Multiple sequence alignment - TraesCS2D01G323100

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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 TraesCS2D01G323100 chr2D 100.000 4282 0 0 1 4282 414961098 414956817 0.000000e+00 7908.0
1 TraesCS2D01G323100 chr2D 87.513 977 66 29 885 1847 416397879 416396945 0.000000e+00 1077.0
2 TraesCS2D01G323100 chr2D 87.322 844 66 19 3453 4282 416390887 416390071 0.000000e+00 928.0
3 TraesCS2D01G323100 chr2D 90.448 513 27 9 1843 2339 416392352 416391846 0.000000e+00 656.0
4 TraesCS2D01G323100 chr2D 86.989 538 49 9 2791 3319 416391414 416390889 1.720000e-163 586.0
5 TraesCS2D01G323100 chr2D 91.549 142 6 1 534 675 464515884 464515749 1.570000e-44 191.0
6 TraesCS2D01G323100 chr2D 100.000 29 0 0 184 212 641483615 641483587 2.000000e-03 54.7
7 TraesCS2D01G323100 chr2A 94.431 1275 41 9 1 1262 581960502 581959245 0.000000e+00 1934.0
8 TraesCS2D01G323100 chr2A 98.320 774 10 1 1441 2214 581945920 581945150 0.000000e+00 1354.0
9 TraesCS2D01G323100 chr2A 91.173 895 45 16 2413 3296 581944580 581943709 0.000000e+00 1184.0
10 TraesCS2D01G323100 chr2A 91.529 850 47 13 3452 4282 581943711 581942868 0.000000e+00 1147.0
11 TraesCS2D01G323100 chr2A 93.706 715 33 7 1610 2313 582635951 582635238 0.000000e+00 1061.0
12 TraesCS2D01G323100 chr2A 89.391 575 38 11 885 1455 582636565 582636010 0.000000e+00 702.0
13 TraesCS2D01G323100 chr2A 87.747 506 43 8 2791 3289 582634715 582634222 1.340000e-159 573.0
14 TraesCS2D01G323100 chr2A 97.814 183 4 0 1259 1441 581950658 581950476 2.490000e-82 316.0
15 TraesCS2D01G323100 chr2A 83.439 157 17 3 2211 2359 581944730 581944575 2.080000e-28 137.0
16 TraesCS2D01G323100 chr2A 83.333 72 9 3 814 884 720950227 720950296 3.570000e-06 63.9
17 TraesCS2D01G323100 chr2A 97.059 34 1 0 452 485 384681360 384681327 1.660000e-04 58.4
18 TraesCS2D01G323100 chr2A 97.059 34 1 0 452 485 384686445 384686412 1.660000e-04 58.4
19 TraesCS2D01G323100 chr2B 87.839 1513 109 33 885 2359 488196724 488195249 0.000000e+00 1705.0
20 TraesCS2D01G323100 chr2B 85.632 863 62 33 2471 3321 488195209 488194397 0.000000e+00 850.0
21 TraesCS2D01G323100 chr2B 93.595 484 19 6 3793 4271 488194090 488193614 0.000000e+00 712.0
22 TraesCS2D01G323100 chr2B 96.875 320 10 0 3450 3769 488194400 488194081 1.750000e-148 536.0
23 TraesCS2D01G323100 chr3D 97.605 167 4 0 673 839 557724664 557724498 1.950000e-73 287.0
24 TraesCS2D01G323100 chr3D 96.970 165 5 0 672 836 486424951 486424787 1.170000e-70 278.0
25 TraesCS2D01G323100 chr3D 82.935 293 38 11 602 886 314150413 314150125 1.980000e-63 254.0
26 TraesCS2D01G323100 chr3D 89.062 192 15 5 252 443 53145947 53145762 2.570000e-57 233.0
27 TraesCS2D01G323100 chr3D 97.101 138 3 1 3318 3455 363329689 363329825 9.260000e-57 231.0
28 TraesCS2D01G323100 chr3D 96.296 135 5 0 3319 3453 348544514 348544380 5.570000e-54 222.0
29 TraesCS2D01G323100 chr3D 94.615 130 7 0 3322 3451 471101903 471102032 7.260000e-48 202.0
30 TraesCS2D01G323100 chr7D 96.988 166 4 1 673 838 171308152 171307988 1.170000e-70 278.0
31 TraesCS2D01G323100 chr7D 94.656 131 7 0 3321 3451 20082932 20083062 2.020000e-48 204.0
32 TraesCS2D01G323100 chr5D 96.407 167 6 0 673 839 472291158 472290992 4.220000e-70 276.0
33 TraesCS2D01G323100 chr5D 89.372 207 16 5 279 484 231475436 231475637 5.490000e-64 255.0
34 TraesCS2D01G323100 chr5D 98.519 135 2 0 3319 3453 542576325 542576459 5.530000e-59 239.0
35 TraesCS2D01G323100 chr5D 91.667 144 4 3 534 675 248193329 248193192 4.370000e-45 193.0
36 TraesCS2D01G323100 chr5D 92.424 132 9 1 3324 3455 310277982 310278112 2.030000e-43 187.0
37 TraesCS2D01G323100 chr5D 84.286 70 8 3 816 884 363676435 363676368 9.940000e-07 65.8
38 TraesCS2D01G323100 chr3B 93.785 177 10 1 664 840 18497638 18497813 9.130000e-67 265.0
39 TraesCS2D01G323100 chr5A 95.122 164 8 0 280 443 456897738 456897901 4.250000e-65 259.0
40 TraesCS2D01G323100 chr5A 92.254 142 5 1 534 675 20531583 20531448 3.380000e-46 196.0
41 TraesCS2D01G323100 chr6B 93.143 175 10 2 269 443 685530952 685531124 5.490000e-64 255.0
42 TraesCS2D01G323100 chr6B 87.324 213 21 5 236 443 542764418 542764207 5.530000e-59 239.0
43 TraesCS2D01G323100 chr6B 85.446 213 23 6 236 443 381742995 381742786 9.330000e-52 215.0
44 TraesCS2D01G323100 chr7A 92.655 177 12 1 272 448 115807695 115807520 1.980000e-63 254.0
45 TraesCS2D01G323100 chr7A 100.000 28 0 0 185 212 36633875 36633902 8.000000e-03 52.8
46 TraesCS2D01G323100 chr6D 93.143 175 9 3 270 443 82196651 82196823 1.980000e-63 254.0
47 TraesCS2D01G323100 chr6D 96.923 130 4 0 3321 3450 427339510 427339639 7.210000e-53 219.0
48 TraesCS2D01G323100 chr6D 88.148 135 15 1 3318 3451 447916553 447916687 4.430000e-35 159.0
49 TraesCS2D01G323100 chr4D 83.045 289 40 8 602 885 314930538 314930254 1.980000e-63 254.0
50 TraesCS2D01G323100 chr4D 92.179 179 12 2 274 452 93338211 93338035 7.110000e-63 252.0
51 TraesCS2D01G323100 chr4D 84.252 254 33 5 602 849 321133838 321133586 1.540000e-59 241.0
52 TraesCS2D01G323100 chr4D 94.815 135 6 1 3321 3455 362783268 362783401 4.340000e-50 209.0
