Multiple sequence alignment - TraesCS7A01G068300

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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 TraesCS7A01G068300 chr7A 100.000 4163 0 0 1 4163 34520642 34516480 0.000000e+00 7688.0
1 TraesCS7A01G068300 chr7A 87.946 589 47 15 1000 1587 34452504 34451939 0.000000e+00 673.0
2 TraesCS7A01G068300 chr7A 83.281 640 48 32 1299 1893 34106314 34105689 6.130000e-148 534.0
3 TraesCS7A01G068300 chr7A 80.618 712 108 14 2423 3126 34451047 34450358 1.330000e-144 523.0
4 TraesCS7A01G068300 chr7A 98.137 161 2 1 4003 4163 34967442 34967601 3.170000e-71 279.0
5 TraesCS7A01G068300 chr7A 96.894 161 5 0 4003 4163 636888006 636887846 1.910000e-68 270.0
6 TraesCS7A01G068300 chr7A 94.798 173 8 1 3992 4163 647184409 647184581 6.860000e-68 268.0
7 TraesCS7A01G068300 chr7A 77.148 512 63 28 2449 2924 34104461 34103968 8.940000e-62 248.0
8 TraesCS7A01G068300 chr7A 75.119 631 89 49 287 884 34453109 34452514 2.500000e-57 233.0
9 TraesCS7A01G068300 chr7A 84.305 223 20 8 30 251 34119441 34119233 1.960000e-48 204.0
10 TraesCS7A01G068300 chr7A 94.643 56 2 1 558 612 34107203 34107148 7.420000e-13 86.1
11 TraesCS7A01G068300 chr4A 88.013 951 106 6 2423 3370 691152472 691153417 0.000000e+00 1118.0
12 TraesCS7A01G068300 chr4A 88.000 925 95 12 2481 3398 690885053 690884138 0.000000e+00 1079.0
13 TraesCS7A01G068300 chr4A 87.898 785 79 11 2599 3372 690879955 690879176 0.000000e+00 909.0
14 TraesCS7A01G068300 chr4A 90.244 656 46 8 1254 1905 690881334 690880693 0.000000e+00 841.0
15 TraesCS7A01G068300 chr4A 85.147 781 99 11 2423 3191 691168556 691169331 0.000000e+00 784.0
16 TraesCS7A01G068300 chr4A 83.844 848 100 17 2423 3254 690936840 690936014 0.000000e+00 773.0
17 TraesCS7A01G068300 chr4A 91.146 576 32 6 1318 1880 691150892 691151461 0.000000e+00 763.0
18 TraesCS7A01G068300 chr4A 88.368 576 64 2 2432 3004 690687681 690687106 0.000000e+00 689.0
19 TraesCS7A01G068300 chr4A 86.003 643 51 24 1286 1905 690937987 690937361 0.000000e+00 652.0
20 TraesCS7A01G068300 chr4A 81.049 839 124 20 2423 3254 691325160 691325970 1.630000e-178 636.0
21 TraesCS7A01G068300 chr4A 88.615 527 51 7 3477 3997 691169465 691169988 2.110000e-177 632.0
22 TraesCS7A01G068300 chr4A 88.694 513 54 4 3481 3992 690883870 690883361 1.270000e-174 623.0
23 TraesCS7A01G068300 chr4A 92.593 432 20 5 1286 1706 690689162 690688732 9.890000e-171 610.0
24 TraesCS7A01G068300 chr4A 85.048 622 53 26 274 861 690882238 690881623 7.700000e-167 597.0
25 TraesCS7A01G068300 chr4A 82.482 685 72 30 1274 1921 691246981 691247654 1.310000e-154 556.0
26 TraesCS7A01G068300 chr4A 82.127 677 65 34 1274 1921 691324074 691324723 2.850000e-146 529.0
27 TraesCS7A01G068300 chr4A 85.741 526 38 20 693 1191 690938571 690938056 4.770000e-144 521.0
28 TraesCS7A01G068300 chr4A 84.423 520 30 24 707 1190 690689736 690689232 8.150000e-127 464.0
29 TraesCS7A01G068300 chr4A 84.137 498 27 22 725 1190 691166216 691166693 6.390000e-118 435.0
30 TraesCS7A01G068300 chr4A 95.595 227 8 2 22 247 690939149 690938924 3.060000e-96 363.0
31 TraesCS7A01G068300 chr4A 87.267 322 34 5 3053 3372 690674473 690674157 1.100000e-95 361.0
32 TraesCS7A01G068300 chr4A 93.074 231 16 0 25 255 691149899 691150129 5.160000e-89 339.0
33 TraesCS7A01G068300 chr4A 92.116 241 12 2 22 255 690690367 690690127 2.400000e-87 333.0
34 TraesCS7A01G068300 chr4A 92.308 234 18 0 22 255 690882527 690882294 2.400000e-87 333.0
35 TraesCS7A01G068300 chr4A 92.544 228 12 4 245 472 691165729 691165951 5.190000e-84 322.0
36 TraesCS7A01G068300 chr4A 92.444 225 16 1 990 1213 690881569 690881345 1.870000e-83 320.0
37 TraesCS7A01G068300 chr4A 89.615 260 9 9 262 521 690938877 690938636 8.690000e-82 315.0
38 TraesCS7A01G068300 chr4A 91.928 223 18 0 991 1213 691246753 691246975 3.120000e-81 313.0
39 TraesCS7A01G068300 chr4A 92.823 209 15 0 991 1199 691323846 691324054 1.880000e-78 303.0
40 TraesCS7A01G068300 chr4A 85.032 314 25 13 245 558 690732207 690731916 2.430000e-77 300.0
41 TraesCS7A01G068300 chr4A 86.742 264 18 10 259 521 691150170 691150417 1.140000e-70 278.0
42 TraesCS7A01G068300 chr4A 96.894 161 5 0 4003 4163 495256486 495256326 1.910000e-68 270.0
43 TraesCS7A01G068300 chr4A 82.934 334 15 18 296 619 690690034 690689733 3.190000e-66 263.0
44 TraesCS7A01G068300 chr4A 76.895 541 70 20 2972 3485 691830035 691829523 5.340000e-64 255.0
45 TraesCS7A01G068300 chr4A 86.498 237 14 7 22 255 690732480 690732259 1.160000e-60 244.0
46 TraesCS7A01G068300 chr4A 91.860 172 9 3 2125 2291 691152128 691152299 6.960000e-58 235.0
47 TraesCS7A01G068300 chr4A 84.109 258 19 12 3477 3731 690673860 690673622 3.240000e-56 230.0
48 TraesCS7A01G068300 chr4A 93.056 144 6 3 1933 2074 239032697 239032556 1.520000e-49 207.0
49 TraesCS7A01G068300 chr4A 94.958 119 6 0 22 140 690888559 690888441 1.980000e-43 187.0
50 TraesCS7A01G068300 chr4A 75.802 405 77 19 3580 3975 584891604 584891212 7.110000e-43 185.0
51 TraesCS7A01G068300 chr4A 77.808 365 36 31 278 612 691471050 691470701 2.560000e-42 183.0
52 TraesCS7A01G068300 chr4A 92.742 124 5 4 1802 1924 690688716 690688596 4.280000e-40 176.0
53 TraesCS7A01G068300 chr4A 81.429 210 17 8 696 901 691150426 691150617 7.210000e-33 152.0
