTTGTGCCTCCCC 58.234 47.619 23.93 5.55 41.31 4.81
91 92 2.497675 AGCAAATCTAGGCTTCTCGTGA 59.502 45.455 0.00 0.00 36.92 4.35
96 97 1.893137 TCTAGGCTTCTCGTGAAAGCA 59.107 47.619 16.68 2.09 32.16 3.91
133 4383 1.334869 CAAGAGGCACAACTGTGGTTC 59.665 52.381 11.63 0.00 45.72 3.62
148 4398 6.518493 ACTGTGGTTCTCGTGAAAGTAAATA 58.482 36.000 0.74 0.00 33.52 1.40
149 4399 7.159372 ACTGTGGTTCTCGTGAAAGTAAATAT 58.841 34.615 0.74 0.00 33.52 1.28
245 4495 6.218746 ACAAATTTGTTCTTCCATGAGAAGC 58.781 36.000 18.13 6.76 41.17 3.86
396 4647 0.670546 CGACCGCTTTGAGTGTGGAT 60.671 55.000 0.00 0.00 38.37 3.41
447 4698 0.035534 ACATGCACATACGGCCAAGA 60.036 50.000 2.24 0.00 0.00 3.02
449 4700 1.265095 CATGCACATACGGCCAAGATC 59.735 52.381 2.24 0.00 0.00 2.75
468 4719 1.180029 CAGTTGGATCTGCCCCTTTG 58.820 55.000 0.00 0.00 34.97 2.77
473 4724 4.078980 AGTTGGATCTGCCCCTTTGATTAT 60.079 41.667 0.00 0.00 34.97 1.28
545 4826 8.662141 TCTTTGTACTACTTTTGTCACTTGTTC 58.338 33.333 0.00 0.00 0.00 3.18
549 4830 9.005777 TGTACTACTTTTGTCACTTGTTCTTTT 57.994 29.630 0.00 0.00 0.00 2.27
550 4831 9.274065 GTACTACTTTTGTCACTTGTTCTTTTG 57.726 33.333 0.00 0.00 0.00 2.44
552 4833 8.357402 ACTACTTTTGTCACTTGTTCTTTTGTT 58.643 29.630 0.00 0.00 0.00 2.83
553 4834 7.406799 ACTTTTGTCACTTGTTCTTTTGTTG 57.593 32.000 0.00 0.00 0.00 3.33
555 4836 7.708752 ACTTTTGTCACTTGTTCTTTTGTTGAA 59.291 29.630 0.00 0.00 0.00 2.69
558 4839 8.600449 TTGTCACTTGTTCTTTTGTTGAATTT 57.400 26.923 0.00 0.00 0.00 1.82
559 4840 8.016497 TGTCACTTGTTCTTTTGTTGAATTTG 57.984 30.769 0.00 0.00 0.00 2.32
560 4841 7.655328 TGTCACTTGTTCTTTTGTTGAATTTGT 59.345 29.630 0.00 0.00 0.00 2.83
561 4842 8.495148 GTCACTTGTTCTTTTGTTGAATTTGTT 58.505 29.630 0.00 0.00 0.00 2.83
577 4867 9.868277 TTGAATTTGTTCATAATGGTCCAATAC 57.132 29.630 0.00 0.00 0.00 1.89
631 4922 8.891671 ATTATGTGATTTGCAGTTGAAGTTTT 57.108 26.923 0.00 0.00 0.00 2.43
718 5010 5.175859 GGAGAAACAATGAATAGACCACGA 58.824 41.667 0.00 0.00 0.00 4.35
720 5012 6.402226 GGAGAAACAATGAATAGACCACGAAC 60.402 42.308 0.00 0.00 0.00 3.95
725 5017 5.867716 ACAATGAATAGACCACGAACTGTAC 59.132 40.000 0.00 0.00 0.00 2.90
750 5042 8.931775 ACGTGCCTTAAATATTTTTGAAAATCC 58.068 29.630 5.91 0.00 39.24 3.01
856 6901 4.632251 TCTTTTGTACTGCAAAGTTCACGA 59.368 37.500 10.60 0.00 46.40 4.35
857 6902 3.936902 TTGTACTGCAAAGTTCACGAC 57.063 42.857 0.00 0.00 33.53 4.34
863 6908 0.935196 GCAAAGTTCACGACGAGGTT 59.065 50.000 0.00 0.00 0.00 3.50
867 6912 2.418983 AGTTCACGACGAGGTTCTTC 57.581 50.000 0.00 0.00 0.00 2.87
873 6918 1.671742 GACGAGGTTCTTCTGGGCA 59.328 57.895 0.00 0.00 0.00 5.36
892 6937 0.831711 AAAAGCCCAGCCCGTTTCAT 60.832 50.000 0.00 0.00 0.00 2.57
893 6938 1.250840 AAAGCCCAGCCCGTTTCATC 61.251 55.000 0.00 0.00 0.00 2.92
894 6939 3.140814 GCCCAGCCCGTTTCATCC 61.141 66.667 0.00 0.00 0.00 3.51
895 6940 2.354729 CCCAGCCCGTTTCATCCA 59.645 61.111 0.00 0.00 0.00 3.41
896 6941 1.076777 CCCAGCCCGTTTCATCCAT 60.077 57.895 0.00 0.00 0.00 3.41
897 6942 1.103398 CCCAGCCCGTTTCATCCATC 61.103 60.000 0.00 0.00 0.00 3.51
899 6944 0.394216 CAGCCCGTTTCATCCATCCA 60.394 55.000 0.00 0.00 0.00 3.41
900 6945 0.552848 AGCCCGTTTCATCCATCCAT 59.447 50.000 0.00 0.00 0.00 3.41
901 6946 1.774254 AGCCCGTTTCATCCATCCATA 59.226 47.619 0.00 0.00 0.00 2.74
902 6947 1.880027 GCCCGTTTCATCCATCCATAC 59.120 52.381 0.00 0.00 0.00 2.39
903 6948 2.143122 CCCGTTTCATCCATCCATACG 58.857 52.381 0.00 0.00 0.00 3.06
904 6949 2.143122 CCGTTTCATCCATCCATACGG 58.857 52.381 0.00 0.00 40.68 4.02
905 6950 1.531149 CGTTTCATCCATCCATACGGC 59.469 52.381 0.00 0.00 0.00 5.68
906 6951 2.571212 GTTTCATCCATCCATACGGCA 58.429 47.619 0.00 0.00 0.00 5.69
907 6952 2.254546 TTCATCCATCCATACGGCAC 57.745 50.000 0.00 0.00 0.00 5.01
920 6965 4.554036 GGCACGATCCTGGGGCTC 62.554 72.222 0.00 0.00 0.00 4.70
921 6966 3.785859 GCACGATCCTGGGGCTCA 61.786 66.667 0.00 0.00 0.00 4.26
922 6967 3.112205 GCACGATCCTGGGGCTCAT 62.112 63.158 0.00 0.00 0.00 2.90
923 6968 1.528824 CACGATCCTGGGGCTCATT 59.471 57.895 0.00 0.00 0.00 2.57
925 6970 0.181350 ACGATCCTGGGGCTCATTTC 59.819 55.000 0.00 0.00 0.00 2.17
928 6973 1.146566 GATCCTGGGGCTCATTTCCAT 59.853 52.381 0.00 0.00 0.00 3.41
930 6975 1.063717 TCCTGGGGCTCATTTCCATTC 60.064 52.381 0.00 0.00 0.00 2.67
931 6976 1.406903 CTGGGGCTCATTTCCATTCC 58.593 55.000 0.00 0.00 0.00 3.01
933 6978 2.175499 CTGGGGCTCATTTCCATTCCTA 59.825 50.000 0.00 0.00 0.00 2.94
