Multiple sequence alignment - TraesCS5D01G039500

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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 TraesCS5D01G039500 chr5D 100.000 8113 0 0 1 8113 40759490 40767602 0.000000e+00 14982.0
1 TraesCS5D01G039500 chr5D 80.790 557 102 4 200 756 40724823 40725374 1.620000e-116 431.0
2 TraesCS5D01G039500 chr5D 86.968 376 35 6 1040 1402 40889005 40889379 2.110000e-110 411.0
3 TraesCS5D01G039500 chr5D 84.252 381 46 10 7371 7748 40783727 40784096 7.740000e-95 359.0
4 TraesCS5D01G039500 chr5D 83.516 364 29 11 6652 7007 40889656 40889996 2.200000e-80 311.0
5 TraesCS5D01G039500 chr5D 83.815 173 22 6 7576 7748 40746275 40746441 8.430000e-35 159.0
6 TraesCS5D01G039500 chr5D 88.393 112 12 1 7249 7359 40906775 40906886 5.110000e-27 134.0
7 TraesCS5D01G039500 chr5D 94.048 84 5 0 6652 6735 40746180 40746263 2.380000e-25 128.0
8 TraesCS5D01G039500 chr4A 94.731 5162 245 16 1413 6551 132699722 132694565 0.000000e+00 8000.0
9 TraesCS5D01G039500 chr1A 94.721 5134 250 10 1438 6551 262931016 262936148 0.000000e+00 7960.0
10 TraesCS5D01G039500 chr3A 94.438 5178 250 21 1402 6551 73297 78464 0.000000e+00 7932.0
11 TraesCS5D01G039500 chr3A 94.636 4847 241 10 1402 6229 719780074 719784920 0.000000e+00 7492.0
12 TraesCS5D01G039500 chr3A 94.954 218 10 1 6335 6551 719780074 719780291 2.800000e-89 340.0
13 TraesCS5D01G039500 chr3A 92.202 218 15 2 6335 6551 23904 24120 2.840000e-79 307.0
14 TraesCS5D01G039500 chr3A 92.202 218 15 2 6335 6551 73297 73513 2.840000e-79 307.0
15 TraesCS5D01G039500 chr3A 91.284 218 17 2 6335 6551 1217 1433 6.160000e-76 296.0
16 TraesCS5D01G039500 chr3A 82.895 76 13 0 1 76 653960462 653960387 1.460000e-07 69.4
17 TraesCS5D01G039500 chr5B 94.443 5147 262 13 1426 6551 2563992 2569135 0.000000e+00 7899.0
18 TraesCS5D01G039500 chr5B 89.105 927 57 15 6552 7466 34544915 34545809 0.000000e+00 1112.0
19 TraesCS5D01G039500 chr5B 90.947 729 42 11 6925 7639 34566689 34567407 0.000000e+00 959.0
20 TraesCS5D01G039500 chr5B 90.059 674 43 11 744 1402 34544256 34544920 0.000000e+00 852.0
21 TraesCS5D01G039500 chr5B 86.310 767 71 14 644 1402 34554635 34555375 0.000000e+00 804.0
22 TraesCS5D01G039500 chr5B 91.929 508 23 7 6925 7425 34555982 34556478 0.000000e+00 695.0
23 TraesCS5D01G039500 chr5B 82.940 762 75 26 644 1402 34565372 34566081 3.190000e-178 636.0
24 TraesCS5D01G039500 chr5B 95.393 369 12 2 6652 7015 34566372 34566740 4.220000e-162 582.0
25 TraesCS5D01G039500 chr5B 87.234 517 47 2 200 716 34543762 34544259 9.130000e-159 571.0
26 TraesCS5D01G039500 chr5B 94.851 369 11 3 6652 7015 34555665 34556030 3.290000e-158 569.0
27 TraesCS5D01G039500 chr5B 78.766 551 108 8 200 748 34287847 34288390 2.150000e-95 361.0
28 TraesCS5D01G039500 chr5B 85.987 314 30 8 981 1293 34608823 34609123 2.820000e-84 324.0
29 TraesCS5D01G039500 chr5B 84.407 295 25 11 881 1167 34288739 34289020 3.730000e-68 270.0
30 TraesCS5D01G039500 chr5B 85.922 206 29 0 1 206 34543515 34543720 3.810000e-53 220.0
31 TraesCS5D01G039500 chr5B 84.444 225 28 5 7517 7741 34547299 34547516 1.770000e-51 215.0
32 TraesCS5D01G039500 chr5B 83.556 225 26 5 6763 6977 34606881 34607104 4.970000e-47 200.0
33 TraesCS5D01G039500 chr5B 88.957 163 15 3 818 977 34607433 34607595 1.790000e-46 198.0
34 TraesCS5D01G039500 chr5B 82.081 173 25 6 7576 7748 34486655 34486821 8.490000e-30 143.0
35 TraesCS5D01G039500 chr7A 94.237 5171 276 13 1401 6551 24210356 24215524 0.000000e+00 7878.0
36 TraesCS5D01G039500 chr7A 92.884 4595 286 18 1432 6007 651789262 651784690 0.000000e+00 6636.0
37 TraesCS5D01G039500 chr7A 94.124 3795 208 8 2771 6551 24026216 24030009 0.000000e+00 5758.0
38 TraesCS5D01G039500 chr7A 94.954 218 10 1 1402 1618 23850674 23850891 2.800000e-89 340.0
39 TraesCS5D01G039500 chr7A 95.714 210 8 1 1410 1618 24215315 24215524 3.630000e-88 337.0
40 TraesCS5D01G039500 chr7A 74.044 366 70 14 387 739 54725460 54725107 8.550000e-25 126.0
41 TraesCS5D01G039500 chr1D 96.453 4764 141 10 1410 6158 423677493 423682243 0.000000e+00 7836.0
42 TraesCS5D01G039500 chr2A 94.345 5040 227 24 1537 6551 27973666 27978672 0.000000e+00 7675.0
