Multiple sequence alignment - TraesCS3A01G281900

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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 TraesCS3A01G281900 chr3A 100.000 3078 0 0 1 3078 510662771 510665848 0.000000e+00 5685.0
1 TraesCS3A01G281900 chr3A 86.325 117 12 4 1460 1574 518642731 518642617 1.160000e-24 124.0
2 TraesCS3A01G281900 chr3B 93.149 2058 86 26 196 2230 507285681 507287706 0.000000e+00 2968.0
3 TraesCS3A01G281900 chr3B 91.165 498 31 5 2424 2917 507287697 507288185 0.000000e+00 664.0
4 TraesCS3A01G281900 chr3B 95.876 194 6 2 2229 2422 34052435 34052626 2.300000e-81 313.0
5 TraesCS3A01G281900 chr3B 95.480 177 8 0 4 180 507285519 507285695 1.810000e-72 283.0
6 TraesCS3A01G281900 chr3B 92.638 163 10 2 2916 3078 507288299 507288459 1.850000e-57 233.0
7 TraesCS3A01G281900 chr3B 87.179 117 11 4 1460 1574 525242494 525242380 2.490000e-26 130.0
8 TraesCS3A01G281900 chr3D 92.143 2049 100 29 196 2223 390040914 390042922 0.000000e+00 2835.0
9 TraesCS3A01G281900 chr3D 87.897 661 35 13 2424 3078 390042933 390043554 0.000000e+00 736.0
10 TraesCS3A01G281900 chr3D 94.022 184 7 1 1 180 390040745 390040928 3.020000e-70 276.0
11 TraesCS3A01G281900 chr3D 87.179 117 11 4 1460 1574 399380487 399380373 2.490000e-26 130.0
12 TraesCS3A01G281900 chr1A 96.410 195 7 0 2229 2423 583115639 583115445 3.830000e-84 322.0
13 TraesCS3A01G281900 chr1A 94.949 198 8 1 2226 2423 6671693 6671498 2.980000e-80 309.0
14 TraesCS3A01G281900 chr1A 84.956 113 16 1 1462 1574 355343728 355343839 2.510000e-21 113.0
15 TraesCS3A01G281900 chr7B 96.354 192 7 0 2227 2418 708843479 708843288 1.780000e-82 316.0
16 TraesCS3A01G281900 chr7B 94.500 200 9 1 2224 2423 718077159 718077356 1.070000e-79 307.0
17 TraesCS3A01G281900 chr5B 95.918 196 6 1 2229 2424 8541837 8541644 1.780000e-82 316.0
18 TraesCS3A01G281900 chr4A 95.408 196 7 1 2229 2424 658241368 658241561 8.290000e-81 311.0
19 TraesCS3A01G281900 chr4A 82.524 103 11 4 2974 3070 555984576 555984677 1.970000e-12 84.2
20 TraesCS3A01G281900 chr4A 81.579 114 10 7 2974 3078 556163820 556163931 1.970000e-12 84.2
21 TraesCS3A01G281900 chr1B 94.500 200 9 1 2224 2423 7989866 7989669 1.070000e-79 307.0
22 TraesCS3A01G281900 chr1B 88.119 101 10 1 2978 3078 681956196 681956294 5.390000e-23 119.0
23 TraesCS3A01G281900 chr1B 84.956 113 16 1 1462 1574 385296796 385296907 2.510000e-21 113.0
24 TraesCS3A01G281900 chr1B 90.323 62 5 1 1217 1278 670202734 670202794 2.540000e-11 80.5
25 TraesCS3A01G281900 chr7A 92.857 210 13 1 2223 2432 732806716 732806509 1.390000e-78 303.0
26 TraesCS3A01G281900 chr1D 84.956 113 16 1 1462 1574 283617844 283617955 2.510000e-21 113.0
27 TraesCS3A01G281900 chr1D 92.857 56 4 0 1229 1284 481603266 481603321 7.070000e-12 82.4
28 TraesCS3A01G281900 chr2D 85.577 104 9 5 2976 3078 601697630 601697728 1.510000e-18 104.0
29 TraesCS3A01G281900 chr2A 84.615 104 10 5 2976 3078 734907356 734907454 7.020000e-17 99.0
30 TraesCS3A01G281900 chr2A 90.566 53 3 2 1233 1284 686214670 686214619 5.510000e-08 69.4
31 TraesCS3A01G281900 chr6B 84.314 102 9 6 2972 3070 448364603 448364700 3.270000e-15 93.5
32 TraesCS3A01G281900 chr2B 90.566 53 3 2 1233 1284 648653128 648653077 5.510000e-08 69.4
33 TraesCS3A01G281900 chr2B 86.667 60 7 1 2804 2863 26510841 26510783 7.120000e-07 65.8
34 TraesCS3A01G281900 chr6D 100.000 33 0 0 2765 2797 400711471 400711439 9.220000e-06 62.1


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 TraesCS3A01G281900 chr3A 510662771 510665848 3077 False 5685.000000 5685 100.000 1 3078 1 chr3A.!!$F1 3077
1 TraesCS3A01G281900 chr3B 507285519 507288459 2940 False 1037.000000 2968 93.108 4 3078 4 chr3B.!!$F2 3074
2 TraesCS3A01G281900 chr3D 390040745 390043554 2809 False 1282.333333 2835 91.354 1 3078 3 chr3D.!!$F1 3077

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
207 212 0.027324 GCGAGCTAACTGCATCAAGC 59.973 55.0 6.27 6.27 45.94 4.01 F
635 644 0.322975 TCAAGCCAAGCCTGTCTCTC 59.677 55.0 0.00 0.00 0.00 3.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1340 1364 0.180171 CATGCCGTCCCAATCCAGTA 59.820 55.0 0.00 0.0 0.00 2.74 R
2390 2425 0.036448 AGTCCGCTATAGCTCCGCTA 59.964 55.0 21.98 0.0 45.55 4.26 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
75 76 2.554893 TGGCTGAACGGGTTTGAATAAC 59.445 45.455 0.00 0.00 0.00 1.89
130 135 1.142185 CGATCGAGCGCACAATCTGT 61.142 55.000 11.25 0.00 0.00 3.41
132 137 0.174389 ATCGAGCGCACAATCTGTCT 59.826 50.000 11.47 0.00 0.00 3.41
149 154 1.017177 TCTGTAACGCGGTGATTGGC 61.017 55.000 7.07 0.00 0.00 4.52
