Multiple sequence alignment - TraesCS5B01G331200

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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 TraesCS5B01G331200 chr5B 100.000 5724 0 0 1 5724 515403184 515397461 0.000000e+00 10571.0
1 TraesCS5B01G331200 chr5B 87.707 1025 80 19 1 989 419774298 419773284 0.000000e+00 1153.0
2 TraesCS5B01G331200 chr5B 87.150 1035 83 24 1 988 114905275 114906306 0.000000e+00 1129.0
3 TraesCS5B01G331200 chr5B 86.994 1038 72 27 1 988 297114328 297113304 0.000000e+00 1110.0
4 TraesCS5B01G331200 chr5B 87.828 838 74 7 3 812 369163873 369163036 0.000000e+00 957.0
5 TraesCS5B01G331200 chr5B 100.000 402 0 0 6015 6416 515397170 515396769 0.000000e+00 743.0
6 TraesCS5B01G331200 chr5B 86.506 415 38 6 6015 6416 222418256 222417847 2.120000e-119 440.0
7 TraesCS5B01G331200 chr5B 86.473 414 41 8 6015 6416 607069125 607068715 2.120000e-119 440.0
8 TraesCS5B01G331200 chr5B 85.990 414 43 8 6015 6416 607124637 607124227 4.600000e-116 429.0
9 TraesCS5B01G331200 chr5B 84.536 194 19 8 800 989 468053025 468052839 1.420000e-41 182.0
10 TraesCS5B01G331200 chr5B 84.659 176 20 7 819 990 668135602 668135774 1.110000e-37 169.0
11 TraesCS5B01G331200 chr5B 84.181 177 21 5 816 989 22030154 22029982 1.430000e-36 165.0
12 TraesCS5B01G331200 chr5A 93.707 3464 159 32 1521 4950 540277854 540274416 0.000000e+00 5134.0
13 TraesCS5B01G331200 chr5A 82.424 990 145 24 1 970 651684371 651685351 0.000000e+00 837.0
14 TraesCS5B01G331200 chr5A 89.394 660 27 5 4951 5587 540274366 540273727 0.000000e+00 791.0
15 TraesCS5B01G331200 chr5A 89.211 380 17 10 1013 1392 540279255 540278900 2.730000e-123 453.0
16 TraesCS5B01G331200 chr5A 96.491 114 4 0 5592 5705 540273694 540273581 8.490000e-44 189.0
17 TraesCS5B01G331200 chr5D 93.959 2367 115 15 2605 4951 425996907 425994549 0.000000e+00 3554.0
18 TraesCS5B01G331200 chr5D 94.479 978 40 5 1013 1985 425998343 425997375 0.000000e+00 1495.0
19 TraesCS5B01G331200 chr5D 95.485 598 15 6 4951 5538 425994500 425993905 0.000000e+00 944.0
20 TraesCS5B01G331200 chr5D 96.053 76 2 1 2535 2610 425997336 425997262 8.740000e-24 122.0
21 TraesCS5B01G331200 chr4D 88.603 2448 213 46 2536 4949 465562836 465560421 0.000000e+00 2915.0
22 TraesCS5B01G331200 chr4D 84.343 677 86 13 1400 2070 465563704 465563042 0.000000e+00 645.0
23 TraesCS5B01G331200 chr4D 83.846 520 68 6 4427 4930 465415340 465414821 1.250000e-131 481.0
24 TraesCS5B01G331200 chr4D 80.690 290 41 12 5194 5478 465414677 465414398 1.810000e-50 211.0
25 TraesCS5B01G331200 chr4D 92.188 128 10 0 2095 2222 465563052 465562925 1.420000e-41 182.0
26 TraesCS5B01G331200 chr4D 84.270 178 21 5 816 990 115402040 115402213 3.980000e-37 167.0
27 TraesCS5B01G331200 chr4D 84.091 176 22 5 814 986 396622285 396622113 1.430000e-36 165.0
28 TraesCS5B01G331200 chr4A 88.582 2391 230 24 2535 4918 4868655 4871009 0.000000e+00 2863.0
29 TraesCS5B01G331200 chr4A 81.406 683 104 18 1400 2067 4867674 4868348 2.630000e-148 536.0
30 TraesCS5B01G331200 chr4A 86.893 412 41 4 6018 6416 605429784 605429373 3.530000e-122 449.0
31 TraesCS5B01G331200 chr4A 86.199 413 43 5 6017 6416 543415560 543415971 9.880000e-118 435.0
32 TraesCS5B01G331200 chr4A 81.651 218 28 5 4735 4946 5020192 5020403 3.080000e-38 171.0
33 TraesCS5B01G331200 chr4A 78.214 280 51 6 5201 5478 5020545 5020816 3.080000e-38 171.0
34 TraesCS5B01G331200 chr4A 91.453 117 9 1 1089 1205 4867483 4867598 6.660000e-35 159.0
35 TraesCS5B01G331200 chr4A 93.023 43 3 0 2101 2143 4868347 4868389 5.370000e-06 63.9
36 TraesCS5B01G331200 chr4B 87.783 2079 191 40 2853 4901 582360757 582358712 0.000000e+00 2374.0
37 TraesCS5B01G331200 chr4B 87.695 1024 92 24 1 996 592200091 592201108 0.000000e+00 1162.0
38 TraesCS5B01G331200 chr4B 86.049 1025 83 17 1 968 404851594 404852615 0.000000e+00 1046.0
39 TraesCS5B01G331200 chr4B 83.900 677 88 14 1400 2070 582362240 582361579 1.520000e-175 627.0
40 TraesCS5B01G331200 chr4B 90.909 330 28 1 1 328 78614898 78615227 5.900000e-120 442.0
41 TraesCS5B01G331200 chr4B 92.208 308 19 5 2535 2841 582361323 582361020 1.280000e-116 431.0
42 TraesCS5B01G331200 chr4B 82.624 282 35 9 5201 5478 582157373 582157102 2.990000e-58 237.0
43 TraesCS5B01G331200 chr4B 80.844 308 43 10 4650 4949 582157810 582157511 1.800000e-55 228.0
44 TraesCS5B01G331200 chr4B 87.943 141 15 2 1066 1205 582362608 582362469 1.430000e-36 165.0
45 TraesCS5B01G331200 chr4B 100.000 45 0 0 2101 2145 582361583 582361539 4.120000e-12 84.2
46 TraesCS5B01G331200 chr4B 90.385 52 4 1 2485 2535 582361413 582361362 4.150000e-07 67.6
47 TraesCS5B01G331200 chr1B 87.846 1012 94 17 1 988 106797384 106796378 0.000000e+00 1160.0
48 TraesCS5B01G331200 chr1B 86.571 417 41 5 6015 6416 564735584 564736000 4.560000e-121 446.0
49 TraesCS5B01G331200 chr1B 88.235 51 4 2 2391 2440 458047864 458047815 6.950000e-05 60.2
50 TraesCS5B01G331200 chr7B 87.745 1020 67 25 3 986 320259311 320260308 0.000000e+00 1138.0
51 TraesCS5B01G331200 chr7B 85.366 1025 112 17 1 990 721498087 721497066 0.000000e+00 1027.0