934 6979 2.791179 TGGGGCTCATTTCCATTCCTAT 59.209 45.455 0.00 0.00 0.00 2.57
935 6980 3.181429 TGGGGCTCATTTCCATTCCTATC 60.181 47.826 0.00 0.00 0.00 2.08
936 6981 3.425659 GGGCTCATTTCCATTCCTATCC 58.574 50.000 0.00 0.00 0.00 2.59
937 6982 3.425659 GGCTCATTTCCATTCCTATCCC 58.574 50.000 0.00 0.00 0.00 3.85
938 6983 3.425659 GCTCATTTCCATTCCTATCCCC 58.574 50.000 0.00 0.00 0.00 4.81
940 6985 4.401925 CTCATTTCCATTCCTATCCCCAC 58.598 47.826 0.00 0.00 0.00 4.61
941 6986 3.149196 CATTTCCATTCCTATCCCCACG 58.851 50.000 0.00 0.00 0.00 4.94
942 6987 2.184088 TTCCATTCCTATCCCCACGA 57.816 50.000 0.00 0.00 0.00 4.35
943 6988 1.717032 TCCATTCCTATCCCCACGAG 58.283 55.000 0.00 0.00 0.00 4.18
944 6989 1.219469 TCCATTCCTATCCCCACGAGA 59.781 52.381 0.00 0.00 0.00 4.04
945 6990 2.047061 CCATTCCTATCCCCACGAGAA 58.953 52.381 0.00 0.00 0.00 2.87
946 6991 2.224305 CCATTCCTATCCCCACGAGAAC 60.224 54.545 0.00 0.00 0.00 3.01
947 6992 1.492764 TTCCTATCCCCACGAGAACC 58.507 55.000 0.00 0.00 0.00 3.62
948 6993 0.398098 TCCTATCCCCACGAGAACCC 60.398 60.000 0.00 0.00 0.00 4.11
949 6994 1.408453 CCTATCCCCACGAGAACCCC 61.408 65.000 0.00 0.00 0.00 4.95
950 6995 0.689745 CTATCCCCACGAGAACCCCA 60.690 60.000 0.00 0.00 0.00 4.96
951 6996 0.252789 TATCCCCACGAGAACCCCAA 60.253 55.000 0.00 0.00 0.00 4.12
952 6997 1.137594 ATCCCCACGAGAACCCCAAA 61.138 55.000 0.00 0.00 0.00 3.28
953 6998 1.137594 TCCCCACGAGAACCCCAAAT 61.138 55.000 0.00 0.00 0.00 2.32
955 7000 0.679960 CCCACGAGAACCCCAAATCC 60.680 60.000 0.00 0.00 0.00 3.01
956 7001 0.679960 CCACGAGAACCCCAAATCCC 60.680 60.000 0.00 0.00 0.00 3.85
959 7004 1.753078 GAGAACCCCAAATCCCCGC 60.753 63.158 0.00 0.00 0.00 6.13
961 7006 4.751820 AACCCCAAATCCCCGCCG 62.752 66.667 0.00 0.00 0.00 6.46
1041 7086 1.388531 GGTGGACCCTCTCCTCAGA 59.611 63.158 0.00 0.00 40.26 3.27
1062 7107 0.749649 ATCTGCCAGATGAGGTCGTC 59.250 55.000 6.37 0.00 32.80 4.20
1192 7258 2.574955 ATCGCTACCGGCCAGGATC 61.575 63.158 18.74 7.31 45.00 3.36
1237 7303 0.898320 CATCCTCACCTTCGACCACT 59.102 55.000 0.00 0.00 0.00 4.00
1275 7341 2.340809 CAACACGTCACCCGGCTA 59.659 61.111 0.00 0.00 42.24 3.93
1282 7348 2.753043 TCACCCGGCTAGACGACC 60.753 66.667 22.46 0.00 35.47 4.79
1333 7399 0.397816 CCTCATCCTCCTCCGTTCCT 60.398 60.000 0.00 0.00 0.00 3.36
1339 7405 1.286849 TCCTCCTCCGTTCCTATGACA 59.713 52.381 0.00 0.00 0.00 3.58
1341 7407 2.379972 CTCCTCCGTTCCTATGACACT 58.620 52.381 0.00 0.00 0.00 3.55
1450 7526 1.672854 CCATCCTTCCGGCGAGTACA 61.673 60.000 9.30 0.00 0.00 2.90
1476 7552 4.247267 TCTGTTGTACGACGAAAATCCT 57.753 40.909 8.73 0.00 0.00 3.24
1481 7557 5.293814 TGTTGTACGACGAAAATCCTGAAAA 59.706 36.000 8.73 0.00 0.00 2.29
1482 7558 5.987777 TGTACGACGAAAATCCTGAAAAA 57.012 34.783 0.00 0.00 0.00 1.94
1483 7559 6.548441 TGTACGACGAAAATCCTGAAAAAT 57.452 33.333 0.00 0.00 0.00 1.82
1484 7560 6.595794 TGTACGACGAAAATCCTGAAAAATC 58.404 36.000 0.00 0.00 0.00 2.17
1488 7564 3.179048 CGAAAATCCTGAAAAATCCGGC 58.821 45.455 0.00 0.00 0.00 6.13
1511 7587 1.482182 TGATGCCTGCTACATCTTCGT 59.518 47.619 13.02 0.00 43.53 3.85
1581 7657 1.133869 GGATGCGTGTTACGGCAAC 59.866 57.895 5.10 2.99 42.82 4.17
1599 7675 1.672356 CGGGGAAGCTGTCCTGTTG 60.672 63.158 12.71 0.88 46.92 3.33
1602 7678 2.328099 GGAAGCTGTCCTGTTGCGG 61.328 63.158 7.46 0.00 43.98 5.69
1624 7940 1.885887 GCAACCTGCATTGGTCAGTAA 59.114 47.619 0.00 0.00 44.26 2.24
1649 7965 2.161609 CGGTTGAGGTTGGAAGCAATAC 59.838 50.000 0.00 0.00 0.00 1.89
1665 7981 8.903820 GGAAGCAATACTATAGTGGTTTTTGAT 58.096 33.333 15.90 7.30 43.34 2.57
1668 7984 9.042008 AGCAATACTATAGTGGTTTTTGATACG 57.958 33.333 15.90 0.00 29.41 3.06
1672 7988 9.745880 ATACTATAGTGGTTTTTGATACGACAG 57.254 33.333 15.90 0.00 0.00 3.51
1709 8025 2.358003 GCGTGCTCCAGTTGCTCT 60.358 61.111 0.00 0.00 0.00 4.09
1710 8026 2.675056 GCGTGCTCCAGTTGCTCTG 61.675 63.158 3.18 3.18 43.27 3.35
1731 8047 4.323417 TGTTCGTTCCTTGCTACAATCAT 58.677 39.130 0.00 0.00 0.00 2.45
1774 8090 2.620251 TGGCATGTACAGCTATGGTC 57.380 50.000 14.28 1.59 0.00 4.02
1777 8093 3.645687 TGGCATGTACAGCTATGGTCATA 59.354 43.478 14.28 0.00 0.00 2.15
1821 8137 2.423577 GTGTTGCCCGACTATGAAAGT 58.576 47.619 0.00 0.00 42.80 2.66
1828 8144 3.616560 GCCCGACTATGAAAGTGAAGTCA 60.617 47.826 0.00 0.00 39.07 3.41
1829 8145 3.927142 CCCGACTATGAAAGTGAAGTCAC 59.073 47.826 3.12 3.12 46.77 3.67
1844 8160 2.755650 AGTCACGACCTTAAAGTGCAG 58.244 47.619 0.00 0.00 35.97 4.41