43 TraesCS5D01G039500 chr5A 89.940 1491 110 17 6652 8108 28905935 28907419 0.000000e+00 1886.0
44 TraesCS5D01G039500 chr5A 92.672 1078 66 5 200 1269 28904477 28905549 0.000000e+00 1541.0
45 TraesCS5D01G039500 chr5A 94.175 206 12 0 1 206 28904230 28904435 1.700000e-81 315.0
46 TraesCS5D01G039500 chr5A 83.582 201 31 2 3 202 28756928 28757127 3.870000e-43 187.0
47 TraesCS5D01G039500 chr5A 92.857 84 6 0 6652 6735 28823179 28823262 1.110000e-23 122.0
48 TraesCS5D01G039500 chr5A 91.781 73 3 3 7475 7546 29123497 29123567 1.860000e-16 99.0
49 TraesCS5D01G039500 chr4B 86.500 200 22 3 7917 8113 575046469 575046272 1.770000e-51 215.0
50 TraesCS5D01G039500 chr2D 85.641 195 25 3 7918 8112 404085827 404085636 1.380000e-47 202.0
51 TraesCS5D01G039500 chr7B 85.354 198 23 3 7918 8113 721090343 721090150 4.970000e-47 200.0
52 TraesCS5D01G039500 chr7B 89.394 66 7 0 1 66 158434391 158434456 5.220000e-12 84.2
53 TraesCS5D01G039500 chr4D 86.096 187 24 1 7927 8113 385521172 385521356 4.970000e-47 200.0
54 TraesCS5D01G039500 chr4D 85.714 189 24 2 7926 8113 460656802 460656616 6.420000e-46 196.0
55 TraesCS5D01G039500 chr4D 85.714 189 24 2 7926 8113 460660902 460660716 6.420000e-46 196.0
56 TraesCS5D01G039500 chr4D 85.714 189 24 2 7926 8113 460663272 460663086 6.420000e-46 196.0
57 TraesCS5D01G039500 chr7D 84.500 200 27 3 7916 8113 413128339 413128536 2.310000e-45 195.0
58 TraesCS5D01G039500 chr7D 94.118 51 3 0 1 51 181342027 181341977 2.430000e-10 78.7
59 TraesCS5D01G039500 chr7D 84.058 69 11 0 2 70 472898555 472898623 5.250000e-07 67.6
60 TraesCS5D01G039500 chr3B 75.704 284 55 8 376 647 180457014 180456733 6.610000e-26 130.0
61 TraesCS5D01G039500 chr2B 88.158 76 9 0 1 76 35401146 35401221 3.120000e-14 91.6
62 TraesCS5D01G039500 chr3D 84.507 71 7 4 1 69 537410158 537410090 5.250000e-07 67.6


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 TraesCS5D01G039500 chr5D 40759490 40767602 8112 False 14982.000000 14982 100.000000 1 8113 1 chr5D.!!$F2 8112
1 TraesCS5D01G039500 chr5D 40724823 40725374 551 False 431.000000 431 80.790000 200 756 1 chr5D.!!$F1 556
2 TraesCS5D01G039500 chr5D 40889005 40889996 991 False 361.000000 411 85.242000 1040 7007 2 chr5D.!!$F6 5967
3 TraesCS5D01G039500 chr4A 132694565 132699722 5157 True 8000.000000 8000 94.731000 1413 6551 1 chr4A.!!$R1 5138
4 TraesCS5D01G039500 chr1A 262931016 262936148 5132 False 7960.000000 7960 94.721000 1438 6551 1 chr1A.!!$F1 5113
5 TraesCS5D01G039500 chr3A 73297 78464 5167 False 7932.000000 7932 94.438000 1402 6551 1 chr3A.!!$F3 5149
6 TraesCS5D01G039500 chr3A 719780074 719784920 4846 False 7492.000000 7492 94.636000 1402 6229 1 chr3A.!!$F5 4827
7 TraesCS5D01G039500 chr5B 2563992 2569135 5143 False 7899.000000 7899 94.443000 1426 6551 1 chr5B.!!$F1 5125
8 TraesCS5D01G039500 chr5B 34565372 34567407 2035 False 725.666667 959 89.760000 644 7639 3 chr5B.!!$F6 6995
9 TraesCS5D01G039500 chr5B 34554635 34556478 1843 False 689.333333 804 91.030000 644 7425 3 chr5B.!!$F5 6781
10 TraesCS5D01G039500 chr5B 34543515 34547516 4001 False 594.000000 1112 87.352800 1 7741 5 chr5B.!!$F4 7740
11 TraesCS5D01G039500 chr5B 34287847 34289020 1173 False 315.500000 361 81.586500 200 1167 2 chr5B.!!$F3 967
12 TraesCS5D01G039500 chr5B 34606881 34609123 2242 False 240.666667 324 86.166667 818 6977 3 chr5B.!!$F7 6159
13 TraesCS5D01G039500 chr7A 651784690 651789262 4572 True 6636.000000 6636 92.884000 1432 6007 1 chr7A.!!$R2 4575
14 TraesCS5D01G039500 chr7A 24026216 24030009 3793 False 5758.000000 5758 94.124000 2771 6551 1 chr7A.!!$F2 3780
15 TraesCS5D01G039500 chr7A 24210356 24215524 5168 False 4107.500000 7878 94.975500 1401 6551 2 chr7A.!!$F3 5150
16 TraesCS5D01G039500 chr1D 423677493 423682243 4750 False 7836.000000 7836 96.453000 1410 6158 1 chr1D.!!$F1 4748
17 TraesCS5D01G039500 chr2A 27973666 27978672 5006 False 7675.000000 7675 94.345000 1537 6551 1 chr2A.!!$F1 5014
18 TraesCS5D01G039500 chr5A 28904230 28907419 3189 False 1247.333333 1886 92.262333 1 8108 3 chr5A.!!$F4 8107

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
590 640 0.521242 CAGGCGCGTCAGTTTAATGC 60.521 55.000 15.58 0.0 0.00 3.56 F