52 TraesCS5B01G331200 chr7B 84.674 1044 97 25 1 986 505463096 505462058 0.000000e+00 983.0
53 TraesCS5B01G331200 chr3B 84.933 1042 98 21 4 989 650352625 650351587 0.000000e+00 1000.0
54 TraesCS5B01G331200 chr3B 87.872 841 64 12 1 812 244387689 244388520 0.000000e+00 953.0
55 TraesCS5B01G331200 chr3B 81.871 171 31 0 2317 2487 560119344 560119174 1.860000e-30 145.0
56 TraesCS5B01G331200 chr3B 96.774 31 1 0 2467 2497 329751233 329751203 1.200000e-02 52.8
57 TraesCS5B01G331200 chr6B 87.006 785 56 19 165 905 155336191 155335409 0.000000e+00 843.0
58 TraesCS5B01G331200 chr6B 87.255 408 40 3 6015 6410 32123582 32123175 7.580000e-124 455.0
59 TraesCS5B01G331200 chr6B 84.659 176 19 6 816 986 716309062 716308890 1.110000e-37 169.0
60 TraesCS5B01G331200 chr3A 87.079 743 88 7 1 738 577628328 577627589 0.000000e+00 833.0
61 TraesCS5B01G331200 chr2A 85.290 809 104 7 8 812 653421121 653420324 0.000000e+00 821.0
62 TraesCS5B01G331200 chr2A 79.290 169 25 10 2317 2481 692760297 692760459 6.800000e-20 110.0
63 TraesCS5B01G331200 chr1D 84.625 826 98 14 4 812 483151891 483151078 0.000000e+00 795.0
64 TraesCS5B01G331200 chr1D 83.908 174 22 4 816 986 442792982 442792812 1.850000e-35 161.0
65 TraesCS5B01G331200 chr1D 75.887 282 51 15 2221 2496 478401978 478401708 1.880000e-25 128.0
66 TraesCS5B01G331200 chr2D 87.229 415 40 4 6015 6416 72626551 72626137 1.630000e-125 460.0
67 TraesCS5B01G331200 chr3D 86.747 415 40 7 6015 6416 609023106 609023518 1.270000e-121 448.0
68 TraesCS5B01G331200 chr3D 80.814 172 31 2 2317 2487 428468912 428468742 4.040000e-27 134.0
69 TraesCS5B01G331200 chr7A 78.598 271 47 8 2222 2491 681817056 681817316 1.110000e-37 169.0
70 TraesCS5B01G331200 chr7D 82.857 105 15 3 2383 2487 611443245 611443346 2.460000e-14 91.6
71 TraesCS5B01G331200 chr6A 100.000 29 0 0 2467 2495 158470242 158470214 3.000000e-03 54.7


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 TraesCS5B01G331200 chr5B 515396769 515403184 6415 True 5657.000000 10571 100.000000 1 6416 2 chr5B.!!$R9 6415
1 TraesCS5B01G331200 chr5B 419773284 419774298 1014 True 1153.000000 1153 87.707000 1 989 1 chr5B.!!$R5 988
2 TraesCS5B01G331200 chr5B 114905275 114906306 1031 False 1129.000000 1129 87.150000 1 988 1 chr5B.!!$F1 987
3 TraesCS5B01G331200 chr5B 297113304 297114328 1024 True 1110.000000 1110 86.994000 1 988 1 chr5B.!!$R3 987
4 TraesCS5B01G331200 chr5B 369163036 369163873 837 True 957.000000 957 87.828000 3 812 1 chr5B.!!$R4 809
5 TraesCS5B01G331200 chr5A 540273581 540279255 5674 True 1641.750000 5134 92.200750 1013 5705 4 chr5A.!!$R1 4692
6 TraesCS5B01G331200 chr5A 651684371 651685351 980 False 837.000000 837 82.424000 1 970 1 chr5A.!!$F1 969
7 TraesCS5B01G331200 chr5D 425993905 425998343 4438 True 1528.750000 3554 94.994000 1013 5538 4 chr5D.!!$R1 4525
8 TraesCS5B01G331200 chr4D 465560421 465563704 3283 True 1247.333333 2915 88.378000 1400 4949 3 chr4D.!!$R3 3549
9 TraesCS5B01G331200 chr4D 465414398 465415340 942 True 346.000000 481 82.268000 4427 5478 2 chr4D.!!$R2 1051
10 TraesCS5B01G331200 chr4A 4867483 4871009 3526 False 905.475000 2863 88.616000 1089 4918 4 chr4A.!!$F2 3829
11 TraesCS5B01G331200 chr4B 592200091 592201108 1017 False 1162.000000 1162 87.695000 1 996 1 chr4B.!!$F3 995
12 TraesCS5B01G331200 chr4B 404851594 404852615 1021 False 1046.000000 1046 86.049000 1 968 1 chr4B.!!$F2 967
13 TraesCS5B01G331200 chr4B 582358712 582362608 3896 True 624.800000 2374 90.369833 1066 4901 6 chr4B.!!$R2 3835
14 TraesCS5B01G331200 chr4B 582157102 582157810 708 True 232.500000 237 81.734000 4650 5478 2 chr4B.!!$R1 828
15 TraesCS5B01G331200 chr1B 106796378 106797384 1006 True 1160.000000 1160 87.846000 1 988 1 chr1B.!!$R1 987
16 TraesCS5B01G331200 chr7B 320259311 320260308 997 False 1138.000000 1138 87.745000 3 986 1 chr7B.!!$F1 983
17 TraesCS5B01G331200 chr7B 721497066 721498087 1021 True 1027.000000 1027 85.366000 1 990 1 chr7B.!!$R2 989
18 TraesCS5B01G331200 chr7B 505462058 505463096 1038 True 983.000000 983 84.674000 1 986 1 chr7B.!!$R1 985
19 TraesCS5B01G331200 chr3B 650351587 650352625 1038 True 1000.000000 1000 84.933000 4 989 1 chr3B.!!$R3 985
20 TraesCS5B01G331200 chr3B 244387689 244388520 831 False 953.000000 953 87.872000 1 812 1 chr3B.!!$F1 811
21 TraesCS5B01G331200 chr6B 155335409 155336191 782 True 843.000000 843 87.006000 165 905 1 chr6B.!!$R2 740
22 TraesCS5B01G331200 chr3A 577627589 577628328 739 True 833.000000 833 87.079000 1 738 1 chr3A.!!$R1 737
23 TraesCS5B01G331200 chr2A 653420324 653421121 797 True 821.000000 821 85.290000 8 812 1 chr2A.!!$R1 804
24 TraesCS5B01G331200 chr1D 483151078 483151891 813 True 795.000000 795 84.625000 4 812 1 chr1D.!!$R3 808

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
986 1137 0.036294 GGCCGTTGGAGTTAGCTCTT 60.036 55.000 6.54 0.0 41.38 2.85 F
1002 1153 0.673644 TCTTAGTGAAGGGCTTGCGC 60.674 55.000 0.00 0.0 33.09 6.09 F
1042 1193 0.759346 CCCTCCACCTGCATACCTAC 59.241 60.000 0.00 0.0 0.00 3.18 F