153 158 0.604243 TAACGCGGTGATTGGCTTGT 60.604 50.000 7.07 0.00 0.00 3.16
160 165 1.743623 TGATTGGCTTGTACGCGGG 60.744 57.895 12.47 0.00 0.00 6.13
180 185 4.394920 CGGGTTACAACTGTATCAAGCATT 59.605 41.667 0.00 0.00 0.00 3.56
181 186 5.106317 CGGGTTACAACTGTATCAAGCATTT 60.106 40.000 0.00 0.00 0.00 2.32
182 187 6.569610 CGGGTTACAACTGTATCAAGCATTTT 60.570 38.462 0.00 0.00 0.00 1.82
183 188 7.151976 GGGTTACAACTGTATCAAGCATTTTT 58.848 34.615 0.00 0.00 0.00 1.94
203 208 2.900122 TTTTGCGAGCTAACTGCATC 57.100 45.000 3.63 0.00 45.94 3.91
204 209 1.807139 TTTGCGAGCTAACTGCATCA 58.193 45.000 3.63 0.00 45.94 3.07
205 210 1.807139 TTGCGAGCTAACTGCATCAA 58.193 45.000 3.63 0.00 45.94 2.57
206 211 1.362768 TGCGAGCTAACTGCATCAAG 58.637 50.000 0.00 0.00 45.94 3.02
207 212 0.027324 GCGAGCTAACTGCATCAAGC 59.973 55.000 6.27 6.27 45.94 4.01
295 300 4.279169 TCATTGTTTCTCCTCCAAGCAAAG 59.721 41.667 0.00 0.00 29.22 2.77
296 301 3.576078 TGTTTCTCCTCCAAGCAAAGA 57.424 42.857 0.00 0.00 0.00 2.52
331 338 3.521531 TCTGTACCAGAATTACCATGCCA 59.478 43.478 0.00 0.00 37.57 4.92
494 501 4.752879 CCGGTCGATGGGTGCGTT 62.753 66.667 0.00 0.00 0.00 4.84
534 541 5.710513 AGCTGACTGATAGATGAGATGAC 57.289 43.478 0.00 0.00 0.00 3.06
547 554 2.033424 TGAGATGACGATGACACCGATC 59.967 50.000 0.00 0.00 0.00 3.69
574 581 4.763073 CAGAGGTTAGTGCATGAGATGAA 58.237 43.478 0.00 0.00 0.00 2.57
632 641 0.767375 TTCTCAAGCCAAGCCTGTCT 59.233 50.000 0.00 0.00 0.00 3.41
635 644 0.322975 TCAAGCCAAGCCTGTCTCTC 59.677 55.000 0.00 0.00 0.00 3.20
637 646 0.612744 AAGCCAAGCCTGTCTCTCTC 59.387 55.000 0.00 0.00 0.00 3.20
643 652 3.065655 CAAGCCTGTCTCTCTCTTGTTG 58.934 50.000 0.00 0.00 31.99 3.33
644 653 2.324541 AGCCTGTCTCTCTCTTGTTGT 58.675 47.619 0.00 0.00 0.00 3.32
645 654 2.703007 AGCCTGTCTCTCTCTTGTTGTT 59.297 45.455 0.00 0.00 0.00 2.83
646 655 3.135530 AGCCTGTCTCTCTCTTGTTGTTT 59.864 43.478 0.00 0.00 0.00 2.83
656 665 2.163613 CTCTTGTTGTTTAATCCCCCGC 59.836 50.000 0.00 0.00 0.00 6.13
781 790 2.628106 GCACATGATACAGGCGCG 59.372 61.111 0.00 0.00 0.00 6.86
782 791 2.628106 CACATGATACAGGCGCGC 59.372 61.111 25.94 25.94 0.00 6.86
783 792 2.961721 ACATGATACAGGCGCGCG 60.962 61.111 28.44 28.44 0.00 6.86
784 793 4.360027 CATGATACAGGCGCGCGC 62.360 66.667 44.40 44.40 41.06 6.86
895 904 4.598257 CCGGTGGCATATCGATCC 57.402 61.111 0.00 0.00 33.82 3.36
908 925 2.923568 GATCCCTACCCCCTCCGC 60.924 72.222 0.00 0.00 0.00 5.54
926 944 4.814294 CCCCCGCTCGTTCTTCCG 62.814 72.222 0.00 0.00 0.00 4.30
927 945 3.755628 CCCCGCTCGTTCTTCCGA 61.756 66.667 0.00 0.00 35.22 4.55
1134 1153 4.124943 ACTAGCGGGAGGAGGCGA 62.125 66.667 0.00 0.00 0.00 5.54
1335 1359 5.006746 CCATAACTCTGCAATTAACTCGGAC 59.993 44.000 0.00 0.00 0.00 4.79
1340 1364 4.385825 TCTGCAATTAACTCGGACTTTGT 58.614 39.130 0.00 0.00 0.00 2.83
1341 1365 5.543714 TCTGCAATTAACTCGGACTTTGTA 58.456 37.500 0.00 0.00 0.00 2.41
1363 1387 1.139520 GATTGGGACGGCATGCAAC 59.860 57.895 21.36 9.63 0.00 4.17
1377 1403 3.429085 CATGCAACGGATTAGTTTGCTC 58.571 45.455 7.04 0.00 32.99 4.26
1389 1415 2.297701 AGTTTGCTCCGTTTGACATGT 58.702 42.857 0.00 0.00 0.00 3.21
1410 1436 3.942130 TCTTGTGCTCTTCGATTGAGA 57.058 42.857 16.88 3.01 33.68 3.27
1472 1500 1.396653 TACGAGCAGGGCTTACTACC 58.603 55.000 0.00 0.00 39.88 3.18
1584 1612 3.357079 CAACCACTCCAGCACGGC 61.357 66.667 0.00 0.00 33.14 5.68
1626 1657 1.959226 CACCGACACCGAAACCCAG 60.959 63.158 0.00 0.00 38.22 4.45
1789 1820 2.614446 CGTGTCGGTCACCTCGTCT 61.614 63.158 0.00 0.00 43.51 4.18
1792 1823 0.957395 TGTCGGTCACCTCGTCTACC 60.957 60.000 0.00 0.00 0.00 3.18
1999 2030 1.743623 CATAGTGTTCCGGCGGCAA 60.744 57.895 23.83 13.88 0.00 4.52
2000 2031 1.095228 CATAGTGTTCCGGCGGCAAT 61.095 55.000 23.83 16.39 0.00 3.56
2001 2032 0.466543 ATAGTGTTCCGGCGGCAATA 59.533 50.000 23.83 18.14 0.00 1.90
2106 2137 0.674895 GTCTGACATGTGGGACAGGC 60.675 60.000 1.15 1.44 41.80 4.85
2119 2150 2.487986 GGGACAGGCCTCCAATAAGATG 60.488 54.545 0.00 0.00 36.66 2.90
2120 2151 2.487986 GGACAGGCCTCCAATAAGATGG 60.488 54.545 0.00 0.00 42.12 3.51
2156 2187 8.945057 ACAAAATTGCAGTTTTAGTTTCATGTT 58.055 25.926 18.19 0.00 30.56 2.71
2157 2188 9.424659 CAAAATTGCAGTTTTAGTTTCATGTTC 57.575 29.630 18.19 0.00 30.56 3.18
2203 2238 7.283807 GGTTAGTTTTCTCACCTTCTTTTGGTA 59.716 37.037 0.00 0.00 40.12 3.25
2215 2250 8.082242 CACCTTCTTTTGGTATACCTTCTTTTG 58.918 37.037 22.41 8.34 35.80 2.44
2223 2258 6.953101 TGGTATACCTTCTTTTGCTCATACA 58.047 36.000 22.41 0.00 36.82 2.29
2224 2259 7.573710 TGGTATACCTTCTTTTGCTCATACAT 58.426 34.615 22.41 0.00 36.82 2.29
2225 2260 8.052748 TGGTATACCTTCTTTTGCTCATACATT 58.947 33.333 22.41 0.00 36.82 2.71