53 TraesCS2D01G323100 chr4D 92.199 141 10 1 3321 3460 345338907 345338767 9.390000e-47 198.0
54 TraesCS2D01G323100 chr4D 92.126 127 10 0 3318 3444 462619486 462619360 3.400000e-41 180.0
55 TraesCS2D01G323100 chr4A 90.860 186 15 2 277 461 582529974 582530158 9.190000e-62 248.0
56 TraesCS2D01G323100 chr4A 79.934 304 35 13 552 849 678143325 678143042 2.610000e-47 200.0
57 TraesCS2D01G323100 chr4A 90.580 138 13 0 3316 3453 14180071 14180208 2.630000e-42 183.0
58 TraesCS2D01G323100 chr4B 91.160 181 12 3 268 448 86060291 86060467 4.280000e-60 243.0
59 TraesCS2D01G323100 chr4B 89.894 188 13 5 256 443 107557034 107556853 1.990000e-58 237.0
60 TraesCS2D01G323100 chr4B 89.894 188 13 5 256 443 220793418 220793599 1.990000e-58 237.0
61 TraesCS2D01G323100 chr4B 91.111 135 11 1 3318 3451 159606467 159606601 9.460000e-42 182.0
62 TraesCS2D01G323100 chr4B 100.000 28 0 0 185 212 408085099 408085126 8.000000e-03 52.8
63 TraesCS2D01G323100 chr1B 91.111 180 14 2 264 443 626862207 626862384 4.280000e-60 243.0
64 TraesCS2D01G323100 chr1B 91.667 60 5 0 222 281 540717723 540717782 2.740000e-12 84.2
65 TraesCS2D01G323100 chr6A 92.308 169 13 0 275 443 287304228 287304060 1.540000e-59 241.0
66 TraesCS2D01G323100 chr6A 89.076 119 6 7 452 568 29293198 29293085 1.610000e-29 141.0
67 TraesCS2D01G323100 chr6A 91.667 60 5 0 222 281 95285676 95285735 2.740000e-12 84.2
68 TraesCS2D01G323100 chr1D 89.418 189 13 6 256 443 275376371 275376553 9.260000e-57 231.0
69 TraesCS2D01G323100 chr1D 88.889 135 15 0 3319 3453 94049922 94049788 2.650000e-37 167.0
70 TraesCS2D01G323100 chr1D 81.553 103 8 11 180 278 454453216 454453121 1.650000e-09 75.0
71 TraesCS2D01G323100 chr1D 84.932 73 6 4 814 884 34807828 34807897 7.680000e-08 69.4
72 TraesCS2D01G323100 chr7B 91.549 142 6 1 534 675 499181569 499181434 1.570000e-44 191.0
73 TraesCS2D01G323100 chr7B 91.549 142 6 1 534 675 501195031 501195166 1.570000e-44 191.0
74 TraesCS2D01G323100 chr7B 100.000 30 0 0 183 212 592622817 592622846 5.980000e-04 56.5
75 TraesCS2D01G323100 chr5B 91.549 142 6 1 534 675 437861002 437860867 1.570000e-44 191.0
76 TraesCS2D01G323100 chr5B 91.667 60 5 0 222 281 598614971 598614912 2.740000e-12 84.2
77 TraesCS2D01G323100 chr1A 91.549 142 6 1 534 675 157432338 157432203 1.570000e-44 191.0
78 TraesCS2D01G323100 chr1A 100.000 28 0 0 185 212 25292159 25292186 8.000000e-03 52.8
79 TraesCS2D01G323100 chrUn 91.603 131 11 0 3321 3451 313778703 313778573 9.460000e-42 182.0
80 TraesCS2D01G323100 chrUn 91.603 131 11 0 3321 3451 337922684 337922554 9.460000e-42 182.0
81 TraesCS2D01G323100 chrUn 91.667 60 5 0 222 281 358211195 358211136 2.740000e-12 84.2


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

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2D01G323100 chr2D 414956817 414961098 4281 True 7908.000000 7908 100.000000 1 4282 1 chr2D.!!$R1 4281
1 TraesCS2D01G323100 chr2D 416396945 416397879 934 True 1077.000000 1077 87.513000 885 1847 1 chr2D.!!$R2 962
2 TraesCS2D01G323100 chr2D 416390071 416392352 2281 True 723.333333 928 88.253000 1843 4282 3 chr2D.!!$R5 2439
3 TraesCS2D01G323100 chr2A 581959245 581960502 1257 True 1934.000000 1934 94.431000 1 1262 1 chr2A.!!$R4 1261
4 TraesCS2D01G323100 chr2A 581942868 581945920 3052 True 955.500000 1354 91.115250 1441 4282 4 chr2A.!!$R5 2841
5 TraesCS2D01G323100 chr2A 582634222 582636565 2343 True 778.666667 1061 90.281333 885 3289 3 chr2A.!!$R6 2404
6 TraesCS2D01G323100 chr2B 488193614 488196724 3110 True 950.750000 1705 90.985250 885 4271 4 chr2B.!!$R1 3386

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
196 197 2.038387 CCGCTTATAAGGCTGGTTGT 57.962 50.000 14.28 0.00 0.0 3.32 F
1304 1325 0.179070 TGTGTGGTTCTGCTGCGTAA 60.179 50.000 0.00 0.00 0.0 3.18 F
1305 1326 0.234884 GTGTGGTTCTGCTGCGTAAC 59.765 55.000 8.03 8.03 0.0 2.50 F
2054 2118 1.000171 GCTGTTTCAAAAGGGAGGCAG 60.000 52.381 0.00 0.00 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2054 2118 0.250467 TGTTCTGTGCTTCTCTGCCC 60.250 55.0 0.00 0.00 0.00 5.36 R
2215 2702 0.465287 TCAAGAGCGGCTCATATGCA 59.535 50.0 29.88 13.19 32.06 3.96 R
2636 3228 0.693049 AGGGCAGGATTGTCGTTCTT 59.307 50.0 0.00 0.00 0.00 2.52 R
3433 4077 0.034337 TAAGGCTGCGTTCGGTTTCT 59.966 50.0 11.22 0.00 0.00 2.52 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
63 64 2.371259 GGGAGAGAACTGAGGGGGC 61.371 68.421 0.00 0.00 0.00 5.80
144 145 2.052047 AACCGGTCTTGGTCCCACTG 62.052 60.000 8.04 0.00 42.89 3.66
196 197 2.038387 CCGCTTATAAGGCTGGTTGT 57.962 50.000 14.28 0.00 0.00 3.32
201 202 4.814234 CGCTTATAAGGCTGGTTGTAATGA 59.186 41.667 14.28 0.00 0.00 2.57
247 248 9.750125 CATACACTCGTATAATGCATATGGTAT 57.250 33.333 0.00 0.00 36.11 2.73
270 271 5.935668 TGGTGTATGATACTACCTCCCTA 57.064 43.478 18.36 3.15 33.71 3.53
271 272 6.283948 TGGTGTATGATACTACCTCCCTAA 57.716 41.667 18.36 2.65 33.71 2.69
272 273 6.871035 TGGTGTATGATACTACCTCCCTAAT 58.129 40.000 18.36 0.00 33.71 1.73
273 274 6.724441 TGGTGTATGATACTACCTCCCTAATG 59.276 42.308 18.36 0.00 33.71 1.90
274 275 6.351117 GGTGTATGATACTACCTCCCTAATGC 60.351 46.154 13.45 0.00 31.49 3.56