2949 4931 0.324943 ATGGCGCCTTCTGTGTTACT 59.675 50.000 29.70 0.0 0.00 2.24 F
3569 5585 1.197721 AGCAGACAGTTAACAATGCGC 59.802 47.619 8.61 0.0 38.65 6.09 F
4581 6624 1.740025 GTGCTCTTCAAGGGATTTCCG 59.260 52.381 0.00 0.0 41.52 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2905 4887 0.618458 ATCCGCCCAAAGTGCTTCTA 59.382 50.000 0.00 0.0 0.00 2.10 R
2949 4931 1.879380 AGCTCGTGTTGCATTGCTTTA 59.121 42.857 10.49 0.0 0.00 1.85 R
3129 5130 5.221803 ACAGATGTTCACCTCATGTTTCTCT 60.222 40.000 0.00 0.0 0.00 3.10 R
4725 6768 0.409876 AGGCCTAGTCTGGTGAGTGA 59.590 55.000 1.29 0.0 0.00 3.41 R
4758 6801 1.133025 CCAATCACCTGCGAATTGGAC 59.867 52.381 7.43 0.0 43.16 4.02 R
6362 8526 0.539986 TCATGGGTCCGTAAAGCTCC 59.460 55.000 0.00 0.0 0.00 4.70 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
186 205 0.801251 ATGTTTCTCGCAGCTTCAGC 59.199 50.000 0.00 0.00 42.49 4.26
253 314 3.213402 CTCGCTCCGTCCTCCTCC 61.213 72.222 0.00 0.00 0.00 4.30
269 330 1.751351 CCTCCGCTCATAGAACTGACA 59.249 52.381 0.00 0.00 0.00 3.58
638 699 2.819595 GCGCATCGACATGGTGGT 60.820 61.111 0.30 0.00 0.00 4.16
665 726 1.464734 CAGCGAGGTTAGTGAGAGGA 58.535 55.000 0.00 0.00 0.00 3.71
880 1020 3.425713 CGCATTGGACACGCTGCT 61.426 61.111 0.00 0.00 32.48 4.24
926 1066 4.091939 GGACGGGCGGCCTAGTTT 62.092 66.667 27.04 4.48 41.04 2.66
974 1125 4.020378 CGTTTGGGTCGGCCGTTG 62.020 66.667 27.15 0.00 34.97 4.10
975 1126 3.666253 GTTTGGGTCGGCCGTTGG 61.666 66.667 27.15 0.00 34.97 3.77
976 1127 3.875023 TTTGGGTCGGCCGTTGGA 61.875 61.111 27.15 1.49 34.97 3.53
977 1128 3.835790 TTTGGGTCGGCCGTTGGAG 62.836 63.158 27.15 0.00 34.97 3.86
979 1130 4.324991 GGGTCGGCCGTTGGAGTT 62.325 66.667 27.15 0.00 34.97 3.01
980 1131 2.658422 GGTCGGCCGTTGGAGTTA 59.342 61.111 27.15 0.00 0.00 2.24
981 1132 1.447314 GGTCGGCCGTTGGAGTTAG 60.447 63.158 27.15 0.00 0.00 2.34
982 1133 2.098831 GTCGGCCGTTGGAGTTAGC 61.099 63.158 27.15 0.06 0.00 3.09
983 1134 2.264794 CGGCCGTTGGAGTTAGCT 59.735 61.111 19.50 0.00 0.00 3.32
984 1135 1.810030 CGGCCGTTGGAGTTAGCTC 60.810 63.158 19.50 0.00 40.93 4.09
985 1136 1.597461 GGCCGTTGGAGTTAGCTCT 59.403 57.895 6.54 0.00 41.38 4.09
986 1137 0.036294 GGCCGTTGGAGTTAGCTCTT 60.036 55.000 6.54 0.00 41.38 2.85
987 1138 1.206371 GGCCGTTGGAGTTAGCTCTTA 59.794 52.381 6.54 0.00 41.38 2.10
988 1139 2.541556 GCCGTTGGAGTTAGCTCTTAG 58.458 52.381 6.54 0.00 41.38 2.18
989 1140 2.094130 GCCGTTGGAGTTAGCTCTTAGT 60.094 50.000 6.54 0.00 41.38 2.24
990 1141 3.512680 CCGTTGGAGTTAGCTCTTAGTG 58.487 50.000 6.54 0.00 41.38 2.74
991 1142 3.192844 CCGTTGGAGTTAGCTCTTAGTGA 59.807 47.826 6.54 0.00 41.38 3.41
992 1143 4.321750 CCGTTGGAGTTAGCTCTTAGTGAA 60.322 45.833 6.54 0.00 41.38 3.18
993 1144 4.859798 CGTTGGAGTTAGCTCTTAGTGAAG 59.140 45.833 6.54 0.00 41.38 3.02
994 1145 5.172205 GTTGGAGTTAGCTCTTAGTGAAGG 58.828 45.833 6.54 0.00 41.38 3.46
995 1146 3.769844 TGGAGTTAGCTCTTAGTGAAGGG 59.230 47.826 6.54 0.00 41.38 3.95
1001 1152 1.363744 CTCTTAGTGAAGGGCTTGCG 58.636 55.000 0.00 0.00 33.09 4.85
1002 1153 0.673644 TCTTAGTGAAGGGCTTGCGC 60.674 55.000 0.00 0.00 33.09 6.09
1042 1193 0.759346 CCCTCCACCTGCATACCTAC 59.241 60.000 0.00 0.00 0.00 3.18
1043 1194 1.692762 CCCTCCACCTGCATACCTACT 60.693 57.143 0.00 0.00 0.00 2.57
1044 1195 2.119495 CCTCCACCTGCATACCTACTT 58.881 52.381 0.00 0.00 0.00 2.24
1045 1196 3.305720 CCTCCACCTGCATACCTACTTA 58.694 50.000 0.00 0.00 0.00 2.24
1046 1197 3.069729 CCTCCACCTGCATACCTACTTAC 59.930 52.174 0.00 0.00 0.00 2.34
1047 1198 3.036091 TCCACCTGCATACCTACTTACC 58.964 50.000 0.00 0.00 0.00 2.85
1048 1199 3.039011 CCACCTGCATACCTACTTACCT 58.961 50.000 0.00 0.00 0.00 3.08
1049 1200 4.079038 TCCACCTGCATACCTACTTACCTA 60.079 45.833 0.00 0.00 0.00 3.08
1144 1295 3.419759 GCGGCGGTGGTTGTACTG 61.420 66.667 9.78 0.00 0.00 2.74
1214 1365 2.759607 GCCAACCAGGTAAGGCACTTG 61.760 57.143 24.66 4.18 44.35 3.16
1235 1387 1.915078 CTCCCAAATCCGCAGTCCCT 61.915 60.000 0.00 0.00 0.00 4.20
1240 1392 1.068333 CAAATCCGCAGTCCCTTGTTG 60.068 52.381 0.00 0.00 0.00 3.33
1253 1405 4.156739 GTCCCTTGTTGGTTCTGATTGATC 59.843 45.833 0.00 0.00 0.00 2.92
1255 1407 3.753272 CCTTGTTGGTTCTGATTGATCGT 59.247 43.478 0.00 0.00 0.00 3.73
1333 1534 2.110721 AGGGGAAGCAATCTTTGGAAGT 59.889 45.455 0.00 0.00 31.48 3.01
1549 2700 8.311836 TGTAGTATGAAGCTATTTATACCCTGC 58.688 37.037 0.00 0.00 38.18 4.85
1614 2773 7.287950 CAAAATTGCATCAGATTTCAGTGTTG 58.712 34.615 0.00 0.00 0.00 3.33
1813 2979 6.541641 AGAAATCAGTGCAGTTATCAGGAATC 59.458 38.462 0.00 0.00 0.00 2.52
1824 2990 8.719648 GCAGTTATCAGGAATCTCAAAGATATG 58.280 37.037 0.00 0.00 32.89 1.78
1966 3133 7.545265 GCTTTCTTATTTGCATATGTGGTTCAA 59.455 33.333 4.29 0.00 0.00 2.69
2071 3242 4.870123 TTGTTCACCATGCTAAGCAATT 57.130 36.364 0.00 0.00 43.62 2.32
2145 3467 5.973565 GGCTTATTGTGCAGCTTAAGTATTG 59.026 40.000 4.02 2.25 36.20 1.90
2376 3703 8.923683 GTCTCATGATGTATCTAATGACATGTG 58.076 37.037 1.15 0.00 36.42 3.21
2435 3762 4.945543 ACTTGGTCGGAGTTTGTAAAGTTT 59.054 37.500 0.00 0.00 0.00 2.66
2444 3771 8.949177 TCGGAGTTTGTAAAGTTTAACTCTTTT 58.051 29.630 20.98 0.00 43.65 2.27