1851 8167 3.941483 CGACCTTAAAGTGCAGGATTGAT 59.059 43.478 0.00 0.00 33.90 2.57
1856 8172 5.337009 CCTTAAAGTGCAGGATTGATTTGCT 60.337 40.000 0.00 0.00 38.60 3.91
1915 8234 2.165998 GTTCTAGGTACGTGGTGGTCT 58.834 52.381 0.00 0.00 0.00 3.85
1962 8284 3.987404 GGCAGATTTGGCGACTGT 58.013 55.556 0.00 0.00 40.30 3.55
1967 8289 2.930887 GCAGATTTGGCGACTGTCTACA 60.931 50.000 6.21 1.87 34.60 2.74
2001 8381 3.005155 GCTCAAGCAAACTCTTGTTCCAT 59.995 43.478 0.00 0.00 42.90 3.41
2006 8386 4.922206 AGCAAACTCTTGTTCCATATCCA 58.078 39.130 0.00 0.00 34.96 3.41
2010 8390 6.096001 GCAAACTCTTGTTCCATATCCATTCT 59.904 38.462 0.00 0.00 34.96 2.40
2013 8393 7.872113 ACTCTTGTTCCATATCCATTCTTTC 57.128 36.000 0.00 0.00 0.00 2.62
2047 8428 3.763897 GGTAAGGTTGTGAATGCTCCATT 59.236 43.478 0.00 0.00 36.72 3.16
2062 8443 3.876320 GCTCCATTCTCAATCTGAAGACC 59.124 47.826 0.00 0.00 0.00 3.85
2067 8448 4.336889 TTCTCAATCTGAAGACCGTTGT 57.663 40.909 0.00 0.00 0.00 3.32
2082 8463 4.610714 TGTGTGTGCCGGCGCTTA 62.611 61.111 37.39 24.40 35.36 3.09
2157 8538 3.306989 CCACCATGAGTTGACTAGCTTCA 60.307 47.826 0.00 0.00 0.00 3.02
2212 8593 1.671328 CTCTCGCTGTTATCTGGTCGA 59.329 52.381 0.00 0.00 0.00 4.20
2220 8601 4.553547 GCTGTTATCTGGTCGAATGCAATC 60.554 45.833 0.00 0.00 0.00 2.67
2225 8606 4.406648 TCTGGTCGAATGCAATCTATGT 57.593 40.909 0.00 0.00 0.00 2.29
2263 8644 2.681848 CCATCTTGAAGGATGTGACTGC 59.318 50.000 2.24 0.00 40.85 4.40
2264 8645 3.607741 CATCTTGAAGGATGTGACTGCT 58.392 45.455 0.00 0.00 38.49 4.24
2265 8646 3.325293 TCTTGAAGGATGTGACTGCTC 57.675 47.619 0.00 0.00 0.00 4.26
2267 8648 3.056250 TCTTGAAGGATGTGACTGCTCTC 60.056 47.826 0.00 0.00 0.00 3.20
2268 8649 1.203287 TGAAGGATGTGACTGCTCTCG 59.797 52.381 0.00 0.00 0.00 4.04
2269 8650 0.108424 AAGGATGTGACTGCTCTCGC 60.108 55.000 0.00 0.00 0.00 5.03
2274 8655 0.958822 TGTGACTGCTCTCGCTGTTA 59.041 50.000 0.00 0.00 46.51 2.41
2275 8656 1.546029 TGTGACTGCTCTCGCTGTTAT 59.454 47.619 0.00 0.00 46.51 1.89
2276 8657 2.189342 GTGACTGCTCTCGCTGTTATC 58.811 52.381 0.00 0.00 46.51 1.75
2278 8659 3.065510 GTGACTGCTCTCGCTGTTATCTA 59.934 47.826 0.00 0.00 46.51 1.98
2280 8661 4.225984 GACTGCTCTCGCTGTTATCTATG 58.774 47.826 0.00 0.00 46.51 2.23
2281 8662 3.634448 ACTGCTCTCGCTGTTATCTATGT 59.366 43.478 0.00 0.00 44.58 2.29
2282 8663 4.098654 ACTGCTCTCGCTGTTATCTATGTT 59.901 41.667 0.00 0.00 44.58 2.71
2283 8664 5.011090 TGCTCTCGCTGTTATCTATGTTT 57.989 39.130 0.00 0.00 36.97 2.83
2284 8665 4.805719 TGCTCTCGCTGTTATCTATGTTTG 59.194 41.667 0.00 0.00 36.97 2.93
2286 8667 5.292101 GCTCTCGCTGTTATCTATGTTTGTT 59.708 40.000 0.00 0.00 0.00 2.83
2287 8668 6.475727 GCTCTCGCTGTTATCTATGTTTGTTA 59.524 38.462 0.00 0.00 0.00 2.41
2288 8669 7.169982 GCTCTCGCTGTTATCTATGTTTGTTAT 59.830 37.037 0.00 0.00 0.00 1.89
2289 8670 8.352752 TCTCGCTGTTATCTATGTTTGTTATG 57.647 34.615 0.00 0.00 0.00 1.90
2290 8671 8.194769 TCTCGCTGTTATCTATGTTTGTTATGA 58.805 33.333 0.00 0.00 0.00 2.15
2291 8672 8.352752 TCGCTGTTATCTATGTTTGTTATGAG 57.647 34.615 0.00 0.00 0.00 2.90
2292 8673 8.194769 TCGCTGTTATCTATGTTTGTTATGAGA 58.805 33.333 0.00 0.00 0.00 3.27
2304 8685 8.870160 TGTTTGTTATGAGAAAGTCATTTTGG 57.130 30.769 0.00 0.00 44.05 3.28
2306 8687 8.968242 GTTTGTTATGAGAAAGTCATTTTGGTC 58.032 33.333 0.00 0.00 44.05 4.02
2307 8688 7.815840 TGTTATGAGAAAGTCATTTTGGTCA 57.184 32.000 0.00 0.00 44.05 4.02
2314 10046 5.598005 AGAAAGTCATTTTGGTCATTGGTCA 59.402 36.000 0.00 0.00 0.00 4.02
2318 10050 3.501828 TCATTTTGGTCATTGGTCAGTCG 59.498 43.478 0.00 0.00 0.00 4.18
2330 10062 5.666969 TTGGTCAGTCGTTGAAGTATTTG 57.333 39.130 0.00 0.00 37.61 2.32
2331 10063 4.062293 TGGTCAGTCGTTGAAGTATTTGG 58.938 43.478 0.00 0.00 37.61 3.28
2333 10065 4.935808 GGTCAGTCGTTGAAGTATTTGGAT 59.064 41.667 0.00 0.00 37.61 3.41
2349 10081 5.596836 TTTGGATGCCAATTAATCTGTCC 57.403 39.130 0.00 0.00 43.55 4.02
2360 10092 2.706339 AATCTGTCCCATGTCTCTGC 57.294 50.000 0.00 0.00 0.00 4.26
2366 10098 2.373169 TGTCCCATGTCTCTGCTTTTCT 59.627 45.455 0.00 0.00 0.00 2.52
2394 10190 1.173913 ACTTGGCCTTTTATCGTGGC 58.826 50.000 3.32 0.00 45.42 5.01
2401 10197 2.029380 GCCTTTTATCGTGGCCTTGTTT 60.029 45.455 3.32 0.00 40.71 2.83
2458 10484 8.660435 AGTTACTATTGGCATAGATACATTGGT 58.340 33.333 9.84 0.00 36.58 3.67
2468 10519 8.850156 GGCATAGATACATTGGTTTATTTGTCT 58.150 33.333 0.00 0.00 0.00 3.41
2503 10554 4.600012 AGTTGTCGATGAAATTAAGGCG 57.400 40.909 0.00 0.00 0.00 5.52