54 TraesCS7A01G068300 chr4A 91.667 96 6 1 3390 3485 690673988 690673895 9.390000e-27 132.0
55 TraesCS7A01G068300 chr4A 91.667 96 6 2 3390 3485 690884001 690883908 9.390000e-27 132.0
56 TraesCS7A01G068300 chr4A 91.358 81 7 0 2155 2235 690885863 690885783 1.220000e-20 111.0
57 TraesCS7A01G068300 chr7D 87.917 960 89 14 2423 3372 34074589 34073647 0.000000e+00 1105.0
58 TraesCS7A01G068300 chr7D 93.272 654 28 7 1285 1924 34076937 34076286 0.000000e+00 950.0
59 TraesCS7A01G068300 chr7D 87.435 772 89 6 2423 3191 34446668 34447434 0.000000e+00 881.0
60 TraesCS7A01G068300 chr7D 90.199 653 39 8 1255 1897 34445192 34445829 0.000000e+00 828.0
61 TraesCS7A01G068300 chr7D 83.491 951 74 49 278 1191 34152421 34151517 0.000000e+00 809.0
62 TraesCS7A01G068300 chr7D 86.186 666 61 16 557 1213 34444537 34445180 0.000000e+00 691.0
63 TraesCS7A01G068300 chr7D 87.960 598 37 15 624 1191 34077574 34076982 0.000000e+00 673.0
64 TraesCS7A01G068300 chr7D 81.830 787 113 16 2423 3191 34010931 34010157 5.870000e-178 634.0
65 TraesCS7A01G068300 chr7D 83.435 658 44 33 1285 1897 33754848 33755485 6.080000e-153 551.0
66 TraesCS7A01G068300 chr7D 87.768 466 47 4 2423 2882 34149977 34149516 1.700000e-148 536.0
67 TraesCS7A01G068300 chr7D 87.445 454 20 17 245 668 34078026 34077580 4.840000e-134 488.0
68 TraesCS7A01G068300 chr7D 87.692 390 26 10 245 619 34168613 34168231 6.390000e-118 435.0
69 TraesCS7A01G068300 chr7D 89.753 283 24 5 3476 3756 34073338 34073059 1.420000e-94 357.0
70 TraesCS7A01G068300 chr7D 92.083 240 13 1 22 255 34078329 34078090 2.400000e-87 333.0
71 TraesCS7A01G068300 chr7D 92.735 234 10 3 22 255 34168907 34168681 8.630000e-87 331.0
72 TraesCS7A01G068300 chr7D 91.250 240 15 1 22 255 34444050 34444289 5.190000e-84 322.0
73 TraesCS7A01G068300 chr7D 87.500 240 19 2 22 255 34152738 34152504 2.470000e-67 267.0
74 TraesCS7A01G068300 chr7D 96.319 163 5 1 4001 4163 223755608 223755769 2.470000e-67 267.0
75 TraesCS7A01G068300 chr7D 92.021 188 9 5 245 432 34444338 34444519 4.130000e-65 259.0
76 TraesCS7A01G068300 chr7D 92.361 144 7 3 1933 2074 445784700 445784841 7.060000e-48 202.0
77 TraesCS7A01G068300 chr7D 77.749 391 40 28 254 612 33753668 33754043 3.280000e-46 196.0
78 TraesCS7A01G068300 chr7D 82.969 229 24 7 24 251 33753387 33753601 4.250000e-45 193.0
79 TraesCS7A01G068300 chr7D 88.889 126 7 5 1784 1905 34150968 34150846 9.320000e-32 148.0
80 TraesCS7A01G068300 chr7D 87.826 115 10 2 2155 2265 34446311 34446425 9.390000e-27 132.0
81 TraesCS7A01G068300 chr7D 89.744 78 6 1 370 445 34168586 34168509 9.520000e-17 99.0
82 TraesCS7A01G068300 chr7D 88.608 79 7 2 370 448 34077999 34077923 1.230000e-15 95.3
83 TraesCS7A01G068300 chr2A 98.137 161 3 0 4003 4163 413332950 413333110 8.810000e-72 281.0
84 TraesCS7A01G068300 chr2A 97.516 161 4 0 4003 4163 605033409 605033569 4.100000e-70 276.0
85 TraesCS7A01G068300 chr2A 92.414 145 6 3 1931 2074 27133100 27132960 7.060000e-48 202.0
86 TraesCS7A01G068300 chr2A 94.444 36 2 0 2313 2348 41269590 41269625 5.810000e-04 56.5
87 TraesCS7A01G068300 chr3D 96.914 162 5 0 4002 4163 582214252 582214091 5.300000e-69 272.0
88 TraesCS7A01G068300 chr1A 95.652 161 7 0 4003 4163 51979651 51979811 4.130000e-65 259.0
89 TraesCS7A01G068300 chrUn 94.815 135 4 2 1932 2065 56941396 56941264 1.520000e-49 207.0
90 TraesCS7A01G068300 chrUn 94.815 135 4 2 1932 2065 287961124 287960992 1.520000e-49 207.0
91 TraesCS7A01G068300 chr5D 93.617 141 5 3 1936 2074 507918734 507918596 1.520000e-49 207.0
92 TraesCS7A01G068300 chr4D 93.617 141 5 3 1936 2074 414149757 414149895 1.520000e-49 207.0
93 TraesCS7A01G068300 chr1D 93.617 141 5 3 1927 2065 230071234 230071096 1.520000e-49 207.0
94 TraesCS7A01G068300 chr2D 93.571 140 5 3 1927 2065 204112952 204112816 5.460000e-49 206.0
95 TraesCS7A01G068300 chr4B 74.734 376 68 14 3580 3935 26820837 26821205 4.340000e-30 143.0
96 TraesCS7A01G068300 chr2B 96.875 32 1 0 2313 2344 381924772 381924803 2.000000e-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 TraesCS7A01G068300 chr7A 34516480 34520642 4162 True 7688.000000 7688 100.000000 1 4163 1 chr7A.!!$R2 4162
1 TraesCS7A01G068300 chr7A 34450358 34453109 2751 True 476.333333 673 81.227667 287 3126 3 chr7A.!!$R5 2839
2 TraesCS7A01G068300 chr7A 34103968 34107203 3235 True 289.366667 534 85.024000 558 2924 3 chr7A.!!$R4 2366
3 TraesCS7A01G068300 chr4A 691165729 691169988 4259 False 543.250000 784 87.610750 245 3997 4 chr4A.!!$F2 3752
4 TraesCS7A01G068300 chr4A 690936014 690939149 3135 True 524.800000 773 88.159600 22 3254 5 chr4A.!!$R10 3232
5 TraesCS7A01G068300 chr4A 690879176 690888559 9383 True 513.200000 1079 90.261900 22 3992 10 chr4A.!!$R9 3970
6 TraesCS7A01G068300 chr4A 691323846 691325970 2124 False 489.333333 636 85.333000 991 3254 3 chr4A.!!$F4 2263
7 TraesCS7A01G068300 chr4A 691149899 691153417 3518 False 480.833333 1118 88.710667 25 3370 6 chr4A.!!$F1 3345
8 TraesCS7A01G068300 chr4A 691246753 691247654 901 False 434.500000 556 87.205000 991 1921 2 chr4A.!!$F3 930
9 TraesCS7A01G068300 chr4A 690687106 690690367 3261 True 422.500000 689 88.862667 22 3004 6 chr4A.!!$R7 2982
10 TraesCS7A01G068300 chr4A 690731916 690732480 564 True 272.000000 300 85.765000 22 558 2 chr4A.!!$R8 536