2501 3829 8.474710 TGGAGGGAGTAGTATATTACAAAGTC 57.525 38.462 8.00 0.00 0.00 3.01
2775 4506 2.133281 TGCTTGGATTGTCTCATGGG 57.867 50.000 0.00 0.00 0.00 4.00
2799 4530 9.832445 GGGAGAAGTCATGTAATAGTCAAAATA 57.168 33.333 0.00 0.00 0.00 1.40
2842 4824 2.095853 CCATGTTTGCGTAACTGCTAGG 59.904 50.000 0.00 0.00 37.64 3.02
2863 4845 7.440856 GCTAGGCTGATTCTATATCTTATTGGC 59.559 40.741 0.00 0.00 0.00 4.52
2893 4875 8.699749 GTGTTTTAATTAGTGATGTTTTCCTGC 58.300 33.333 0.00 0.00 0.00 4.85
2897 4879 9.995003 TTTAATTAGTGATGTTTTCCTGCATTT 57.005 25.926 0.00 0.00 0.00 2.32
2905 4887 6.267471 TGATGTTTTCCTGCATTTTAGGTTCT 59.733 34.615 0.00 0.00 36.67 3.01
2934 4916 2.592861 GGGCGGATGACTGATGGC 60.593 66.667 0.00 0.00 0.00 4.40
2940 4922 1.162800 GGATGACTGATGGCGCCTTC 61.163 60.000 30.12 30.12 0.00 3.46
2949 4931 0.324943 ATGGCGCCTTCTGTGTTACT 59.675 50.000 29.70 0.00 0.00 2.24
3129 5130 1.361204 TCCATCCTGCTTCCTTGACA 58.639 50.000 0.00 0.00 0.00 3.58
3208 5209 8.923609 CTGCATATCAGTATATGTGACCTTAG 57.076 38.462 7.11 0.00 44.66 2.18
3223 5224 6.014925 TGTGACCTTAGCACATGAAGTAGTTA 60.015 38.462 0.00 0.00 41.00 2.24
3252 5253 4.457949 CAGGTTGGGTAGTTCCATTTGTAC 59.542 45.833 0.00 0.00 36.58 2.90
3339 5349 9.420118 AGTTTTCATGGTATAAGCATATTCCAA 57.580 29.630 10.76 0.00 40.87 3.53
3499 5512 2.237392 AGCTGGTATGTTCTCTTGGACC 59.763 50.000 0.00 0.00 0.00 4.46
3569 5585 1.197721 AGCAGACAGTTAACAATGCGC 59.802 47.619 8.61 0.00 38.65 6.09
3578 5594 5.629020 ACAGTTAACAATGCGCATAAACTTG 59.371 36.000 25.61 20.53 0.00 3.16
3582 5598 8.026607 AGTTAACAATGCGCATAAACTTGTAAT 58.973 29.630 25.61 12.59 30.33 1.89
3590 5606 5.640732 CGCATAAACTTGTAATCCTTTGCT 58.359 37.500 0.00 0.00 0.00 3.91
3847 5864 8.783093 TCTGATTTTAGTAAATGTTGACACTGG 58.217 33.333 0.00 0.00 34.16 4.00
3969 5986 2.092968 CCTCTGTTGCTAGGTATGCCAA 60.093 50.000 1.54 0.00 37.19 4.52
3983 6000 2.996249 TGCCAATCACTTGCCAAAAA 57.004 40.000 0.00 0.00 0.00 1.94
3984 6001 2.836262 TGCCAATCACTTGCCAAAAAG 58.164 42.857 0.00 0.00 0.00 2.27
3999 6019 9.573133 CTTGCCAAAAAGAATTTATACTGTAGG 57.427 33.333 0.00 0.00 37.28 3.18
4050 6071 2.863809 TCAGCTGATCTAGGCGTATCA 58.136 47.619 13.74 0.00 0.00 2.15
4115 6136 7.119846 GGTTAACTCACATCATCTGCTTACTTT 59.880 37.037 5.42 0.00 0.00 2.66
4118 6139 8.798859 AACTCACATCATCTGCTTACTTTAAT 57.201 30.769 0.00 0.00 0.00 1.40
4164 6186 5.288015 TGCATTGTAACTTGAATGGTTGTG 58.712 37.500 0.00 0.00 31.38 3.33
4172 6194 6.538945 AACTTGAATGGTTGTGTTTAGGTT 57.461 33.333 0.00 0.00 0.00 3.50
4252 6274 6.532657 CCCATGTTTCTAGATGTTTGAATTGC 59.467 38.462 0.00 0.00 0.00 3.56
4263 6285 7.669427 AGATGTTTGAATTGCTATGTTTTGGA 58.331 30.769 0.00 0.00 0.00 3.53
4286 6308 2.170166 TGGCCTTTTGGTTGCTCTATG 58.830 47.619 3.32 0.00 42.99 2.23
4469 6498 2.721274 TGGGTCATTGTTTCAATGCG 57.279 45.000 15.04 0.00 0.00 4.73
4556 6599 6.215845 ACTGGTACTGCAATTGAAAAATCAC 58.784 36.000 10.34 0.00 0.00 3.06
4561 6604 3.058450 TGCAATTGAAAAATCACGCAGG 58.942 40.909 10.34 0.00 0.00 4.85
4581 6624 1.740025 GTGCTCTTCAAGGGATTTCCG 59.260 52.381 0.00 0.00 41.52 4.30
4813 6860 7.310664 CACAATAATATTGATCAGATGGGCAC 58.689 38.462 18.78 0.00 0.00 5.01
4870 6917 7.717875 TGCCAATTCCATAGTTTATAGGTGTAC 59.282 37.037 0.00 0.00 0.00 2.90
4918 6977 6.065976 TGTACATTTGATGGTTGAGGAGAT 57.934 37.500 0.00 0.00 33.60 2.75
4920 6979 7.629157 TGTACATTTGATGGTTGAGGAGATAA 58.371 34.615 0.00 0.00 33.60 1.75
4921 6980 7.552687 TGTACATTTGATGGTTGAGGAGATAAC 59.447 37.037 0.00 0.00 33.60 1.89
4922 6981 6.484288 ACATTTGATGGTTGAGGAGATAACA 58.516 36.000 0.00 0.00 33.60 2.41
4923 6982 7.121382 ACATTTGATGGTTGAGGAGATAACAT 58.879 34.615 0.00 0.00 33.60 2.71
4924 6983 7.284034 ACATTTGATGGTTGAGGAGATAACATC 59.716 37.037 0.00 0.00 33.60 3.06
4925 6984 6.566079 TTGATGGTTGAGGAGATAACATCT 57.434 37.500 0.00 0.00 43.70 2.90
4951 7010 6.401474 GCATGTGCATATATCAGTTTACTCGG 60.401 42.308 0.00 0.00 41.59 4.63
4953 7012 5.983118 TGTGCATATATCAGTTTACTCGGTG 59.017 40.000 0.00 0.00 0.00 4.94
4954 7013 5.983720 GTGCATATATCAGTTTACTCGGTGT 59.016 40.000 0.00 0.00 0.00 4.16
4955 7014 6.479001 GTGCATATATCAGTTTACTCGGTGTT 59.521 38.462 0.00 0.00 0.00 3.32
4957 7016 6.129168 GCATATATCAGTTTACTCGGTGTTCG 60.129 42.308 0.00 0.00 40.90 3.95
4959 7018 3.004024 TCAGTTTACTCGGTGTTCGTC 57.996 47.619 0.00 0.00 40.32 4.20
5013 7131 4.496840 CCCAACGAACTCCAACTGTTTAAC 60.497 45.833 0.00 0.00 0.00 2.01
5029 7147 4.396790 TGTTTAACGAAAAGGTGTTGAGCT 59.603 37.500 0.00 0.00 0.00 4.09
5032 7150 6.680874 TTAACGAAAAGGTGTTGAGCTTAA 57.319 33.333 0.00 0.00 39.03 1.85
5060 7178 6.349611 CCAAGTTGTTTCAGCATGTATAGCTT 60.350 38.462 1.45 0.00 41.14 3.74
5245 7378 7.239438 TGTACCCAAATAAATTGTACCAGGAA 58.761 34.615 0.00 0.00 37.32 3.36
5275 7408 9.206870 GATTTCTTTTTCATTGTCTTTGCCATA 57.793 29.630 0.00 0.00 0.00 2.74
5396 7532 7.178628 AGGTAAGCTTACACTCTGAATCTGTTA 59.821 37.037 31.98 0.00 35.37 2.41
5422 7558 5.843019 TCCATTTACTTCCTTGTTCCTCT 57.157 39.130 0.00 0.00 0.00 3.69
5518 7654 4.054780 TGTCGTTAGAGCAACTTCAAGT 57.945 40.909 0.00 0.00 34.77 3.16
5587 7723 7.286087 ACCGTAAAATTCAAGGGAAGTTAACTT 59.714 33.333 20.67 20.67 40.14 2.66