2228 2263 6.442513 ACCTTCTTTTGCTCATACATTAGC 57.557 37.500 0.00 0.00 39.25 3.09
2245 2280 7.506296 ACATTAGCAAAGTTTTAAATAGCGC 57.494 32.000 0.00 0.00 0.00 5.92
2246 2281 6.250527 ACATTAGCAAAGTTTTAAATAGCGCG 59.749 34.615 0.00 0.00 0.00 6.86
2247 2282 2.914838 AGCAAAGTTTTAAATAGCGCGC 59.085 40.909 26.66 26.66 0.00 6.86
2248 2283 2.914838 GCAAAGTTTTAAATAGCGCGCT 59.085 40.909 38.01 38.01 0.00 5.92
2249 2284 4.092816 GCAAAGTTTTAAATAGCGCGCTA 58.907 39.130 39.72 39.72 0.00 4.26
2250 2285 4.555747 GCAAAGTTTTAAATAGCGCGCTAA 59.444 37.500 40.90 26.03 31.73 3.09
2251 2286 5.275280 GCAAAGTTTTAAATAGCGCGCTAAG 60.275 40.000 40.90 16.80 31.73 2.18
2252 2287 3.936661 AGTTTTAAATAGCGCGCTAAGC 58.063 40.909 40.90 27.92 43.95 3.09
2264 2299 1.413382 CGCTAAGCATCTTAGAGGCG 58.587 55.000 13.23 9.96 44.44 5.52
2265 2300 1.789506 GCTAAGCATCTTAGAGGCGG 58.210 55.000 13.23 8.81 44.44 6.13
2266 2301 1.341531 GCTAAGCATCTTAGAGGCGGA 59.658 52.381 13.23 4.56 44.44 5.54
2267 2302 2.864489 GCTAAGCATCTTAGAGGCGGAC 60.864 54.545 13.23 1.27 44.44 4.79
2268 2303 0.466124 AAGCATCTTAGAGGCGGACC 59.534 55.000 13.23 0.00 44.44 4.46
2280 2315 1.428448 GGCGGACCTTTTTCAAATGC 58.572 50.000 0.00 0.00 0.00 3.56
2281 2316 1.000843 GGCGGACCTTTTTCAAATGCT 59.999 47.619 0.00 0.00 0.00 3.79
2282 2317 2.230266 GGCGGACCTTTTTCAAATGCTA 59.770 45.455 0.00 0.00 0.00 3.49
2283 2318 3.119137 GGCGGACCTTTTTCAAATGCTAT 60.119 43.478 0.00 0.00 0.00 2.97
2284 2319 4.097286 GGCGGACCTTTTTCAAATGCTATA 59.903 41.667 0.00 0.00 0.00 1.31
2285 2320 5.393678 GGCGGACCTTTTTCAAATGCTATAA 60.394 40.000 0.00 0.00 0.00 0.98
2286 2321 5.515270 GCGGACCTTTTTCAAATGCTATAAC 59.485 40.000 0.00 0.00 0.00 1.89
2287 2322 5.737290 CGGACCTTTTTCAAATGCTATAACG 59.263 40.000 0.00 0.00 0.00 3.18
2288 2323 6.617879 GGACCTTTTTCAAATGCTATAACGT 58.382 36.000 0.00 0.00 0.00 3.99
2289 2324 6.526674 GGACCTTTTTCAAATGCTATAACGTG 59.473 38.462 0.00 0.00 0.00 4.49
2290 2325 5.861787 ACCTTTTTCAAATGCTATAACGTGC 59.138 36.000 0.00 0.00 0.00 5.34
2291 2326 6.092748 CCTTTTTCAAATGCTATAACGTGCT 58.907 36.000 0.00 0.00 0.00 4.40
2292 2327 7.094549 ACCTTTTTCAAATGCTATAACGTGCTA 60.095 33.333 0.00 0.00 0.00 3.49
2293 2328 7.915397 CCTTTTTCAAATGCTATAACGTGCTAT 59.085 33.333 0.00 0.00 0.00 2.97
2294 2329 9.929722 CTTTTTCAAATGCTATAACGTGCTATA 57.070 29.630 0.00 0.00 0.00 1.31
2295 2330 9.929722 TTTTTCAAATGCTATAACGTGCTATAG 57.070 29.630 9.14 9.14 35.70 1.31
2296 2331 8.657074 TTTCAAATGCTATAACGTGCTATAGT 57.343 30.769 13.32 0.00 35.24 2.12
2297 2332 7.637709 TCAAATGCTATAACGTGCTATAGTG 57.362 36.000 13.32 6.34 35.24 2.74
2298 2333 6.645003 TCAAATGCTATAACGTGCTATAGTGG 59.355 38.462 13.32 0.00 35.24 4.00
2299 2334 5.977489 ATGCTATAACGTGCTATAGTGGA 57.023 39.130 13.32 2.54 35.24 4.02
2300 2335 5.372547 TGCTATAACGTGCTATAGTGGAG 57.627 43.478 13.32 0.00 35.24 3.86
2301 2336 4.167268 GCTATAACGTGCTATAGTGGAGC 58.833 47.826 13.32 1.32 40.53 4.70
2302 2337 4.082679 GCTATAACGTGCTATAGTGGAGCT 60.083 45.833 13.32 0.00 40.76 4.09
2303 2338 5.123502 GCTATAACGTGCTATAGTGGAGCTA 59.876 44.000 13.32 0.00 40.76 3.32
2304 2339 6.183360 GCTATAACGTGCTATAGTGGAGCTAT 60.183 42.308 13.32 0.00 42.63 2.97
2305 2340 7.012138 GCTATAACGTGCTATAGTGGAGCTATA 59.988 40.741 13.32 0.00 40.61 1.31
2323 2358 5.618561 GCTATAGCGCGCTATTTAAAATGT 58.381 37.500 46.76 28.88 39.65 2.71
2324 2359 6.077838 GCTATAGCGCGCTATTTAAAATGTT 58.922 36.000 46.76 28.22 39.65 2.71
2325 2360 6.577427 GCTATAGCGCGCTATTTAAAATGTTT 59.423 34.615 46.76 27.75 39.65 2.83
2326 2361 7.112984 GCTATAGCGCGCTATTTAAAATGTTTT 59.887 33.333 46.76 27.57 39.65 2.43
2327 2362 7.749539 ATAGCGCGCTATTTAAAATGTTTTT 57.250 28.000 40.32 19.71 35.92 1.94
2328 2363 8.844441 ATAGCGCGCTATTTAAAATGTTTTTA 57.156 26.923 40.32 18.29 35.92 1.52
2329 2364 7.749539 AGCGCGCTATTTAAAATGTTTTTAT 57.250 28.000 35.79 0.00 0.00 1.40
2330 2365 8.180317 AGCGCGCTATTTAAAATGTTTTTATT 57.820 26.923 35.79 0.00 0.00 1.40
2331 2366 8.318167 AGCGCGCTATTTAAAATGTTTTTATTC 58.682 29.630 35.79 0.00 0.00 1.75
2332 2367 8.105135 GCGCGCTATTTAAAATGTTTTTATTCA 58.895 29.630 26.67 0.00 0.00 2.57
2345 2380 8.970859 ATGTTTTTATTCATTTGTTTGGACCA 57.029 26.923 0.00 0.00 0.00 4.02
2346 2381 8.792830 TGTTTTTATTCATTTGTTTGGACCAA 57.207 26.923 1.69 1.69 0.00 3.67
2347 2382 9.231297 TGTTTTTATTCATTTGTTTGGACCAAA 57.769 25.926 15.89 15.89 36.34 3.28
2348 2383 9.715123 GTTTTTATTCATTTGTTTGGACCAAAG 57.285 29.630 20.14 8.25 35.45 2.77
2349 2384 9.454859 TTTTTATTCATTTGTTTGGACCAAAGT 57.545 25.926 20.14 4.29 35.45 2.66