11 TraesCS7A01G068300 chr4A 691829523 691830035 512 True 255.000000 255 76.895000 2972 3485 1 chr4A.!!$R5 513
12 TraesCS7A01G068300 chr4A 690673622 690674473 851 True 241.000000 361 87.681000 3053 3731 3 chr4A.!!$R6 678
13 TraesCS7A01G068300 chr7D 34010157 34010931 774 True 634.000000 634 81.830000 2423 3191 1 chr7D.!!$R1 768
14 TraesCS7A01G068300 chr7D 34073059 34078329 5270 True 571.614286 1105 89.576857 22 3756 7 chr7D.!!$R2 3734
15 TraesCS7A01G068300 chr7D 34444050 34447434 3384 False 518.833333 881 89.152833 22 3191 6 chr7D.!!$F4 3169
16 TraesCS7A01G068300 chr7D 34149516 34152738 3222 True 440.000000 809 86.912000 22 2882 4 chr7D.!!$R3 2860
17 TraesCS7A01G068300 chr7D 33753387 33755485 2098 False 313.333333 551 81.384333 24 1897 3 chr7D.!!$F3 1873
18 TraesCS7A01G068300 chr7D 34168231 34168907 676 True 288.333333 435 90.057000 22 619 3 chr7D.!!$R4 597

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
884 1683 0.179108 GACTCCATCGTTTCCCCTCG 60.179 60.0 0.0 0.0 0.0 4.63 F
988 1912 0.961753 AGTGATCTCTGTGTGCGTGA 59.038 50.0 0.0 0.0 0.0 4.35 F
2294 11341 0.455633 CGACATGCCTTTTGAGCTGC 60.456 55.0 0.0 0.0 0.0 5.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 9133 0.247185 CCCCACTCGCAAATTGCAAT 59.753 50.0 18.65 5.99 45.36 3.56 R
2987 12691 1.006825 CATGCCGTTCGTCGTCTTGA 61.007 55.0 0.00 0.00 37.94 3.02 R
4002 13939 0.036294 AGCTCCAAAACGCCCTACTC 60.036 55.0 0.00 0.00 0.00 2.59 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
186 571 4.580167 GCATATGCACACCCTTCTTTATCA 59.420 41.667 22.84 0.00 41.59 2.15
197 582 4.938226 CCCTTCTTTATCAGTTCACCAGAC 59.062 45.833 0.00 0.00 0.00 3.51
287 770 6.003950 CCTTGTGGAACTTGATTTCCTCTTA 58.996 40.000 3.66 0.00 44.89 2.10
383 866 5.633830 TTCTGCTGCTTAATTTCCTCTTG 57.366 39.130 0.00 0.00 0.00 3.02
521 1060 0.395586 TGGTGGTTATGCTGGCCATC 60.396 55.000 5.51 1.26 35.34 3.51
566 1139 4.195334 ATGGCGGTGGGGATCAGC 62.195 66.667 0.00 0.00 40.26 4.26
608 1182 3.000727 CGTGGAGATTTTTAAGGTCGCT 58.999 45.455 0.00 0.00 0.00 4.93
609 1183 3.181520 CGTGGAGATTTTTAAGGTCGCTG 60.182 47.826 0.00 0.00 0.00 5.18
617 1217 3.764237 TTTAAGGTCGCTGTCCTTTCT 57.236 42.857 10.89 0.00 41.86 2.52
621 1221 1.585006 GTCGCTGTCCTTTCTCGGA 59.415 57.895 0.00 0.00 0.00 4.55
622 1222 0.456995 GTCGCTGTCCTTTCTCGGAG 60.457 60.000 0.00 0.00 32.70 4.63
678 1341 2.685380 CTCTCTCCCCTTGCCGGT 60.685 66.667 1.90 0.00 0.00 5.28
680 1343 3.003173 CTCTCCCCTTGCCGGTGA 61.003 66.667 1.90 0.00 0.00 4.02
695 1358 4.954118 TGAGGACCACCGTGGCCT 62.954 66.667 25.06 25.06 43.50 5.19
703 1409 4.887190 ACCGTGGCCTTGGCGTTT 62.887 61.111 13.09 0.00 0.00 3.60
742 1461 2.297597 CACTTCTCCTCTGGAACGAACT 59.702 50.000 0.00 0.00 0.00 3.01
753 1472 6.351117 CCTCTGGAACGAACTTAACTAATCCT 60.351 42.308 0.00 0.00 0.00 3.24
793 1591 7.726033 AGCTTGGCAGTAGCTATATATAACT 57.274 36.000 11.86 1.47 46.66 2.24
844 1643 2.635443 CCCATCACCGGCAACAACC 61.635 63.158 0.00 0.00 0.00 3.77
849 1648 0.605319 TCACCGGCAACAACCTCATC 60.605 55.000 0.00 0.00 0.00 2.92
861 1660 1.834822 CCTCATCCCCCTCGACTCC 60.835 68.421 0.00 0.00 0.00 3.85
863 1662 0.470833 CTCATCCCCCTCGACTCCAT 60.471 60.000 0.00 0.00 0.00 3.41
864 1663 0.470080 TCATCCCCCTCGACTCCATC 60.470 60.000 0.00 0.00 0.00 3.51
884 1683 0.179108 GACTCCATCGTTTCCCCTCG 60.179 60.000 0.00 0.00 0.00 4.63
908 1737 1.776667 CCTGCTCCCTCCCATCAATTA 59.223 52.381 0.00 0.00 0.00 1.40
910 1758 3.560882 CCTGCTCCCTCCCATCAATTATC 60.561 52.174 0.00 0.00 0.00 1.75
916 1780 3.261897 CCCTCCCATCAATTATCGCTAGT 59.738 47.826 0.00 0.00 0.00 2.57
918 1782 4.692625 CCTCCCATCAATTATCGCTAGTTG 59.307 45.833 0.00 0.00 0.00 3.16
919 1783 5.290493 TCCCATCAATTATCGCTAGTTGT 57.710 39.130 2.12 0.00 0.00 3.32
923 1793 5.294306 CCATCAATTATCGCTAGTTGTGTGT 59.706 40.000 2.12 0.00 0.00 3.72
942 1812 4.080919 TGTGTAGCATTTCACTCCAGCTAT 60.081 41.667 0.00 0.00 39.65 2.97
984 1908 5.720371 ATCCTATAGTGATCTCTGTGTGC 57.280 43.478 7.56 0.00 0.00 4.57
988 1912 0.961753 AGTGATCTCTGTGTGCGTGA 59.038 50.000 0.00 0.00 0.00 4.35
1017 1969 1.487976 ACCATGAGCATCTCCGTGAAT 59.512 47.619 0.00 0.00 34.92 2.57
1199 2151 4.217118 GTGCATGAGTTCCTTTGTTCATCT 59.783 41.667 0.00 0.00 0.00 2.90
1205 2157 6.826668 TGAGTTCCTTTGTTCATCTTCTACA 58.173 36.000 0.00 0.00 0.00 2.74
1212 2164 5.717078 TTGTTCATCTTCTACACTACCGT 57.283 39.130 0.00 0.00 0.00 4.83
1230 2182 4.134563 ACCGTGTAGTTTCAAGAATGCTT 58.865 39.130 0.00 0.00 33.74 3.91
1231 2183 4.578928 ACCGTGTAGTTTCAAGAATGCTTT 59.421 37.500 0.00 0.00 30.14 3.51
1233 2185 6.261381 ACCGTGTAGTTTCAAGAATGCTTTTA 59.739 34.615 0.00 0.00 30.14 1.52
1234 2186 7.040686 ACCGTGTAGTTTCAAGAATGCTTTTAT 60.041 33.333 0.00 0.00 30.14 1.40
1236 2188 9.988350 CGTGTAGTTTCAAGAATGCTTTTATAT 57.012 29.630 0.00 0.00 30.14 0.86
1253 2205 9.078753 GCTTTTATATTATAGAACGGAGAGAGC 57.921 37.037 0.00 0.00 0.00 4.09
1256 2208 8.865420 TTATATTATAGAACGGAGAGAGCAGT 57.135 34.615 0.00 0.00 0.00 4.40
1641 8078 1.762957 CCAGTGACTCATTCCCGGTAT 59.237 52.381 0.00 0.00 0.00 2.73
1870 8552 2.282783 GGTGGTGGTTGGGAATGGC 61.283 63.158 0.00 0.00 0.00 4.40
1884 8743 4.041617 TGGCGACACACATGACAC 57.958 55.556 0.00 0.00 33.40 3.67
1885 8744 1.144936 TGGCGACACACATGACACA 59.855 52.632 0.00 0.00 33.40 3.72
1902 9133 6.527057 TGACACATGATGCAATGGAATTAA 57.473 33.333 0.00 0.00 32.46 1.40