2530 10581 1.000938 CCTCTTTGTTGACCAGCAAGC 60.001 52.381 0.01 0.00 37.12 4.01
2531 10582 1.677576 CTCTTTGTTGACCAGCAAGCA 59.322 47.619 0.00 0.00 37.12 3.91
2563 10614 8.195436 AGATTTTTAGTCATGAATCCATTGCAG 58.805 33.333 0.00 0.00 30.67 4.41
2567 10618 2.028876 TCATGAATCCATTGCAGCTGG 58.971 47.619 17.12 10.39 34.93 4.85
2586 10637 4.744631 GCTGGTTAGGTGTTGAAATGTTTG 59.255 41.667 0.00 0.00 0.00 2.93
2587 10638 4.688021 TGGTTAGGTGTTGAAATGTTTGC 58.312 39.130 0.00 0.00 0.00 3.68
2588 10639 4.404073 TGGTTAGGTGTTGAAATGTTTGCT 59.596 37.500 0.00 0.00 0.00 3.91
2589 10640 5.594725 TGGTTAGGTGTTGAAATGTTTGCTA 59.405 36.000 0.00 0.00 0.00 3.49
2590 10641 6.266558 TGGTTAGGTGTTGAAATGTTTGCTAT 59.733 34.615 0.00 0.00 0.00 2.97
2591 10642 7.448777 TGGTTAGGTGTTGAAATGTTTGCTATA 59.551 33.333 0.00 0.00 0.00 1.31
2592 10643 7.968405 GGTTAGGTGTTGAAATGTTTGCTATAG 59.032 37.037 0.00 0.00 0.00 1.31
2593 10644 8.512138 GTTAGGTGTTGAAATGTTTGCTATAGT 58.488 33.333 0.84 0.00 0.00 2.12
2594 10645 7.524717 AGGTGTTGAAATGTTTGCTATAGTT 57.475 32.000 0.84 0.00 0.00 2.24
2595 10646 7.593825 AGGTGTTGAAATGTTTGCTATAGTTC 58.406 34.615 0.84 0.00 0.00 3.01
2596 10647 6.806739 GGTGTTGAAATGTTTGCTATAGTTCC 59.193 38.462 0.84 0.00 0.00 3.62
2603 10654 4.834534 TGTTTGCTATAGTTCCGCCTTTA 58.165 39.130 0.84 0.00 0.00 1.85
2612 10663 2.423538 AGTTCCGCCTTTATGTTGCATC 59.576 45.455 0.00 0.00 0.00 3.91
2619 10670 2.159254 CCTTTATGTTGCATCGTTGGGG 60.159 50.000 0.00 0.00 0.00 4.96
2623 10674 1.626686 TGTTGCATCGTTGGGGATTT 58.373 45.000 0.00 0.00 0.00 2.17
2630 10681 1.821216 TCGTTGGGGATTTTCTCTGC 58.179 50.000 0.00 0.00 0.00 4.26
2639 10690 3.382865 GGGATTTTCTCTGCCATTTCTCC 59.617 47.826 0.00 0.00 0.00 3.71
2652 10703 4.775236 CCATTTCTCCTTAGCTGCTAACT 58.225 43.478 17.67 0.00 0.00 2.24
2653 10704 4.574013 CCATTTCTCCTTAGCTGCTAACTG 59.426 45.833 17.67 11.91 0.00 3.16
2657 10708 5.995565 TCTCCTTAGCTGCTAACTGTTTA 57.004 39.130 17.67 0.00 0.00 2.01
2664 10715 5.690997 AGCTGCTAACTGTTTAAAGGAAC 57.309 39.130 0.00 0.00 0.00 3.62
2676 10727 7.014615 ACTGTTTAAAGGAACTGATGCTTCATT 59.985 33.333 2.33 0.00 38.99 2.57
2677 10728 8.402798 TGTTTAAAGGAACTGATGCTTCATTA 57.597 30.769 2.33 0.00 38.99 1.90
2678 10729 9.023962 TGTTTAAAGGAACTGATGCTTCATTAT 57.976 29.630 2.33 0.00 38.99 1.28
2685 10762 9.905713 AGGAACTGATGCTTCATTATAACTAAA 57.094 29.630 2.33 0.00 37.18 1.85
2692 10769 9.722056 GATGCTTCATTATAACTAAAACCTGTG 57.278 33.333 0.00 0.00 0.00 3.66
2697 10774 9.461312 TTCATTATAACTAAAACCTGTGCTGAT 57.539 29.630 0.00 0.00 0.00 2.90
2702 10779 1.839424 AAAACCTGTGCTGATAGGCC 58.161 50.000 0.00 0.00 37.61 5.19
2726 10803 1.954382 GAAAGGTTTGTCAGGTCCCAC 59.046 52.381 0.00 0.00 0.00 4.61
2746 10823 0.980423 GCTGGGTTCCTCTTGAGACT 59.020 55.000 0.00 0.00 0.00 3.24
2749 10826 3.406764 CTGGGTTCCTCTTGAGACTTTG 58.593 50.000 0.00 0.00 0.00 2.77
2750 10827 2.777692 TGGGTTCCTCTTGAGACTTTGT 59.222 45.455 0.00 0.00 0.00 2.83
2757 10834 3.748568 CCTCTTGAGACTTTGTAACTGCC 59.251 47.826 0.00 0.00 0.00 4.85
2761 10838 1.807142 GAGACTTTGTAACTGCCAGGC 59.193 52.381 3.66 3.66 0.00 4.85
2769 10846 2.094675 GTAACTGCCAGGCATGTTCAT 58.905 47.619 24.28 10.57 38.13 2.57
2770 10847 1.636148 AACTGCCAGGCATGTTCATT 58.364 45.000 16.64 0.00 38.13 2.57
2779 10856 4.021719 CCAGGCATGTTCATTTTTCTCTGT 60.022 41.667 0.00 0.00 0.00 3.41
2782 10859 5.069516 AGGCATGTTCATTTTTCTCTGTTGT 59.930 36.000 0.00 0.00 0.00 3.32
2784 10861 6.292488 GGCATGTTCATTTTTCTCTGTTGTTG 60.292 38.462 0.00 0.00 0.00 3.33
2806 10894 5.636123 TGCTGTCCACTAAGGGAAATTTTA 58.364 37.500 0.00 0.00 39.05 1.52
2808 10896 7.406916 TGCTGTCCACTAAGGGAAATTTTATA 58.593 34.615 0.00 0.00 39.05 0.98
2837 10925 2.224137 TGTCTCAAGCAGAGGACAACAG 60.224 50.000 6.38 0.00 44.81 3.16
2863 10955 1.171308 ATGGCAGTGCAGCTGTAAAG 58.829 50.000 18.61 7.96 46.64 1.85
2871 10963 3.826157 AGTGCAGCTGTAAAGGCAATTTA 59.174 39.130 16.64 0.00 38.10 1.40
2899 10999 6.328672 AGCTCCCTCTCATCAGTTGTATTATT 59.671 38.462 0.00 0.00 0.00 1.40
2902 11002 6.615316 TCCCTCTCATCAGTTGTATTATTCCA 59.385 38.462 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.219469 TGTCCTTCTCGGATATGGGGA 59.781 52.381 0.00 0.00 45.44 4.81
12 13 2.434336 TGGTTGTCCTTCTCGGATATGG 59.566 50.000 0.00 0.00 45.44 2.74
13 14 3.819564 TGGTTGTCCTTCTCGGATATG 57.180 47.619 0.00 0.00 45.44 1.78
19 20 1.734465 GAAGCATGGTTGTCCTTCTCG 59.266 52.381 16.18 0.00 34.23 4.04