275 276 6.210784 GTGTATGATACTACCTCCCTAATGCA 59.789 42.308 4.03 0.00 0.00 3.96
276 277 6.959954 TGTATGATACTACCTCCCTAATGCAT 59.040 38.462 4.03 0.00 0.00 3.96
277 278 8.119891 TGTATGATACTACCTCCCTAATGCATA 58.880 37.037 0.00 0.00 0.00 3.14
278 279 7.667575 ATGATACTACCTCCCTAATGCATAG 57.332 40.000 0.00 0.00 0.00 2.23
279 280 6.562228 TGATACTACCTCCCTAATGCATAGT 58.438 40.000 0.00 0.00 0.00 2.12
280 281 7.705700 TGATACTACCTCCCTAATGCATAGTA 58.294 38.462 0.00 0.81 0.00 1.82
281 282 7.614583 TGATACTACCTCCCTAATGCATAGTAC 59.385 40.741 0.00 0.00 0.00 2.73
282 283 5.966684 ACTACCTCCCTAATGCATAGTACT 58.033 41.667 0.00 0.00 0.00 2.73
283 284 6.382925 ACTACCTCCCTAATGCATAGTACTT 58.617 40.000 0.00 0.00 0.00 2.24
284 285 5.810080 ACCTCCCTAATGCATAGTACTTC 57.190 43.478 0.00 0.00 0.00 3.01
285 286 5.468658 ACCTCCCTAATGCATAGTACTTCT 58.531 41.667 0.00 0.00 0.00 2.85
286 287 5.905913 ACCTCCCTAATGCATAGTACTTCTT 59.094 40.000 0.00 0.00 0.00 2.52
287 288 6.042208 ACCTCCCTAATGCATAGTACTTCTTC 59.958 42.308 0.00 0.00 0.00 2.87
288 289 6.420913 TCCCTAATGCATAGTACTTCTTCC 57.579 41.667 0.00 0.00 0.00 3.46
292 293 6.761714 CCTAATGCATAGTACTTCTTCCGTTT 59.238 38.462 0.00 0.00 0.00 3.60
385 386 7.550906 AGAGTGTAGATTTACTCATTTTGCTCC 59.449 37.037 7.09 0.00 44.41 4.70
413 414 7.946655 TGTAGTCACTTGTTGAAATGTCTAG 57.053 36.000 0.00 0.00 35.39 2.43
417 418 8.506168 AGTCACTTGTTGAAATGTCTAGAAAA 57.494 30.769 0.00 0.00 35.39 2.29
452 455 9.535170 TTAGAAATGGAGGGAGTCATATACTAG 57.465 37.037 0.00 0.00 39.07 2.57
512 516 4.959596 TGTATGGTCAGTCTAGAACGTC 57.040 45.455 0.00 0.00 0.00 4.34
531 535 8.304596 AGAACGTCTTATATTTGTGAACAGAGA 58.695 33.333 0.00 0.00 0.00 3.10
606 610 9.534565 AGTAGCATAGCATTTATTATGATACGG 57.465 33.333 11.77 0.00 46.16 4.02
640 644 6.723298 TGATACTCAATCCTCTCTTTCTCC 57.277 41.667 0.00 0.00 33.22 3.71
652 656 9.933240 ATCCTCTCTTTCTCCATTTAATTCAAT 57.067 29.630 0.00 0.00 0.00 2.57
675 679 6.801539 TGACACCTCATCAAAATTGTCTAC 57.198 37.500 0.00 0.00 35.45 2.59
696 700 4.098894 ACTCCCTCCGTTCCTAAATGTAA 58.901 43.478 0.00 0.00 0.00 2.41
728 732 4.716784 AGAGCTTCCACTATGAACCACATA 59.283 41.667 0.00 0.00 40.07 2.29
786 790 6.597672 TCATTCATTTTGCTCCGTATGTAGTT 59.402 34.615 0.00 0.00 0.00 2.24
789 793 5.350365 TCATTTTGCTCCGTATGTAGTTCAC 59.650 40.000 0.00 0.00 0.00 3.18
796 800 4.847198 TCCGTATGTAGTTCACCTAGTGA 58.153 43.478 0.00 0.00 41.09 3.41
878 892 9.640963 GATACTGGAGTATGATACATTACAACC 57.359 37.037 5.28 0.00 40.99 3.77
949 963 2.284699 CCACCCCCGTCTTCTCCT 60.285 66.667 0.00 0.00 0.00 3.69
1137 1157 3.160047 CCTCCTGCTCCCGCTGAT 61.160 66.667 0.00 0.00 37.28 2.90
1262 1283 4.617520 TTGGAGCGCGCTGGTTGA 62.618 61.111 41.82 16.65 0.00 3.18
1263 1284 3.899981 TTGGAGCGCGCTGGTTGAT 62.900 57.895 41.82 13.69 0.00 2.57
1264 1285 3.127533 GGAGCGCGCTGGTTGATT 61.128 61.111 41.82 12.72 0.00 2.57
1272 1293 0.673644 CGCTGGTTGATTCGTTCCCT 60.674 55.000 0.00 0.00 0.00 4.20
1304 1325 0.179070 TGTGTGGTTCTGCTGCGTAA 60.179 50.000 0.00 0.00 0.00 3.18
1305 1326 0.234884 GTGTGGTTCTGCTGCGTAAC 59.765 55.000 8.03 8.03 0.00 2.50
1315 1336 1.235724 GCTGCGTAACCAGGAAGTTT 58.764 50.000 0.00 0.00 33.44 2.66
1335 1356 4.137872 GTCGATCCCGCCCGTGAA 62.138 66.667 0.00 0.00 35.37 3.18
1383 1404 2.041265 AAGGGCGAGGTGGAGGAT 59.959 61.111 0.00 0.00 0.00 3.24
2054 2118 1.000171 GCTGTTTCAAAAGGGAGGCAG 60.000 52.381 0.00 0.00 0.00 4.85
2267 2762 6.665680 AGTTCACTATGACATACTTCCTCTGT 59.334 38.462 0.00 0.00 0.00 3.41
2362 2857 9.469807 GATTTATCATCATAGCTAATACTCCGG 57.530 37.037 0.00 0.00 0.00 5.14
2363 2858 7.956328 TTATCATCATAGCTAATACTCCGGT 57.044 36.000 0.00 0.00 0.00 5.28
2364 2859 9.470399 TTTATCATCATAGCTAATACTCCGGTA 57.530 33.333 0.00 0.00 0.00 4.02
2365 2860 7.956328 ATCATCATAGCTAATACTCCGGTAA 57.044 36.000 0.00 0.00 0.00 2.85
2366 2861 7.392494 TCATCATAGCTAATACTCCGGTAAG 57.608 40.000 0.00 0.00 0.00 2.34
2367 2862 7.173032 TCATCATAGCTAATACTCCGGTAAGA 58.827 38.462 0.00 0.00 0.00 2.10
2368 2863 7.834681 TCATCATAGCTAATACTCCGGTAAGAT 59.165 37.037 0.00 0.00 0.00 2.40
2369 2864 8.470805 CATCATAGCTAATACTCCGGTAAGATT 58.529 37.037 0.00 0.06 0.00 2.40
2370 2865 9.696572 ATCATAGCTAATACTCCGGTAAGATTA 57.303 33.333 0.00 1.31 0.00 1.75
2371 2866 9.524496 TCATAGCTAATACTCCGGTAAGATTAA 57.476 33.333 0.00 0.00 0.00 1.40
2374 2869 8.653036 AGCTAATACTCCGGTAAGATTAATCT 57.347 34.615 12.37 12.37 39.22 2.40
2376 2871 9.708092 GCTAATACTCCGGTAAGATTAATCTTT 57.292 33.333 30.39 16.15 44.28 2.52
2381 2876 8.904099 ACTCCGGTAAGATTAATCTTTTATGG 57.096 34.615 30.39 24.87 44.28 2.74
2382 2877 8.711170 ACTCCGGTAAGATTAATCTTTTATGGA 58.289 33.333 30.39 26.79 44.28 3.41
2383 2878 9.209175 CTCCGGTAAGATTAATCTTTTATGGAG 57.791 37.037 29.69 29.69 44.28 3.86
2384 2879 8.711170 TCCGGTAAGATTAATCTTTTATGGAGT 58.289 33.333 30.39 10.22 44.28 3.85
2385 2880 9.991906 CCGGTAAGATTAATCTTTTATGGAGTA 57.008 33.333 30.39 10.88 44.28 2.59
2396 2891 9.911788 AATCTTTTATGGAGTATCAACTGATGT 57.088 29.630 2.36 0.00 35.56 3.06
2399 2894 9.823647 CTTTTATGGAGTATCAACTGATGTAGT 57.176 33.333 2.36 0.00 42.89 2.73
2401 2896 9.817809 TTTATGGAGTATCAACTGATGTAGTTC 57.182 33.333 2.36 0.00 46.55 3.01