1924 9156 1.501741 CAATTTGCGAGTGGGGACG 59.498 57.895 0.00 0.00 0.00 4.79
1927 9159 1.910580 ATTTGCGAGTGGGGACGGAT 61.911 55.000 0.00 0.00 0.00 4.18
1928 9160 2.796483 TTTGCGAGTGGGGACGGATG 62.796 60.000 0.00 0.00 0.00 3.51
1931 9163 1.952102 GCGAGTGGGGACGGATGTTA 61.952 60.000 0.00 0.00 0.00 2.41
1932 9164 0.750850 CGAGTGGGGACGGATGTTAT 59.249 55.000 0.00 0.00 0.00 1.89
1933 9165 1.958579 CGAGTGGGGACGGATGTTATA 59.041 52.381 0.00 0.00 0.00 0.98
1934 9166 2.288030 CGAGTGGGGACGGATGTTATAC 60.288 54.545 0.00 0.00 0.00 1.47
1936 9168 4.147321 GAGTGGGGACGGATGTTATACTA 58.853 47.826 0.00 0.00 0.00 1.82
1939 9171 2.564504 GGGGACGGATGTTATACTACCC 59.435 54.545 0.00 0.00 0.00 3.69
1940 9172 2.564504 GGGACGGATGTTATACTACCCC 59.435 54.545 0.00 0.00 0.00 4.95
1943 9175 3.504375 ACGGATGTTATACTACCCCTCC 58.496 50.000 0.00 0.00 0.00 4.30
1946 9178 3.899980 GGATGTTATACTACCCCTCCGTT 59.100 47.826 0.00 0.00 0.00 4.44
1947 9179 4.346127 GGATGTTATACTACCCCTCCGTTT 59.654 45.833 0.00 0.00 0.00 3.60
1948 9180 5.510349 GGATGTTATACTACCCCTCCGTTTC 60.510 48.000 0.00 0.00 0.00 2.78
1949 9181 4.613437 TGTTATACTACCCCTCCGTTTCT 58.387 43.478 0.00 0.00 0.00 2.52
1951 9183 5.484998 TGTTATACTACCCCTCCGTTTCTTT 59.515 40.000 0.00 0.00 0.00 2.52
1952 9184 6.013466 TGTTATACTACCCCTCCGTTTCTTTT 60.013 38.462 0.00 0.00 0.00 2.27
1958 9190 3.079578 CCCCTCCGTTTCTTTTTAGTCC 58.920 50.000 0.00 0.00 0.00 3.85
1959 9191 2.740447 CCCTCCGTTTCTTTTTAGTCCG 59.260 50.000 0.00 0.00 0.00 4.79
1960 9192 2.159037 CCTCCGTTTCTTTTTAGTCCGC 59.841 50.000 0.00 0.00 0.00 5.54
1962 9194 3.404899 TCCGTTTCTTTTTAGTCCGCAT 58.595 40.909 0.00 0.00 0.00 4.73
1964 9196 5.180271 TCCGTTTCTTTTTAGTCCGCATAT 58.820 37.500 0.00 0.00 0.00 1.78
1966 9198 6.817641 TCCGTTTCTTTTTAGTCCGCATATAA 59.182 34.615 0.00 0.00 0.00 0.98
1970 9202 8.456471 GTTTCTTTTTAGTCCGCATATAAGGTT 58.544 33.333 0.00 0.00 0.00 3.50
1973 9205 6.687081 TTTTAGTCCGCATATAAGGTTTGG 57.313 37.500 0.00 0.00 0.00 3.28
1974 9206 3.926058 AGTCCGCATATAAGGTTTGGT 57.074 42.857 0.00 0.00 0.00 3.67
1975 9207 3.805207 AGTCCGCATATAAGGTTTGGTC 58.195 45.455 0.00 0.00 0.00 4.02
1977 9209 3.942748 GTCCGCATATAAGGTTTGGTCAA 59.057 43.478 0.00 0.00 0.00 3.18
1978 9210 4.396790 GTCCGCATATAAGGTTTGGTCAAA 59.603 41.667 0.00 0.00 0.00 2.69
1979 9211 4.638421 TCCGCATATAAGGTTTGGTCAAAG 59.362 41.667 0.00 0.00 0.00 2.77
1981 9213 5.448632 CCGCATATAAGGTTTGGTCAAAGTC 60.449 44.000 0.00 0.00 0.00 3.01
1983 9215 6.348950 CGCATATAAGGTTTGGTCAAAGTCAA 60.349 38.462 0.00 0.00 0.00 3.18
1989 9221 4.953579 AGGTTTGGTCAAAGTCAAGCTTTA 59.046 37.500 0.00 0.00 44.95 1.85
1993 9225 8.736244 GGTTTGGTCAAAGTCAAGCTTTATATA 58.264 33.333 0.00 0.00 44.95 0.86
1994 9226 9.774742 GTTTGGTCAAAGTCAAGCTTTATATAG 57.225 33.333 0.00 0.00 44.95 1.31
2173 10783 7.553881 AATAATCGAATAGTGGACCTTTGTG 57.446 36.000 0.00 0.00 0.00 3.33
2202 10812 3.531538 ACACCGGCATATGACAAACTAG 58.468 45.455 9.77 0.00 0.00 2.57
2294 11341 0.455633 CGACATGCCTTTTGAGCTGC 60.456 55.000 0.00 0.00 0.00 5.25
2305 11352 4.327680 CTTTTGAGCTGCCTTAGGTAGTT 58.672 43.478 17.29 11.82 37.73 2.24
2309 11356 2.696187 GAGCTGCCTTAGGTAGTTAGCT 59.304 50.000 17.29 14.76 41.30 3.32
2311 11358 3.118592 AGCTGCCTTAGGTAGTTAGCTTG 60.119 47.826 17.29 0.00 37.75 4.01
2314 11361 5.086104 TGCCTTAGGTAGTTAGCTTGAAG 57.914 43.478 0.00 0.00 35.39 3.02
2315 11362 4.775780 TGCCTTAGGTAGTTAGCTTGAAGA 59.224 41.667 0.00 0.00 35.39 2.87
2316 11363 5.247564 TGCCTTAGGTAGTTAGCTTGAAGAA 59.752 40.000 0.00 0.00 35.39 2.52
2318 11365 6.698380 CCTTAGGTAGTTAGCTTGAAGAACA 58.302 40.000 0.00 0.00 35.39 3.18
2321 11368 9.220767 CTTAGGTAGTTAGCTTGAAGAACATTT 57.779 33.333 0.00 0.00 35.39 2.32
2323 11370 8.465273 AGGTAGTTAGCTTGAAGAACATTTTT 57.535 30.769 0.00 0.00 0.00 1.94
2324 11371 9.569122 AGGTAGTTAGCTTGAAGAACATTTTTA 57.431 29.630 0.00 0.00 0.00 1.52
2349 11396 6.838401 ATTATGAGATGGAGGGAGAAGTTT 57.162 37.500 0.00 0.00 0.00 2.66
2360 11454 6.040842 TGGAGGGAGAAGTTTCTTTGAAAATG 59.959 38.462 0.00 0.00 37.73 2.32
2361 11455 6.040955 GGAGGGAGAAGTTTCTTTGAAAATGT 59.959 38.462 0.00 0.00 37.73 2.71
2364 11458 8.977412 AGGGAGAAGTTTCTTTGAAAATGTAAA 58.023 29.630 0.00 0.00 37.73 2.01
2428 12059 3.546815 GCGCGCTTGATTAGTCAATTGAT 60.547 43.478 26.67 3.70 43.08 2.57
2460 12098 6.834168 TCCGTATCATATGAGCAGATACAA 57.166 37.500 11.78 0.00 42.52 2.41
2464 12102 4.277515 TCATATGAGCAGATACAAGGCC 57.722 45.455 0.00 0.00 0.00 5.19
2466 12104 5.086621 TCATATGAGCAGATACAAGGCCTA 58.913 41.667 5.16 0.00 0.00 3.93
2794 12492 0.740868 CAACCCATCATCGTCAGCGT 60.741 55.000 0.00 0.00 39.49 5.07
2888 12589 4.351938 CGAGCACGTCGTCCCCAA 62.352 66.667 0.00 0.00 44.20 4.12
2987 12691 1.458777 TCTCTGACCCCACGTTGGT 60.459 57.895 6.23 6.23 39.32 3.67
3012 12716 0.248907 CGACGAACGGCATGTCCTAT 60.249 55.000 0.11 0.00 38.46 2.57
3056 12763 1.682684 CCTCCTACTCTGGCGGTGT 60.683 63.158 6.27 6.27 0.00 4.16
3058 12765 0.681564 CTCCTACTCTGGCGGTGTCT 60.682 60.000 3.98 0.00 0.00 3.41
3112 12819 3.695606 GCGACCTGTGGAGCCTGA 61.696 66.667 0.00 0.00 0.00 3.86
3150 12857 1.607713 CTACACGCAGACTTGACGAG 58.392 55.000 0.00 0.00 0.00 4.18
3152 12859 1.007271 CACGCAGACTTGACGAGGT 60.007 57.895 0.00 0.00 0.00 3.85
3191 12898 0.174389 ATGCTGACACTGTCCTAGCG 59.826 55.000 13.88 0.00 35.32 4.26