22 23 2.352127 GCAAGAAGCATGGTTGTCCTTC 60.352 50.000 16.18 7.59 44.79 3.46
54 55 3.068881 CTTCTCGGGGAGGCACAA 58.931 61.111 0.00 0.00 0.00 3.33
64 65 2.611225 AGCCTAGATTTGCTTCTCGG 57.389 50.000 0.00 0.00 32.94 4.63
133 4383 8.276325 GGATAAGCACATATTTACTTTCACGAG 58.724 37.037 0.00 0.00 0.00 4.18
148 4398 5.664294 TTTTGCATTCAGGATAAGCACAT 57.336 34.783 0.00 0.00 34.56 3.21
149 4399 5.465532 TTTTTGCATTCAGGATAAGCACA 57.534 34.783 0.00 0.00 34.56 4.57
192 4442 5.163343 GGTAGGAACACAACTATGCATCCTA 60.163 44.000 0.19 2.23 37.38 2.94
194 4444 3.877508 GGTAGGAACACAACTATGCATCC 59.122 47.826 0.19 0.00 0.00 3.51
197 4447 3.580895 TCTGGTAGGAACACAACTATGCA 59.419 43.478 0.00 0.00 0.00 3.96
245 4495 4.034626 TGTGTCACGTGGTACAGATTTTTG 59.965 41.667 17.00 0.00 41.80 2.44
298 4548 6.604396 TCCATGAGATGCACAGATTTATTTGT 59.396 34.615 0.00 0.00 0.00 2.83
299 4549 7.034685 TCCATGAGATGCACAGATTTATTTG 57.965 36.000 0.00 0.00 0.00 2.32
300 4550 7.558807 TCTTCCATGAGATGCACAGATTTATTT 59.441 33.333 0.00 0.00 0.00 1.40
301 4551 7.058525 TCTTCCATGAGATGCACAGATTTATT 58.941 34.615 0.00 0.00 0.00 1.40
302 4552 6.598503 TCTTCCATGAGATGCACAGATTTAT 58.401 36.000 0.00 0.00 0.00 1.40
303 4553 5.993055 TCTTCCATGAGATGCACAGATTTA 58.007 37.500 0.00 0.00 0.00 1.40
304 4554 4.851843 TCTTCCATGAGATGCACAGATTT 58.148 39.130 0.00 0.00 0.00 2.17
354 4605 6.153170 TCGATAAGTAACACCATCCAACTGTA 59.847 38.462 0.00 0.00 0.00 2.74
356 4607 5.291128 GTCGATAAGTAACACCATCCAACTG 59.709 44.000 0.00 0.00 0.00 3.16
396 4647 2.039216 ACCCCGTCAATGTAATGTGTCA 59.961 45.455 0.00 0.00 0.00 3.58
411 4662 1.354101 TGTCAATCCAACTACCCCGT 58.646 50.000 0.00 0.00 0.00 5.28
413 4664 2.024414 GCATGTCAATCCAACTACCCC 58.976 52.381 0.00 0.00 0.00 4.95
447 4698 1.302907 AAGGGGCAGATCCAACTGAT 58.697 50.000 0.00 0.00 39.94 2.90
449 4700 1.180029 CAAAGGGGCAGATCCAACTG 58.820 55.000 0.00 0.00 40.43 3.16
509 4768 7.838771 AAAGTAGTACAAAGAAACGTGAACT 57.161 32.000 2.52 0.00 0.00 3.01
518 4777 8.556213 ACAAGTGACAAAAGTAGTACAAAGAA 57.444 30.769 2.52 0.00 0.00 2.52
553 4834 9.868277 TTGTATTGGACCATTATGAACAAATTC 57.132 29.630 0.00 0.00 35.18 2.17
558 4839 8.811017 ACAAATTGTATTGGACCATTATGAACA 58.189 29.630 0.00 0.00 34.56 3.18
561 4842 8.629158 GCTACAAATTGTATTGGACCATTATGA 58.371 33.333 6.27 0.00 31.66 2.15
640 4932 2.338577 ATCTTCAGCCGGAAATCCTG 57.661 50.000 5.05 1.86 34.44 3.86
652 4944 6.258287 CCTAACTTCTCATCAGCAATCTTCAG 59.742 42.308 0.00 0.00 0.00 3.02
705 4997 3.503363 ACGTACAGTTCGTGGTCTATTCA 59.497 43.478 4.19 0.00 40.07 2.57
718 5010 8.569641 TCAAAAATATTTAAGGCACGTACAGTT 58.430 29.630 0.01 0.00 0.00 3.16
720 5012 8.958175 TTCAAAAATATTTAAGGCACGTACAG 57.042 30.769 0.01 0.00 0.00 2.74
725 5017 8.107564 CGGATTTTCAAAAATATTTAAGGCACG 58.892 33.333 0.01 0.00 38.64 5.34
836 6881 3.242155 CGTCGTGAACTTTGCAGTACAAA 60.242 43.478 0.00 0.00 46.01 2.83
840 6885 2.390938 CTCGTCGTGAACTTTGCAGTA 58.609 47.619 0.00 0.00 30.68 2.74
846 6891 2.884894 AGAACCTCGTCGTGAACTTT 57.115 45.000 0.00 0.00 0.00 2.66
849 6894 2.052157 CAGAAGAACCTCGTCGTGAAC 58.948 52.381 0.00 0.00 30.11 3.18
856 6901 0.472471 TTTGCCCAGAAGAACCTCGT 59.528 50.000 0.00 0.00 0.00 4.18
857 6902 1.537202 CTTTTGCCCAGAAGAACCTCG 59.463 52.381 0.00 0.00 0.00 4.63
873 6918 0.831711 ATGAAACGGGCTGGGCTTTT 60.832 50.000 0.00 0.00 0.00 2.27
886 6931 2.290641 GTGCCGTATGGATGGATGAAAC 59.709 50.000 4.73 0.00 37.49 2.78
892 6937 0.317160 GATCGTGCCGTATGGATGGA 59.683 55.000 4.73 0.00 37.49 3.41
893 6938 0.670546 GGATCGTGCCGTATGGATGG 60.671 60.000 4.73 0.00 37.49 3.51
894 6939 0.318441 AGGATCGTGCCGTATGGATG 59.682 55.000 4.73 0.00 37.49 3.51
895 6940 0.318441 CAGGATCGTGCCGTATGGAT 59.682 55.000 4.73 0.00 37.49 3.41
896 6941 1.739667 CAGGATCGTGCCGTATGGA 59.260 57.895 4.73 0.00 37.49 3.41
897 6942 1.300931 CCAGGATCGTGCCGTATGG 60.301 63.158 9.95 0.00 38.77 2.74
899 6944 2.507854 CCCCAGGATCGTGCCGTAT 61.508 63.158 9.95 0.00 0.00 3.06
900 6945 3.151710 CCCCAGGATCGTGCCGTA 61.152 66.667 9.95 0.00 0.00 4.02
903 6948 4.554036 GAGCCCCAGGATCGTGCC 62.554 72.222 9.95 1.03 0.00 5.01
904 6949 2.615227 AATGAGCCCCAGGATCGTGC 62.615 60.000 9.95 0.00 41.58 5.34
905 6950 0.107017 AAATGAGCCCCAGGATCGTG 60.107 55.000 8.47 8.47 41.58 4.35
906 6951 0.181350 GAAATGAGCCCCAGGATCGT 59.819 55.000 0.00 0.00 41.58 3.73
907 6952 0.536006 GGAAATGAGCCCCAGGATCG 60.536 60.000 0.00 0.00 41.58 3.69
908 6953 0.552848 TGGAAATGAGCCCCAGGATC 59.447 55.000 0.00 0.00 38.78 3.36