5588 7724 8.139350 CCGTAAAATTCAAGGGAAGTTAACTTT 58.861 33.333 21.40 3.78 40.14 2.66
5648 7812 5.805728 TCCTAAACTCTTCCTGTGAATTCC 58.194 41.667 2.27 0.00 0.00 3.01
5690 7854 7.936496 TCTCATAAACAAGCATACAAATGGA 57.064 32.000 0.00 0.00 33.38 3.41
6115 8279 4.712425 GCGGTGCAGCTTGGCTTG 62.712 66.667 14.92 0.00 36.40 4.01
6116 8280 4.047059 CGGTGCAGCTTGGCTTGG 62.047 66.667 14.92 0.00 36.40 3.61
6117 8281 2.914097 GGTGCAGCTTGGCTTGGT 60.914 61.111 9.07 0.00 36.40 3.67
6118 8282 2.501602 GGTGCAGCTTGGCTTGGTT 61.502 57.895 9.07 0.00 36.40 3.67
6119 8283 1.300388 GTGCAGCTTGGCTTGGTTG 60.300 57.895 0.00 0.00 36.40 3.77
6120 8284 2.356673 GCAGCTTGGCTTGGTTGC 60.357 61.111 0.00 0.00 36.40 4.17
6121 8285 2.049802 CAGCTTGGCTTGGTTGCG 60.050 61.111 0.00 0.00 36.40 4.85
6122 8286 3.297620 AGCTTGGCTTGGTTGCGG 61.298 61.111 0.00 0.00 33.89 5.69
6123 8287 3.605664 GCTTGGCTTGGTTGCGGT 61.606 61.111 0.00 0.00 0.00 5.68
6124 8288 2.644992 CTTGGCTTGGTTGCGGTC 59.355 61.111 0.00 0.00 0.00 4.79
6125 8289 2.909965 TTGGCTTGGTTGCGGTCC 60.910 61.111 0.00 0.00 0.00 4.46
6229 8393 2.925170 CCCCCGGCCCAGATCTAG 60.925 72.222 0.00 0.00 0.00 2.43
6230 8394 2.925170 CCCCGGCCCAGATCTAGG 60.925 72.222 2.31 2.31 0.00 3.02
6235 8399 3.631046 GCCCAGATCTAGGCCCGG 61.631 72.222 20.41 4.23 43.76 5.73
6236 8400 3.631046 CCCAGATCTAGGCCCGGC 61.631 72.222 0.00 0.00 0.00 6.13
6237 8401 3.996124 CCAGATCTAGGCCCGGCG 61.996 72.222 0.00 0.00 0.00 6.46
6238 8402 3.996124 CAGATCTAGGCCCGGCGG 61.996 72.222 21.46 21.46 0.00 6.13
6255 8419 2.203938 GGCCCCATCCGGATCCTA 60.204 66.667 15.88 0.00 0.00 2.94
6256 8420 2.294078 GGCCCCATCCGGATCCTAG 61.294 68.421 15.88 2.83 0.00 3.02
6257 8421 2.960688 GCCCCATCCGGATCCTAGC 61.961 68.421 15.88 11.62 0.00 3.42
6258 8422 2.650116 CCCCATCCGGATCCTAGCG 61.650 68.421 15.88 1.56 0.00 4.26
6259 8423 2.650116 CCCATCCGGATCCTAGCGG 61.650 68.421 15.88 11.72 0.00 5.52
6260 8424 2.650116 CCATCCGGATCCTAGCGGG 61.650 68.421 15.88 7.19 0.00 6.13
6261 8425 2.997897 ATCCGGATCCTAGCGGGC 60.998 66.667 12.38 0.00 34.39 6.13
6287 8451 4.681978 GGCGTGGCCTCGTTGTCT 62.682 66.667 26.41 0.00 46.69 3.41
6288 8452 3.414700 GCGTGGCCTCGTTGTCTG 61.415 66.667 26.41 0.00 0.00 3.51
6289 8453 3.414700 CGTGGCCTCGTTGTCTGC 61.415 66.667 18.86 0.00 0.00 4.26
6290 8454 3.414700 GTGGCCTCGTTGTCTGCG 61.415 66.667 3.32 0.00 0.00 5.18
6291 8455 4.680237 TGGCCTCGTTGTCTGCGG 62.680 66.667 3.32 0.00 0.00 5.69
6292 8456 4.681978 GGCCTCGTTGTCTGCGGT 62.682 66.667 0.00 0.00 0.00 5.68
6293 8457 3.414700 GCCTCGTTGTCTGCGGTG 61.415 66.667 0.00 0.00 0.00 4.94
6294 8458 3.414700 CCTCGTTGTCTGCGGTGC 61.415 66.667 0.00 0.00 0.00 5.01
6295 8459 3.767230 CTCGTTGTCTGCGGTGCG 61.767 66.667 0.00 0.00 0.00 5.34
6298 8462 4.012895 GTTGTCTGCGGTGCGGTG 62.013 66.667 0.00 0.00 36.18 4.94
6299 8463 4.228567 TTGTCTGCGGTGCGGTGA 62.229 61.111 0.00 0.00 36.18 4.02
6300 8464 4.662961 TGTCTGCGGTGCGGTGAG 62.663 66.667 0.00 0.00 36.18 3.51
6306 8470 4.135153 CGGTGCGGTGAGGAGGAG 62.135 72.222 0.00 0.00 0.00 3.69
6307 8471 4.459089 GGTGCGGTGAGGAGGAGC 62.459 72.222 0.00 0.00 0.00 4.70
6308 8472 4.803426 GTGCGGTGAGGAGGAGCG 62.803 72.222 0.00 0.00 37.38 5.03
6312 8476 3.844090 GGTGAGGAGGAGCGGCTC 61.844 72.222 21.57 21.57 0.00 4.70
6313 8477 3.071206 GTGAGGAGGAGCGGCTCA 61.071 66.667 29.33 7.77 31.08 4.26
6314 8478 2.757508 TGAGGAGGAGCGGCTCAG 60.758 66.667 29.33 0.00 31.08 3.35
6315 8479 2.441164 GAGGAGGAGCGGCTCAGA 60.441 66.667 29.33 0.00 31.08 3.27
6316 8480 1.832167 GAGGAGGAGCGGCTCAGAT 60.832 63.158 29.33 15.73 31.08 2.90
6317 8481 1.382420 AGGAGGAGCGGCTCAGATT 60.382 57.895 29.33 12.90 31.08 2.40
6318 8482 0.980231 AGGAGGAGCGGCTCAGATTT 60.980 55.000 29.33 10.53 31.08 2.17
6319 8483 0.813210 GGAGGAGCGGCTCAGATTTG 60.813 60.000 29.33 0.00 31.08 2.32
6320 8484 0.813210 GAGGAGCGGCTCAGATTTGG 60.813 60.000 29.33 0.00 31.08 3.28
6321 8485 1.821332 GGAGCGGCTCAGATTTGGG 60.821 63.158 29.33 0.00 31.08 4.12
6322 8486 1.821332 GAGCGGCTCAGATTTGGGG 60.821 63.158 24.42 0.00 0.00 4.96
6323 8487 3.521796 GCGGCTCAGATTTGGGGC 61.522 66.667 0.00 0.00 46.43 5.80
6325 8489 2.830370 GGCTCAGATTTGGGGCGG 60.830 66.667 0.00 0.00 40.89 6.13
6326 8490 3.521796 GCTCAGATTTGGGGCGGC 61.522 66.667 0.00 0.00 0.00 6.53
6327 8491 3.204827 CTCAGATTTGGGGCGGCG 61.205 66.667 0.51 0.51 0.00 6.46
6328 8492 3.680620 CTCAGATTTGGGGCGGCGA 62.681 63.158 12.98 0.00 0.00 5.54
6329 8493 3.508840 CAGATTTGGGGCGGCGAC 61.509 66.667 12.98 8.16 0.00 5.19
6369 8533 4.767255 CGCGAGGGCAGGAGCTTT 62.767 66.667 0.00 0.00 41.70 3.51
6370 8534 2.584608 GCGAGGGCAGGAGCTTTA 59.415 61.111 0.00 0.00 41.70 1.85
6371 8535 1.815840 GCGAGGGCAGGAGCTTTAC 60.816 63.158 0.00 0.00 41.70 2.01
6372 8536 1.519455 CGAGGGCAGGAGCTTTACG 60.519 63.158 0.00 0.00 41.70 3.18
6373 8537 1.153349 GAGGGCAGGAGCTTTACGG 60.153 63.158 0.00 0.00 41.70 4.02
6374 8538 1.612442 AGGGCAGGAGCTTTACGGA 60.612 57.895 0.00 0.00 41.70 4.69
6375 8539 1.449778 GGGCAGGAGCTTTACGGAC 60.450 63.158 0.00 0.00 41.70 4.79
6376 8540 1.449778 GGCAGGAGCTTTACGGACC 60.450 63.158 0.00 0.00 41.70 4.46