2350 2385 8.655651 TTTATTCATTTGTTTGGACCAAAGTC 57.344 30.769 20.14 10.01 42.73 3.01
2351 2386 5.930837 TTCATTTGTTTGGACCAAAGTCT 57.069 34.783 20.14 2.95 43.05 3.24
2352 2387 5.514274 TCATTTGTTTGGACCAAAGTCTC 57.486 39.130 20.14 8.94 43.05 3.36
2353 2388 5.200483 TCATTTGTTTGGACCAAAGTCTCT 58.800 37.500 20.14 1.91 43.05 3.10
2354 2389 5.656416 TCATTTGTTTGGACCAAAGTCTCTT 59.344 36.000 20.14 1.05 43.05 2.85
2355 2390 6.831353 TCATTTGTTTGGACCAAAGTCTCTTA 59.169 34.615 20.14 1.24 43.05 2.10
2356 2391 6.693315 TTTGTTTGGACCAAAGTCTCTTAG 57.307 37.500 20.14 0.00 43.05 2.18
2357 2392 4.134563 TGTTTGGACCAAAGTCTCTTAGC 58.865 43.478 20.14 5.76 43.05 3.09
2358 2393 2.743636 TGGACCAAAGTCTCTTAGCG 57.256 50.000 0.00 0.00 43.05 4.26
2359 2394 1.337823 TGGACCAAAGTCTCTTAGCGC 60.338 52.381 0.00 0.00 43.05 5.92
2360 2395 1.337823 GGACCAAAGTCTCTTAGCGCA 60.338 52.381 11.47 0.00 43.05 6.09
2361 2396 2.413837 GACCAAAGTCTCTTAGCGCAA 58.586 47.619 11.47 0.50 40.10 4.85
2362 2397 2.413453 GACCAAAGTCTCTTAGCGCAAG 59.587 50.000 11.47 11.67 40.10 4.01
2363 2398 2.037251 ACCAAAGTCTCTTAGCGCAAGA 59.963 45.455 11.47 15.40 41.10 3.02
2364 2399 2.413453 CCAAAGTCTCTTAGCGCAAGAC 59.587 50.000 11.47 16.26 38.39 3.01
2365 2400 2.371910 AAGTCTCTTAGCGCAAGACC 57.628 50.000 21.13 13.52 40.21 3.85
2366 2401 1.551452 AGTCTCTTAGCGCAAGACCT 58.449 50.000 21.13 14.93 40.21 3.85
2367 2402 1.896465 AGTCTCTTAGCGCAAGACCTT 59.104 47.619 21.13 7.87 40.21 3.50
2368 2403 2.300437 AGTCTCTTAGCGCAAGACCTTT 59.700 45.455 21.13 7.34 40.21 3.11
2369 2404 3.067833 GTCTCTTAGCGCAAGACCTTTT 58.932 45.455 11.47 0.00 38.39 2.27
2370 2405 3.067106 TCTCTTAGCGCAAGACCTTTTG 58.933 45.455 11.47 4.34 38.39 2.44
2371 2406 2.808543 CTCTTAGCGCAAGACCTTTTGT 59.191 45.455 11.47 0.00 38.39 2.83
2372 2407 3.994392 CTCTTAGCGCAAGACCTTTTGTA 59.006 43.478 11.47 0.00 38.39 2.41
2373 2408 4.382291 TCTTAGCGCAAGACCTTTTGTAA 58.618 39.130 11.47 0.00 38.39 2.41
2374 2409 4.817464 TCTTAGCGCAAGACCTTTTGTAAA 59.183 37.500 11.47 0.00 38.39 2.01
2375 2410 3.349488 AGCGCAAGACCTTTTGTAAAC 57.651 42.857 11.47 0.00 43.02 2.01
2376 2411 2.041244 GCGCAAGACCTTTTGTAAACG 58.959 47.619 0.30 0.00 43.02 3.60
2377 2412 2.041244 CGCAAGACCTTTTGTAAACGC 58.959 47.619 0.00 0.00 43.02 4.84
2378 2413 2.286772 CGCAAGACCTTTTGTAAACGCT 60.287 45.455 0.00 0.00 43.02 5.07
2379 2414 3.059461 CGCAAGACCTTTTGTAAACGCTA 60.059 43.478 0.00 0.00 43.02 4.26
2380 2415 4.378046 CGCAAGACCTTTTGTAAACGCTAT 60.378 41.667 0.00 0.00 43.02 2.97
2381 2416 5.163933 CGCAAGACCTTTTGTAAACGCTATA 60.164 40.000 0.00 0.00 43.02 1.31
2382 2417 6.248631 GCAAGACCTTTTGTAAACGCTATAG 58.751 40.000 0.00 0.00 0.00 1.31
2383 2418 6.248631 CAAGACCTTTTGTAAACGCTATAGC 58.751 40.000 15.09 15.09 37.78 2.97
2397 2432 3.326733 CTATAGCGTGCTATAGCGGAG 57.673 52.381 27.04 13.65 46.26 4.63
2398 2433 0.171455 ATAGCGTGCTATAGCGGAGC 59.829 55.000 22.98 22.98 45.83 4.70
2421 2456 7.710766 GCTATAGCGGACTATTTAAAACAGT 57.289 36.000 9.40 5.72 39.81 3.55
2422 2457 7.564988 GCTATAGCGGACTATTTAAAACAGTG 58.435 38.462 9.40 0.00 39.81 3.66
2457 2492 4.974368 AGAAGAATCTGAGGTCAGTACG 57.026 45.455 6.87 0.00 44.12 3.67
2482 2517 4.122046 TGCACATATTGATTGGACGAGAG 58.878 43.478 0.00 0.00 0.00 3.20
2485 2520 5.468072 GCACATATTGATTGGACGAGAGATT 59.532 40.000 0.00 0.00 0.00 2.40
2493 2528 1.285078 TGGACGAGAGATTGAGAGGGA 59.715 52.381 0.00 0.00 0.00 4.20
2499 2534 4.956700 ACGAGAGATTGAGAGGGATACAAA 59.043 41.667 0.00 0.00 39.74 2.83
2542 2577 8.684386 TTGGTTGAATCATTTGTCTTGTAGTA 57.316 30.769 0.00 0.00 0.00 1.82
2545 2580 9.431887 GGTTGAATCATTTGTCTTGTAGTAGTA 57.568 33.333 0.00 0.00 0.00 1.82
2634 2676 3.002246 TCTTCAACTTTTGCACTGCTACG 59.998 43.478 1.98 0.00 0.00 3.51
2695 2740 6.514705 GCATGAAGAGGATAAGCTTGAATTCC 60.515 42.308 9.86 10.00 0.00 3.01
2717 2762 1.818060 CATGGCGGTGGAAATCTTTCA 59.182 47.619 5.14 0.00 38.92 2.69
2815 2860 8.113462 TGTCCTAATTAAGCCAAACTTCCTTAT 58.887 33.333 0.00 0.00 39.97 1.73
2876 2921 7.136772 CACAACATCAAATGTATAGAGCATGG 58.863 38.462 0.00 0.00 44.07 3.66
2989 3149 4.141937 GGCTTAAAATAAGGGCCTCTTTGG 60.142 45.833 6.46 6.38 39.68 3.28
2994 3154 4.337264 AATAAGGGCCTCTTTGGTTCAT 57.663 40.909 6.46 0.00 36.93 2.57
2996 3156 3.372440 AAGGGCCTCTTTGGTTCATAG 57.628 47.619 6.46 0.00 38.35 2.23
3020 3181 5.008712 GGATTCTAAAAACGCTGGAATAGGG 59.991 44.000 0.00 0.00 44.41 3.53
3025 3186 5.538849 AAAAACGCTGGAATAGGGAAAAA 57.461 34.783 0.00 0.00 41.61 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
75 76 4.882427 TGCCATGATGCAAATTTTAATGGG 59.118 37.500 6.80 0.00 38.56 4.00
130 135 1.017177 GCCAATCACCGCGTTACAGA 61.017 55.000 4.92 0.00 0.00 3.41