910 6955 1.009997 AATGGAAATGAGCCCCAGGA 58.990 50.000 0.00 0.00 32.90 3.86
911 6956 1.406903 GAATGGAAATGAGCCCCAGG 58.593 55.000 0.00 0.00 32.90 4.45
912 6957 1.063417 AGGAATGGAAATGAGCCCCAG 60.063 52.381 0.00 0.00 32.90 4.45
915 6960 3.425659 GGATAGGAATGGAAATGAGCCC 58.574 50.000 0.00 0.00 0.00 5.19
916 6961 3.425659 GGGATAGGAATGGAAATGAGCC 58.574 50.000 0.00 0.00 0.00 4.70
918 6963 4.401925 GTGGGGATAGGAATGGAAATGAG 58.598 47.826 0.00 0.00 0.00 2.90
919 6964 3.181445 CGTGGGGATAGGAATGGAAATGA 60.181 47.826 0.00 0.00 0.00 2.57
920 6965 3.149196 CGTGGGGATAGGAATGGAAATG 58.851 50.000 0.00 0.00 0.00 2.32
921 6966 3.053077 TCGTGGGGATAGGAATGGAAAT 58.947 45.455 0.00 0.00 0.00 2.17
922 6967 2.438021 CTCGTGGGGATAGGAATGGAAA 59.562 50.000 0.00 0.00 0.00 3.13
923 6968 2.047061 CTCGTGGGGATAGGAATGGAA 58.953 52.381 0.00 0.00 0.00 3.53
925 6970 1.717032 TCTCGTGGGGATAGGAATGG 58.283 55.000 0.00 0.00 0.00 3.16
928 6973 1.492764 GGTTCTCGTGGGGATAGGAA 58.507 55.000 0.00 0.00 0.00 3.36
930 6975 1.408453 GGGGTTCTCGTGGGGATAGG 61.408 65.000 0.00 0.00 0.00 2.57
931 6976 0.689745 TGGGGTTCTCGTGGGGATAG 60.690 60.000 0.00 0.00 0.00 2.08
933 6978 1.137594 TTTGGGGTTCTCGTGGGGAT 61.138 55.000 0.00 0.00 0.00 3.85
934 6979 1.137594 ATTTGGGGTTCTCGTGGGGA 61.138 55.000 0.00 0.00 0.00 4.81
935 6980 0.679960 GATTTGGGGTTCTCGTGGGG 60.680 60.000 0.00 0.00 0.00 4.96
936 6981 0.679960 GGATTTGGGGTTCTCGTGGG 60.680 60.000 0.00 0.00 0.00 4.61
937 6982 0.679960 GGGATTTGGGGTTCTCGTGG 60.680 60.000 0.00 0.00 0.00 4.94
938 6983 0.679960 GGGGATTTGGGGTTCTCGTG 60.680 60.000 0.00 0.00 0.00 4.35
940 6985 1.451387 CGGGGATTTGGGGTTCTCG 60.451 63.158 0.00 0.00 0.00 4.04
941 6986 1.753078 GCGGGGATTTGGGGTTCTC 60.753 63.158 0.00 0.00 0.00 2.87
942 6987 2.359011 GCGGGGATTTGGGGTTCT 59.641 61.111 0.00 0.00 0.00 3.01
943 6988 2.758327 GGCGGGGATTTGGGGTTC 60.758 66.667 0.00 0.00 0.00 3.62
944 6989 4.751820 CGGCGGGGATTTGGGGTT 62.752 66.667 0.00 0.00 0.00 4.11
1041 7086 1.039068 CGACCTCATCTGGCAGATCT 58.961 55.000 26.62 5.84 31.32 2.75
1043 7088 0.749649 GACGACCTCATCTGGCAGAT 59.250 55.000 24.01 24.01 34.74 2.90
1062 7107 0.965439 GGACGAGGATCTCCCAGATG 59.035 60.000 0.00 0.00 34.53 2.90
1092 7137 1.524849 GCAGCGGAGGAGGGATTTC 60.525 63.158 0.00 0.00 0.00 2.17
1275 7341 1.302351 ACGAGAGAACGGGTCGTCT 60.302 57.895 0.00 0.00 43.19 4.18
1282 7348 1.803943 CCTCCAGACGAGAGAACGG 59.196 63.158 0.00 0.00 41.63 4.44
1333 7399 6.773200 CAGATGGAGAAGTAGGTAGTGTCATA 59.227 42.308 0.00 0.00 0.00 2.15
1339 7405 5.892686 GGTTACAGATGGAGAAGTAGGTAGT 59.107 44.000 0.00 0.00 0.00 2.73
1341 7407 5.206587 GGGTTACAGATGGAGAAGTAGGTA 58.793 45.833 0.00 0.00 0.00 3.08
1450 7526 6.128634 GGATTTTCGTCGTACAACAGAATTCT 60.129 38.462 0.88 0.88 0.00 2.40
1467 7543 3.179048 GCCGGATTTTTCAGGATTTTCG 58.821 45.455 5.05 0.00 0.00 3.46
1476 7552 1.065401 GCATCATCGCCGGATTTTTCA 59.935 47.619 5.05 0.00 0.00 2.69
1488 7564 2.452295 AGATGTAGCAGGCATCATCG 57.548 50.000 16.63 0.00 43.66 3.84
1511 7587 3.713650 GCTGGACAGAGCCCACTA 58.286 61.111 3.00 0.00 32.35 2.74
1530 7606 1.983224 CCACCTGATGTTCCTCGGT 59.017 57.895 0.00 0.00 0.00 4.69
1561 7637 2.125269 GCCGTAACACGCATCCCT 60.125 61.111 0.00 0.00 40.91 4.20
1599 7675 4.440127 CAATGCAGGTTGCCCCGC 62.440 66.667 0.00 0.00 44.23 6.13
1602 7678 1.880819 CTGACCAATGCAGGTTGCCC 61.881 60.000 0.00 0.00 44.23 5.36
1624 7940 1.886655 GCTTCCAACCTCAACCGGATT 60.887 52.381 9.46 0.00 0.00 3.01
1649 7965 6.757010 AGCTGTCGTATCAAAAACCACTATAG 59.243 38.462 0.00 0.00 0.00 1.31
1709 8025 3.734463 TGATTGTAGCAAGGAACGAACA 58.266 40.909 0.00 0.00 0.00 3.18
1710 8026 4.631813 AGATGATTGTAGCAAGGAACGAAC 59.368 41.667 0.00 0.00 0.00 3.95
1731 8047 3.503363 GCACACCATCAATCTCAAACAGA 59.497 43.478 0.00 0.00 34.78 3.41
1774 8090 6.529477 CAGATATTGATGGTAGTCGCAGTATG 59.471 42.308 0.00 0.00 40.87 2.39
1777 8093 4.262207 CCAGATATTGATGGTAGTCGCAGT 60.262 45.833 0.00 0.00 0.00 4.40
1821 8137 3.128349 GCACTTTAAGGTCGTGACTTCA 58.872 45.455 0.00 0.00 0.00 3.02
1828 8144 3.074412 CAATCCTGCACTTTAAGGTCGT 58.926 45.455 0.00 0.00 34.94 4.34
1829 8145 3.334691 TCAATCCTGCACTTTAAGGTCG 58.665 45.455 0.00 0.00 34.94 4.79
1844 8160 7.095857 CGATCTCAGTAACTAGCAAATCAATCC 60.096 40.741 0.00 0.00 0.00 3.01
1851 8167 4.098044 CCCTCGATCTCAGTAACTAGCAAA 59.902 45.833 0.00 0.00 0.00 3.68
1856 8172 2.175069 AGCCCCTCGATCTCAGTAACTA 59.825 50.000 0.00 0.00 0.00 2.24