2402 2897 7.667575 ATGGAGTATCAACTGATGTAGTTCT 57.332 36.000 2.36 0.00 46.55 3.01
2403 2898 7.101652 TGGAGTATCAACTGATGTAGTTCTC 57.898 40.000 2.36 0.00 46.55 2.87
2404 2899 6.892456 TGGAGTATCAACTGATGTAGTTCTCT 59.108 38.462 2.36 0.00 46.55 3.10
2405 2900 7.397476 TGGAGTATCAACTGATGTAGTTCTCTT 59.603 37.037 2.36 0.00 46.55 2.85
2406 2901 8.254508 GGAGTATCAACTGATGTAGTTCTCTTT 58.745 37.037 2.36 0.00 46.55 2.52
2463 2967 8.289618 TCTTTGTATGACTTGATTTTACACAGC 58.710 33.333 0.00 0.00 0.00 4.40
2605 3196 4.463050 TCATGTGGGTTTTAAACTCCCT 57.537 40.909 21.23 5.92 41.58 4.20
2606 3197 4.810345 TCATGTGGGTTTTAAACTCCCTT 58.190 39.130 21.23 9.34 41.58 3.95
2607 3198 5.954757 TCATGTGGGTTTTAAACTCCCTTA 58.045 37.500 21.23 13.78 41.58 2.69
2608 3199 6.557568 TCATGTGGGTTTTAAACTCCCTTAT 58.442 36.000 21.23 14.89 41.58 1.73
2609 3200 6.661805 TCATGTGGGTTTTAAACTCCCTTATC 59.338 38.462 21.23 12.96 41.58 1.75
2610 3201 6.208840 TGTGGGTTTTAAACTCCCTTATCT 57.791 37.500 21.23 0.00 41.58 1.98
2611 3202 7.332433 TGTGGGTTTTAAACTCCCTTATCTA 57.668 36.000 21.23 4.84 41.58 1.98
2612 3203 7.399634 TGTGGGTTTTAAACTCCCTTATCTAG 58.600 38.462 21.23 0.00 41.58 2.43
2615 3206 9.114938 TGGGTTTTAAACTCCCTTATCTAGTTA 57.885 33.333 21.23 2.71 41.58 2.24
2662 3254 0.333993 ACAATCCTGCCCTGCTCAAT 59.666 50.000 0.00 0.00 0.00 2.57
2692 3287 4.276183 TCAGCTCTTTATCTAGGCTACACG 59.724 45.833 0.00 0.00 0.00 4.49
2693 3288 4.036971 CAGCTCTTTATCTAGGCTACACGT 59.963 45.833 0.00 0.00 0.00 4.49
2701 3296 3.845178 TCTAGGCTACACGTGTTGAATG 58.155 45.455 29.93 16.86 0.00 2.67
2704 3299 3.067106 AGGCTACACGTGTTGAATGAAG 58.933 45.455 29.93 18.92 0.00 3.02
2705 3300 2.412847 GGCTACACGTGTTGAATGAAGC 60.413 50.000 29.93 26.18 0.00 3.86
2719 3314 7.042725 TGTTGAATGAAGCTGTATTATCGTAGC 60.043 37.037 0.00 0.00 36.45 3.58
2747 3342 6.757897 TGGTCAATGGCAGAACTAAAATAG 57.242 37.500 0.00 0.00 0.00 1.73
2748 3343 5.652014 TGGTCAATGGCAGAACTAAAATAGG 59.348 40.000 0.00 0.00 0.00 2.57
2785 3390 2.095567 CGGTTGATGAAACAGAAGCCTG 60.096 50.000 0.00 0.00 45.76 4.85
2889 3520 7.093945 GGAGACCAAAATGCCAAAACTAGATTA 60.094 37.037 0.00 0.00 0.00 1.75
2929 3565 6.712095 ACAGATGAAACGGTATAATGATGCAT 59.288 34.615 0.00 0.00 0.00 3.96
2930 3566 7.877612 ACAGATGAAACGGTATAATGATGCATA 59.122 33.333 0.00 0.00 0.00 3.14
2931 3567 8.720562 CAGATGAAACGGTATAATGATGCATAA 58.279 33.333 0.00 0.00 0.00 1.90
2932 3568 8.721478 AGATGAAACGGTATAATGATGCATAAC 58.279 33.333 0.00 0.00 0.00 1.89
2933 3569 7.793927 TGAAACGGTATAATGATGCATAACA 57.206 32.000 0.00 0.00 0.00 2.41
2934 3570 8.214721 TGAAACGGTATAATGATGCATAACAA 57.785 30.769 0.00 0.00 0.00 2.83
2935 3571 8.678199 TGAAACGGTATAATGATGCATAACAAA 58.322 29.630 0.00 0.00 0.00 2.83
2936 3572 9.677567 GAAACGGTATAATGATGCATAACAAAT 57.322 29.630 0.00 0.00 0.00 2.32
2986 3625 7.195839 AGATCTGAGTGAAAGCAAGTAAAAC 57.804 36.000 0.00 0.00 0.00 2.43
2995 3634 7.390718 AGTGAAAGCAAGTAAAACTAGTATGGG 59.609 37.037 0.00 0.00 0.00 4.00
2998 3637 6.555463 AGCAAGTAAAACTAGTATGGGCTA 57.445 37.500 0.00 0.00 0.00 3.93
3109 3751 1.570501 AGGCTGCCCCTTGAATGATAA 59.429 47.619 16.57 0.00 43.06 1.75
3298 3942 3.067833 GTTGAAGCAGAGAGGGTAACAC 58.932 50.000 0.00 0.00 39.74 3.32
3321 3965 5.359576 ACCTCAGTGCTAGAGTGATTCTTAG 59.640 44.000 0.00 0.00 37.36 2.18
3322 3966 5.221224 CCTCAGTGCTAGAGTGATTCTTAGG 60.221 48.000 0.00 0.00 37.36 2.69
3323 3967 4.098654 TCAGTGCTAGAGTGATTCTTAGGC 59.901 45.833 0.00 0.00 37.36 3.93
3324 3968 3.386402 AGTGCTAGAGTGATTCTTAGGCC 59.614 47.826 0.00 0.00 37.36 5.19
3325 3969 2.700897 TGCTAGAGTGATTCTTAGGCCC 59.299 50.000 0.00 0.00 37.36 5.80
3326 3970 2.969262 GCTAGAGTGATTCTTAGGCCCT 59.031 50.000 0.00 0.00 37.36 5.19
3327 3971 3.244044 GCTAGAGTGATTCTTAGGCCCTG 60.244 52.174 0.00 0.00 37.36 4.45
3328 3972 2.839228 AGAGTGATTCTTAGGCCCTGT 58.161 47.619 0.00 0.00 29.61 4.00
3329 3973 3.185455 AGAGTGATTCTTAGGCCCTGTT 58.815 45.455 0.00 0.00 29.61 3.16
3330 3974 3.198853 AGAGTGATTCTTAGGCCCTGTTC 59.801 47.826 0.00 0.00 29.61 3.18
3331 3975 2.093447 AGTGATTCTTAGGCCCTGTTCG 60.093 50.000 0.00 0.00 0.00 3.95
3332 3976 1.209504 TGATTCTTAGGCCCTGTTCGG 59.790 52.381 0.00 0.00 0.00 4.30
3333 3977 1.485066 GATTCTTAGGCCCTGTTCGGA 59.515 52.381 0.00 0.00 33.16 4.55
3334 3978 1.354101 TTCTTAGGCCCTGTTCGGAA 58.646 50.000 0.00 0.00 33.16 4.30
3335 3979 0.611714 TCTTAGGCCCTGTTCGGAAC 59.388 55.000 13.86 13.86 33.16 3.62
3336 3980 0.613777 CTTAGGCCCTGTTCGGAACT 59.386 55.000 20.53 3.18 33.16 3.01
3337 3981 1.003233 CTTAGGCCCTGTTCGGAACTT 59.997 52.381 20.53 3.85 33.16 2.66
3338 3982 0.323629 TAGGCCCTGTTCGGAACTTG 59.676 55.000 20.53 13.22 33.16 3.16
3339 3983 2.626780 GGCCCTGTTCGGAACTTGC 61.627 63.158 20.53 18.04 33.16 4.01
3340 3984 2.626780 GCCCTGTTCGGAACTTGCC 61.627 63.158 20.53 4.79 33.16 4.52
3341 3985 1.971695 CCCTGTTCGGAACTTGCCC 60.972 63.158 20.53 0.00 33.16 5.36
3343 3987 2.966309 CTGTTCGGAACTTGCCCGC 61.966 63.158 20.53 0.00 46.10 6.13
3344 3988 2.668550 GTTCGGAACTTGCCCGCT 60.669 61.111 13.49 0.00 46.10 5.52
3345 3989 2.358247 TTCGGAACTTGCCCGCTC 60.358 61.111 0.00 0.00 46.10 5.03