3192 12899 1.153745 GCTGACACTGTCCTAGCGG 60.154 63.158 6.72 0.00 0.00 5.52
3193 12900 1.595993 GCTGACACTGTCCTAGCGGA 61.596 60.000 6.72 0.00 36.83 5.54
3257 12974 3.275617 AGCTAATACCATCGCACCAAA 57.724 42.857 0.00 0.00 0.00 3.28
3266 12983 2.094597 CCATCGCACCAAATGAATGTGT 60.095 45.455 0.00 0.00 32.62 3.72
3308 13025 8.500773 TGAACTAAAACCACAACGAGAATTATC 58.499 33.333 0.00 0.00 0.00 1.75
3310 13027 8.561738 ACTAAAACCACAACGAGAATTATCAT 57.438 30.769 0.35 0.00 0.00 2.45
3319 13036 6.043243 ACAACGAGAATTATCATATGGAGGGT 59.957 38.462 2.13 0.00 0.00 4.34
3328 13045 7.733773 TTATCATATGGAGGGTGTACATAGG 57.266 40.000 0.00 0.00 31.35 2.57
3344 13062 5.021033 ACATAGGAAGATGCAAGAGTCAG 57.979 43.478 0.00 0.00 0.00 3.51
3346 13064 3.331478 AGGAAGATGCAAGAGTCAGTG 57.669 47.619 0.00 0.00 0.00 3.66
3385 13133 8.621286 AGGTGTCATACAGAAAAAGTAAAAGTG 58.379 33.333 0.00 0.00 0.00 3.16
3440 13327 9.003658 CCTATCCAAAGACAATATTACATGTCC 57.996 37.037 0.00 0.00 45.55 4.02
3444 13331 7.709182 TCCAAAGACAATATTACATGTCCTACG 59.291 37.037 0.00 0.00 45.55 3.51
3460 13347 6.240894 TGTCCTACGGAAAAGTAGAAGTAGA 58.759 40.000 5.79 0.00 45.07 2.59
3461 13348 6.888632 TGTCCTACGGAAAAGTAGAAGTAGAT 59.111 38.462 5.79 0.00 45.07 1.98
3509 13440 0.325671 CTCCCCCTAGTGCCTCTTCA 60.326 60.000 0.00 0.00 0.00 3.02
3513 13444 0.761802 CCCTAGTGCCTCTTCATCCC 59.238 60.000 0.00 0.00 0.00 3.85
3539 13472 4.047883 CCCTTTATATATCCCCTCCCCAG 58.952 52.174 0.00 0.00 0.00 4.45
3544 13477 2.079161 ATATCCCCTCCCCAGCCCAT 62.079 60.000 0.00 0.00 0.00 4.00
3578 13511 4.660938 ACTTTCGCACCCCTGCCC 62.661 66.667 0.00 0.00 40.73 5.36
3609 13542 0.250684 TTGCACCGATGACCATGTGT 60.251 50.000 0.00 0.00 0.00 3.72
3619 13552 2.268920 CCATGTGTGGGTAGCGCT 59.731 61.111 17.26 17.26 42.11 5.92
3635 13568 0.541863 CGCTCCTTGGACTATGGGTT 59.458 55.000 0.00 0.00 0.00 4.11
3661 13594 3.957468 GCAATAGCTTTGTGGCATCTAC 58.043 45.455 0.00 0.00 37.91 2.59
3662 13595 3.629398 GCAATAGCTTTGTGGCATCTACT 59.371 43.478 0.00 0.00 37.91 2.57
3669 13602 0.339859 TGTGGCATCTACTCTCCCCT 59.660 55.000 0.00 0.00 0.00 4.79
3677 13610 3.827817 TCTACTCTCCCCTGTTCTTCA 57.172 47.619 0.00 0.00 0.00 3.02
3717 13652 5.121811 AGCTGTCTAACATGATTGTGATCC 58.878 41.667 0.00 0.00 35.83 3.36
3733 13668 9.459640 GATTGTGATCCATCAGATGTAATTTTG 57.540 33.333 9.64 0.00 37.51 2.44
3735 13670 7.118060 TGTGATCCATCAGATGTAATTTTGGA 58.882 34.615 9.64 0.00 37.51 3.53
3739 13674 7.337480 TCCATCAGATGTAATTTTGGATGTG 57.663 36.000 9.64 0.00 0.00 3.21
3812 13749 5.879223 TGTTTTGGTTCTTTGTTGCATGATT 59.121 32.000 0.00 0.00 0.00 2.57
3817 13754 5.982516 TGGTTCTTTGTTGCATGATTTGTAC 59.017 36.000 0.00 0.00 0.00 2.90
3820 13757 7.171337 GGTTCTTTGTTGCATGATTTGTACATT 59.829 33.333 0.00 0.00 0.00 2.71
3826 13763 9.486497 TTGTTGCATGATTTGTACATTTACATT 57.514 25.926 0.00 0.00 38.05 2.71
3827 13764 9.138062 TGTTGCATGATTTGTACATTTACATTC 57.862 29.630 0.00 0.00 38.05 2.67
3857 13794 9.277783 CTAATCTATTAGTTTTGCACTAGCCAT 57.722 33.333 0.00 0.00 39.28 4.40
3863 13800 3.059166 GTTTTGCACTAGCCATGTTTGG 58.941 45.455 0.00 0.00 46.66 3.28
3866 13803 2.093890 TGCACTAGCCATGTTTGGATG 58.906 47.619 0.00 0.00 46.92 3.51
3881 13818 8.775527 CATGTTTGGATGATTGATCTCTAAGAG 58.224 37.037 0.00 0.00 0.00 2.85
3909 13846 6.040054 AGTTCTGTATGTTGGTTGGGTTTAAC 59.960 38.462 0.00 0.00 0.00 2.01
3921 13858 6.225318 GGTTGGGTTTAACCTTCCAAATAAC 58.775 40.000 14.27 6.75 45.29 1.89
3925 13862 7.480437 TGGGTTTAACCTTCCAAATAACCTAT 58.520 34.615 14.27 0.00 38.64 2.57
3947 13884 2.297701 TGAGTGGCAGAAAGACCAAAC 58.702 47.619 0.00 0.00 37.79 2.93
3949 13886 2.687935 GAGTGGCAGAAAGACCAAACAA 59.312 45.455 0.00 0.00 37.79 2.83
3957 13894 5.273944 CAGAAAGACCAAACAAGCTTGTAC 58.726 41.667 31.31 18.90 41.31 2.90
3968 13905 5.108385 ACAAGCTTGTACTGTGTTATTGC 57.892 39.130 30.25 0.00 40.16 3.56
3978 13915 6.649141 TGTACTGTGTTATTGCCACTAAAGAG 59.351 38.462 0.00 0.00 33.92 2.85
3991 13928 7.224297 TGCCACTAAAGAGAAACAAGATAGTT 58.776 34.615 0.00 0.00 0.00 2.24
3997 13934 7.674471 AAAGAGAAACAAGATAGTTGCCTAC 57.326 36.000 0.00 0.00 0.00 3.18
3998 13935 6.613153 AGAGAAACAAGATAGTTGCCTACT 57.387 37.500 0.00 0.00 41.04 2.57
3999 13936 7.719871 AGAGAAACAAGATAGTTGCCTACTA 57.280 36.000 0.00 0.00 43.29 1.82
4000 13937 7.777095 AGAGAAACAAGATAGTTGCCTACTAG 58.223 38.462 2.75 0.00 42.44 2.57
4001 13938 6.879400 AGAAACAAGATAGTTGCCTACTAGG 58.121 40.000 0.00 0.00 42.44 3.02
4002 13939 5.615925 AACAAGATAGTTGCCTACTAGGG 57.384 43.478 4.18 0.00 42.44 3.53
4003 13940 4.880164 ACAAGATAGTTGCCTACTAGGGA 58.120 43.478 4.18 0.00 42.44 4.20
4004 13941 4.896482 ACAAGATAGTTGCCTACTAGGGAG 59.104 45.833 4.18 0.00 42.44 4.30
4005 13942 4.817874 AGATAGTTGCCTACTAGGGAGT 57.182 45.455 4.18 0.00 42.44 3.85
4006 13943 5.926580 AGATAGTTGCCTACTAGGGAGTA 57.073 43.478 4.18 0.00 42.44 2.59
4014 13951 2.834638 TACTAGGGAGTAGGGCGTTT 57.165 50.000 0.00 0.00 37.10 3.60
4015 13952 1.948391 ACTAGGGAGTAGGGCGTTTT 58.052 50.000 0.00 0.00 32.65 2.43
4016 13953 1.553704 ACTAGGGAGTAGGGCGTTTTG 59.446 52.381 0.00 0.00 32.65 2.44
4017 13954 0.906775 TAGGGAGTAGGGCGTTTTGG 59.093 55.000 0.00 0.00 0.00 3.28
4018 13955 0.838987 AGGGAGTAGGGCGTTTTGGA 60.839 55.000 0.00 0.00 0.00 3.53
4019 13956 0.392595 GGGAGTAGGGCGTTTTGGAG 60.393 60.000 0.00 0.00 0.00 3.86