1915 8234 1.962807 CAAGTCACCATTTCCAGGCAA 59.037 47.619 0.00 0.00 0.00 4.52
1959 8281 5.237127 TGAGCTTCAATTGTGTTGTAGACAG 59.763 40.000 5.13 0.00 39.39 3.51
1962 8284 5.277974 GCTTGAGCTTCAATTGTGTTGTAGA 60.278 40.000 5.13 0.00 35.59 2.59
1967 8289 4.389890 TTGCTTGAGCTTCAATTGTGTT 57.610 36.364 5.13 0.00 42.66 3.32
2001 8381 5.476599 CACCTTGTGTTGGAAAGAATGGATA 59.523 40.000 0.00 0.00 0.00 2.59
2006 8386 3.642141 ACCACCTTGTGTTGGAAAGAAT 58.358 40.909 0.00 0.00 0.00 2.40
2010 8390 3.292460 CCTTACCACCTTGTGTTGGAAA 58.708 45.455 0.00 0.00 0.00 3.13
2013 8393 2.358322 ACCTTACCACCTTGTGTTGG 57.642 50.000 0.00 0.00 0.00 3.77
2047 8428 3.069586 ACACAACGGTCTTCAGATTGAGA 59.930 43.478 0.00 0.00 0.00 3.27
2050 8431 2.872245 ACACACAACGGTCTTCAGATTG 59.128 45.455 0.00 0.00 0.00 2.67
2067 8448 0.673956 TTTATAAGCGCCGGCACACA 60.674 50.000 28.98 9.03 43.41 3.72
2082 8463 7.720957 TGCAGATACAAACATCTAGGCATTTAT 59.279 33.333 0.00 0.00 32.20 1.40
2197 8578 2.279741 TGCATTCGACCAGATAACAGC 58.720 47.619 0.00 0.00 0.00 4.40
2205 8586 5.163723 ACAAACATAGATTGCATTCGACCAG 60.164 40.000 3.08 0.00 0.00 4.00
2212 8593 7.171337 GGTGTCAAAACAAACATAGATTGCATT 59.829 33.333 0.00 0.00 37.08 3.56
2220 8601 5.068460 TGGAAGGGTGTCAAAACAAACATAG 59.932 40.000 0.00 0.00 37.08 2.23
2225 8606 4.285863 AGATGGAAGGGTGTCAAAACAAA 58.714 39.130 0.00 0.00 37.08 2.83
2263 8644 6.893958 AACAAACATAGATAACAGCGAGAG 57.106 37.500 0.00 0.00 0.00 3.20
2264 8645 8.194769 TCATAACAAACATAGATAACAGCGAGA 58.805 33.333 0.00 0.00 0.00 4.04
2265 8646 8.352752 TCATAACAAACATAGATAACAGCGAG 57.647 34.615 0.00 0.00 0.00 5.03
2267 8648 8.352752 TCTCATAACAAACATAGATAACAGCG 57.647 34.615 0.00 0.00 0.00 5.18
2278 8659 9.480053 CCAAAATGACTTTCTCATAACAAACAT 57.520 29.630 0.00 0.00 38.82 2.71
2280 8661 8.871686 ACCAAAATGACTTTCTCATAACAAAC 57.128 30.769 0.00 0.00 38.82 2.93
2281 8662 8.690884 TGACCAAAATGACTTTCTCATAACAAA 58.309 29.630 0.00 0.00 38.82 2.83
2282 8663 8.231692 TGACCAAAATGACTTTCTCATAACAA 57.768 30.769 0.00 0.00 38.82 2.83
2283 8664 7.815840 TGACCAAAATGACTTTCTCATAACA 57.184 32.000 0.00 0.00 38.82 2.41
2284 8665 9.132521 CAATGACCAAAATGACTTTCTCATAAC 57.867 33.333 0.00 0.00 38.82 1.89
2286 8667 7.451255 ACCAATGACCAAAATGACTTTCTCATA 59.549 33.333 0.00 0.00 38.82 2.15
2287 8668 6.268387 ACCAATGACCAAAATGACTTTCTCAT 59.732 34.615 0.00 0.00 41.85 2.90
2288 8669 5.598005 ACCAATGACCAAAATGACTTTCTCA 59.402 36.000 0.00 0.00 0.00 3.27
2289 8670 6.089249 ACCAATGACCAAAATGACTTTCTC 57.911 37.500 0.00 0.00 0.00 2.87
2290 8671 5.598005 TGACCAATGACCAAAATGACTTTCT 59.402 36.000 0.00 0.00 0.00 2.52
2291 8672 5.841810 TGACCAATGACCAAAATGACTTTC 58.158 37.500 0.00 0.00 0.00 2.62
2292 8673 5.363580 ACTGACCAATGACCAAAATGACTTT 59.636 36.000 0.00 0.00 0.00 2.66
2303 8684 2.163818 TCAACGACTGACCAATGACC 57.836 50.000 0.00 0.00 0.00 4.02
2304 8685 3.131396 ACTTCAACGACTGACCAATGAC 58.869 45.455 0.00 0.00 32.21 3.06
2306 8687 5.862924 AATACTTCAACGACTGACCAATG 57.137 39.130 0.00 0.00 32.21 2.82
2307 8688 5.181245 CCAAATACTTCAACGACTGACCAAT 59.819 40.000 0.00 0.00 32.21 3.16
2314 10046 3.689649 GGCATCCAAATACTTCAACGACT 59.310 43.478 0.00 0.00 0.00 4.18
2330 10062 3.565307 TGGGACAGATTAATTGGCATCC 58.435 45.455 0.00 0.00 0.00 3.51
2349 10081 5.702670 TCAGTTAAGAAAAGCAGAGACATGG 59.297 40.000 0.00 0.00 0.00 3.66
2360 10092 6.149129 AGGCCAAGTTTCAGTTAAGAAAAG 57.851 37.500 5.01 0.00 39.05 2.27
2366 10098 6.263617 ACGATAAAAGGCCAAGTTTCAGTTAA 59.736 34.615 5.01 0.00 0.00 2.01
2394 10190 6.393171 GGATCATCTCCAAAGAAAAACAAGG 58.607 40.000 0.00 0.00 44.26 3.61
2442 10238 8.850156 AGACAAATAAACCAATGTATCTATGCC 58.150 33.333 0.00 0.00 0.00 4.40
2462 10488 9.997482 GACAACTACATCAAAAGTTTAGACAAA 57.003 29.630 0.00 0.00 33.72 2.83
2464 10490 7.707464 TCGACAACTACATCAAAAGTTTAGACA 59.293 33.333 0.00 0.00 33.72 3.41
2468 10519 8.596271 TCATCGACAACTACATCAAAAGTTTA 57.404 30.769 0.00 0.00 33.72 2.01
2469 10520 7.490962 TCATCGACAACTACATCAAAAGTTT 57.509 32.000 0.00 0.00 33.72 2.66
2478 10529 6.238103 CGCCTTAATTTCATCGACAACTACAT 60.238 38.462 0.00 0.00 0.00 2.29
2484 10535 3.601435 TCCGCCTTAATTTCATCGACAA 58.399 40.909 0.00 0.00 0.00 3.18
2487 10538 5.642063 GGATAATCCGCCTTAATTTCATCGA 59.358 40.000 0.00 0.00 0.00 3.59
2503 10554 4.336713 GCTGGTCAACAAAGAGGATAATCC 59.663 45.833 0.00 0.00 36.58 3.01
2530 10581 8.866956 GGATTCATGACTAAAAATCTTTTGCTG 58.133 33.333 0.00 0.00 0.00 4.41