132 137 0.604243 AAGCCAATCACCGCGTTACA 60.604 50.000 4.92 0.00 0.00 2.41
149 154 1.458064 CAGTTGTAACCCGCGTACAAG 59.542 52.381 17.85 6.90 34.80 3.16
153 158 2.491298 TGATACAGTTGTAACCCGCGTA 59.509 45.455 4.92 0.00 33.76 4.42
183 188 2.551887 TGATGCAGTTAGCTCGCAAAAA 59.448 40.909 0.00 0.00 45.94 1.94
184 189 2.150390 TGATGCAGTTAGCTCGCAAAA 58.850 42.857 0.00 0.00 45.94 2.44
185 190 1.807139 TGATGCAGTTAGCTCGCAAA 58.193 45.000 0.00 0.00 45.94 3.68
186 191 1.733912 CTTGATGCAGTTAGCTCGCAA 59.266 47.619 0.00 0.00 45.94 4.85
187 192 1.362768 CTTGATGCAGTTAGCTCGCA 58.637 50.000 0.00 0.00 45.94 5.10
188 193 0.027324 GCTTGATGCAGTTAGCTCGC 59.973 55.000 8.89 0.00 45.94 5.03
199 204 0.524414 TGCACTGTCATGCTTGATGC 59.476 50.000 15.92 15.92 46.28 3.91
200 205 2.081462 TCTGCACTGTCATGCTTGATG 58.919 47.619 5.49 1.74 46.28 3.07
201 206 2.082231 GTCTGCACTGTCATGCTTGAT 58.918 47.619 5.49 0.00 46.28 2.57
202 207 1.071228 AGTCTGCACTGTCATGCTTGA 59.929 47.619 0.00 0.00 46.28 3.02
203 208 1.520494 AGTCTGCACTGTCATGCTTG 58.480 50.000 0.00 0.00 46.28 4.01
204 209 3.070018 GTTAGTCTGCACTGTCATGCTT 58.930 45.455 0.00 0.00 46.28 3.91
205 210 2.613977 GGTTAGTCTGCACTGTCATGCT 60.614 50.000 0.00 0.00 46.28 3.79
206 211 1.734465 GGTTAGTCTGCACTGTCATGC 59.266 52.381 0.00 0.00 46.32 4.06
207 212 3.325293 AGGTTAGTCTGCACTGTCATG 57.675 47.619 0.00 0.00 33.62 3.07
208 213 4.344978 TCTAGGTTAGTCTGCACTGTCAT 58.655 43.478 0.00 0.00 33.62 3.06
209 214 3.759086 CTCTAGGTTAGTCTGCACTGTCA 59.241 47.826 0.00 0.00 33.62 3.58
216 221 5.881443 TGTCTAGAACTCTAGGTTAGTCTGC 59.119 44.000 12.71 0.00 44.60 4.26
295 300 2.231721 GGTACAGACCTGGTGTTCTCTC 59.768 54.545 2.82 0.00 43.16 3.20
296 301 2.249139 GGTACAGACCTGGTGTTCTCT 58.751 52.381 2.82 0.00 43.16 3.10
331 338 4.577693 CAGCTACATGCATGACCAGTAAAT 59.422 41.667 32.75 9.69 45.94 1.40
494 501 3.068732 CAGCTGTCCCTTCGATCTCAATA 59.931 47.826 5.25 0.00 0.00 1.90
534 541 2.286559 GCGTCGATCGGTGTCATCG 61.287 63.158 16.41 0.00 43.77 3.84
547 554 0.458543 ATGCACTAACCTCTGCGTCG 60.459 55.000 0.00 0.00 36.08 5.12
574 581 1.520666 CGACGCCTCCCCAACTATT 59.479 57.895 0.00 0.00 0.00 1.73
632 641 4.564821 CGGGGGATTAAACAACAAGAGAGA 60.565 45.833 0.00 0.00 0.00 3.10
635 644 2.163613 GCGGGGGATTAAACAACAAGAG 59.836 50.000 0.00 0.00 0.00 2.85
637 646 1.203758 GGCGGGGGATTAAACAACAAG 59.796 52.381 0.00 0.00 0.00 3.16
643 652 1.820906 GACGGGCGGGGGATTAAAC 60.821 63.158 0.00 0.00 0.00 2.01
644 653 2.591198 GACGGGCGGGGGATTAAA 59.409 61.111 0.00 0.00 0.00 1.52
645 654 3.852307 CGACGGGCGGGGGATTAA 61.852 66.667 0.00 0.00 36.03 1.40
888 897 1.470165 GGAGGGGGTAGGGATCGAT 59.530 63.158 0.00 0.00 0.00 3.59
889 898 2.940951 GGAGGGGGTAGGGATCGA 59.059 66.667 0.00 0.00 0.00 3.59
890 899 2.600769 CGGAGGGGGTAGGGATCG 60.601 72.222 0.00 0.00 0.00 3.69
891 900 2.923568 GCGGAGGGGGTAGGGATC 60.924 72.222 0.00 0.00 0.00 3.36
892 901 4.576374 GGCGGAGGGGGTAGGGAT 62.576 72.222 0.00 0.00 0.00 3.85
919 936 1.897133 TCGGAAATGGAGTCGGAAGAA 59.103 47.619 0.00 0.00 45.01 2.52
926 944 1.854227 GACCGATCGGAAATGGAGTC 58.146 55.000 39.55 20.14 38.96 3.36
927 945 0.102481 CGACCGATCGGAAATGGAGT 59.898 55.000 39.55 15.57 44.99 3.85
1134 1153 1.016130 CCACTCGCTTCTGCAACGAT 61.016 55.000 0.00 0.00 39.64 3.73
1287 1306 6.257193 GGTGACTTAAATTAGGTCGTACATGG 59.743 42.308 10.07 0.00 37.58 3.66
1335 1359 2.356135 CCGTCCCAATCCAGTACAAAG 58.644 52.381 0.00 0.00 0.00 2.77
1340 1364 0.180171 CATGCCGTCCCAATCCAGTA 59.820 55.000 0.00 0.00 0.00 2.74
1341 1365 1.077501 CATGCCGTCCCAATCCAGT 60.078 57.895 0.00 0.00 0.00 4.00
1377 1403 2.033299 AGCACAAGAACATGTCAAACGG 59.967 45.455 0.00 0.00 0.00 4.44
1379 1405 4.558538 AGAGCACAAGAACATGTCAAAC 57.441 40.909 0.00 0.00 0.00 2.93
1381 1407 3.248363 CGAAGAGCACAAGAACATGTCAA 59.752 43.478 0.00 0.00 0.00 3.18
1389 1415 3.990469 GTCTCAATCGAAGAGCACAAGAA 59.010 43.478 12.07 0.00 43.63 2.52
1421 1449 1.067295 ACCCAGATCAGCAAACCTCA 58.933 50.000 0.00 0.00 0.00 3.86
1609 1637 2.424302 CTGGGTTTCGGTGTCGGT 59.576 61.111 0.00 0.00 36.95 4.69
1705 1736 3.138798 GGGCTCGCGGTGACTAGA 61.139 66.667 6.13 0.00 0.00 2.43
1777 1808 1.991099 GCGAGGTAGACGAGGTGACC 61.991 65.000 0.00 0.00 0.00 4.02
1789 1820 1.751927 GACTTCGGAGGGCGAGGTA 60.752 63.158 0.00 0.00 0.00 3.08
1792 1823 3.114647 CTCGACTTCGGAGGGCGAG 62.115 68.421 27.45 27.45 41.78 5.03
1919 1950 0.246635 TCTTCTTCGCTTCCTTCCCG 59.753 55.000 0.00 0.00 0.00 5.14
1928 1959 2.254703 ATCGCGTCGTCTTCTTCGCT 62.255 55.000 5.77 0.00 45.25 4.93
1975 2006 1.523711 CCGGAACACTATGGCGCAT 60.524 57.895 10.83 3.40 0.00 4.73