3346 3990 3.894547 TTCGGAACTTGCCCGCTCC 62.895 63.158 0.00 0.00 46.10 4.70
3348 3992 4.699522 GGAACTTGCCCGCTCCGT 62.700 66.667 0.00 0.00 0.00 4.69
3349 3993 3.423154 GAACTTGCCCGCTCCGTG 61.423 66.667 0.00 0.00 0.00 4.94
3356 4000 4.760047 CCCGCTCCGTGGAGTTGG 62.760 72.222 16.88 17.21 43.70 3.77
3357 4001 4.760047 CCGCTCCGTGGAGTTGGG 62.760 72.222 16.88 11.89 43.70 4.12
3358 4002 4.760047 CGCTCCGTGGAGTTGGGG 62.760 72.222 16.88 0.00 43.70 4.96
3359 4003 3.319198 GCTCCGTGGAGTTGGGGA 61.319 66.667 16.88 0.00 43.70 4.81
3360 4004 2.982130 CTCCGTGGAGTTGGGGAG 59.018 66.667 7.79 0.00 40.05 4.30
3361 4005 3.316573 CTCCGTGGAGTTGGGGAGC 62.317 68.421 7.79 0.00 39.60 4.70
3362 4006 3.322466 CCGTGGAGTTGGGGAGCT 61.322 66.667 0.00 0.00 0.00 4.09
3363 4007 2.046892 CGTGGAGTTGGGGAGCTG 60.047 66.667 0.00 0.00 0.00 4.24
3364 4008 2.352805 GTGGAGTTGGGGAGCTGG 59.647 66.667 0.00 0.00 0.00 4.85
3365 4009 2.935481 TGGAGTTGGGGAGCTGGG 60.935 66.667 0.00 0.00 0.00 4.45
3366 4010 2.936032 GGAGTTGGGGAGCTGGGT 60.936 66.667 0.00 0.00 0.00 4.51
3367 4011 2.539081 GGAGTTGGGGAGCTGGGTT 61.539 63.158 0.00 0.00 0.00 4.11
3368 4012 1.460699 GAGTTGGGGAGCTGGGTTT 59.539 57.895 0.00 0.00 0.00 3.27
3369 4013 0.178961 GAGTTGGGGAGCTGGGTTTT 60.179 55.000 0.00 0.00 0.00 2.43
3370 4014 0.469892 AGTTGGGGAGCTGGGTTTTG 60.470 55.000 0.00 0.00 0.00 2.44
3371 4015 1.152355 TTGGGGAGCTGGGTTTTGG 60.152 57.895 0.00 0.00 0.00 3.28
3372 4016 2.997315 GGGGAGCTGGGTTTTGGC 60.997 66.667 0.00 0.00 0.00 4.52
3373 4017 2.203625 GGGAGCTGGGTTTTGGCA 60.204 61.111 0.00 0.00 0.00 4.92
3374 4018 2.278330 GGGAGCTGGGTTTTGGCAG 61.278 63.158 0.00 0.00 0.00 4.85
3375 4019 2.653115 GAGCTGGGTTTTGGCAGC 59.347 61.111 0.00 0.00 40.66 5.25
3376 4020 2.199535 AGCTGGGTTTTGGCAGCT 59.800 55.556 0.00 0.00 45.07 4.24
3377 4021 1.905354 AGCTGGGTTTTGGCAGCTC 60.905 57.895 0.00 0.00 46.74 4.09
3378 4022 2.935740 GCTGGGTTTTGGCAGCTCC 61.936 63.158 0.00 0.00 37.66 4.70
3379 4023 1.531365 CTGGGTTTTGGCAGCTCCA 60.531 57.895 1.25 1.25 44.85 3.86
3380 4024 0.901580 CTGGGTTTTGGCAGCTCCAT 60.902 55.000 5.83 0.00 46.04 3.41
3381 4025 0.407528 TGGGTTTTGGCAGCTCCATA 59.592 50.000 5.83 0.00 46.04 2.74
3382 4026 1.203112 TGGGTTTTGGCAGCTCCATAA 60.203 47.619 5.83 5.22 46.04 1.90
3383 4027 1.899142 GGGTTTTGGCAGCTCCATAAA 59.101 47.619 5.83 6.94 46.04 1.40
3384 4028 2.301583 GGGTTTTGGCAGCTCCATAAAA 59.698 45.455 5.83 2.91 46.04 1.52
3385 4029 3.055167 GGGTTTTGGCAGCTCCATAAAAT 60.055 43.478 5.83 0.00 46.04 1.82
3386 4030 4.565444 GGGTTTTGGCAGCTCCATAAAATT 60.565 41.667 5.83 0.00 46.04 1.82
3387 4031 5.337975 GGGTTTTGGCAGCTCCATAAAATTA 60.338 40.000 5.83 0.00 46.04 1.40
3388 4032 6.169800 GGTTTTGGCAGCTCCATAAAATTAA 58.830 36.000 5.83 0.00 46.04 1.40
3389 4033 6.313658 GGTTTTGGCAGCTCCATAAAATTAAG 59.686 38.462 5.83 0.00 46.04 1.85
3390 4034 4.654091 TGGCAGCTCCATAAAATTAAGC 57.346 40.909 1.25 0.00 40.72 3.09
3391 4035 4.280819 TGGCAGCTCCATAAAATTAAGCT 58.719 39.130 1.25 0.00 43.81 3.74
3392 4036 5.445069 TGGCAGCTCCATAAAATTAAGCTA 58.555 37.500 1.25 0.00 41.19 3.32
3393 4037 5.890985 TGGCAGCTCCATAAAATTAAGCTAA 59.109 36.000 1.25 0.00 41.19 3.09
3394 4038 6.379703 TGGCAGCTCCATAAAATTAAGCTAAA 59.620 34.615 1.25 0.00 41.19 1.85
3395 4039 6.920210 GGCAGCTCCATAAAATTAAGCTAAAG 59.080 38.462 0.00 0.00 41.19 1.85
3396 4040 7.416777 GGCAGCTCCATAAAATTAAGCTAAAGT 60.417 37.037 0.00 0.00 41.19 2.66
3397 4041 7.645735 GCAGCTCCATAAAATTAAGCTAAAGTC 59.354 37.037 0.00 0.00 41.19 3.01
3398 4042 8.897752 CAGCTCCATAAAATTAAGCTAAAGTCT 58.102 33.333 0.00 0.00 41.19 3.24
3399 4043 8.897752 AGCTCCATAAAATTAAGCTAAAGTCTG 58.102 33.333 0.00 0.00 41.32 3.51
3400 4044 8.131731 GCTCCATAAAATTAAGCTAAAGTCTGG 58.868 37.037 0.00 0.00 0.00 3.86
3401 4045 9.178758 CTCCATAAAATTAAGCTAAAGTCTGGT 57.821 33.333 0.00 0.00 0.00 4.00
3402 4046 9.174166 TCCATAAAATTAAGCTAAAGTCTGGTC 57.826 33.333 0.00 0.00 0.00 4.02
3403 4047 8.406297 CCATAAAATTAAGCTAAAGTCTGGTCC 58.594 37.037 0.00 0.00 0.00 4.46
3404 4048 8.956426 CATAAAATTAAGCTAAAGTCTGGTCCA 58.044 33.333 0.00 0.00 0.00 4.02
3405 4049 6.819397 AAATTAAGCTAAAGTCTGGTCCAC 57.181 37.500 0.00 0.00 0.00 4.02
3406 4050 5.763876 ATTAAGCTAAAGTCTGGTCCACT 57.236 39.130 0.00 0.00 0.00 4.00
3407 4051 3.686916 AAGCTAAAGTCTGGTCCACTC 57.313 47.619 0.00 0.00 0.00 3.51
3408 4052 1.903183 AGCTAAAGTCTGGTCCACTCC 59.097 52.381 0.00 0.00 0.00 3.85
3409 4053 1.066071 GCTAAAGTCTGGTCCACTCCC 60.066 57.143 0.00 0.00 0.00 4.30
3410 4054 1.204941 CTAAAGTCTGGTCCACTCCCG 59.795 57.143 0.00 0.00 0.00 5.14
3411 4055 1.481056 AAAGTCTGGTCCACTCCCGG 61.481 60.000 0.00 0.00 0.00 5.73
3412 4056 2.283676 GTCTGGTCCACTCCCGGA 60.284 66.667 0.73 0.00 34.95 5.14
3413 4057 2.037367 TCTGGTCCACTCCCGGAG 59.963 66.667 13.31 13.31 35.10 4.63
3426 4070 4.874534 CGGAGCGGAGTTAAACGA 57.125 55.556 0.00 0.00 0.00 3.85
3427 4071 2.650163 CGGAGCGGAGTTAAACGAG 58.350 57.895 0.00 0.00 0.00 4.18
3428 4072 1.411493 CGGAGCGGAGTTAAACGAGC 61.411 60.000 0.00 0.00 0.00 5.03
3429 4073 1.082679 GGAGCGGAGTTAAACGAGCC 61.083 60.000 0.00 0.00 0.00 4.70
3430 4074 1.411493 GAGCGGAGTTAAACGAGCCG 61.411 60.000 0.00 0.00 44.47 5.52