833 1232 0.594602 TGAAGACTGCATGTGCTTGC 59.405 50.000 6.55 3.5 42.66 4.01 F
1148 2794 0.668535 AAGAAGGGCAAGAAACGTGC 59.331 50.000 0.00 0.0 41.45 5.34 F
1407 3065 1.165907 ACTTGGTCATGTGTGTGCGG 61.166 55.000 0.00 0.0 0.00 5.69 F
3340 5013 1.078143 GAAGATCTGCCCGCCACTT 60.078 57.895 0.00 0.0 0.00 3.16 F
4179 5914 0.453282 CCGAAACATGAGCTTGCGTG 60.453 55.000 0.00 0.0 0.00 5.34 F
4187 5922 0.934496 TGAGCTTGCGTGTGTTGTAC 59.066 50.000 0.00 0.0 0.00 2.90 F
4349 6084 0.942252 ACGCTTCGTCCCAAAACTTC 59.058 50.000 0.00 0.0 33.69 3.01 F
5909 7664 1.589630 GGATGTTTTTCACCCGGCC 59.410 57.895 0.00 0.0 0.00 6.13 F
6344 8149 1.147376 GTATACCATGTGCGGGGCA 59.853 57.895 0.00 0.0 35.60 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1407 3065 0.323957 AGGGTAAGACGTTTCTGCCC 59.676 55.000 9.65 9.65 43.45 5.36 R
2676 4345 0.182537 CAAGGGCATGGTATTCCCGA 59.817 55.000 0.00 0.00 44.70 5.14 R
3157 4830 4.481195 CACAGGTGAACCAGGTGG 57.519 61.111 13.56 0.00 38.85 4.61 R
3347 5020 0.251916 AGAAAATCCCGTGCATCCGA 59.748 50.000 0.00 0.00 0.00 4.55 R
4349 6084 0.030235 CTCATGCGTCCATGCCATTG 59.970 55.000 0.00 0.00 46.69 2.82 R
4995 6734 0.250513 AAGGATCAGGCCACGAAGAC 59.749 55.000 5.01 0.00 0.00 3.01 R
5909 7664 1.372499 TTTTCGTCGCAGTCCCTCG 60.372 57.895 0.00 0.00 0.00 4.63 R
6340 8145 0.323957 AGGGTAAGACGTTTCTGCCC 59.676 55.000 9.65 9.65 43.45 5.36 R
6973 9034 1.273495 TGTCAGCCTCCTCTTCATCCT 60.273 52.381 0.00 0.00 0.00 3.24 R
8020 11610 0.169230 ACTCGCTGCAGTTCTCGTAG 59.831 55.000 16.64 11.26 0.00 3.51 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
52 53 3.519510 TCCCATGGTCTACTTTTCCTCAG 59.480 47.826 11.73 0.00 0.00 3.35
83 84 1.772063 GCCGCAGACGTGTTGACTTT 61.772 55.000 0.00 0.00 37.70 2.66
94 95 2.612212 GTGTTGACTTTGTCATCGTGGT 59.388 45.455 1.05 0.00 42.40 4.16
95 96 2.611751 TGTTGACTTTGTCATCGTGGTG 59.388 45.455 1.05 0.00 42.40 4.17
128 129 4.719369 GCGGAGTTGGCGACGTCT 62.719 66.667 14.70 0.00 0.00 4.18
172 173 0.762418 TCCACCGTCACATCAACCTT 59.238 50.000 0.00 0.00 0.00 3.50
176 177 1.140052 ACCGTCACATCAACCTTCACA 59.860 47.619 0.00 0.00 0.00 3.58
212 261 1.908619 TCAGCTTATTGGACAGCCTGA 59.091 47.619 0.00 0.00 36.62 3.86
248 297 2.039480 CCCATGGTGATGTCATCCTAGG 59.961 54.545 11.73 0.82 0.00 3.02
307 356 2.182842 CAAGCCAGCCAGTATCCGC 61.183 63.158 0.00 0.00 0.00 5.54
308 357 2.370445 AAGCCAGCCAGTATCCGCT 61.370 57.895 0.00 0.00 35.10 5.52
419 469 1.077212 GCCATGCCATGTCTCCTGT 60.077 57.895 3.63 0.00 0.00 4.00
447 497 2.914777 GATGGAGAGCGGAGGTGTGC 62.915 65.000 0.00 0.00 40.55 4.57
461 511 3.969802 GTGCTGCGGCTGTTGCTT 61.970 61.111 20.27 0.00 39.59 3.91
535 585 2.515523 GCCAGCATGCAGACGGAT 60.516 61.111 21.98 0.00 31.97 4.18
590 640 0.521242 CAGGCGCGTCAGTTTAATGC 60.521 55.000 15.58 0.00 0.00 3.56
679 731 1.284408 GGCGCGTGTTTCAATTCCA 59.716 52.632 8.43 0.00 0.00 3.53
684 736 1.537202 GCGTGTTTCAATTCCAGCTCT 59.463 47.619 0.00 0.00 0.00 4.09
702 754 3.607741 CTCTAGTGAGAGGTTACGTCCA 58.392 50.000 0.00 0.00 44.92 4.02
761 844 2.342648 GAAAGGGTGCGGTCGAGT 59.657 61.111 0.00 0.00 0.00 4.18
782 865 2.591193 AAAGGGTTTTGGGTGGGCGA 62.591 55.000 0.00 0.00 0.00 5.54
784 867 2.114411 GGTTTTGGGTGGGCGAGA 59.886 61.111 0.00 0.00 0.00 4.04
787 870 1.976474 TTTTGGGTGGGCGAGATGC 60.976 57.895 0.00 0.00 45.38 3.91
799 882 3.180891 GCGAGATGCCCTTAGTAAACT 57.819 47.619 0.00 0.00 37.76 2.66
800 883 2.866762 GCGAGATGCCCTTAGTAAACTG 59.133 50.000 0.00 0.00 37.76 3.16
801 884 3.679083 GCGAGATGCCCTTAGTAAACTGT 60.679 47.826 0.00 0.00 37.76 3.55
803 886 5.041940 CGAGATGCCCTTAGTAAACTGTAC 58.958 45.833 0.00 0.00 0.00 2.90
804 887 5.163540 CGAGATGCCCTTAGTAAACTGTACT 60.164 44.000 0.00 0.00 0.00 2.73
805 888 6.039047 CGAGATGCCCTTAGTAAACTGTACTA 59.961 42.308 0.00 0.00 0.00 1.82
806 889 7.110043 AGATGCCCTTAGTAAACTGTACTAC 57.890 40.000 0.00 0.00 30.54 2.73
807 890 5.314923 TGCCCTTAGTAAACTGTACTACG 57.685 43.478 0.00 0.00 30.54 3.51
808 891 5.009631 TGCCCTTAGTAAACTGTACTACGA 58.990 41.667 0.00 0.00 30.54 3.43
809 892 5.653769 TGCCCTTAGTAAACTGTACTACGAT 59.346 40.000 0.00 0.00 30.54 3.73
811 894 5.975939 CCCTTAGTAAACTGTACTACGATGC 59.024 44.000 0.00 0.00 30.54 3.91