4020 13957 1.025113 GGAGTAGGGCGTTTTGGAGC 61.025 60.000 0.00 0.00 0.00 4.70
4021 13958 0.036294 GAGTAGGGCGTTTTGGAGCT 60.036 55.000 0.00 0.00 0.00 4.09
4022 13959 0.036294 AGTAGGGCGTTTTGGAGCTC 60.036 55.000 4.71 4.71 0.00 4.09
4023 13960 1.079405 TAGGGCGTTTTGGAGCTCG 60.079 57.895 7.83 0.00 39.21 5.03
4024 13961 2.515996 TAGGGCGTTTTGGAGCTCGG 62.516 60.000 7.83 0.00 39.21 4.63
4025 13962 4.103103 GGCGTTTTGGAGCTCGGC 62.103 66.667 7.83 4.17 41.00 5.54
4026 13963 4.103103 GCGTTTTGGAGCTCGGCC 62.103 66.667 7.83 0.00 0.00 6.13
4027 13964 2.358737 CGTTTTGGAGCTCGGCCT 60.359 61.111 7.83 0.00 0.00 5.19
4028 13965 2.391389 CGTTTTGGAGCTCGGCCTC 61.391 63.158 7.83 0.00 0.00 4.70
4034 13971 3.157252 GAGCTCGGCCTCCATGGA 61.157 66.667 15.27 15.27 38.35 3.41
4035 13972 3.160047 AGCTCGGCCTCCATGGAG 61.160 66.667 31.69 31.69 41.63 3.86
4043 13980 3.244616 CTCCATGGAGGCCGGATT 58.755 61.111 31.14 0.00 38.51 3.01
4044 13981 1.533711 CTCCATGGAGGCCGGATTT 59.466 57.895 31.14 0.00 38.51 2.17
4045 13982 0.106519 CTCCATGGAGGCCGGATTTT 60.107 55.000 31.14 0.00 38.51 1.82
4046 13983 0.334676 TCCATGGAGGCCGGATTTTT 59.665 50.000 11.44 0.00 37.29 1.94
4079 14016 8.824159 TTCAAAATTCACACTTTTCAGTTTCA 57.176 26.923 0.00 0.00 0.00 2.69
4080 14017 8.824159 TCAAAATTCACACTTTTCAGTTTCAA 57.176 26.923 0.00 0.00 0.00 2.69
4081 14018 9.265901 TCAAAATTCACACTTTTCAGTTTCAAA 57.734 25.926 0.00 0.00 0.00 2.69
4082 14019 9.875675 CAAAATTCACACTTTTCAGTTTCAAAA 57.124 25.926 0.00 0.00 0.00 2.44
4156 14093 8.893563 TGTAAAATTTGAGGATGAAATACCCT 57.106 30.769 0.00 0.00 28.06 4.34
4157 14094 9.983024 TGTAAAATTTGAGGATGAAATACCCTA 57.017 29.630 0.00 0.00 28.06 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
176 561 6.708054 ACTTGTCTGGTGAACTGATAAAGAAG 59.292 38.462 8.87 0.00 32.66 2.85
186 571 4.487714 TTCTTGACTTGTCTGGTGAACT 57.512 40.909 2.35 0.00 0.00 3.01
197 582 3.629398 AGTGGAACAGCTTTCTTGACTTG 59.371 43.478 8.05 0.00 41.80 3.16
383 866 7.523219 TCATGGTTGACGTTGTCATAAATTAC 58.477 34.615 0.00 0.00 42.40 1.89
521 1060 0.680921 AAATCATCAGGCACCACGGG 60.681 55.000 0.00 0.00 0.00 5.28
566 1139 2.209690 AAACCATACCCCAAACCGAG 57.790 50.000 0.00 0.00 0.00 4.63
608 1182 0.251832 AGGAGCTCCGAGAAAGGACA 60.252 55.000 26.95 0.00 42.08 4.02
609 1183 0.458260 GAGGAGCTCCGAGAAAGGAC 59.542 60.000 26.95 7.49 42.08 3.85
621 1221 1.771255 GAGAGAGAGAGAGGAGGAGCT 59.229 57.143 0.00 0.00 0.00 4.09
622 1222 1.771255 AGAGAGAGAGAGAGGAGGAGC 59.229 57.143 0.00 0.00 0.00 4.70
678 1341 4.954118 AGGCCACGGTGGTCCTCA 62.954 66.667 27.19 0.00 45.08 3.86
680 1343 3.953775 CAAGGCCACGGTGGTCCT 61.954 66.667 27.19 27.14 45.08 3.85
695 1358 0.472471 ACCTTGAGAGGAAACGCCAA 59.528 50.000 0.00 0.00 46.74 4.52
700 1399 2.230660 CCACCAACCTTGAGAGGAAAC 58.769 52.381 0.00 0.00 46.74 2.78
703 1409 1.059584 TGCCACCAACCTTGAGAGGA 61.060 55.000 0.00 0.00 46.74 3.71
742 1461 9.155785 AGCTAGCCTTGTAATAGGATTAGTTAA 57.844 33.333 12.13 0.00 37.50 2.01
805 1603 2.550639 GGTGCAAGGAAACAATGGCAAT 60.551 45.455 0.00 0.00 0.00 3.56
844 1643 0.470833 ATGGAGTCGAGGGGGATGAG 60.471 60.000 0.00 0.00 0.00 2.90
865 1664 0.179108 CGAGGGGAAACGATGGAGTC 60.179 60.000 0.00 0.00 0.00 3.36
866 1665 1.898154 CGAGGGGAAACGATGGAGT 59.102 57.895 0.00 0.00 0.00 3.85
908 1737 3.526931 ATGCTACACACAACTAGCGAT 57.473 42.857 0.00 0.00 38.61 4.58
910 1758 3.431912 TGAAATGCTACACACAACTAGCG 59.568 43.478 0.00 0.00 38.61 4.26
916 1780 3.814625 TGGAGTGAAATGCTACACACAA 58.185 40.909 0.00 0.00 39.18 3.33
918 1782 2.160417 GCTGGAGTGAAATGCTACACAC 59.840 50.000 0.00 0.00 39.18 3.82
919 1783 2.038952 AGCTGGAGTGAAATGCTACACA 59.961 45.455 0.00 0.00 39.18 3.72
923 1793 6.778069 ACTACTATAGCTGGAGTGAAATGCTA 59.222 38.462 11.52 0.00 39.97 3.49
976 1846 0.666274 GATCGGTTCACGCACACAGA 60.666 55.000 0.00 0.00 43.86 3.41
984 1908 0.108377 TCATGGTGGATCGGTTCACG 60.108 55.000 0.00 0.00 46.11 4.35
988 1912 0.548031 ATGCTCATGGTGGATCGGTT 59.452 50.000 0.00 0.00 0.00 4.44
1205 2157 4.689345 GCATTCTTGAAACTACACGGTAGT 59.311 41.667 9.95 9.95 0.00 2.73
1230 2182 9.298250 ACTGCTCTCTCCGTTCTATAATATAAA 57.702 33.333 0.00 0.00 0.00 1.40
1231 2183 8.865420 ACTGCTCTCTCCGTTCTATAATATAA 57.135 34.615 0.00 0.00 0.00 0.98
1233 2185 7.768807 AACTGCTCTCTCCGTTCTATAATAT 57.231 36.000 0.00 0.00 0.00 1.28
1234 2186 7.426410 CAAACTGCTCTCTCCGTTCTATAATA 58.574 38.462 0.00 0.00 0.00 0.98
1236 2188 5.651530 CAAACTGCTCTCTCCGTTCTATAA 58.348 41.667 0.00 0.00 0.00 0.98
1237 2189 4.440250 GCAAACTGCTCTCTCCGTTCTATA 60.440 45.833 0.00 0.00 40.96 1.31
1238 2190 3.677424 GCAAACTGCTCTCTCCGTTCTAT 60.677 47.826 0.00 0.00 40.96 1.98
1239 2191 2.352814 GCAAACTGCTCTCTCCGTTCTA 60.353 50.000 0.00 0.00 40.96 2.10
1240 2192 1.606737 GCAAACTGCTCTCTCCGTTCT 60.607 52.381 0.00 0.00 40.96 3.01
1241 2193 0.793250 GCAAACTGCTCTCTCCGTTC 59.207 55.000 0.00 0.00 40.96 3.95
1242 2194 0.106708 TGCAAACTGCTCTCTCCGTT 59.893 50.000 0.00 0.00 45.31 4.44
1243 2195 0.322975 ATGCAAACTGCTCTCTCCGT 59.677 50.000 0.00 0.00 45.31 4.69
1244 2196 1.005340 GATGCAAACTGCTCTCTCCG 58.995 55.000 0.00 0.00 45.31 4.63
1245 2197 2.399916 AGATGCAAACTGCTCTCTCC 57.600 50.000 0.00 0.00 45.31 3.71
1246 2198 3.332919 TCAAGATGCAAACTGCTCTCTC 58.667 45.455 0.00 0.00 45.31 3.20
1247 2199 3.413846 TCAAGATGCAAACTGCTCTCT 57.586 42.857 0.00 0.08 45.31 3.10