2029 2060 1.305381 CTCGACCTTGACCCCTCCT 60.305 63.158 0.00 0.00 0.00 3.69
2094 2125 1.217057 ATTGGAGGCCTGTCCCACAT 61.217 55.000 12.00 5.46 35.49 3.21
2119 2150 1.531883 GCAATTTTGTCCGCTCGATCC 60.532 52.381 0.00 0.00 0.00 3.36
2120 2151 1.130373 TGCAATTTTGTCCGCTCGATC 59.870 47.619 0.00 0.00 0.00 3.69
2121 2152 1.131126 CTGCAATTTTGTCCGCTCGAT 59.869 47.619 0.00 0.00 0.00 3.59
2122 2153 0.516877 CTGCAATTTTGTCCGCTCGA 59.483 50.000 0.00 0.00 0.00 4.04
2156 2187 1.295792 ACAAAAGCGCAAGAGAACGA 58.704 45.000 11.47 0.00 43.02 3.85
2157 2188 1.775208 CAACAAAAGCGCAAGAGAACG 59.225 47.619 11.47 0.00 43.02 3.95
2203 2238 7.775093 TGCTAATGTATGAGCAAAAGAAGGTAT 59.225 33.333 1.33 0.00 45.47 2.73
2223 2258 5.229260 GCGCGCTATTTAAAACTTTGCTAAT 59.771 36.000 26.67 0.00 0.00 1.73
2224 2259 4.555747 GCGCGCTATTTAAAACTTTGCTAA 59.444 37.500 26.67 0.00 0.00 3.09
2225 2260 4.092816 GCGCGCTATTTAAAACTTTGCTA 58.907 39.130 26.67 0.00 0.00 3.49
2227 2262 2.914838 AGCGCGCTATTTAAAACTTTGC 59.085 40.909 35.79 0.00 0.00 3.68
2228 2263 5.275280 GCTTAGCGCGCTATTTAAAACTTTG 60.275 40.000 38.51 15.49 0.00 2.77
2230 2265 4.142773 TGCTTAGCGCGCTATTTAAAACTT 60.143 37.500 38.51 13.94 43.27 2.66
2231 2266 3.372822 TGCTTAGCGCGCTATTTAAAACT 59.627 39.130 38.51 14.50 43.27 2.66
2232 2267 3.676540 TGCTTAGCGCGCTATTTAAAAC 58.323 40.909 38.51 22.00 43.27 2.43
2233 2268 4.272504 AGATGCTTAGCGCGCTATTTAAAA 59.727 37.500 38.51 24.43 43.27 1.52
2234 2269 3.807622 AGATGCTTAGCGCGCTATTTAAA 59.192 39.130 38.51 25.16 43.27 1.52
2235 2270 3.390135 AGATGCTTAGCGCGCTATTTAA 58.610 40.909 38.51 25.53 43.27 1.52
2236 2271 3.026630 AGATGCTTAGCGCGCTATTTA 57.973 42.857 38.51 26.65 43.27 1.40
2237 2272 1.871080 AGATGCTTAGCGCGCTATTT 58.129 45.000 38.51 23.54 43.27 1.40
2238 2273 1.871080 AAGATGCTTAGCGCGCTATT 58.129 45.000 38.51 26.01 43.27 1.73
2239 2274 2.229062 TCTAAGATGCTTAGCGCGCTAT 59.771 45.455 38.51 26.50 43.27 2.97
2240 2275 1.607148 TCTAAGATGCTTAGCGCGCTA 59.393 47.619 35.48 35.48 43.27 4.26
2241 2276 0.385751 TCTAAGATGCTTAGCGCGCT 59.614 50.000 38.01 38.01 43.27 5.92
2242 2277 0.781191 CTCTAAGATGCTTAGCGCGC 59.219 55.000 26.66 26.66 43.27 6.86
2243 2278 1.413382 CCTCTAAGATGCTTAGCGCG 58.587 55.000 0.00 0.00 43.27 6.86
2244 2279 1.144136 GCCTCTAAGATGCTTAGCGC 58.856 55.000 0.00 0.00 39.77 5.92
2245 2280 1.413382 CGCCTCTAAGATGCTTAGCG 58.587 55.000 8.89 7.01 36.06 4.26
2246 2281 1.341531 TCCGCCTCTAAGATGCTTAGC 59.658 52.381 8.89 0.00 0.00 3.09
2247 2282 2.288518 GGTCCGCCTCTAAGATGCTTAG 60.289 54.545 7.68 7.68 0.00 2.18
2248 2283 1.687123 GGTCCGCCTCTAAGATGCTTA 59.313 52.381 0.00 0.00 0.00 3.09
2249 2284 0.466124 GGTCCGCCTCTAAGATGCTT 59.534 55.000 0.00 0.00 0.00 3.91
2250 2285 0.397816 AGGTCCGCCTCTAAGATGCT 60.398 55.000 0.00 0.00 42.67 3.79
2251 2286 0.466124 AAGGTCCGCCTCTAAGATGC 59.534 55.000 0.00 0.00 46.33 3.91
2252 2287 2.990066 AAAGGTCCGCCTCTAAGATG 57.010 50.000 0.00 0.00 46.33 2.90
2253 2288 3.263425 TGAAAAAGGTCCGCCTCTAAGAT 59.737 43.478 0.00 0.00 46.33 2.40
2254 2289 2.635915 TGAAAAAGGTCCGCCTCTAAGA 59.364 45.455 0.00 0.00 46.33 2.10
2255 2290 3.053831 TGAAAAAGGTCCGCCTCTAAG 57.946 47.619 0.00 0.00 46.33 2.18
2256 2291 3.495434 TTGAAAAAGGTCCGCCTCTAA 57.505 42.857 0.00 0.00 46.33 2.10
2257 2292 3.495434 TTTGAAAAAGGTCCGCCTCTA 57.505 42.857 0.00 0.00 46.33 2.43
2258 2293 2.358322 TTTGAAAAAGGTCCGCCTCT 57.642 45.000 0.00 0.00 46.33 3.69
2259 2294 2.926586 GCATTTGAAAAAGGTCCGCCTC 60.927 50.000 0.00 0.00 46.33 4.70
2261 2296 1.000843 AGCATTTGAAAAAGGTCCGCC 59.999 47.619 0.00 0.00 0.00 6.13
2262 2297 2.438868 AGCATTTGAAAAAGGTCCGC 57.561 45.000 0.00 0.00 0.00 5.54
2263 2298 5.737290 CGTTATAGCATTTGAAAAAGGTCCG 59.263 40.000 0.00 0.00 0.00 4.79
2264 2299 6.526674 CACGTTATAGCATTTGAAAAAGGTCC 59.473 38.462 0.00 0.00 0.00 4.46
2265 2300 6.033513 GCACGTTATAGCATTTGAAAAAGGTC 59.966 38.462 0.00 0.00 0.00 3.85
2266 2301 5.861787 GCACGTTATAGCATTTGAAAAAGGT 59.138 36.000 0.00 0.00 0.00 3.50
2267 2302 6.092748 AGCACGTTATAGCATTTGAAAAAGG 58.907 36.000 0.00 0.00 0.00 3.11
2268 2303 8.841444 ATAGCACGTTATAGCATTTGAAAAAG 57.159 30.769 0.00 0.00 0.00 2.27
2269 2304 9.929722 CTATAGCACGTTATAGCATTTGAAAAA 57.070 29.630 2.21 0.00 29.57 1.94
2270 2305 9.104965 ACTATAGCACGTTATAGCATTTGAAAA 57.895 29.630 12.28 0.00 37.20 2.29
2271 2306 8.547894 CACTATAGCACGTTATAGCATTTGAAA 58.452 33.333 12.28 0.00 37.20 2.69
2272 2307 7.170828 CCACTATAGCACGTTATAGCATTTGAA 59.829 37.037 12.28 0.00 37.20 2.69
2273 2308 6.645003 CCACTATAGCACGTTATAGCATTTGA 59.355 38.462 12.28 0.00 37.20 2.69