6377 8541 1.449778 GCAGGAGCTTTACGGACCC 60.450 63.158 0.00 0.00 37.91 4.46
6378 8542 1.980052 CAGGAGCTTTACGGACCCA 59.020 57.895 0.00 0.00 0.00 4.51
6379 8543 0.541863 CAGGAGCTTTACGGACCCAT 59.458 55.000 0.00 0.00 0.00 4.00
6380 8544 0.541863 AGGAGCTTTACGGACCCATG 59.458 55.000 0.00 0.00 0.00 3.66
6381 8545 0.539986 GGAGCTTTACGGACCCATGA 59.460 55.000 0.00 0.00 0.00 3.07
6382 8546 1.473434 GGAGCTTTACGGACCCATGAG 60.473 57.143 0.00 0.00 0.00 2.90
6383 8547 0.541863 AGCTTTACGGACCCATGAGG 59.458 55.000 0.00 0.00 43.78 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
186 205 2.768492 GCAGGCCGCTCAATTGAGG 61.768 63.158 31.41 20.55 42.29 3.86
253 314 4.259570 CGACAAATGTCAGTTCTATGAGCG 60.260 45.833 13.51 0.00 44.99 5.03
269 330 1.935873 CGCAGGACATCATCGACAAAT 59.064 47.619 0.00 0.00 0.00 2.32
396 457 3.157252 GATCTGGCGCCTCTCCCA 61.157 66.667 29.70 4.55 0.00 4.37
654 715 1.752683 GTCTCGCCTCCTCTCACTAA 58.247 55.000 0.00 0.00 0.00 2.24
738 813 0.236187 ATGTTCGCGCGCTTGTTTTA 59.764 45.000 30.48 9.05 0.00 1.52
827 963 1.136690 CCGCGCGCTTTTAGATCATA 58.863 50.000 30.48 0.00 0.00 2.15
921 1061 6.902408 TGTCCCTTCTTTTTGTCCTAAACTA 58.098 36.000 0.00 0.00 0.00 2.24
924 1064 7.483580 TTTTGTCCCTTCTTTTTGTCCTAAA 57.516 32.000 0.00 0.00 0.00 1.85
925 1065 6.406512 GCTTTTGTCCCTTCTTTTTGTCCTAA 60.407 38.462 0.00 0.00 0.00 2.69
926 1066 5.068591 GCTTTTGTCCCTTCTTTTTGTCCTA 59.931 40.000 0.00 0.00 0.00 2.94
933 1073 1.068588 GGCGCTTTTGTCCCTTCTTTT 59.931 47.619 7.64 0.00 0.00 2.27
937 1077 2.183858 GACGGCGCTTTTGTCCCTTC 62.184 60.000 6.90 0.00 0.00 3.46
940 1080 3.733960 GGACGGCGCTTTTGTCCC 61.734 66.667 22.38 10.70 45.14 4.46
971 1122 5.172205 CCTTCACTAAGAGCTAACTCCAAC 58.828 45.833 0.00 0.00 44.65 3.77
972 1123 4.223032 CCCTTCACTAAGAGCTAACTCCAA 59.777 45.833 0.00 0.00 44.65 3.53
973 1124 3.769844 CCCTTCACTAAGAGCTAACTCCA 59.230 47.826 0.00 0.00 44.65 3.86
974 1125 3.431068 GCCCTTCACTAAGAGCTAACTCC 60.431 52.174 0.00 0.00 44.65 3.85
975 1126 3.449377 AGCCCTTCACTAAGAGCTAACTC 59.551 47.826 0.00 0.00 44.19 3.01
976 1127 3.445987 AGCCCTTCACTAAGAGCTAACT 58.554 45.455 0.00 0.00 44.19 2.24
977 1128 3.897141 AGCCCTTCACTAAGAGCTAAC 57.103 47.619 0.00 0.00 44.19 2.34
978 1129 3.619979 GCAAGCCCTTCACTAAGAGCTAA 60.620 47.826 0.00 0.00 45.16 3.09
979 1130 2.093447 GCAAGCCCTTCACTAAGAGCTA 60.093 50.000 0.00 0.00 45.16 3.32
981 1132 1.090728 GCAAGCCCTTCACTAAGAGC 58.909 55.000 0.00 0.00 36.74 4.09
982 1133 1.363744 CGCAAGCCCTTCACTAAGAG 58.636 55.000 0.00 0.00 34.37 2.85
983 1134 3.532896 CGCAAGCCCTTCACTAAGA 57.467 52.632 0.00 0.00 34.37 2.10
1003 1154 1.446272 GTGAGGGAGCCGAAGAACG 60.446 63.158 0.00 0.00 42.18 3.95
1004 1155 1.079057 GGTGAGGGAGCCGAAGAAC 60.079 63.158 0.00 0.00 0.00 3.01
1005 1156 2.291043 GGGTGAGGGAGCCGAAGAA 61.291 63.158 0.00 0.00 30.84 2.52
1006 1157 2.683933 GGGTGAGGGAGCCGAAGA 60.684 66.667 0.00 0.00 30.84 2.87
1007 1158 3.787001 GGGGTGAGGGAGCCGAAG 61.787 72.222 0.00 0.00 43.98 3.79
1042 1193 4.857509 AGAAATAGCGGCTCTAGGTAAG 57.142 45.455 5.39 0.00 0.00 2.34
1043 1194 4.038883 GGAAGAAATAGCGGCTCTAGGTAA 59.961 45.833 5.39 0.00 0.00 2.85
1044 1195 3.573110 GGAAGAAATAGCGGCTCTAGGTA 59.427 47.826 5.39 0.00 0.00 3.08
1045 1196 2.365941 GGAAGAAATAGCGGCTCTAGGT 59.634 50.000 5.39 0.00 0.00 3.08
1046 1197 2.630580 AGGAAGAAATAGCGGCTCTAGG 59.369 50.000 5.39 0.00 0.00 3.02
1047 1198 3.305744 GGAGGAAGAAATAGCGGCTCTAG 60.306 52.174 5.39 0.00 0.00 2.43
1048 1199 2.628657 GGAGGAAGAAATAGCGGCTCTA 59.371 50.000 5.39 0.00 0.00 2.43
1049 1200 1.414550 GGAGGAAGAAATAGCGGCTCT 59.585 52.381 5.39 0.00 0.00 4.09
1214 1365 0.744771 GGACTGCGGATTTGGGAGAC 60.745 60.000 0.00 0.00 0.00 3.36
1235 1387 4.133820 ACACGATCAATCAGAACCAACAA 58.866 39.130 0.00 0.00 0.00 2.83
1240 1392 3.334691 TCCAACACGATCAATCAGAACC 58.665 45.455 0.00 0.00 0.00 3.62
1253 1405 0.810031 CGCCCCTCTAATCCAACACG 60.810 60.000 0.00 0.00 0.00 4.49
1255 1407 1.483415 GTACGCCCCTCTAATCCAACA 59.517 52.381 0.00 0.00 0.00 3.33
1476 1715 4.177026 CGATGAAGGTGTAAGGAACAGAG 58.823 47.826 0.00 0.00 39.29 3.35
1491 1733 6.373779 AGTAAAATTCAACAGCACGATGAAG 58.626 36.000 0.00 0.00 39.48 3.02
1549 2700 6.239064 CCTTAAGCTGTAGGAGTACTGGTATG 60.239 46.154 0.00 0.00 37.71 2.39
1752 2917 6.201806 CCTTGAAGTCAACTGTAGTTTGAGAG 59.798 42.308 0.00 0.00 35.83 3.20
1758 2923 5.497474 ACAACCTTGAAGTCAACTGTAGTT 58.503 37.500 0.00 0.00 39.12 2.24
2054 3225 5.726980 AAAGAAATTGCTTAGCATGGTGA 57.273 34.783 8.05 0.00 38.76 4.02
2150 3472 8.538409 TGTACATATTGCATAGCATGAGTTAG 57.462 34.615 0.00 0.00 38.76 2.34
2259 3586 9.945904 AACTTCACAAGGTTTGGTTTAAAAATA 57.054 25.926 0.00 0.00 34.12 1.40
2261 3588 8.560374 CAAACTTCACAAGGTTTGGTTTAAAAA 58.440 29.630 9.75 0.00 44.68 1.94
2262 3589 7.931948 TCAAACTTCACAAGGTTTGGTTTAAAA 59.068 29.630 15.36 0.00 46.86 1.52
2263 3590 7.385478 GTCAAACTTCACAAGGTTTGGTTTAAA 59.615 33.333 15.36 0.00 46.86 1.52
2264 3591 6.869388 GTCAAACTTCACAAGGTTTGGTTTAA 59.131 34.615 15.36 0.00 46.86 1.52
2265 3592 6.391537 GTCAAACTTCACAAGGTTTGGTTTA 58.608 36.000 15.36 0.00 46.86 2.01