812 895 6.405065 CCCTTAGTAAACTGTACTACGATGCA 60.405 42.308 0.00 0.00 30.54 3.96
813 896 7.031372 CCTTAGTAAACTGTACTACGATGCAA 58.969 38.462 0.00 0.00 30.54 4.08
814 897 7.705325 CCTTAGTAAACTGTACTACGATGCAAT 59.295 37.037 0.00 0.00 30.54 3.56
816 899 6.627243 AGTAAACTGTACTACGATGCAATGA 58.373 36.000 0.00 0.00 0.00 2.57
817 900 7.094631 AGTAAACTGTACTACGATGCAATGAA 58.905 34.615 0.00 0.00 0.00 2.57
818 901 6.408858 AAACTGTACTACGATGCAATGAAG 57.591 37.500 0.00 0.00 0.00 3.02
821 904 5.105716 ACTGTACTACGATGCAATGAAGACT 60.106 40.000 0.00 0.00 0.00 3.24
833 1232 0.594602 TGAAGACTGCATGTGCTTGC 59.405 50.000 6.55 3.50 42.66 4.01
905 1305 8.153479 TGGATAGAAAATATTTCATGACGTGG 57.847 34.615 0.10 0.00 0.00 4.94
1017 2644 3.196207 AATGGGGACTGCGCACTGT 62.196 57.895 5.66 3.19 0.00 3.55
1086 2732 6.631971 AAAAGGCAAGAGAAGAAGAAGAAG 57.368 37.500 0.00 0.00 0.00 2.85
1087 2733 5.559148 AAGGCAAGAGAAGAAGAAGAAGA 57.441 39.130 0.00 0.00 0.00 2.87
1088 2734 4.893608 AGGCAAGAGAAGAAGAAGAAGAC 58.106 43.478 0.00 0.00 0.00 3.01
1089 2735 3.677596 GGCAAGAGAAGAAGAAGAAGACG 59.322 47.826 0.00 0.00 0.00 4.18
1090 2736 4.551388 GCAAGAGAAGAAGAAGAAGACGA 58.449 43.478 0.00 0.00 0.00 4.20
1131 2777 2.430332 TGGAAACAACCAAGGCAAGAAG 59.570 45.455 0.00 0.00 36.96 2.85
1148 2794 0.668535 AAGAAGGGCAAGAAACGTGC 59.331 50.000 0.00 0.00 41.45 5.34
1289 2943 8.811017 TCTCTTCACAAGAAAGACAAGATAGAT 58.189 33.333 0.00 0.00 37.02 1.98
1290 2944 9.434420 CTCTTCACAAGAAAGACAAGATAGATT 57.566 33.333 0.00 0.00 37.02 2.40
1292 2946 9.212641 CTTCACAAGAAAGACAAGATAGATTGA 57.787 33.333 0.00 0.00 32.08 2.57
1293 2947 8.539770 TCACAAGAAAGACAAGATAGATTGAC 57.460 34.615 0.00 0.00 34.20 3.18
1294 2948 7.604164 TCACAAGAAAGACAAGATAGATTGACC 59.396 37.037 0.00 0.00 34.20 4.02
1331 2988 9.710900 ATTTTGTACATTGATTCCCTTTTTCTC 57.289 29.630 0.00 0.00 0.00 2.87
1359 3016 1.412079 TGGCCATGGAATGCATAACC 58.588 50.000 18.40 13.77 44.97 2.85
1383 3041 9.553064 ACCTTGCATAGATTTAGAGACTAAATG 57.447 33.333 17.61 8.90 0.00 2.32
1407 3065 1.165907 ACTTGGTCATGTGTGTGCGG 61.166 55.000 0.00 0.00 0.00 5.69
1408 3066 1.855213 CTTGGTCATGTGTGTGCGGG 61.855 60.000 0.00 0.00 0.00 6.13
1466 3124 4.039488 ACGTGTTATATAGGGGATTGCGAA 59.961 41.667 0.00 0.00 0.00 4.70
1584 3247 5.995565 AAACTACCATGCGGCTATCTATA 57.004 39.130 0.00 0.00 34.57 1.31
1903 3568 5.657302 TCCAGACCTAACTCCTTCAAGATAC 59.343 44.000 0.00 0.00 0.00 2.24
1904 3569 5.659079 CCAGACCTAACTCCTTCAAGATACT 59.341 44.000 0.00 0.00 0.00 2.12
2208 3876 1.679032 GGTGGGTGCATGTAGGAACTC 60.679 57.143 0.00 0.00 41.75 3.01
2245 3913 3.507233 CAGCAAAAGAAATGTCTGGCCTA 59.493 43.478 3.32 0.00 33.05 3.93
2274 3942 6.354794 TGTTAAGTACTGAAGTGCACCTAT 57.645 37.500 14.63 0.00 32.87 2.57
2375 4043 2.490168 GGAGTGGGTGTGGGTTTACAAT 60.490 50.000 0.00 0.00 31.36 2.71
2455 4123 1.241165 CATCCTTGTGCTGCTTCACA 58.759 50.000 0.00 7.37 44.39 3.58
2505 4173 6.157645 TCTCCTAGATCCTTGAGAGCAAATTT 59.842 38.462 0.00 0.00 31.44 1.82
2570 4238 8.375608 AGATGAGCTTGTGACAATAATATCAC 57.624 34.615 0.00 0.00 44.56 3.06
2669 4337 2.157738 AGCCAAGTGTCTGCATCTTTC 58.842 47.619 0.00 0.00 0.00 2.62
2676 4345 3.070734 AGTGTCTGCATCTTTCACTGAGT 59.929 43.478 8.00 0.00 37.85 3.41
2745 4414 3.808466 TCTAGCTTGCACACATAGGAG 57.192 47.619 0.00 0.00 0.00 3.69
3157 4830 1.273327 CCTCTTCAATTGTGTTGGGCC 59.727 52.381 5.13 0.00 0.00 5.80
3340 5013 1.078143 GAAGATCTGCCCGCCACTT 60.078 57.895 0.00 0.00 0.00 3.16
3347 5020 3.292159 GCCCGCCACTTTCGGTTT 61.292 61.111 0.66 0.00 45.09 3.27
3462 5135 1.448365 ATGAGCTCGTGATTGCGCA 60.448 52.632 5.66 5.66 42.50 6.09
3943 5678 4.512944 AGCCGACATATGATCACAACAATC 59.487 41.667 10.38 0.00 0.00 2.67
4016 5751 5.767816 TTTCTTTTTGAAGTAGAGCACCC 57.232 39.130 0.00 0.00 35.89 4.61
4179 5914 0.453282 CCGAAACATGAGCTTGCGTG 60.453 55.000 0.00 0.00 0.00 5.34
4187 5922 0.934496 TGAGCTTGCGTGTGTTGTAC 59.066 50.000 0.00 0.00 0.00 2.90
4349 6084 0.942252 ACGCTTCGTCCCAAAACTTC 59.058 50.000 0.00 0.00 33.69 3.01
4393 6128 2.165998 GAGAGCAAGGCCAACTTCAAT 58.834 47.619 5.01 0.00 37.29 2.57
4402 6137 4.406456 AGGCCAACTTCAATAATGTGACA 58.594 39.130 5.01 0.00 0.00 3.58
4601 6339 4.337274 ACTTGGAAAACGTCGGATCTTTTT 59.663 37.500 0.00 0.00 0.00 1.94