3431 4075 1.444895 GCGGAGTTAAACGAGCCGA 60.445 57.895 0.00 0.00 44.43 5.54
3432 4076 1.411493 GCGGAGTTAAACGAGCCGAG 61.411 60.000 0.00 0.00 44.43 4.63
3433 4077 0.169672 CGGAGTTAAACGAGCCGAGA 59.830 55.000 0.00 0.00 44.43 4.04
3434 4078 1.794437 CGGAGTTAAACGAGCCGAGAG 60.794 57.143 0.00 0.00 44.43 3.20
3435 4079 1.471684 GGAGTTAAACGAGCCGAGAGA 59.528 52.381 1.50 0.00 0.00 3.10
3436 4080 2.094854 GGAGTTAAACGAGCCGAGAGAA 60.095 50.000 1.50 0.00 0.00 2.87
3437 4081 3.572584 GAGTTAAACGAGCCGAGAGAAA 58.427 45.455 1.50 0.00 0.00 2.52
3438 4082 3.315418 AGTTAAACGAGCCGAGAGAAAC 58.685 45.455 1.50 0.00 0.00 2.78
3439 4083 2.358939 TAAACGAGCCGAGAGAAACC 57.641 50.000 1.50 0.00 0.00 3.27
3440 4084 0.666577 AAACGAGCCGAGAGAAACCG 60.667 55.000 1.50 0.00 0.00 4.44
3441 4085 1.521450 AACGAGCCGAGAGAAACCGA 61.521 55.000 1.50 0.00 0.00 4.69
3442 4086 1.211969 CGAGCCGAGAGAAACCGAA 59.788 57.895 0.00 0.00 0.00 4.30
3443 4087 1.071567 CGAGCCGAGAGAAACCGAAC 61.072 60.000 0.00 0.00 0.00 3.95
3444 4088 1.071567 GAGCCGAGAGAAACCGAACG 61.072 60.000 0.00 0.00 0.00 3.95
3445 4089 2.727684 GCCGAGAGAAACCGAACGC 61.728 63.158 0.00 0.00 0.00 4.84
3446 4090 1.372499 CCGAGAGAAACCGAACGCA 60.372 57.895 0.00 0.00 0.00 5.24
3447 4091 1.344942 CCGAGAGAAACCGAACGCAG 61.345 60.000 0.00 0.00 0.00 5.18
3448 4092 1.782181 GAGAGAAACCGAACGCAGC 59.218 57.895 0.00 0.00 0.00 5.25
3449 4093 1.627550 GAGAGAAACCGAACGCAGCC 61.628 60.000 0.00 0.00 0.00 4.85
3450 4094 1.668151 GAGAAACCGAACGCAGCCT 60.668 57.895 0.00 0.00 0.00 4.58
3451 4095 1.227853 AGAAACCGAACGCAGCCTT 60.228 52.632 0.00 0.00 0.00 4.35
3452 4096 0.034337 AGAAACCGAACGCAGCCTTA 59.966 50.000 0.00 0.00 0.00 2.69
3508 4153 9.608617 GAATGTACTTTCCTTAGCAAAAACTAC 57.391 33.333 9.76 0.00 0.00 2.73
3534 4179 9.364989 CTCTCTGAATTTTCCTTTAGAGTAGTG 57.635 37.037 0.00 0.00 38.99 2.74
3581 4236 7.255569 TCACTTAGTGTATTTAGTGTCATCCG 58.744 38.462 12.41 0.00 39.16 4.18
3848 4509 2.039613 TGGTCTGTGCATTGTATGGTCA 59.960 45.455 0.00 0.00 0.00 4.02
3896 4557 5.463392 CCATATATTCTTGACCACTCACACG 59.537 44.000 0.00 0.00 0.00 4.49
4009 4674 6.324770 TCTCTAAGTAGTTCATGCCATCATCA 59.675 38.462 0.00 0.00 0.00 3.07
4010 4675 7.015974 TCTCTAAGTAGTTCATGCCATCATCAT 59.984 37.037 0.00 0.00 0.00 2.45
4011 4676 7.157347 TCTAAGTAGTTCATGCCATCATCATC 58.843 38.462 0.00 0.00 0.00 2.92
4049 4719 6.478016 CAGATCGCAATCTCTTATCTTGTGAA 59.522 38.462 2.37 0.00 40.38 3.18
4149 4819 5.700373 TGTGCTCCCTTAAATTTTGCAATTC 59.300 36.000 0.00 0.00 30.80 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 2.507992 CAGCCTCTGTCTTCGCGG 60.508 66.667 6.13 0.00 0.00 6.46
105 106 1.826709 GACCCAGCTAGCTCCTTCC 59.173 63.158 16.15 0.00 0.00 3.46
144 145 3.443045 CCAATGTGGCGCCTGACC 61.443 66.667 29.70 13.27 0.00 4.02
225 226 7.549134 ACCAATACCATATGCATTATACGAGTG 59.451 37.037 3.54 0.00 0.00 3.51
229 230 7.609760 ACACCAATACCATATGCATTATACG 57.390 36.000 3.54 0.00 0.00 3.06
247 248 5.152306 AGGGAGGTAGTATCATACACCAA 57.848 43.478 14.98 0.00 34.45 3.67
256 257 7.835181 AGTACTATGCATTAGGGAGGTAGTATC 59.165 40.741 3.54 0.00 31.68 2.24
270 271 6.407202 AGAAACGGAAGAAGTACTATGCATT 58.593 36.000 3.54 0.00 0.00 3.56
271 272 5.978814 AGAAACGGAAGAAGTACTATGCAT 58.021 37.500 3.79 3.79 0.00 3.96
272 273 5.401531 AGAAACGGAAGAAGTACTATGCA 57.598 39.130 0.00 0.00 0.00 3.96
273 274 7.823149 TTTAGAAACGGAAGAAGTACTATGC 57.177 36.000 0.00 0.00 0.00 3.14
280 281 9.503399 AGACAAATATTTAGAAACGGAAGAAGT 57.497 29.630 0.00 0.00 0.00 3.01
364 365 6.663944 ACGGAGCAAAATGAGTAAATCTAC 57.336 37.500 0.00 0.00 0.00 2.59
385 386 7.116376 AGACATTTCAACAAGTGACTACATACG 59.884 37.037 0.00 0.00 35.39 3.06
417 418 9.190317 GACTCCCTCCATTTCTAAATATTTGTT 57.810 33.333 11.05 0.00 0.00 2.83
430 431 8.457757 AGTACTAGTATATGACTCCCTCCATTT 58.542 37.037 5.75 0.00 39.81 2.32
640 644 9.642327 TTTGATGAGGTGTCATTGAATTAAATG 57.358 29.630 9.04 9.04 43.92 2.32
652 656 6.533730 AGTAGACAATTTTGATGAGGTGTCA 58.466 36.000 4.60 0.00 38.24 3.58
675 679 4.161754 ACTTACATTTAGGAACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
696 700 5.717178 TCATAGTGGAAGCTCTACAAAGACT 59.283 40.000 0.00 0.00 29.47 3.24
786 790 7.451877 AGTCTTTGTAGAGATTTCACTAGGTGA 59.548 37.037 0.00 0.00 41.09 4.02
878 892 1.855360 GATTCGAGCGAGTTTAGGCTG 59.145 52.381 0.00 0.00 40.16 4.85
949 963 2.875933 CAAAACAAGGTTCTGGAGCGTA 59.124 45.455 0.00 0.00 0.00 4.42
1084 1103 2.514824 GTGCGATGGAGAAGGGCC 60.515 66.667 0.00 0.00 0.00 5.80
1137 1157 3.444388 ACCAAAACTAAACAGAAACGGCA 59.556 39.130 0.00 0.00 0.00 5.69
1262 1283 4.099573 ACATCGATCAGTAAGGGAACGAAT 59.900 41.667 0.00 0.00 41.69 3.34
1263 1284 3.446161 ACATCGATCAGTAAGGGAACGAA 59.554 43.478 0.00 0.00 41.69 3.85
1264 1285 3.021695 ACATCGATCAGTAAGGGAACGA 58.978 45.455 0.00 0.00 42.38 3.85
1272 1293 3.953712 ACCACACACATCGATCAGTAA 57.046 42.857 0.00 0.00 0.00 2.24
1304 1325 2.612221 GGATCGACGAAAACTTCCTGGT 60.612 50.000 0.00 0.00 0.00 4.00
1305 1326 2.000447 GGATCGACGAAAACTTCCTGG 59.000 52.381 0.00 0.00 0.00 4.45
1335 1356 1.032014 GCTCGAAGATGAGGCTCTCT 58.968 55.000 16.72 12.64 36.47 3.10