1248 2200 4.874966 AGTATCAAGATGCAAACTGCTCTC 59.125 41.667 0.00 0.00 45.31 3.20
1249 2201 4.841422 AGTATCAAGATGCAAACTGCTCT 58.159 39.130 0.00 0.00 45.31 4.09
1250 2202 5.353678 AGAAGTATCAAGATGCAAACTGCTC 59.646 40.000 0.00 0.00 45.31 4.26
1251 2203 5.251764 AGAAGTATCAAGATGCAAACTGCT 58.748 37.500 0.00 0.00 45.31 4.24
1252 2204 5.448360 GGAGAAGTATCAAGATGCAAACTGC 60.448 44.000 0.00 0.00 45.29 4.40
1253 2205 5.879223 AGGAGAAGTATCAAGATGCAAACTG 59.121 40.000 0.00 0.00 0.00 3.16
1254 2206 5.879223 CAGGAGAAGTATCAAGATGCAAACT 59.121 40.000 0.00 0.00 0.00 2.66
1255 2207 5.645497 ACAGGAGAAGTATCAAGATGCAAAC 59.355 40.000 0.00 0.00 0.00 2.93
1256 2208 5.809001 ACAGGAGAAGTATCAAGATGCAAA 58.191 37.500 0.00 0.00 0.00 3.68
1361 2327 0.836606 TGTCCTTGTGGCTGAACAGA 59.163 50.000 5.97 0.00 0.00 3.41
1607 8038 0.824759 CACTGGAGTAGTAGGTGGCC 59.175 60.000 0.00 0.00 37.60 5.36
1641 8078 3.266254 AGGGACTGTACTAGTAGAGCACA 59.734 47.826 23.29 10.53 40.53 4.57
1661 8104 5.067153 CAGTATTGTACAGTCTGGAGAGAGG 59.933 48.000 4.53 0.00 0.00 3.69
1870 8552 2.475022 GCATCATGTGTCATGTGTGTCG 60.475 50.000 9.13 0.00 0.00 4.35
1902 9133 0.247185 CCCCACTCGCAAATTGCAAT 59.753 50.000 18.65 5.99 45.36 3.56
1924 9156 3.504375 ACGGAGGGGTAGTATAACATCC 58.496 50.000 0.00 0.00 33.63 3.51
1927 9159 4.613437 AGAAACGGAGGGGTAGTATAACA 58.387 43.478 0.00 0.00 0.00 2.41
1928 9160 5.604758 AAGAAACGGAGGGGTAGTATAAC 57.395 43.478 0.00 0.00 0.00 1.89
1931 9163 5.509832 AAAAAGAAACGGAGGGGTAGTAT 57.490 39.130 0.00 0.00 0.00 2.12
1932 9164 4.980339 AAAAAGAAACGGAGGGGTAGTA 57.020 40.909 0.00 0.00 0.00 1.82
1933 9165 3.870538 AAAAAGAAACGGAGGGGTAGT 57.129 42.857 0.00 0.00 0.00 2.73
1934 9166 4.903054 ACTAAAAAGAAACGGAGGGGTAG 58.097 43.478 0.00 0.00 0.00 3.18
1936 9168 3.497405 GGACTAAAAAGAAACGGAGGGGT 60.497 47.826 0.00 0.00 0.00 4.95
1939 9171 2.159037 GCGGACTAAAAAGAAACGGAGG 59.841 50.000 0.00 0.00 0.00 4.30
1940 9172 2.803956 TGCGGACTAAAAAGAAACGGAG 59.196 45.455 0.00 0.00 0.00 4.63
1943 9175 7.123830 CCTTATATGCGGACTAAAAAGAAACG 58.876 38.462 0.00 0.00 0.00 3.60
1946 9178 8.455682 CAAACCTTATATGCGGACTAAAAAGAA 58.544 33.333 0.00 0.00 0.00 2.52
1947 9179 7.066525 CCAAACCTTATATGCGGACTAAAAAGA 59.933 37.037 0.00 0.00 0.00 2.52
1948 9180 7.148137 ACCAAACCTTATATGCGGACTAAAAAG 60.148 37.037 0.00 0.00 0.00 2.27
1949 9181 6.660094 ACCAAACCTTATATGCGGACTAAAAA 59.340 34.615 0.00 0.00 0.00 1.94
1951 9183 5.747342 ACCAAACCTTATATGCGGACTAAA 58.253 37.500 0.00 0.00 0.00 1.85
1952 9184 5.104859 TGACCAAACCTTATATGCGGACTAA 60.105 40.000 0.00 0.00 0.00 2.24
1958 9190 5.123186 TGACTTTGACCAAACCTTATATGCG 59.877 40.000 0.00 0.00 0.00 4.73
1959 9191 6.509418 TGACTTTGACCAAACCTTATATGC 57.491 37.500 0.00 0.00 0.00 3.14
1960 9192 7.029563 GCTTGACTTTGACCAAACCTTATATG 58.970 38.462 0.00 0.00 0.00 1.78
1962 9194 6.303839 AGCTTGACTTTGACCAAACCTTATA 58.696 36.000 0.00 0.00 0.00 0.98
1964 9196 4.532834 AGCTTGACTTTGACCAAACCTTA 58.467 39.130 0.00 0.00 0.00 2.69
1966 9198 3.018423 AGCTTGACTTTGACCAAACCT 57.982 42.857 0.00 0.00 0.00 3.50
2056 9715 6.260700 TCTACCCATAGTTAAATGGTGCAT 57.739 37.500 5.62 0.00 44.29 3.96
2092 9982 7.054751 GGACCAAGGACTTAACTTTGCTATAT 58.945 38.462 0.00 0.00 0.00 0.86
2112 10007 1.203262 AGCAGTAGTACCAAGGGACCA 60.203 52.381 0.00 0.00 0.00 4.02
2113 10008 1.207329 CAGCAGTAGTACCAAGGGACC 59.793 57.143 0.00 0.00 0.00 4.46
2202 10812 3.373130 GCTCGGTAATGGAGGTTTGTTAC 59.627 47.826 0.00 0.00 32.10 2.50
2271 11256 2.421424 AGCTCAAAAGGCATGTCGATTC 59.579 45.455 0.00 0.00 0.00 2.52
2272 11257 2.163010 CAGCTCAAAAGGCATGTCGATT 59.837 45.455 0.00 0.00 0.00 3.34
2294 11341 6.698380 TGTTCTTCAAGCTAACTACCTAAGG 58.302 40.000 0.00 0.00 0.00 2.69
2321 11368 9.621239 ACTTCTCCCTCCATCTCATAATATAAA 57.379 33.333 0.00 0.00 0.00 1.40
2323 11370 9.621239 AAACTTCTCCCTCCATCTCATAATATA 57.379 33.333 0.00 0.00 0.00 0.86
2324 11371 8.517323 AAACTTCTCCCTCCATCTCATAATAT 57.483 34.615 0.00 0.00 0.00 1.28
2326 11373 6.619023 AGAAACTTCTCCCTCCATCTCATAAT 59.381 38.462 0.00 0.00 29.94 1.28
2329 11376 4.369872 AGAAACTTCTCCCTCCATCTCAT 58.630 43.478 0.00 0.00 29.94 2.90
2331 11378 4.835284 AAGAAACTTCTCCCTCCATCTC 57.165 45.455 0.00 0.00 36.28 2.75
2332 11379 4.599241 TCAAAGAAACTTCTCCCTCCATCT 59.401 41.667 0.00 0.00 36.28 2.90
2333 11380 4.911390 TCAAAGAAACTTCTCCCTCCATC 58.089 43.478 0.00 0.00 36.28 3.51
2334 11381 5.324832 TTCAAAGAAACTTCTCCCTCCAT 57.675 39.130 0.00 0.00 36.28 3.41
2335 11382 4.788925 TTCAAAGAAACTTCTCCCTCCA 57.211 40.909 0.00 0.00 36.28 3.86
2336 11383 6.040955 ACATTTTCAAAGAAACTTCTCCCTCC 59.959 38.462 0.00 0.00 36.28 4.30
2337 11384 7.043961 ACATTTTCAAAGAAACTTCTCCCTC 57.956 36.000 0.00 0.00 36.28 4.30
2339 11386 9.764363 ATTTACATTTTCAAAGAAACTTCTCCC 57.236 29.630 0.00 0.00 36.28 4.30
2388 11862 2.992744 GCGTGACGAGCTTAATTACC 57.007 50.000 10.10 0.00 0.00 2.85
2428 12059 5.125578 GCTCATATGATACGGATAGACACCA 59.874 44.000 5.72 0.00 0.00 4.17
2489 12130 2.044806 GATGACCCACCCATCCTCCG 62.045 65.000 0.00 0.00 35.56 4.63
2496 12137 3.716195 CGGCAGATGACCCACCCA 61.716 66.667 0.00 0.00 0.00 4.51
2585 12241 2.181777 CGCCGACTAGCTTGCTGA 59.818 61.111 5.26 0.00 0.00 4.26
2794 12492 1.545428 GCTGTTGATCAGGTGGTCCAA 60.545 52.381 0.00 0.00 43.78 3.53
2965 12669 2.681778 CGTGGGGTCAGAGAGGCT 60.682 66.667 0.00 0.00 0.00 4.58