4640 6378 5.276395 CCACGAAAACTTGCTATAGTCATCG 60.276 44.000 0.84 8.15 39.75 3.84
4836 6575 5.357032 CCAACATACGGGAGCTTATTTTTCT 59.643 40.000 0.00 0.00 0.00 2.52
4984 6723 2.100197 CCCTCGAACACATCTACCTCA 58.900 52.381 0.00 0.00 0.00 3.86
5242 6983 6.313658 CACGATATTTCTCCTTCATTGTCACA 59.686 38.462 0.00 0.00 0.00 3.58
5292 7033 2.126189 GCCACTGTCGACGTACCC 60.126 66.667 11.62 0.00 0.00 3.69
5335 7076 3.914579 ATCCGCAGCAGCAGCAAGT 62.915 57.895 10.77 0.00 45.49 3.16
5395 7140 1.675714 CGATACCAGCAGTCTTTGGCA 60.676 52.381 0.86 0.00 38.03 4.92
5898 7653 4.344865 AGGGCCGTGCGGATGTTT 62.345 61.111 15.45 0.00 37.50 2.83
5909 7664 1.589630 GGATGTTTTTCACCCGGCC 59.410 57.895 0.00 0.00 0.00 6.13
6318 8088 4.813809 AGGCTAGATGAGATTGGAAGAGA 58.186 43.478 0.00 0.00 0.00 3.10
6340 8145 1.502231 GCTCTGTATACCATGTGCGG 58.498 55.000 0.00 0.00 0.00 5.69
6341 8146 1.873903 GCTCTGTATACCATGTGCGGG 60.874 57.143 0.00 0.00 0.00 6.13
6344 8149 1.147376 GTATACCATGTGCGGGGCA 59.853 57.895 0.00 0.00 35.60 5.36
6402 8207 5.047235 GTGTTATATAGGGGATTGCGAGTCT 60.047 44.000 0.00 0.00 0.00 3.24
6455 8260 5.046950 ACATGACTTGAGGGAGAAGAAGTAC 60.047 44.000 0.00 0.00 0.00 2.73
6532 8338 7.330946 CGGCTATCTATCTTATCTATCTCCTCG 59.669 44.444 0.00 0.00 0.00 4.63
6551 8357 5.124297 TCCTCGTACATATCTCGTTTGACAA 59.876 40.000 0.00 0.00 0.00 3.18
6552 8358 5.977725 CCTCGTACATATCTCGTTTGACAAT 59.022 40.000 0.00 0.00 0.00 2.71
6553 8359 6.074835 CCTCGTACATATCTCGTTTGACAATG 60.075 42.308 0.00 0.00 0.00 2.82
6554 8360 6.327154 TCGTACATATCTCGTTTGACAATGT 58.673 36.000 0.00 0.00 33.39 2.71
6555 8361 6.252655 TCGTACATATCTCGTTTGACAATGTG 59.747 38.462 0.00 0.00 32.07 3.21
6556 8362 5.221891 ACATATCTCGTTTGACAATGTGC 57.778 39.130 0.00 0.00 29.96 4.57
6643 8459 3.953712 TCATGTTCCGAGCTCACTTTA 57.046 42.857 15.40 0.00 0.00 1.85
6654 8666 7.033791 TCCGAGCTCACTTTATAGTTAACTTG 58.966 38.462 14.49 4.90 30.26 3.16
6700 8712 2.856032 CGGCTTGAGAACGTGCAG 59.144 61.111 0.00 0.00 0.00 4.41
6777 8805 8.349983 TCTAGGTGCAATTTTCTTAACTTTGAC 58.650 33.333 0.00 0.00 0.00 3.18
6973 9034 1.062581 CAATGAGGAGGAGGAGGAGGA 60.063 57.143 0.00 0.00 0.00 3.71
7015 9079 0.560688 GAGGATGAGGAGGAGGAGGT 59.439 60.000 0.00 0.00 0.00 3.85
7016 9080 0.264359 AGGATGAGGAGGAGGAGGTG 59.736 60.000 0.00 0.00 0.00 4.00
7017 9081 0.762461 GGATGAGGAGGAGGAGGTGG 60.762 65.000 0.00 0.00 0.00 4.61
7068 9186 0.803117 GGATCAGACTGACGACGACA 59.197 55.000 7.47 0.00 0.00 4.35
7070 9188 2.243407 GATCAGACTGACGACGACAAC 58.757 52.381 7.47 0.00 0.00 3.32
7094 9212 2.329379 GACCAGACTGACGATGACAAC 58.671 52.381 3.32 0.00 0.00 3.32
7112 9230 2.840066 CGGCGAGGACCTCAGCTAG 61.840 68.421 26.51 20.03 33.26 3.42
7195 9313 7.411486 TCTTCTGGGCAGCTATATTATCTAC 57.589 40.000 0.00 0.00 0.00 2.59
7196 9314 6.381420 TCTTCTGGGCAGCTATATTATCTACC 59.619 42.308 0.00 0.00 0.00 3.18
7198 9318 4.694512 TGGGCAGCTATATTATCTACCCA 58.305 43.478 0.00 0.00 40.25 4.51
7199 9319 4.716784 TGGGCAGCTATATTATCTACCCAG 59.283 45.833 0.00 0.00 38.24 4.45
7253 9374 3.690422 CACGTACGCATGCCAATTTATT 58.310 40.909 16.72 0.00 0.00 1.40
7260 9381 5.288804 ACGCATGCCAATTTATTTATGTCC 58.711 37.500 13.15 0.00 0.00 4.02
7316 9437 7.068716 GCTAGTGAAACATTCTAATTTGGGGAT 59.931 37.037 0.00 0.00 41.43 3.85
7554 11136 2.288213 CGCTCAACCGAGAATAGCCATA 60.288 50.000 0.00 0.00 42.34 2.74
7593 11178 4.142038 GTGAAAACCTGACCACCTACAAT 58.858 43.478 0.00 0.00 0.00 2.71
7601 11186 4.326826 CTGACCACCTACAATCACAACAT 58.673 43.478 0.00 0.00 0.00 2.71
7610 11195 6.590292 ACCTACAATCACAACATTAGAGTTCG 59.410 38.462 0.00 0.00 0.00 3.95
7628 11213 4.828387 AGTTCGGTGAAGTAGAGAGAACTT 59.172 41.667 2.55 0.00 42.55 2.66
7727 11313 2.101582 CCTTGACCTTGGTATCCTCGAG 59.898 54.545 5.13 5.13 0.00 4.04
7735 11321 2.388735 TGGTATCCTCGAGCTCAACAT 58.611 47.619 15.40 2.22 0.00 2.71
7867 11454 3.550431 CGTCCATCGGCCCTGGAT 61.550 66.667 21.39 5.45 44.34 3.41
7869 11456 2.040988 TCCATCGGCCCTGGATGA 60.041 61.111 17.79 0.00 43.07 2.92
8015 11605 6.753913 TTCAGATCCATAAACCATCTAGCT 57.246 37.500 0.00 0.00 0.00 3.32
8017 11607 7.233389 TCAGATCCATAAACCATCTAGCTAC 57.767 40.000 0.00 0.00 0.00 3.58
8020 11610 5.449107 TCCATAAACCATCTAGCTACGAC 57.551 43.478 0.00 0.00 0.00 4.34