2269 3596 3.194542 TGGTCAAACTTCACAAGGTTTGG 59.805 43.478 15.36 1.99 46.86 3.28
2476 3803 7.230108 CGACTTTGTAATATACTACTCCCTCCA 59.770 40.741 0.00 0.00 0.00 3.86
2501 3829 6.264841 ACTAAGTAAGGGTCAGAGTAAACG 57.735 41.667 0.00 0.00 0.00 3.60
2799 4530 5.015817 TGGTTGGAGGGTTTACCAGAAATAT 59.984 40.000 0.69 0.00 43.89 1.28
2812 4543 1.178534 CGCAAACATGGTTGGAGGGT 61.179 55.000 24.41 0.00 0.00 4.34
2842 4824 7.555554 ACATGGCCAATAAGATATAGAATCAGC 59.444 37.037 10.96 0.00 0.00 4.26
2893 4875 7.308435 CCAAAGTGCTTCTAGAACCTAAAATG 58.692 38.462 0.00 0.00 0.00 2.32
2897 4879 4.806286 GCCCAAAGTGCTTCTAGAACCTAA 60.806 45.833 0.00 0.00 0.00 2.69
2905 4887 0.618458 ATCCGCCCAAAGTGCTTCTA 59.382 50.000 0.00 0.00 0.00 2.10
2934 4916 3.064207 TGCTTTAGTAACACAGAAGGCG 58.936 45.455 0.00 0.00 0.00 5.52
2940 4922 5.518812 TGTTGCATTGCTTTAGTAACACAG 58.481 37.500 10.49 0.00 33.90 3.66
2949 4931 1.879380 AGCTCGTGTTGCATTGCTTTA 59.121 42.857 10.49 0.00 0.00 1.85
3129 5130 5.221803 ACAGATGTTCACCTCATGTTTCTCT 60.222 40.000 0.00 0.00 0.00 3.10
3208 5209 5.220739 CCTGCAGAATAACTACTTCATGTGC 60.221 44.000 17.39 0.00 0.00 4.57
3223 5224 2.290960 GGAACTACCCAACCTGCAGAAT 60.291 50.000 17.39 0.00 0.00 2.40
3499 5512 0.738975 TCCGCAATAGAGACCACTCG 59.261 55.000 0.00 0.00 46.64 4.18
3569 5585 8.184192 CAGGTAGCAAAGGATTACAAGTTTATG 58.816 37.037 0.00 0.00 0.00 1.90
3590 5606 0.618458 GGTGTCCTGGAATGCAGGTA 59.382 55.000 20.23 8.40 40.59 3.08
3812 5828 9.236006 ACATTTACTAAAATCAGAGCAATGACT 57.764 29.630 0.00 0.00 32.87 3.41
3813 5829 9.846248 AACATTTACTAAAATCAGAGCAATGAC 57.154 29.630 0.00 0.00 32.87 3.06
3831 5848 6.072673 CCTTTACCTCCAGTGTCAACATTTAC 60.073 42.308 0.00 0.00 0.00 2.01
3847 5864 4.409247 TCTTTCTATCAGGCCCTTTACCTC 59.591 45.833 0.00 0.00 34.42 3.85
3896 5913 1.583054 AGGCAACACGTCTCAGTTTC 58.417 50.000 0.00 0.00 41.41 2.78
3953 5970 3.545703 AGTGATTGGCATACCTAGCAAC 58.454 45.455 0.00 0.00 38.80 4.17
3969 5986 9.643693 CAGTATAAATTCTTTTTGGCAAGTGAT 57.356 29.630 0.00 0.00 0.00 3.06
3983 6000 8.589338 CAGCACCTATCCTACAGTATAAATTCT 58.411 37.037 0.00 0.00 0.00 2.40
3984 6001 8.585881 TCAGCACCTATCCTACAGTATAAATTC 58.414 37.037 0.00 0.00 0.00 2.17
3999 6019 3.691118 TGCTCAAACAATCAGCACCTATC 59.309 43.478 0.00 0.00 38.25 2.08
4004 6024 4.797471 TGTATTGCTCAAACAATCAGCAC 58.203 39.130 0.00 0.00 42.85 4.40
4050 6071 1.270305 CCCGACGAGGATGTATGCAAT 60.270 52.381 0.00 0.00 45.00 3.56
4094 6115 8.043113 TCATTAAAGTAAGCAGATGATGTGAGT 58.957 33.333 0.00 0.00 0.00 3.41
4164 6186 8.303876 ACATCCAAACATATCAACAACCTAAAC 58.696 33.333 0.00 0.00 0.00 2.01
4172 6194 7.068103 GGTAATCCACATCCAAACATATCAACA 59.932 37.037 0.00 0.00 0.00 3.33
4252 6274 5.412286 CCAAAAGGCCAATTCCAAAACATAG 59.588 40.000 5.01 0.00 0.00 2.23
4263 6285 2.049372 AGAGCAACCAAAAGGCCAATT 58.951 42.857 5.01 0.00 0.00 2.32
4286 6308 9.004717 AGAAAAAGAAAGCCAGAGTCTTATAAC 57.995 33.333 0.00 0.00 31.41 1.89
4530 6568 6.922957 TGATTTTTCAATTGCAGTACCAGTTC 59.077 34.615 0.00 0.00 0.00 3.01
4535 6578 4.089923 GCGTGATTTTTCAATTGCAGTACC 59.910 41.667 0.00 0.00 0.00 3.34
4561 6604 1.740025 CGGAAATCCCTTGAAGAGCAC 59.260 52.381 0.00 0.00 0.00 4.40
4581 6624 2.859165 TCAAGGTGTCACATTCCTCC 57.141 50.000 5.12 0.00 0.00 4.30
4620 6663 3.907474 TGGAAGATGACCCTGTACTCAAA 59.093 43.478 0.00 0.00 0.00 2.69
4725 6768 0.409876 AGGCCTAGTCTGGTGAGTGA 59.590 55.000 1.29 0.00 0.00 3.41
4758 6801 1.133025 CCAATCACCTGCGAATTGGAC 59.867 52.381 7.43 0.00 43.16 4.02
4813 6860 1.605202 CCGGCAACAAAACCATCCTTG 60.605 52.381 0.00 0.00 0.00 3.61
4870 6917 5.055642 TGGTCACTCAAGTGTACGATAAG 57.944 43.478 9.82 0.00 45.76 1.73
4875 6928 3.245797 CATCTGGTCACTCAAGTGTACG 58.754 50.000 9.82 0.00 45.76 3.67
4951 7010 2.726832 AGGTTCTGCTAGACGAACAC 57.273 50.000 19.65 12.35 40.88 3.32
4953 7012 4.261530 GGGTATAGGTTCTGCTAGACGAAC 60.262 50.000 13.26 13.26 38.95 3.95
4954 7013 3.887716 GGGTATAGGTTCTGCTAGACGAA 59.112 47.826 0.00 0.00 0.00 3.85
4955 7014 3.137913 AGGGTATAGGTTCTGCTAGACGA 59.862 47.826 0.00 0.00 0.00 4.20
4957 7016 4.471548 TGAGGGTATAGGTTCTGCTAGAC 58.528 47.826 0.00 0.00 0.00 2.59
4959 7018 3.829601 CCTGAGGGTATAGGTTCTGCTAG 59.170 52.174 0.00 0.00 0.00 3.42
4996 7113 5.969435 CCTTTTCGTTAAACAGTTGGAGTTC 59.031 40.000 0.00 0.00 0.00 3.01
5013 7131 4.319549 GGACTTAAGCTCAACACCTTTTCG 60.320 45.833 1.29 0.00 0.00 3.46
5029 7147 5.359576 ACATGCTGAAACAACTTGGACTTAA 59.640 36.000 0.00 0.00 0.00 1.85
5032 7150 3.290710 ACATGCTGAAACAACTTGGACT 58.709 40.909 0.00 0.00 0.00 3.85
5060 7178 4.501571 GCCGCTAAACTCTAATGGATCAGA 60.502 45.833 0.00 0.00 0.00 3.27
5245 7378 6.405278 AAGACAATGAAAAAGAAATCGGGT 57.595 33.333 0.00 0.00 0.00 5.28
5275 7408 3.262660 TGTTGGAGATCTGAGCTCACAAT 59.737 43.478 22.82 9.50 34.07 2.71
5396 7532 6.735556 AGGAACAAGGAAGTAAATGGATCAT 58.264 36.000 0.00 0.00 0.00 2.45
5422 7558 3.296709 GAGAGGCAAAGCGACGGGA 62.297 63.158 0.00 0.00 0.00 5.14
5570 7706 9.245481 TGAAAAGTAAAGTTAACTTCCCTTGAA 57.755 29.630 20.78 11.35 36.17 2.69
5603 7767 7.339482 AGGAGAACTGAGAAAAGTAAAGTTGT 58.661 34.615 0.00 0.00 31.45 3.32