2274 2309 6.645003 TCCACTATAGCACGTTATAGCATTTG 59.355 38.462 12.28 5.43 37.20 2.32
2275 2310 6.755206 TCCACTATAGCACGTTATAGCATTT 58.245 36.000 12.28 0.00 37.20 2.32
2276 2311 6.340962 TCCACTATAGCACGTTATAGCATT 57.659 37.500 12.28 0.00 37.20 3.56
2277 2312 5.622460 GCTCCACTATAGCACGTTATAGCAT 60.622 44.000 12.28 1.65 39.83 3.79
2278 2313 4.321008 GCTCCACTATAGCACGTTATAGCA 60.321 45.833 12.28 0.12 39.83 3.49
2279 2314 4.082679 AGCTCCACTATAGCACGTTATAGC 60.083 45.833 12.28 1.28 42.62 2.97
2280 2315 5.630661 AGCTCCACTATAGCACGTTATAG 57.369 43.478 11.19 11.19 42.62 1.31
2291 2326 1.400846 GCGCGCTATAGCTCCACTATA 59.599 52.381 26.67 0.00 41.91 1.31
2292 2327 0.171455 GCGCGCTATAGCTCCACTAT 59.829 55.000 26.67 0.00 44.12 2.12
2293 2328 0.889638 AGCGCGCTATAGCTCCACTA 60.890 55.000 35.79 0.00 39.98 2.74
2294 2329 0.889638 TAGCGCGCTATAGCTCCACT 60.890 55.000 35.48 11.63 43.44 4.00
2295 2330 0.171455 ATAGCGCGCTATAGCTCCAC 59.829 55.000 43.42 7.86 43.44 4.02
2296 2331 0.888619 AATAGCGCGCTATAGCTCCA 59.111 50.000 43.81 24.51 43.44 3.86
2297 2332 1.997669 AAATAGCGCGCTATAGCTCC 58.002 50.000 43.81 10.26 43.44 4.70
2298 2333 5.511088 TTTTAAATAGCGCGCTATAGCTC 57.489 39.130 43.81 13.77 43.44 4.09
2299 2334 5.408604 ACATTTTAAATAGCGCGCTATAGCT 59.591 36.000 43.81 33.17 46.53 3.32
2300 2335 5.618561 ACATTTTAAATAGCGCGCTATAGC 58.381 37.500 43.81 15.09 38.20 2.97
2301 2336 8.488979 AAAACATTTTAAATAGCGCGCTATAG 57.511 30.769 43.81 29.40 38.20 1.31
2302 2337 8.844441 AAAAACATTTTAAATAGCGCGCTATA 57.156 26.923 43.81 31.73 38.20 1.31
2303 2338 7.749539 AAAAACATTTTAAATAGCGCGCTAT 57.250 28.000 40.32 40.32 40.63 2.97
2304 2339 8.844441 ATAAAAACATTTTAAATAGCGCGCTA 57.156 26.923 39.72 39.72 0.00 4.26
2305 2340 7.749539 ATAAAAACATTTTAAATAGCGCGCT 57.250 28.000 38.01 38.01 0.00 5.92
2306 2341 8.105135 TGAATAAAAACATTTTAAATAGCGCGC 58.895 29.630 26.66 26.66 0.00 6.86
2319 2354 9.401058 TGGTCCAAACAAATGAATAAAAACATT 57.599 25.926 0.00 0.00 38.18 2.71
2320 2355 8.970859 TGGTCCAAACAAATGAATAAAAACAT 57.029 26.923 0.00 0.00 0.00 2.71
2321 2356 8.792830 TTGGTCCAAACAAATGAATAAAAACA 57.207 26.923 0.40 0.00 0.00 2.83
2322 2357 9.715123 CTTTGGTCCAAACAAATGAATAAAAAC 57.285 29.630 13.26 0.00 37.22 2.43
2323 2358 9.454859 ACTTTGGTCCAAACAAATGAATAAAAA 57.545 25.926 13.26 0.00 37.22 1.94
2324 2359 9.103861 GACTTTGGTCCAAACAAATGAATAAAA 57.896 29.630 13.26 0.00 37.22 1.52
2325 2360 8.482128 AGACTTTGGTCCAAACAAATGAATAAA 58.518 29.630 13.26 0.00 43.05 1.40
2326 2361 8.017418 AGACTTTGGTCCAAACAAATGAATAA 57.983 30.769 13.26 0.00 43.05 1.40
2327 2362 7.505585 AGAGACTTTGGTCCAAACAAATGAATA 59.494 33.333 13.26 0.00 43.05 1.75
2328 2363 6.324770 AGAGACTTTGGTCCAAACAAATGAAT 59.675 34.615 13.26 0.00 43.05 2.57
2329 2364 5.656416 AGAGACTTTGGTCCAAACAAATGAA 59.344 36.000 13.26 0.00 43.05 2.57
2330 2365 5.200483 AGAGACTTTGGTCCAAACAAATGA 58.800 37.500 13.26 0.00 43.05 2.57
2331 2366 5.520376 AGAGACTTTGGTCCAAACAAATG 57.480 39.130 13.26 6.01 43.05 2.32
2332 2367 6.239036 GCTAAGAGACTTTGGTCCAAACAAAT 60.239 38.462 13.26 0.00 43.05 2.32
2333 2368 5.067283 GCTAAGAGACTTTGGTCCAAACAAA 59.933 40.000 13.26 0.00 43.05 2.83
2334 2369 4.578928 GCTAAGAGACTTTGGTCCAAACAA 59.421 41.667 13.26 0.00 43.05 2.83
2335 2370 4.134563 GCTAAGAGACTTTGGTCCAAACA 58.865 43.478 13.26 0.00 43.05 2.83
2336 2371 3.186613 CGCTAAGAGACTTTGGTCCAAAC 59.813 47.826 13.26 4.96 43.05 2.93
2337 2372 3.399330 CGCTAAGAGACTTTGGTCCAAA 58.601 45.455 16.26 16.26 43.05 3.28
2338 2373 2.870435 GCGCTAAGAGACTTTGGTCCAA 60.870 50.000 0.00 0.00 43.05 3.53
2339 2374 1.337823 GCGCTAAGAGACTTTGGTCCA 60.338 52.381 0.00 0.00 43.05 4.02
2340 2375 1.337823 TGCGCTAAGAGACTTTGGTCC 60.338 52.381 9.73 0.00 43.05 4.46
2341 2376 2.080286 TGCGCTAAGAGACTTTGGTC 57.920 50.000 9.73 0.00 42.41 4.02
2342 2377 2.037251 TCTTGCGCTAAGAGACTTTGGT 59.963 45.455 9.73 0.00 40.43 3.67
2343 2378 2.413453 GTCTTGCGCTAAGAGACTTTGG 59.587 50.000 18.44 0.00 45.71 3.28
2344 2379 2.413453 GGTCTTGCGCTAAGAGACTTTG 59.587 50.000 22.91 0.00 45.71 2.77
2345 2380 2.300437 AGGTCTTGCGCTAAGAGACTTT 59.700 45.455 22.91 14.31 45.71 2.66
2346 2381 1.896465 AGGTCTTGCGCTAAGAGACTT 59.104 47.619 22.91 17.23 45.71 3.01
2347 2382 1.551452 AGGTCTTGCGCTAAGAGACT 58.449 50.000 22.91 18.83 45.71 3.24
2348 2383 2.371910 AAGGTCTTGCGCTAAGAGAC 57.628 50.000 18.44 18.59 45.71 3.36
2349 2384 3.067106 CAAAAGGTCTTGCGCTAAGAGA 58.933 45.455 18.44 9.99 45.71 3.10
2350 2385 2.808543 ACAAAAGGTCTTGCGCTAAGAG 59.191 45.455 18.44 10.73 45.71 2.85
2351 2386 2.846193 ACAAAAGGTCTTGCGCTAAGA 58.154 42.857 9.73 13.31 43.01 2.10
2352 2387 4.742438 TTACAAAAGGTCTTGCGCTAAG 57.258 40.909 9.73 11.02 37.76 2.18