8024 11614 4.548991 AAACCATCTAGCTACGACTACG 57.451 45.455 0.00 0.00 45.75 3.51
8026 11616 3.391965 ACCATCTAGCTACGACTACGAG 58.608 50.000 0.00 0.00 42.66 4.18
8032 11622 1.397692 AGCTACGACTACGAGAACTGC 59.602 52.381 0.00 0.00 42.66 4.40
8084 11674 3.136750 CTCCCTCATCGGAGCTGG 58.863 66.667 0.00 0.00 43.01 4.85
8094 11684 2.629656 CGGAGCTGGGCAAACCTTG 61.630 63.158 0.00 0.00 41.11 3.61
8108 11698 7.689384 GGGCAAACCTTGTTGTAGTAGACAAT 61.689 42.308 0.00 0.00 42.51 2.71
8109 11699 9.380027 GGGCAAACCTTGTTGTAGTAGACAATC 62.380 44.444 0.00 0.00 42.51 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 4.386951 CCCGCCACCACGATGACA 62.387 66.667 0.00 0.00 34.06 3.58
137 138 1.354368 GTGGAGGAATTTGACTGGGGA 59.646 52.381 0.00 0.00 0.00 4.81
172 173 4.206375 TGAGAAAGAAGGCATGTTTGTGA 58.794 39.130 0.00 0.00 0.00 3.58
176 177 3.494332 AGCTGAGAAAGAAGGCATGTTT 58.506 40.909 0.00 0.00 0.00 2.83
419 469 2.091830 TCCGCTCTCCATCTCCTCTTTA 60.092 50.000 0.00 0.00 0.00 1.85
447 497 2.253452 GTCAAGCAACAGCCGCAG 59.747 61.111 0.00 0.00 0.00 5.18
461 511 5.414454 GCTATTTAAATGTGGTCAGGTGTCA 59.586 40.000 11.05 0.00 0.00 3.58
679 731 3.272581 GACGTAACCTCTCACTAGAGCT 58.727 50.000 0.00 0.00 46.84 4.09
684 736 3.008813 AGAGTGGACGTAACCTCTCACTA 59.991 47.826 20.92 0.00 46.58 2.74
702 754 2.414994 CATTCATGCTGGTCCAGAGT 57.585 50.000 23.77 6.85 32.44 3.24
729 781 2.017049 CCTTTCCTACCCAAAGCGATG 58.983 52.381 0.00 0.00 30.61 3.84
737 789 2.598787 CCGCACCCTTTCCTACCCA 61.599 63.158 0.00 0.00 0.00 4.51
740 792 1.447314 CGACCGCACCCTTTCCTAC 60.447 63.158 0.00 0.00 0.00 3.18
741 793 1.601419 CTCGACCGCACCCTTTCCTA 61.601 60.000 0.00 0.00 0.00 2.94
761 844 1.051556 GCCCACCCAAAACCCTTTCA 61.052 55.000 0.00 0.00 0.00 2.69
782 865 6.183360 CGTAGTACAGTTTACTAAGGGCATCT 60.183 42.308 0.38 0.00 32.49 2.90
784 867 5.653769 TCGTAGTACAGTTTACTAAGGGCAT 59.346 40.000 8.83 0.00 32.77 4.40
787 870 5.975939 GCATCGTAGTACAGTTTACTAAGGG 59.024 44.000 8.83 4.55 32.77 3.95
788 871 6.558009 TGCATCGTAGTACAGTTTACTAAGG 58.442 40.000 8.83 1.27 32.77 2.69
789 872 8.532341 CATTGCATCGTAGTACAGTTTACTAAG 58.468 37.037 0.38 1.05 32.49 2.18
791 874 7.764331 TCATTGCATCGTAGTACAGTTTACTA 58.236 34.615 0.38 0.00 0.00 1.82
792 875 6.627243 TCATTGCATCGTAGTACAGTTTACT 58.373 36.000 0.38 0.00 0.00 2.24
794 877 7.274904 GTCTTCATTGCATCGTAGTACAGTTTA 59.725 37.037 0.38 0.00 0.00 2.01
795 878 6.090898 GTCTTCATTGCATCGTAGTACAGTTT 59.909 38.462 0.38 0.00 0.00 2.66
798 881 5.230936 CAGTCTTCATTGCATCGTAGTACAG 59.769 44.000 0.38 0.00 0.00 2.74
799 882 5.102313 CAGTCTTCATTGCATCGTAGTACA 58.898 41.667 0.38 0.00 0.00 2.90
800 883 4.026475 GCAGTCTTCATTGCATCGTAGTAC 60.026 45.833 0.00 0.00 40.02 2.73
801 884 4.112634 GCAGTCTTCATTGCATCGTAGTA 58.887 43.478 0.00 0.00 40.02 1.82
803 886 2.931969 TGCAGTCTTCATTGCATCGTAG 59.068 45.455 0.00 0.00 44.72 3.51
804 887 2.971307 TGCAGTCTTCATTGCATCGTA 58.029 42.857 0.00 0.00 44.72 3.43
805 888 1.812235 TGCAGTCTTCATTGCATCGT 58.188 45.000 0.00 0.00 44.72 3.73
811 894 3.242518 CAAGCACATGCAGTCTTCATTG 58.757 45.455 6.64 0.00 45.16 2.82
812 895 2.352421 GCAAGCACATGCAGTCTTCATT 60.352 45.455 6.64 0.00 45.70 2.57
813 896 1.201647 GCAAGCACATGCAGTCTTCAT 59.798 47.619 6.64 0.00 45.70 2.57
814 897 0.594602 GCAAGCACATGCAGTCTTCA 59.405 50.000 6.64 0.00 45.70 3.02
816 899 1.577922 CGCAAGCACATGCAGTCTT 59.422 52.632 6.64 0.00 46.76 3.01
817 900 3.260931 CGCAAGCACATGCAGTCT 58.739 55.556 6.64 0.00 46.76 3.24
833 1232 0.998669 TACACGTCAATCATGCAGCG 59.001 50.000 0.00 0.00 0.00 5.18
905 1305 5.098893 TGCACACATTAAAATTGATACGCC 58.901 37.500 0.00 0.00 0.00 5.68
919 1319 1.855513 GCACACAACATGCACACATT 58.144 45.000 0.00 0.00 42.88 2.71
1068 2702 4.551388 TCGTCTTCTTCTTCTTCTCTTGC 58.449 43.478 0.00 0.00 0.00 4.01
1079 2725 1.603172 CGCCACTGTTCGTCTTCTTCT 60.603 52.381 0.00 0.00 0.00 2.85
1081 2727 0.600255 CCGCCACTGTTCGTCTTCTT 60.600 55.000 0.00 0.00 0.00 2.52
1082 2728 1.006102 CCGCCACTGTTCGTCTTCT 60.006 57.895 0.00 0.00 0.00 2.85
1083 2729 0.878961 AACCGCCACTGTTCGTCTTC 60.879 55.000 0.00 0.00 0.00 2.87
1084 2730 0.878961 GAACCGCCACTGTTCGTCTT 60.879 55.000 0.00 0.00 33.48 3.01
1085 2731 1.300697 GAACCGCCACTGTTCGTCT 60.301 57.895 0.00 0.00 33.48 4.18