1998 2059 5.344743 AATCAAGCGTGAGATCCTTAAGA 57.655 39.130 8.63 0.00 37.14 2.10
2054 2118 0.250467 TGTTCTGTGCTTCTCTGCCC 60.250 55.000 0.00 0.00 0.00 5.36
2215 2702 0.465287 TCAAGAGCGGCTCATATGCA 59.535 50.000 29.88 13.19 32.06 3.96
2309 2804 9.832445 TGAACAAGACTTTATACTTGAGAAAGT 57.168 29.630 12.69 0.00 44.12 2.66
2355 2850 9.991906 CCATAAAAGATTAATCTTACCGGAGTA 57.008 33.333 26.90 12.91 45.83 2.59
2356 2851 8.711170 TCCATAAAAGATTAATCTTACCGGAGT 58.289 33.333 26.90 10.18 45.83 3.85
2357 2852 9.209175 CTCCATAAAAGATTAATCTTACCGGAG 57.791 37.037 28.96 28.96 45.83 4.63
2358 2853 8.711170 ACTCCATAAAAGATTAATCTTACCGGA 58.289 33.333 26.90 24.86 45.83 5.14
2359 2854 8.904099 ACTCCATAAAAGATTAATCTTACCGG 57.096 34.615 26.90 22.79 45.83 5.28
2370 2865 9.911788 ACATCAGTTGATACTCCATAAAAGATT 57.088 29.630 0.00 0.00 32.63 2.40
2373 2868 9.823647 ACTACATCAGTTGATACTCCATAAAAG 57.176 33.333 0.00 0.00 31.59 2.27
2402 2897 9.524496 TGGTGATAAACAGTACTCTACTAAAGA 57.476 33.333 0.00 0.00 37.23 2.52
2463 2967 8.539770 AATACATAATTCTCCTAAGCACATCG 57.460 34.615 0.00 0.00 0.00 3.84
2636 3228 0.693049 AGGGCAGGATTGTCGTTCTT 59.307 50.000 0.00 0.00 0.00 2.52
2673 3268 5.502153 ACACGTGTAGCCTAGATAAAGAG 57.498 43.478 21.98 0.00 0.00 2.85
2692 3287 7.005062 ACGATAATACAGCTTCATTCAACAC 57.995 36.000 0.00 0.00 0.00 3.32
2693 3288 7.042725 GCTACGATAATACAGCTTCATTCAACA 60.043 37.037 0.00 0.00 0.00 3.33
2701 3296 6.528423 CCATACTGCTACGATAATACAGCTTC 59.472 42.308 0.00 0.00 35.05 3.86
2704 3299 5.710984 ACCATACTGCTACGATAATACAGC 58.289 41.667 0.00 0.00 34.56 4.40
2705 3300 6.909909 TGACCATACTGCTACGATAATACAG 58.090 40.000 0.00 0.00 0.00 2.74
2719 3314 3.614092 AGTTCTGCCATTGACCATACTG 58.386 45.455 0.00 0.00 0.00 2.74
2759 3364 2.844946 TCTGTTTCATCAACCGAGCAA 58.155 42.857 0.00 0.00 33.97 3.91
2785 3390 1.001641 ATGAGGCCCTGAGCACAAC 60.002 57.895 0.00 0.00 46.50 3.32
2857 3488 1.092348 GCATTTTGGTCTCCCCGTAC 58.908 55.000 0.00 0.00 35.15 3.67
2904 3540 6.054941 TGCATCATTATACCGTTTCATCTGT 58.945 36.000 0.00 0.00 0.00 3.41
2986 3625 7.246171 ACTTGGATATGTTAGCCCATACTAG 57.754 40.000 0.00 0.00 31.88 2.57
2995 3634 7.096147 GCTAGTCGTTAACTTGGATATGTTAGC 60.096 40.741 3.71 1.68 39.55 3.09
2998 3637 6.875076 AGCTAGTCGTTAACTTGGATATGTT 58.125 36.000 3.71 0.00 39.55 2.71
3298 3942 4.734398 AAGAATCACTCTAGCACTGAGG 57.266 45.455 5.79 0.00 35.98 3.86
3321 3965 2.626780 GCAAGTTCCGAACAGGGCC 61.627 63.158 13.69 0.00 41.52 5.80
3322 3966 2.626780 GGCAAGTTCCGAACAGGGC 61.627 63.158 13.69 12.31 41.52 5.19
3323 3967 1.971695 GGGCAAGTTCCGAACAGGG 60.972 63.158 13.69 3.68 41.52 4.45
3324 3968 3.668386 GGGCAAGTTCCGAACAGG 58.332 61.111 13.69 6.01 42.97 4.00
3331 3975 4.699522 ACGGAGCGGGCAAGTTCC 62.700 66.667 5.29 5.29 38.03 3.62
3332 3976 3.423154 CACGGAGCGGGCAAGTTC 61.423 66.667 0.00 0.00 0.00 3.01
3339 3983 4.760047 CCAACTCCACGGAGCGGG 62.760 72.222 13.16 10.66 45.54 6.13
3340 3984 4.760047 CCCAACTCCACGGAGCGG 62.760 72.222 13.16 13.11 45.54 5.52
3341 3985 4.760047 CCCCAACTCCACGGAGCG 62.760 72.222 13.16 4.69 45.54 5.03
3342 3986 3.316573 CTCCCCAACTCCACGGAGC 62.317 68.421 13.16 0.00 45.54 4.70
3343 3987 2.982130 CTCCCCAACTCCACGGAG 59.018 66.667 11.67 11.67 46.91 4.63
3344 3988 3.319198 GCTCCCCAACTCCACGGA 61.319 66.667 0.00 0.00 0.00 4.69
3345 3989 3.322466 AGCTCCCCAACTCCACGG 61.322 66.667 0.00 0.00 0.00 4.94
3346 3990 2.046892 CAGCTCCCCAACTCCACG 60.047 66.667 0.00 0.00 0.00 4.94
3347 3991 2.352805 CCAGCTCCCCAACTCCAC 59.647 66.667 0.00 0.00 0.00 4.02
3348 3992 2.935481 CCCAGCTCCCCAACTCCA 60.935 66.667 0.00 0.00 0.00 3.86
3349 3993 2.081585 AAACCCAGCTCCCCAACTCC 62.082 60.000 0.00 0.00 0.00 3.85
3350 3994 0.178961 AAAACCCAGCTCCCCAACTC 60.179 55.000 0.00 0.00 0.00 3.01
3351 3995 0.469892 CAAAACCCAGCTCCCCAACT 60.470 55.000 0.00 0.00 0.00 3.16
3352 3996 1.471829 CCAAAACCCAGCTCCCCAAC 61.472 60.000 0.00 0.00 0.00 3.77
3353 3997 1.152355 CCAAAACCCAGCTCCCCAA 60.152 57.895 0.00 0.00 0.00 4.12
3354 3998 2.525592 CCAAAACCCAGCTCCCCA 59.474 61.111 0.00 0.00 0.00 4.96
3355 3999 2.997315 GCCAAAACCCAGCTCCCC 60.997 66.667 0.00 0.00 0.00 4.81
3356 4000 2.203625 TGCCAAAACCCAGCTCCC 60.204 61.111 0.00 0.00 0.00 4.30
3357 4001 3.369921 CTGCCAAAACCCAGCTCC 58.630 61.111 0.00 0.00 0.00 4.70
3361 4005 1.531365 TGGAGCTGCCAAAACCCAG 60.531 57.895 1.53 0.00 45.87 4.45
3362 4006 2.605873 TGGAGCTGCCAAAACCCA 59.394 55.556 1.53 0.00 45.87 4.51
3370 4014 4.926140 AGCTTAATTTTATGGAGCTGCC 57.074 40.909 1.53 0.00 41.75 4.85
3371 4015 7.484140 ACTTTAGCTTAATTTTATGGAGCTGC 58.516 34.615 0.00 0.00 43.06 5.25
3372 4016 8.897752 AGACTTTAGCTTAATTTTATGGAGCTG 58.102 33.333 6.44 0.00 43.06 4.24
3373 4017 8.897752 CAGACTTTAGCTTAATTTTATGGAGCT 58.102 33.333 0.00 1.58 45.01 4.09
3374 4018 8.131731 CCAGACTTTAGCTTAATTTTATGGAGC 58.868 37.037 0.00 0.00 0.00 4.70
3375 4019 9.178758 ACCAGACTTTAGCTTAATTTTATGGAG 57.821 33.333 0.00 0.00 0.00 3.86
3376 4020 9.174166 GACCAGACTTTAGCTTAATTTTATGGA 57.826 33.333 0.00 0.00 0.00 3.41
3377 4021 8.406297 GGACCAGACTTTAGCTTAATTTTATGG 58.594 37.037 0.00 0.00 0.00 2.74
3378 4022 8.956426 TGGACCAGACTTTAGCTTAATTTTATG 58.044 33.333 0.00 0.00 0.00 1.90