2531 10582 8.587608 TGGATTCATGACTAAAAATCTTTTGCT 58.412 29.630 0.00 0.00 0.00 3.91
2537 10588 8.070034 TGCAATGGATTCATGACTAAAAATCT 57.930 30.769 0.00 0.00 33.18 2.40
2563 10614 4.584327 AACATTTCAACACCTAACCAGC 57.416 40.909 0.00 0.00 0.00 4.85
2567 10618 8.512138 ACTATAGCAAACATTTCAACACCTAAC 58.488 33.333 0.00 0.00 0.00 2.34
2586 10637 4.319549 GCAACATAAAGGCGGAACTATAGC 60.320 45.833 0.00 0.00 0.00 2.97
2587 10638 4.814234 TGCAACATAAAGGCGGAACTATAG 59.186 41.667 0.00 0.00 0.00 1.31
2588 10639 4.771903 TGCAACATAAAGGCGGAACTATA 58.228 39.130 0.00 0.00 0.00 1.31
2589 10640 3.616219 TGCAACATAAAGGCGGAACTAT 58.384 40.909 0.00 0.00 0.00 2.12
2590 10641 3.060736 TGCAACATAAAGGCGGAACTA 57.939 42.857 0.00 0.00 0.00 2.24
2591 10642 1.904287 TGCAACATAAAGGCGGAACT 58.096 45.000 0.00 0.00 0.00 3.01
2592 10643 2.791158 CGATGCAACATAAAGGCGGAAC 60.791 50.000 0.00 0.00 0.00 3.62
2593 10644 1.400142 CGATGCAACATAAAGGCGGAA 59.600 47.619 0.00 0.00 0.00 4.30
2594 10645 1.013596 CGATGCAACATAAAGGCGGA 58.986 50.000 0.00 0.00 0.00 5.54
2595 10646 0.732571 ACGATGCAACATAAAGGCGG 59.267 50.000 0.00 0.00 0.00 6.13
2596 10647 2.176369 CAACGATGCAACATAAAGGCG 58.824 47.619 0.00 0.00 0.00 5.52
2603 10654 1.851304 AATCCCCAACGATGCAACAT 58.149 45.000 0.00 0.00 0.00 2.71
2612 10663 0.811281 GGCAGAGAAAATCCCCAACG 59.189 55.000 0.00 0.00 0.00 4.10
2619 10670 5.911378 AAGGAGAAATGGCAGAGAAAATC 57.089 39.130 0.00 0.00 0.00 2.17
2623 10674 3.521126 AGCTAAGGAGAAATGGCAGAGAA 59.479 43.478 0.00 0.00 0.00 2.87
2630 10681 4.574013 CAGTTAGCAGCTAAGGAGAAATGG 59.426 45.833 15.55 0.00 0.00 3.16
2639 10690 7.173390 AGTTCCTTTAAACAGTTAGCAGCTAAG 59.827 37.037 15.55 7.45 0.00 2.18
2652 10703 6.899393 ATGAAGCATCAGTTCCTTTAAACA 57.101 33.333 0.00 0.00 39.39 2.83
2657 10708 8.814038 AGTTATAATGAAGCATCAGTTCCTTT 57.186 30.769 0.00 0.00 39.39 3.11
2664 10715 9.941664 CAGGTTTTAGTTATAATGAAGCATCAG 57.058 33.333 0.00 0.00 39.39 2.90
2676 10727 6.990349 GCCTATCAGCACAGGTTTTAGTTATA 59.010 38.462 0.00 0.00 34.18 0.98
2677 10728 5.823045 GCCTATCAGCACAGGTTTTAGTTAT 59.177 40.000 0.00 0.00 34.18 1.89
2678 10729 5.183228 GCCTATCAGCACAGGTTTTAGTTA 58.817 41.667 0.00 0.00 34.18 2.24
2685 10762 1.221840 CGGCCTATCAGCACAGGTT 59.778 57.895 0.00 0.00 34.18 3.50
2687 10764 0.531532 CTTCGGCCTATCAGCACAGG 60.532 60.000 0.00 0.00 34.85 4.00
2692 10769 1.134371 ACCTTTCTTCGGCCTATCAGC 60.134 52.381 0.00 0.00 0.00 4.26
2697 10774 2.105134 TGACAAACCTTTCTTCGGCCTA 59.895 45.455 0.00 0.00 0.00 3.93
2698 10775 1.133915 TGACAAACCTTTCTTCGGCCT 60.134 47.619 0.00 0.00 0.00 5.19
2702 10779 2.548480 GGACCTGACAAACCTTTCTTCG 59.452 50.000 0.00 0.00 0.00 3.79
2726 10803 0.390472 GTCTCAAGAGGAACCCAGCG 60.390 60.000 0.00 0.00 0.00 5.18
2746 10823 1.993956 ACATGCCTGGCAGTTACAAA 58.006 45.000 27.20 0.00 43.65 2.83
2749 10826 1.533625 TGAACATGCCTGGCAGTTAC 58.466 50.000 27.20 20.14 43.65 2.50
2750 10827 2.512692 ATGAACATGCCTGGCAGTTA 57.487 45.000 27.20 16.94 43.65 2.24
2757 10834 5.130292 ACAGAGAAAAATGAACATGCCTG 57.870 39.130 0.00 0.00 0.00 4.85
2761 10838 6.477688 AGCAACAACAGAGAAAAATGAACATG 59.522 34.615 0.00 0.00 0.00 3.21
2769 10846 3.761218 TGGACAGCAACAACAGAGAAAAA 59.239 39.130 0.00 0.00 0.00 1.94
2770 10847 3.128589 GTGGACAGCAACAACAGAGAAAA 59.871 43.478 0.00 0.00 0.00 2.29
2779 10856 1.771854 TCCCTTAGTGGACAGCAACAA 59.228 47.619 0.00 0.00 38.35 2.83
2782 10859 3.806949 ATTTCCCTTAGTGGACAGCAA 57.193 42.857 0.00 0.00 38.35 3.91
2784 10861 6.775594 ATAAAATTTCCCTTAGTGGACAGC 57.224 37.500 0.00 0.00 38.35 4.40
2806 10894 5.474578 TCTGCTTGAGACAAGACAAGTAT 57.525 39.130 14.44 0.00 43.41 2.12
2808 10896 3.494048 CCTCTGCTTGAGACAAGACAAGT 60.494 47.826 14.44 0.00 45.39 3.16
2837 10925 0.039437 GCTGCACTGCCATATGATGC 60.039 55.000 3.65 8.98 36.81 3.91
2863 10955 3.763897 TGAGAGGGAGCTTTTAAATTGCC 59.236 43.478 9.25 4.36 0.00 4.52
2871 10963 3.073650 ACAACTGATGAGAGGGAGCTTTT 59.926 43.478 0.00 0.00 0.00 2.27
2899 10999 2.567169 ACGACAGTCATCCTTCAATGGA 59.433 45.455 0.41 0.00 40.82 3.41
2902 11002 3.189287 GCAAACGACAGTCATCCTTCAAT 59.811 43.478 0.41 0.00 0.00 2.57
2908 11008 2.668457 CAGTAGCAAACGACAGTCATCC 59.332 50.000 0.41 0.00 0.00 3.51
2934 11035 5.192923 TGCCCCTGTACTGGAAAATAATACT 59.807 40.000 19.66 0.00 0.00 2.12
2942 11043 1.145571 AACTGCCCCTGTACTGGAAA 58.854 50.000 19.66 4.44 0.00 3.13


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

AutoCloner maintained by Alex Coulton.