1086 2732 0.949105 ATGAACCGCCACTGTTCGTC 60.949 55.000 0.00 0.00 43.95 4.20
1087 2733 0.949105 GATGAACCGCCACTGTTCGT 60.949 55.000 0.00 0.00 43.95 3.85
1088 2734 1.635663 GGATGAACCGCCACTGTTCG 61.636 60.000 0.00 0.00 43.95 3.95
1089 2735 2.171635 GGATGAACCGCCACTGTTC 58.828 57.895 0.00 0.00 41.91 3.18
1090 2736 4.397348 GGATGAACCGCCACTGTT 57.603 55.556 0.00 0.00 0.00 3.16
1131 2777 1.082104 CGCACGTTTCTTGCCCTTC 60.082 57.895 0.00 0.00 36.57 3.46
1289 2943 3.505680 ACAAAATGCTGCTATTCGGTCAA 59.494 39.130 0.00 0.00 0.00 3.18
1290 2944 3.081061 ACAAAATGCTGCTATTCGGTCA 58.919 40.909 0.00 0.00 0.00 4.02
1292 2946 4.006989 TGTACAAAATGCTGCTATTCGGT 58.993 39.130 0.00 4.44 0.00 4.69
1293 2947 4.614555 TGTACAAAATGCTGCTATTCGG 57.385 40.909 0.00 0.00 0.00 4.30
1294 2948 6.257423 TCAATGTACAAAATGCTGCTATTCG 58.743 36.000 0.00 0.00 0.00 3.34
1331 2988 2.681319 TTCCATGGCCATATGGGAAG 57.319 50.000 25.09 10.30 46.16 3.46
1373 3031 9.601217 ACATGACCAAGTATTACATTTAGTCTC 57.399 33.333 0.00 0.00 0.00 3.36
1383 3041 4.435518 CGCACACACATGACCAAGTATTAC 60.436 45.833 0.00 0.00 0.00 1.89
1407 3065 0.323957 AGGGTAAGACGTTTCTGCCC 59.676 55.000 9.65 9.65 43.45 5.36
1408 3066 2.074576 GAAGGGTAAGACGTTTCTGCC 58.925 52.381 0.00 0.00 29.98 4.85
1466 3124 5.221722 ACAGAATTGTATGCGTATCAGGGAT 60.222 40.000 0.00 0.00 35.25 3.85
1584 3247 9.483916 CGAGATATGTACGAGGAGATAGATAAT 57.516 37.037 0.00 0.00 0.00 1.28
1880 3545 5.659079 AGTATCTTGAAGGAGTTAGGTCTGG 59.341 44.000 0.00 0.00 0.00 3.86
1903 3568 4.946157 AGCAGAAATCATTTGGGTACAGAG 59.054 41.667 0.00 0.00 0.00 3.35
1904 3569 4.701651 CAGCAGAAATCATTTGGGTACAGA 59.298 41.667 0.00 0.00 0.00 3.41
2208 3876 6.264832 TCTTTTGCTGTCAACAAAGTATGTG 58.735 36.000 1.92 0.00 42.99 3.21
2245 3913 6.202954 GTGCACTTCAGTACTTAACATTGACT 59.797 38.462 10.32 0.00 0.00 3.41
2295 3963 2.447047 ACACTTTTGGGTCCAGAGGATT 59.553 45.455 0.00 0.00 32.73 3.01
2455 4123 8.773033 AATTGCATTACTTCCTAGGAATTGAT 57.227 30.769 24.48 17.53 32.34 2.57
2505 4173 5.104900 GGACTCTTGAAGGATTTAGGTGCTA 60.105 44.000 0.00 0.00 0.00 3.49
2570 4238 7.377398 TCCATGTTTGTTCTCATTTATGTTGG 58.623 34.615 0.00 0.00 0.00 3.77
2578 4246 4.473444 ACACCTCCATGTTTGTTCTCATT 58.527 39.130 0.00 0.00 0.00 2.57
2669 4337 2.826428 CATGGTATTCCCGACTCAGTG 58.174 52.381 0.00 0.00 35.15 3.66
2676 4345 0.182537 CAAGGGCATGGTATTCCCGA 59.817 55.000 0.00 0.00 44.70 5.14
3157 4830 4.481195 CACAGGTGAACCAGGTGG 57.519 61.111 13.56 0.00 38.85 4.61
3211 4884 4.209080 GCAAGGTTTGATTCAACCGAAAAG 59.791 41.667 0.00 0.00 34.01 2.27
3340 5013 2.030401 CCGTGCATCCGAAACCGAA 61.030 57.895 0.00 0.00 0.00 4.30
3347 5020 0.251916 AGAAAATCCCGTGCATCCGA 59.748 50.000 0.00 0.00 0.00 4.55
3462 5135 2.370445 CCCTGATTCAGACGGGCCT 61.370 63.158 15.36 0.00 32.44 5.19
3554 5280 4.008933 GCGACAGTGGCCTGGACT 62.009 66.667 3.32 0.00 43.36 3.85
3790 5519 0.405198 TGGGCCTCATCACATGTGTT 59.595 50.000 24.63 14.55 0.00 3.32
3943 5678 2.512692 TGATCAAGGGGGTGTTGATG 57.487 50.000 3.13 0.00 43.26 3.07
4016 5751 2.270923 TCTGATCTTCATCCAAACGCG 58.729 47.619 3.53 3.53 0.00 6.01
4179 5914 0.319813 AACCTACGCCCGTACAACAC 60.320 55.000 0.00 0.00 0.00 3.32
4187 5922 3.441011 CTGGCCTAACCTACGCCCG 62.441 68.421 3.32 0.00 42.29 6.13
4349 6084 0.030235 CTCATGCGTCCATGCCATTG 59.970 55.000 0.00 0.00 46.69 2.82
4393 6128 2.217750 AGCGCAAACACTGTCACATTA 58.782 42.857 11.47 0.00 0.00 1.90
4402 6137 1.226686 CTCAGCTGAGCGCAAACACT 61.227 55.000 29.79 0.00 42.61 3.55
4601 6339 9.720769 AAGTTTTCGTGGATCTATCTTCTTAAA 57.279 29.630 0.00 0.00 0.00 1.52
4640 6378 6.020041 GGCACACTTACTACGTAAGCTTTATC 60.020 42.308 3.20 0.00 46.46 1.75
4805 6544 1.079405 CCCGTATGTTGGTGAGCGT 60.079 57.895 0.00 0.00 0.00 5.07
4960 6699 2.541556 GTAGATGTGTTCGAGGGCTTC 58.458 52.381 0.00 0.00 0.00 3.86
4984 6723 3.432326 GGCCACGAAGACAATCCTCTATT 60.432 47.826 0.00 0.00 0.00 1.73
4995 6734 0.250513 AAGGATCAGGCCACGAAGAC 59.749 55.000 5.01 0.00 0.00 3.01
5035 6774 9.329913 CTTGATAATCACGTTTTCTCGAATTTT 57.670 29.630 0.00 0.00 34.70 1.82
5242 6983 5.280945 CACATCACCAACGAACTTGAAAAT 58.719 37.500 0.00 0.00 30.42 1.82
5292 7033 1.538204 CCTATGGGATCGACACCAACG 60.538 57.143 13.27 7.74 40.73 4.10