3379 4023 8.957466 GTGGACCAGACTTTAGCTTAATTTTAT 58.043 33.333 0.00 0.00 0.00 1.40
3380 4024 8.161425 AGTGGACCAGACTTTAGCTTAATTTTA 58.839 33.333 0.00 0.00 0.00 1.52
3381 4025 7.004691 AGTGGACCAGACTTTAGCTTAATTTT 58.995 34.615 0.00 0.00 0.00 1.82
3382 4026 6.543735 AGTGGACCAGACTTTAGCTTAATTT 58.456 36.000 0.00 0.00 0.00 1.82
3383 4027 6.128138 AGTGGACCAGACTTTAGCTTAATT 57.872 37.500 0.00 0.00 0.00 1.40
3384 4028 5.338463 GGAGTGGACCAGACTTTAGCTTAAT 60.338 44.000 0.00 0.00 0.00 1.40
3385 4029 4.020485 GGAGTGGACCAGACTTTAGCTTAA 60.020 45.833 0.00 0.00 0.00 1.85
3386 4030 3.514309 GGAGTGGACCAGACTTTAGCTTA 59.486 47.826 0.00 0.00 0.00 3.09
3387 4031 2.303311 GGAGTGGACCAGACTTTAGCTT 59.697 50.000 0.00 0.00 0.00 3.74
3388 4032 1.903183 GGAGTGGACCAGACTTTAGCT 59.097 52.381 0.00 0.00 0.00 3.32
3389 4033 1.066071 GGGAGTGGACCAGACTTTAGC 60.066 57.143 0.00 0.00 0.00 3.09
3390 4034 1.204941 CGGGAGTGGACCAGACTTTAG 59.795 57.143 0.00 0.00 0.00 1.85
3391 4035 1.263356 CGGGAGTGGACCAGACTTTA 58.737 55.000 0.00 0.00 0.00 1.85
3392 4036 1.481056 CCGGGAGTGGACCAGACTTT 61.481 60.000 0.00 0.00 0.00 2.66
3393 4037 1.913762 CCGGGAGTGGACCAGACTT 60.914 63.158 0.00 0.00 0.00 3.01
3394 4038 2.283966 CCGGGAGTGGACCAGACT 60.284 66.667 0.00 0.00 0.00 3.24
3395 4039 2.283676 TCCGGGAGTGGACCAGAC 60.284 66.667 0.00 0.00 31.53 3.51
3396 4040 2.037367 CTCCGGGAGTGGACCAGA 59.963 66.667 16.15 0.00 33.48 3.86
3397 4041 3.775654 GCTCCGGGAGTGGACCAG 61.776 72.222 24.30 0.00 33.48 4.00
3409 4053 1.411493 GCTCGTTTAACTCCGCTCCG 61.411 60.000 0.00 0.00 0.00 4.63
3410 4054 1.082679 GGCTCGTTTAACTCCGCTCC 61.083 60.000 0.00 0.00 0.00 4.70
3411 4055 1.411493 CGGCTCGTTTAACTCCGCTC 61.411 60.000 7.19 0.00 33.36 5.03
3412 4056 1.445582 CGGCTCGTTTAACTCCGCT 60.446 57.895 7.19 0.00 33.36 5.52
3413 4057 1.411493 CTCGGCTCGTTTAACTCCGC 61.411 60.000 12.77 4.24 39.90 5.54
3414 4058 0.169672 TCTCGGCTCGTTTAACTCCG 59.830 55.000 11.83 11.83 41.30 4.63
3415 4059 1.471684 TCTCTCGGCTCGTTTAACTCC 59.528 52.381 0.00 0.00 0.00 3.85
3416 4060 2.915738 TCTCTCGGCTCGTTTAACTC 57.084 50.000 0.00 0.00 0.00 3.01
3417 4061 3.315418 GTTTCTCTCGGCTCGTTTAACT 58.685 45.455 0.00 0.00 0.00 2.24
3418 4062 2.411069 GGTTTCTCTCGGCTCGTTTAAC 59.589 50.000 0.00 0.00 0.00 2.01
3419 4063 2.680577 GGTTTCTCTCGGCTCGTTTAA 58.319 47.619 0.00 0.00 0.00 1.52
3420 4064 1.401931 CGGTTTCTCTCGGCTCGTTTA 60.402 52.381 0.00 0.00 0.00 2.01
3421 4065 0.666577 CGGTTTCTCTCGGCTCGTTT 60.667 55.000 0.00 0.00 0.00 3.60
3422 4066 1.080705 CGGTTTCTCTCGGCTCGTT 60.081 57.895 0.00 0.00 0.00 3.85
3423 4067 1.521450 TTCGGTTTCTCTCGGCTCGT 61.521 55.000 0.00 0.00 0.00 4.18
3424 4068 1.071567 GTTCGGTTTCTCTCGGCTCG 61.072 60.000 0.00 0.00 0.00 5.03
3425 4069 1.071567 CGTTCGGTTTCTCTCGGCTC 61.072 60.000 0.00 0.00 0.00 4.70
3426 4070 1.080705 CGTTCGGTTTCTCTCGGCT 60.081 57.895 0.00 0.00 0.00 5.52
3427 4071 2.727684 GCGTTCGGTTTCTCTCGGC 61.728 63.158 0.00 0.00 0.00 5.54
3428 4072 1.344942 CTGCGTTCGGTTTCTCTCGG 61.345 60.000 0.00 0.00 0.00 4.63
3429 4073 1.945776 GCTGCGTTCGGTTTCTCTCG 61.946 60.000 0.00 0.00 0.00 4.04
3430 4074 1.627550 GGCTGCGTTCGGTTTCTCTC 61.628 60.000 0.00 0.00 0.00 3.20
3431 4075 1.668151 GGCTGCGTTCGGTTTCTCT 60.668 57.895 0.00 0.00 0.00 3.10
3432 4076 1.228657 AAGGCTGCGTTCGGTTTCTC 61.229 55.000 1.08 0.00 0.00 2.87
3433 4077 0.034337 TAAGGCTGCGTTCGGTTTCT 59.966 50.000 11.22 0.00 0.00 2.52
3434 4078 0.869730 TTAAGGCTGCGTTCGGTTTC 59.130 50.000 11.22 0.00 0.00 2.78
3435 4079 1.310904 TTTAAGGCTGCGTTCGGTTT 58.689 45.000 11.22 0.00 0.00 3.27
3436 4080 1.310904 TTTTAAGGCTGCGTTCGGTT 58.689 45.000 11.22 0.00 0.00 4.44
3437 4081 1.265905 CTTTTTAAGGCTGCGTTCGGT 59.734 47.619 11.22 0.00 0.00 4.69
3438 4082 1.401018 CCTTTTTAAGGCTGCGTTCGG 60.401 52.381 11.22 2.55 42.78 4.30
3439 4083 1.963747 CCTTTTTAAGGCTGCGTTCG 58.036 50.000 11.22 0.00 42.78 3.95
3449 4093 6.038714 ACTCTCTTGCAGAACACCTTTTTAAG 59.961 38.462 0.00 0.00 0.00 1.85
3450 4094 5.885912 ACTCTCTTGCAGAACACCTTTTTAA 59.114 36.000 0.00 0.00 0.00 1.52
3451 4095 5.296780 CACTCTCTTGCAGAACACCTTTTTA 59.703 40.000 0.00 0.00 0.00 1.52
3452 4096 4.096984 CACTCTCTTGCAGAACACCTTTTT 59.903 41.667 0.00 0.00 0.00 1.94
3508 4153 9.364989 CACTACTCTAAAGGAAAATTCAGAGAG 57.635 37.037 12.53 10.90 34.84 3.20
3534 4179 4.385358 TGGCACTTTCAGGAAAAGAAAC 57.615 40.909 4.64 0.00 46.18 2.78
3564 4219 6.103997 GGTTCTTCGGATGACACTAAATACA 58.896 40.000 0.00 0.00 0.00 2.29
3569 4224 3.056107 CAGGGTTCTTCGGATGACACTAA 60.056 47.826 0.00 0.00 0.00 2.24
3581 4236 3.551846 TGAACTTCAACCAGGGTTCTTC 58.448 45.455 0.00 1.53 38.86 2.87
3848 4509 7.951806 TGGAAATCATGAGGGATAAATATTGCT 59.048 33.333 0.09 0.00 0.00 3.91
3896 4557 1.246056 TGCTTGGTGCCAATCAGAGC 61.246 55.000 3.91 4.66 42.00 4.09
4009 4674 1.689273 GATCTGCGAACCTAGGTGGAT 59.311 52.381 17.14 13.58 39.71 3.41
4010 4675 1.112113 GATCTGCGAACCTAGGTGGA 58.888 55.000 17.14 4.00 39.71 4.02
4011 4676 0.249073 CGATCTGCGAACCTAGGTGG 60.249 60.000 17.14 12.06 44.57 4.61
4049 4719 9.685276 TTATCAGAGTTATCCACACAAATTGAT 57.315 29.630 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.