2987 12691 1.006825 CATGCCGTTCGTCGTCTTGA 61.007 55.000 0.00 0.00 37.94 3.02
3056 12763 0.680280 GGAGGGAGTGTACAGCGAGA 60.680 60.000 0.00 0.00 0.00 4.04
3058 12765 2.044555 CGGAGGGAGTGTACAGCGA 61.045 63.158 0.00 0.00 0.00 4.93
3063 12770 1.888736 GGTGACGGAGGGAGTGTAC 59.111 63.158 0.00 0.00 0.00 2.90
3064 12771 4.428845 GGTGACGGAGGGAGTGTA 57.571 61.111 0.00 0.00 0.00 2.90
3150 12857 1.804748 CGACAGCCTTAAAACAGGACC 59.195 52.381 0.00 0.00 35.71 4.46
3152 12859 1.695242 TCCGACAGCCTTAAAACAGGA 59.305 47.619 0.00 0.00 35.71 3.86
3246 12963 3.220507 ACACATTCATTTGGTGCGATG 57.779 42.857 0.00 0.00 36.00 3.84
3257 12974 8.855110 CAGGAGTACTAGAATCTACACATTCAT 58.145 37.037 0.00 0.00 35.51 2.57
3308 13025 5.780282 TCTTCCTATGTACACCCTCCATATG 59.220 44.000 0.00 0.00 0.00 1.78
3310 13027 5.412617 TCTTCCTATGTACACCCTCCATA 57.587 43.478 0.00 0.00 0.00 2.74
3319 13036 5.422012 TGACTCTTGCATCTTCCTATGTACA 59.578 40.000 0.00 0.00 0.00 2.90
3328 13045 1.392853 CGCACTGACTCTTGCATCTTC 59.607 52.381 0.00 0.00 38.76 2.87
3404 13291 3.386402 GTCTTTGGATAGGACCTCCTCTG 59.614 52.174 0.00 0.00 44.77 3.35
3509 13440 4.304659 GGGATATATAAAGGGGTCGGGAT 58.695 47.826 0.00 0.00 0.00 3.85
3513 13444 3.710165 GGAGGGGATATATAAAGGGGTCG 59.290 52.174 0.00 0.00 0.00 4.79
3539 13472 0.813184 CCGCATATTCATGGATGGGC 59.187 55.000 0.00 0.00 35.33 5.36
3544 13477 3.576078 AAGTTCCCGCATATTCATGGA 57.424 42.857 0.00 0.00 32.36 3.41
3572 13505 1.001181 CAACAAAGTTGATGGGGCAGG 59.999 52.381 3.91 0.00 0.00 4.85
3578 13511 1.336440 TCGGTGCAACAAAGTTGATGG 59.664 47.619 13.58 0.42 39.98 3.51
3609 13542 2.284331 TCCAAGGAGCGCTACCCA 60.284 61.111 18.20 0.00 0.00 4.51
3619 13552 3.561313 GCTTTGAACCCATAGTCCAAGGA 60.561 47.826 0.00 0.00 0.00 3.36
3660 13593 4.168101 TGTATTGAAGAACAGGGGAGAGT 58.832 43.478 0.00 0.00 0.00 3.24
3661 13594 4.826274 TGTATTGAAGAACAGGGGAGAG 57.174 45.455 0.00 0.00 0.00 3.20
3662 13595 5.576563 TTTGTATTGAAGAACAGGGGAGA 57.423 39.130 0.00 0.00 0.00 3.71
3717 13652 8.626526 TCATCACATCCAAAATTACATCTGATG 58.373 33.333 15.83 15.83 34.93 3.07
3781 13718 8.734386 TGCAACAAAGAACCAAAACAAAATAAT 58.266 25.926 0.00 0.00 0.00 1.28
3785 13722 6.205464 TCATGCAACAAAGAACCAAAACAAAA 59.795 30.769 0.00 0.00 0.00 2.44
3844 13781 2.591923 TCCAAACATGGCTAGTGCAAA 58.408 42.857 0.00 0.00 41.91 3.68
3857 13794 8.082672 TCTCTTAGAGATCAATCATCCAAACA 57.917 34.615 8.00 0.00 33.35 2.83
3881 13818 4.003648 CCCAACCAACATACAGAACTCTC 58.996 47.826 0.00 0.00 0.00 3.20
3888 13825 5.128992 GGTTAAACCCAACCAACATACAG 57.871 43.478 0.17 0.00 46.14 2.74
3909 13846 6.058183 CCACTCAGATAGGTTATTTGGAAGG 58.942 44.000 0.00 0.00 0.00 3.46
3947 13884 4.023279 TGGCAATAACACAGTACAAGCTTG 60.023 41.667 24.84 24.84 0.00 4.01
3949 13886 3.502211 GTGGCAATAACACAGTACAAGCT 59.498 43.478 0.00 0.00 38.67 3.74
3957 13894 6.801539 TTCTCTTTAGTGGCAATAACACAG 57.198 37.500 6.93 2.87 41.21 3.66
3968 13905 7.361286 GGCAACTATCTTGTTTCTCTTTAGTGG 60.361 40.741 0.00 0.00 0.00 4.00
3997 13934 1.134491 CCAAAACGCCCTACTCCCTAG 60.134 57.143 0.00 0.00 0.00 3.02
3998 13935 0.906775 CCAAAACGCCCTACTCCCTA 59.093 55.000 0.00 0.00 0.00 3.53
3999 13936 0.838987 TCCAAAACGCCCTACTCCCT 60.839 55.000 0.00 0.00 0.00 4.20
4000 13937 0.392595 CTCCAAAACGCCCTACTCCC 60.393 60.000 0.00 0.00 0.00 4.30
4001 13938 1.025113 GCTCCAAAACGCCCTACTCC 61.025 60.000 0.00 0.00 0.00 3.85
4002 13939 0.036294 AGCTCCAAAACGCCCTACTC 60.036 55.000 0.00 0.00 0.00 2.59
4003 13940 0.036294 GAGCTCCAAAACGCCCTACT 60.036 55.000 0.87 0.00 0.00 2.57
4004 13941 1.359459 CGAGCTCCAAAACGCCCTAC 61.359 60.000 8.47 0.00 0.00 3.18
4005 13942 1.079405 CGAGCTCCAAAACGCCCTA 60.079 57.895 8.47 0.00 0.00 3.53
4006 13943 2.358737 CGAGCTCCAAAACGCCCT 60.359 61.111 8.47 0.00 0.00 5.19
4007 13944 3.431725 CCGAGCTCCAAAACGCCC 61.432 66.667 8.47 0.00 0.00 6.13
4008 13945 4.103103 GCCGAGCTCCAAAACGCC 62.103 66.667 8.47 0.00 0.00 5.68
4009 13946 4.103103 GGCCGAGCTCCAAAACGC 62.103 66.667 8.47 0.23 0.00 4.84
4010 13947 2.358737 AGGCCGAGCTCCAAAACG 60.359 61.111 8.47 0.00 0.00 3.60
4011 13948 2.041115 GGAGGCCGAGCTCCAAAAC 61.041 63.158 8.47 0.00 39.45 2.43
4012 13949 2.351276 GGAGGCCGAGCTCCAAAA 59.649 61.111 8.47 0.00 39.45 2.44
4013 13950 2.927856 TGGAGGCCGAGCTCCAAA 60.928 61.111 8.96 0.00 45.68 3.28
4016 13953 4.247380 CCATGGAGGCCGAGCTCC 62.247 72.222 5.56 0.00 40.05 4.70
4017 13954 3.157252 TCCATGGAGGCCGAGCTC 61.157 66.667 11.44 2.73 37.29 4.09
4018 13955 3.160047 CTCCATGGAGGCCGAGCT 61.160 66.667 31.14 0.00 38.51 4.09
4026 13963 0.106519 AAAATCCGGCCTCCATGGAG 60.107 55.000 31.69 31.69 41.63 3.86
4027 13964 0.334676 AAAAATCCGGCCTCCATGGA 59.665 50.000 15.27 15.27 38.35 3.41
4028 13965 2.900547 AAAAATCCGGCCTCCATGG 58.099 52.632 4.97 4.97 39.35 3.66
4053 13990 9.434420 TGAAACTGAAAAGTGTGAATTTTGAAT 57.566 25.926 0.00 0.00 30.22 2.57
4054 13991 8.824159 TGAAACTGAAAAGTGTGAATTTTGAA 57.176 26.923 0.00 0.00 30.22 2.69
4055 13992 8.824159 TTGAAACTGAAAAGTGTGAATTTTGA 57.176 26.923 0.00 0.00 30.22 2.69
4056 13993 9.875675 TTTTGAAACTGAAAAGTGTGAATTTTG 57.124 25.926 0.00 0.00 30.22 2.44
4130 14067 9.492730 AGGGTATTTCATCCTCAAATTTTACAT 57.507 29.630 0.00 0.00 0.00 2.29
4131 14068 8.893563 AGGGTATTTCATCCTCAAATTTTACA 57.106 30.769 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.