6098 8262 4.712425 CAAGCCAAGCTGCACCGC 62.712 66.667 1.02 0.00 39.62 5.68
6099 8263 4.047059 CCAAGCCAAGCTGCACCG 62.047 66.667 1.02 0.00 39.62 4.94
6100 8264 2.501602 AACCAAGCCAAGCTGCACC 61.502 57.895 1.02 0.00 39.62 5.01
6101 8265 1.300388 CAACCAAGCCAAGCTGCAC 60.300 57.895 1.02 0.00 39.62 4.57
6102 8266 3.131155 CAACCAAGCCAAGCTGCA 58.869 55.556 1.02 0.00 39.62 4.41
6103 8267 2.356673 GCAACCAAGCCAAGCTGC 60.357 61.111 0.00 0.00 39.62 5.25
6104 8268 2.049802 CGCAACCAAGCCAAGCTG 60.050 61.111 0.00 0.00 39.62 4.24
6105 8269 3.297620 CCGCAACCAAGCCAAGCT 61.298 61.111 0.00 0.00 42.56 3.74
6106 8270 3.558099 GACCGCAACCAAGCCAAGC 62.558 63.158 0.00 0.00 0.00 4.01
6107 8271 2.644992 GACCGCAACCAAGCCAAG 59.355 61.111 0.00 0.00 0.00 3.61
6108 8272 2.909965 GGACCGCAACCAAGCCAA 60.910 61.111 0.00 0.00 0.00 4.52
6212 8376 2.925170 CTAGATCTGGGCCGGGGG 60.925 72.222 13.58 0.00 0.00 5.40
6213 8377 2.925170 CCTAGATCTGGGCCGGGG 60.925 72.222 12.76 0.71 0.00 5.73
6219 8383 3.631046 GCCGGGCCTAGATCTGGG 61.631 72.222 20.42 20.42 0.00 4.45
6220 8384 3.996124 CGCCGGGCCTAGATCTGG 61.996 72.222 14.55 1.30 0.00 3.86
6221 8385 3.996124 CCGCCGGGCCTAGATCTG 61.996 72.222 14.55 0.00 0.00 2.90
6237 8401 3.864983 TAGGATCCGGATGGGGCCC 62.865 68.421 24.82 18.17 36.01 5.80
6238 8402 2.203938 TAGGATCCGGATGGGGCC 60.204 66.667 24.82 16.93 36.01 5.80
6239 8403 2.960688 GCTAGGATCCGGATGGGGC 61.961 68.421 24.82 16.14 36.01 5.80
6240 8404 2.650116 CGCTAGGATCCGGATGGGG 61.650 68.421 24.82 13.00 36.01 4.96
6241 8405 2.973899 CGCTAGGATCCGGATGGG 59.026 66.667 24.82 12.00 35.24 4.00
6271 8435 3.414700 CAGACAACGAGGCCACGC 61.415 66.667 23.09 6.14 36.70 5.34
6272 8436 3.414700 GCAGACAACGAGGCCACG 61.415 66.667 21.59 21.59 39.31 4.94
6273 8437 3.414700 CGCAGACAACGAGGCCAC 61.415 66.667 5.01 0.00 0.00 5.01
6274 8438 4.680237 CCGCAGACAACGAGGCCA 62.680 66.667 5.01 0.00 0.00 5.36
6275 8439 4.681978 ACCGCAGACAACGAGGCC 62.682 66.667 0.00 0.00 0.00 5.19
6276 8440 3.414700 CACCGCAGACAACGAGGC 61.415 66.667 0.00 0.00 0.00 4.70
6277 8441 3.414700 GCACCGCAGACAACGAGG 61.415 66.667 0.00 0.00 0.00 4.63
6278 8442 3.767230 CGCACCGCAGACAACGAG 61.767 66.667 0.00 0.00 0.00 4.18
6281 8445 4.012895 CACCGCACCGCAGACAAC 62.013 66.667 0.00 0.00 0.00 3.32
6282 8446 4.228567 TCACCGCACCGCAGACAA 62.229 61.111 0.00 0.00 0.00 3.18
6283 8447 4.662961 CTCACCGCACCGCAGACA 62.663 66.667 0.00 0.00 0.00 3.41
6289 8453 4.135153 CTCCTCCTCACCGCACCG 62.135 72.222 0.00 0.00 0.00 4.94
6290 8454 4.459089 GCTCCTCCTCACCGCACC 62.459 72.222 0.00 0.00 0.00 5.01
6291 8455 4.803426 CGCTCCTCCTCACCGCAC 62.803 72.222 0.00 0.00 0.00 5.34
6295 8459 3.844090 GAGCCGCTCCTCCTCACC 61.844 72.222 9.42 0.00 0.00 4.02
6296 8460 3.071206 TGAGCCGCTCCTCCTCAC 61.071 66.667 17.81 0.00 31.16 3.51
6297 8461 2.580155 ATCTGAGCCGCTCCTCCTCA 62.580 60.000 17.81 0.00 34.68 3.86
6298 8462 1.398958 AATCTGAGCCGCTCCTCCTC 61.399 60.000 17.81 0.00 0.00 3.71
6299 8463 0.980231 AAATCTGAGCCGCTCCTCCT 60.980 55.000 17.81 0.00 0.00 3.69
6300 8464 0.813210 CAAATCTGAGCCGCTCCTCC 60.813 60.000 17.81 0.00 0.00 4.30
6301 8465 0.813210 CCAAATCTGAGCCGCTCCTC 60.813 60.000 17.81 0.00 0.00 3.71
6302 8466 1.222936 CCAAATCTGAGCCGCTCCT 59.777 57.895 17.81 0.00 0.00 3.69
6303 8467 1.821332 CCCAAATCTGAGCCGCTCC 60.821 63.158 17.81 0.61 0.00 4.70
6304 8468 1.821332 CCCCAAATCTGAGCCGCTC 60.821 63.158 13.81 13.81 0.00 5.03
6305 8469 2.273449 CCCCAAATCTGAGCCGCT 59.727 61.111 0.00 0.00 0.00 5.52
6306 8470 3.521796 GCCCCAAATCTGAGCCGC 61.522 66.667 0.00 0.00 0.00 6.53
6307 8471 3.204827 CGCCCCAAATCTGAGCCG 61.205 66.667 0.00 0.00 0.00 5.52
6308 8472 2.830370 CCGCCCCAAATCTGAGCC 60.830 66.667 0.00 0.00 0.00 4.70
6309 8473 3.521796 GCCGCCCCAAATCTGAGC 61.522 66.667 0.00 0.00 0.00 4.26
6310 8474 3.204827 CGCCGCCCCAAATCTGAG 61.205 66.667 0.00 0.00 0.00 3.35
6311 8475 3.711814 TCGCCGCCCCAAATCTGA 61.712 61.111 0.00 0.00 0.00 3.27
6312 8476 3.508840 GTCGCCGCCCCAAATCTG 61.509 66.667 0.00 0.00 0.00 2.90
6352 8516 3.371097 TAAAGCTCCTGCCCTCGCG 62.371 63.158 0.00 0.00 40.80 5.87
6353 8517 1.815840 GTAAAGCTCCTGCCCTCGC 60.816 63.158 0.00 0.00 40.80 5.03
6354 8518 1.519455 CGTAAAGCTCCTGCCCTCG 60.519 63.158 0.00 0.00 40.80 4.63
6355 8519 1.153349 CCGTAAAGCTCCTGCCCTC 60.153 63.158 0.00 0.00 40.80 4.30
6356 8520 1.612442 TCCGTAAAGCTCCTGCCCT 60.612 57.895 0.00 0.00 40.80 5.19
6357 8521 1.449778 GTCCGTAAAGCTCCTGCCC 60.450 63.158 0.00 0.00 40.80 5.36
6358 8522 1.449778 GGTCCGTAAAGCTCCTGCC 60.450 63.158 0.00 0.00 40.80 4.85
6359 8523 1.449778 GGGTCCGTAAAGCTCCTGC 60.450 63.158 0.00 0.00 40.05 4.85
6360 8524 0.541863 ATGGGTCCGTAAAGCTCCTG 59.458 55.000 0.00 0.00 0.00 3.86
6361 8525 0.541863 CATGGGTCCGTAAAGCTCCT 59.458 55.000 0.00 0.00 0.00 3.69
6362 8526 0.539986 TCATGGGTCCGTAAAGCTCC 59.460 55.000 0.00 0.00 0.00 4.70
6363 8527 1.473434 CCTCATGGGTCCGTAAAGCTC 60.473 57.143 0.00 0.00 0.00 4.09
6364 8528 0.541863 CCTCATGGGTCCGTAAAGCT 59.458 55.000 0.00 0.00 0.00 3.74
6365 8529 3.080647 CCTCATGGGTCCGTAAAGC 57.919 57.895 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.