2353 2388 4.553156 CGTTTACAAAAGGTCTTGCGCTAA 60.553 41.667 9.73 0.00 0.00 3.09
2354 2389 3.059461 CGTTTACAAAAGGTCTTGCGCTA 60.059 43.478 9.73 0.00 0.00 4.26
2355 2390 2.286772 CGTTTACAAAAGGTCTTGCGCT 60.287 45.455 9.73 0.00 0.00 5.92
2356 2391 2.041244 CGTTTACAAAAGGTCTTGCGC 58.959 47.619 0.00 0.00 0.00 6.09
2357 2392 2.041244 GCGTTTACAAAAGGTCTTGCG 58.959 47.619 0.00 0.00 0.00 4.85
2358 2393 3.349488 AGCGTTTACAAAAGGTCTTGC 57.651 42.857 0.00 0.00 0.00 4.01
2359 2394 6.248631 GCTATAGCGTTTACAAAAGGTCTTG 58.751 40.000 9.40 0.00 31.10 3.02
2360 2395 6.418585 GCTATAGCGTTTACAAAAGGTCTT 57.581 37.500 9.40 0.00 31.10 3.01
2378 2413 1.400846 GCTCCGCTATAGCACGCTATA 59.599 52.381 23.99 15.99 42.21 1.31
2379 2414 0.171455 GCTCCGCTATAGCACGCTAT 59.829 55.000 23.99 15.45 42.21 2.97
2380 2415 0.889638 AGCTCCGCTATAGCACGCTA 60.890 55.000 23.99 0.39 42.62 4.26
2381 2416 0.889638 TAGCTCCGCTATAGCACGCT 60.890 55.000 25.78 25.78 42.62 5.07
2382 2417 1.579932 TAGCTCCGCTATAGCACGC 59.420 57.895 23.99 20.26 42.62 5.34
2390 2425 0.036448 AGTCCGCTATAGCTCCGCTA 59.964 55.000 21.98 0.00 45.55 4.26
2391 2426 0.036448 TAGTCCGCTATAGCTCCGCT 59.964 55.000 21.98 15.56 43.41 5.52
2392 2427 1.096416 ATAGTCCGCTATAGCTCCGC 58.904 55.000 21.98 9.68 36.24 5.54
2393 2428 3.851976 AAATAGTCCGCTATAGCTCCG 57.148 47.619 21.98 9.66 36.95 4.63
2394 2429 6.927381 TGTTTTAAATAGTCCGCTATAGCTCC 59.073 38.462 21.98 9.66 36.95 4.70
2395 2430 7.652507 ACTGTTTTAAATAGTCCGCTATAGCTC 59.347 37.037 21.98 12.14 36.95 4.09
2396 2431 7.438459 CACTGTTTTAAATAGTCCGCTATAGCT 59.562 37.037 21.98 6.31 36.95 3.32
2397 2432 7.224167 ACACTGTTTTAAATAGTCCGCTATAGC 59.776 37.037 15.09 15.09 36.95 2.97
2398 2433 8.644318 ACACTGTTTTAAATAGTCCGCTATAG 57.356 34.615 4.13 0.00 36.95 1.31
2399 2434 9.520204 GTACACTGTTTTAAATAGTCCGCTATA 57.480 33.333 4.13 0.00 36.95 1.31
2400 2435 8.036575 TGTACACTGTTTTAAATAGTCCGCTAT 58.963 33.333 4.13 0.00 39.46 2.97
2401 2436 7.377398 TGTACACTGTTTTAAATAGTCCGCTA 58.623 34.615 4.13 0.00 29.72 4.26
2402 2437 6.225318 TGTACACTGTTTTAAATAGTCCGCT 58.775 36.000 4.13 0.00 29.72 5.52
2403 2438 6.470557 TGTACACTGTTTTAAATAGTCCGC 57.529 37.500 4.13 0.00 29.72 5.54
2405 2440 9.983804 GCTAATGTACACTGTTTTAAATAGTCC 57.016 33.333 4.13 0.00 29.72 3.85
2421 2456 6.591448 CAGATTCTTCTGTGTGCTAATGTACA 59.409 38.462 0.00 0.00 43.73 2.90
2422 2457 6.998338 CAGATTCTTCTGTGTGCTAATGTAC 58.002 40.000 0.00 0.00 43.73 2.90
2449 2484 5.966636 TCAATATGTGCAATCGTACTGAC 57.033 39.130 0.00 0.00 0.00 3.51
2450 2485 6.018016 CCAATCAATATGTGCAATCGTACTGA 60.018 38.462 0.00 0.00 0.00 3.41
2453 2488 6.136071 GTCCAATCAATATGTGCAATCGTAC 58.864 40.000 0.00 0.00 0.00 3.67
2457 2492 5.237127 TCTCGTCCAATCAATATGTGCAATC 59.763 40.000 0.00 0.00 0.00 2.67
2482 2517 3.821748 GGGGTTTGTATCCCTCTCAATC 58.178 50.000 0.96 0.00 44.07 2.67
2499 2534 2.437651 CCAAACCATTGACAAAAGGGGT 59.562 45.455 12.92 6.66 38.94 4.95
2542 2577 7.509546 ACCGGAGTATTGAATTGATGAATACT 58.490 34.615 9.46 0.00 42.78 2.12
2545 2580 5.466728 CGACCGGAGTATTGAATTGATGAAT 59.533 40.000 9.46 0.00 0.00 2.57
2546 2581 4.808895 CGACCGGAGTATTGAATTGATGAA 59.191 41.667 9.46 0.00 0.00 2.57
2547 2582 4.368315 CGACCGGAGTATTGAATTGATGA 58.632 43.478 9.46 0.00 0.00 2.92
2548 2583 3.059597 GCGACCGGAGTATTGAATTGATG 60.060 47.826 9.46 0.00 0.00 3.07
2549 2584 3.131396 GCGACCGGAGTATTGAATTGAT 58.869 45.455 9.46 0.00 0.00 2.57
2550 2585 2.546778 GCGACCGGAGTATTGAATTGA 58.453 47.619 9.46 0.00 0.00 2.57
2551 2586 1.597663 GGCGACCGGAGTATTGAATTG 59.402 52.381 9.46 0.00 0.00 2.32
2552 2587 1.805120 CGGCGACCGGAGTATTGAATT 60.805 52.381 9.46 0.00 44.15 2.17
2634 2676 3.689649 CCTTGACCTAGGCAATGTACAAC 59.310 47.826 9.30 0.00 0.00 3.32
2695 2740 1.755179 AAGATTTCCACCGCCATGAG 58.245 50.000 0.00 0.00 0.00 2.90
2717 2762 5.474532 TGCTTGACAAGTAATTGCTGAGATT 59.525 36.000 16.39 0.00 0.00 2.40
2860 2905 9.632638 AAGTACATTTCCATGCTCTATACATTT 57.367 29.630 0.00 0.00 33.05 2.32
2963 3123 4.023980 AGAGGCCCTTATTTTAAGCCAAC 58.976 43.478 0.00 0.00 46.35 3.77
2989 3149 6.315393 TCCAGCGTTTTTAGAATCCTATGAAC 59.685 38.462 0.00 0.00 0.00 3.18
2994 3154 6.990349 CCTATTCCAGCGTTTTTAGAATCCTA 59.010 38.462 0.00 0.00 0.00 2.94
2996 3156 5.008712 CCCTATTCCAGCGTTTTTAGAATCC 59.991 44.000 0.00 0.00 0.00 3.01
3025 3186 6.891361 TGACCATGACATTTCAATCCTATGTT 59.109 34.615 0.00 0.00 34.61 2.71
3026 3187 6.425735 TGACCATGACATTTCAATCCTATGT 58.574 36.000 0.00 0.00 34.61 2.29
3037 3198 5.763355 AGGATTGAGATGACCATGACATTT 58.237 37.500 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.