5335 7076 2.106511 CTCCTCCCAAGACAAGGACAAA 59.893 50.000 0.00 0.00 35.38 2.83
5395 7140 2.700897 CTGTGGTAAGCTAGGGCATACT 59.299 50.000 0.00 0.00 40.93 2.12
5909 7664 1.372499 TTTTCGTCGCAGTCCCTCG 60.372 57.895 0.00 0.00 0.00 4.63
6192 7947 1.820519 ACCCGCACGAACTATGTTCTA 59.179 47.619 8.51 0.00 0.00 2.10
6266 8021 1.242076 CATTAGTGCCCTAGCCATGC 58.758 55.000 0.00 0.00 38.69 4.06
6318 8088 2.483714 CGCACATGGTATACAGAGCCTT 60.484 50.000 5.01 0.00 0.00 4.35
6340 8145 0.323957 AGGGTAAGACGTTTCTGCCC 59.676 55.000 9.65 9.65 43.45 5.36
6341 8146 2.074576 GAAGGGTAAGACGTTTCTGCC 58.925 52.381 0.00 0.00 29.98 4.85
6344 8149 2.230750 CCTCGAAGGGTAAGACGTTTCT 59.769 50.000 0.00 0.00 0.00 2.52
6402 8207 4.365899 ACAGAATTGTACGCGTATCAGA 57.634 40.909 23.56 9.10 35.25 3.27
6455 8260 9.968870 GGTTGTAACTATACTTCTTATCTCCTG 57.031 37.037 0.00 0.00 32.98 3.86
6505 8311 8.041143 AGGAGATAGATAAGATAGATAGCCGT 57.959 38.462 0.00 0.00 0.00 5.68
6532 8338 6.183360 TGCACATTGTCAAACGAGATATGTAC 60.183 38.462 0.00 0.00 29.93 2.90
6551 8357 6.740411 AACAAAAATCAAACTTGTGCACAT 57.260 29.167 22.39 3.15 33.67 3.21
6552 8358 6.551385 AAACAAAAATCAAACTTGTGCACA 57.449 29.167 17.42 17.42 33.67 4.57
6553 8359 7.850268 AAAAACAAAAATCAAACTTGTGCAC 57.150 28.000 10.75 10.75 33.67 4.57
6606 8422 7.008628 CGGAACATGAATTGCTCAAAATAGTTC 59.991 37.037 0.00 0.00 37.67 3.01
6607 8423 6.808212 CGGAACATGAATTGCTCAAAATAGTT 59.192 34.615 0.00 0.00 37.67 2.24
6608 8424 6.150976 TCGGAACATGAATTGCTCAAAATAGT 59.849 34.615 0.00 0.00 37.67 2.12
6643 8459 5.989477 TCTGCATGGTAGCAAGTTAACTAT 58.011 37.500 8.92 0.89 45.13 2.12
6654 8666 1.134580 TCAGCTCTTCTGCATGGTAGC 60.135 52.381 0.00 0.00 42.56 3.58
6700 8712 0.105039 CATCGTCCCAAGAGGTAGGC 59.895 60.000 0.00 0.00 36.75 3.93
6777 8805 5.469479 ACCAAAATTAATTCGCAAGTCCAG 58.531 37.500 0.10 0.00 39.48 3.86
6973 9034 1.273495 TGTCAGCCTCCTCTTCATCCT 60.273 52.381 0.00 0.00 0.00 3.24
7015 9079 3.062466 CGTCTCCGTCAGCCTCCA 61.062 66.667 0.00 0.00 0.00 3.86
7016 9080 3.827898 CCGTCTCCGTCAGCCTCC 61.828 72.222 0.00 0.00 0.00 4.30
7017 9081 3.063084 ACCGTCTCCGTCAGCCTC 61.063 66.667 0.00 0.00 0.00 4.70
7068 9186 2.338984 GTCAGTCTGGTCGCCGTT 59.661 61.111 0.00 0.00 0.00 4.44
7070 9188 3.052620 ATCGTCAGTCTGGTCGCCG 62.053 63.158 0.00 0.00 0.00 6.46
7094 9212 2.829003 TAGCTGAGGTCCTCGCCG 60.829 66.667 23.51 12.93 33.20 6.46
7112 9230 2.878406 TGTCTTAAGCACAACTTGGAGC 59.122 45.455 0.00 0.00 39.58 4.70
7198 9318 7.415206 GGTTCAATACAAACACAACAGACTTCT 60.415 37.037 0.00 0.00 0.00 2.85
7199 9319 6.691388 GGTTCAATACAAACACAACAGACTTC 59.309 38.462 0.00 0.00 0.00 3.01
7253 9374 7.704899 CAGAAACATAGTGATACACGGACATAA 59.295 37.037 0.00 0.00 39.64 1.90
7260 9381 8.683550 TTTAGACAGAAACATAGTGATACACG 57.316 34.615 0.00 0.00 39.64 4.49
7316 9437 7.796660 GCGCATAATTACTCGACAAATGAAATA 59.203 33.333 0.30 0.00 0.00 1.40
7445 9577 6.150140 AGCAAGTCTGTTGGAATCAAATAGTC 59.850 38.462 0.00 0.00 34.28 2.59
7593 11178 4.594123 TCACCGAACTCTAATGTTGTGA 57.406 40.909 0.00 0.00 33.46 3.58
7601 11186 5.802465 TCTCTCTACTTCACCGAACTCTAA 58.198 41.667 0.00 0.00 0.00 2.10
7610 11195 6.655848 TGTCTCTAAGTTCTCTCTACTTCACC 59.344 42.308 0.00 0.00 37.12 4.02
7628 11213 3.724374 CGTTGTGGTCCTTTTGTCTCTA 58.276 45.455 0.00 0.00 0.00 2.43
7727 11313 1.457346 CCCTCTGGAACATGTTGAGC 58.543 55.000 17.58 1.00 38.20 4.26
7867 11454 4.758251 CGCCATCCACGCCTGTCA 62.758 66.667 0.00 0.00 0.00 3.58
7993 11583 6.071896 CGTAGCTAGATGGTTTATGGATCTGA 60.072 42.308 0.00 0.00 0.00 3.27
8004 11594 3.801698 TCGTAGTCGTAGCTAGATGGTT 58.198 45.455 0.00 0.00 38.33 3.67
8009 11599 4.111198 CAGTTCTCGTAGTCGTAGCTAGA 58.889 47.826 0.00 0.00 38.33 2.43
8015 11605 1.129998 GCTGCAGTTCTCGTAGTCGTA 59.870 52.381 16.64 0.00 38.33 3.43
8017 11607 1.128724 CGCTGCAGTTCTCGTAGTCG 61.129 60.000 16.64 1.93 38.55 4.18
8020 11610 0.169230 ACTCGCTGCAGTTCTCGTAG 59.831 55.000 16.64 11.26 0.00 3.51
8024 11614 3.163655 GCACTCGCTGCAGTTCTC 58.836 61.111 16.64 0.00 46.29 2.87
8084 11674 4.131596 TGTCTACTACAACAAGGTTTGCC 58.868 43.478 0.00 0.00 34.29 4.52


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

AutoCloner maintained by Alex Coulton.